From 5558c301fa1cb940fd26f2c1d1004cf69a599c83 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <daniel.mentock@mpie.de>
Date: Mon, 6 Dec 2021 14:22:52 +0100
Subject: [PATCH 001/133] added fist typehints for _grid module

---
 python/damask/_grid.py        | 158 ++++++++++++++++++++--------------
 python/damask/grid_filters.py |  12 +--
 2 files changed, 101 insertions(+), 69 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 135cc6b66..99991a534 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -3,6 +3,8 @@ import copy
 import warnings
 import multiprocessing as mp
 from functools import partial
+from typing import Union, Optional, TextIO, List, Sequence
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -13,7 +15,7 @@ from . import VTK
 from . import util
 from . import grid_filters
 from . import Rotation
-
+from . import Table
 
 class Grid:
     """
@@ -25,7 +27,11 @@ class Grid:
     the physical size.
     """
 
-    def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
+    def __init__(self,
+                 material: np.ndarray,
+                 size,
+                 origin = [0.0,0.0,0.0],
+                 comments = []):
         """
         New geometry definition for grid solvers.
 
@@ -43,12 +49,12 @@ class Grid:
 
         """
         self.material = material
-        self.size     = size
-        self.origin   = origin
+        self._size    = size
+        self._origin  = origin
         self.comments = comments
 
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """Basic information on grid definition."""
         mat_min = np.nanmin(self.material)
         mat_max = np.nanmax(self.material)
@@ -62,14 +68,14 @@ class Grid:
               ])
 
 
-    def __copy__(self):
+    def __copy__(self) -> "Grid":
         """Create deep copy."""
         return copy.deepcopy(self)
 
     copy = __copy__
 
 
-    def __eq__(self,other):
+    def __eq__(self, other):
         """
         Test equality of other.
 
@@ -79,6 +85,8 @@ class Grid:
             Grid to compare self against.
 
         """
+        if not isinstance(other, Grid):
+            raise TypeError
         return (np.allclose(other.size,self.size)
             and np.allclose(other.origin,self.origin)
             and np.all(other.cells == self.cells)
@@ -86,15 +94,15 @@ class Grid:
 
 
     @property
-    def material(self):
+    def material(self) -> np.ndarray:
         """Material indices."""
         return self._material
 
     @material.setter
-    def material(self,material):
+    def material(self, material: np.ndarray):
         if len(material.shape) != 3:
             raise ValueError(f'invalid material shape {material.shape}')
-        elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
+        elif material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
             raise TypeError(f'invalid material data type {material.dtype}')
         else:
             self._material = np.copy(material)
@@ -105,53 +113,53 @@ class Grid:
 
 
     @property
-    def size(self):
+    def size(self) -> np.ndarray:
         """Physical size of grid in meter."""
         return self._size
 
     @size.setter
-    def size(self,size):
+    def size(self, size: Union[Sequence[float], np.ndarray]):
         if len(size) != 3 or any(np.array(size) < 0):
             raise ValueError(f'invalid size {size}')
         else:
             self._size = np.array(size)
 
     @property
-    def origin(self):
+    def origin(self) -> Union[Sequence[float], np.ndarray]:
         """Coordinates of grid origin in meter."""
         return self._origin
 
     @origin.setter
-    def origin(self,origin):
+    def origin(self, origin: np.ndarray):
         if len(origin) != 3:
             raise ValueError(f'invalid origin {origin}')
         else:
             self._origin = np.array(origin)
 
     @property
-    def comments(self):
+    def comments(self) -> List[str]:
         """Comments, e.g. history of operations."""
         return self._comments
 
     @comments.setter
-    def comments(self,comments):
+    def comments(self, comments: Union[str, Sequence[str]]):
         self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
 
 
     @property
-    def cells(self):
+    def cells(self) -> np.ndarray:
         """Number of cells in x,y,z direction."""
         return np.asarray(self.material.shape)
 
 
     @property
-    def N_materials(self):
+    def N_materials(self) -> int:
         """Number of (unique) material indices within grid."""
         return np.unique(self.material).size
 
 
     @staticmethod
-    def load(fname):
+    def load(fname: Union[str, Path]) -> "Grid":
         """
         Load from VTK image data file.
 
@@ -198,15 +206,17 @@ class Grid:
 
         """
         warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
-        try:
+        if isinstance(fname, (str, Path)):
             f = open(fname)
-        except TypeError:
+        elif isinstance(fname, TextIO):
             f = fname
+        else:
+            raise TypeError
 
         f.seek(0)
         try:
-            header_length,keyword = f.readline().split()[:2]
-            header_length = int(header_length)
+            header_length_,keyword = f.readline().split()[:2]
+            header_length = int(header_length_)
         except ValueError:
             header_length,keyword = (-1, 'invalid')
         if not keyword.startswith('head') or header_length < 3:
@@ -215,10 +225,10 @@ class Grid:
         comments = []
         content = f.readlines()
         for i,line in enumerate(content[:header_length]):
-            items = line.split('#')[0].lower().strip().split()
+            items: List[str] = line.split('#')[0].lower().strip().split()
             key = items[0] if items else ''
             if   key == 'grid':
-                cells  = np.array([  int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
+                cells  = np.array([int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
             elif key == 'size':
                 size   = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
             elif key == 'origin':
@@ -226,19 +236,19 @@ class Grid:
             else:
                 comments.append(line.strip())
 
-        material = np.empty(cells.prod())                                                           # initialize as flat array
+        material = np.empty(int(cells.prod()))                                                         # initialize as flat array
         i = 0
         for line in content[header_length:]:
             items = line.split('#')[0].split()
             if len(items) == 3:
-                if   items[1].lower() == 'of':
-                    items = np.ones(int(items[0]))*float(items[2])
+                if items[1].lower() == 'of':
+                    material_entry = np.ones(int(items[0]))*float(items[2])
                 elif items[1].lower() == 'to':
-                    items = np.linspace(int(items[0]),int(items[2]),
+                    material_entry = np.linspace(int(items[0]),int(items[2]),
                                         abs(int(items[2])-int(items[0]))+1,dtype=float)
-                else:                        items = list(map(float,items))
-            else:                            items = list(map(float,items))
-            material[i:i+len(items)] = items
+                else:                        material_entry = list(map(float, items))
+            else:                            material_entry = list(map(float, items))
+            material[i:i+len(material_entry)] = material_entry
             i += len(items)
 
         if i != cells.prod():
@@ -251,7 +261,7 @@ class Grid:
 
 
     @staticmethod
-    def load_Neper(fname):
+    def load_Neper(fname: Union[str, Path]) -> "Grid":
         """
         Load from Neper VTK file.
 
@@ -276,10 +286,10 @@ class Grid:
 
 
     @staticmethod
-    def load_DREAM3D(fname,
-                     feature_IDs=None,cell_data=None,
-                     phases='Phases',Euler_angles='EulerAngles',
-                     base_group=None):
+    def load_DREAM3D(fname: str,
+                     feature_IDs: str = None, cell_data: str = None,
+                     phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
+                     base_group: str = None) -> "Grid":
         """
         Load DREAM.3D (HDF5) file.
 
@@ -339,7 +349,7 @@ class Grid:
 
 
     @staticmethod
-    def from_table(table,coordinates,labels):
+    def from_table(table: Table, coordinates: str, labels: Union[str, Sequence[str]]) -> "Grid":
         """
         Create grid from ASCII table.
 
@@ -372,11 +382,16 @@ class Grid:
 
 
     @staticmethod
-    def _find_closest_seed(seeds, weights, point):
+    def _find_closest_seed(seeds: np.ndarray, weights: np.ndarray, point: np.ndarray) -> np.integer:
         return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
 
     @staticmethod
-    def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
+    def from_Laguerre_tessellation(cells,
+                                   size,
+                                   seeds,
+                                   weights,
+                                   material = None,
+                                   periodic = True):
         """
         Create grid from Laguerre tessellation.
 
@@ -412,7 +427,6 @@ class Grid:
             seeds_p   = seeds
 
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
-
         pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
         result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), coords)
         pool.close()
@@ -428,7 +442,11 @@ class Grid:
 
 
     @staticmethod
-    def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
+    def from_Voronoi_tessellation(cells: np.ndarray,
+                                  size: Union[Sequence[float], np.ndarray],
+                                  seeds: np.ndarray,
+                                  material: np.ndarray = None,
+                                  periodic: bool = True) -> "Grid":
         """
         Create grid from Voronoi tessellation.
 
@@ -509,7 +527,12 @@ class Grid:
 
 
     @staticmethod
-    def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
+    def from_minimal_surface(cells: np.ndarray,
+                             size: Union[Sequence[float], np.ndarray],
+                             surface: str,
+                             threshold: float = 0.0,
+                             periods: int = 1,
+                             materials: tuple = (0,1)) -> "Grid":
         """
         Create grid from definition of triply periodic minimal surface.
 
@@ -595,7 +618,7 @@ class Grid:
                    )
 
 
-    def save(self,fname,compress=True):
+    def save(self, fname: Union[str, Path], compress: bool = True):
         """
         Save as VTK image data file.
 
@@ -614,7 +637,7 @@ class Grid:
         v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
 
 
-    def save_ASCII(self,fname):
+    def save_ASCII(self, fname: Union[str, TextIO]):
         """
         Save as geom file.
 
@@ -649,8 +672,14 @@ class Grid:
         VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
 
 
-    def add_primitive(self,dimension,center,exponent,
-                      fill=None,R=Rotation(),inverse=False,periodic=True):
+    def add_primitive(self,
+                      dimension: np.ndarray,
+                      center: np.ndarray,
+                      exponent: Union[np.ndarray, float],
+                      fill: int = None,
+                      R: Rotation = Rotation(),
+                      inverse: bool = False,
+                      periodic: bool = True) -> "Grid":
         """
         Insert a primitive geometric object at a given position.
 
@@ -734,7 +763,7 @@ class Grid:
                    )
 
 
-    def mirror(self,directions,reflect=False):
+    def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
         """
         Mirror grid along given directions.
 
@@ -769,7 +798,7 @@ class Grid:
         if not set(directions).issubset(valid):
             raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
 
-        limits = [None,None] if reflect else [-2,0]
+        limits: Sequence[Optional[int]] = [None,None] if reflect else [-2,0]
         mat = self.material.copy()
 
         if 'x' in directions:
@@ -786,7 +815,7 @@ class Grid:
                    )
 
 
-    def flip(self,directions):
+    def flip(self, directions: Sequence[str]) -> "Grid":
         """
         Flip grid along given directions.
 
@@ -815,7 +844,7 @@ class Grid:
                    )
 
 
-    def scale(self,cells,periodic=True):
+    def scale(self, cells: np.ndarray, periodic: bool = True) -> "Grid":
         """
         Scale grid to new cells.
 
@@ -859,7 +888,7 @@ class Grid:
                    )
 
 
-    def clean(self,stencil=3,selection=None,periodic=True):
+    def clean(self, stencil: int = 3, selection: Sequence[float] = None, periodic: bool = True) -> "Grid":
         """
         Smooth grid by selecting most frequent material index within given stencil at each location.
 
@@ -878,7 +907,7 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def mostFrequent(arr,selection=None):
+        def mostFrequent(arr, selection = None):
             me = arr[arr.size//2]
             if selection is None or me in selection:
                 unique, inverse = np.unique(arr, return_inverse=True)
@@ -899,7 +928,7 @@ class Grid:
                    )
 
 
-    def renumber(self):
+    def renumber(self) -> "Grid":
         """
         Renumber sorted material indices as 0,...,N-1.
 
@@ -918,7 +947,7 @@ class Grid:
                    )
 
 
-    def rotate(self,R,fill=None):
+    def rotate(self, R: Rotation, fill: Union[int, float] = None) -> "Grid":
         """
         Rotate grid (pad if required).
 
@@ -956,7 +985,7 @@ class Grid:
                    )
 
 
-    def canvas(self,cells=None,offset=None,fill=None):
+    def canvas(self, cells = None, offset = None, fill = None):
         """
         Crop or enlarge/pad grid.
 
@@ -1008,7 +1037,7 @@ class Grid:
                    )
 
 
-    def substitute(self,from_material,to_material):
+    def substitute(self, from_material: np.ndarray, to_material: np.ndarray) -> "Grid":
         """
         Substitute material indices.
 
@@ -1025,7 +1054,7 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def mp(entry,mapper):
+        def mp(entry, mapper):
             return mapper[entry] if entry in mapper else entry
 
         mp = np.vectorize(mp)
@@ -1038,7 +1067,7 @@ class Grid:
                    )
 
 
-    def sort(self):
+    def sort(self) -> "Grid":
         """
         Sort material indices such that min(material) is located at (0,0,0).
 
@@ -1060,7 +1089,11 @@ class Grid:
                    )
 
 
-    def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
+    def vicinity_offset(self,
+                        vicinity: int = 1,
+                        offset: int = None,
+                        trigger: Sequence[int] = [],
+                        periodic: bool = True) -> "Grid":
         """
         Offset material index of points in the vicinity of xxx.
 
@@ -1088,8 +1121,7 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def tainted_neighborhood(stencil,trigger):
-
+        def tainted_neighborhood(stencil, trigger):
             me = stencil[stencil.shape[0]//2]
             return np.any(stencil != me if len(trigger) == 0 else
                           np.in1d(stencil,np.array(list(set(trigger) - {me}))))
@@ -1108,7 +1140,7 @@ class Grid:
                    )
 
 
-    def get_grain_boundaries(self,periodic=True,directions='xyz'):
+    def get_grain_boundaries(self, periodic = True, directions = 'xyz'):
         """
         Create VTK unstructured grid containing grain boundaries.
 
diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py
index 42b5a16c4..1b83e99f8 100644
--- a/python/damask/grid_filters.py
+++ b/python/damask/grid_filters.py
@@ -130,9 +130,9 @@ def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
 
 
-def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
-                       size: _np.ndarray,
-                       origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
+def coordinates0_point(cells: Union[_np.ndarray, Sequence[int]],
+                       size: Union[_np.ndarray, Sequence[float]],
+                       origin: Union[_np.ndarray, Sequence[float]] = _np.zeros(3)) -> _np.ndarray:
     """
     Cell center positions (undeformed).
 
@@ -305,9 +305,9 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
     return (cells,size,origin)
 
 
-def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
-                      size: _np.ndarray,
-                      origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
+def coordinates0_node(cells: Union[_np.ndarray, Sequence[int]],
+                      size: Union[_np.ndarray, Sequence[int]],
+                      origin: Union[_np.ndarray, Sequence[int]] = _np.zeros(3)) -> _np.ndarray:
     """
     Nodal positions (undeformed).
 

From 1de12bb40289c2a2c8845559145c0d283f501df5 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <daniel.mentock@mpie.de>
Date: Mon, 6 Dec 2021 15:48:19 +0100
Subject: [PATCH 002/133] removed direct attribute assignments for size and
 origin

---
 python/damask/_grid.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 99991a534..1bda19d4e 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -49,8 +49,8 @@ class Grid:
 
         """
         self.material = material
-        self._size    = size
-        self._origin  = origin
+        self.size    = size
+        self.origin  = origin
         self.comments = comments
 
 

From 7c7c3926b783201c6f2464efad553137cf6a1437 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <daniel.mentock@mpie.de>
Date: Mon, 6 Dec 2021 15:48:57 +0100
Subject: [PATCH 003/133] added array conversion to ambiguous types in
 grid_filters.coordinates0_point function

---
 python/damask/grid_filters.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py
index 1b83e99f8..9d0e055c8 100644
--- a/python/damask/grid_filters.py
+++ b/python/damask/grid_filters.py
@@ -151,8 +151,8 @@ def coordinates0_point(cells: Union[_np.ndarray, Sequence[int]],
         Undeformed cell center coordinates.
 
     """
-    start = origin        + size/_np.array(cells)*.5
-    end   = origin + size - size/_np.array(cells)*.5
+    start = _np.array(origin)                   + size/_np.array(cells)*.5
+    end   = _np.array(origin) + _np.array(size) - size/_np.array(cells)*.5
 
     return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],cells[0]),
                                   _np.linspace(start[1],end[1],cells[1]),

From d66b9e1896b227f963704e93ff936c820efacf0c Mon Sep 17 00:00:00 2001
From: Sheng Zhang <sheng.zhang@student.kuleuven.be>
Date: Mon, 6 Dec 2021 16:00:37 +0100
Subject: [PATCH 004/133] subdivision of interaction matrix for hcp

---
 .../mechanical/plastic/phenopowerlaw_Mg.yaml  | 10 ++-
 .../mechanical/plastic/phenopowerlaw_Ti.yaml  |  7 ++-
 src/lattice.f90                               | 63 ++++++++++---------
 3 files changed, 44 insertions(+), 36 deletions(-)

diff --git a/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml b/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
index 0ae04928d..5bc4a2e03 100644
--- a/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
+++ b/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
@@ -23,9 +23,13 @@ f_sat_sl-tw: 10.0
 h_0_sl-sl: 500.0e+6
 h_0_tw-tw:  50.0e+6
 h_0_tw-sl: 150.0e+6
-h_sl-sl:  [1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,
-           1.0,  1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
-           1.0,  1.0,  1.0, -1.0,  1.0,  1.0, -1.0,  1.0, +1.0,  1.0]  # unused entries are indicated by -1.0
+h_sl-sl: [+1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,
+          +1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0, -1.0,
+          -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
+          -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
+          -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,  1.0,  1.0,  1.0,  1.0,
+          +1.0,  1.0, -1.0, -1.0, -1.0, -1.0,  1.0,  1.0,  1.0,  1.0,
+          -1.0, -1.0, -1.0, -1.0,  1.0,  1.0,  1.0,  1.0,  1.0]  # unused entries are indicated by -1.0
 h_tw-tw: [+1.0,  1.0, -1.0, -1.0, -1.0, -1.0,  1.0, -1.0,  1.0,  1.0,
           -1.0,  1.0]  # unused entries are indicated by -1.0
 h_tw-sl:  [1.0, -1.0,  1.0, -1.0,  1.0, -1.0,  1.0, -1.0,  1.0, -1.0,
diff --git a/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml b/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
index 1db6adc6b..c238e6afb 100644
--- a/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
+++ b/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
@@ -20,5 +20,8 @@ xi_inf_sl: [568.e+6, 150.e+7, 0.0, 3420.e+6]
 # L. Wang et al. :
 # xi_0_sl:   [127.e+6, 96.e+6, 0.0, 240.e+6]
 
-h_sl-sl: [+1.0,  1.0,  1.0,  1.0,  1.0,  1.0, -1.0, -1.0, -1.0, -1.0,
-          -1.0, -1.0, +1.0,  1.0, -1.0,  1.0,  1.0, -1.0,  1.0,  1.0] # unused entries are indicated by -1.0
+h_sl-sl: [+1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0, -1.0, -1.0,
+          -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,  1.0,
+          +1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,
+          +1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,  1.0,
+          +1.0,  1.0,  1.0,  1.0,  1.0,  1.0] # unused entries are indicated by -1.0
diff --git a/src/lattice.f90 b/src/lattice.f90
index 50d4b6c51..68240390f 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -750,40 +750,41 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
   integer, dimension(HEX_NSLIP,HEX_NSLIP), parameter :: &
     HEX_INTERACTIONSLIPSLIP = reshape( [&
     ! basal      prism      1. pyr<a>           1. pyr<c+a>                           2. pyr<c+a>
-       1, 2, 2,   3, 3, 3,   7, 7, 7, 7, 7, 7,  13,13,13,13,13,13,13,13,13,13,13,13,  21,21,21,21,21,21, & ! -----> acting (forest)
-       2, 1, 2,   3, 3, 3,   7, 7, 7, 7, 7, 7,  13,13,13,13,13,13,13,13,13,13,13,13,  21,21,21,21,21,21, & ! | basal
-       2, 2, 1,   3, 3, 3,   7, 7, 7, 7, 7, 7,  13,13,13,13,13,13,13,13,13,13,13,13,  21,21,21,21,21,21, & ! |
-                                                                                                           ! v
-       6, 6, 6,   4, 5, 5,   8, 8, 8, 8, 8, 8,  14,14,14,14,14,14,14,14,14,14,14,14,  22,22,22,22,22,22, & ! reacting (primary)
-       6, 6, 6,   5, 4, 5,   8, 8, 8, 8, 8, 8,  14,14,14,14,14,14,14,14,14,14,14,14,  22,22,22,22,22,22, & ! prism
-       6, 6, 6,   5, 5, 4,   8, 8, 8, 8, 8, 8,  14,14,14,14,14,14,14,14,14,14,14,14,  22,22,22,22,22,22, &
+       1, 2, 2,   3, 4, 4,   9,10,9,9,10,9,      20,21,22,22,21,20,20,21,22,22,21,20,  47,47,48,47,47,48, & ! -----> acting (forest)
+       2, 1, 2,   4, 3, 4,   10,9,9,10,9,9,      22,22,21,20,20,21,22,22,21,20,20,21,  47,48,47,47,48,47, & ! | basal
+       2, 2, 1,   4, 4, 3,   9,9,10,9,9,10,      21,20,20,21,22,22,21,20,20,21,22,22,  48,47,47,48,47,47, & ! |
+                                                                                                                      ! v
+       7, 8, 8,   5, 6, 6,   11,12,11,11,12,11,  23,24,25,25,24,23,23,24,25,25,24,23,  49,49,50,49,49,50, & ! reacting (primary)
+       8, 7, 8,   6, 5, 6,   12,11,11,12,11,11,  25,25,24,23,23,24,25,25,24,23,23,24,  49,50,49,49,50,49, & ! prism
+       8, 8, 7,   6, 6, 5,   11,11,12,11,11,12,  24,23,23,24,25,25,24,23,23,24,25,25,  50,49,49,50,49,49, &
 
-      12,12,12,  11,11,11,   9,10,10,10,10,10,  15,15,15,15,15,15,15,15,15,15,15,15,  23,23,23,23,23,23, &
-      12,12,12,  11,11,11,  10, 9,10,10,10,10,  15,15,15,15,15,15,15,15,15,15,15,15,  23,23,23,23,23,23, &
-      12,12,12,  11,11,11,  10,10, 9,10,10,10,  15,15,15,15,15,15,15,15,15,15,15,15,  23,23,23,23,23,23, &
-      12,12,12,  11,11,11,  10,10,10, 9,10,10,  15,15,15,15,15,15,15,15,15,15,15,15,  23,23,23,23,23,23, & ! 1. pyr<a>
-      12,12,12,  11,11,11,  10,10,10,10, 9,10,  15,15,15,15,15,15,15,15,15,15,15,15,  23,23,23,23,23,23, &
-      12,12,12,  11,11,11,  10,10,10,10,10, 9,  15,15,15,15,15,15,15,15,15,15,15,15,  23,23,23,23,23,23, &
 
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  16,17,17,17,17,17,17,17,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,16,17,17,17,17,17,17,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,16,17,17,17,17,17,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,16,17,17,17,17,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,16,17,17,17,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,16,17,17,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,17,16,17,17,17,17,17,  24,24,24,24,24,24, & ! 1. pyr<c+a>
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,17,17,16,17,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,17,17,17,16,17,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,17,17,17,17,16,17,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,17,17,17,17,17,16,17,  24,24,24,24,24,24, &
-      20,20,20,  19,19,19,  18,18,18,18,18,18,  17,17,17,17,17,17,17,17,17,17,17,16,  24,24,24,24,24,24, &
+      18,19,18,  16,17,16,   13,14,14,15,14,14,  26,26,27,28,28,27,29,29,27,28,28,27,  51,52,51,51,52,51, &
+      19,18,18,  17,16,16,   14,13,14,14,15,14,  28,27,26,26,27,28,28,27,29,29,27,28,  51,51,52,51,51,52, &
+      18,18,19,  16,16,17,   14,14,13,14,14,15,  27,28,28,27,26,26,27,28,28,27,29,29,  52,51,51,52,51,51, &
+      18,19,18,  16,17,16,   15,14,14,13,14,14,  29,29,27,28,28,27,26,26,27,28,28,27,  51,52,51,51,52,51, & ! 1. pyr<a>
+      19,18,18,  17,16,16,   14,15,14,14,13,14,  28,27,29,29,27,28,28,27,26,26,27,28,  51,51,52,51,51,52, &
+      18,18,19,  16,16,17,   14,14,15,14,14,13,  27,28,28,27,29,29,27,28,28,27,26,26,  52,51,51,52,51,51, &
 
-      30,30,30,  29,29,29,  28,28,28,28,28,28,  27,27,27,27,27,27,27,27,27,27,27,27,  25,26,26,26,26,26, &
-      30,30,30,  29,29,29,  28,28,28,28,28,28,  27,27,27,27,27,27,27,27,27,27,27,27,  26,25,26,26,26,26, &
-      30,30,30,  29,29,29,  28,28,28,28,28,28,  27,27,27,27,27,27,27,27,27,27,27,27,  26,26,25,26,26,26, &
-      30,30,30,  29,29,29,  28,28,28,28,28,28,  27,27,27,27,27,27,27,27,27,27,27,27,  26,26,26,25,26,26, & ! 2. pyr<c+a>
-      30,30,30,  29,29,29,  28,28,28,28,28,28,  27,27,27,27,27,27,27,27,27,27,27,27,  26,26,26,26,25,26, &
-      30,30,30,  29,29,29,  28,28,28,28,28,28,  27,27,27,27,27,27,27,27,27,27,27,27,  26,26,26,26,26,25  &
+      44,45,46,  41,42,43,   37,38,39,40,38,39,  30,31,32,32,32,33,34,35,32,32,32,36,  53,54,55,53,54,56, &
+      46,45,44,  43,42,41,   37,39,38,40,39,38,  31,30,36,32,32,32,35,34,33,32,32,32,  56,54,53,55,54,53, &
+      45,46,44,  42,43,41,   39,37,38,39,40,38,  32,36,30,31,32,32,32,33,34,35,32,32,  56,53,54,55,53,54, &
+      45,44,46,  42,41,43,   38,37,39,38,40,39,  32,32,31,30,36,32,32,32,35,34,33,32,  53,56,54,53,55,54, &
+      46,44,45,  43,41,42,   38,39,37,38,39,40,  32,32,32,36,30,31,32,32,32,33,34,35,  54,56,53,54,55,53, &
+      44,46,45,  41,43,42,   39,38,37,39,38,40,  33,32,32,32,31,30,36,32,32,32,35,34,  54,53,56,54,53,55, &
+      44,45,46,  41,42,43,   40,38,39,37,38,39,  34,35,32,32,32,36,30,31,32,32,32,33,  53,54,56,53,54,55, & ! 1. pyr<c+a>
+      46,45,44,  43,42,41,   40,39,38,37,39,38,  35,34,33,32,32,32,31,30,36,32,32,32,  55,54,53,56,54,53, &
+      45,46,44,  42,43,41,   39,40,38,39,37,38,  32,33,34,35,32,32,32,36,30,31,32,32,  55,53,54,56,53,54, &
+      45,44,46,  42,41,43,   38,40,39,38,37,39,  32,32,35,34,33,32,32,32,31,30,36,32,  53,55,54,53,56,54, &
+      46,44,45,  43,41,42,   38,39,40,38,39,37,  32,32,32,33,34,35,32,32,32,36,30,31,  54,55,53,54,56,53, &
+      44,46,45,  41,43,42,   39,38,40,39,38,37,  36,32,32,32,35,34,33,32,32,32,31,30,  54,53,55,54,53,56, &
+
+      68,68,69,  66,66,67,   64,64,65,64,65,65,  60,61,61,60,62,62,60,63,63,60,62,62,  57,58,58,59,58,58, &
+      68,69,68,  66,67,66,   65,64,64,65,64,64,  62,62,60,61,61,60,62,62,60,63,63,60,  58,57,58,58,59,58, &
+      69,68,68,  67,66,66,   64,65,64,64,65,64,  63,60,62,62,60,61,61,60,62,62,60,63,  58,58,57,58,58,59, &
+      68,68,69,  66,66,67,   64,64,65,64,64,65,  60,63,63,60,62,62,60,61,61,60,62,62,  59,58,58,57,58,58, & ! 2. pyr<c+a>
+      68,69,68,  66,67,66,   65,64,64,65,64,64,  62,62,60,63,63,60,62,62,60,61,61,60,  58,59,58,58,57,58, &
+      69,68,68,  67,66,66,   64,65,64,64,65,64,  61,60,62,62,60,63,63,60,62,62,60,61,  58,58,59,58,58,57  &
       ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme)
 
   integer, dimension(BCT_NSLIP,BCT_NSLIP), parameter :: &

From ea25c8ff40c82764788279793102230a8f2442cc Mon Sep 17 00:00:00 2001
From: Sheng Zhang <sheng.zhang@student.kuleuven.be>
Date: Mon, 6 Dec 2021 16:55:24 +0100
Subject: [PATCH 005/133] updated tests to have new # of interactions

---
 PRIVATE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PRIVATE b/PRIVATE
index e6e1f93a3..fb4dd2478 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit e6e1f93a36d63348359a81d7c373083a39977694
+Subproject commit fb4dd2478c00eedf2b5e977b4c2c00dfab523632

From a23a714bd0c8f1ee9547035534eb1824ae234f4c Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 7 Dec 2021 19:10:24 +0100
Subject: [PATCH 006/133] polishing

---
 src/lattice.f90 | 63 ++++++++++++++++++++++++-------------------------
 1 file changed, 31 insertions(+), 32 deletions(-)

diff --git a/src/lattice.f90 b/src/lattice.f90
index 68240390f..a93144f42 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -750,41 +750,40 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
   integer, dimension(HEX_NSLIP,HEX_NSLIP), parameter :: &
     HEX_INTERACTIONSLIPSLIP = reshape( [&
     ! basal      prism      1. pyr<a>           1. pyr<c+a>                           2. pyr<c+a>
-       1, 2, 2,   3, 4, 4,   9,10,9,9,10,9,      20,21,22,22,21,20,20,21,22,22,21,20,  47,47,48,47,47,48, & ! -----> acting (forest)
-       2, 1, 2,   4, 3, 4,   10,9,9,10,9,9,      22,22,21,20,20,21,22,22,21,20,20,21,  47,48,47,47,48,47, & ! | basal
-       2, 2, 1,   4, 4, 3,   9,9,10,9,9,10,      21,20,20,21,22,22,21,20,20,21,22,22,  48,47,47,48,47,47, & ! |
-                                                                                                                      ! v
-       7, 8, 8,   5, 6, 6,   11,12,11,11,12,11,  23,24,25,25,24,23,23,24,25,25,24,23,  49,49,50,49,49,50, & ! reacting (primary)
-       8, 7, 8,   6, 5, 6,   12,11,11,12,11,11,  25,25,24,23,23,24,25,25,24,23,23,24,  49,50,49,49,50,49, & ! prism
-       8, 8, 7,   6, 6, 5,   11,11,12,11,11,12,  24,23,23,24,25,25,24,23,23,24,25,25,  50,49,49,50,49,49, &
+       1, 2, 2,   3, 4, 4,   9,10, 9, 9,10, 9,  20,21,22,22,21,20,20,21,22,22,21,20,  47,47,48,47,47,48, & ! -----> acting (forest)
+       2, 1, 2,   4, 3, 4,  10, 9, 9,10, 9, 9,  22,22,21,20,20,21,22,22,21,20,20,21,  47,48,47,47,48,47, & ! | basal
+       2, 2, 1,   4, 4, 3,   9, 9,10, 9, 9,10,  21,20,20,21,22,22,21,20,20,21,22,22,  48,47,47,48,47,47, & ! |
+                                                                                                           ! v
+       7, 8, 8,   5, 6, 6,  11,12,11,11,12,11,  23,24,25,25,24,23,23,24,25,25,24,23,  49,49,50,49,49,50, & ! reacting (primary)
+       8, 7, 8,   6, 5, 6,  12,11,11,12,11,11,  25,25,24,23,23,24,25,25,24,23,23,24,  49,50,49,49,50,49, & ! prism
+       8, 8, 7,   6, 6, 5,  11,11,12,11,11,12,  24,23,23,24,25,25,24,23,23,24,25,25,  50,49,49,50,49,49, &
 
+      18,19,18,  16,17,16,  13,14,14,15,14,14,  26,26,27,28,28,27,29,29,27,28,28,27,  51,52,51,51,52,51, &
+      19,18,18,  17,16,16,  14,13,14,14,15,14,  28,27,26,26,27,28,28,27,29,29,27,28,  51,51,52,51,51,52, &
+      18,18,19,  16,16,17,  14,14,13,14,14,15,  27,28,28,27,26,26,27,28,28,27,29,29,  52,51,51,52,51,51, &
+      18,19,18,  16,17,16,  15,14,14,13,14,14,  29,29,27,28,28,27,26,26,27,28,28,27,  51,52,51,51,52,51, & ! 1. pyr<a>
+      19,18,18,  17,16,16,  14,15,14,14,13,14,  28,27,29,29,27,28,28,27,26,26,27,28,  51,51,52,51,51,52, &
+      18,18,19,  16,16,17,  14,14,15,14,14,13,  27,28,28,27,29,29,27,28,28,27,26,26,  52,51,51,52,51,51, &
 
-      18,19,18,  16,17,16,   13,14,14,15,14,14,  26,26,27,28,28,27,29,29,27,28,28,27,  51,52,51,51,52,51, &
-      19,18,18,  17,16,16,   14,13,14,14,15,14,  28,27,26,26,27,28,28,27,29,29,27,28,  51,51,52,51,51,52, &
-      18,18,19,  16,16,17,   14,14,13,14,14,15,  27,28,28,27,26,26,27,28,28,27,29,29,  52,51,51,52,51,51, &
-      18,19,18,  16,17,16,   15,14,14,13,14,14,  29,29,27,28,28,27,26,26,27,28,28,27,  51,52,51,51,52,51, & ! 1. pyr<a>
-      19,18,18,  17,16,16,   14,15,14,14,13,14,  28,27,29,29,27,28,28,27,26,26,27,28,  51,51,52,51,51,52, &
-      18,18,19,  16,16,17,   14,14,15,14,14,13,  27,28,28,27,29,29,27,28,28,27,26,26,  52,51,51,52,51,51, &
+      44,45,46,  41,42,43,  37,38,39,40,38,39,  30,31,32,32,32,33,34,35,32,32,32,36,  53,54,55,53,54,56, &
+      46,45,44,  43,42,41,  37,39,38,40,39,38,  31,30,36,32,32,32,35,34,33,32,32,32,  56,54,53,55,54,53, &
+      45,46,44,  42,43,41,  39,37,38,39,40,38,  32,36,30,31,32,32,32,33,34,35,32,32,  56,53,54,55,53,54, &
+      45,44,46,  42,41,43,  38,37,39,38,40,39,  32,32,31,30,36,32,32,32,35,34,33,32,  53,56,54,53,55,54, &
+      46,44,45,  43,41,42,  38,39,37,38,39,40,  32,32,32,36,30,31,32,32,32,33,34,35,  54,56,53,54,55,53, &
+      44,46,45,  41,43,42,  39,38,37,39,38,40,  33,32,32,32,31,30,36,32,32,32,35,34,  54,53,56,54,53,55, &
+      44,45,46,  41,42,43,  40,38,39,37,38,39,  34,35,32,32,32,36,30,31,32,32,32,33,  53,54,56,53,54,55, & ! 1. pyr<c+a>
+      46,45,44,  43,42,41,  40,39,38,37,39,38,  35,34,33,32,32,32,31,30,36,32,32,32,  55,54,53,56,54,53, &
+      45,46,44,  42,43,41,  39,40,38,39,37,38,  32,33,34,35,32,32,32,36,30,31,32,32,  55,53,54,56,53,54, &
+      45,44,46,  42,41,43,  38,40,39,38,37,39,  32,32,35,34,33,32,32,32,31,30,36,32,  53,55,54,53,56,54, &
+      46,44,45,  43,41,42,  38,39,40,38,39,37,  32,32,32,33,34,35,32,32,32,36,30,31,  54,55,53,54,56,53, &
+      44,46,45,  41,43,42,  39,38,40,39,38,37,  36,32,32,32,35,34,33,32,32,32,31,30,  54,53,55,54,53,56, &
 
-      44,45,46,  41,42,43,   37,38,39,40,38,39,  30,31,32,32,32,33,34,35,32,32,32,36,  53,54,55,53,54,56, &
-      46,45,44,  43,42,41,   37,39,38,40,39,38,  31,30,36,32,32,32,35,34,33,32,32,32,  56,54,53,55,54,53, &
-      45,46,44,  42,43,41,   39,37,38,39,40,38,  32,36,30,31,32,32,32,33,34,35,32,32,  56,53,54,55,53,54, &
-      45,44,46,  42,41,43,   38,37,39,38,40,39,  32,32,31,30,36,32,32,32,35,34,33,32,  53,56,54,53,55,54, &
-      46,44,45,  43,41,42,   38,39,37,38,39,40,  32,32,32,36,30,31,32,32,32,33,34,35,  54,56,53,54,55,53, &
-      44,46,45,  41,43,42,   39,38,37,39,38,40,  33,32,32,32,31,30,36,32,32,32,35,34,  54,53,56,54,53,55, &
-      44,45,46,  41,42,43,   40,38,39,37,38,39,  34,35,32,32,32,36,30,31,32,32,32,33,  53,54,56,53,54,55, & ! 1. pyr<c+a>
-      46,45,44,  43,42,41,   40,39,38,37,39,38,  35,34,33,32,32,32,31,30,36,32,32,32,  55,54,53,56,54,53, &
-      45,46,44,  42,43,41,   39,40,38,39,37,38,  32,33,34,35,32,32,32,36,30,31,32,32,  55,53,54,56,53,54, &
-      45,44,46,  42,41,43,   38,40,39,38,37,39,  32,32,35,34,33,32,32,32,31,30,36,32,  53,55,54,53,56,54, &
-      46,44,45,  43,41,42,   38,39,40,38,39,37,  32,32,32,33,34,35,32,32,32,36,30,31,  54,55,53,54,56,53, &
-      44,46,45,  41,43,42,   39,38,40,39,38,37,  36,32,32,32,35,34,33,32,32,32,31,30,  54,53,55,54,53,56, &
-
-      68,68,69,  66,66,67,   64,64,65,64,65,65,  60,61,61,60,62,62,60,63,63,60,62,62,  57,58,58,59,58,58, &
-      68,69,68,  66,67,66,   65,64,64,65,64,64,  62,62,60,61,61,60,62,62,60,63,63,60,  58,57,58,58,59,58, &
-      69,68,68,  67,66,66,   64,65,64,64,65,64,  63,60,62,62,60,61,61,60,62,62,60,63,  58,58,57,58,58,59, &
-      68,68,69,  66,66,67,   64,64,65,64,64,65,  60,63,63,60,62,62,60,61,61,60,62,62,  59,58,58,57,58,58, & ! 2. pyr<c+a>
-      68,69,68,  66,67,66,   65,64,64,65,64,64,  62,62,60,63,63,60,62,62,60,61,61,60,  58,59,58,58,57,58, &
-      69,68,68,  67,66,66,   64,65,64,64,65,64,  61,60,62,62,60,63,63,60,62,62,60,61,  58,58,59,58,58,57  &
+      68,68,69,  66,66,67,  64,64,65,64,65,65,  60,61,61,60,62,62,60,63,63,60,62,62,  57,58,58,59,58,58, &
+      68,69,68,  66,67,66,  65,64,64,65,64,64,  62,62,60,61,61,60,62,62,60,63,63,60,  58,57,58,58,59,58, &
+      69,68,68,  67,66,66,  64,65,64,64,65,64,  63,60,62,62,60,61,61,60,62,62,60,63,  58,58,57,58,58,59, &
+      68,68,69,  66,66,67,  64,64,65,64,64,65,  60,63,63,60,62,62,60,61,61,60,62,62,  59,58,58,57,58,58, & ! 2. pyr<c+a>
+      68,69,68,  66,67,66,  65,64,64,65,64,64,  62,62,60,63,63,60,62,62,60,61,61,60,  58,59,58,58,57,58, &
+      69,68,68,  67,66,66,  64,65,64,64,65,64,  61,60,62,62,60,63,63,60,62,62,60,61,  58,58,59,58,58,57  &
       ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme)
 
   integer, dimension(BCT_NSLIP,BCT_NSLIP), parameter :: &

From 1ddf1e569499829bba4ccbff288dad3711cd62cf Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 21 Dec 2021 23:01:00 +0100
Subject: [PATCH 007/133] support for PETSc with 64bit integers

compiles, but untested
---
 src/grid/grid_damage_spectral.f90            | 12 ++++++------
 src/grid/grid_mech_FEM.f90                   | 18 +++++++++---------
 src/grid/grid_mech_spectral_basic.f90        | 12 ++++++------
 src/grid/grid_mech_spectral_polarisation.f90 | 12 ++++++------
 src/grid/grid_thermal_spectral.f90           | 12 ++++++------
 src/prec.f90                                 |  9 +++++++++
 6 files changed, 42 insertions(+), 33 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index ef229368e..69370b211 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -108,16 +108,16 @@ subroutine grid_damage_spectral_init()
 ! initialize solver specific parts of PETSc
   call SNESCreate(PETSC_COMM_WORLD,damage_snes,ierr); CHKERRQ(ierr)
   call SNESSetOptionsPrefix(damage_snes,'damage_',ierr);CHKERRQ(ierr)
-  localK            = 0
-  localK(worldrank) = grid3
+  localK            = 0_pPetscInt
+  localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
   call DMDACreate3D(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
-         grid(1),grid(2),grid(3), &                                                                 ! global grid
-         1, 1, worldsize, &
-         1, 0, &                                                                                    ! #dof (damage phase field), ghost boundary width (domain overlap)
-         [grid(1)],[grid(2)],localK, &                                                              ! local grid
+         int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), &                    ! global grid
+         1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
+         1_pPetscInt, 0_pPetscInt, &                                                                ! #dof (phi, scalar), ghost boundary width (domain overlap)
+         [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          damage_grid,ierr)                                                                          ! handle, error
   CHKERRQ(ierr)
   call SNESSetDM(damage_snes,damage_grid,ierr); CHKERRQ(ierr)                                       ! connect snes to da
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index e1dc3dabe..c4a8588d6 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -164,16 +164,16 @@ subroutine grid_mechanical_FEM_init
   CHKERRQ(ierr)
   call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',ierr)
   CHKERRQ(ierr)
-  localK            = 0
-  localK(worldrank) = grid3
+  localK            = 0_pPetscInt
+  localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
   call DMDACreate3d(PETSC_COMM_WORLD, &
          DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, &
          DMDA_STENCIL_BOX, &
-         grid(1),grid(2),grid(3), &
-         1, 1, worldsize, &
-         3, 1, &
-         [grid(1)],[grid(2)],localK, &
+         int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), &                    ! global grid
+         1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
+         3_pPetscInt, 1_pPetscInt, &                                                                ! #dof (u, vector), ghost boundary width (domain overlap)
+         [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          mechanical_grid,ierr)
   CHKERRQ(ierr)
   call SNESSetDM(mechanical_snes,mechanical_grid,ierr)
@@ -196,7 +196,7 @@ subroutine grid_mechanical_FEM_init
   CHKERRQ(ierr)
   call SNESSetConvergenceTest(mechanical_snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr)   ! specify custom convergence check function "_converged"
   CHKERRQ(ierr)
-  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1), ierr)                                ! ignore linear solve failures
+  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPetscInt), ierr)                      ! ignore linear solve failures
   CHKERRQ(ierr)
   call SNESSetFromOptions(mechanical_snes,ierr)                                                     ! pull it all together with additional cli arguments
   CHKERRQ(ierr)
@@ -687,7 +687,7 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
             matmul(transpose(BMatFull), &
                    matmul(reshape(reshape(homogenization_dPdF(1:3,1:3,1:3,1:3,ele), &
                                           shape=[3,3,3,3], order=[2,1,4,3]),shape=[9,9]),BMatFull))*detJ
-    call MatSetValuesStencil(Jac,24,row,24,col,K_ele,ADD_VALUES,ierr)
+    call MatSetValuesStencil(Jac,24_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,ierr)
     CHKERRQ(ierr)
   enddo; enddo; enddo
   call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
@@ -700,7 +700,7 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
   diag = (C_volAvg(1,1,1,1)/delta(1)**2 + &
           C_volAvg(2,2,2,2)/delta(2)**2 + &
           C_volAvg(3,3,3,3)/delta(3)**2)*detJ
-  call MatZeroRowsColumns(Jac,size(rows),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,ierr)
+  call MatZeroRowsColumns(Jac,size(rows,kind=pPetscInt),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,ierr)
   CHKERRQ(ierr)
   call DMGetGlobalVector(da_local,coordinates,ierr); CHKERRQ(ierr)
   call DMDAVecGetArrayF90(da_local,coordinates,x_scal,ierr); CHKERRQ(ierr)
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 66b703ed6..0a267ecca 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -159,16 +159,16 @@ subroutine grid_mechanical_spectral_basic_init
 ! initialize solver specific parts of PETSc
   call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
   call SNESSetOptionsPrefix(snes,'mechanical_',ierr);CHKERRQ(ierr)
-  localK            = 0
-  localK(worldrank) = grid3
+  localK            = 0_pPetscInt
+  localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
   call DMDACreate3d(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
-         grid(1),grid(2),grid(3), &                                                                 ! global grid
-         1 , 1, worldsize, &
-         9, 0, &                                                                                    ! #dof (F tensor), ghost boundary width (domain overlap)
-         [grid(1)],[grid(2)],localK, &                                                              ! local grid
+         int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), &                    ! global grid
+         1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
+         9_pPetscInt, 0_pPetscInt, &                                                                ! #dof (F, tensor), ghost boundary width (domain overlap)
+         [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          da,ierr)                                                                                   ! handle, error
   CHKERRQ(ierr)
   call SNESSetDM(snes,da,ierr); CHKERRQ(ierr)                                                       ! connect snes to da
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index 3d524029c..5bfce5e3f 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -179,16 +179,16 @@ subroutine grid_mechanical_spectral_polarisation_init
 ! initialize solver specific parts of PETSc
   call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
   call SNESSetOptionsPrefix(snes,'mechanical_',ierr);CHKERRQ(ierr)
-  localK            = 0
-  localK(worldrank) = grid3
+  localK            = 0_pPetscInt
+  localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
   call DMDACreate3d(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
-         grid(1),grid(2),grid(3), &                                                                 ! global grid
-         1 , 1, worldsize, &
-         18, 0, &                                                                                   ! #dof (F tensor), ghost boundary width (domain overlap)
-         [grid(1)],[grid(2)],localK, &                                                              ! local grid
+         int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), &                    ! global grid
+         1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
+         18_pPetscInt, 0_pPetscInt, &                                                               ! #dof (2xtensor), ghost boundary width (domain overlap)
+         [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          da,ierr)                                                                                   ! handle, error
   CHKERRQ(ierr)
   call SNESSetDM(snes,da,ierr); CHKERRQ(ierr)                                                       ! connect snes to da
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 67c7ba1c3..548fa4b3c 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -103,16 +103,16 @@ subroutine grid_thermal_spectral_init(T_0)
 ! initialize solver specific parts of PETSc
   call SNESCreate(PETSC_COMM_WORLD,thermal_snes,ierr); CHKERRQ(ierr)
   call SNESSetOptionsPrefix(thermal_snes,'thermal_',ierr);CHKERRQ(ierr)
-  localK            = 0
-  localK(worldrank) = grid3
+  localK            = 0_pPetscInt
+  localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
   call DMDACreate3D(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
-         grid(1),grid(2),grid(3), &                                                                 ! global grid
-         1, 1, worldsize, &
-         1, 0, &                                                                                    ! #dof (T field), ghost boundary width (domain overlap)
-         [grid(1)],[grid(2)],localK, &                                                              ! local grid
+         int(grid(1),pPetscInt),int(grid(2),pPetscInt),int(grid(3),pPetscInt), &                    ! global grid
+         1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
+         1_pPetscInt, 0_pPetscInt, &                                                                ! #dof (T, scalar), ghost boundary width (domain overlap)
+         [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          thermal_grid,ierr)                                                                         ! handle, error
   CHKERRQ(ierr)
   call SNESSetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr)                                     ! connect snes to da
diff --git a/src/prec.f90 b/src/prec.f90
index 843033219..fe3e7fc20 100644
--- a/src/prec.f90
+++ b/src/prec.f90
@@ -10,6 +10,11 @@ module prec
   use, intrinsic :: IEEE_arithmetic
   use, intrinsic :: ISO_C_binding
 
+#ifdef PETSC
+#include <petsc/finclude/petscsys.h>
+  use PETScSys
+#endif
+
   implicit none
   public
 
@@ -21,6 +26,10 @@ module prec
   integer,     parameter :: pInt       = pI64
 #else
   integer,     parameter :: pInt       = pI32
+#endif
+#ifdef PETSC
+  PetscInt,    private   :: dummy
+  integer,     parameter :: pPetscInt  = kind(dummy)
 #endif
   integer,     parameter :: pStringLen = 256                                                        !< default string length
   integer,     parameter :: pPathLen   = 4096                                                       !< maximum length of a path name on linux

From e0e13ec659c286d7d1ad43ea385ef8f5a89b4028 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 27 Dec 2021 12:41:55 +0100
Subject: [PATCH 008/133] testing 64bit integer compilation

---
 .gitlab-ci.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6f18e3f1e..9fe88bba0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -93,6 +93,13 @@ test_mesh_GNU:
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU
 
+test_grid_GNU-64bit:
+  stage: compile
+  script:
+    - module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
+    - cd PRIVATE/testing/pytest
+    - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU-64bit
+
 test_mesh_IntelLLVM:
   stage: compile
   script:

From 1e965c42b7bfea0ec8957ac1ad4c5e0f478a7423 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 27 Dec 2021 17:44:22 +0100
Subject: [PATCH 009/133] don't rely on ML

avoid dependencies to external packages as much as possible
---
 src/grid/grid_mech_FEM.f90 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index c4a8588d6..6030e9a74 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -145,8 +145,7 @@ subroutine grid_mechanical_FEM_init
 ! set default and user defined options for PETSc
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS, &
                                 '-mechanical_snes_type newtonls -mechanical_ksp_type fgmres &
-                                &-mechanical_ksp_max_it 25 -mechanical_pc_type ml &
-                                &-mechanical_mg_levels_ksp_type chebyshev', &
+                                &-mechanical_ksp_max_it 25 -mechanical_mg_levels_ksp_type chebyshev', &
                                 ierr)
   CHKERRQ(ierr)
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)

From 56c22a91a560955005fe03562f993dccced2243b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 27 Dec 2021 18:59:33 +0100
Subject: [PATCH 010/133] testing grid with Intel LLVM works now

ML is no longer the default preconditioner for FEM.
Theoretically, installation of ML with all standard conforming compilers
should be possible, but --download-ml failed for unknown reasons.
---
 .gitlab-ci.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9fe88bba0..055a40815 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -100,6 +100,13 @@ test_grid_GNU-64bit:
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU-64bit
 
+test_grid_IntelLLVM:
+  stage: compile
+  script:
+    - module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
+    - cd PRIVATE/testing/pytest
+    - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_IntelLLVM
+
 test_mesh_IntelLLVM:
   stage: compile
   script:
@@ -128,7 +135,6 @@ test_Marc:
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and Marc' --basetemp ${TESTROOT}/compile_Marc
 
-
 setup_grid:
   stage: compile
   script:

From 95c64f7a0aefaebcfa6c82802a6205bba5a19a22 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 21:53:00 +0100
Subject: [PATCH 011/133] avoid failing self test

increase number of samples to have less corner cases.
Needs to be allocatable to avoid stack/heap issue on ifort
---
 src/math.f90 | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/math.f90 b/src/math.f90
index 34cb6eecb..3ea4d6a08 100644
--- a/src/math.f90
+++ b/src/math.f90
@@ -1432,9 +1432,11 @@ subroutine selfTest
     error stop 'math_LeviCivita'
 
   normal_distribution: block
-    real(pReal), dimension(500000) :: r
+    integer, parameter :: N = 1000000
+    real(pReal), dimension(:), allocatable :: r
     real(pReal) :: mu, sigma
 
+    allocate(r(N))
     call random_number(mu)
     call random_number(sigma)
 
@@ -1443,11 +1445,11 @@ subroutine selfTest
 
     call math_normal(r,mu,sigma)
 
-    if (abs(mu -sum(r)/real(size(r),pReal))>5.0e-2_pReal) &
+    if (abs(mu -sum(r)/real(N,pReal))>5.0e-2_pReal) &
       error stop 'math_normal(mu)'
 
-    mu = sum(r)/real(size(r),pReal)
-    if (abs(sigma**2 -1.0_pReal/real(size(r)-1,pReal) * sum((r-mu)**2))/sigma > 5.0e-2_pReal) &
+    mu = sum(r)/real(N,pReal)
+    if (abs(sigma**2 -1.0_pReal/real(N-1,pReal) * sum((r-mu)**2))/sigma > 5.0e-2_pReal) &
       error stop 'math_normal(sigma)'
   end block normal_distribution
 

From de9183af4e78d4663c062d2b0174ab2dc2db0910 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 21:55:49 +0100
Subject: [PATCH 012/133] functions without side-effects are 'pure'

basically all 'getter' functions should be pure
---
 src/phase_mechanical.f90         | 6 +++---
 src/phase_mechanical_elastic.f90 | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/phase_mechanical.f90 b/src/phase_mechanical.f90
index 37e6fe7bf..1917d81c9 100644
--- a/src/phase_mechanical.f90
+++ b/src/phase_mechanical.f90
@@ -168,17 +168,17 @@ submodule(phase) mechanical
       integer,     intent(in) :: ph,en
     end function plastic_dislotwin_homogenizedC
 
-    module function elastic_C66(ph,en) result(C66)
+    pure module function elastic_C66(ph,en) result(C66)
       real(pReal), dimension(6,6) :: C66
       integer,     intent(in) :: ph, en
     end function elastic_C66
 
-    module function elastic_mu(ph,en) result(mu)
+    pure module function elastic_mu(ph,en) result(mu)
       real(pReal) :: mu
       integer, intent(in) :: ph, en
     end function elastic_mu
 
-    module function elastic_nu(ph,en) result(nu)
+    pure module function elastic_nu(ph,en) result(nu)
       real(pReal) :: nu
       integer, intent(in) :: ph, en
     end function elastic_nu
diff --git a/src/phase_mechanical_elastic.f90 b/src/phase_mechanical_elastic.f90
index acbbac236..24797a880 100644
--- a/src/phase_mechanical_elastic.f90
+++ b/src/phase_mechanical_elastic.f90
@@ -86,7 +86,7 @@ end subroutine elastic_init
 !--------------------------------------------------------------------------------------------------
 !> @brief return 6x6 elasticity tensor
 !--------------------------------------------------------------------------------------------------
-module function elastic_C66(ph,en) result(C66)
+pure module function elastic_C66(ph,en) result(C66)
 
   integer, intent(in) :: &
     ph, &
@@ -140,7 +140,7 @@ end function elastic_C66
 !--------------------------------------------------------------------------------------------------
 !> @brief return shear modulus
 !--------------------------------------------------------------------------------------------------
-module function elastic_mu(ph,en) result(mu)
+pure module function elastic_mu(ph,en) result(mu)
 
   integer, intent(in) :: &
     ph, &
@@ -157,7 +157,7 @@ end function elastic_mu
 !--------------------------------------------------------------------------------------------------
 !> @brief return Poisson ratio
 !--------------------------------------------------------------------------------------------------
-module function elastic_nu(ph,en) result(nu)
+pure module function elastic_nu(ph,en) result(nu)
 
   integer, intent(in) :: &
     ph, &

From 1661b815b21db384545f5476294ce3b4332c3c43 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 22:02:29 +0100
Subject: [PATCH 013/133] correct calculation of temperature dependent stacking
 fault energy

---
 src/phase_mechanical_plastic_dislotwin.f90 | 13 +++++++------
 src/phase_mechanical_plastic_nonlocal.f90  |  2 +-
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 78681fa24..805b3cc43 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -153,10 +153,10 @@ module function plastic_dislotwin_init() result(myPlasticity)
   print'(/,a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
 
   print'(/,1x,a)', 'A. Ma and F. Roters, Acta Materialia 52(12):3603–3612, 2004'
-  print'(  1x,a)', 'https://doi.org/10.1016/j.actamat.2004.04.012'//IO_EOL
+  print'(  1x,a)', 'https://doi.org/10.1016/j.actamat.2004.04.012'
 
   print'(/,1x,a)', 'F. Roters et al., Computational Materials Science 39:91–95, 2007'
-  print'(  1x,a)', 'https://doi.org/10.1016/j.commatsci.2006.04.014'//IO_EOL
+  print'(  1x,a)', 'https://doi.org/10.1016/j.commatsci.2006.04.014'
 
   print'(/,1x,a)', 'S.L. Wong et al., Acta Materialia 118:140–151, 2016'
   print'(  1x,a)', 'https://doi.org/10.1016/j.actamat.2016.07.032'
@@ -656,12 +656,14 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
     dot_gamma_tr
   real(pReal) :: &
     mu, &
-    nu
+    nu, &
+    Gamma
 
   associate(prm => param(ph), stt => state(ph), dot => dotState(ph), dst => dependentState(ph))
 
     mu = elastic_mu(ph,en)
     nu = elastic_nu(ph,en)
+    Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
 
     f_matrix = 1.0_pReal &
              - sum(stt%f_tw(1:prm%sum_N_tw,en)) &
@@ -689,8 +691,7 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
         else
           ! Argon & Moffat, Acta Metallurgica, Vol. 29, pg 293 to 299, 1981
           sigma_cl = dot_product(prm%n0_sl(1:3,i),matmul(Mp,prm%n0_sl(1:3,i)))
-          b_d = merge(24.0_pReal*PI*(1.0_pReal - nu)/(2.0_pReal + nu) &
-                        * (prm%Gamma_sf(1) + prm%Gamma_sf(2) * T) / (mu*prm%b_sl(i)), &
+          b_d = merge(24.0_pReal*PI*(1.0_pReal - nu)/(2.0_pReal + nu) * Gamma / (mu*prm%b_sl(i)), &
                       1.0_pReal, &
                       prm%ExtendedDislocations)
           v_cl = 2.0_pReal*prm%omega*b_d**2*exp(-prm%Q_cl/(K_B*T)) &
@@ -756,7 +757,7 @@ module subroutine dislotwin_dependentState(T,ph,en)
     sumf_tw = sum(stt%f_tw(1:prm%sum_N_tw,en))
     sumf_tr = sum(stt%f_tr(1:prm%sum_N_tr,en))
 
-    Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * T
+    Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
 
     !* rescaled volume fraction for topology
     f_over_t_tw = stt%f_tw(1:prm%sum_N_tw,en)/prm%t_tw                                              ! this is per system ...
diff --git a/src/phase_mechanical_plastic_nonlocal.f90 b/src/phase_mechanical_plastic_nonlocal.f90
index 7118055fe..9d88fb5fc 100644
--- a/src/phase_mechanical_plastic_nonlocal.f90
+++ b/src/phase_mechanical_plastic_nonlocal.f90
@@ -203,7 +203,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
   print'(/,a,i0)', ' # phases: ',Ninstances; flush(IO_STDOUT)
 
   print'(/,1x,a)', 'C. Reuber et al., Acta Materialia 71:333–348, 2014'
-  print'(  1x,a)', 'https://doi.org/10.1016/j.actamat.2014.03.012'//IO_EOL
+  print'(  1x,a)', 'https://doi.org/10.1016/j.actamat.2014.03.012'
 
   print'(/,1x,a)', 'C. Kords, Dissertation RWTH Aachen, 2014'
   print'(  1x,a)', 'http://publications.rwth-aachen.de/record/229993'

From da00f33487f5020310788273797abd425762713a Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 22:09:53 +0100
Subject: [PATCH 014/133] transformation is only for fcc

---
 src/phase_mechanical_plastic_dislotwin.f90 | 48 ++++++++--------------
 1 file changed, 18 insertions(+), 30 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 805b3cc43..b94a135f1 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -25,9 +25,9 @@ submodule(phase:plastic) dislotwin
       xi_sb               = 1.0_pReal, &                                                            !< value for shearband resistance
       v_sb                = 1.0_pReal, &                                                            !< value for shearband velocity_0
       E_sb                = 1.0_pReal, &                                                            !< activation energy for shear bands
-      delta_G             = 1.0_pReal, &                                                            !< Free energy difference between austensite and martensite
+      delta_G             = 1.0_pReal, &                                                            !< free energy difference between austensite and martensite
       i_tr                = 1.0_pReal, &                                                            !< adjustment parameter to calculate MFP for transformation
-      h                   = 1.0_pReal, &                                                            !< Stack height of hex nucleus
+      h                   = 1.0_pReal, &                                                            !< stack height of hex nucleus
       T_ref               = T_ROOM, &
       a_cI                = 1.0_pReal, &
       a_cF                = 1.0_pReal
@@ -40,14 +40,13 @@ submodule(phase:plastic) dislotwin
       Q_sl,&                                                                                        !< activation energy for glide [J] for each slip system
       v_0, &                                                                                        !< dislocation velocity prefactor [m/s] for each slip system
       dot_N_0_tw, &                                                                                 !< twin nucleation rate [1/m³s] for each twin system
-      dot_N_0_tr, &                                                                                 !< trans nucleation rate [1/m³s] for each trans system
       t_tw, &                                                                                       !< twin thickness [m] for each twin system
       i_sl, &                                                                                       !< Adj. parameter for distance between 2 forest dislocations for each slip system
       t_tr, &                                                                                       !< martensite lamellar thickness [m] for each trans system
       p, &                                                                                          !< p-exponent in glide velocity
       q, &                                                                                          !< q-exponent in glide velocity
-      r, &                                                                                          !< r-exponent in twin nucleation rate
-      s, &                                                                                          !< s-exponent in trans nucleation rate
+      r, &                                                                                          !< exponent in twin nucleation rate
+      s, &                                                                                          !< exponent in trans nucleation rate
       tau_0, &                                                                                      !< strength due to elements in solid solution
       gamma_char, &                                                                                 !< characteristic shear for twins
       B, &                                                                                          !< drag coefficient
@@ -306,10 +305,10 @@ module function plastic_dislotwin_init() result(myPlasticity)
       prm%b_tr = pl%get_as1dFloat('b_tr')
       prm%b_tr = math_expand(prm%b_tr,prm%N_tr)
 
-      prm%h             = pl%get_asFloat('h',       defaultVal=0.0_pReal) ! ToDo: How to handle that???
-      prm%i_tr          = pl%get_asFloat('i_tr',    defaultVal=0.0_pReal) ! ToDo: How to handle that???
+      prm%h             = pl%get_asFloat('h',       defaultVal=0.0_pReal) ! ToDo: This is not optional!
+      prm%i_tr          = pl%get_asFloat('i_tr',    defaultVal=0.0_pReal) ! ToDo: This is not optional!
       prm%delta_G       = pl%get_asFloat('delta_G')
-      prm%x_c_tr        = pl%get_asFloat('x_c_tr',  defaultVal=0.0_pReal) ! ToDo: How to handle that???
+      prm%x_c_tr        = pl%get_asFloat('x_c_tr',  defaultVal=0.0_pReal) ! ToDo: This is not optional!
       prm%L_tr          = pl%get_asFloat('L_tr')
       prm%a_cI          = pl%get_asFloat('a_cI',    defaultVal=0.0_pReal)
       prm%a_cF          = pl%get_asFloat('a_cF',    defaultVal=0.0_pReal)
@@ -324,10 +323,6 @@ module function plastic_dislotwin_init() result(myPlasticity)
                                                prm%a_cI, &
                                                prm%a_cF)
 
-      if (phase_lattice(ph) /= 'cF') then
-        prm%dot_N_0_tr = pl%get_as1dFloat('dot_N_0_tr')
-        prm%dot_N_0_tr = math_expand(prm%dot_N_0_tr,prm%N_tr)
-      endif
       prm%t_tr = pl%get_as1dFloat('t_tr')
       prm%t_tr = math_expand(prm%t_tr,prm%N_tr)
       prm%s    = pl%get_as1dFloat('p_tr',defaultVal=[0.0_pReal])
@@ -339,11 +334,8 @@ module function plastic_dislotwin_init() result(myPlasticity)
       if (    prm%i_tr          < 0.0_pReal)  extmsg = trim(extmsg)//' i_tr'
       if (any(prm%t_tr          < 0.0_pReal)) extmsg = trim(extmsg)//' t_tr'
       if (any(prm%s             < 0.0_pReal)) extmsg = trim(extmsg)//' p_tr'
-      if (phase_lattice(ph) /= 'cF') then
-        if (any(prm%dot_N_0_tr  < 0.0_pReal)) extmsg = trim(extmsg)//' dot_N_0_tr'
-      end if
     else transActive
-      allocate(prm%s,prm%b_tr,prm%t_tr,prm%dot_N_0_tr,source=emptyRealArray)
+      allocate(prm%s,prm%b_tr,prm%t_tr,source=emptyRealArray)
       allocate(prm%h_tr_tr(0,0))
     end if transActive
 
@@ -1042,20 +1034,16 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
     do i = 1, prm%sum_N_tr
       tau(i) = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
-      isFCC: if (prm%fccTwinTransNucleation) then
-        s1=prm%fcc_twinNucleationSlipPair(1,i)
-        s2=prm%fcc_twinNucleationSlipPair(2,i)
-        if (tau(i) < dst%tau_r_tr(i,en)) then                                                       ! ToDo: correct?
-          Ndot0=(abs(dot_gamma_sl(s1))*(stt%rho_mob(s2,en)+stt%rho_dip(s2,en))+&
-                 abs(dot_gamma_sl(s2))*(stt%rho_mob(s1,en)+stt%rho_dip(s1,en)))/&
-                  (prm%L_tr*prm%b_sl(i))*&
-                  (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tr(i,en)-tau(i))))
-        else
-          Ndot0=0.0_pReal
-        end if
-      else isFCC
-        Ndot0=prm%dot_N_0_tr(i)
-      end if isFCC
+      s1=prm%fcc_twinNucleationSlipPair(1,i)
+      s2=prm%fcc_twinNucleationSlipPair(2,i)
+      if (tau(i) < dst%tau_r_tr(i,en)) then                                                         ! ToDo: correct?
+        Ndot0=(abs(dot_gamma_sl(s1))*(stt%rho_mob(s2,en)+stt%rho_dip(s2,en))+&
+               abs(dot_gamma_sl(s2))*(stt%rho_mob(s1,en)+stt%rho_dip(s1,en)))/&
+                (prm%L_tr*prm%b_sl(i))*&
+                (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tr(i,en)-tau(i))))
+      else
+        Ndot0=0.0_pReal
+      end if
     end do
 
     significantStress: where(tau > tol_math_check)

From d130225c9f90939676bb4ff3cfd66420574b2c23 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 22:13:48 +0100
Subject: [PATCH 015/133] polishing

---
 src/phase_mechanical_plastic_dislotwin.f90 | 42 +++++++++++-----------
 src/phase_mechanical_plastic_nonlocal.f90  |  1 -
 2 files changed, 21 insertions(+), 22 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index b94a135f1..09c7ca35c 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -779,9 +779,8 @@ module subroutine dislotwin_dependentState(T,ph,en)
                          + 3.0_pReal*prm%b_tr*mu/(prm%L_tr*prm%b_tr) &
                          + prm%h*prm%delta_G/(3.0_pReal*prm%b_tr)
 
-    dst%V_tw(:,en) = (PI/4.0_pReal)*prm%t_tw*dst%Lambda_tw(:,en)**2
-    dst%V_tr(:,en) = (PI/4.0_pReal)*prm%t_tr*dst%Lambda_tr(:,en)**2
-
+    dst%V_tw(:,en) = PI/4.0_pReal*dst%Lambda_tw(:,en)**2*prm%t_tw
+    dst%V_tr(:,en) = PI/4.0_pReal*dst%Lambda_tr(:,en)**2*prm%t_tr
 
     x0 = mu*prm%b_tw**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                  ! ToDo: In the paper, this is the Burgers vector for slip
     dst%tau_r_tw(:,en) = mu*prm%b_tw/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(pi/3.0_pReal)/x0)
@@ -954,11 +953,12 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
 
   real, dimension(param(ph)%sum_N_tw) :: &
     tau, &
-    Ndot0, &
+    dot_N_0, &
     stressRatio_r, &
     ddot_gamma_dtau
-
-  integer :: i,s1,s2
+  integer, dimension(2) :: &
+    s
+  integer :: i
 
 
   associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
@@ -966,24 +966,23 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
     do i = 1, prm%sum_N_tw
       tau(i) = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
       isFCC: if (prm%fccTwinTransNucleation) then
-        s1=prm%fcc_twinNucleationSlipPair(1,i)
-        s2=prm%fcc_twinNucleationSlipPair(2,i)
         if (tau(i) < dst%tau_r_tw(i,en)) then                                                       ! ToDo: correct?
-          Ndot0=(abs(dot_gamma_sl(s1))*(stt%rho_mob(s2,en)+stt%rho_dip(s2,en))+&
-                 abs(dot_gamma_sl(s2))*(stt%rho_mob(s1,en)+stt%rho_dip(s1,en)))/&
+          s=prm%fcc_twinNucleationSlipPair(1:2,i)
+          dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
+                   abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
                   (prm%L_tw*prm%b_sl(i))*&
                   (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tw(i,en)-tau(i))))
         else
-          Ndot0=0.0_pReal
+          dot_N_0=0.0_pReal
         end if
       else isFCC
-        Ndot0=prm%dot_N_0_tw(i)
+        dot_N_0=prm%dot_N_0_tw(i)
       end if isFCC
     end do
 
     significantStress: where(tau > tol_math_check)
       StressRatio_r   = (dst%tau_hat_tw(:,en)/tau)**prm%r
-      dot_gamma_tw    = prm%gamma_char * dst%V_tw(:,en) * Ndot0*exp(-StressRatio_r)
+      dot_gamma_tw    = prm%gamma_char * dst%V_tw(:,en) * dot_N_0*exp(-StressRatio_r)
       ddot_gamma_dtau = (dot_gamma_tw*prm%r/tau)*StressRatio_r
     else where significantStress
       dot_gamma_tw    = 0.0_pReal
@@ -1024,31 +1023,32 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
   real, dimension(param(ph)%sum_N_tr) :: &
     tau, &
-    Ndot0, &
+    dot_N_0, &
     stressRatio_s, &
     ddot_gamma_dtau
-  integer :: i,s1,s2
+  integer, dimension(2) :: &
+    s
+  integer :: i
 
 
   associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
 
     do i = 1, prm%sum_N_tr
       tau(i) = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
-      s1=prm%fcc_twinNucleationSlipPair(1,i)
-      s2=prm%fcc_twinNucleationSlipPair(2,i)
       if (tau(i) < dst%tau_r_tr(i,en)) then                                                         ! ToDo: correct?
-        Ndot0=(abs(dot_gamma_sl(s1))*(stt%rho_mob(s2,en)+stt%rho_dip(s2,en))+&
-               abs(dot_gamma_sl(s2))*(stt%rho_mob(s1,en)+stt%rho_dip(s1,en)))/&
+        s=prm%fcc_twinNucleationSlipPair(1:2,i)
+        dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
+                 abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
                 (prm%L_tr*prm%b_sl(i))*&
                 (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tr(i,en)-tau(i))))
       else
-        Ndot0=0.0_pReal
+        dot_N_0=0.0_pReal
       end if
     end do
 
     significantStress: where(tau > tol_math_check)
       StressRatio_s   = (dst%tau_hat_tr(:,en)/tau)**prm%s
-      dot_gamma_tr    = dst%V_tr(:,en) * Ndot0*exp(-StressRatio_s)
+      dot_gamma_tr    = dst%V_tr(:,en) * dot_N_0*exp(-StressRatio_s)
       ddot_gamma_dtau = (dot_gamma_tr*prm%s/tau)*StressRatio_s
     else where significantStress
       dot_gamma_tr  = 0.0_pReal
diff --git a/src/phase_mechanical_plastic_nonlocal.f90 b/src/phase_mechanical_plastic_nonlocal.f90
index 9d88fb5fc..1715af2d9 100644
--- a/src/phase_mechanical_plastic_nonlocal.f90
+++ b/src/phase_mechanical_plastic_nonlocal.f90
@@ -1570,7 +1570,6 @@ subroutine stateInit(ini,phase,Nentries)
     upto, &
     s
   real(pReal), dimension(2) :: &
-    noise, &
     rnd
   real(pReal) :: &
     meanDensity, &

From f2b6ddece1f44ffb23e587a362cef195e6c890a4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 22:36:06 +0100
Subject: [PATCH 016/133] reduce memory footprint

---
 src/phase_mechanical_plastic_dislotwin.f90 | 42 ++++++++++++++--------
 1 file changed, 27 insertions(+), 15 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 09c7ca35c..e96c0dbbf 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -103,9 +103,7 @@ submodule(phase:plastic) dislotwin
       tau_hat_tw, &                                                                                 !< threshold stress for twinning
       tau_hat_tr, &                                                                                 !< threshold stress for transformation
       V_tw, &                                                                                       !< volume of a new twin
-      V_tr, &                                                                                       !< volume of a new martensite disc
-      tau_r_tw, &                                                                                   !< stress to bring partials close together (twin)
-      tau_r_tr                                                                                      !< stress to bring partials close together (trans)
+      V_tr                                                                                          !< volume of a new martensite disc
   end type tDislotwinDependentState
 
 !--------------------------------------------------------------------------------------------------
@@ -435,12 +433,10 @@ module function plastic_dislotwin_init() result(myPlasticity)
 
     allocate(dst%Lambda_tw             (prm%sum_N_tw,Nmembers),source=0.0_pReal)
     allocate(dst%tau_hat_tw            (prm%sum_N_tw,Nmembers),source=0.0_pReal)
-    allocate(dst%tau_r_tw              (prm%sum_N_tw,Nmembers),source=0.0_pReal)
     allocate(dst%V_tw                  (prm%sum_N_tw,Nmembers),source=0.0_pReal)
 
     allocate(dst%Lambda_tr             (prm%sum_N_tr,Nmembers),source=0.0_pReal)
     allocate(dst%tau_hat_tr            (prm%sum_N_tr,Nmembers),source=0.0_pReal)
-    allocate(dst%tau_r_tr              (prm%sum_N_tr,Nmembers),source=0.0_pReal)
     allocate(dst%V_tr                  (prm%sum_N_tr,Nmembers),source=0.0_pReal)
 
     end associate
@@ -782,12 +778,6 @@ module subroutine dislotwin_dependentState(T,ph,en)
     dst%V_tw(:,en) = PI/4.0_pReal*dst%Lambda_tw(:,en)**2*prm%t_tw
     dst%V_tr(:,en) = PI/4.0_pReal*dst%Lambda_tr(:,en)**2*prm%t_tr
 
-    x0 = mu*prm%b_tw**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                  ! ToDo: In the paper, this is the Burgers vector for slip
-    dst%tau_r_tw(:,en) = mu*prm%b_tw/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(pi/3.0_pReal)/x0)
-
-    x0 = mu*prm%b_tr**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                  ! ToDo: In the paper, this is the Burgers vector for slip
-    dst%tau_r_tr(:,en) = mu*prm%b_tr/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(pi/3.0_pReal)/x0)
-
   end associate
 
 end subroutine dislotwin_dependentState
@@ -956,6 +946,11 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
     dot_N_0, &
     stressRatio_r, &
     ddot_gamma_dtau
+  real :: &
+    x0, &
+    tau_r, &
+    Gamma, &
+    mu, nu
   integer, dimension(2) :: &
     s
   integer :: i
@@ -963,15 +958,21 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
 
   associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
 
+    mu = elastic_mu(ph,en)
+    nu = elastic_nu(ph,en)
+    Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
+
     do i = 1, prm%sum_N_tw
       tau(i) = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
       isFCC: if (prm%fccTwinTransNucleation) then
-        if (tau(i) < dst%tau_r_tw(i,en)) then                                                       ! ToDo: correct?
+        x0 = mu*prm%b_tw(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                   ! ToDo: In the paper, this is the Burgers vector for slip
+        tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(pi/3.0_pReal)/x0)
+        if (tau(i) < tau_r) then                                                                    ! ToDo: correct?
           s=prm%fcc_twinNucleationSlipPair(1:2,i)
           dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
                    abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
                   (prm%L_tw*prm%b_sl(i))*&
-                  (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tw(i,en)-tau(i))))
+                  (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
         else
           dot_N_0=0.0_pReal
         end if
@@ -1026,6 +1027,11 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
     dot_N_0, &
     stressRatio_s, &
     ddot_gamma_dtau
+  real :: &
+    x0, &
+    tau_r, &
+    Gamma, &
+    mu, nu
   integer, dimension(2) :: &
     s
   integer :: i
@@ -1033,14 +1039,20 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
   associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
 
+    mu = elastic_mu(ph,en)
+    nu = elastic_nu(ph,en)
+    Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
+
     do i = 1, prm%sum_N_tr
       tau(i) = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
-      if (tau(i) < dst%tau_r_tr(i,en)) then                                                         ! ToDo: correct?
+      x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, this is the Burgers vector for slip              ! ToDo: In the paper, this is the Burgers vector for slip
+      tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(pi/3.0_pReal)/x0)
+      if (tau(i) < tau_r) then                                                                      ! ToDo: correct?
         s=prm%fcc_twinNucleationSlipPair(1:2,i)
         dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
                  abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
                 (prm%L_tr*prm%b_sl(i))*&
-                (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(dst%tau_r_tr(i,en)-tau(i))))
+                (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
       else
         dot_N_0=0.0_pReal
       end if

From 0116e2dae605a062d0f6586a9a18239b7cf208df Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 30 Dec 2021 22:38:39 +0100
Subject: [PATCH 017/133] bugfix: write only to active twin/trans system

---
 src/phase_mechanical_plastic_dislotwin.f90 | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index e96c0dbbf..b8f3516ed 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -969,15 +969,14 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
         tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(pi/3.0_pReal)/x0)
         if (tau(i) < tau_r) then                                                                    ! ToDo: correct?
           s=prm%fcc_twinNucleationSlipPair(1:2,i)
-          dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                   abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
-                  (prm%L_tw*prm%b_sl(i))*&
-                  (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
+          dot_N_0(i)=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
+                      abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
+                     (prm%L_tw*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
         else
-          dot_N_0=0.0_pReal
+          dot_N_0(i)=0.0_pReal
         end if
       else isFCC
-        dot_N_0=prm%dot_N_0_tw(i)
+        dot_N_0(i)=prm%dot_N_0_tw(i)
       end if isFCC
     end do
 
@@ -1045,16 +1044,15 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
     do i = 1, prm%sum_N_tr
       tau(i) = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
-      x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, this is the Burgers vector for slip              ! ToDo: In the paper, this is the Burgers vector for slip
+      x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, this is the Burgers vector for slip
       tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(pi/3.0_pReal)/x0)
       if (tau(i) < tau_r) then                                                                      ! ToDo: correct?
         s=prm%fcc_twinNucleationSlipPair(1:2,i)
-        dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                 abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
-                (prm%L_tr*prm%b_sl(i))*&
-                (1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
+        dot_N_0(i)=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
+                    abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
+                   (prm%L_tr*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
       else
-        dot_N_0=0.0_pReal
+        dot_N_0(i)=0.0_pReal
       end if
     end do
 

From 017c182640a079b2b4cfdfc37d35506d95d0a0f7 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 31 Dec 2021 08:45:55 +0100
Subject: [PATCH 018/133] branch only once

---
 src/phase_mechanical_plastic_dislotwin.f90 | 36 +++++++++-------------
 1 file changed, 15 insertions(+), 21 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index b8f3516ed..5e4b757c7 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -966,7 +966,7 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
       tau(i) = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
       isFCC: if (prm%fccTwinTransNucleation) then
         x0 = mu*prm%b_tw(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                   ! ToDo: In the paper, this is the Burgers vector for slip
-        tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(pi/3.0_pReal)/x0)
+        tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0)
         if (tau(i) < tau_r) then                                                                    ! ToDo: correct?
           s=prm%fcc_twinNucleationSlipPair(1:2,i)
           dot_N_0(i)=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
@@ -1022,13 +1022,12 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
     ddot_gamma_dtau_tr
 
   real, dimension(param(ph)%sum_N_tr) :: &
-    tau, &
-    dot_N_0, &
-    stressRatio_s, &
     ddot_gamma_dtau
   real :: &
+    stressRatio_s, &
+    tau, tau_r, &
+    dot_N_0, &
     x0, &
-    tau_r, &
     Gamma, &
     mu, nu
   integer, dimension(2) :: &
@@ -1043,28 +1042,23 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
     Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
 
     do i = 1, prm%sum_N_tr
-      tau(i) = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
+      tau = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
       x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, this is the Burgers vector for slip
-      tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(pi/3.0_pReal)/x0)
-      if (tau(i) < tau_r) then                                                                      ! ToDo: correct?
+      tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0)
+      if (tau > tol_math_check .and. tau < tau_r) then
         s=prm%fcc_twinNucleationSlipPair(1:2,i)
-        dot_N_0(i)=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                    abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
-                   (prm%L_tr*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
+        dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
+                 abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
+                (prm%L_tr*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau)))
+        StressRatio_s = (dst%tau_hat_tr(i,en)/tau)**prm%s(i)
+        dot_gamma_tr(i) = dst%V_tr(i,en) * dot_N_0*exp(-StressRatio_s)
+        ddot_gamma_dtau(i) = (dot_gamma_tr(i)*prm%s(i)/tau)*StressRatio_s
       else
-        dot_N_0(i)=0.0_pReal
+        dot_gamma_tr(i) = 0.0_pReal
+        ddot_gamma_dtau(i) = 0.0_pReal
       end if
     end do
 
-    significantStress: where(tau > tol_math_check)
-      StressRatio_s   = (dst%tau_hat_tr(:,en)/tau)**prm%s
-      dot_gamma_tr    = dst%V_tr(:,en) * dot_N_0*exp(-StressRatio_s)
-      ddot_gamma_dtau = (dot_gamma_tr*prm%s/tau)*StressRatio_s
-    else where significantStress
-      dot_gamma_tr  = 0.0_pReal
-      ddot_gamma_dtau = 0.0_pReal
-    end where significantStress
-
   end associate
 
   if (present(ddot_gamma_dtau_tr)) ddot_gamma_dtau_tr = ddot_gamma_dtau

From e678b231d99859f098e12f65f97b5214b2ee3608 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 31 Dec 2021 09:01:23 +0100
Subject: [PATCH 019/133] following naming convention

---
 src/phase_mechanical_plastic_dislotwin.f90 | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 5e4b757c7..3c666934a 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -944,7 +944,7 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
   real, dimension(param(ph)%sum_N_tw) :: &
     tau, &
     dot_N_0, &
-    stressRatio_r, &
+    ratio_tau_r, &
     ddot_gamma_dtau
   real :: &
     x0, &
@@ -981,11 +981,11 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
     end do
 
     significantStress: where(tau > tol_math_check)
-      StressRatio_r   = (dst%tau_hat_tw(:,en)/tau)**prm%r
-      dot_gamma_tw    = prm%gamma_char * dst%V_tw(:,en) * dot_N_0*exp(-StressRatio_r)
-      ddot_gamma_dtau = (dot_gamma_tw*prm%r/tau)*StressRatio_r
+      ratio_tau_r = (dst%tau_hat_tw(:,en)/tau)**prm%r
+      dot_gamma_tw = prm%gamma_char * dst%V_tw(:,en) * dot_N_0*exp(-ratio_tau_r)
+      ddot_gamma_dtau = (dot_gamma_tw*prm%r/tau)*ratio_tau_r
     else where significantStress
-      dot_gamma_tw    = 0.0_pReal
+      dot_gamma_tw = 0.0_pReal
       ddot_gamma_dtau = 0.0_pReal
     end where significantStress
 
@@ -1024,7 +1024,7 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
   real, dimension(param(ph)%sum_N_tr) :: &
     ddot_gamma_dtau
   real :: &
-    stressRatio_s, &
+    ratio_tau_s, &
     tau, tau_r, &
     dot_N_0, &
     x0, &
@@ -1046,13 +1046,16 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
       x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, this is the Burgers vector for slip
       tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0)
       if (tau > tol_math_check .and. tau < tau_r) then
+
+        ratio_tau_s = (dst%tau_hat_tr(i,en)/tau)**prm%s(i)
+
         s=prm%fcc_twinNucleationSlipPair(1:2,i)
         dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
                  abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
                 (prm%L_tr*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau)))
-        StressRatio_s = (dst%tau_hat_tr(i,en)/tau)**prm%s(i)
-        dot_gamma_tr(i) = dst%V_tr(i,en) * dot_N_0*exp(-StressRatio_s)
-        ddot_gamma_dtau(i) = (dot_gamma_tr(i)*prm%s(i)/tau)*StressRatio_s
+
+        dot_gamma_tr(i) = dst%V_tr(i,en) * dot_N_0*exp(-ratio_tau_s)
+        ddot_gamma_dtau(i) = (dot_gamma_tr(i)*prm%s(i)/tau)*ratio_tau_s
       else
         dot_gamma_tr(i) = 0.0_pReal
         ddot_gamma_dtau(i) = 0.0_pReal

From 770cf33667739b80daa68b170f666d2f16d9b66f Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 1 Jan 2022 11:37:04 +0100
Subject: [PATCH 020/133] correct calculation of tangent.

thanks to Seyedamirhossein Motaman (RWTH Aachen) for reporting
---
 src/phase_mechanical_plastic_dislotwin.f90 | 116 ++++++++++++---------
 1 file changed, 64 insertions(+), 52 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 3c666934a..5d2191726 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -17,8 +17,8 @@ submodule(phase:plastic) dislotwin
       p_sb                = 1.0_pReal, &                                                            !< p-exponent in shear band velocity
       q_sb                = 1.0_pReal, &                                                            !< q-exponent in shear band velocity
       i_tw                = 1.0_pReal, &                                                            !< adjustment parameter to calculate MFP for twinning
-      L_tw                = 1.0_pReal, &                                                            !< Length of twin nuclei in Burgers vectors
-      L_tr                = 1.0_pReal, &                                                            !< Length of trans nuclei in Burgers vectors
+      L_tw                = 1.0_pReal, &                                                            !< length of twin nuclei in Burgers vectors: TODO unit should be meters
+      L_tr                = 1.0_pReal, &                                                            !< length of trans nuclei in Burgers vectors: TODO unit should be meters
       x_c_tw              = 1.0_pReal, &                                                            !< critical distance for formation of twin nucleus
       x_c_tr              = 1.0_pReal, &                                                            !< critical distance for formation of trans nucleus
       V_cs                = 1.0_pReal, &                                                            !< cross slip volume
@@ -731,8 +731,6 @@ module subroutine dislotwin_dependentState(T,ph,en)
    real(pReal), dimension(param(ph)%sum_N_tr) :: &
     inv_lambda_tr_tr, &                                                                             !< 1/mean free distance between 2 martensite stacks from different systems seen by a growing martensite
     f_over_t_tr
-  real(pReal), dimension(:), allocatable :: &
-    x0
   real(pReal) :: &
     mu, &
     nu
@@ -941,16 +939,15 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
   real(pReal), dimension(param(ph)%sum_N_tw), optional, intent(out) :: &
     ddot_gamma_dtau_tw
 
-  real, dimension(param(ph)%sum_N_tw) :: &
-    tau, &
-    dot_N_0, &
-    ratio_tau_r, &
-    ddot_gamma_dtau
   real :: &
+    ratio_tau_s, &
+    tau, tau_r, &
+    dot_N_0, &
     x0, &
-    tau_r, &
     Gamma, &
-    mu, nu
+    mu, nu, &
+    P_ncs, dP_ncs_dtau, &
+    P, dP_dtau
   integer, dimension(2) :: &
     s
   integer :: i
@@ -958,41 +955,53 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
 
   associate(prm => param(ph), stt => state(ph), dst => dependentState(ph))
 
-    mu = elastic_mu(ph,en)
-    nu = elastic_nu(ph,en)
-    Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
+    isFCC: if (prm%fccTwinTransNucleation) then
+      mu = elastic_mu(ph,en)
+      nu = elastic_nu(ph,en)
+      Gamma = prm%Gamma_sf(1) + prm%Gamma_sf(2) * (T-prm%T_ref)
 
-    do i = 1, prm%sum_N_tw
-      tau(i) = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
-      isFCC: if (prm%fccTwinTransNucleation) then
-        x0 = mu*prm%b_tw(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                   ! ToDo: In the paper, this is the Burgers vector for slip
+      do i = 1, prm%sum_N_tw
+        tau = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
+        x0 = mu*prm%b_tw(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                   ! ToDo: In the paper, the Burgers vector for slip is used
         tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0)
-        if (tau(i) < tau_r) then                                                                    ! ToDo: correct?
-          s=prm%fcc_twinNucleationSlipPair(1:2,i)
-          dot_N_0(i)=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                      abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
-                     (prm%L_tw*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau(i))))
-        else
-          dot_N_0(i)=0.0_pReal
-        end if
-      else isFCC
-        dot_N_0(i)=prm%dot_N_0_tw(i)
-      end if isFCC
-    end do
 
-    significantStress: where(tau > tol_math_check)
-      ratio_tau_r = (dst%tau_hat_tw(:,en)/tau)**prm%r
-      dot_gamma_tw = prm%gamma_char * dst%V_tw(:,en) * dot_N_0*exp(-ratio_tau_r)
-      ddot_gamma_dtau = (dot_gamma_tw*prm%r/tau)*ratio_tau_r
-    else where significantStress
-      dot_gamma_tw = 0.0_pReal
-      ddot_gamma_dtau = 0.0_pReal
-    end where significantStress
+        if (tau > tol_math_check .and. tau < tau_r) then
+          ratio_tau_s = (dst%tau_hat_tw(i,en)/tau)**prm%r(i)
+          P = exp(-ratio_tau_s)
+          dP_dTau = prm%r(i) * ratio_tau_s/tau * P
+
+          s=prm%fcc_twinNucleationSlipPair(1:2,i)
+          dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
+                   abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/(prm%L_tw*prm%b_sl(i))
+
+          P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
+          dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
+
+          dot_gamma_tw(i) = dst%V_tw(i,en)*dot_N_0*P_ncs*P
+          if (present(ddot_gamma_dtau_tw)) &
+            ddot_gamma_dtau_tw(i) = dst%V_tw(i,en)*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
+        else
+          dot_gamma_tw(i) = 0.0_pReal
+          if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
+        end if
+      end do
+
+    else isFCC
+      do i = 1, prm%sum_N_tw
+        error stop 'not implemented'
+        tau = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
+        if (tau > tol_math_check) then
+          dot_gamma_tw(i) = 0.0_pReal
+          if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
+        else
+          dot_gamma_tw(i) = 0.0_pReal
+          if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
+        end if
+      end do
+    end if isFCC
 
   end associate
 
-  if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw = ddot_gamma_dtau
-
 end subroutine kinetics_tw
 
 
@@ -1021,15 +1030,15 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
   real(pReal), dimension(param(ph)%sum_N_tr), optional, intent(out) :: &
     ddot_gamma_dtau_tr
 
-  real, dimension(param(ph)%sum_N_tr) :: &
-    ddot_gamma_dtau
   real :: &
     ratio_tau_s, &
     tau, tau_r, &
     dot_N_0, &
     x0, &
     Gamma, &
-    mu, nu
+    mu, nu, &
+    P_ncs, dP_ncs_dtau, &
+    P, dP_dtau
   integer, dimension(2) :: &
     s
   integer :: i
@@ -1043,29 +1052,32 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
     do i = 1, prm%sum_N_tr
       tau = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
-      x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, this is the Burgers vector for slip
+      x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, the Burgers vector for slip is used
       tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0)
-      if (tau > tol_math_check .and. tau < tau_r) then
 
+      if (tau > tol_math_check .and. tau < tau_r) then
         ratio_tau_s = (dst%tau_hat_tr(i,en)/tau)**prm%s(i)
+        P = exp(-ratio_tau_s)
+        dP_dTau = prm%s(i) * ratio_tau_s/tau * P
 
         s=prm%fcc_twinNucleationSlipPair(1:2,i)
         dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                 abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/&
-                (prm%L_tr*prm%b_sl(i))*(1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau)))
+                 abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/(prm%L_tr*prm%b_sl(i))
 
-        dot_gamma_tr(i) = dst%V_tr(i,en) * dot_N_0*exp(-ratio_tau_s)
-        ddot_gamma_dtau(i) = (dot_gamma_tr(i)*prm%s(i)/tau)*ratio_tau_s
+        P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
+        dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
+
+        dot_gamma_tr(i) = dst%V_tr(i,en)*dot_N_0*P_ncs*P
+        if (present(ddot_gamma_dtau_tr)) &
+          ddot_gamma_dtau_tr(i) = dst%V_tr(i,en)*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
       else
         dot_gamma_tr(i) = 0.0_pReal
-        ddot_gamma_dtau(i) = 0.0_pReal
+        if (present(ddot_gamma_dtau_tr)) ddot_gamma_dtau_tr(i) = 0.0_pReal
       end if
     end do
 
   end associate
 
-  if (present(ddot_gamma_dtau_tr)) ddot_gamma_dtau_tr = ddot_gamma_dtau
-
 end subroutine kinetics_tr
 
 end submodule dislotwin

From d181b988c14ba48469658e115424c0b5bc62970d Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 1 Jan 2022 10:47:15 +0100
Subject: [PATCH 021/133] using vector access

---
 src/phase_mechanical_plastic_dislotwin.f90 | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 5d2191726..a2f0ce732 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -970,9 +970,9 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
           P = exp(-ratio_tau_s)
           dP_dTau = prm%r(i) * ratio_tau_s/tau * P
 
-          s=prm%fcc_twinNucleationSlipPair(1:2,i)
-          dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                   abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/(prm%L_tw*prm%b_sl(i))
+          s = prm%fcc_twinNucleationSlipPair(1:2,i)
+          dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &
+                  / (prm%L_tw*prm%b_sl(i))
 
           P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
           dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
@@ -1060,9 +1060,9 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
         P = exp(-ratio_tau_s)
         dP_dTau = prm%s(i) * ratio_tau_s/tau * P
 
-        s=prm%fcc_twinNucleationSlipPair(1:2,i)
-        dot_N_0=(abs(dot_gamma_sl(s(1)))*(stt%rho_mob(s(2),en)+stt%rho_dip(s(2),en))+&
-                 abs(dot_gamma_sl(s(2)))*(stt%rho_mob(s(1),en)+stt%rho_dip(s(1),en)))/(prm%L_tr*prm%b_sl(i))
+        s = prm%fcc_twinNucleationSlipPair(1:2,i)
+        dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &
+                / (prm%L_tr*prm%b_sl(i))
 
         P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
         dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)

From 03c6708629ce603ff560555aaaa0c5389b1456bd Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 1 Jan 2022 11:26:31 +0100
Subject: [PATCH 022/133] polishing

---
 src/phase_mechanical_plastic_dislotwin.f90 | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index a2f0ce732..6a9043cde 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -940,7 +940,7 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
     ddot_gamma_dtau_tw
 
   real :: &
-    ratio_tau_s, &
+    ratio_tau_r, &
     tau, tau_r, &
     dot_N_0, &
     x0, &
@@ -962,13 +962,13 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
 
       do i = 1, prm%sum_N_tw
         tau = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
-        x0 = mu*prm%b_tw(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                   ! ToDo: In the paper, the Burgers vector for slip is used
-        tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0)
+        x0 = mu*prm%b_tr(i)**2*(2.0_pReal+nu)/(Gamma*8.0_pReal*PI*(1.0_pReal-nu))                   ! ToDo: In the paper, the Burgers vector for slip is used
+        tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0)      ! ToDo: In the paper, the Burgers vector for slip is used
 
         if (tau > tol_math_check .and. tau < tau_r) then
-          ratio_tau_s = (dst%tau_hat_tw(i,en)/tau)**prm%r(i)
-          P = exp(-ratio_tau_s)
-          dP_dTau = prm%r(i) * ratio_tau_s/tau * P
+          ratio_tau_r = (dst%tau_hat_tw(i,en)/tau)**prm%r(i)
+          P = exp(-ratio_tau_r)
+          dP_dTau = prm%r(i) * ratio_tau_r/tau * P
 
           s = prm%fcc_twinNucleationSlipPair(1:2,i)
           dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &
@@ -1052,8 +1052,8 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
     do i = 1, prm%sum_N_tr
       tau = math_tensordot(Mp,prm%P_tr(1:3,1:3,i))
-      x0 = mu*prm%b_tr(i)**2/(Gamma*8.0_pReal*PI)*(2.0_pReal+nu)/(1.0_pReal-nu)                     ! ToDo: In the paper, the Burgers vector for slip is used
-      tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0)
+      x0 = mu*prm%b_tr(i)**2*(2.0_pReal+nu)/(Gamma*8.0_pReal*PI*(1.0_pReal-nu))                     ! ToDo: In the paper, the Burgers vector for slip is used
+      tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0)        ! ToDo: In the paper, the Burgers vector for slip is used
 
       if (tau > tol_math_check .and. tau < tau_r) then
         ratio_tau_s = (dst%tau_hat_tr(i,en)/tau)**prm%s(i)

From 4a7f23069c87fe0c4a04970ab36d92312e6dfeff Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 4 Jan 2022 07:32:56 +0100
Subject: [PATCH 023/133] avoid misleading variable name

---
 src/phase_mechanical_plastic_dislotwin.f90 | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 6a9043cde..e1ccf3f5f 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -940,7 +940,6 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
     ddot_gamma_dtau_tw
 
   real :: &
-    ratio_tau_r, &
     tau, tau_r, &
     dot_N_0, &
     x0, &
@@ -966,9 +965,8 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
         tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0)      ! ToDo: In the paper, the Burgers vector for slip is used
 
         if (tau > tol_math_check .and. tau < tau_r) then
-          ratio_tau_r = (dst%tau_hat_tw(i,en)/tau)**prm%r(i)
-          P = exp(-ratio_tau_r)
-          dP_dTau = prm%r(i) * ratio_tau_r/tau * P
+          P = exp(-(dst%tau_hat_tw(i,en)/tau)**prm%r(i))
+          dP_dTau = prm%r(i) * (dst%tau_hat_tw(i,en)/tau)**prm%r(i)/tau * P
 
           s = prm%fcc_twinNucleationSlipPair(1:2,i)
           dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &
@@ -1031,7 +1029,6 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
     ddot_gamma_dtau_tr
 
   real :: &
-    ratio_tau_s, &
     tau, tau_r, &
     dot_N_0, &
     x0, &
@@ -1056,9 +1053,8 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
       tau_r = mu*prm%b_tr(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tr)+cos(PI/3.0_pReal)/x0)        ! ToDo: In the paper, the Burgers vector for slip is used
 
       if (tau > tol_math_check .and. tau < tau_r) then
-        ratio_tau_s = (dst%tau_hat_tr(i,en)/tau)**prm%s(i)
-        P = exp(-ratio_tau_s)
-        dP_dTau = prm%s(i) * ratio_tau_s/tau * P
+        P = exp(-(dst%tau_hat_tr(i,en)/tau)**prm%s(i))
+        dP_dTau = prm%s(i) * (dst%tau_hat_tr(i,en)/tau)**prm%s(i)/tau * P
 
         s = prm%fcc_twinNucleationSlipPair(1:2,i)
         dot_N_0 = sum(abs(dot_gamma_sl(s(2:1:-1)))*(stt%rho_mob(s,en)+stt%rho_dip(s,en))) &

From 03e3fbd98f0b55d492c434a33cf0decde7f511c4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 4 Jan 2022 07:40:58 +0100
Subject: [PATCH 024/133] compute only when needed

---
 src/phase_mechanical_plastic_dislotwin.f90 | 25 +++++++++-------------
 1 file changed, 10 insertions(+), 15 deletions(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index e1ccf3f5f..41b4854a7 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -101,9 +101,7 @@ submodule(phase:plastic) dislotwin
       Lambda_tr, &                                                                                  !< mean free path between 2 obstacles seen by a growing martensite
       tau_pass, &                                                                                   !< threshold stress for slip
       tau_hat_tw, &                                                                                 !< threshold stress for twinning
-      tau_hat_tr, &                                                                                 !< threshold stress for transformation
-      V_tw, &                                                                                       !< volume of a new twin
-      V_tr                                                                                          !< volume of a new martensite disc
+      tau_hat_tr                                                                                    !< threshold stress for transformation
   end type tDislotwinDependentState
 
 !--------------------------------------------------------------------------------------------------
@@ -433,11 +431,9 @@ module function plastic_dislotwin_init() result(myPlasticity)
 
     allocate(dst%Lambda_tw             (prm%sum_N_tw,Nmembers),source=0.0_pReal)
     allocate(dst%tau_hat_tw            (prm%sum_N_tw,Nmembers),source=0.0_pReal)
-    allocate(dst%V_tw                  (prm%sum_N_tw,Nmembers),source=0.0_pReal)
 
     allocate(dst%Lambda_tr             (prm%sum_N_tr,Nmembers),source=0.0_pReal)
     allocate(dst%tau_hat_tr            (prm%sum_N_tr,Nmembers),source=0.0_pReal)
-    allocate(dst%V_tr                  (prm%sum_N_tr,Nmembers),source=0.0_pReal)
 
     end associate
 
@@ -773,9 +769,6 @@ module subroutine dislotwin_dependentState(T,ph,en)
                          + 3.0_pReal*prm%b_tr*mu/(prm%L_tr*prm%b_tr) &
                          + prm%h*prm%delta_G/(3.0_pReal*prm%b_tr)
 
-    dst%V_tw(:,en) = PI/4.0_pReal*dst%Lambda_tw(:,en)**2*prm%t_tw
-    dst%V_tr(:,en) = PI/4.0_pReal*dst%Lambda_tr(:,en)**2*prm%t_tr
-
   end associate
 
 end subroutine dislotwin_dependentState
@@ -942,7 +935,7 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
   real :: &
     tau, tau_r, &
     dot_N_0, &
-    x0, &
+    x0, V, &
     Gamma, &
     mu, nu, &
     P_ncs, dP_ncs_dtau, &
@@ -975,9 +968,10 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
           P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
           dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
 
-          dot_gamma_tw(i) = dst%V_tw(i,en)*dot_N_0*P_ncs*P
+          V = PI/4.0_pReal*dst%Lambda_tw(i,en)**2*prm%t_tw(i)
+          dot_gamma_tw(i) = V*dot_N_0*P_ncs*P
           if (present(ddot_gamma_dtau_tw)) &
-            ddot_gamma_dtau_tw(i) = dst%V_tw(i,en)*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
+            ddot_gamma_dtau_tw(i) = V*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
         else
           dot_gamma_tw(i) = 0.0_pReal
           if (present(ddot_gamma_dtau_tw)) ddot_gamma_dtau_tw(i) = 0.0_pReal
@@ -1031,7 +1025,7 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
   real :: &
     tau, tau_r, &
     dot_N_0, &
-    x0, &
+    x0, V, &
     Gamma, &
     mu, nu, &
     P_ncs, dP_ncs_dtau, &
@@ -1062,10 +1056,11 @@ pure subroutine kinetics_tr(Mp,T,dot_gamma_sl,ph,en,&
 
         P_ncs = 1.0_pReal-exp(-prm%V_cs/(K_B*T)*(tau_r-tau))
         dP_ncs_dtau = prm%V_cs / (K_B * T) * (P_ncs - 1.0_pReal)
-
-        dot_gamma_tr(i) = dst%V_tr(i,en)*dot_N_0*P_ncs*P
+        
+        V = PI/4.0_pReal*dst%Lambda_tr(i,en)**2*prm%t_tr(i)
+        dot_gamma_tr(i) = V*dot_N_0*P_ncs*P
         if (present(ddot_gamma_dtau_tr)) &
-          ddot_gamma_dtau_tr(i) = dst%V_tr(i,en)*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
+          ddot_gamma_dtau_tr(i) = V*dot_N_0*(P*dP_ncs_dtau + P_ncs*dP_dtau)
       else
         dot_gamma_tr(i) = 0.0_pReal
         if (present(ddot_gamma_dtau_tr)) ddot_gamma_dtau_tr(i) = 0.0_pReal

From 1140625b1272754102adc6f8a276563cb241eb32 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 4 Jan 2022 17:29:19 +0100
Subject: [PATCH 025/133] copy and paste error

---
 src/phase_mechanical_plastic_dislotwin.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/phase_mechanical_plastic_dislotwin.f90 b/src/phase_mechanical_plastic_dislotwin.f90
index 41b4854a7..bc6fb0ee6 100644
--- a/src/phase_mechanical_plastic_dislotwin.f90
+++ b/src/phase_mechanical_plastic_dislotwin.f90
@@ -954,7 +954,7 @@ pure subroutine kinetics_tw(Mp,T,dot_gamma_sl,ph,en,&
 
       do i = 1, prm%sum_N_tw
         tau = math_tensordot(Mp,prm%P_tw(1:3,1:3,i))
-        x0 = mu*prm%b_tr(i)**2*(2.0_pReal+nu)/(Gamma*8.0_pReal*PI*(1.0_pReal-nu))                   ! ToDo: In the paper, the Burgers vector for slip is used
+        x0 = mu*prm%b_tw(i)**2*(2.0_pReal+nu)/(Gamma*8.0_pReal*PI*(1.0_pReal-nu))                   ! ToDo: In the paper, the Burgers vector for slip is used
         tau_r = mu*prm%b_tw(i)/(2.0_pReal*PI)*(1.0_pReal/(x0+prm%x_c_tw)+cos(PI/3.0_pReal)/x0)      ! ToDo: In the paper, the Burgers vector for slip is used
 
         if (tau > tol_math_check .and. tau < tau_r) then

From e60d41d5e4d0674342334579bb42b98502313285 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <daniel.mentock@mpie.de>
Date: Wed, 5 Jan 2022 14:06:06 +0100
Subject: [PATCH 026/133] merge with current development branch

---
 python/damask/_grid.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 1bda19d4e..a6340ce9b 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -205,7 +205,7 @@ class Grid:
             Grid-based geometry from file.
 
         """
-        warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
+        warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
         if isinstance(fname, (str, Path)):
             f = open(fname)
         elif isinstance(fname, TextIO):
@@ -652,7 +652,7 @@ class Grid:
             Compress geometry with 'x of y' and 'a to b'.
 
         """
-        warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
+        warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
         header =  [f'{len(self.comments)+4} header'] + self.comments \
                 + ['grid   a {} b {} c {}'.format(*self.cells),
                    'size   x {} y {} z {}'.format(*self.size),

From 1026d56842662ca8397c4b7f0038dcc3380644f2 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 9 Jan 2022 08:05:42 +0100
Subject: [PATCH 027/133] credit where credit is due

referencing DOI gives faster access to actual data
---
 src/lattice.f90 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/lattice.f90 b/src/lattice.f90
index c4b26c679..469bfa556 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -587,8 +587,8 @@ function lattice_C66_trans(Ntrans,C_parent66,lattice_target, &
 
 !--------------------------------------------------------------------------------------------------
 !> @brief Non-schmid projections for bcc with up to 6 coefficients
-! Koester et al. 2012, Acta Materialia 60 (2012) 3894–3901, eq. (17)
-! Gröger et al. 2008, Acta Materialia 56 (2008) 5412–5425, table 1
+! https://doi.org/10.1016/j.actamat.2012.03.053, eq. (17)
+! https://doi.org/10.1016/j.actamat.2008.07.037, table 1
 !--------------------------------------------------------------------------------------------------
 function lattice_nonSchmidMatrix(Nslip,nonSchmidCoefficients,sense) result(nonSchmidMatrix)
 
@@ -602,6 +602,7 @@ function lattice_nonSchmidMatrix(Nslip,nonSchmidCoefficients,sense) result(nonSc
   type(rotation)                                       :: R
   integer                                              :: i
 
+
   if (abs(sense) /= 1) error stop 'Sense in lattice_nonSchmidMatrix'
 
   coordinateSystem  = buildCoordinateSystem(Nslip,BCC_NSLIPSYSTEM,BCC_SYSTEMSLIP,'cI',0.0_pReal)
@@ -634,7 +635,9 @@ end function lattice_nonSchmidMatrix
 
 !--------------------------------------------------------------------------------------------------
 !> @brief Slip-slip interaction matrix
-!> details only active slip systems are considered
+!> @details only active slip systems are considered
+!> @details https://doi.org/10.1016/j.actamat.2016.12.040 (fcc: Tab S4-1, bcc: Tab S5-1)
+!> @details https://doi.org/10.1016/j.ijplas.2014.06.010 (hex: Tab 3b)
 !--------------------------------------------------------------------------------------------------
 function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(interactionMatrix)
 
@@ -646,6 +649,7 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
   integer, dimension(:),   allocatable :: NslipMax
   integer, dimension(:,:), allocatable :: interactionTypes
 
+
   integer, dimension(FCC_NSLIP,FCC_NSLIP), parameter :: &
     FCC_INTERACTIONSLIPSLIP = reshape( [&
        1, 2, 2, 4, 7, 5, 3, 5, 5, 4, 6, 7,  10,11,10,11,12,13, & ! -----> acting (forest)

From 0f0108f60330f1470c93879a1003937809180f90 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 9 Jan 2022 08:14:31 +0100
Subject: [PATCH 028/133] polishing

---
 examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml | 2 +-
 examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml b/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
index 5bc4a2e03..8a3147604 100644
--- a/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
+++ b/examples/config/phase/mechanical/plastic/phenopowerlaw_Mg.yaml
@@ -6,7 +6,7 @@ references:
 
 output: [xi_sl, xi_tw]
 
-N_sl: [3, 3, 6, 0, 6]  # basal, prism, -, 1. pyr<a>, -, 2. pyr<c+a>
+N_sl: [3, 3, 6, 0, 6]  # basal, prism, 1. pyr<a>, -, 2. pyr<c+a>
 N_tw: [6, 0, 6]        # tension, -, compression
 
 xi_0_sl:   [10.e+6,  55.e+6,  60.e+6, 0.,  60.e+6]
diff --git a/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml b/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
index c238e6afb..890f580cc 100644
--- a/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
+++ b/examples/config/phase/mechanical/plastic/phenopowerlaw_Ti.yaml
@@ -8,7 +8,7 @@ references:
     https://doi.org/10.1016/j.actamat.2017.05.015
 output: [gamma_sl]
 
-N_sl: [3, 3, 0, 12]   # basal, 1. prism, -, 1. pyr<c+a>
+N_sl: [3, 3, 0, 12]   # basal, prism, -, 1. pyr<c+a>
 n_sl: 20
 a_sl: 2.0
 dot_gamma_0_sl: 0.001

From 410a515afc178b232d0ef24650f3de80b00ad628 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 13:18:38 +0000
Subject: [PATCH 029/133] allow flexible arguments for 1D arguments

---
 python/damask/__init__.py     |   1 +
 python/damask/_colormap.py    |  25 +++--
 python/damask/_typehints.py   |  11 +++
 python/damask/grid_filters.py | 171 +++++++++++++++++-----------------
 python/damask/mechanics.py    |   4 +-
 python/damask/seeds.py        |  33 ++++---
 6 files changed, 130 insertions(+), 115 deletions(-)
 create mode 100644 python/damask/_typehints.py

diff --git a/python/damask/__init__.py b/python/damask/__init__.py
index 231fa8b30..584a97e87 100644
--- a/python/damask/__init__.py
+++ b/python/damask/__init__.py
@@ -8,6 +8,7 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
     version = _re.sub(r'^v','',_f.readline().strip())
     __version__ = version
 
+from .                 import _typehints       # noqa
 from .                 import util             # noqa
 from .                 import seeds            # noqa
 from .                 import tensor           # noqa
diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index c2721e0fa..2da92ae3f 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -3,13 +3,9 @@ import json
 import functools
 import colorsys
 from pathlib import Path
-from typing import Sequence, Union, TextIO
+from typing import Union, TextIO
 
 import numpy as np
-try:
-    from numpy.typing import ArrayLike
-except ImportError:
-    ArrayLike = Union[np.ndarray,Sequence[float]] # type: ignore
 import scipy.interpolate as interp
 import matplotlib as mpl
 if os.name == 'posix' and 'DISPLAY' not in os.environ:
@@ -18,6 +14,7 @@ import matplotlib.pyplot as plt
 from matplotlib import cm
 from PIL import Image
 
+from ._typehints import FloatSequence, FileHandle
 from . import util
 from . import Table
 
@@ -82,8 +79,8 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def from_range(low: ArrayLike,
-                   high: ArrayLike,
+    def from_range(low: FloatSequence,
+                   high: FloatSequence,
                    name: str = 'DAMASK colormap',
                    N: int = 256,
                    model: str = 'rgb') -> 'Colormap':
@@ -197,7 +194,7 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     def at(self,
-           fraction : Union[float,Sequence[float]]) -> np.ndarray:
+           fraction : Union[float,FloatSequence]) -> np.ndarray:
         """
         Interpolate color at fraction.
 
@@ -229,7 +226,7 @@ class Colormap(mpl.colors.ListedColormap):
 
     def shade(self,
               field: np.ndarray,
-              bounds: ArrayLike = None,
+              bounds: FloatSequence = None,
               gap: float = None) -> Image:
         """
         Generate PIL image of 2D field using colormap.
@@ -296,7 +293,7 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     def _get_file_handle(self,
-                         fname: Union[TextIO, str, Path, None],
+                         fname: Union[FileHandle, None],
                          suffix: str = '') -> TextIO:
         """
         Provide file handle.
@@ -323,7 +320,7 @@ class Colormap(mpl.colors.ListedColormap):
             return fname
 
 
-    def save_paraview(self, fname: Union[TextIO, str, Path] = None):
+    def save_paraview(self, fname: FileHandle = None):
         """
         Save as JSON file for use in Paraview.
 
@@ -350,7 +347,7 @@ class Colormap(mpl.colors.ListedColormap):
         fhandle.write('\n')
 
 
-    def save_ASCII(self, fname: Union[TextIO, str, Path] = None):
+    def save_ASCII(self, fname: FileHandle = None):
         """
         Save as ASCII file.
 
@@ -365,7 +362,7 @@ class Colormap(mpl.colors.ListedColormap):
         t.save(self._get_file_handle(fname,'.txt'))
 
 
-    def save_GOM(self, fname: Union[TextIO, str, Path] = None):
+    def save_GOM(self, fname: FileHandle = None):
         """
         Save as ASCII file for use in GOM Aramis.
 
@@ -385,7 +382,7 @@ class Colormap(mpl.colors.ListedColormap):
         self._get_file_handle(fname,'.legend').write(GOM_str)
 
 
-    def save_gmsh(self, fname: Union[TextIO, str, Path] = None):
+    def save_gmsh(self, fname: FileHandle = None):
         """
         Save as ASCII file for use in gmsh.
 
diff --git a/python/damask/_typehints.py b/python/damask/_typehints.py
new file mode 100644
index 000000000..67e920957
--- /dev/null
+++ b/python/damask/_typehints.py
@@ -0,0 +1,11 @@
+"""Functionality for typehints."""
+
+from typing import Sequence, Union, TextIO
+from pathlib import Path
+
+import numpy as np
+
+
+FloatSequence = Union[np.ndarray,Sequence[float]]
+IntSequence = Union[np.ndarray,Sequence[int]]
+FileHandle = Union[TextIO, str, Path]
diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py
index 42b5a16c4..d9d658d0b 100644
--- a/python/damask/grid_filters.py
+++ b/python/damask/grid_filters.py
@@ -12,21 +12,23 @@ the following operations are required for tensorial data:
 
 """
 
-from typing import Sequence, Tuple, Union
+from typing import Tuple as _Tuple
 
 from scipy import spatial as _spatial
 import numpy as _np
 
+from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
 
-def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order: bool = False) -> _np.ndarray:
+
+def _ks(size: _FloatSequence, cells: _IntSequence, first_order: bool = False) -> _np.ndarray:
     """
     Get wave numbers operator.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    cells : numpy.ndarray of shape (3)
+    cells : sequence of int, len (3)
         Number of cells.
     first_order : bool, optional
         Correction for first order derivatives, defaults to False.
@@ -45,20 +47,20 @@ def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order:
     return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
 
 
-def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
+def curl(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate curl of a vector or tensor field in Fourier space.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
+    f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
         Periodic field of which the curl is calculated.
 
     Returns
     -------
-    ∇ × f : numpy.ndarray
+    ∇ × f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
         Curl of f.
 
     """
@@ -76,20 +78,20 @@ def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(curl_,axes=(0,1,2),s=f.shape[:3])
 
 
-def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
+def divergence(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate divergence of a vector or tensor field in Fourier space.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
+    f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
         Periodic field of which the divergence is calculated.
 
     Returns
     -------
-    ∇ · f : numpy.ndarray
+    ∇ · f : numpy.ndarray, shape (:,:,:,1) or (:,:,:,3)
         Divergence of f.
 
     """
@@ -103,20 +105,20 @@ def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(div_,axes=(0,1,2),s=f.shape[:3])
 
 
-def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
+def gradient(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
     u"""
-    Calculate gradient of a scalar or vector fieldin Fourier space.
+    Calculate gradient of a scalar or vector field in Fourier space.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    f : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
+    f : numpy.ndarray, shape (:,:,:,1) or (:,:,:,3)
         Periodic field of which the gradient is calculated.
 
     Returns
     -------
-    ∇ f : numpy.ndarray
+    ∇ f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
         Divergence of f.
 
     """
@@ -130,29 +132,30 @@ def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
 
 
-def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
-                       size: _np.ndarray,
-                       origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
+def coordinates0_point(cells: _IntSequence,
+                       size: _FloatSequence,
+                       origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
     """
     Cell center positions (undeformed).
 
     Parameters
     ----------
-    cells : numpy.ndarray of shape (3)
+    cells : sequence of int, len (3)
         Number of cells.
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    origin : numpy.ndarray, optional
+    origin : sequence of float, len(3), optional
         Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
 
     Returns
     -------
-    x_p_0 : numpy.ndarray
+    x_p_0 : numpy.ndarray, shape (:,:,:,3)
         Undeformed cell center coordinates.
 
     """
-    start = origin        + size/_np.array(cells)*.5
-    end   = origin + size - size/_np.array(cells)*.5
+    size_ = _np.array(size,float)
+    start = origin         + size_/_np.array(cells,int)*.5
+    end   = origin + size_ - size_/_np.array(cells,int)*.5
 
     return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],cells[0]),
                                   _np.linspace(start[1],end[1],cells[1]),
@@ -160,24 +163,24 @@ def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
                      axis = -1)
 
 
-def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def displacement_fluct_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from fluctuation part of the deformation gradient field.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
 
     Returns
     -------
-    u_p_fluct : numpy.ndarray
+    u_p_fluct : numpy.ndarray, shape (:,:,:,3)
         Fluctuating part of the cell center displacements.
 
     """
-    integrator = 0.5j*size/_np.pi
+    integrator = 0.5j*_np.array(size,float)/_np.pi
 
     k_s = _ks(size,F.shape[:3],False)
     k_s_squared = _np.einsum('...l,...l',k_s,k_s)
@@ -192,20 +195,20 @@ def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
 
 
-def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def displacement_avg_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from average part of the deformation gradient field.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
 
     Returns
     -------
-    u_p_avg : numpy.ndarray
+    u_p_avg : numpy.ndarray, shape (:,:,:,3)
         Average part of the cell center displacements.
 
     """
@@ -213,42 +216,42 @@ def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
 
 
-def displacement_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def displacement_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from deformation gradient field.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
 
     Returns
     -------
-    u_p : numpy.ndarray
+    u_p : numpy.ndarray, shape (:,:,:,3)
         Cell center displacements.
 
     """
     return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
 
 
-def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
+def coordinates_point(size: _FloatSequence, F: _np.ndarray, origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
     """
     Cell center positions.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
-    origin : numpy.ndarray of shape (3), optional
+    origin : sequence of float, len(3), optional
         Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
 
     Returns
     -------
-    x_p : numpy.ndarray
+    x_p : numpy.ndarray, shape (:,:,:,3)
         Cell center coordinates.
 
     """
@@ -256,14 +259,14 @@ def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _
 
 
 def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
-                                       ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
+                                       ordered: bool = True) -> _Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
     """
     Return grid 'DNA', i.e. cells, size, and origin from 1D array of point positions.
 
     Parameters
     ----------
-    coordinates0 : numpy.ndarray of shape (:,3)
-        Undeformed cell coordinates.
+    coordinates0 : numpy.ndarray, shape (:,3)
+        Undeformed cell center coordinates.
     ordered : bool, optional
         Expect coordinates0 data to be ordered (x fast, z slow).
         Defaults to True.
@@ -277,7 +280,7 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
     coords    = [_np.unique(coordinates0[:,i]) for i in range(3)]
     mincorner = _np.array(list(map(min,coords)))
     maxcorner = _np.array(list(map(max,coords)))
-    cells     = _np.array(list(map(len,coords)),'i')
+    cells     = _np.array(list(map(len,coords)),int)
     size      = cells/_np.maximum(cells-1,1) * (maxcorner-mincorner)
     delta     = size/cells
     origin    = mincorner - delta*.5
@@ -305,24 +308,24 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
     return (cells,size,origin)
 
 
-def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
-                      size: _np.ndarray,
-                      origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
+def coordinates0_node(cells: _IntSequence,
+                      size: _FloatSequence,
+                      origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
     """
     Nodal positions (undeformed).
 
     Parameters
     ----------
-    cells : numpy.ndarray of shape (3)
+    cells : sequence of int, len (3)
         Number of cells.
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    origin : numpy.ndarray of shape (3), optional
+    origin : sequence of float, len(3), optional
         Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
 
     Returns
     -------
-    x_n_0 : numpy.ndarray
+    x_n_0 : numpy.ndarray, shape (:,:,:,3)
         Undeformed nodal coordinates.
 
     """
@@ -332,40 +335,40 @@ def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
                      axis = -1)
 
 
-def displacement_fluct_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def displacement_fluct_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from fluctuation part of the deformation gradient field.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
 
     Returns
     -------
-    u_n_fluct : numpy.ndarray
+    u_n_fluct : numpy.ndarray, shape (:,:,:,3)
         Fluctuating part of the nodal displacements.
 
     """
     return point_to_node(displacement_fluct_point(size,F))
 
 
-def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def displacement_avg_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from average part of the deformation gradient field.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
 
     Returns
     -------
-    u_n_avg : numpy.ndarray
+    u_n_avg : numpy.ndarray, shape (:,:,:,3)
         Average part of the nodal displacements.
 
     """
@@ -373,42 +376,42 @@ def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
 
 
-def displacement_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def displacement_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from deformation gradient field.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
 
     Returns
     -------
-    u_p : numpy.ndarray
+    u_p : numpy.ndarray, shape (:,:,:,3)
         Nodal displacements.
 
     """
     return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
 
 
-def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
+def coordinates_node(size: _FloatSequence, F: _np.ndarray, origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
     """
     Nodal positions.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the periodic field.
-    F : numpy.ndarray
+    F : numpy.ndarray, shape (:,:,:,3,3)
         Deformation gradient field.
-    origin : numpy.ndarray of shape (3), optional
+    origin : sequence of float, len(3), optional
         Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
 
     Returns
     -------
-    x_n : numpy.ndarray
+    x_n : numpy.ndarray, shape (:,:,:,3)
         Nodal coordinates.
 
     """
@@ -416,13 +419,13 @@ def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _n
 
 
 def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
-                                      ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
+                                      ordered: bool = True) -> _Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
     """
     Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
 
     Parameters
     ----------
-    coordinates0 : numpy.ndarray of shape (:,3)
+    coordinates0 : numpy.ndarray, shape (:,3)
         Undeformed nodal coordinates.
     ordered : bool, optional
         Expect coordinates0 data to be ordered (x fast, z slow).
@@ -437,7 +440,7 @@ def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
     coords    = [_np.unique(coordinates0[:,i]) for i in range(3)]
     mincorner = _np.array(list(map(min,coords)))
     maxcorner = _np.array(list(map(max,coords)))
-    cells     = _np.array(list(map(len,coords)),'i') - 1
+    cells     = _np.array(list(map(len,coords)),int) - 1
     size      = maxcorner-mincorner
     origin    = mincorner
 
@@ -463,12 +466,12 @@ def point_to_node(cell_data: _np.ndarray) -> _np.ndarray:
 
     Parameters
     ----------
-    cell_data : numpy.ndarray of shape (:,:,:,...)
+    cell_data : numpy.ndarray, shape (:,:,:,...)
         Data defined on the cell centers of a periodic grid.
 
     Returns
     -------
-    node_data : numpy.ndarray of shape (:,:,:,...)
+    node_data : numpy.ndarray, shape (:,:,:,...)
         Data defined on the nodes of a periodic grid.
 
     """
@@ -485,12 +488,12 @@ def node_to_point(node_data: _np.ndarray) -> _np.ndarray:
 
     Parameters
     ----------
-    node_data : numpy.ndarray of shape (:,:,:,...)
+    node_data : numpy.ndarray, shape (:,:,:,...)
         Data defined on the nodes of a periodic grid.
 
     Returns
     -------
-    cell_data : numpy.ndarray of shape (:,:,:,...)
+    cell_data : numpy.ndarray, shape (:,:,:,...)
         Data defined on the cell centers of a periodic grid.
 
     """
@@ -507,7 +510,7 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
 
     Parameters
     ----------
-    coordinates0 : numpy.ndarray
+    coordinates0 : numpy.ndarray, shape (:,3)
         Array of undeformed cell coordinates.
 
     Returns
@@ -523,17 +526,17 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
         return False
 
 
-def regrid(size: _np.ndarray, F: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]]) -> _np.ndarray:
+def regrid(size: _FloatSequence, F: _np.ndarray, cells: _IntSequence) -> _np.ndarray:
     """
     Return mapping from coordinates in deformed configuration to a regular grid.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size.
-    F : numpy.ndarray of shape (:,:,:,3,3)
+    F : numpy.ndarray, shape (:,:,:,3,3), shape (:,:,:,3,3)
         Deformation gradient field.
-    cells : numpy.ndarray of shape (3)
+    cells : sequence of int, len (3)
         Cell count along x,y,z of remapping grid.
 
     """
diff --git a/python/damask/mechanics.py b/python/damask/mechanics.py
index 22e3aeabf..7c1af6c5f 100644
--- a/python/damask/mechanics.py
+++ b/python/damask/mechanics.py
@@ -5,7 +5,7 @@ All routines operate on numpy.ndarrays of shape (...,3,3).
 
 """
 
-from typing import Sequence
+from typing import Sequence as _Sequence
 
 import numpy as _np
 
@@ -243,7 +243,7 @@ def stretch_right(T: _np.ndarray) -> _np.ndarray:
     return _polar_decomposition(T,'U')[0]
 
 
-def _polar_decomposition(T: _np.ndarray, requested: Sequence[str]) -> tuple:
+def _polar_decomposition(T: _np.ndarray, requested: _Sequence[str]) -> tuple:
     """
     Perform singular value decomposition.
 
diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index 4d5a8c624..7e01a40e6 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -1,25 +1,27 @@
 """Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
 
-from typing import Sequence,Tuple
+from typing import Tuple as _Tuple
 
 from scipy import spatial as _spatial
 import numpy as _np
 
+from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
 from . import util as _util
 from . import grid_filters as _grid_filters
 
 
-def from_random(size: _np.ndarray, N_seeds: int, cells: _np.ndarray = None, rng_seed=None) -> _np.ndarray:
+def from_random(size: _FloatSequence, N_seeds: int, cells: _IntSequence = None,
+                rng_seed=None) -> _np.ndarray:
     """
     Place seeds randomly in space.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the seeding domain.
     N_seeds : int
         Number of seeds.
-    cells : numpy.ndarray of shape (3), optional.
+    cells : sequence of int, len (3), optional.
         If given, ensures that each seed results in a grain when a standard Voronoi
         tessellation is performed using the given grid resolution (i.e. size/cells).
     rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@@ -28,29 +30,30 @@ def from_random(size: _np.ndarray, N_seeds: int, cells: _np.ndarray = None, rng_
 
     Returns
     -------
-    coords : numpy.ndarray of shape (N_seeds,3)
+    coords : numpy.ndarray, shape (N_seeds,3)
         Seed coordinates in 3D space.
 
     """
+    size_ = _np.array(size,float)
     rng = _np.random.default_rng(rng_seed)
     if cells is None:
-        coords = rng.random((N_seeds,3)) * size
+        coords = rng.random((N_seeds,3)) * size_
     else:
         grid_coords = _grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
         coords = grid_coords[rng.choice(_np.prod(cells),N_seeds, replace=False)] \
-               + _np.broadcast_to(size/cells,(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25)          # wobble without leaving cells
+               + _np.broadcast_to(size_/_np.array(cells,int),(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25) # wobble w/o leaving grid
 
     return coords
 
 
-def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distance: float,
+def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, distance: float,
                       periodic: bool = True, rng_seed=None) -> _np.ndarray:
     """
     Place seeds according to a Poisson disc distribution.
 
     Parameters
     ----------
-    size : numpy.ndarray of shape (3)
+    size : sequence of float, len (3)
         Physical size of the seeding domain.
     N_seeds : int
         Number of seeds.
@@ -66,13 +69,13 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
 
     Returns
     -------
-    coords : numpy.ndarray of shape (N_seeds,3)
+    coords : numpy.ndarray, shape (N_seeds,3)
         Seed coordinates in 3D space.
 
     """
     rng = _np.random.default_rng(rng_seed)
     coords = _np.empty((N_seeds,3))
-    coords[0] = rng.random(3) * size
+    coords[0] = rng.random(3) * _np.array(size,float)
 
     s = 1
     i = 0
@@ -96,8 +99,8 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
     return coords
 
 
-def from_grid(grid, selection: Sequence[int] = None,
-              invert: bool = False, average: bool = False, periodic: bool = True) -> Tuple[_np.ndarray, _np.ndarray]:
+def from_grid(grid, selection: _IntSequence = None,
+              invert: bool = False, average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
     """
     Create seeds from grid description.
 
@@ -105,7 +108,7 @@ def from_grid(grid, selection: Sequence[int] = None,
     ----------
     grid : damask.Grid
         Grid from which the material IDs are used as seeds.
-    selection : iterable of integers, optional
+    selection : sequence of int, optional
         Material IDs to consider.
     invert : boolean, false
         Consider all material IDs except those in selection. Defaults to False.
@@ -116,7 +119,7 @@ def from_grid(grid, selection: Sequence[int] = None,
 
     Returns
     -------
-    coords, materials : numpy.ndarray of shape (:,3), numpy.ndarray of shape (:)
+    coords, materials : numpy.ndarray, shape (:,3); numpy.ndarray, shape (:)
         Seed coordinates in 3D space, material IDs.
 
     """

From a87db2ba0b683f090e33b2801ba8dc5afa3d15af Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 16:56:24 +0100
Subject: [PATCH 030/133] test for long long integer

---
 src/parallelization.f90 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/parallelization.f90 b/src/parallelization.f90
index ebb9573d4..17f9698a5 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -86,6 +86,10 @@ subroutine parallelization_init
   if (err /= 0)                              error stop 'Could not determine MPI integer size'
   if (typeSize*8 /= bit_size(0))             error stop 'Mismatch between MPI and DAMASK integer'
 
+  call MPI_Type_size(MPI_INTEGER8,typeSize,err)
+  if (err /= 0)                              error stop 'Could not determine MPI integer size'
+  if (typeSize*8 /= bit_size(0_pI64))        error stop 'Mismatch between MPI and DAMASK integer (long long)'
+
   call MPI_Type_size(MPI_DOUBLE,typeSize,err)
   if (err /= 0)                              error stop 'Could not determine MPI real size'
   if (typeSize*8 /= storage_size(0.0_pReal)) error stop 'Mismatch between MPI and DAMASK real'

From ffa80f6bef02525b3f1a9477c3a4460e04a46df3 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Wed, 12 Jan 2022 17:10:13 +0100
Subject: [PATCH 031/133] added typehints for table module

---
 python/damask/_table.py | 86 ++++++++++++++++++++++++-----------------
 1 file changed, 51 insertions(+), 35 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index a65971f39..04ab426ce 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -1,5 +1,7 @@
 import re
 import copy
+from typing import Union, Optional, Tuple, List, TextIO, Set
+import pathlib
 
 import pandas as pd
 import numpy as np
@@ -9,7 +11,7 @@ from . import util
 class Table:
     """Manipulate multi-dimensional spreadsheet-like data."""
 
-    def __init__(self,data,shapes,comments=None):
+    def __init__(self, data: np.ndarray, shapes: dict, comments: Optional[Union[str, list]] = None):
         """
         New spreadsheet.
 
@@ -30,7 +32,7 @@ class Table:
         self._relabel('uniform')
 
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """Brief overview."""
         self._relabel('shapes')
         data_repr = self.data.__repr__()
@@ -38,7 +40,7 @@ class Table:
         return '\n'.join(['# '+c for c in self.comments])+'\n'+data_repr
 
 
-    def __getitem__(self,item):
+    def __getitem__(self, item: Union[slice, Tuple[slice, ...]]) -> "Table":
         """
         Slice the Table according to item.
 
@@ -85,19 +87,19 @@ class Table:
                               comments=self.comments)
 
 
-    def __len__(self):
+    def __len__(self) -> int:
         """Number of rows."""
         return len(self.data)
 
 
-    def __copy__(self):
+    def __copy__(self) -> "Table":
         """Create deep copy."""
         return copy.deepcopy(self)
 
     copy = __copy__
 
 
-    def _label(self,what,how):
+    def _label(self, what: Union[str, List[str]], how: str) -> List[str]:
         """
         Expand labels according to data shape.
 
@@ -128,7 +130,7 @@ class Table:
         return labels
 
 
-    def _relabel(self,how):
+    def _relabel(self, how: str):
         """
         Modify labeling of data in-place.
 
@@ -141,17 +143,21 @@ class Table:
             'linear'  ==> 1_v 2_v 3_v
 
         """
-        self.data.columns = self._label(self.shapes,how)
+        self.data.columns = self._label(self.shapes,how) #type: ignore
 
 
-    def _add_comment(self,label,shape,info):
+    def _add_comment(self, label: str, shape: Tuple[int, ...], info: Optional[str]):
         if info is not None:
             specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
             general  = util.execution_stamp('Table')
             self.comments.append(f'{specific} / {general}')
 
 
-    def isclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
+    def isclose(self,
+                    other: "Table",
+                    rtol: float = 1e-5,
+                    atol: float = 1e-8,
+                    equal_nan: bool = True) -> np.ndarray:
         """
         Report where values are approximately equal to corresponding ones of other Table.
 
@@ -179,7 +185,11 @@ class Table:
                           equal_nan=equal_nan)
 
 
-    def allclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
+    def allclose(self,
+                 other: "Table",
+                 rtol: float = 1e-5,
+                 atol: float = 1e-8,
+                 equal_nan: bool = True) -> bool:
         """
         Test whether all values are approximately equal to corresponding ones of other Table.
 
@@ -208,7 +218,7 @@ class Table:
 
 
     @staticmethod
-    def load(fname):
+    def load(fname: Union[TextIO, str, pathlib.Path]) -> "Table":
         """
         Load from ASCII table file.
 
@@ -229,11 +239,13 @@ class Table:
             Table data from file.
 
         """
-        try:
-            f = open(fname)
-        except TypeError:
+        if isinstance(fname, TextIO):
             f = fname
             f.seek(0)
+        elif isinstance(fname, (str, pathlib.Path)):
+            f = open(fname)
+        else:
+            raise TypeError
 
         comments = []
         line = f.readline().strip()
@@ -261,7 +273,7 @@ class Table:
 
 
     @staticmethod
-    def load_ang(fname):
+    def load_ang(fname: Union[TextIO, str, pathlib.Path]) -> "Table":
         """
         Load from ang file.
 
@@ -286,11 +298,13 @@ class Table:
             Table data from file.
 
         """
-        try:
-            f = open(fname)
-        except TypeError:
+        if isinstance(fname, TextIO):
             f = fname
             f.seek(0)
+        elif isinstance(fname, (str, pathlib.Path)):
+            f = open(fname)
+        else:
+            raise TypeError
 
         content = f.readlines()
 
@@ -312,11 +326,11 @@ class Table:
 
 
     @property
-    def labels(self):
+    def labels(self) -> List[Tuple[int, ...]]:
         return list(self.shapes)
 
 
-    def get(self,label):
+    def get(self, label: str) -> np.ndarray:
         """
         Get column data.
 
@@ -336,7 +350,7 @@ class Table:
         return data.astype(type(data.flatten()[0]))
 
 
-    def set(self,label,data,info=None):
+    def set(self, label: str, data: np.ndarray, info: str = None) -> "Table":
         """
         Set column data.
 
@@ -356,7 +370,7 @@ class Table:
 
         """
         dup = self.copy()
-        dup._add_comment(label,data.shape[1:],info)
+        dup._add_comment(label, data.shape[1:],info)
         m = re.match(r'(.*)\[((\d+,)*(\d+))\]',label)
         if m:
             key = m.group(1)
@@ -369,7 +383,7 @@ class Table:
         return dup
 
 
-    def add(self,label,data,info=None):
+    def add(self, label: str, data: np.ndarray, info: str = None) -> "Table":
         """
         Add column data.
 
@@ -401,7 +415,7 @@ class Table:
         return dup
 
 
-    def delete(self,label):
+    def delete(self, label: str) -> "Table":
         """
         Delete column data.
 
@@ -422,7 +436,7 @@ class Table:
         return dup
 
 
-    def rename(self,old,new,info=None):
+    def rename(self, old: Union[str, List[str]], new: Union[str, List[str]], info: str = None) -> "Table":
         """
         Rename column data.
 
@@ -448,7 +462,7 @@ class Table:
         return dup
 
 
-    def sort_by(self,labels,ascending=True):
+    def sort_by(self, labels: Union[str, List[str]], ascending: Union[bool, List[bool]] = True) -> "Table":
         """
         Sort table by values of given labels.
 
@@ -481,7 +495,7 @@ class Table:
         return dup
 
 
-    def append(self,other):
+    def append(self, other: "Table") -> "Table":
         """
         Append other table vertically (similar to numpy.vstack).
 
@@ -506,7 +520,7 @@ class Table:
             return dup
 
 
-    def join(self,other):
+    def join(self, other: "Table") -> "Table":
         """
         Append other table horizontally (similar to numpy.hstack).
 
@@ -533,7 +547,7 @@ class Table:
             return dup
 
 
-    def save(self,fname):
+    def save(self, fname: Union[TextIO, str, pathlib.Path]):
         """
         Save as plain text file.
 
@@ -543,9 +557,9 @@ class Table:
             Filename or file for writing.
 
         """
-        seen = set()
+        seen: Set = set()
         labels = []
-        for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
+        for l in [x for x in self.data.columns if x not in seen]:
             if self.shapes[l] == (1,):
                 labels.append(f'{l}')
             elif len(self.shapes[l]) == 1:
@@ -555,10 +569,12 @@ class Table:
                 labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                           for i in range(np.prod(self.shapes[l]))]
 
-        try:
-            fhandle = open(fname,'w',newline='\n')
-        except TypeError:
+        if isinstance(fname, TextIO):
             fhandle = fname
+        elif isinstance(fname, (str, pathlib.Path)):
+            fhandle = open(fname,'w',newline='\n')
+        else:
+            raise TypeError
 
         fhandle.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
         self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)

From 18913bb94ea6af197d714d6688a12c6093449673 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 17:33:14 +0100
Subject: [PATCH 032/133] autodetect datatype

---
 src/results.f90 | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/results.f90 b/src/results.f90
index 7c2346095..4028d0307 100644
--- a/src/results.f90
+++ b/src/results.f90
@@ -507,6 +507,7 @@ subroutine results_mapping_phase(ID,entry,label)
     totalShape                                                                                      !< shape of the dataset (all processes)
 
   integer(HID_T) :: &
+    pI64_t, & ! NOT YET 64 bit!
     loc_id, &                                                                                       !< identifier of group in file
     dtype_id, &                                                                                     !< identifier of compound data type
     label_id, &                                                                                     !< identifier of label (string) in compound data type
@@ -567,14 +568,15 @@ subroutine results_mapping_phase(ID,entry,label)
   call h5tget_size_f(dt_id, type_size_string, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5tget_size_f(H5T_NATIVE_INTEGER, type_size_int, hdferr)
+  pI64_t = h5kind_to_type(kind(entryGlobal),H5_INTEGER_KIND)
+  call h5tget_size_f(pI64_t, type_size_int, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
   call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
   call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(dtype_id, 'entry', type_size_string, pI64_t, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
 !--------------------------------------------------------------------------------------------------
@@ -586,7 +588,7 @@ subroutine results_mapping_phase(ID,entry,label)
 
   call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, pI64_t, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
   call h5tclose_f(dt_id, hdferr)
@@ -660,6 +662,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
     totalShape                                                                                      !< shape of the dataset (all processes)
 
   integer(HID_T) :: &
+    pI64_t, & ! NOT YET 64 bit!
     loc_id, &                                                                                       !< identifier of group in file
     dtype_id, &                                                                                     !< identifier of compound data type
     label_id, &                                                                                     !< identifier of label (string) in compound data type
@@ -716,14 +719,15 @@ subroutine results_mapping_homogenization(ID,entry,label)
   call h5tget_size_f(dt_id, type_size_string, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5tget_size_f(H5T_NATIVE_INTEGER, type_size_int, hdferr)
+  pI64_t = h5kind_to_type(kind(entryGlobal),H5_INTEGER_KIND)
+  call h5tget_size_f(pI64_t, type_size_int, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
   call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
   call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(dtype_id, 'entry', type_size_string, pI64_t, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
 !--------------------------------------------------------------------------------------------------
@@ -735,7 +739,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
 
   call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
+  call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, pI64_t, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
   call h5tclose_f(dt_id, hdferr)

From ae0eead748409ce5557dacc476b88efa8f920a60 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 17:44:07 +0100
Subject: [PATCH 033/133] write out mapping as 64 bit integer

---
 src/results.f90 | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/results.f90 b/src/results.f90
index 4028d0307..31f3bb173 100644
--- a/src/results.f90
+++ b/src/results.f90
@@ -497,9 +497,9 @@ subroutine results_mapping_phase(ID,entry,label)
   integer,          dimension(:,:), intent(in) :: entry                                             !< phase entry at (co,ce)
   character(len=*), dimension(:),   intent(in) :: label                                             !< label of each phase section
 
-  integer, dimension(size(entry,1),size(entry,2)) :: &
+  integer(pI64), dimension(size(entry,1),size(entry,2)) :: &
     entryGlobal
-  integer, dimension(size(label),0:worldsize-1) :: entryOffset                                      !< offset in entry counting per process
+  integer, dimension(size(label),0:worldsize-1) :: entryOffset                                       !< offset in entry counting per process
   integer, dimension(0:worldsize-1)             :: writeSize                                        !< amount of data written per process
   integer(HSIZE_T), dimension(2) :: &
     myShape, &                                                                                      !< shape of the dataset (this process)
@@ -507,7 +507,7 @@ subroutine results_mapping_phase(ID,entry,label)
     totalShape                                                                                      !< shape of the dataset (all processes)
 
   integer(HID_T) :: &
-    pI64_t, & ! NOT YET 64 bit!
+    pI64_t, &                                                                                       !< HDF5 type for pI64 (8 bit integer)
     loc_id, &                                                                                       !< identifier of group in file
     dtype_id, &                                                                                     !< identifier of compound data type
     label_id, &                                                                                     !< identifier of label (string) in compound data type
@@ -529,7 +529,7 @@ subroutine results_mapping_phase(ID,entry,label)
   if(hdferr < 0) error stop 'HDF5 error'
 
 #ifndef PETSC
-  entryGlobal = entry -1                                                                            ! 0-based
+  entryGlobal = int(entry -1,pI64)                                                                  ! 0-based
 #else
 !--------------------------------------------------------------------------------------------------
 ! MPI settings and communication
@@ -550,7 +550,7 @@ subroutine results_mapping_phase(ID,entry,label)
   entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
   do co = 1, size(ID,1)
     do ce = 1, size(ID,2)
-      entryGlobal(co,ce) = entry(co,ce) -1 + entryOffset(ID(co,ce),worldrank)
+      entryGlobal(co,ce) = int(entry(co,ce) -1 + entryOffset(ID(co,ce),worldrank),pI64)
     end do
   end do
 #endif
@@ -652,7 +652,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
   integer,          dimension(:), intent(in) :: entry                                               !< homogenization entry at (ce)
   character(len=*), dimension(:), intent(in) :: label                                               !< label of each homogenization section
 
-  integer, dimension(size(entry,1)) :: &
+  integer(pI64), dimension(size(entry,1)) :: &
     entryGlobal
   integer, dimension(size(label),0:worldsize-1) :: entryOffset                                      !< offset in entry counting per process
   integer, dimension(0:worldsize-1)             :: writeSize                                        !< amount of data written per process
@@ -662,7 +662,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
     totalShape                                                                                      !< shape of the dataset (all processes)
 
   integer(HID_T) :: &
-    pI64_t, & ! NOT YET 64 bit!
+    pI64_t, &                                                                                       !< HDF5 type for pI64 (8 bit integer)
     loc_id, &                                                                                       !< identifier of group in file
     dtype_id, &                                                                                     !< identifier of compound data type
     label_id, &                                                                                     !< identifier of label (string) in compound data type
@@ -684,7 +684,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
   if(hdferr < 0) error stop 'HDF5 error'
 
 #ifndef PETSC
-  entryGlobal = entry -1                                                                            ! 0-based
+  entryGlobal = int(entry -1,pI64)                                                                  ! 0-based
 #else
 !--------------------------------------------------------------------------------------------------
 ! MPI settings and communication
@@ -702,7 +702,7 @@ subroutine results_mapping_homogenization(ID,entry,label)
   if(ierr /= 0) error stop 'MPI error'
   entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
   do ce = 1, size(ID,1)
-    entryGlobal(ce) = entry(ce) -1 + entryOffset(ID(ce),worldrank)
+    entryGlobal(ce) = int(entry(ce) -1 + entryOffset(ID(ce),worldrank),pI64)
   end do
 #endif
 

From fd3c18ea4db4e252031f9422f2c888d9b1754ed7 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 17:58:44 +0100
Subject: [PATCH 034/133] calculate global entry in 64 bit

---
 src/HDF5_utilities.f90  |  4 ++--
 src/parallelization.f90 |  3 ++-
 src/results.f90         | 28 ++++++++++++++--------------
 3 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90
index e064997e5..7645189c6 100644
--- a/src/HDF5_utilities.f90
+++ b/src/HDF5_utilities.f90
@@ -1877,7 +1877,7 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
   if (parallel) then
     call H5Pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
     if(hdferr < 0) error stop 'HDF5 error'
-    call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)       ! get total output size over each process
+    call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,ierr)   ! get total output size over each process
     if (ierr /= 0) error stop 'MPI error'
   end if
 #endif
@@ -1977,7 +1977,7 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
   writeSize(worldrank+1) = int(myShape(ubound(myShape,1)))
 #ifdef PETSC
   if (parallel) then
-    call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)      ! get total output size over each process
+    call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,ierr)  ! get total output size over each process
     if (ierr /= 0) error stop 'MPI error'
   end if
 #endif
diff --git a/src/parallelization.f90 b/src/parallelization.f90
index 17f9698a5..a4f7e5ae1 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -88,7 +88,8 @@ subroutine parallelization_init
 
   call MPI_Type_size(MPI_INTEGER8,typeSize,err)
   if (err /= 0)                              error stop 'Could not determine MPI integer size'
-  if (typeSize*8 /= bit_size(0_pI64))        error stop 'Mismatch between MPI and DAMASK integer (long long)'
+  if (int(typeSize,pI64)*8_pI64 /= bit_size(0_pI64)) &
+                                             error stop 'Mismatch between MPI and DAMASK integer (long long)'
 
   call MPI_Type_size(MPI_DOUBLE,typeSize,err)
   if (err /= 0)                              error stop 'Could not determine MPI real size'
diff --git a/src/results.f90 b/src/results.f90
index 31f3bb173..48cce82f9 100644
--- a/src/results.f90
+++ b/src/results.f90
@@ -499,8 +499,8 @@ subroutine results_mapping_phase(ID,entry,label)
 
   integer(pI64), dimension(size(entry,1),size(entry,2)) :: &
     entryGlobal
-  integer, dimension(size(label),0:worldsize-1) :: entryOffset                                       !< offset in entry counting per process
-  integer, dimension(0:worldsize-1)             :: writeSize                                        !< amount of data written per process
+  integer(pI64), dimension(size(label),0:worldsize-1) :: entryOffset                                 !< offset in entry counting per process
+  integer, dimension(0:worldsize-1) :: writeSize                                                    !< amount of data written per process
   integer(HSIZE_T), dimension(2) :: &
     myShape, &                                                                                      !< shape of the dataset (this process)
     myOffset, &
@@ -536,21 +536,21 @@ subroutine results_mapping_phase(ID,entry,label)
   call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr)          ! get output at each process
+  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)      ! get output at each process
   if(ierr /= 0) error stop 'MPI error'
 
-  entryOffset = 0
+  entryOffset = 0_pI64
   do co = 1, size(ID,1)
     do ce = 1, size(ID,2)
-      entryOffset(ID(co,ce),worldrank) = entryOffset(ID(co,ce),worldrank) +1
+      entryOffset(ID(co,ce),worldrank) = entryOffset(ID(co,ce),worldrank) +1_pI64
     end do
   end do
-  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
+  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
   if(ierr /= 0) error stop 'MPI error'
   entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
   do co = 1, size(ID,1)
     do ce = 1, size(ID,2)
-      entryGlobal(co,ce) = int(entry(co,ce) -1 + entryOffset(ID(co,ce),worldrank),pI64)
+      entryGlobal(co,ce) = int(entry(co,ce),pI64) -1_pI64 + entryOffset(ID(co,ce),worldrank)
     end do
   end do
 #endif
@@ -654,8 +654,8 @@ subroutine results_mapping_homogenization(ID,entry,label)
 
   integer(pI64), dimension(size(entry,1)) :: &
     entryGlobal
-  integer, dimension(size(label),0:worldsize-1) :: entryOffset                                      !< offset in entry counting per process
-  integer, dimension(0:worldsize-1)             :: writeSize                                        !< amount of data written per process
+  integer(pI64), dimension(size(label),0:worldsize-1) :: entryOffset                                !< offset in entry counting per process
+  integer, dimension(0:worldsize-1) :: writeSize                                                    !< amount of data written per process
   integer(HSIZE_T), dimension(1) :: &
     myShape, &                                                                                      !< shape of the dataset (this process)
     myOffset, &
@@ -691,18 +691,18 @@ subroutine results_mapping_homogenization(ID,entry,label)
   call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr)          ! get output at each process
+  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)      ! get output at each process
   if(ierr /= 0) error stop 'MPI error'
 
-  entryOffset = 0
+  entryOffset = 0_pI64
   do ce = 1, size(ID,1)
-    entryOffset(ID(ce),worldrank) = entryOffset(ID(ce),worldrank) +1
+    entryOffset(ID(ce),worldrank) = entryOffset(ID(ce),worldrank) +1_pI64
   end do
-  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INT,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
+  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
   if(ierr /= 0) error stop 'MPI error'
   entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
   do ce = 1, size(ID,1)
-    entryGlobal(ce) = int(entry(ce) -1 + entryOffset(ID(ce),worldrank),pI64)
+    entryGlobal(ce) = int(entry(ce),pI64) -1_pI64 + entryOffset(ID(ce),worldrank)
   end do
 #endif
 

From 2c1231a806bfcefa8f8a09102fb9eda531545398 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 20:34:29 +0100
Subject: [PATCH 035/133] using best practices from grid_filters

---
 python/damask/_grid.py    | 255 ++++++++++++++++++++------------------
 python/damask/_vtk.py     |   2 +-
 python/tests/test_Grid.py |  21 +++-
 3 files changed, 153 insertions(+), 125 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index a6340ce9b..a65f4eb30 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -3,6 +3,7 @@ import copy
 import warnings
 import multiprocessing as mp
 from functools import partial
+import typing
 from typing import Union, Optional, TextIO, List, Sequence
 from pathlib import Path
 
@@ -16,6 +17,7 @@ from . import util
 from . import grid_filters
 from . import Rotation
 from . import Table
+from ._typehints import FloatSequence, IntSequence
 
 class Grid:
     """
@@ -29,9 +31,9 @@ class Grid:
 
     def __init__(self,
                  material: np.ndarray,
-                 size,
-                 origin = [0.0,0.0,0.0],
-                 comments = []):
+                 size: FloatSequence,
+                 origin: FloatSequence = np.zeros(3),
+                 comments: Union[str, Sequence[str]] = []):
         """
         New geometry definition for grid solvers.
 
@@ -40,18 +42,18 @@ class Grid:
         material : numpy.ndarray of shape (:,:,:)
             Material indices. The shape of the material array defines
             the number of cells.
-        size : list or numpy.ndarray of shape (3)
+        size : sequence of float, len (3)
             Physical size of grid in meter.
-        origin : list or numpy.ndarray of shape (3), optional
-            Coordinates of grid origin in meter.
-        comments : list of str, optional
+        origin : sequence of float, len (3), optional
+            Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
+        comments : (list of) str, optional
             Comments, e.g. history of operations.
 
         """
         self.material = material
-        self.size    = size
-        self.origin  = origin
-        self.comments = comments
+        self.size = size                                                                            # type: ignore
+        self.origin = origin                                                                        # type: ignore
+        self.comments = comments                                                                    # type: ignore
 
 
     def __repr__(self) -> str:
@@ -75,7 +77,7 @@ class Grid:
     copy = __copy__
 
 
-    def __eq__(self, other):
+    def __eq__(self, other: object) -> bool:
         """
         Test equality of other.
 
@@ -86,8 +88,8 @@ class Grid:
 
         """
         if not isinstance(other, Grid):
-            raise TypeError
-        return (np.allclose(other.size,self.size)
+            return NotImplemented
+        return bool(np.allclose(other.size,self.size)
             and np.allclose(other.origin,self.origin)
             and np.all(other.cells == self.cells)
             and np.all(other.material == self.material))
@@ -118,19 +120,19 @@ class Grid:
         return self._size
 
     @size.setter
-    def size(self, size: Union[Sequence[float], np.ndarray]):
+    def size(self, size: FloatSequence):
         if len(size) != 3 or any(np.array(size) < 0):
             raise ValueError(f'invalid size {size}')
         else:
             self._size = np.array(size)
 
     @property
-    def origin(self) -> Union[Sequence[float], np.ndarray]:
+    def origin(self) -> np.ndarray:
         """Coordinates of grid origin in meter."""
         return self._origin
 
     @origin.setter
-    def origin(self, origin: np.ndarray):
+    def origin(self, origin: FloatSequence):
         if len(origin) != 3:
             raise ValueError(f'invalid origin {origin}')
         else:
@@ -165,7 +167,7 @@ class Grid:
 
         Parameters
         ----------
-        fname : str or or pathlib.Path
+        fname : str or pathlib.Path
             Grid file to read. Valid extension is .vti, which will be appended
             if not given.
 
@@ -186,8 +188,9 @@ class Grid:
                     comments=comments)
 
 
+    @typing. no_type_check
     @staticmethod
-    def load_ASCII(fname):
+    def load_ASCII(fname)-> "Grid":
         """
         Load from geom file.
 
@@ -225,10 +228,10 @@ class Grid:
         comments = []
         content = f.readlines()
         for i,line in enumerate(content[:header_length]):
-            items: List[str] = line.split('#')[0].lower().strip().split()
+            items = line.split('#')[0].lower().strip().split()
             key = items[0] if items else ''
             if   key == 'grid':
-                cells  = np.array([int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
+                cells  = np.array([  int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
             elif key == 'size':
                 size   = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
             elif key == 'origin':
@@ -236,7 +239,7 @@ class Grid:
             else:
                 comments.append(line.strip())
 
-        material = np.empty(int(cells.prod()))                                                         # initialize as flat array
+        material = np.empty(int(cells.prod()))                                                      # initialize as flat array
         i = 0
         for line in content[header_length:]:
             items = line.split('#')[0].split()
@@ -267,7 +270,7 @@ class Grid:
 
         Parameters
         ----------
-        fname : str, pathlib.Path, or file handle
+        fname : str or pathlib.Path
             Geometry file to read.
 
         Returns
@@ -286,7 +289,7 @@ class Grid:
 
 
     @staticmethod
-    def load_DREAM3D(fname: str,
+    def load_DREAM3D(fname: Union[str, Path],
                      feature_IDs: str = None, cell_data: str = None,
                      phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
                      base_group: str = None) -> "Grid":
@@ -300,24 +303,24 @@ class Grid:
 
         Parameters
         ----------
-        fname : str
+        fname : str or or pathlib.Path
             Filename of the DREAM.3D (HDF5) file.
-        feature_IDs : str
+        feature_IDs : str, optional
             Name of the dataset containing the mapping between cells and
             grain-wise data. Defaults to 'None', in which case cell-wise
             data is used.
-        cell_data : str
+        cell_data : str, optional
             Name of the group (folder) containing cell-wise data. Defaults to
             None in wich case it is automatically detected.
-        phases : str
+        phases : str, optional
             Name of the dataset containing the phase ID. It is not used for
             grain-wise data, i.e. when feature_IDs is not None.
             Defaults to 'Phases'.
-        Euler_angles : str
+        Euler_angles : str, optional
             Name of the dataset containing the crystallographic orientation as
             Euler angles in radians It is not used for grain-wise data, i.e.
             when feature_IDs is not None. Defaults to 'EulerAngles'.
-        base_group : str
+        base_group : str, optional
             Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
             and grain- or cell-wise data. Defaults to None, in which case
             it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
@@ -349,7 +352,9 @@ class Grid:
 
 
     @staticmethod
-    def from_table(table: Table, coordinates: str, labels: Union[str, Sequence[str]]) -> "Grid":
+    def from_table(table: Table,
+                   coordinates: str,
+                   labels: Union[str, Sequence[str]]) -> "Grid":
         """
         Create grid from ASCII table.
 
@@ -360,7 +365,7 @@ class Grid:
         coordinates : str
             Label of the vector column containing the spatial coordinates.
             Need to be ordered (1./x fast, 3./z slow).
-        labels : str or list of str
+        labels : (list of) str
             Label(s) of the columns containing the material definition.
             Each unique combination of values results in one material ID.
 
@@ -386,26 +391,26 @@ class Grid:
         return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
 
     @staticmethod
-    def from_Laguerre_tessellation(cells,
-                                   size,
-                                   seeds,
-                                   weights,
-                                   material = None,
-                                   periodic = True):
+    def from_Laguerre_tessellation(cells: IntSequence,
+                                   size: FloatSequence,
+                                   seeds: np.ndarray,
+                                   weights: FloatSequence,
+                                   material: IntSequence = None,
+                                   periodic: bool = True):
         """
         Create grid from Laguerre tessellation.
 
         Parameters
         ----------
-        cells : int numpy.ndarray of shape (3)
+        cells : sequence of int, len (3)
             Number of cells in x,y,z direction.
-        size : list or numpy.ndarray of shape (3)
+        size : sequence of float, len (3)
             Physical size of the grid in meter.
         seeds : numpy.ndarray of shape (:,3)
             Position of the seed points in meter. All points need to lay within the box.
-        weights : numpy.ndarray of shape (seeds.shape[0])
+        weights : sequence of float, len (seeds.shape[0])
             Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
-        material : numpy.ndarray of shape (seeds.shape[0]), optional
+        material : sequence of int, len (seeds.shape[0]), optional
             Material ID of the seeds.
             Defaults to None, in which case materials are consecutively numbered.
         periodic : Boolean, optional
@@ -427,6 +432,7 @@ class Grid:
             seeds_p   = seeds
 
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
+
         pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
         result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), coords)
         pool.close()
@@ -435,30 +441,30 @@ class Grid:
 
         if periodic: material_ %= len(weights)
 
-        return Grid(material = material_ if material is None else material[material_],
+        return Grid(material = material_ if material is None else np.array(material)[material_],
                     size     = size,
                     comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
                    )
 
 
     @staticmethod
-    def from_Voronoi_tessellation(cells: np.ndarray,
-                                  size: Union[Sequence[float], np.ndarray],
+    def from_Voronoi_tessellation(cells: IntSequence,
+                                  size: FloatSequence,
                                   seeds: np.ndarray,
-                                  material: np.ndarray = None,
+                                  material: IntSequence = None,
                                   periodic: bool = True) -> "Grid":
         """
         Create grid from Voronoi tessellation.
 
         Parameters
         ----------
-        cells : int numpy.ndarray of shape (3)
+        cells : sequence of int, len (3)
             Number of cells in x,y,z direction.
-        size : list or numpy.ndarray of shape (3)
+        size : sequence of float, len (3)
             Physical size of the grid in meter.
         seeds : numpy.ndarray of shape (:,3)
             Position of the seed points in meter. All points need to lay within the box.
-        material : numpy.ndarray of shape (seeds.shape[0]), optional
+        material : sequence of int, len (seeds.shape[0]), optional
             Material ID of the seeds.
             Defaults to None, in which case materials are consecutively numbered.
         periodic : Boolean, optional
@@ -478,7 +484,7 @@ class Grid:
         except TypeError:
             material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1]    # scipy <1.6
 
-        return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
+        return Grid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
                     size     = size,
                     comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
                    )
@@ -527,20 +533,20 @@ class Grid:
 
 
     @staticmethod
-    def from_minimal_surface(cells: np.ndarray,
-                             size: Union[Sequence[float], np.ndarray],
+    def from_minimal_surface(cells: IntSequence,
+                             size: FloatSequence,
                              surface: str,
                              threshold: float = 0.0,
                              periods: int = 1,
-                             materials: tuple = (0,1)) -> "Grid":
+                             materials: IntSequence = (0,1)) -> "Grid":
         """
         Create grid from definition of triply periodic minimal surface.
 
         Parameters
         ----------
-        cells : int numpy.ndarray of shape (3)
+        cells : sequence of int, len (3)
             Number of cells in x,y,z direction.
-        size : list or numpy.ndarray of shape (3)
+        size : sequence of float, len (3)
             Physical size of the grid in meter.
         surface : str
             Type of the minimal surface. See notes for details.
@@ -548,7 +554,7 @@ class Grid:
             Threshold of the minimal surface. Defaults to 0.0.
         periods : integer, optional.
             Number of periods per unit cell. Defaults to 1.
-        materials : (int, int), optional
+        materials : sequence of int, len (2)
             Material IDs. Defaults to (0,1).
 
         Returns
@@ -589,22 +595,21 @@ class Grid:
 
         >>> import numpy as np
         >>> import damask
-        >>> damask.Grid.from_minimal_surface(np.array([64]*3,int),np.ones(3),
-        ...                                  'Gyroid')
-        cells  a b c: 64 x 64 x 64
-        size   x y z: 1.0 x 1.0 x 1.0
-        origin x y z: 0.0   0.0   0.0
+        >>> damask.Grid.from_minimal_surface([64]*3,np.ones(3)*1.e-4,'Gyroid')
+        cells : 64 x 64 x 64
+        size  : 0.0001 x 0.0001 x 0.0001 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 2
 
         Minimal surface of 'Neovius' type. non-default material IDs.
 
         >>> import numpy as np
         >>> import damask
-        >>> damask.Grid.from_minimal_surface(np.array([80]*3,int),np.ones(3),
+        >>> damask.Grid.from_minimal_surface([80]*3,np.ones(3)*5.e-4,
         ...                                  'Neovius',materials=(1,5))
-        cells  a b c: 80 x 80 x 80
-        size   x y z: 1.0 x 1.0 x 1.0
-        origin x y z: 0.0   0.0   0.0
+        cells : 80 x 80 x 80
+        size  : 0.0005 x 0.0005 x 0.0005 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 2 (min: 1, max: 5)
 
         """
@@ -634,7 +639,7 @@ class Grid:
         v.add(self.material.flatten(order='F'),'material')
         v.add_comments(self.comments)
 
-        v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
+        v.save(fname,parallel=False,compress=compress)
 
 
     def save_ASCII(self, fname: Union[str, TextIO]):
@@ -667,15 +672,15 @@ class Grid:
                    header='\n'.join(header), fmt=format_string, comments='')
 
 
-    def show(self):
+    def show(self) -> None:
         """Show on screen."""
         VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
 
 
     def add_primitive(self,
-                      dimension: np.ndarray,
-                      center: np.ndarray,
-                      exponent: Union[np.ndarray, float],
+                      dimension: Union[FloatSequence, IntSequence],
+                      center: Union[FloatSequence, IntSequence],
+                      exponent: Union[FloatSequence, float],
                       fill: int = None,
                       R: Rotation = Rotation(),
                       inverse: bool = False,
@@ -685,14 +690,15 @@ class Grid:
 
         Parameters
         ----------
-        dimension : int or float numpy.ndarray of shape (3)
-            Dimension (diameter/side length) of the primitive. If given as
-            integers, cell centers are addressed.
-            If given as floats, coordinates are addressed.
-        center : int or float numpy.ndarray of shape (3)
-            Center of the primitive. If given as integers, cell centers are addressed.
-            If given as floats, coordinates in space are addressed.
-        exponent : numpy.ndarray of shape (3) or float
+        dimension : sequence of int or float, len (3)
+            Dimension (diameter/side length) of the primitive.
+            If given as integers, cell centers are addressed.
+            If given as floats, physical coordinates are addressed.
+        center : sequence of int or float, len (3)
+            Center of the primitive.
+            If given as integers, cell centers are addressed.
+            If given as floats, physical coordinates are addressed.
+        exponent : float or sequence of float, len (3)
             Exponents for the three axes.
             0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
             1 gives sphere     (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
@@ -719,9 +725,9 @@ class Grid:
         >>> import damask
         >>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
         >>> g.add_primitive(np.ones(3)*5e-5,np.ones(3)*5e-5,1)
-        cells  a b c: 64 x 64 x 64
-        size   x y z: 0.0001 x 0.0001 x 0.0001
-        origin x y z: 0.0   0.0   0.0
+        cells : 64 x 64 x 64
+        size  : 0.0001 x 0.0001 x 0.0001 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 2
 
         Add a cube at the origin.
@@ -730,9 +736,9 @@ class Grid:
         >>> import damask
         >>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
         >>> g.add_primitive(np.ones(3,int)*32,np.zeros(3),np.inf)
-        cells  a b c: 64 x 64 x 64
-        size   x y z: 0.0001 x 0.0001 x 0.0001
-        origin x y z: 0.0   0.0   0.0
+        cells : 64 x 64 x 64
+        size  : 0.0001 x 0.0001 x 0.0001 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 2
 
         """
@@ -769,7 +775,7 @@ class Grid:
 
         Parameters
         ----------
-        directions : iterable containing str
+        directions : (sequence of) str
             Direction(s) along which the grid is mirrored.
             Valid entries are 'x', 'y', 'z'.
         reflect : bool, optional
@@ -788,9 +794,9 @@ class Grid:
         >>> import damask
         >>> g = damask.Grid(np.zeros([32]*3,int), np.ones(3)*1e-4)
         >>> g.mirror('xy',True)
-        cells  a b c: 64 x 64 x 32
-        size   x y z: 0.0002 x 0.0002 x 0.0001
-        origin x y z: 0.0   0.0   0.0
+        cells : 64 x 64 x 32
+        size  : 0.0002 x 0.0002 x 0.0001 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 1
 
         """
@@ -821,7 +827,7 @@ class Grid:
 
         Parameters
         ----------
-        directions : iterable containing str
+        directions : (sequence of) str
             Direction(s) along which the grid is flipped.
             Valid entries are 'x', 'y', 'z'.
 
@@ -844,13 +850,13 @@ class Grid:
                    )
 
 
-    def scale(self, cells: np.ndarray, periodic: bool = True) -> "Grid":
+    def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
         """
         Scale grid to new cells.
 
         Parameters
         ----------
-        cells : numpy.ndarray of shape (3)
+        cells : sequence of int, len (3)
             Number of cells in x,y,z direction.
         periodic : Boolean, optional
             Assume grid to be periodic. Defaults to True.
@@ -868,9 +874,9 @@ class Grid:
         >>> import damask
         >>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
         >>> g.scale(g.cells*2)
-        cells  a b c: 64 x 64 x 64
-        size   x y z: 0.0001 x 0.0001 x 0.0001
-        origin x y z: 0.0   0.0   0.0
+        cells : 64 x 64 x 64
+        size  : 0.0001 x 0.0001 x 0.0001 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 1
 
         """
@@ -888,7 +894,10 @@ class Grid:
                    )
 
 
-    def clean(self, stencil: int = 3, selection: Sequence[float] = None, periodic: bool = True) -> "Grid":
+    def clean(self,
+              stencil: int = 3,
+              selection: IntSequence = None,
+              periodic: bool = True) -> "Grid":
         """
         Smooth grid by selecting most frequent material index within given stencil at each location.
 
@@ -896,7 +905,7 @@ class Grid:
         ----------
         stencil : int, optional
             Size of smoothing stencil.
-        selection : list, optional
+        selection : sequence of int, optional
             Field values that can be altered. Defaults to all.
         periodic : Boolean, optional
             Assume grid to be periodic. Defaults to True.
@@ -907,7 +916,7 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def mostFrequent(arr, selection = None):
+        def mostFrequent(arr: np.ndarray, selection = None):
             me = arr[arr.size//2]
             if selection is None or me in selection:
                 unique, inverse = np.unique(arr, return_inverse=True)
@@ -947,7 +956,7 @@ class Grid:
                    )
 
 
-    def rotate(self, R: Rotation, fill: Union[int, float] = None) -> "Grid":
+    def rotate(self, R: Rotation, fill: int = None) -> "Grid":
         """
         Rotate grid (pad if required).
 
@@ -955,7 +964,7 @@ class Grid:
         ----------
         R : damask.Rotation
             Rotation to apply to the grid.
-        fill : int or float, optional
+        fill : int, optional
             Material index to fill the corners. Defaults to material.max() + 1.
 
         Returns
@@ -985,17 +994,20 @@ class Grid:
                    )
 
 
-    def canvas(self, cells = None, offset = None, fill = None):
+    def canvas(self,
+               cells: IntSequence = None,
+               offset: IntSequence = None,
+               fill: int = None) -> "Grid":
         """
         Crop or enlarge/pad grid.
 
         Parameters
         ----------
-        cells : numpy.ndarray of shape (3)
+        cells : sequence of int, len (3), optional
             Number of cells  x,y,z direction.
-        offset : numpy.ndarray of shape (3)
+        offset : sequence of int, len (3), optional
             Offset (measured in cells) from old to new grid [0,0,0].
-        fill : int or float, optional
+        fill : int, optional
             Material index to fill the background. Defaults to material.max() + 1.
 
         Returns
@@ -1010,42 +1022,43 @@ class Grid:
         >>> import numpy as np
         >>> import damask
         >>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
-        >>> g.canvas(np.array([32,32,16],int))
-        cells  a b c: 33 x 32 x 16
-        size   x y z: 0.0001 x 0.0001 x 5e-05
-        origin x y z: 0.0   0.0   0.0
+        >>> g.canvas([32,32,16])
+        cells : 33 x 32 x 16
+        size  : 0.0001 x 0.0001 x 5e-05 / m³
+        origin: 0.0   0.0   0.0 / m
         # materials: 1
 
         """
-        if offset is None: offset = 0
+        offset_ = np.array(offset,int) if offset is not None else np.zeros(3,int)
+        cells_ = np.array(cells,int) if cells is not None else self.cells
         if fill is None: fill = np.nanmax(self.material) + 1
         dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
 
-        canvas = np.full(self.cells if cells is None else cells,fill,dtype)
+        canvas = np.full(cells_,fill,dtype)
 
-        LL = np.clip( offset,           0,np.minimum(self.cells,     cells+offset))
-        UR = np.clip( offset+cells,     0,np.minimum(self.cells,     cells+offset))
-        ll = np.clip(-offset,           0,np.minimum(     cells,self.cells-offset))
-        ur = np.clip(-offset+self.cells,0,np.minimum(     cells,self.cells-offset))
+        LL = np.clip( offset_,           0,np.minimum(self.cells,     cells_+offset_))
+        UR = np.clip( offset_+cells_,    0,np.minimum(self.cells,     cells_+offset_))
+        ll = np.clip(-offset_,           0,np.minimum(     cells_,self.cells-offset_))
+        ur = np.clip(-offset_+self.cells,0,np.minimum(     cells_,self.cells-offset_))
 
         canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
 
         return Grid(material = canvas,
                     size     = self.size/self.cells*np.asarray(canvas.shape),
-                    origin   = self.origin+offset*self.size/self.cells,
+                    origin   = self.origin+offset_*self.size/self.cells,
                     comments = self.comments+[util.execution_stamp('Grid','canvas')],
                    )
 
 
-    def substitute(self, from_material: np.ndarray, to_material: np.ndarray) -> "Grid":
+    def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
         """
         Substitute material indices.
 
         Parameters
         ----------
-        from_material : iterable of ints
+        from_material : sequence of int
             Material indices to be substituted.
-        to_material : iterable of ints
+        to_material : sequence of int
             New material indices.
 
         Returns
@@ -1092,7 +1105,7 @@ class Grid:
     def vicinity_offset(self,
                         vicinity: int = 1,
                         offset: int = None,
-                        trigger: Sequence[int] = [],
+                        trigger: IntSequence = [],
                         periodic: bool = True) -> "Grid":
         """
         Offset material index of points in the vicinity of xxx.
@@ -1109,7 +1122,7 @@ class Grid:
         offset : int, optional
             Offset (positive or negative) to tag material indices,
             defaults to material.max()+1.
-        trigger : list of ints, optional
+        trigger : sequence of int, optional
             List of material indices that trigger a change.
             Defaults to [], meaning that any different neighbor triggers a change.
         periodic : Boolean, optional
@@ -1121,7 +1134,7 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def tainted_neighborhood(stencil, trigger):
+        def tainted_neighborhood(stencil: np.ndarray, trigger):
             me = stencil[stencil.shape[0]//2]
             return np.any(stencil != me if len(trigger) == 0 else
                           np.in1d(stencil,np.array(list(set(trigger) - {me}))))
@@ -1140,7 +1153,7 @@ class Grid:
                    )
 
 
-    def get_grain_boundaries(self, periodic = True, directions = 'xyz'):
+    def get_grain_boundaries(self, periodic: bool = True, directions: Sequence[str] = 'xyz'):
         """
         Create VTK unstructured grid containing grain boundaries.
 
@@ -1148,7 +1161,7 @@ class Grid:
         ----------
         periodic : Boolean, optional
             Assume grid to be periodic. Defaults to True.
-        directions : iterable containing str, optional
+        directions : (sequence of) string, optional
             Direction(s) along which the boundaries are determined.
             Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.
 
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index cbf70c37a..95cea4542 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -419,7 +419,7 @@ class VTK:
         return writer.GetOutputString()
 
 
-    def show(self):
+    def show(self) -> None:
         """
         Render.
 
diff --git a/python/tests/test_Grid.py b/python/tests/test_Grid.py
index 3538e3dd8..2b9ca22f4 100644
--- a/python/tests/test_Grid.py
+++ b/python/tests/test_Grid.py
@@ -237,12 +237,27 @@ class TestGrid:
                           modified)
 
 
-    def test_canvas(self,default):
+    def test_canvas_extend(self,default):
         cells = default.cells
-        grid_add = np.random.randint(0,30,(3))
-        modified = default.canvas(cells + grid_add)
+        cells_add = np.random.randint(0,30,(3))
+        modified = default.canvas(cells + cells_add)
         assert np.all(modified.material[:cells[0],:cells[1],:cells[2]] == default.material)
 
+    @pytest.mark.parametrize('sign',[+1,-1])
+    @pytest.mark.parametrize('extra_offset',[0,-1])
+    def test_canvas_move_out(self,sign,extra_offset):
+        g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
+        o = sign*np.ones(3)*g.cells.min() +extra_offset*sign
+        if extra_offset == 0:
+            assert np.all(g.canvas(offset=o).material == 1)
+        else:
+            assert np.all(np.unique(g.canvas(offset=o).material) == (0,1))
+
+    def test_canvas_cells(self,default):
+        g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
+        cells = np.random.randint(1,30,(3))
+        offset = np.random.randint(-30,30,(3))
+        assert np.all(g.canvas(cells,offset).cells == cells)
 
     @pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
                                                 (np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])

From 7410463067e4e0a77a2fec7099329cc0927824e0 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Wed, 12 Jan 2022 23:41:05 +0100
Subject: [PATCH 036/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-379-g731222d09

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index d9749c5a9..fe2ec0531 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-375-g76fe2d2b3
+v3.0.0-alpha5-379-g731222d09

From 3acabcdc7feac3c585e9c1b997e9f56700f3b34f Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 12 Jan 2022 23:13:38 +0100
Subject: [PATCH 037/133] docstring adjustments

---
 python/damask/_colormap.py    |  2 +-
 python/damask/_grid.py        | 22 +++++++++++-----------
 python/damask/_orientation.py | 12 ++++++------
 python/damask/_result.py      |  2 +-
 python/damask/_rotation.py    | 22 +++++++++++-----------
 python/damask/_vtk.py         |  6 +++---
 python/damask/seeds.py        | 14 +++++++-------
 python/tests/test_seeds.py    |  2 +-
 8 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 2da92ae3f..2c7f01d94 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -205,7 +205,7 @@ class Colormap(mpl.colors.ListedColormap):
 
         Returns
         -------
-        color : np.ndarray, shape(...,4)
+        color : numpy.ndarray, shape(...,4)
             RGBA values of interpolated color(s).
 
         Examples
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index a65f4eb30..5006e1b40 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -39,7 +39,7 @@ class Grid:
 
         Parameters
         ----------
-        material : numpy.ndarray of shape (:,:,:)
+        material : numpy.ndarray, shape (:,:,:)
             Material indices. The shape of the material array defines
             the number of cells.
         size : sequence of float, len (3)
@@ -406,14 +406,14 @@ class Grid:
             Number of cells in x,y,z direction.
         size : sequence of float, len (3)
             Physical size of the grid in meter.
-        seeds : numpy.ndarray of shape (:,3)
+        seeds : numpy.ndarray, shape (:,3)
             Position of the seed points in meter. All points need to lay within the box.
         weights : sequence of float, len (seeds.shape[0])
             Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
         material : sequence of int, len (seeds.shape[0]), optional
             Material ID of the seeds.
             Defaults to None, in which case materials are consecutively numbered.
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
         Returns
@@ -462,12 +462,12 @@ class Grid:
             Number of cells in x,y,z direction.
         size : sequence of float, len (3)
             Physical size of the grid in meter.
-        seeds : numpy.ndarray of shape (:,3)
+        seeds : numpy.ndarray, shape (:,3)
             Position of the seed points in meter. All points need to lay within the box.
         material : sequence of int, len (seeds.shape[0]), optional
             Material ID of the seeds.
             Defaults to None, in which case materials are consecutively numbered.
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
         Returns
@@ -706,10 +706,10 @@ class Grid:
             Fill value for primitive. Defaults to material.max()+1.
         R : damask.Rotation, optional
             Rotation of primitive. Defaults to no rotation.
-        inverse : Boolean, optional
+        inverse : bool, optional
             Retain original materials within primitive and fill outside.
             Defaults to False.
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
         Returns
@@ -858,7 +858,7 @@ class Grid:
         ----------
         cells : sequence of int, len (3)
             Number of cells in x,y,z direction.
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
         Returns
@@ -907,7 +907,7 @@ class Grid:
             Size of smoothing stencil.
         selection : sequence of int, optional
             Field values that can be altered. Defaults to all.
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
         Returns
@@ -1125,7 +1125,7 @@ class Grid:
         trigger : sequence of int, optional
             List of material indices that trigger a change.
             Defaults to [], meaning that any different neighbor triggers a change.
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
 
         Returns
@@ -1159,7 +1159,7 @@ class Grid:
 
         Parameters
         ----------
-        periodic : Boolean, optional
+        periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
         directions : (sequence of) string, optional
             Direction(s) along which the boundaries are determined.
diff --git a/python/damask/_orientation.py b/python/damask/_orientation.py
index 2fc2a7d4a..b7a43e0fb 100644
--- a/python/damask/_orientation.py
+++ b/python/damask/_orientation.py
@@ -393,8 +393,8 @@ class Orientation(Rotation,Crystal):
 
         Returns
         -------
-        in : numpy.ndarray of quaternion.shape
-           Boolean array indicating whether Rodrigues-Frank vector falls into fundamental zone.
+        in : numpy.ndarray of bool, quaternion.shape
+            Whether Rodrigues-Frank vector falls into fundamental zone.
 
         Notes
         -----
@@ -437,8 +437,8 @@ class Orientation(Rotation,Crystal):
 
         Returns
         -------
-        in : numpy.ndarray of quaternion.shape
-           Boolean array indicating whether Rodrigues-Frank vector falls into disorientation FZ.
+        in : numpy.ndarray of bool, quaternion.shape
+            Whether Rodrigues-Frank vector falls into disorientation FZ.
 
         References
         ----------
@@ -651,8 +651,8 @@ class Orientation(Rotation,Crystal):
 
         Returns
         -------
-        in : numpy.ndarray of shape (...)
-           Boolean array indicating whether vector falls into SST.
+        in : numpy.ndarray, shape (...)
+            Whether vector falls into SST.
 
         """
         if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:
diff --git a/python/damask/_result.py b/python/damask/_result.py
index f47a7da80..c87b51a89 100644
--- a/python/damask/_result.py
+++ b/python/damask/_result.py
@@ -1817,7 +1817,7 @@ class Result:
         output : (list of) str, optional
             Names of the datasets to export to the file.
             Defaults to '*', in which case all datasets are exported.
-        overwrite : boolean, optional
+        overwrite : bool, optional
             Overwrite existing configuration files.
             Defaults to False.
 
diff --git a/python/damask/_rotation.py b/python/damask/_rotation.py
index ac921d70a..fd19ec31b 100644
--- a/python/damask/_rotation.py
+++ b/python/damask/_rotation.py
@@ -671,7 +671,7 @@ class Rotation:
         ----------
         q : numpy.ndarray of shape (...,4)
             Unit quaternion (q_0, q_1, q_2, q_3) in positive real hemisphere, i.e. ǀqǀ = 1, q_0 ≥ 0.
-        accept_homomorph : boolean, optional
+        accept_homomorph : bool, optional
             Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
             Defaults to False.
         P : int ∈ {-1,1}, optional
@@ -706,7 +706,7 @@ class Rotation:
         phi : numpy.ndarray of shape (...,3)
             Euler angles (φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π])
             or (φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]) if degrees == True.
-        degrees : boolean, optional
+        degrees : bool, optional
             Euler angles are given in degrees. Defaults to False.
 
         Notes
@@ -737,9 +737,9 @@ class Rotation:
         axis_angle : numpy.ndarray of shape (...,4)
             Axis and angle (n_1, n_2, n_3, ω) with ǀnǀ = 1 and ω ∈ [0,π]
             or ω ∈ [0,180] if degrees == True.
-        degrees : boolean, optional
+        degrees : bool, optional
             Angle ω is given in degrees. Defaults to False.
-        normalize: boolean, optional
+        normalize: bool, optional
             Allow ǀnǀ ≠ 1. Defaults to False.
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
@@ -773,9 +773,9 @@ class Rotation:
         ----------
         basis : numpy.ndarray of shape (...,3,3)
             Three three-dimensional lattice basis vectors.
-        orthonormal : boolean, optional
+        orthonormal : bool, optional
             Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
-        reciprocal : boolean, optional
+        reciprocal : bool, optional
             Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
 
         """
@@ -851,7 +851,7 @@ class Rotation:
         ----------
         rho : numpy.ndarray of shape (...,4)
             Rodrigues–Frank vector (n_1, n_2, n_3, tan(ω/2)) with ǀnǀ = 1  and ω ∈ [0,π].
-        normalize : boolean, optional
+        normalize : bool, optional
             Allow ǀnǀ ≠ 1. Defaults to False.
         P : int ∈ {-1,1}, optional
             Sign convention. Defaults to -1.
@@ -977,9 +977,9 @@ class Rotation:
         N : integer, optional
             Number of discrete orientations to be sampled from the given ODF.
             Defaults to 500.
-        degrees : boolean, optional
+        degrees : bool, optional
             Euler space grid coordinates are in degrees. Defaults to True.
-        fractions : boolean, optional
+        fractions : bool, optional
             ODF values correspond to volume fractions, not probability densities.
             Defaults to True.
         rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@@ -1033,7 +1033,7 @@ class Rotation:
             Standard deviation of (Gaussian) misorientation distribution.
         N : int, optional
             Number of samples. Defaults to 500.
-        degrees : boolean, optional
+        degrees : bool, optional
             sigma is given in degrees. Defaults to True.
         rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
             A seed to initialize the BitGenerator.
@@ -1072,7 +1072,7 @@ class Rotation:
             Defaults to 0.
         N : int, optional
             Number of samples. Defaults to 500.
-        degrees : boolean, optional
+        degrees : bool, optional
             sigma, alpha, and beta are given in degrees.
         rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
             A seed to initialize the BitGenerator.
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index 95cea4542..dbbfb1b10 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -28,8 +28,8 @@ class VTK:
         ----------
         vtk_data : subclass of vtk.vtkDataSet
             Description of geometry and topology, optionally with attached data.
-            Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid,
-            or vtk.vtkPolyData.
+            Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
+            vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
 
         """
         self.vtk_data = vtk_data
@@ -242,7 +242,7 @@ class VTK:
         ----------
         fname : str or pathlib.Path
             Filename for writing.
-        parallel : boolean, optional
+        parallel : bool, optional
             Write data in parallel background process. Defaults to True.
         compress : bool, optional
             Compress with zlib algorithm. Defaults to True.
diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index 7e01a40e6..6ff150df3 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -61,7 +61,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
         Number of candidates to consider for finding best candidate.
     distance : float
         Minimum acceptable distance to other seeds.
-    periodic : boolean, optional
+    periodic : bool, optional
         Calculate minimum distance for periodically repeated grid.
     rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
         A seed to initialize the BitGenerator. Defaults to None.
@@ -99,8 +99,8 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
     return coords
 
 
-def from_grid(grid, selection: _IntSequence = None,
-              invert: bool = False, average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
+def from_grid(grid, selection: _IntSequence = None, invert_selection: bool = False,
+              average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
     """
     Create seeds from grid description.
 
@@ -110,11 +110,11 @@ def from_grid(grid, selection: _IntSequence = None,
         Grid from which the material IDs are used as seeds.
     selection : sequence of int, optional
         Material IDs to consider.
-    invert : boolean, false
+    invert_selection : bool, optional
         Consider all material IDs except those in selection. Defaults to False.
-    average : boolean, optional
+    average : bool, optional
         Seed corresponds to center of gravity of material ID cloud.
-    periodic : boolean, optional
+    periodic : bool, optional
         Center of gravity accounts for periodic boundaries.
 
     Returns
@@ -125,7 +125,7 @@ def from_grid(grid, selection: _IntSequence = None,
     """
     material = grid.material.reshape((-1,1),order='F')
     mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
-           _np.isin(material,selection,invert=invert).flatten()
+           _np.isin(material,selection,invert=invert_selection).flatten()
     coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
 
     if not average:
diff --git a/python/tests/test_seeds.py b/python/tests/test_seeds.py
index e68260aa4..ca5cd6f6d 100644
--- a/python/tests/test_seeds.py
+++ b/python/tests/test_seeds.py
@@ -67,5 +67,5 @@ class TestSeeds:
         coords = seeds.from_random(size,N_seeds,cells)
         grid = Grid.from_Voronoi_tessellation(cells,size,coords)
         selection=np.random.randint(N_seeds)+1
-        coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert=invert,selection=[selection])
+        coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert_selection=invert,selection=[selection])
         assert selection not in material if invert else (selection==material).all()

From 4727652856c8062791ebe92057e21274facf09b4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 07:37:38 +0100
Subject: [PATCH 038/133] default integer is set via a compiler flag

---
 src/CPFEM.f90       | 34 +++++++++++++++++-----------------
 src/DAMASK_Marc.f90 |  6 +++---
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/src/CPFEM.f90 b/src/CPFEM.f90
index 8f1217a88..8ee26ffe7 100644
--- a/src/CPFEM.f90
+++ b/src/CPFEM.f90
@@ -32,18 +32,18 @@ module CPFEM
   real(pReal), dimension (:,:,:,:), allocatable, private :: &
     CPFEM_dcsdE_knownGood                                                                           !< known good tangent
 
-  integer(pInt),                                 public :: &
-    cycleCounter =  0_pInt                                                                          !< needs description
+  integer,                                       public :: &
+    cycleCounter = 0                                                                                !< needs description
 
-  integer(pInt), parameter,                      public :: &
-    CPFEM_CALCRESULTS     = 2_pInt**0_pInt, &
-    CPFEM_AGERESULTS      = 2_pInt**1_pInt, &
-    CPFEM_BACKUPJACOBIAN  = 2_pInt**2_pInt, &
-    CPFEM_RESTOREJACOBIAN = 2_pInt**3_pInt
+  integer, parameter,                            public :: &
+    CPFEM_CALCRESULTS     = 2**0, &
+    CPFEM_AGERESULTS      = 2**1, &
+    CPFEM_BACKUPJACOBIAN  = 2**2, &
+    CPFEM_RESTOREJACOBIAN = 2**3
 
   type, private :: tNumerics
     integer :: &
-      iJacoStiffness                                                                                !< frequency of stiffness update
+      iJacoStiffness                                                                                 !< frequency of stiffness update
   end type tNumerics
 
   type(tNumerics), private :: num
@@ -134,12 +134,12 @@ end subroutine CPFEM_init
 !--------------------------------------------------------------------------------------------------
 subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyStress, jacobian)
 
-  integer(pInt), intent(in) ::                        elFE, &                                       !< FE element number
+  integer, intent(in) ::                              elFE, &                                       !< FE element number
                                                       ip                                            !< integration point number
   real(pReal), intent(in) ::                          dt                                            !< time increment
   real(pReal), dimension (3,3), intent(in) ::         ffn, &                                        !< deformation gradient for t=t0
                                                       ffn1                                          !< deformation gradient for t=t1
-  integer(pInt), intent(in) ::                        mode                                          !< computation mode  1: regular computation plus aging of results
+  integer, intent(in) ::                              mode                                          !< computation mode  1: regular computation plus aging of results
   real(pReal), intent(in) ::                          temperature_inp                               !< temperature
   real(pReal), dimension(6), intent(out) ::           cauchyStress                                  !< stress as 6 vector
   real(pReal), dimension(6,6), intent(out) ::         jacobian                                      !< jacobian as 66 tensor (Consistent tangent dcs/dE)
@@ -150,7 +150,7 @@ subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyS
   real(pReal), dimension (3,3,3,3) ::                 H_sym, &
                                                       H
 
-  integer(pInt)                                       elCP, &                                       ! crystal plasticity element number
+  integer                                             elCP, &                                       ! crystal plasticity element number
                                                       i, j, k, l, m, n, ph, homog, mySource,ce
 
   real(pReal), parameter ::                          ODD_STRESS    = 1e15_pReal, &                  !< return value for stress if terminallyIll
@@ -171,17 +171,17 @@ subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyS
     print'(a,/)', '#############################################'; flush (6)
   endif
 
-  if (iand(mode, CPFEM_BACKUPJACOBIAN) /= 0_pInt) &
+  if (iand(mode, CPFEM_BACKUPJACOBIAN) /= 0) &
     CPFEM_dcsde_knownGood = CPFEM_dcsde
-  if (iand(mode, CPFEM_RESTOREJACOBIAN) /= 0_pInt) &
+  if (iand(mode, CPFEM_RESTOREJACOBIAN) /= 0) &
     CPFEM_dcsde = CPFEM_dcsde_knownGood
 
-  if (iand(mode, CPFEM_AGERESULTS) /= 0_pInt) call CPFEM_forward
+  if (iand(mode, CPFEM_AGERESULTS) /= 0) call CPFEM_forward
 
     homogenization_F0(1:3,1:3,ce) = ffn
     homogenization_F(1:3,1:3,ce) = ffn1
 
-  if (iand(mode, CPFEM_CALCRESULTS) /= 0_pInt) then
+  if (iand(mode, CPFEM_CALCRESULTS) /= 0) then
 
     validCalculation: if (terminallyIll) then
       call random_number(rnd)
@@ -264,8 +264,8 @@ end subroutine CPFEM_forward
 !--------------------------------------------------------------------------------------------------
 subroutine CPFEM_results(inc,time)
 
-  integer(pInt), intent(in) :: inc
-  real(pReal),   intent(in) :: time
+  integer,     intent(in) :: inc
+  real(pReal), intent(in) :: time
 
   call results_openJobFile
   call results_addIncrement(inc,time)
diff --git a/src/DAMASK_Marc.f90 b/src/DAMASK_Marc.f90
index 0525db323..6e969ced4 100644
--- a/src/DAMASK_Marc.f90
+++ b/src/DAMASK_Marc.f90
@@ -223,9 +223,9 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
   integer :: computationMode, i, node, CPnodeID
   integer(pI32) :: defaultNumThreadsInt                                                             !< default value set by Marc
 
-  integer(pInt), save :: &
-    theInc       = -1_pInt, &                                                                       !< needs description
-    lastLovl     =  0_pInt                                                                          !< lovl in previous call to marc hypela2
+  integer, save :: &
+    theInc       = -1, &                                                                            !< needs description
+    lastLovl     =  0                                                                               !< lovl in previous call to marc hypela2
   real(pReal), save :: &
     theTime      = 0.0_pReal, &                                                                     !< needs description
     theDelta     = 0.0_pReal

From 3fb5bd459c79f992cbd9c457d4a86060b888fe11 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 07:43:53 +0100
Subject: [PATCH 039/133] pInt leftovers

---
 src/base64.f90                   |  2 +-
 src/grid/discretization_grid.f90 |  4 ++--
 src/mesh/FEM_utilities.f90       |  6 +++---
 src/prec.f90                     | 16 ++++++++--------
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/base64.f90 b/src/base64.f90
index 7bc00a1f9..448f57d2a 100644
--- a/src/base64.f90
+++ b/src/base64.f90
@@ -151,7 +151,7 @@ pure logical function validBase64(base64_str)
   l = len(base64_str,pI64)
   validBase64 = .true.
 
-  if(mod(l,4_pI64)/=0_pI64 .or. l < 4_pInt)                                  validBase64 = .false.
+  if(mod(l,4_pI64)/=0_pI64 .or. l < 4_pI64)                                  validBase64 = .false.
   if(verify(base64_str(:l-2_pI64),base64_encoding,     kind=pI64) /= 0_pI64) validBase64 = .false.
   if(verify(base64_str(l-1_pI64:),base64_encoding//'=',kind=pI64) /= 0_pI64) validBase64 = .false.
 
diff --git a/src/grid/discretization_grid.f90 b/src/grid/discretization_grid.f90
index ddc9efd80..54851c1fe 100644
--- a/src/grid/discretization_grid.f90
+++ b/src/grid/discretization_grid.f90
@@ -307,7 +307,7 @@ subroutine readVTI(grid,geomSize,origin,material, &
       case('Float64')
         as_Int = int(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)))
       case default
-        call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
+        call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
     end select
 
   end function as_Int
@@ -335,7 +335,7 @@ subroutine readVTI(grid,geomSize,origin,material, &
       case('Float64')
         as_pReal = real(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
       case default
-        call IO_error(844_pInt,ext_msg='unknown data type: '//trim(dataType))
+        call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
     end select
 
   end function as_pReal
diff --git a/src/mesh/FEM_utilities.f90 b/src/mesh/FEM_utilities.f90
index df16fa8e2..86fb52b36 100644
--- a/src/mesh/FEM_utilities.f90
+++ b/src/mesh/FEM_utilities.f90
@@ -92,7 +92,7 @@ subroutine FEM_utilities_init
     p_i                                                                                             !< integration order (quadrature rule)
   character(len=*), parameter :: &
     PETSCDEBUG = ' -snes_view -snes_monitor '
-  PetscErrorCode            :: ierr
+  PetscErrorCode :: ierr
   logical :: debugPETSc                                                                             !< use some in debug defined options for more verbose PETSc solution
 
 
@@ -103,9 +103,9 @@ subroutine FEM_utilities_init
   p_s = num_mesh%get_asInt('p_s',defaultVal = 2)
   p_i = num_mesh%get_asInt('p_i',defaultVal = p_s)
 
-  if (p_s < 1_pInt .or. p_s > size(FEM_nQuadrature,2)) &
+  if (p_s < 1 .or. p_s > size(FEM_nQuadrature,2)) &
     call IO_error(821,ext_msg='shape function order (p_s) out of bounds')
-  if (p_i < max(1_pInt,p_s-1_pInt) .or. p_i > p_s) &
+  if (p_i < max(1,p_s-1) .or. p_i > p_s) &
     call IO_error(821,ext_msg='integration order (p_i) out of bounds')
 
   debug_mesh  => config_debug%get('mesh',defaultVal=emptyList)
diff --git a/src/prec.f90 b/src/prec.f90
index fe3e7fc20..2616a6dcf 100644
--- a/src/prec.f90
+++ b/src/prec.f90
@@ -29,10 +29,10 @@ module prec
 #endif
 #ifdef PETSC
   PetscInt,    private   :: dummy
-  integer,     parameter :: pPetscInt  = kind(dummy)
+  integer,     parameter :: pPETSCINT  = kind(dummy)
 #endif
-  integer,     parameter :: pStringLen = 256                                                        !< default string length
-  integer,     parameter :: pPathLen   = 4096                                                       !< maximum length of a path name on linux
+  integer,     parameter :: pSTRINGLEN = 256                                                        !< default string length
+  integer,     parameter :: pPATHLEN   = 4096                                                       !< maximum length of a path name on linux
 
   real(pReal), parameter :: tol_math_check = 1.0e-8_pReal                                           !< tolerance for internal math self-checks (rotation)
 
@@ -277,7 +277,7 @@ subroutine selfTest
 
   integer, allocatable, dimension(:) :: realloc_lhs_test
   real(pReal),   dimension(1) :: f
-  integer(pInt), dimension(1) :: i
+  integer(pI64), dimension(1) :: i
   real(pReal),   dimension(2) :: r
 
 
@@ -298,11 +298,11 @@ subroutine selfTest
   f = real(prec_bytesToC_DOUBLE(int([0,0,0,-32,+119,+65,+115,65],C_SIGNED_CHAR)),pReal)
   if (dNeq(f(1),20191102.0_pReal,0.0_pReal)) error stop 'prec_bytesToC_DOUBLE'
 
-  i = int(prec_bytesToC_INT32_T(int([+126,+23,+52,+1],C_SIGNED_CHAR)),pInt)
-  if (i(1) /= 20191102_pInt)                 error stop 'prec_bytesToC_INT32_T'
+  i = int(prec_bytesToC_INT32_T(int([+126,+23,+52,+1],C_SIGNED_CHAR)),pI64)
+  if (i(1) /= 20191102_pI64)                 error stop 'prec_bytesToC_INT32_T'
 
-  i = int(prec_bytesToC_INT64_T(int([+126,+23,+52,+1,0,0,0,0],C_SIGNED_CHAR)),pInt)
-  if (i(1) /= 20191102_pInt)                 error stop 'prec_bytesToC_INT64_T'
+  i = int(prec_bytesToC_INT64_T(int([+126,+23,+52,+1,0,0,0,0],C_SIGNED_CHAR)),pI64)
+  if (i(1) /= 20191102_pI64)                 error stop 'prec_bytesToC_INT64_T'
 
 end subroutine selfTest
 

From 8223dc7fa7b01b3e540f040fb2a82b90394db287 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 08:17:31 +0100
Subject: [PATCH 040/133] polishing

MPI, HDF5, PETSc, and DAMASK might have different integer kinds ..
---
 src/grid/spectral_utilities.f90 |  4 ++--
 src/parallelization.f90         | 14 +++++++-------
 src/quit.f90                    | 26 +++++++++++++++-----------
 3 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index f40025039..415c4f838 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -292,12 +292,12 @@ subroutine spectral_utilities_init
                                         tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
                                                        tensorField_real, tensorField_fourier, &     ! input data, output data
                                                                PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
-  if (.not. C_ASSOCIATED(planTensorForth)) error stop 'FFTW error'
+  if (.not. c_associated(planTensorForth)) error stop 'FFTW error'
   planTensorBack  = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], &          ! dimension, logical length in each dimension in reversed order
                                        tensorSize,  FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
                                                         tensorField_fourier,tensorField_real, &     ! input data, output data
                                                                PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
-  if (.not. C_ASSOCIATED(planTensorBack)) error stop 'FFTW error'
+  if (.not. c_associated(planTensorBack)) error stop 'FFTW error'
 
 !--------------------------------------------------------------------------------------------------
 ! vector MPI fftw plans
diff --git a/src/parallelization.f90 b/src/parallelization.f90
index a4f7e5ae1..6e1dedd70 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -50,7 +50,7 @@ subroutine parallelization_init
 !$ character(len=6) NumThreadsString
 
 
-  PetscErrorCode :: petsc_err
+  PetscErrorCode :: err_PETSc
 #ifdef _OPENMP
   ! If openMP is enabled, check if the MPI libary supports it and initialize accordingly.
   ! Otherwise, the first call to PETSc will do the initialization.
@@ -60,18 +60,18 @@ subroutine parallelization_init
 #endif
 
 #if defined(DEBUG)
-  call PetscInitialize(PETSC_NULL_CHARACTER,petsc_err)
+  call PetscInitialize(PETSC_NULL_CHARACTER,err_PETSc)
 #else
-  call PetscInitializeNoArguments(petsc_err)
+  call PetscInitializeNoArguments(err_PETSc)
 #endif
-  CHKERRQ(petsc_err)
+  CHKERRQ(err_PETSc)
 
 #if defined(DEBUG) && defined(__INTEL_COMPILER)
-  call PetscSetFPTrap(PETSC_FP_TRAP_ON,petsc_err)
+  call PetscSetFPTrap(PETSC_FP_TRAP_ON,err_PETSc)
 #else
-  call PetscSetFPTrap(PETSC_FP_TRAP_OFF,petsc_err)
+  call PetscSetFPTrap(PETSC_FP_TRAP_OFF,err_PETSc)
 #endif
-  CHKERRQ(petsc_err)
+  CHKERRQ(err_PETSc)
 
   call MPI_Comm_rank(MPI_COMM_WORLD,worldrank,err)
   if (err /= 0)                              error stop 'Could not determine worldrank'
diff --git a/src/quit.f90 b/src/quit.f90
index 6361ff783..3f9aabdf5 100644
--- a/src/quit.f90
+++ b/src/quit.f90
@@ -15,20 +15,21 @@ subroutine quit(stop_id)
   implicit none
   integer, intent(in) :: stop_id
   integer, dimension(8) :: dateAndTime
-  integer :: error
-  PetscErrorCode :: ierr = 0
+  integer :: err_HDF5
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  PetscErrorCode :: err_PETSc
  
-  call h5open_f(error)
-  if (error /= 0) write(6,'(a,i5)') ' Error in h5open_f ',error                                     ! prevents error if not opened yet
-  call h5close_f(error)
-  if (error /= 0) write(6,'(a,i5)') ' Error in h5close_f ',error
+  call h5open_f(err_HDF5)
+  if (err_HDF5 /= 0) write(6,'(a,i5)') ' Error in h5open_f ',err_HDF5                               ! prevents error if not opened yet
+  call h5close_f(err_HDF5)
+  if (err_HDF5 /= 0) write(6,'(a,i5)') ' Error in h5close_f ',err_HDF5
  
-  call PetscFinalize(ierr)
-  CHKERRQ(ierr)
+  call PetscFinalize(err_PETSc)
+  CHKERRQ(err_PETSc)
  
 #ifdef _OPENMP
-  call MPI_finalize(error)
-  if (error /= 0) write(6,'(a,i5)') ' Error in MPI_finalize',error
+  call MPI_finalize(err_MPI)
+  if (err_MPI /= 0) write(6,'(a,i5)') ' Error in MPI_finalize',err_MPI
 #endif
   
   call date_and_time(values = dateAndTime)
@@ -40,7 +41,10 @@ subroutine quit(stop_id)
                                                         dateAndTime(6),':',&
                                                         dateAndTime(7)
  
-  if (stop_id == 0 .and. ierr == 0 .and. error == 0) stop 0                                         ! normal termination
+  if (stop_id == 0 .and. &
+      err_HDF5 == 0 .and. &
+      err_MPI == 0_MPI_INTEGER_KIND .and. &
+      err_PETSC == 0) stop 0                                                                        ! normal termination
   stop 1                                                                                            ! error (message from IO_error)
 
 end subroutine quit

From 1c46e7ea1a73a70eeac965a84683244beadc421b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 08:30:46 +0100
Subject: [PATCH 041/133] not needed

---
 src/prec.f90 | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/prec.f90 b/src/prec.f90
index 2616a6dcf..8de82fee8 100644
--- a/src/prec.f90
+++ b/src/prec.f90
@@ -22,11 +22,6 @@ module prec
   integer,     parameter :: pReal      = IEEE_selected_real_kind(15,307)                            !< number with 15 significant digits, up to 1e+-307 (typically 64 bit)
   integer,     parameter :: pI32       = selected_int_kind(9)                                       !< number with at least up to +-1e9 (typically 32 bit)
   integer,     parameter :: pI64       = selected_int_kind(18)                                      !< number with at least up to +-1e18 (typically 64 bit)
-#if(INT==8)
-  integer,     parameter :: pInt       = pI64
-#else
-  integer,     parameter :: pInt       = pI32
-#endif
 #ifdef PETSC
   PetscInt,    private   :: dummy
   integer,     parameter :: pPETSCINT  = kind(dummy)

From a3a3388855fd16765b27b6d0d7f7956479f6f3cd Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 08:43:39 +0100
Subject: [PATCH 042/133] decouple DAMASK default integer from MPI default
 integer

---
 src/grid/spectral_utilities.f90 | 90 +++++++++++++++++----------------
 src/parallelization.f90         | 64 ++++++++++++++---------
 src/results.f90                 | 22 ++++----
 3 files changed, 98 insertions(+), 78 deletions(-)

diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index 415c4f838..35803481c 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -144,7 +144,7 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine spectral_utilities_init
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   integer        :: i, j, k, &
     FFTW_planner_flag
   integer, dimension(3) :: k_s
@@ -193,13 +193,13 @@ subroutine spectral_utilities_init
                  'add more using the "PETSc_options" keyword in numerics.yaml'
   flush(IO_STDOUT)
 
-  call PetscOptionsClear(PETSC_NULL_OPTIONS,ierr)
-  CHKERRQ(ierr)
-  if (debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),ierr)
-  CHKERRQ(ierr)
+  call PetscOptionsClear(PETSC_NULL_OPTIONS,err_PETSc)
+  CHKERRQ(err_PETSc)
+  if (debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),err_PETSc)
+  CHKERRQ(err_PETSc)
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS,&
-                                num_grid%get_asString('PETSc_options',defaultVal=''),ierr)
-  CHKERRQ(ierr)
+                                num_grid%get_asString('PETSc_options',defaultVal=''),err_PETSc)
+  CHKERRQ(err_PETSc)
 
   grid1Red = grid(1)/2 + 1
   wgt = 1.0/real(product(grid),pReal)
@@ -559,8 +559,9 @@ end subroutine utilities_fourierGreenConvolution
 !--------------------------------------------------------------------------------------------------
 real(pReal) function utilities_divergenceRMS()
 
-  integer :: i, j, k, ierr
-  complex(pReal), dimension(3)   :: rescaledGeom
+  integer :: i, j, k
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  complex(pReal), dimension(3) :: rescaledGeom
 
   print'(/,1x,a)', '... calculating divergence ................................................'
   flush(IO_STDOUT)
@@ -589,8 +590,8 @@ real(pReal) function utilities_divergenceRMS()
                                   conjg(-xi1st(1:3,grid1Red,j,k))*rescaledGeom))**2)
   enddo; enddo
   if (grid(1) == 1) utilities_divergenceRMS = utilities_divergenceRMS * 0.5_pReal                   ! counted twice in case of grid(1) == 1
-  call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
-  if (ierr /=0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   utilities_divergenceRMS = sqrt(utilities_divergenceRMS) * wgt                                     ! RMS in real space calculated with Parsevals theorem from Fourier space
 
 end function utilities_divergenceRMS
@@ -601,7 +602,8 @@ end function utilities_divergenceRMS
 !--------------------------------------------------------------------------------------------------
 real(pReal) function utilities_curlRMS()
 
-  integer  ::  i, j, k, l, ierr
+  integer  ::  i, j, k, l
+  integer(MPI_INTEGER_KIND) :: err_MPI
   complex(pReal), dimension(3,3) :: curl_fourier
   complex(pReal), dimension(3)   :: rescaledGeom
 
@@ -649,8 +651,8 @@ real(pReal) function utilities_curlRMS()
                       + sum(curl_fourier%re**2 + curl_fourier%im**2)                                ! this layer (Nyquist) does not have a conjugate complex counterpart (if grid(1) /= 1)
   enddo; enddo
 
-  call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
-  if (ierr /=0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   utilities_curlRMS = sqrt(utilities_curlRMS) * wgt
   if (grid(1) == 1) utilities_curlRMS = utilities_curlRMS * 0.5_pReal                               ! counted twice in case of grid(1) == 1
 
@@ -799,8 +801,8 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
   type(rotation), intent(in),  optional                             :: rotation_BC                  !< rotation of load frame
 
 
-  integer :: &
-    i,ierr
+  integer :: i
+  integer(MPI_INTEGER_KIND) :: err_MPI
   real(pReal), dimension(3,3,3,3) :: dPdF_max,      dPdF_min
   real(pReal)                     :: dPdF_norm_max, dPdF_norm_min
   real(pReal), dimension(2) :: valueAndRank                                                         !< pair of min/max norm of dPdF to synchronize min/max of dPdF
@@ -818,7 +820,8 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
 
   P = reshape(homogenization_P, [3,3,grid(1),grid(2),grid3])
   P_av = sum(sum(sum(P,dim=5),dim=4),dim=3) * wgt
-  call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   if (debugRotation) print'(/,1x,a,/,2(3(2x,f12.4,1x)/),3(2x,f12.4,1x))', &
     'Piola--Kirchhoff stress (lab) / MPa =', transpose(P_av)*1.e-6_pReal
   if (present(rotation_BC)) P_av = rotation_BC%rotate(P_av)
@@ -842,22 +845,22 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
   enddo
 
   valueAndRank = [dPdF_norm_max,real(worldrank,pReal)]
-  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MAXLOC, MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
-  call MPI_Bcast(dPdF_max,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MAXLOC, MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Bcast(dPdF_max,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   valueAndRank = [dPdF_norm_min,real(worldrank,pReal)]
-  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MINLOC, MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
-  call MPI_Bcast(dPdF_min,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MINLOC, MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Bcast(dPdF_min,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   C_minmaxAvg = 0.5_pReal*(dPdF_max + dPdF_min)
 
   C_volAvg = sum(homogenization_dPdF,dim=5)
-  call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   C_volAvg = C_volAvg * wgt
 
 
@@ -906,12 +909,13 @@ function utilities_forwardField(Delta_t,field_lastInc,rate,aim)
   real(pReal),                       dimension(3,3,grid(1),grid(2),grid3) :: &
     utilities_forwardField
   real(pReal),                       dimension(3,3)                       :: fieldDiff              !< <a + adot*t> - aim
-  PetscErrorCode :: ierr
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
   utilities_forwardField = field_lastInc + rate*Delta_t
   if (present(aim)) then                                                                            !< correct to match average
     fieldDiff = sum(sum(sum(utilities_forwardField,dim=5),dim=4),dim=3)*wgt
-    call MPI_Allreduce(MPI_IN_PLACE,fieldDiff,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+    call MPI_Allreduce(MPI_IN_PLACE,fieldDiff,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     fieldDiff = fieldDiff - aim
     utilities_forwardField = utilities_forwardField - &
                      spread(spread(spread(fieldDiff,3,grid(1)),4,grid(2)),5,grid3)
@@ -982,8 +986,8 @@ subroutine utilities_updateCoords(F)
   integer :: &
     i,j,k,n, &
     rank_t, rank_b, &
-    c, &
-    ierr
+    c
+  integer(MPI_INTEGER_KIND) :: err_MPI
 #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
   type(MPI_Request), dimension(4) :: request
   type(MPI_Status),  dimension(4) :: status
@@ -1025,8 +1029,8 @@ subroutine utilities_updateCoords(F)
  !--------------------------------------------------------------------------------------------------
  ! average F
   if (grid3Offset == 0) Favg = real(tensorField_fourier(1:3,1:3,1,1,1),pReal)*wgt
-  call MPI_Bcast(Favg,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-  if (ierr /=0) error stop 'MPI error'
+  call MPI_Bcast(Favg,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
  !--------------------------------------------------------------------------------------------------
  ! pad cell center fluctuations along z-direction (needed when running MPI simulation)
@@ -1036,19 +1040,19 @@ subroutine utilities_updateCoords(F)
   rank_b = modulo(worldrank-1,worldsize)
 
   ! send bottom layer to process below
-  call MPI_Isend(IPfluct_padded(:,:,:,2),      c,MPI_DOUBLE,rank_b,0,MPI_COMM_WORLD,request(1),ierr)
-  if (ierr /=0) error stop 'MPI error'
-  call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,MPI_COMM_WORLD,request(2),ierr)
-  if (ierr /=0) error stop 'MPI error'
+  call MPI_Isend(IPfluct_padded(:,:,:,2),      c,MPI_DOUBLE,rank_b,0,MPI_COMM_WORLD,request(1),err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,MPI_COMM_WORLD,request(2),err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   ! send top layer to process above
-  call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1,MPI_COMM_WORLD,request(3),ierr)
-  if (ierr /=0) error stop 'MPI error'
-  call MPI_Irecv(IPfluct_padded(:,:,:,1),      c,MPI_DOUBLE,rank_b,1,MPI_COMM_WORLD,request(4),ierr)
-  if (ierr /=0) error stop 'MPI error'
+  call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1,MPI_COMM_WORLD,request(3),err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Irecv(IPfluct_padded(:,:,:,1),      c,MPI_DOUBLE,rank_b,1,MPI_COMM_WORLD,request(4),err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
-  call MPI_Waitall(4,request,status,ierr)
-  if (ierr /=0) error stop 'MPI error'
+  call MPI_Waitall(4,request,status,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
   ! ToDo
 #else
diff --git a/src/parallelization.f90 b/src/parallelization.f90
index 6e1dedd70..94bf6d343 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -20,12 +20,19 @@ module parallelization
   implicit none
   private
 
-  integer, protected, public :: &
-    worldrank = 0, &                                                                                !< MPI worldrank (/=0 for MPI simulations only)
-    worldsize = 1                                                                                   !< MPI worldsize (/=1 for MPI simulations only)
+#ifndef PETSC
+  integer, parameter, public :: &
+    MPI_INTEGER_KIND = pI64
+  integer(MPI_INTEGER_KIND), parameter, public :: &
+    worldrank = 0_MPI_INTEGER_KIND, &                                                               !< MPI dummy worldrank
+    worldsize = 1_MPI_INTEGER_KIND                                                                  !< MPI dummy worldsize
+#else
+  integer(MPI_INTEGER_KIND), protected, public :: &
+    worldrank = 0_MPI_INTEGER_KIND, &                                                               !< MPI worldrank (/=0 for MPI simulations only)
+    worldsize = 1_MPI_INTEGER_KIND                                                                  !< MPI worldsize (/=1 for MPI simulations only)
+#endif
 
 #ifndef PETSC
-public :: parallelization_bcast_str
 
 contains
 subroutine parallelization_bcast_str(string)
@@ -44,7 +51,7 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine parallelization_init
 
-  integer :: err, typeSize
+  integer(MPI_INTEGER_KIND) :: err_MPI, typeSize
 !$ integer :: got_env, threadLevel
 !$ integer(pI32) :: OMP_NUM_THREADS
 !$ character(len=6) NumThreadsString
@@ -54,8 +61,8 @@ subroutine parallelization_init
 #ifdef _OPENMP
   ! If openMP is enabled, check if the MPI libary supports it and initialize accordingly.
   ! Otherwise, the first call to PETSc will do the initialization.
-  call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,err)
-  if (err /= 0)                        error stop 'MPI init failed'
+  call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND)   error stop 'MPI init failed'
   if (threadLevel<MPI_THREAD_FUNNELED) error stop 'MPI library does not support OpenMP'
 #endif
 
@@ -73,27 +80,34 @@ subroutine parallelization_init
 #endif
   CHKERRQ(err_PETSc)
 
-  call MPI_Comm_rank(MPI_COMM_WORLD,worldrank,err)
-  if (err /= 0)                              error stop 'Could not determine worldrank'
+  call MPI_Comm_rank(MPI_COMM_WORLD,worldrank,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) &
+    error stop 'Could not determine worldrank'
 
   if (worldrank == 0) print'(/,1x,a)', '<<<+-  parallelization init  -+>>>'
 
-  call MPI_Comm_size(MPI_COMM_WORLD,worldsize,err)
-  if (err /= 0)                              error stop 'Could not determine worldsize'
+  call MPI_Comm_size(MPI_COMM_WORLD,worldsize,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) &
+    error stop 'Could not determine worldsize'
   if (worldrank == 0) print'(/,1x,a,i3)', 'MPI processes: ',worldsize
 
-  call MPI_Type_size(MPI_INTEGER,typeSize,err)
-  if (err /= 0)                              error stop 'Could not determine MPI integer size'
-  if (typeSize*8 /= bit_size(0))             error stop 'Mismatch between MPI and DAMASK integer'
+  call MPI_Type_size(MPI_INTEGER,typeSize,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) &
+    error stop 'Could not determine size of MPI_INTEGER'
+  if (typeSize*8_MPI_INTEGER_KIND /= int(bit_size(0),MPI_INTEGER_KIND)) &
+    error stop 'Mismatch between MPI_INTEGER and DAMASK default integer'
 
-  call MPI_Type_size(MPI_INTEGER8,typeSize,err)
-  if (err /= 0)                              error stop 'Could not determine MPI integer size'
-  if (int(typeSize,pI64)*8_pI64 /= bit_size(0_pI64)) &
-                                             error stop 'Mismatch between MPI and DAMASK integer (long long)'
+  call MPI_Type_size(MPI_INTEGER8,typeSize,err_MPI)
+  if (err_MPI /= 0) &
+    error stop 'Could not determine size of MPI_INTEGER8'
+  if (typeSize*8_MPI_INTEGER_KIND /= int(bit_size(0_pI64),MPI_INTEGER_KIND)) &
+    error stop 'Mismatch between MPI_INTEGER8 and DAMASK pI64'
 
-  call MPI_Type_size(MPI_DOUBLE,typeSize,err)
-  if (err /= 0)                              error stop 'Could not determine MPI real size'
-  if (typeSize*8 /= storage_size(0.0_pReal)) error stop 'Mismatch between MPI and DAMASK real'
+  call MPI_Type_size(MPI_DOUBLE,typeSize,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) &
+    error stop 'Could not determine size of MPI_DOUBLE'
+  if (typeSize*8_MPI_INTEGER_KIND /= int(storage_size(0.0_pReal),MPI_INTEGER_KIND)) &
+    error stop 'Mismatch between MPI_DOUBLE and DAMASK pReal'
 
   if (worldrank /= 0) then
     close(OUTPUT_UNIT)                                                                              ! disable output
@@ -124,14 +138,14 @@ subroutine parallelization_bcast_str(string)
 
   character(len=:), allocatable, intent(inout) :: string
 
-  integer :: strlen, ierr                                                                           ! pI64 for strlen not supported by MPI
+  integer(MPI_INTEGER_KIND) :: strlen, err_MPI
 
 
-  if (worldrank == 0) strlen = len(string)
-  call MPI_Bcast(strlen,1,MPI_INTEGER,0,MPI_COMM_WORLD, ierr)
+  if (worldrank == 0) strlen = len(string,MPI_INTEGER_KIND)
+  call MPI_Bcast(strlen,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
   if (worldrank /= 0) allocate(character(len=strlen)::string)
 
-  call MPI_Bcast(string,strlen,MPI_CHARACTER,0,MPI_COMM_WORLD, ierr)
+  call MPI_Bcast(string,strlen,MPI_CHARACTER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
 
 
 end subroutine parallelization_bcast_str
diff --git a/src/results.f90 b/src/results.f90
index 48cce82f9..d85a30dc0 100644
--- a/src/results.f90
+++ b/src/results.f90
@@ -519,7 +519,8 @@ subroutine results_mapping_phase(ID,entry,label)
     dt_id
 
   integer(SIZE_T) :: type_size_string, type_size_int
-  integer         :: hdferr, ierr, ce, co
+  integer         :: hdferr, ce, co
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
 
   writeSize = 0
@@ -536,8 +537,8 @@ subroutine results_mapping_phase(ID,entry,label)
   call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)      ! get output at each process
-  if(ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)   ! get output at each process
+  if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   entryOffset = 0_pI64
   do co = 1, size(ID,1)
@@ -545,8 +546,8 @@ subroutine results_mapping_phase(ID,entry,label)
       entryOffset(ID(co,ce),worldrank) = entryOffset(ID(co,ce),worldrank) +1_pI64
     end do
   end do
-  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
-  if(ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,err_MPI)! get offset at each process
+  if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
   do co = 1, size(ID,1)
     do ce = 1, size(ID,2)
@@ -674,7 +675,8 @@ subroutine results_mapping_homogenization(ID,entry,label)
     dt_id
 
   integer(SIZE_T) :: type_size_string, type_size_int
-  integer         :: hdferr, ierr, ce
+  integer         :: hdferr, ce
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
 
   writeSize = 0
@@ -691,15 +693,15 @@ subroutine results_mapping_homogenization(ID,entry,label)
   call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)      ! get output at each process
-  if(ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)   ! get output at each process
+  if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   entryOffset = 0_pI64
   do ce = 1, size(ID,1)
     entryOffset(ID(ce),worldrank) = entryOffset(ID(ce),worldrank) +1_pI64
   end do
-  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,ierr)! get offset at each process
-  if(ierr /= 0) error stop 'MPI error'
+  call MPI_Allreduce(MPI_IN_PLACE,entryOffset,size(entryOffset),MPI_INTEGER8,MPI_SUM,MPI_COMM_WORLD,err_MPI)! get offset at each process
+  if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   entryOffset(:,worldrank) = sum(entryOffset(:,0:worldrank-1),2)
   do ce = 1, size(ID,1)
     entryGlobal(ce) = int(entry(ce),pI64) -1_pI64 + entryOffset(ID(ce),worldrank)

From 64395d4b2b53b8321133df5676d59414edc1c2fd Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 10:18:17 +0100
Subject: [PATCH 043/133] not needed anymore

setting precision is done via compiler flag. Theoretically, it would
work to simply use pI64 for the interface (hypela2 and uedinc) but
stupid common blocks would need to be adjusted as well
---
 install/MarcMentat/2020/Marc_tools/include_linux64.patch    | 6 ++----
 install/MarcMentat/2021.2/Marc_tools/include_linux64.patch  | 6 ++----
 .../MarcMentat/2021.3.1/Marc_tools/include_linux64.patch    | 6 ++----
 3 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/install/MarcMentat/2020/Marc_tools/include_linux64.patch b/install/MarcMentat/2020/Marc_tools/include_linux64.patch
index c28b41b9e..9849584fa 100644
--- a/install/MarcMentat/2020/Marc_tools/include_linux64.patch
+++ b/install/MarcMentat/2020/Marc_tools/include_linux64.patch
@@ -12,17 +12,15 @@
  
  # AEM
  if test "$MARCDLLOUTDIR" = ""; then
-@@ -390,8 +395,8 @@
+@@ -390,7 +395,7 @@
    I8DEFINES=
    I8CDEFINES=
  else
 -  I8FFLAGS="-i8"
--  I8DEFINES="-DI64"
 +  I8FFLAGS="-i8 -integer-size 64"
-+  I8DEFINES="-DI64 -DINT=8"
+   I8DEFINES="-DI64"
    I8CDEFINES="-U_DOUBLE -D_SINGLE"
  fi
- 
 @@ -498,7 +503,7 @@
  PROFILE=" $PROFILE -pg"
  fi
diff --git a/install/MarcMentat/2021.2/Marc_tools/include_linux64.patch b/install/MarcMentat/2021.2/Marc_tools/include_linux64.patch
index 430d5bc61..5ff02dae6 100644
--- a/install/MarcMentat/2021.2/Marc_tools/include_linux64.patch
+++ b/install/MarcMentat/2021.2/Marc_tools/include_linux64.patch
@@ -12,17 +12,15 @@
  
  # AEM
  if test "$MARCDLLOUTDIR" = ""; then
-@@ -439,8 +444,8 @@
+@@ -439,7 +444,7 @@
    I8DEFINES=
    I8CDEFINES=
  else
 -  I8FFLAGS="-i8"
--  I8DEFINES="-DI64"
 +  I8FFLAGS="-i8 -integer-size 64"
-+  I8DEFINES="-DI64 -DINT=8"
+   I8DEFINES="-DI64"
    I8CDEFINES="-U_DOUBLE -D_SINGLE"
  fi
- 
 @@ -556,7 +561,7 @@
  PROFILE=" $PROFILE -pg"
  fi
diff --git a/install/MarcMentat/2021.3.1/Marc_tools/include_linux64.patch b/install/MarcMentat/2021.3.1/Marc_tools/include_linux64.patch
index 91e2b1b59..e1cc543c6 100644
--- a/install/MarcMentat/2021.3.1/Marc_tools/include_linux64.patch
+++ b/install/MarcMentat/2021.3.1/Marc_tools/include_linux64.patch
@@ -12,17 +12,15 @@
  # AEM
  if test "$MARCDLLOUTDIR" = ""; then
   DLLOUTDIR="$MARC_LIB"
-@@ -439,8 +444,8 @@ if test "$MARC_INTEGER_SIZE" = "i4" ; then
+@@ -439,7 +444,7 @@ if test "$MARC_INTEGER_SIZE" = "i4" ; then
    I8DEFINES=
    I8CDEFINES=
  else
 -  I8FFLAGS="-i8"
--  I8DEFINES="-DI64"
 +  I8FFLAGS="-i8 -integer-size 64"
-+  I8DEFINES="-DI64 -DINT=8"
+   I8DEFINES="-DI64"
    I8CDEFINES="-U_DOUBLE -D_SINGLE"
  fi
- 
 @@ -556,7 +561,7 @@ then
  PROFILE=" $PROFILE -pg"
  fi

From a7417a7ad76c78a2d6fc96fa331c2981849c2a88 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 10:41:36 +0100
Subject: [PATCH 044/133] default integer, PETSc integer, and MPI integer might
 be different

---
 src/HDF5_utilities.f90                       |  15 +-
 src/grid/DAMASK_grid.f90                     |  14 +-
 src/grid/discretization_grid.f90             |  39 +-
 src/grid/grid_mech_FEM.f90                   | 277 ++++++-------
 src/grid/grid_mech_spectral_basic.f90        | 119 +++---
 src/grid/grid_mech_spectral_polarisation.f90 | 126 +++---
 src/mesh/DAMASK_mesh.f90                     |   6 +-
 src/mesh/FEM_utilities.f90                   |  58 +--
 src/mesh/discretization_mesh.f90             |  97 ++---
 src/mesh/mesh_mech_FEM.f90                   | 386 ++++++++++---------
 src/results.f90                              |   2 +-
 11 files changed, 607 insertions(+), 532 deletions(-)

diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90
index 7645189c6..d2076c2cc 100644
--- a/src/HDF5_utilities.f90
+++ b/src/HDF5_utilities.f90
@@ -1857,13 +1857,13 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
     localShape
   integer(HSIZE_T),  intent(out), dimension(size(localShape,1)):: &
     myStart, &
-    globalShape                                                                                    !< shape of the dataset (all processes)
+    globalShape                                                                                     !< shape of the dataset (all processes)
   integer(HID_T),    intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
 
   integer, dimension(worldsize) :: &
     readSize                                                                                        !< contribution of all processes
-  integer :: ierr
   integer :: hdferr
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
 !-------------------------------------------------------------------------------------------------
 ! creating a property list for transfer properties (is collective for MPI)
@@ -1877,8 +1877,8 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
   if (parallel) then
     call H5Pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
     if(hdferr < 0) error stop 'HDF5 error'
-    call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,ierr)   ! get total output size over each process
-    if (ierr /= 0) error stop 'MPI error'
+    call MPI_allreduce(MPI_IN_PLACE,readSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,err_MPI) ! get total output size over each process
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   end if
 #endif
   myStart                   = int(0,HSIZE_T)
@@ -1956,7 +1956,8 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
 
   integer, dimension(worldsize) :: writeSize                                                        !< contribution of all processes
   integer(HID_T) ::  dcpl
-  integer :: ierr, hdferr
+  integer :: hdferr
+  integer(MPI_INTEGER_KIND) :: err_MPI
   integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
 
 
@@ -1977,8 +1978,8 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
   writeSize(worldrank+1) = int(myShape(ubound(myShape,1)))
 #ifdef PETSC
   if (parallel) then
-    call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,ierr)  ! get total output size over each process
-    if (ierr /= 0) error stop 'MPI error'
+    call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,err_MPI) ! get total output size over each process
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   end if
 #endif
   myStart                   = int(0,HSIZE_T)
diff --git a/src/grid/DAMASK_grid.f90 b/src/grid/DAMASK_grid.f90
index b1da0c2a2..6377748be 100644
--- a/src/grid/DAMASK_grid.f90
+++ b/src/grid/DAMASK_grid.f90
@@ -75,7 +75,6 @@ program DAMASK_grid
   integer :: &
     i, j, m, field, &
     errorID = 0, &
-    ierr,&
     cutBackLevel = 0, &                                                                             !< cut back level \f$ t = \frac{t_{inc}}{2^l} \f$
     stepFraction = 0, &                                                                             !< fraction of current time interval
     l = 0, &                                                                                        !< current load case
@@ -86,6 +85,7 @@ program DAMASK_grid
     nActiveFields = 0, &
     maxCutBack, &                                                                                   !< max number of cut backs
     stagItMax                                                                                       !< max number of field level staggered iterations
+  integer(MPI_INTEGER_KIND) :: err_MPI
   character(len=pStringLen) :: &
     incInfo
 
@@ -455,23 +455,23 @@ program DAMASK_grid
           print'(/,1x,a,i0,a)', 'increment ', totalIncsCounter, ' NOT converged'
         endif; flush(IO_STDOUT)
 
-        call MPI_Allreduce(interface_SIGUSR1,signal,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
-        if (ierr /= 0) error stop 'MPI error'
+        call MPI_Allreduce(interface_SIGUSR1,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+        if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
         if (mod(inc,loadCases(l)%f_out) == 0 .or. signal) then
           print'(/,1x,a)', '... writing results to file ...............................................'
           flush(IO_STDOUT)
           call CPFEM_results(totalIncsCounter,t)
         endif
         if (signal) call interface_setSIGUSR1(.false.)
-        call MPI_Allreduce(interface_SIGUSR2,signal,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
-        if (ierr /= 0) error stop 'MPI error'
+        call MPI_Allreduce(interface_SIGUSR2,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+        if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
         if (mod(inc,loadCases(l)%f_restart) == 0 .or. signal) then
           call mechanical_restartWrite
           call CPFEM_restartWrite
         endif
         if (signal) call interface_setSIGUSR2(.false.)
-        call MPI_Allreduce(interface_SIGTERM,signal,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
-        if (ierr /= 0) error stop 'MPI error'
+        call MPI_Allreduce(interface_SIGTERM,signal,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+        if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
         if (signal) exit loadCaseLooping
       endif skipping
 
diff --git a/src/grid/discretization_grid.f90 b/src/grid/discretization_grid.f90
index 54851c1fe..93b3cbc91 100644
--- a/src/grid/discretization_grid.f90
+++ b/src/grid/discretization_grid.f90
@@ -27,14 +27,14 @@ module discretization_grid
   private
 
   integer,     dimension(3), public, protected :: &
-    grid                                                                                            !< (global) grid
+    grid                                                                                           !< (global) grid
   integer,                   public, protected :: &
-    grid3, &                                                                                        !< (local) grid in 3rd direction
+    grid3, &                                                                                       !< (local) grid in 3rd direction
     grid3Offset                                                                                     !< (local) grid offset in 3rd direction
   real(pReal), dimension(3), public, protected :: &
-    geomSize                                                                                        !< (global) physical size
+    geomSize                                                                                       !< (global) physical size
   real(pReal),               public, protected :: &
-    size3, &                                                                                        !< (local) size in 3rd direction
+    size3, &                                                                                       !< (local) size in 3rd direction
     size3offset                                                                                     !< (local) size offset in 3rd direction
 
   public :: &
@@ -62,8 +62,8 @@ subroutine discretization_grid_init(restart)
 
   integer :: &
     j, &
-    debug_element, debug_ip, &
-    ierr
+    debug_element, debug_ip
+  integer(MPI_INTEGER_KIND) :: err_MPI
   integer(C_INTPTR_T) :: &
     devNull, z, z_offset
   integer, dimension(worldsize) :: &
@@ -88,13 +88,13 @@ subroutine discretization_grid_init(restart)
   end if
 
 
-  call MPI_Bcast(grid,3,MPI_INTEGER,0,MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Bcast(grid,3,MPI_INTEGER,0,MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   if (grid(1) < 2) call IO_error(844, ext_msg='cells(1) must be larger than 1')
-  call MPI_Bcast(geomSize,3,MPI_DOUBLE,0,MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
-  call MPI_Bcast(origin,3,MPI_DOUBLE,0,MPI_COMM_WORLD, ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Bcast(geomSize,3,MPI_DOUBLE,0,MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Bcast(origin,3,MPI_DOUBLE,0,MPI_COMM_WORLD, err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   print'(/,1x,a,3(i12,1x))',    'cells  a b c: ', grid
   print  '(1x,a,3(es12.5,1x))', 'size   x y z: ', geomSize
@@ -118,14 +118,17 @@ subroutine discretization_grid_init(restart)
   myGrid = [grid(1:2),grid3]
   mySize = [geomSize(1:2),size3]
 
-  call MPI_Gather(product(grid(1:2))*grid3Offset,1,MPI_INTEGER,displs,    1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
-  if (ierr /= 0) error stop 'MPI error'
-  call MPI_Gather(product(myGrid),               1,MPI_INTEGER,sendcounts,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Gather(product(grid(1:2))*grid3Offset, 1_MPI_INTEGER_KIND,MPI_INTEGER,displs,&
+                  1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Gather(product(myGrid),               1_MPI_INTEGER_KIND,MPI_INTEGER,sendcounts,&
+                  1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   allocate(materialAt(product(myGrid)))
-  call MPI_Scatterv(materialAt_global,sendcounts,displs,MPI_INTEGER,materialAt,size(materialAt),MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
-  if (ierr /= 0) error stop 'MPI error'
+  call MPI_Scatterv(materialAt_global,sendcounts,displs,MPI_INTEGER,materialAt,size(materialAt),&
+                    MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   call discretization_init(materialAt, &
                            IPcoordinates0(myGrid,mySize,grid3Offset), &
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 6030e9a74..dbb87440b 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -107,7 +107,8 @@ subroutine grid_mechanical_FEM_init
                        1.0_pReal,-1.0_pReal,-1.0_pReal,-1.0_pReal, &
                        1.0_pReal, 1.0_pReal, 1.0_pReal, 1.0_pReal], [4,8])
   real(pReal), dimension(3,3,3,3) :: devNull
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
   PetscScalar, pointer, dimension(:,:,:,:) :: &
     u_current,u_lastInc
   PetscInt, dimension(0:worldsize-1) :: localK
@@ -146,10 +147,10 @@ subroutine grid_mechanical_FEM_init
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS, &
                                 '-mechanical_snes_type newtonls -mechanical_ksp_type fgmres &
                                 &-mechanical_ksp_max_it 25 -mechanical_mg_levels_ksp_type chebyshev', &
-                                ierr)
-  CHKERRQ(ierr)
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
-  CHKERRQ(ierr)
+                                err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! allocate global fields
@@ -159,13 +160,14 @@ subroutine grid_mechanical_FEM_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,ierr)
-  CHKERRQ(ierr)
-  call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',ierr)
-  CHKERRQ(ierr)
+  call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',err_PETSc)
+  CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
-  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   call DMDACreate3d(PETSC_COMM_WORLD, &
          DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, &
          DMDA_STENCIL_BOX, &
@@ -173,45 +175,45 @@ subroutine grid_mechanical_FEM_init
          1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
          3_pPetscInt, 1_pPetscInt, &                                                                ! #dof (u, vector), ghost boundary width (domain overlap)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
-         mechanical_grid,ierr)
-  CHKERRQ(ierr)
-  call SNESSetDM(mechanical_snes,mechanical_grid,ierr)
-  CHKERRQ(ierr)
-  call DMsetFromOptions(mechanical_grid,ierr)
-  CHKERRQ(ierr)
-  call DMsetUp(mechanical_grid,ierr)
-  CHKERRQ(ierr)
-  call DMDASetUniformCoordinates(mechanical_grid,0.0_pReal,geomSize(1),0.0_pReal,geomSize(2),0.0_pReal,geomSize(3),ierr)
-  CHKERRQ(ierr)
-  call DMCreateGlobalVector(mechanical_grid,solution_current,ierr)
-  CHKERRQ(ierr)
-  call DMCreateGlobalVector(mechanical_grid,solution_lastInc,ierr)
-  CHKERRQ(ierr)
-  call DMCreateGlobalVector(mechanical_grid,solution_rate   ,ierr)
-  CHKERRQ(ierr)
-  call DMSNESSetFunctionLocal(mechanical_grid,formResidual,PETSC_NULL_SNES,ierr)
-  CHKERRQ(ierr)
-  call DMSNESSetJacobianLocal(mechanical_grid,formJacobian,PETSC_NULL_SNES,ierr)
-  CHKERRQ(ierr)
-  call SNESSetConvergenceTest(mechanical_snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr)   ! specify custom convergence check function "_converged"
-  CHKERRQ(ierr)
-  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPetscInt), ierr)                      ! ignore linear solve failures
-  CHKERRQ(ierr)
-  call SNESSetFromOptions(mechanical_snes,ierr)                                                     ! pull it all together with additional cli arguments
-  CHKERRQ(ierr)
+         mechanical_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetDM(mechanical_snes,mechanical_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMsetFromOptions(mechanical_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMsetUp(mechanical_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDASetUniformCoordinates(mechanical_grid,0.0_pReal,geomSize(1),0.0_pReal,geomSize(2),0.0_pReal,geomSize(3),err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(mechanical_grid,solution_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(mechanical_grid,solution_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(mechanical_grid,solution_rate   ,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMSNESSetFunctionLocal(mechanical_grid,formResidual,PETSC_NULL_SNES,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMSNESSetJacobianLocal(mechanical_grid,formJacobian,PETSC_NULL_SNES,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetConvergenceTest(mechanical_snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "_converged"
+  CHKERRQ(err_PETSc)
+  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPetscInt), err_PETSc)                 ! ignore linear solve failures
+  CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(mechanical_snes,err_PETSc)                                                ! pull it all together with additional cli arguments
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call VecSet(solution_current,0.0_pReal,ierr);CHKERRQ(ierr)
-  call VecSet(solution_lastInc,0.0_pReal,ierr);CHKERRQ(ierr)
-  call VecSet(solution_rate   ,0.0_pReal,ierr);CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
-  CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
-  CHKERRQ(ierr)
+  call VecSet(solution_current,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
+  call VecSet(solution_lastInc,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
+  call VecSet(solution_rate   ,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
-  call DMDAGetCorners(mechanical_grid,xstart,ystart,zstart,xend,yend,zend,ierr)                           ! local grid extent
-  CHKERRQ(ierr)
+  call DMDAGetCorners(mechanical_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)                ! local grid extent
+  CHKERRQ(err_PETSc)
   xend = xstart+xend-1
   yend = ystart+yend-1
   zend = zstart+zend-1
@@ -239,17 +241,17 @@ subroutine grid_mechanical_FEM_init
     groupHandle = HDF5_openGroup(fileHandle,'solver')
 
     call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
-    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if(ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
-    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if(ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if(ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
-    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if(ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F,groupHandle,'F')
     call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
     call HDF5_read(u_current,groupHandle,'u')
@@ -265,19 +267,19 @@ subroutine grid_mechanical_FEM_init
   call utilities_constitutiveResponse(P_current,P_av,C_volAvg,devNull, &                            ! stress field, stress avg, global average of stiffness and (min+max)/2
                                       F, &                                                          ! target F
                                       0.0_pReal)                                                    ! time increment
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
-  CHKERRQ(ierr)
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
-  CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   restartRead2: if (interface_restartInc > 0) then
     print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
     call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
-    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if(ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+    if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if(ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+    if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
@@ -300,7 +302,7 @@ function grid_mechanical_FEM_solution(incInfoIn) result(solution)
     solution
 !--------------------------------------------------------------------------------------------------
 ! PETSc Data
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   SNESConvergedReason :: reason
 
   incInfo = incInfoIn
@@ -311,13 +313,13 @@ function grid_mechanical_FEM_solution(incInfoIn) result(solution)
 
 !--------------------------------------------------------------------------------------------------
 ! solve BVP
-  call SNESsolve(mechanical_snes,PETSC_NULL_VEC,solution_current,ierr)
-  CHKERRQ(ierr)
+  call SNESsolve(mechanical_snes,PETSC_NULL_VEC,solution_current,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! check convergence
-  call SNESGetConvergedReason(mechanical_snes,reason,ierr)
-  CHKERRQ(ierr)
+  call SNESGetConvergedReason(mechanical_snes,reason,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   solution%converged = reason > 0
   solution%iterationsNeeded = totalIter
@@ -347,22 +349,22 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
     deformation_BC
   type(rotation),           intent(in) :: &
     rotation_BC
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   PetscScalar, pointer, dimension(:,:,:,:) :: &
     u_current,u_lastInc
 
 
-  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
-  CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
-  CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (cutBack) then
     C_volAvg = C_volAvgLastInc
   else
     C_volAvgLastInc    = C_volAvg
 
-    F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess)  ! estimate deformation rate for prescribed stress components
+    F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess) ! estimate deformation rate for prescribed stress components
     F_aim_lastInc = F_aim
 
     !-----------------------------------------------------------------------------------------------
@@ -379,13 +381,14 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
     endif
 
     if (guess) then
-      call VecWAXPY(solution_rate,-1.0_pReal,solution_lastInc,solution_current,ierr)
-      CHKERRQ(ierr)
-      call VecScale(solution_rate,1.0_pReal/Delta_t_old,ierr); CHKERRQ(ierr)
+      call VecWAXPY(solution_rate,-1.0_pReal,solution_lastInc,solution_current,err_PETSc)
+      CHKERRQ(err_PETSc)
+      call VecScale(solution_rate,1.0_pReal/Delta_t_old,err_PETSc)
+      CHKERRQ(err_PETSc)
     else
-      call VecSet(solution_rate,0.0_pReal,ierr); CHKERRQ(ierr)
+      call VecSet(solution_rate,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
     endif
-    call VecCopy(solution_current,solution_lastInc,ierr); CHKERRQ(ierr)
+    call VecCopy(solution_current,solution_lastInc,err_PETSc); CHKERRQ(err_PETSc)
 
     F_lastInc = F
 
@@ -400,12 +403,12 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
   if (stress_BC%myType=='dot_P') P_aim = P_aim &
                                        + merge(.0_pReal,stress_BC%values,stress_BC%mask)*Delta_t
 
-  call VecAXPY(solution_current,Delta_t,solution_rate,ierr); CHKERRQ(ierr)
-
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
-  CHKERRQ(ierr)
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
-  CHKERRQ(ierr)
+  call VecAXPY(solution_current,Delta_t,solution_rate,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! set module wide available data
@@ -431,15 +434,15 @@ end subroutine grid_mechanical_FEM_updateCoords
 !--------------------------------------------------------------------------------------------------
 subroutine grid_mechanical_FEM_restartWrite
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   integer(HID_T) :: fileHandle, groupHandle
   PetscScalar, dimension(:,:,:,:), pointer :: u_current,u_lastInc
 
 
-  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
-  CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
-  CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
@@ -465,10 +468,10 @@ subroutine grid_mechanical_FEM_restartWrite
     call HDF5_closeFile(fileHandle)
   endif
 
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
-  CHKERRQ(ierr)
-  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)
-  CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_FEM_restartWrite
 
@@ -476,7 +479,7 @@ end subroutine grid_mechanical_FEM_restartWrite
 !--------------------------------------------------------------------------------------------------
 !> @brief convergence check
 !--------------------------------------------------------------------------------------------------
-subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,ierr)
+subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,err_PETSc)
 
   SNES :: snes_local
   PetscInt,  intent(in) :: PETScIter
@@ -486,7 +489,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,i
     fnorm
   SNESConvergedReason :: reason
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   real(pReal) :: &
     err_div, &
     divTol, &
@@ -520,7 +523,7 @@ end subroutine converged
 !> @brief forms the residual vector
 !--------------------------------------------------------------------------------------------------
 subroutine formResidual(da_local,x_local, &
-                        f_local,dummy,ierr)
+                        f_local,dummy,err_PETSc)
 
   DM                   :: da_local
   Vec                  :: x_local, f_local
@@ -531,13 +534,14 @@ subroutine formResidual(da_local,x_local, &
     PETScIter, &
     nfuncs
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
   real(pReal), dimension(3,3,3,3) :: devNull
 
-  call SNESGetNumberFunctionEvals(mechanical_snes,nfuncs,ierr)
-  CHKERRQ(ierr)
-  call SNESGetIterationNumber(mechanical_snes,PETScIter,ierr)
-  CHKERRQ(ierr)
+  call SNESGetNumberFunctionEvals(mechanical_snes,nfuncs,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetIterationNumber(mechanical_snes,PETScIter,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1                                              ! new increment
 
@@ -555,7 +559,7 @@ subroutine formResidual(da_local,x_local, &
 
 !--------------------------------------------------------------------------------------------------
 ! get deformation gradient
-  call DMDAVecGetArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
   do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
     ctr = 0
     do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
@@ -565,14 +569,15 @@ subroutine formResidual(da_local,x_local, &
     ii = i-xstart+1; jj = j-ystart+1; kk = k-zstart+1
     F(1:3,1:3,ii,jj,kk) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
   enddo; enddo; enddo
-  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! evaluate constitutive response
   call utilities_constitutiveResponse(P_current,&
                                       P_av,C_volAvg,devNull, &
                                       F,params%Delta_t,params%rotation_BC)
-  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+  if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 !--------------------------------------------------------------------------------------------------
 ! stress BC handling
@@ -581,9 +586,9 @@ subroutine formResidual(da_local,x_local, &
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  call VecSet(f_local,0.0_pReal,ierr);CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
+  call VecSet(f_local,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
   ele = 0
   do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
     ctr = 0
@@ -603,12 +608,12 @@ subroutine formResidual(da_local,x_local, &
       f_scal(0:2,i+ii,j+jj,k+kk) = f_scal(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
     enddo; enddo; enddo
   enddo; enddo; enddo
-  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,ierr);CHKERRQ(ierr)
-  call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
-  call DMDAVecGetArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
   if (zstart == 0) then
     f_scal(0:2,xstart,ystart,zstart) = 0.0
     f_scal(0:2,xend+1,ystart,zstart) = 0.0
@@ -621,7 +626,7 @@ subroutine formResidual(da_local,x_local, &
     f_scal(0:2,xstart,yend+1,zend+1) = 0.0
     f_scal(0:2,xend+1,yend+1,zend+1) = 0.0
   endif
-  call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,ierr);CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
 
 end subroutine formResidual
 
@@ -629,7 +634,7 @@ end subroutine formResidual
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the FEM stiffness matrix
 !--------------------------------------------------------------------------------------------------
-subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
+subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
 
   DM                                   :: da_local
   Vec                                  :: x_local, coordinates
@@ -643,15 +648,17 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
   PetscScalar                          :: diag
   PetscObject                          :: dummy
   MatNullSpace                         :: matnull
-  PetscErrorCode                       :: ierr
+  PetscErrorCode                       :: err_PETSc
 
   BMatFull = 0.0
   BMatFull(1:3,1 :8 ) = BMat
   BMatFull(4:6,9 :16) = BMat
   BMatFull(7:9,17:24) = BMat
-  call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,ierr); CHKERRQ(ierr)
-  call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,ierr); CHKERRQ(ierr)
-  call MatZeroEntries(Jac,ierr); CHKERRQ(ierr)
+  call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatZeroEntries(Jac,err_PETSc); CHKERRQ(err_PETSc)
   ele = 0
   do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
     ctr = 0
@@ -686,34 +693,42 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,ierr)
             matmul(transpose(BMatFull), &
                    matmul(reshape(reshape(homogenization_dPdF(1:3,1:3,1:3,1:3,ele), &
                                           shape=[3,3,3,3], order=[2,1,4,3]),shape=[9,9]),BMatFull))*detJ
-    call MatSetValuesStencil(Jac,24_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,ierr)
-    CHKERRQ(ierr)
+    call MatSetValuesStencil(Jac,24_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo; enddo; enddo
-  call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
+  call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
   diag = (C_volAvg(1,1,1,1)/delta(1)**2 + &
           C_volAvg(2,2,2,2)/delta(2)**2 + &
           C_volAvg(3,3,3,3)/delta(3)**2)*detJ
-  call MatZeroRowsColumns(Jac,size(rows,kind=pPetscInt),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,ierr)
-  CHKERRQ(ierr)
-  call DMGetGlobalVector(da_local,coordinates,ierr); CHKERRQ(ierr)
-  call DMDAVecGetArrayF90(da_local,coordinates,x_scal,ierr); CHKERRQ(ierr)
+  call MatZeroRowsColumns(Jac,size(rows,kind=pPetscInt),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetGlobalVector(da_local,coordinates,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,coordinates,x_scal,err_PETSc)
+  CHKERRQ(err_PETSc)
   ele = 0
   do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
     ele = ele + 1
     x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ele)
   enddo; enddo; enddo
-  call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,ierr); CHKERRQ(ierr)                      ! initialize to undeformed coordinates (ToDo: use ip coordinates)
-  call MatNullSpaceCreateRigidBody(coordinates,matnull,ierr); CHKERRQ(ierr)                         ! get rigid body deformation modes
-  call DMRestoreGlobalVector(da_local,coordinates,ierr); CHKERRQ(ierr)
-  call MatSetNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
-  call MatSetNearNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
-  call MatNullSpaceDestroy(matnull,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,err_PETSc)
+  CHKERRQ(err_PETSc)                                                                          ! initialize to undeformed coordinates (ToDo: use ip coordinates)
+  call MatNullSpaceCreateRigidBody(coordinates,matnull,err_PETSc)
+  CHKERRQ(err_PETSc)                                                                          ! get rigid body deformation modes
+  call DMRestoreGlobalVector(da_local,coordinates,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatSetNullSpace(Jac,matnull,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatSetNearNullSpace(Jac,matnull,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatNullSpaceDestroy(matnull,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine formJacobian
 
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 0a267ecca..2d5376781 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -97,7 +97,8 @@ contains
 subroutine grid_mechanical_spectral_basic_init
 
   real(pReal), dimension(3,3,grid(1),grid(2),grid3) :: P
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
   PetscScalar, pointer, dimension(:,:,:,:) :: &
     F                                                                                               ! pointer to solution data
   PetscInt, dimension(0:worldsize-1) :: localK
@@ -145,10 +146,10 @@ subroutine grid_mechanical_spectral_basic_init
 
 !--------------------------------------------------------------------------------------------------
 ! set default and user defined options for PETSc
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',ierr)
-  CHKERRQ(ierr)
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
-  CHKERRQ(ierr)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! allocate global fields
@@ -157,11 +158,12 @@ subroutine grid_mechanical_spectral_basic_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
-  call SNESSetOptionsPrefix(snes,'mechanical_',ierr);CHKERRQ(ierr)
+  call SNESCreate(PETSC_COMM_WORLD,snes,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(snes,'mechanical_',err_PETSc);CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
-  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   call DMDACreate3d(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
@@ -169,21 +171,21 @@ subroutine grid_mechanical_spectral_basic_init
          1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
          9_pPetscInt, 0_pPetscInt, &                                                                ! #dof (F, tensor), ghost boundary width (domain overlap)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
-         da,ierr)                                                                                   ! handle, error
-  CHKERRQ(ierr)
-  call SNESSetDM(snes,da,ierr); CHKERRQ(ierr)                                                       ! connect snes to da
-  call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
-  call DMsetUp(da,ierr); CHKERRQ(ierr)
-  call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)                                    ! global solution vector (grid x 9, i.e. every def grad tensor)
-  call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr)                 ! residual vector of same shape as solution vector
-  CHKERRQ(ierr)
-  call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr)              ! specify custom convergence check function "converged"
-  CHKERRQ(ierr)
-  call SNESsetFromOptions(snes,ierr); CHKERRQ(ierr)                                                 ! pull it all together with additional CLI arguments
+         da,err_PETSc)                                                                              ! handle, error
+  CHKERRQ(err_PETSc)
+  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
+  call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
+  call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
+  call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 9, i.e. every def grad tensor)
+  call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)            ! residual vector of same shape as solution vector
+  CHKERRQ(err_PETSc)
+  call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)         ! specify custom convergence check function "converged"
+  CHKERRQ(err_PETSc)
+  call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc)                                       ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)                                   ! places pointer on PETSc data
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)                          ! places pointer on PETSc data
 
   restartRead: if (interface_restartInc > 0) then
     print'(/,1x,a,i0,a)', 'reading restart data of increment ', interface_restartInc, ' from file'
@@ -192,17 +194,17 @@ subroutine grid_mechanical_spectral_basic_init
     groupHandle = HDF5_openGroup(fileHandle,'solver')
 
     call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
-    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
-    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
-    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F,groupHandle,'F')
     call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
 
@@ -216,24 +218,27 @@ subroutine grid_mechanical_spectral_basic_init
   call utilities_constitutiveResponse(P,P_av,C_volAvg,C_minMaxAvg, &                                ! stress field, stress avg, global average of stiffness and (min+max)/2
                                       reshape(F,shape(F_lastInc)), &                                ! target F
                                       0.0_pReal)                                                    ! time increment
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)                                ! deassociate pointer
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)                      ! deassociate pointer
 
   restartRead2: if (interface_restartInc > 0) then
     print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
     call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
-    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
 
     call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
-                       MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,ierr)
-    call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,ierr)
-    call MPI_File_close(fileUnit,ierr)
+                       MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+    call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+    call MPI_File_close(fileUnit,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   end if restartRead2
 
   call utilities_updateGamma(C_minMaxAvg)
@@ -255,7 +260,7 @@ function grid_mechanical_spectral_basic_solution(incInfoIn) result(solution)
     solution
 !--------------------------------------------------------------------------------------------------
 ! PETSc Data
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   SNESConvergedReason :: reason
 
   incInfo = incInfoIn
@@ -267,11 +272,11 @@ function grid_mechanical_spectral_basic_solution(incInfoIn) result(solution)
 
 !--------------------------------------------------------------------------------------------------
 ! solve BVP
-  call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
+  call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! check convergence
-  call SNESGetConvergedReason(snes,reason,ierr); CHKERRQ(ierr)
+  call SNESGetConvergedReason(snes,reason,err_PETSc); CHKERRQ(err_PETSc)
 
   solution%converged = reason > 0
   solution%iterationsNeeded = totalIter
@@ -301,11 +306,11 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
     deformation_BC
   type(rotation),           intent(in) :: &
     rotation_BC
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   PetscScalar, pointer, dimension(:,:,:,:) :: F
 
 
-  call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
 
   if (cutBack) then
     C_volAvg    = C_volAvgLastInc
@@ -314,7 +319,7 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
     C_volAvgLastInc    = C_volAvg
     C_minMaxAvgLastInc = C_minMaxAvg
 
-    F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess)  ! estimate deformation rate for prescribed stress components
+    F_aimDot = merge(merge(.0_pReal,(F_aim-F_aim_lastInc)/Delta_t_old,stress_BC%mask),.0_pReal,guess) ! estimate deformation rate for prescribed stress components
     F_aim_lastInc = F_aim
 
     !-----------------------------------------------------------------------------------------------
@@ -348,7 +353,7 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
 
   F = reshape(utilities_forwardField(Delta_t,F_lastInc,Fdot, &                                      ! estimate of F at end of time+Delta_t that matches rotated F_aim on average
               rotation_BC%rotate(F_aim,active=.true.)),[9,grid(1),grid(2),grid3])
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! set module wide available data
@@ -364,12 +369,12 @@ end subroutine grid_mechanical_spectral_basic_forward
 !--------------------------------------------------------------------------------------------------
 subroutine grid_mechanical_spectral_basic_updateCoords
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   PetscScalar, dimension(:,:,:,:), pointer :: F
 
-  call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
   call utilities_updateCoords(F)
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_basic_updateCoords
 
@@ -379,11 +384,11 @@ end subroutine grid_mechanical_spectral_basic_updateCoords
 !--------------------------------------------------------------------------------------------------
 subroutine grid_mechanical_spectral_basic_restartWrite
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   integer(HID_T) :: fileHandle, groupHandle
   PetscScalar, dimension(:,:,:,:), pointer :: F
 
-  call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
 
   print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
@@ -410,7 +415,7 @@ subroutine grid_mechanical_spectral_basic_restartWrite
 
   if (num%update_gamma) call utilities_saveReferenceStiffness
 
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_basic_restartWrite
 
@@ -418,7 +423,7 @@ end subroutine grid_mechanical_spectral_basic_restartWrite
 !--------------------------------------------------------------------------------------------------
 !> @brief convergence check
 !--------------------------------------------------------------------------------------------------
-subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,ierr)
+subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,err_PETSc)
 
   SNES :: snes_local
   PetscInt,  intent(in) :: PETScIter
@@ -428,7 +433,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
     devNull3
   SNESConvergedReason :: reason
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   real(pReal) :: &
     divTol, &
     BCTol
@@ -460,7 +465,7 @@ end subroutine converged
 !> @brief forms the residual vector
 !--------------------------------------------------------------------------------------------------
 subroutine formResidual(in, F, &
-                        residuum, dummy, ierr)
+                        residuum, dummy, err_PETSc)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: in                                              !< DMDA info (needs to be named "in" for macros like XRANGE to work)
   PetscScalar, dimension(3,3,XG_RANGE,YG_RANGE,ZG_RANGE), &
@@ -473,10 +478,11 @@ subroutine formResidual(in, F, &
     PETScIter, &
     nfuncs
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
-  call SNESGetNumberFunctionEvals(snes,nfuncs,ierr); CHKERRQ(ierr)
-  call SNESGetIterationNumber(snes,PETScIter,ierr);  CHKERRQ(ierr)
+  call SNESGetNumberFunctionEvals(snes,nfuncs,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESGetIterationNumber(snes,PETScIter,err_PETSc);  CHKERRQ(err_PETSc)
 
   if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1                                              ! new increment
 
@@ -497,7 +503,8 @@ subroutine formResidual(in, F, &
   call utilities_constitutiveResponse(residuum, &                                                   ! "residuum" gets field of first PK stress (to save memory)
                                       P_av,C_volAvg,C_minMaxAvg, &
                                       F,params%Delta_t,params%rotation_BC)
-  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 !--------------------------------------------------------------------------------------------------
 ! stress BC handling
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index 5bfce5e3f..a6ce8d173 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -108,7 +108,8 @@ contains
 subroutine grid_mechanical_spectral_polarisation_init
 
   real(pReal), dimension(3,3,grid(1),grid(2),grid3) :: P
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
   PetscScalar, pointer, dimension(:,:,:,:) :: &
     FandF_tau, &                                                                                    ! overall pointer to solution data
     F, &                                                                                            ! specific (sub)pointer
@@ -163,10 +164,10 @@ subroutine grid_mechanical_spectral_polarisation_init
 
 !--------------------------------------------------------------------------------------------------
 ! set default and user defined options for PETSc
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',ierr)
-  CHKERRQ(ierr)
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
-  CHKERRQ(ierr)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type ngmres',err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! allocate global fields
@@ -177,11 +178,12 @@ subroutine grid_mechanical_spectral_polarisation_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
-  call SNESSetOptionsPrefix(snes,'mechanical_',ierr);CHKERRQ(ierr)
+  call SNESCreate(PETSC_COMM_WORLD,snes,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(snes,'mechanical_',err_PETSc);CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
-  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   call DMDACreate3d(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
@@ -189,21 +191,21 @@ subroutine grid_mechanical_spectral_polarisation_init
          1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
          18_pPetscInt, 0_pPetscInt, &                                                               ! #dof (2xtensor), ghost boundary width (domain overlap)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
-         da,ierr)                                                                                   ! handle, error
-  CHKERRQ(ierr)
-  call SNESSetDM(snes,da,ierr); CHKERRQ(ierr)                                                       ! connect snes to da
-  call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
-  call DMsetUp(da,ierr); CHKERRQ(ierr)
-  call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)                                    ! global solution vector (grid x 18, i.e. every def grad tensor)
-  call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr)                 ! residual vector of same shape as solution vector
-  CHKERRQ(ierr)
-  call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,ierr)              ! specify custom convergence check function "converged"
-  CHKERRQ(ierr)
-  call SNESsetFromOptions(snes,ierr); CHKERRQ(ierr)                                                 ! pull it all together with additional CLI arguments
+         da,err_PETSc)                                                                              ! handle, error
+  CHKERRQ(err_PETSc)
+  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
+  call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
+  call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
+  call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 18, i.e. every def grad tensor)
+  call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)            ! residual vector of same shape as solution vector
+  CHKERRQ(err_PETSc)
+  call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)         ! specify custom convergence check function "converged"
+  CHKERRQ(err_PETSc)
+  call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc)                                       ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)                             ! places pointer on PETSc data
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)                  ! places pointer on PETSc data
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
@@ -214,17 +216,17 @@ subroutine grid_mechanical_spectral_polarisation_init
     groupHandle = HDF5_openGroup(fileHandle,'solver')
 
     call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
-    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
-    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
-    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F,groupHandle,'F')
     call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
     call HDF5_read(F_tau,groupHandle,'F_tau')
@@ -242,24 +244,28 @@ subroutine grid_mechanical_spectral_polarisation_init
   call utilities_constitutiveResponse(P,P_av,C_volAvg,C_minMaxAvg, &                                ! stress field, stress avg, global average of stiffness and (min+max)/2
                                       reshape(F,shape(F_lastInc)), &                                ! target F
                                       0.0_pReal)                                                    ! time increment
-  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)                        ! deassociate pointer
+  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)                                  ! deassociate pointer
+  CHKERRQ(err_PETSc)
 
   restartRead2: if (interface_restartInc > 0) then
     print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
     call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
-    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,ierr)
-    if (ierr /=0) error stop 'MPI error'
+    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
     call HDF5_closeFile(fileHandle)
 
     call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
-                       MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,ierr)
-    call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,ierr)
-    call MPI_File_close(fileUnit,ierr)
+                       MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+    call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+    call MPI_File_close(fileUnit,err_MPI)
+    if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   end if restartRead2
 
   call utilities_updateGamma(C_minMaxAvg)
@@ -283,7 +289,7 @@ function grid_mechanical_spectral_polarisation_solution(incInfoIn) result(soluti
     solution
 !--------------------------------------------------------------------------------------------------
 ! PETSc Data
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   SNESConvergedReason :: reason
 
   incInfo = incInfoIn
@@ -299,11 +305,11 @@ function grid_mechanical_spectral_polarisation_solution(incInfoIn) result(soluti
 
 !--------------------------------------------------------------------------------------------------
 ! solve BVP
-  call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
+  call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! check convergence
-  call SNESGetConvergedReason(snes,reason,ierr); CHKERRQ(ierr)
+  call SNESGetConvergedReason(snes,reason,err_PETSc); CHKERRQ(err_PETSc)
 
   solution%converged = reason > 0
   solution%iterationsNeeded = totalIter
@@ -333,13 +339,13 @@ subroutine grid_mechanical_spectral_polarisation_forward(cutBack,guess,Delta_t,D
     deformation_BC
   type(rotation),           intent(in) :: &
     rotation_BC
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   PetscScalar, pointer, dimension(:,:,:,:) :: FandF_tau, F, F_tau
   integer :: i, j, k
   real(pReal), dimension(3,3) :: F_lambda33
 
 
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
@@ -402,7 +408,8 @@ subroutine grid_mechanical_spectral_polarisation_forward(cutBack,guess,Delta_t,D
     end do; end do; end do
   end if
 
-  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! set module wide available data
@@ -418,12 +425,14 @@ end subroutine grid_mechanical_spectral_polarisation_forward
 !--------------------------------------------------------------------------------------------------
 subroutine grid_mechanical_spectral_polarisation_updateCoords
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau
 
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  CHKERRQ(err_PETSc)
   call utilities_updateCoords(FandF_tau(0:8,:,:,:))
-  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_polarisation_updateCoords
 
@@ -433,11 +442,11 @@ end subroutine grid_mechanical_spectral_polarisation_updateCoords
 !--------------------------------------------------------------------------------------------------
 subroutine grid_mechanical_spectral_polarisation_restartWrite
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   integer(HID_T) :: fileHandle, groupHandle
   PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
 
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
@@ -467,7 +476,8 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
 
   if (num%update_gamma) call utilities_saveReferenceStiffness
 
-  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_polarisation_restartWrite
 
@@ -475,7 +485,7 @@ end subroutine grid_mechanical_spectral_polarisation_restartWrite
 !--------------------------------------------------------------------------------------------------
 !> @brief convergence check
 !--------------------------------------------------------------------------------------------------
-subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,ierr)
+subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dummy,err_PETSc)
 
   SNES :: snes_local
   PetscInt,  intent(in) :: PETScIter
@@ -485,7 +495,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
     devNull3
   SNESConvergedReason :: reason
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   real(pReal) :: &
     curlTol, &
     divTol, &
@@ -521,7 +531,7 @@ end subroutine converged
 !> @brief forms the residual vector
 !--------------------------------------------------------------------------------------------------
 subroutine formResidual(in, FandF_tau, &
-                        residuum, dummy,ierr)
+                        residuum, dummy,err_PETSc)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: in                                              !< DMDA info (needs to be named "in" for macros like XRANGE to work)
   PetscScalar, dimension(3,3,2,XG_RANGE,YG_RANGE,ZG_RANGE), &
@@ -537,8 +547,9 @@ subroutine formResidual(in, FandF_tau, &
     PETScIter, &
     nfuncs
   PetscObject :: dummy
-  PetscErrorCode :: ierr
- integer :: &
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  integer :: &
     i, j, k, e
 
 !---------------------------------------------------------------------------------------------------
@@ -553,10 +564,11 @@ subroutine formResidual(in, FandF_tau, &
                              X_RANGE, Y_RANGE, Z_RANGE)
 
   F_av = sum(sum(sum(F,dim=5),dim=4),dim=3) * wgt
-  call MPI_Allreduce(MPI_IN_PLACE,F_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,F_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
-  call SNESGetNumberFunctionEvals(snes,nfuncs,ierr); CHKERRQ(ierr)
-  call SNESGetIterationNumber(snes,PETScIter,ierr);  CHKERRQ(ierr)
+  call SNESGetNumberFunctionEvals(snes,nfuncs,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESGetIterationNumber(snes,PETScIter,err_PETSc);  CHKERRQ(err_PETSc)
 
   if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1                                              ! new increment
 
@@ -597,7 +609,7 @@ subroutine formResidual(in, FandF_tau, &
   call utilities_constitutiveResponse(residual_F, &                                                 ! "residuum" gets field of first PK stress (to save memory)
                                       P_av,C_volAvg,C_minMaxAvg, &
                                       F - residual_F_tau/num%beta,params%Delta_t,params%rotation_BC)
-  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
 
 !--------------------------------------------------------------------------------------------------
 ! stress BC handling
diff --git a/src/mesh/DAMASK_mesh.f90 b/src/mesh/DAMASK_mesh.f90
index 14872bf15..aa156ec2d 100644
--- a/src/mesh/DAMASK_mesh.f90
+++ b/src/mesh/DAMASK_mesh.f90
@@ -78,7 +78,7 @@ program DAMASK_mesh
   type(tLoadCase), allocatable, dimension(:) :: loadCases                                           !< array of all load cases
   type(tSolutionState), allocatable, dimension(:) :: solres
   PetscInt :: faceSet, currentFaceSet, dimPlex
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   integer(kind(COMPONENT_UNDEFINED_ID)) :: ID
   external :: &
     quit
@@ -98,8 +98,8 @@ program DAMASK_mesh
   if (maxCutBack < 0) call IO_error(301,ext_msg='maxCutBack')
 
 ! reading basic information from load case file and allocate data structure containing load cases
-  call DMGetDimension(geomMesh,dimPlex,ierr)                                                        !< dimension of mesh (2D or 3D)
-  CHKERRA(ierr)
+  call DMGetDimension(geomMesh,dimPlex,err_PETSc)                                                   !< dimension of mesh (2D or 3D)
+  CHKERRA(err_PETSc)
   allocate(solres(1))
 
 !--------------------------------------------------------------------------------------------------
diff --git a/src/mesh/FEM_utilities.f90 b/src/mesh/FEM_utilities.f90
index 86fb52b36..ce97e7776 100644
--- a/src/mesh/FEM_utilities.f90
+++ b/src/mesh/FEM_utilities.f90
@@ -92,7 +92,7 @@ subroutine FEM_utilities_init
     p_i                                                                                             !< integration order (quadrature rule)
   character(len=*), parameter :: &
     PETSCDEBUG = ' -snes_view -snes_monitor '
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   logical :: debugPETSc                                                                             !< use some in debug defined options for more verbose PETSc solution
 
 
@@ -116,20 +116,20 @@ subroutine FEM_utilities_init
                  trim(PETScDebug), &
                  'add more using the "PETSc_options" keyword in numerics.yaml'
   flush(IO_STDOUT)
-  call PetscOptionsClear(PETSC_NULL_OPTIONS,ierr)
-  CHKERRQ(ierr)
-  if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),ierr)
-  CHKERRQ(ierr)
+  call PetscOptionsClear(PETSC_NULL_OPTIONS,err_PETSc)
+  CHKERRQ(err_PETSc)
+  if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),err_PETSc)
+  CHKERRQ(err_PETSc)
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type newtonls &
                                &-mechanical_snes_linesearch_type cp -mechanical_snes_ksp_ew &
                                &-mechanical_snes_ksp_ew_rtol0 0.01 -mechanical_snes_ksp_ew_rtolmax 0.01 &
-                               &-mechanical_ksp_type fgmres -mechanical_ksp_max_it 25', ierr)
-  CHKERRQ(ierr)
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_mesh%get_asString('PETSc_options',defaultVal=''),ierr)
-  CHKERRQ(ierr)
+                               &-mechanical_ksp_type fgmres -mechanical_ksp_max_it 25', err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_mesh%get_asString('PETSc_options',defaultVal=''),err_PETSc)
+  CHKERRQ(err_PETSc)
   write(petsc_optionsOrder,'(a,i0)') '-mechFE_petscspace_degree ', p_s
-  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(petsc_optionsOrder),ierr)
-  CHKERRQ(ierr)
+  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(petsc_optionsOrder),err_PETSc)
+  CHKERRQ(err_PETSc)
 
   wgt = 1.0/real(mesh_maxNips*mesh_NcpElemsGlobal,pReal)
 
@@ -144,10 +144,9 @@ subroutine utilities_constitutiveResponse(timeinc,P_av,forwardData)
 
   real(pReal), intent(in)                 :: timeinc                                                !< loading time
   logical,     intent(in)                 :: forwardData                                            !< age results
-
   real(pReal),intent(out), dimension(3,3) :: P_av                                                   !< average PK stress
 
-  PetscErrorCode :: ierr
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
   print'(/,1x,a)', '... evaluating constitutive response ......................................'
 
@@ -157,7 +156,9 @@ subroutine utilities_constitutiveResponse(timeinc,P_av,forwardData)
   cutBack = .false.
 
   P_av = sum(homogenization_P,dim=3) * wgt
-  call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+
 
 end subroutine utilities_constitutiveResponse
 
@@ -174,26 +175,29 @@ subroutine utilities_projectBCValues(localVec,section,field,comp,bcPointsIS,BCVa
   PetscInt,    pointer :: bcPoints(:)
   PetscScalar, pointer :: localArray(:)
   PetscScalar          :: BCValue,BCDotValue,timeinc
-  PetscErrorCode       :: ierr
+  PetscErrorCode       :: err_PETSc
 
 
-  call PetscSectionGetFieldComponents(section,field,numComp,ierr); CHKERRQ(ierr)
-  call ISGetSize(bcPointsIS,nBcPoints,ierr); CHKERRQ(ierr)
-  if (nBcPoints > 0) call ISGetIndicesF90(bcPointsIS,bcPoints,ierr)
-  call VecGetArrayF90(localVec,localArray,ierr); CHKERRQ(ierr)
+  call PetscSectionGetFieldComponents(section,field,numComp,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call ISGetSize(bcPointsIS,nBcPoints,err_PETSc)
+  CHKERRQ(err_PETSc)
+  if (nBcPoints > 0) call ISGetIndicesF90(bcPointsIS,bcPoints,err_PETSc)
+  call VecGetArrayF90(localVec,localArray,err_PETSc); CHKERRQ(err_PETSc)
   do point = 1, nBcPoints
-    call PetscSectionGetFieldDof(section,bcPoints(point),field,numDof,ierr)
-    CHKERRQ(ierr)
-    call PetscSectionGetFieldOffset(section,bcPoints(point),field,offset,ierr)
-    CHKERRQ(ierr)
+    call PetscSectionGetFieldDof(section,bcPoints(point),field,numDof,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call PetscSectionGetFieldOffset(section,bcPoints(point),field,offset,err_PETSc)
+    CHKERRQ(err_PETSc)
     do dof = offset+comp+1, offset+numDof, numComp
       localArray(dof) = localArray(dof) + BCValue + BCDotValue*timeinc
     end do
   end do
-  call VecRestoreArrayF90(localVec,localArray,ierr); CHKERRQ(ierr)
-  call VecAssemblyBegin(localVec, ierr); CHKERRQ(ierr)
-  call VecAssemblyEnd  (localVec, ierr); CHKERRQ(ierr)
-  if (nBcPoints > 0) call ISRestoreIndicesF90(bcPointsIS,bcPoints,ierr)
+  call VecRestoreArrayF90(localVec,localArray,err_PETSc); CHKERRQ(err_PETSc)
+  call VecAssemblyBegin(localVec, err_PETSc); CHKERRQ(err_PETSc)
+  call VecAssemblyEnd  (localVec, err_PETSc); CHKERRQ(err_PETSc)
+  if (nBcPoints > 0) call ISRestoreIndicesF90(bcPointsIS,bcPoints,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine utilities_projectBCValues
 
diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90
index 2446bc0de..172101976 100644
--- a/src/mesh/discretization_mesh.f90
+++ b/src/mesh/discretization_mesh.f90
@@ -80,7 +80,8 @@ subroutine discretization_mesh_init(restart)
   PetscInt :: nFaceSets
   PetscInt, pointer, dimension(:) :: pFaceSets
   IS :: faceSetIS
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
+  integer(MPI_INTEGER_KIND) :: err_MPI
   integer, dimension(:), allocatable :: &
     materialAt
   class(tNode), pointer :: &
@@ -100,56 +101,60 @@ subroutine discretization_mesh_init(restart)
   debug_element = config_debug%get_asInt('element',defaultVal=1)
   debug_ip      = config_debug%get_asInt('integrationpoint',defaultVal=1)
 
-  call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,ierr)
-  CHKERRQ(ierr)
-  call DMGetDimension(globalMesh,dimPlex,ierr)
-  CHKERRQ(ierr)
-  call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr)
-  CHKERRQ(ierr)
+  call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetDimension(globalMesh,dimPlex,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,err_PETSc)
+  CHKERRQ(err_PETSc)
   print'()'
-  call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,ierr)
-  CHKERRQ(ierr)
+  call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   ! get number of IDs in face sets (for boundary conditions?)
-  call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr)
-  CHKERRQ(ierr)
-  call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
-  call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
-  call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
+  call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
+  call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   if (worldrank == 0) then
-    call DMClone(globalMesh,geomMesh,ierr)
+    call DMClone(globalMesh,geomMesh,err_PETSc)
   else
-    call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr)
+    call DMPlexDistribute(globalMesh,0,sf,geomMesh,err_PETSc)
   endif
-  CHKERRQ(ierr)
+  CHKERRQ(err_PETSc)
 
   allocate(mesh_boundaries(mesh_Nboundaries), source = 0)
-  call DMGetLabelSize(globalMesh,'Face Sets',nFaceSets,ierr)
-  CHKERRQ(ierr)
-  call DMGetLabelIdIS(globalMesh,'Face Sets',faceSetIS,ierr)
-  CHKERRQ(ierr)
+  call DMGetLabelSize(globalMesh,'Face Sets',nFaceSets,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetLabelIdIS(globalMesh,'Face Sets',faceSetIS,err_PETSc)
+  CHKERRQ(err_PETSc)
   if (nFaceSets > 0) then
-    call ISGetIndicesF90(faceSetIS,pFaceSets,ierr)
-    CHKERRQ(ierr)
+    call ISGetIndicesF90(faceSetIS,pFaceSets,err_PETSc)
+    CHKERRQ(err_PETSc)
     mesh_boundaries(1:nFaceSets) = pFaceSets
-    CHKERRQ(ierr)
-    call ISRestoreIndicesF90(faceSetIS,pFaceSets,ierr)
+    CHKERRQ(err_PETSc)
+    call ISRestoreIndicesF90(faceSetIS,pFaceSets,err_PETSc)
   endif
-  call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
+  call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
-  call DMDestroy(globalMesh,ierr); CHKERRQ(ierr)
+  call DMDestroy(globalMesh,err_PETSc); CHKERRQ(err_PETSc)
 
-  call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,ierr)
-  CHKERRQ(ierr)
-  call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
-  CHKERRQ(ierr)
+  call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 ! Get initial nodal coordinates
-  call DMGetCoordinates(geomMesh,coords_node0,ierr)
-  CHKERRQ(ierr)
-  call VecGetArrayF90(coords_node0, mesh_node0_temp,ierr)
-  CHKERRQ(ierr)
+  call DMGetCoordinates(geomMesh,coords_node0,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecGetArrayF90(coords_node0, mesh_node0_temp,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   mesh_maxNips = FEM_nQuadrature(dimPlex,p_i)
 
@@ -158,8 +163,8 @@ subroutine discretization_mesh_init(restart)
 
   allocate(materialAt(mesh_NcpElems))
   do j = 1, mesh_NcpElems
-    call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),ierr)
-    CHKERRQ(ierr)
+    call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo
   materialAt = materialAt + 1
 
@@ -188,16 +193,17 @@ subroutine mesh_FEM_build_ipVolumes(dimPlex)
   PetscReal          :: vol
   PetscReal, pointer,dimension(:) :: pCent, pNorm
   PetscInt           :: cellStart, cellEnd, cell
-  PetscErrorCode     :: ierr
+  PetscErrorCode     :: err_PETSc
 
   allocate(mesh_ipVolume(mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
 
-  call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
+  call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
   allocate(pCent(dimPlex))
   allocate(pNorm(dimPlex))
   do cell = cellStart, cellEnd-1
-    call  DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
-    CHKERRQ(ierr)
+    call  DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,err_PETSc)
+    CHKERRQ(err_PETSc)
     mesh_ipVolume(:,cell+1) = vol/real(mesh_maxNips,pReal)
   enddo
 
@@ -215,7 +221,7 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
   PetscReal,        pointer,dimension(:) :: pV0, pCellJ, pInvcellJ
   PetscReal                 :: detJ
   PetscInt                  :: cellStart, cellEnd, cell, qPt, dirI, dirJ, qOffset
-  PetscErrorCode            :: ierr
+  PetscErrorCode            :: err_PETSc
 
 
   allocate(mesh_ipCoordinates(3,mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
@@ -223,10 +229,11 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
   allocate(pV0(dimPlex))
   allocatE(pCellJ(dimPlex**2))
   allocatE(pinvCellJ(dimPlex**2))
-  call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
+  call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
   do cell = cellStart, cellEnd-1                                                                     !< loop over all elements
-    call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
-    CHKERRQ(ierr)
+    call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
+    CHKERRQ(err_PETSc)
     qOffset = 0
     do qPt = 1, mesh_maxNips
       do dirI = 1, dimPlex
diff --git a/src/mesh/mesh_mech_FEM.f90 b/src/mesh/mesh_mech_FEM.f90
index c1c0d8e3d..bb7bfaece 100644
--- a/src/mesh/mesh_mech_FEM.f90
+++ b/src/mesh/mesh_mech_FEM.f90
@@ -108,7 +108,7 @@ subroutine FEM_mechanical_init(fieldBC)
   PetscScalar,       allocatable, target ::  x_scal(:)
 
   character(len=*), parameter            :: prefix = 'mechFE_'
-  PetscErrorCode                         :: ierr
+  PetscErrorCode                         :: err_PETSc
   real(pReal), dimension(3,3) :: devNull
   class(tNode), pointer :: &
     num_mesh
@@ -130,8 +130,8 @@ subroutine FEM_mechanical_init(fieldBC)
 
 !--------------------------------------------------------------------------------------------------
 ! Setup FEM mech mesh
-  call DMClone(geomMesh,mechanical_mesh,ierr); CHKERRQ(ierr)
-  call DMGetDimension(mechanical_mesh,dimPlex,ierr); CHKERRQ(ierr)
+  call DMClone(geomMesh,mechanical_mesh,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetDimension(mechanical_mesh,dimPlex,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! Setup FEM mech discretization
@@ -140,35 +140,37 @@ subroutine FEM_mechanical_init(fieldBC)
   nQuadrature = FEM_nQuadrature(    dimPlex,num%p_i)
   qPointsP  => qPoints
   qWeightsP => qWeights
-  call PetscQuadratureCreate(PETSC_COMM_SELF,mechQuad,ierr); CHKERRQ(ierr)
-  CHKERRQ(ierr)
+  call PetscQuadratureCreate(PETSC_COMM_SELF,mechQuad,err_PETSc)
+  CHKERRQ(err_PETSc)
   nc = dimPlex
-  call PetscQuadratureSetData(mechQuad,dimPlex,nc,nQuadrature,qPointsP,qWeightsP,ierr)
-  CHKERRQ(ierr)
+  call PetscQuadratureSetData(mechQuad,dimPlex,nc,nQuadrature,qPointsP,qWeightsP,err_PETSc)
+  CHKERRQ(err_PETSc)
   call PetscFECreateDefault(PETSC_COMM_SELF,dimPlex,nc,PETSC_TRUE,prefix, &
-                            num%p_i,mechFE,ierr); CHKERRQ(ierr)
-  call PetscFESetQuadrature(mechFE,mechQuad,ierr); CHKERRQ(ierr)
-  call PetscFEGetDimension(mechFE,nBasis,ierr); CHKERRQ(ierr)
+                            num%p_i,mechFE,err_PETSc); CHKERRQ(err_PETSc)
+  call PetscFESetQuadrature(mechFE,mechQuad,err_PETSc); CHKERRQ(err_PETSc)
+  call PetscFEGetDimension(mechFE,nBasis,err_PETSc); CHKERRQ(err_PETSc)
   nBasis = nBasis/nc
-  call DMAddField(mechanical_mesh,PETSC_NULL_DMLABEL,mechFE,ierr); CHKERRQ(ierr)
-  call DMCreateDS(mechanical_mesh,ierr); CHKERRQ(ierr)
-  call DMGetDS(mechanical_mesh,mechDS,ierr); CHKERRQ(ierr)
-  call PetscDSGetTotalDimension(mechDS,cellDof,ierr); CHKERRQ(ierr)
-  call PetscFEDestroy(mechFE,ierr); CHKERRQ(ierr)
-  call PetscQuadratureDestroy(mechQuad,ierr); CHKERRQ(ierr)
+  call DMAddField(mechanical_mesh,PETSC_NULL_DMLABEL,mechFE,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMCreateDS(mechanical_mesh,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetDS(mechanical_mesh,mechDS,err_PETSc); CHKERRQ(err_PETSc)
+  call PetscDSGetTotalDimension(mechDS,cellDof,err_PETSc); CHKERRQ(err_PETSc)
+  call PetscFEDestroy(mechFE,err_PETSc); CHKERRQ(err_PETSc)
+  call PetscQuadratureDestroy(mechQuad,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! Setup FEM mech boundary conditions
-  call DMGetLabel(mechanical_mesh,'Face Sets',BCLabel,ierr); CHKERRQ(ierr)
-  call DMPlexLabelComplete(mechanical_mesh,BCLabel,ierr); CHKERRQ(ierr)
-  call DMGetLocalSection(mechanical_mesh,section,ierr); CHKERRQ(ierr)
+  call DMGetLabel(mechanical_mesh,'Face Sets',BCLabel,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMPlexLabelComplete(mechanical_mesh,BCLabel,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetLocalSection(mechanical_mesh,section,err_PETSc); CHKERRQ(err_PETSc)
   allocate(pnumComp(1), source=dimPlex)
   allocate(pnumDof(0:dimPlex), source = 0)
   do topologDim = 0, dimPlex
-    call DMPlexGetDepthStratum(mechanical_mesh,topologDim,cellStart,cellEnd,ierr)
-    CHKERRQ(ierr)
-    call PetscSectionGetDof(section,cellStart,pnumDof(topologDim),ierr)
-    CHKERRQ(ierr)
+    call DMPlexGetDepthStratum(mechanical_mesh,topologDim,cellStart,cellEnd,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call PetscSectionGetDof(section,cellStart,pnumDof(topologDim),err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo
   numBC = 0
   do field = 1, dimPlex; do faceSet = 1, mesh_Nboundaries
@@ -181,55 +183,61 @@ subroutine FEM_mechanical_init(fieldBC)
   do field = 1, dimPlex; do faceSet = 1, mesh_Nboundaries
     if (fieldBC%componentBC(field)%Mask(faceSet)) then
       numBC = numBC + 1
-      call ISCreateGeneral(PETSC_COMM_WORLD,1,[field-1],PETSC_COPY_VALUES,pbcComps(numBC),ierr)
-      CHKERRQ(ierr)
-      call DMGetStratumSize(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcSize,ierr)
-      CHKERRQ(ierr)
+      call ISCreateGeneral(PETSC_COMM_WORLD,1,[field-1],PETSC_COPY_VALUES,pbcComps(numBC),err_PETSc)
+      CHKERRQ(err_PETSc)
+      call DMGetStratumSize(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcSize,err_PETSc)
+      CHKERRQ(err_PETSc)
       if (bcSize > 0) then
-        call DMGetStratumIS(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcPoint,ierr)
-        CHKERRQ(ierr)
-        call ISGetIndicesF90(bcPoint,pBcPoint,ierr); CHKERRQ(ierr)
-        call ISCreateGeneral(PETSC_COMM_WORLD,bcSize,pBcPoint,PETSC_COPY_VALUES,pbcPoints(numBC),ierr)
-        CHKERRQ(ierr)
-        call ISRestoreIndicesF90(bcPoint,pBcPoint,ierr); CHKERRQ(ierr)
-        call ISDestroy(bcPoint,ierr); CHKERRQ(ierr)
+        call DMGetStratumIS(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcPoint,err_PETSc)
+        CHKERRQ(err_PETSc)
+        call ISGetIndicesF90(bcPoint,pBcPoint,err_PETSc); CHKERRQ(err_PETSc)
+        call ISCreateGeneral(PETSC_COMM_WORLD,bcSize,pBcPoint,PETSC_COPY_VALUES,pbcPoints(numBC),err_PETSc)
+        CHKERRQ(err_PETSc)
+        call ISRestoreIndicesF90(bcPoint,pBcPoint,err_PETSc); CHKERRQ(err_PETSc)
+        call ISDestroy(bcPoint,err_PETSc); CHKERRQ(err_PETSc)
       else
-        call ISCreateGeneral(PETSC_COMM_WORLD,0,[0],PETSC_COPY_VALUES,pbcPoints(numBC),ierr)
-        CHKERRQ(ierr)
+        call ISCreateGeneral(PETSC_COMM_WORLD,0,[0],PETSC_COPY_VALUES,pbcPoints(numBC),err_PETSc)
+        CHKERRQ(err_PETSc)
       endif
     endif
   enddo; enddo
   call DMPlexCreateSection(mechanical_mesh,nolabel,pNumComp,pNumDof, &
-                           numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,ierr)
-  CHKERRQ(ierr)
-  call DMSetSection(mechanical_mesh,section,ierr); CHKERRQ(ierr)
+                           numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMSetSection(mechanical_mesh,section,err_PETSc); CHKERRQ(err_PETSc)
   do faceSet = 1, numBC
-    call ISDestroy(pbcPoints(faceSet),ierr); CHKERRQ(ierr)
+    call ISDestroy(pbcPoints(faceSet),err_PETSc); CHKERRQ(err_PETSc)
   enddo
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,ierr);CHKERRQ(ierr)
-  call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',ierr);CHKERRQ(ierr)
-  call SNESSetDM(mechanical_snes,mechanical_mesh,ierr); CHKERRQ(ierr)                                           !< set the mesh for non-linear solver
-  call DMCreateGlobalVector(mechanical_mesh,solution        ,ierr); CHKERRQ(ierr)                         !< locally owned displacement Dofs
-  call DMCreateGlobalVector(mechanical_mesh,solution_rate   ,ierr); CHKERRQ(ierr)                         !< locally owned velocity Dofs to guess solution at next load step
-  call DMCreateLocalVector (mechanical_mesh,solution_local  ,ierr); CHKERRQ(ierr)                         !< locally owned velocity Dofs to guess solution at next load step
-  call DMSNESSetFunctionLocal(mechanical_mesh,FEM_mechanical_formResidual,PETSC_NULL_VEC,ierr)                  !< function to evaluate residual forces
-  CHKERRQ(ierr)
-  call DMSNESSetJacobianLocal(mechanical_mesh,FEM_mechanical_formJacobian,PETSC_NULL_VEC,ierr)                  !< function to evaluate stiffness matrix
-  CHKERRQ(ierr)
-  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1), ierr); CHKERRQ(ierr)                       !< ignore linear solve failures
-  call SNESSetConvergenceTest(mechanical_snes,FEM_mechanical_converged,PETSC_NULL_VEC,PETSC_NULL_FUNCTION,ierr)
-  CHKERRQ(ierr)
-  call SNESSetTolerances(mechanical_snes,1.0,0.0,0.0,num%itmax,num%itmax,ierr)
-  CHKERRQ(ierr)
-  call SNESSetFromOptions(mechanical_snes,ierr); CHKERRQ(ierr)
+  call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,err_PETSc);CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetDM(mechanical_snes,mechanical_mesh,err_PETSc)                                         ! set the mesh for non-linear solver
+  CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(mechanical_mesh,solution, err_PETSc)                                    ! locally owned displacement Dofs
+  CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(mechanical_mesh,solution_rate, err_PETSc)                               ! locally owned velocity Dofs to guess solution at next load step
+  CHKERRQ(err_PETSc)
+  call DMCreateLocalVector (mechanical_mesh,solution_local,err_PETSc)                               ! locally owned velocity Dofs to guess solution at next load step
+  CHKERRQ(err_PETSc)
+  call DMSNESSetFunctionLocal(mechanical_mesh,FEM_mechanical_formResidual,PETSC_NULL_VEC,err_PETSc) ! function to evaluate residual forces
+  CHKERRQ(err_PETSc)
+  call DMSNESSetJacobianLocal(mechanical_mesh,FEM_mechanical_formJacobian,PETSC_NULL_VEC,err_PETSc) ! function to evaluate stiffness matrix
+  CHKERRQ(err_PETSc)
+  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1), err_PETSc)                           ! ignore linear solve failures CHKERRQ(err_PETSc)                                                                                !< ignore linear solve failures
+  CHKERRQ(err_PETSc)
+  call SNESSetConvergenceTest(mechanical_snes,FEM_mechanical_converged,PETSC_NULL_VEC,PETSC_NULL_FUNCTION,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetTolerances(mechanical_snes,1.0,0.0,0.0,num%itmax,num%itmax,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(mechanical_snes,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call VecSet(solution        ,0.0,ierr); CHKERRQ(ierr)
-  call VecSet(solution_rate   ,0.0,ierr); CHKERRQ(ierr)
+  call VecSet(solution        ,0.0,err_PETSc); CHKERRQ(err_PETSc)
+  call VecSet(solution_rate   ,0.0,err_PETSc); CHKERRQ(err_PETSc)
   allocate(x_scal(cellDof))
   allocate(nodalWeightsP(1))
   allocate(nodalPointsP(dimPlex))
@@ -237,26 +245,26 @@ subroutine FEM_mechanical_init(fieldBC)
   allocate(pcellJ(dimPlex**2))
   allocate(pinvcellJ(dimPlex**2))
   allocate(cellJMat(dimPlex,dimPlex))
-  call PetscDSGetDiscretization(mechDS,0,mechFE,ierr)
-  CHKERRQ(ierr)
-  call PetscFEGetDualSpace(mechFE,mechDualSpace,ierr); CHKERRQ(ierr)
-  call DMPlexGetHeightStratum(mechanical_mesh,0,cellStart,cellEnd,ierr)
-  CHKERRQ(ierr)
+  call PetscDSGetDiscretization(mechDS,0,mechFE,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscFEGetDualSpace(mechFE,mechDualSpace,err_PETSc); CHKERRQ(err_PETSc)
+  call DMPlexGetHeightStratum(mechanical_mesh,0,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
   do cell = cellStart, cellEnd-1                                                                    !< loop over all elements
     x_scal = 0.0_pReal
-    call  DMPlexComputeCellGeometryAffineFEM(mechanical_mesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
-    CHKERRQ(ierr)
+    call  DMPlexComputeCellGeometryAffineFEM(mechanical_mesh,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
+    CHKERRQ(err_PETSc)
     cellJMat = reshape(pCellJ,shape=[dimPlex,dimPlex])
     do basis = 0, nBasis*dimPlex-1, dimPlex
-      call PetscDualSpaceGetFunctional(mechDualSpace,basis,functional,ierr)
-      CHKERRQ(ierr)
-      call PetscQuadratureGetData(functional,dimPlex,nc,nNodalPoints,nodalPointsP,nodalWeightsP,ierr)
-      CHKERRQ(ierr)
+      call PetscDualSpaceGetFunctional(mechDualSpace,basis,functional,err_PETSc)
+      CHKERRQ(err_PETSc)
+      call PetscQuadratureGetData(functional,dimPlex,nc,nNodalPoints,nodalPointsP,nodalWeightsP,err_PETSc)
+      CHKERRQ(err_PETSc)
       x_scal(basis+1:basis+dimPlex) = pV0 + matmul(transpose(cellJMat),nodalPointsP + 1.0_pReal)
     enddo
     px_scal => x_scal
-    call DMPlexVecSetClosure(mechanical_mesh,section,solution_local,cell,px_scal,5,ierr)
-    CHKERRQ(ierr)
+    call DMPlexVecSetClosure(mechanical_mesh,section,solution_local,cell,px_scal,5,err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo
   call utilities_constitutiveResponse(0.0_pReal,devNull,.true.)
 
@@ -279,7 +287,7 @@ type(tSolutionState) function FEM_mechanical_solution( &
   character(len=*), intent(in) :: &
     incInfoIn
 
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   SNESConvergedReason :: reason
 
   incInfo = incInfoIn
@@ -289,8 +297,10 @@ type(tSolutionState) function FEM_mechanical_solution( &
   params%timeinc = timeinc
   params%fieldBC = fieldBC
 
-  call SNESSolve(mechanical_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr)                       ! solve mechanical_snes based on solution guess (result in solution)
-  call SNESGetConvergedReason(mechanical_snes,reason,ierr); CHKERRQ(ierr)                           ! solution converged?
+  call SNESSolve(mechanical_snes,PETSC_NULL_VEC,solution,err_PETSc)                                 ! solve mechanical_snes based on solution guess (result in solution)
+  CHKERRQ(err_PETSc)
+  call SNESGetConvergedReason(mechanical_snes,reason,err_PETSc)                                     ! solution converged?
+  CHKERRQ(err_PETSc)
   terminallyIll = .false.
 
   if (reason < 1) then                                                                              ! 0: still iterating (will not occur), negative -> convergence error
@@ -298,8 +308,8 @@ type(tSolutionState) function FEM_mechanical_solution( &
     FEM_mechanical_solution%iterationsNeeded = num%itmax
   else                                                                                              ! >= 1 proper convergence (or terminally ill)
     FEM_mechanical_solution%converged = .true.
-    call SNESGetIterationNumber(mechanical_snes,FEM_mechanical_solution%iterationsNeeded,ierr)
-    CHKERRQ(ierr)
+    call SNESGetIterationNumber(mechanical_snes,FEM_mechanical_solution%iterationsNeeded,err_PETSc)
+    CHKERRQ(err_PETSc)
   endif
 
   print'(/,1x,a)', '==========================================================================='
@@ -311,11 +321,12 @@ end function FEM_mechanical_solution
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the FEM residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
+subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,err_PETSc)
 
   DM                                 :: dm_local
   PetscObject,intent(in)             :: dummy
-  PetscErrorCode                     :: ierr
+  PetscErrorCode                     :: err_PETSc
+  integer(MPI_INTEGER_KIND)          :: err_MPI
 
   PetscDS                            :: prob
   Vec                                :: x_local, f_local, xx_local
@@ -339,22 +350,23 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
   allocate(pinvcellJ(dimPlex**2))
   allocate(x_scal(cellDof))
 
-  call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
-  call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr)
-  call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,ierr)
-  CHKERRQ(ierr)
-  call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
-  call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
-  call VecWAXPY(x_local,1.0,xx_local,solution_local,ierr); CHKERRQ(ierr)
+  call DMGetLocalSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetDS(dm_local,prob,err_PETSc); CHKERRQ(err_PETSc)
+  call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
+  call VecWAXPY(x_local,1.0,xx_local,solution_local,err_PETSc); CHKERRQ(err_PETSc)
   do field = 1, dimPlex; do face = 1, mesh_Nboundaries
     if (params%fieldBC%componentBC(field)%Mask(face)) then
-      call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,ierr)
+      call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
       if (bcSize > 0) then
-        call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,ierr)
-        CHKERRQ(ierr)
+        call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
+        CHKERRQ(err_PETSc)
         call utilities_projectBCValues(x_local,section,0,field-1,bcPoints, &
                                        0.0_pReal,params%fieldBC%componentBC(field)%Value(face),params%timeinc)
-        call ISDestroy(bcPoints,ierr); CHKERRQ(ierr)
+        call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
       endif
     endif
   enddo; enddo
@@ -363,12 +375,12 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
 ! evaluate field derivatives
   do cell = cellStart, cellEnd-1                                                                    !< loop over all elements
 
-    call PetscSectionGetNumFields(section,numFields,ierr)
-    CHKERRQ(ierr)
-    call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr)                             !< get Dofs belonging to element
-    CHKERRQ(ierr)
-    call  DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
-    CHKERRQ(ierr)
+    call PetscSectionGetNumFields(section,numFields,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)                        !< get Dofs belonging to element
+    CHKERRQ(err_PETSc)
+    call  DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
+    CHKERRQ(err_PETSc)
     IcellJMat = reshape(pInvcellJ,shape=[dimPlex,dimPlex])
     do qPt = 0, nQuadrature-1
       m = cell*nQuadrature + qPt+1
@@ -392,23 +404,24 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
 
       enddo
     endif
-    call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,ierr)
-    CHKERRQ(ierr)
+    call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo
 
 !--------------------------------------------------------------------------------------------------
 ! evaluate constitutive response
   call utilities_constitutiveResponse(params%timeinc,P_av,ForwardData)
-  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   ForwardData = .false.
 
 !--------------------------------------------------------------------------------------------------
 ! integrating residual
   do cell = cellStart, cellEnd-1                                                                    !< loop over all elements
-    call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr)                             !< get Dofs belonging to element
-    CHKERRQ(ierr)
-    call  DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
-    CHKERRQ(ierr)
+    call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)                        !< get Dofs belonging to element
+    CHKERRQ(err_PETSc)
+    call  DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
+    CHKERRQ(err_PETSc)
     IcellJMat = reshape(pInvcellJ,shape=[dimPlex,dimPlex])
     f_scal = 0.0
     do qPt = 0, nQuadrature-1
@@ -429,12 +442,12 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,ierr)
     enddo
     f_scal = f_scal*abs(detJ)
     pf_scal => f_scal
-    call DMPlexVecSetClosure(dm_local,section,f_local,cell,pf_scal,ADD_VALUES,ierr)
-    CHKERRQ(ierr)
-    call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,ierr)
-    CHKERRQ(ierr)
+    call DMPlexVecSetClosure(dm_local,section,f_local,cell,pf_scal,ADD_VALUES,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo
-  call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
+  call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
 
 end subroutine FEM_mechanical_formResidual
 
@@ -442,13 +455,13 @@ end subroutine FEM_mechanical_formResidual
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the FEM stiffness matrix
 !--------------------------------------------------------------------------------------------------
-subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
+subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,err_PETSc)
 
 
   DM                      :: dm_local
   Mat                     :: Jac_pre, Jac
   PetscObject, intent(in) :: dummy
-  PetscErrorCode          :: ierr
+  PetscErrorCode          :: err_PETSc
 
   PetscDS                              :: prob
   Vec                                  :: x_local, xx_local
@@ -478,34 +491,43 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
   allocate(pcellJ(dimPlex**2))
   allocate(pinvcellJ(dimPlex**2))
 
-  call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,ierr); CHKERRQ(ierr)
-  call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,ierr); CHKERRQ(ierr)
-  call MatZeroEntries(Jac,ierr); CHKERRQ(ierr)
-  call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr)
-  call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,ierr)
-  call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
-  call DMGetGlobalSection(dm_local,gSection,ierr); CHKERRQ(ierr)
+  call MatSetOption(Jac,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatZeroEntries(Jac,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetDS(dm_local,prob,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscDSGetTabulation(prob,0_pPETSCINT,basisField,basisFieldDer,err_PETSc)
+  call DMGetLocalSection(dm_local,section,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetGlobalSection(dm_local,gSection,err_PETSc)
+  CHKERRQ(err_PETSc)
 
-  call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
-  call VecWAXPY(x_local,1.0_pReal,xx_local,solution_local,ierr); CHKERRQ(ierr)
+  call DMGetLocalVector(dm_local,x_local,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecWAXPY(x_local,1.0_pReal,xx_local,solution_local,err_PETSc)
+  CHKERRQ(err_PETSc)
   do field = 1, dimPlex; do face = 1, mesh_Nboundaries
     if (params%fieldBC%componentBC(field)%Mask(face)) then
-      call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,ierr)
+      call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
       if (bcSize > 0) then
-        call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,ierr)
-        CHKERRQ(ierr)
+        call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
+        CHKERRQ(err_PETSc)
         call utilities_projectBCValues(x_local,section,0,field-1,bcPoints, &
                                        0.0_pReal,params%fieldBC%componentBC(field)%Value(face),params%timeinc)
-        call ISDestroy(bcPoints,ierr); CHKERRQ(ierr)
+        call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
       endif
     endif
   enddo; enddo
-  call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
+  call DMPlexGetHeightStratum(dm_local,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
   do cell = cellStart, cellEnd-1                                                                    !< loop over all elements
-    call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr)                             !< get Dofs belonging to element
-    CHKERRQ(ierr)
-    call  DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
-    CHKERRQ(ierr)
+    call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)                        !< get Dofs belonging to element
+    CHKERRQ(err_PETSc)
+    call  DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)
+    CHKERRQ(err_PETSc)
     K_eA = 0.0
     K_eB = 0.0
     MatB = 0.0
@@ -558,27 +580,27 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
     ! https://software.intel.com/en-us/forums/intel-fortran-compiler/topic/782230 (bug)
     allocate(pK_e(cellDOF**2),source = reshape(K_e,[cellDOF**2]))
 #endif
-    call DMPlexMatSetClosure(dm_local,section,gSection,Jac,cell,pK_e,ADD_VALUES,ierr)
-    CHKERRQ(ierr)
-    call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,ierr)
-    CHKERRQ(ierr)
+    call DMPlexMatSetClosure(dm_local,section,gSection,Jac,cell,pK_e,ADD_VALUES,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMPlexVecRestoreClosure(dm_local,section,x_local,cell,x_scal,err_PETSc)
+    CHKERRQ(err_PETSc)
   enddo
-  call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,ierr); CHKERRQ(ierr)
-  call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
+  call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! apply boundary conditions
 #if (PETSC_VERSION_MINOR < 14)
-  call DMPlexCreateRigidBody(dm_local,matnull,ierr); CHKERRQ(ierr)
+  call DMPlexCreateRigidBody(dm_local,matnull,err_PETSc); CHKERRQ(err_PETSc)
 #else
-  call DMPlexCreateRigidBody(dm_local,0,matnull,ierr); CHKERRQ(ierr)
+  call DMPlexCreateRigidBody(dm_local,0,matnull,err_PETSc); CHKERRQ(err_PETSc)
 #endif
-  call MatSetNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
-  call MatSetNearNullSpace(Jac,matnull,ierr); CHKERRQ(ierr)
-  call MatNullSpaceDestroy(matnull,ierr); CHKERRQ(ierr)
+  call MatSetNullSpace(Jac,matnull,err_PETSc); CHKERRQ(err_PETSc)
+  call MatSetNearNullSpace(Jac,matnull,err_PETSc); CHKERRQ(err_PETSc)
+  call MatNullSpaceDestroy(matnull,err_PETSc); CHKERRQ(err_PETSc)
 
 end subroutine FEM_mechanical_formJacobian
 
@@ -601,43 +623,43 @@ subroutine FEM_mechanical_forward(guess,timeinc,timeinc_old,fieldBC)
   Vec            :: x_local
   PetscSection   :: section
   IS             :: bcPoints
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
 
 !--------------------------------------------------------------------------------------------------
 ! forward last inc
   if (guess .and. .not. cutBack) then
     ForwardData = .True.
     homogenization_F0 = homogenization_F
-    call SNESGetDM(mechanical_snes,dm_local,ierr); CHKERRQ(ierr)                                          !< retrieve mesh info from mechanical_snes into dm_local
-    call DMGetSection(dm_local,section,ierr); CHKERRQ(ierr)
-    call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
-    call VecSet(x_local,0.0_pReal,ierr); CHKERRQ(ierr)
-    call DMGlobalToLocalBegin(dm_local,solution,INSERT_VALUES,x_local,ierr)                         !< retrieve my partition of global solution vector
-    CHKERRQ(ierr)
-    call DMGlobalToLocalEnd(dm_local,solution,INSERT_VALUES,x_local,ierr)
-    CHKERRQ(ierr)
-    call VecAXPY(solution_local,1.0,x_local,ierr); CHKERRQ(ierr)
+    call SNESGetDM(mechanical_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)                               !< retrieve mesh info from mechanical_snes into dm_local
+    call DMGetSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
+    call DMGetLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
+    call VecSet(x_local,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+    call DMGlobalToLocalBegin(dm_local,solution,INSERT_VALUES,x_local,err_PETSc)                         !< retrieve my partition of global solution vector
+    CHKERRQ(err_PETSc)
+    call DMGlobalToLocalEnd(dm_local,solution,INSERT_VALUES,x_local,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call VecAXPY(solution_local,1.0,x_local,err_PETSc); CHKERRQ(err_PETSc)
     do field = 1, dimPlex; do face = 1, mesh_Nboundaries
       if (fieldBC%componentBC(field)%Mask(face)) then
-        call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,ierr)
+        call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
         if (bcSize > 0) then
-          call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,ierr)
-          CHKERRQ(ierr)
+          call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
+          CHKERRQ(err_PETSc)
           call utilities_projectBCValues(solution_local,section,0,field-1,bcPoints, &
                                          0.0_pReal,fieldBC%componentBC(field)%Value(face),timeinc_old)
-          call ISDestroy(bcPoints,ierr); CHKERRQ(ierr)
+          call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
         endif
       endif
     enddo; enddo
-    call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
+    call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! update rate and forward last inc
-    call VecCopy(solution,solution_rate,ierr); CHKERRQ(ierr)
-    call VecScale(solution_rate,1.0/timeinc_old,ierr); CHKERRQ(ierr)
+    call VecCopy(solution,solution_rate,err_PETSc); CHKERRQ(err_PETSc)
+    call VecScale(solution_rate,1.0/timeinc_old,err_PETSc); CHKERRQ(err_PETSc)
   endif
-  call VecCopy(solution_rate,solution,ierr); CHKERRQ(ierr)
-  call VecScale(solution,timeinc,ierr); CHKERRQ(ierr)
+  call VecCopy(solution_rate,solution,err_PETSc); CHKERRQ(err_PETSc)
+  call VecScale(solution,timeinc,err_PETSc); CHKERRQ(err_PETSc)
 
 end subroutine FEM_mechanical_forward
 
@@ -645,20 +667,20 @@ end subroutine FEM_mechanical_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief reporting
 !--------------------------------------------------------------------------------------------------
-subroutine FEM_mechanical_converged(snes_local,PETScIter,xnorm,snorm,fnorm,reason,dummy,ierr)
+subroutine FEM_mechanical_converged(snes_local,PETScIter,xnorm,snorm,fnorm,reason,dummy,err_PETSc)
 
   SNES :: snes_local
   PetscInt :: PETScIter
   PetscReal :: xnorm,snorm,fnorm,divTol
   SNESConvergedReason :: reason
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
 
 !--------------------------------------------------------------------------------------------------
 ! report
   divTol = max(maxval(abs(P_av(1:dimPlex,1:dimPlex)))*num%eps_struct_rtol,num%eps_struct_atol)
-  call SNESConvergedDefault(snes_local,PETScIter,xnorm,snorm,fnorm/divTol,reason,dummy,ierr)
-  CHKERRQ(ierr)
+  call SNESConvergedDefault(snes_local,PETScIter,xnorm,snorm,fnorm/divTol,reason,dummy,err_PETSc)
+  CHKERRQ(err_PETSc)
   if (terminallyIll) reason = SNES_DIVERGED_FUNCTION_DOMAIN
   print'(/,1x,a,a,i0,a,i0,f0.3)', trim(incInfo), &
                   ' @ Iteration ',PETScIter,' mechanical residual norm = ', &
@@ -690,7 +712,7 @@ subroutine FEM_mechanical_updateCoords()
 
   DM  :: dm_local
   Vec :: x_local
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
   PetscInt :: pStart, pEnd, p, s, e, q, &
               cellStart, cellEnd, c, n
   PetscSection :: section
@@ -698,34 +720,37 @@ subroutine FEM_mechanical_updateCoords()
   PetscReal,      dimension(:),  pointer :: basisField, basisFieldDer
   PetscScalar, dimension(:),   pointer :: x_scal
 
-  call SNESGetDM(mechanical_snes,dm_local,ierr); CHKERRQ(ierr)
-  call DMGetDS(dm_local,mechQuad,ierr); CHKERRQ(ierr)
-  call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
-  call DMGetLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
-  call DMGetDimension(dm_local,dimPlex,ierr); CHKERRQ(ierr)
+  call SNESGetDM(mechanical_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetDS(dm_local,mechQuad,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetLocalSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
+  call DMGetDimension(dm_local,dimPlex,err_PETSc); CHKERRQ(err_PETSc)
 
   ! write cell vertex displacements
-  call DMPlexGetDepthStratum(dm_local,0,pStart,pEnd,ierr); CHKERRQ(ierr)
+  call DMPlexGetDepthStratum(dm_local,0,pStart,pEnd,err_PETSc); CHKERRQ(err_PETSc)
   allocate(nodeCoords(3,pStart:pEnd-1),source=0.0_pReal)
-  call VecGetArrayF90(x_local,nodeCoords_linear,ierr); CHKERRQ(ierr)
+  call VecGetArrayF90(x_local,nodeCoords_linear,err_PETSc); CHKERRQ(err_PETSc)
   do p=pStart, pEnd-1
-    call DMPlexGetPointLocal(dm_local, p, s, e, ierr); CHKERRQ(ierr)
+    call DMPlexGetPointLocal(dm_local, p, s, e, err_PETSc); CHKERRQ(err_PETSc)
     nodeCoords(1:dimPlex,p)=nodeCoords_linear(s+1:e)
   enddo
 
   call discretization_setNodeCoords(nodeCoords)
-  call VecRestoreArrayF90(x_local,nodeCoords_linear,ierr); CHKERRQ(ierr)
+  call VecRestoreArrayF90(x_local,nodeCoords_linear,err_PETSc); CHKERRQ(err_PETSc)
 
   ! write ip displacements
-  call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
-  call PetscDSGetTabulation(mechQuad,0,basisField,basisFieldDer,ierr); CHKERRQ(ierr)
+  call DMPlexGetHeightStratum(dm_local,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call PetscDSGetTabulation(mechQuad,0_pPETSCINT,basisField,basisFieldDer,err_PETSc)
+  CHKERRQ(err_PETSc)
   allocate(ipCoords(3,nQuadrature,mesh_NcpElems),source=0.0_pReal)
   do c=cellStart,cellEnd-1
     qOffset=0
-    call DMPlexVecGetClosure(dm_local,section,x_local,c,x_scal,ierr); CHKERRQ(ierr)                             !< get nodal coordinates of each element
+    call DMPlexVecGetClosure(dm_local,section,x_local,c,x_scal,err_PETSc)                           !< get nodal coordinates of each element
+    CHKERRQ(err_PETSc)
     do qPt=0,nQuadrature-1
       qOffset= qPt * (size(basisField)/nQuadrature)
-      do comp=0,dimPlex-1                                                                                       !< loop over components
+      do comp=0,dimPlex-1                                                                           !< loop over components
         nOffset=0
         q = comp
         do n=0,nBasis-1
@@ -737,10 +762,11 @@ subroutine FEM_mechanical_updateCoords()
         enddo
       enddo
     enddo
-    call DMPlexVecRestoreClosure(dm_local,section,x_local,c,x_scal,ierr); CHKERRQ(ierr)
+    call DMPlexVecRestoreClosure(dm_local,section,x_local,c,x_scal,err_PETSc)
+    CHKERRQ(err_PETSc)
   end do
   call discretization_setIPcoords(reshape(ipCoords,[3,mesh_NcpElems*nQuadrature]))
-  call DMRestoreLocalVector(dm_local,x_local,ierr); CHKERRQ(ierr)
+  call DMRestoreLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
 
 end subroutine FEM_mechanical_updateCoords
 
diff --git a/src/results.f90 b/src/results.f90
index d85a30dc0..dc77d5a7f 100644
--- a/src/results.f90
+++ b/src/results.f90
@@ -499,7 +499,7 @@ subroutine results_mapping_phase(ID,entry,label)
 
   integer(pI64), dimension(size(entry,1),size(entry,2)) :: &
     entryGlobal
-  integer(pI64), dimension(size(label),0:worldsize-1) :: entryOffset                                 !< offset in entry counting per process
+  integer(pI64), dimension(size(label),0:worldsize-1) :: entryOffset                                !< offset in entry counting per process
   integer, dimension(0:worldsize-1) :: writeSize                                                    !< amount of data written per process
   integer(HSIZE_T), dimension(2) :: &
     myShape, &                                                                                      !< shape of the dataset (this process)

From d7dbb6ffc2b06278c42793bcf86f0cde32c5c044 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 12:03:22 +0100
Subject: [PATCH 045/133] needs to be public for Marc

---
 src/parallelization.f90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/parallelization.f90 b/src/parallelization.f90
index 94bf6d343..d9ca15981 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -33,6 +33,7 @@ module parallelization
 #endif
 
 #ifndef PETSC
+public :: parallelization_bcast_str
 
 contains
 subroutine parallelization_bcast_str(string)

From 91a3ea96ec82c719d2de60738a4998b853a6ad3a Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 12:41:11 +0100
Subject: [PATCH 046/133] final MPI-DAMASK integer kind decoupling

bugfix: set error for openMP-calucations
---
 src/grid/grid_damage_spectral.f90  | 100 ++++++++++++++++-------------
 src/grid/grid_thermal_spectral.f90 |  90 +++++++++++++++-----------
 src/quit.f90                       |   8 ++-
 3 files changed, 114 insertions(+), 84 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 69370b211..480f3c944 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -69,7 +69,8 @@ subroutine grid_damage_spectral_init()
   PetscInt, dimension(0:worldsize-1) :: localK
   DM :: damage_grid
   Vec :: uBound, lBound
-  PetscErrorCode :: ierr
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  PetscErrorCode :: err_PETSc
   class(tNode), pointer :: &
     num_grid, &
     num_generic
@@ -99,18 +100,19 @@ subroutine grid_damage_spectral_init()
 !--------------------------------------------------------------------------------------------------
 ! set default and user defined options for PETSc
  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-damage_snes_type newtonls -damage_snes_mf &
-                               &-damage_snes_ksp_ew -damage_ksp_type fgmres',ierr)
- CHKERRQ(ierr)
- call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
- CHKERRQ(ierr)
+                               &-damage_snes_ksp_ew -damage_ksp_type fgmres',err_PETSc)
+ CHKERRQ(err_PETSc)
+ call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
+ CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,damage_snes,ierr); CHKERRQ(ierr)
-  call SNESSetOptionsPrefix(damage_snes,'damage_',ierr);CHKERRQ(ierr)
+  call SNESCreate(PETSC_COMM_WORLD,damage_snes,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(damage_snes,'damage_',err_PETSc);CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
-  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   call DMDACreate3D(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
@@ -118,31 +120,31 @@ subroutine grid_damage_spectral_init()
          1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
          1_pPetscInt, 0_pPetscInt, &                                                                ! #dof (phi, scalar), ghost boundary width (domain overlap)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
-         damage_grid,ierr)                                                                          ! handle, error
-  CHKERRQ(ierr)
-  call SNESSetDM(damage_snes,damage_grid,ierr); CHKERRQ(ierr)                                       ! connect snes to da
-  call DMsetFromOptions(damage_grid,ierr); CHKERRQ(ierr)
-  call DMsetUp(damage_grid,ierr); CHKERRQ(ierr)
-  call DMCreateGlobalVector(damage_grid,solution_vec,ierr); CHKERRQ(ierr)                           ! global solution vector (grid x 1, i.e. every def grad tensor)
-  call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr)        ! residual vector of same shape as solution vector
-  CHKERRQ(ierr)
-  call SNESSetFromOptions(damage_snes,ierr); CHKERRQ(ierr)                                          ! pull it all together with additional CLI arguments
-  call SNESGetType(damage_snes,snes_type,ierr); CHKERRQ(ierr)
+         damage_grid,err_PETSc)                                                                     ! handle, error
+  CHKERRQ(err_PETSc)
+  call SNESSetDM(damage_snes,damage_grid,err_PETSc); CHKERRQ(err_PETSc)                             ! connect snes to da
+  call DMsetFromOptions(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
+  call DMsetUp(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                 ! global solution vector (grid x 1, i.e. every def grad tensor)
+  call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)   ! residual vector of same shape as solution vector
+  CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(damage_snes,err_PETSc); CHKERRQ(err_PETSc)                                ! pull it all together with additional CLI arguments
+  call SNESGetType(damage_snes,snes_type,err_PETSc); CHKERRQ(err_PETSc)
   if (trim(snes_type) == 'vinewtonrsls' .or. &
       trim(snes_type) == 'vinewtonssls') then
-    call DMGetGlobalVector(damage_grid,lBound,ierr); CHKERRQ(ierr)
-    call DMGetGlobalVector(damage_grid,uBound,ierr); CHKERRQ(ierr)
-    call VecSet(lBound,0.0_pReal,ierr); CHKERRQ(ierr)
-    call VecSet(uBound,1.0_pReal,ierr); CHKERRQ(ierr)
-    call SNESVISetVariableBounds(damage_snes,lBound,uBound,ierr)                                    ! variable bounds for variational inequalities like contact mechanics, damage etc.
-    call DMRestoreGlobalVector(damage_grid,lBound,ierr); CHKERRQ(ierr)
-    call DMRestoreGlobalVector(damage_grid,uBound,ierr); CHKERRQ(ierr)
+    call DMGetGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
+    call DMGetGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
+    call VecSet(lBound,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+    call VecSet(uBound,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+    call SNESVISetVariableBounds(damage_snes,lBound,uBound,err_PETSc)                                ! variable bounds for variational inequalities like contact mechanics, damage etc.
+    call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
+    call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
   end if
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAGetCorners(damage_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
-  CHKERRQ(ierr)
+  call DMDAGetCorners(damage_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)
+  CHKERRQ(err_PETSc)
   xend = xstart + xend - 1
   yend = ystart + yend - 1
   zend = zstart + zend - 1
@@ -150,7 +152,7 @@ subroutine grid_damage_spectral_init()
   allocate(phi_lastInc(grid(1),grid(2),grid3), source=1.0_pReal)
   allocate(phi_stagInc(grid(1),grid(2),grid3), source=1.0_pReal)
 
-  call VecSet(solution_vec,1.0_pReal,ierr); CHKERRQ(ierr)
+  call VecSet(solution_vec,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
 
   call updateReference
 
@@ -169,7 +171,8 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
   PetscInt  :: devNull
   PetscReal :: phi_min, phi_max, stagNorm
 
-  PetscErrorCode :: ierr
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  PetscErrorCode :: err_PETSc
   SNESConvergedReason :: reason
 
   solution%converged =.false.
@@ -178,8 +181,10 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
 ! set module wide availabe data
   params%Delta_t = Delta_t
 
-  call SNESSolve(damage_snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
-  call SNESGetConvergedReason(damage_snes,reason,ierr); CHKERRQ(ierr)
+  call SNESSolve(damage_snes,PETSC_NULL_VEC,solution_vec,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetConvergedReason(damage_snes,reason,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (reason < 1) then
     solution%converged = .false.
@@ -189,9 +194,11 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
     solution%iterationsNeeded = totalIter
   end if
   stagNorm = maxval(abs(phi_current - phi_stagInc))
-  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   solution%stagConverged = stagNorm < max(num%eps_damage_atol, num%eps_damage_rtol*maxval(phi_current))
-  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   phi_stagInc = phi_current
 
 !--------------------------------------------------------------------------------------------------
@@ -202,8 +209,8 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
     call homogenization_set_phi(phi_current(i,j,k),ce)
   end do; end do; end do
 
-  call VecMin(solution_vec,devNull,phi_min,ierr); CHKERRQ(ierr)
-  call VecMax(solution_vec,devNull,phi_max,ierr); CHKERRQ(ierr)
+  call VecMin(solution_vec,devNull,phi_min,err_PETSc); CHKERRQ(err_PETSc)
+  call VecMax(solution_vec,devNull,phi_max,err_PETSc); CHKERRQ(err_PETSc)
   if (solution%converged) &
     print'(/,1x,a)', '... nonlocal damage converged .....................................'
   print'(/,1x,a,f8.6,2x,f8.6,2x,e11.4)', 'Minimum|Maximum|Delta Damage      = ', phi_min, phi_max, stagNorm
@@ -222,17 +229,19 @@ subroutine grid_damage_spectral_forward(cutBack)
   integer :: i, j, k, ce
   DM :: dm_local
   PetscScalar,  dimension(:,:,:), pointer :: x_scal
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
 
   if (cutBack) then
     phi_current = phi_lastInc
     phi_stagInc = phi_lastInc
 !--------------------------------------------------------------------------------------------------
 ! reverting damage field state
-    call SNESGetDM(damage_snes,dm_local,ierr); CHKERRQ(ierr)
-    call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr)                       !< get the data out of PETSc to work with
+    call SNESGetDM(damage_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
+    call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
+    CHKERRQ(err_PETSc)
     x_scal(xstart:xend,ystart:yend,zstart:zend) = phi_current
-    call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr)
+    call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
+    CHKERRQ(err_PETSc)
     ce = 0
     do k = 1, grid3;  do j = 1, grid(2);  do i = 1,grid(1)
       ce = ce + 1
@@ -249,7 +258,7 @@ end subroutine grid_damage_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the spectral damage residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
+subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
     in
@@ -260,7 +269,7 @@ subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
     X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
     f_scal
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: dummy_err
   integer :: i, j, k, ce
 
 
@@ -311,7 +320,8 @@ end subroutine formResidual
 !--------------------------------------------------------------------------------------------------
 subroutine updateReference()
 
-  integer :: ce,ierr
+  integer :: ce
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
 
   K_ref = 0.0_pReal
@@ -322,9 +332,11 @@ subroutine updateReference()
   end do
 
   K_ref = K_ref*wgt
-  call MPI_Allreduce(MPI_IN_PLACE,K_ref,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,K_ref,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   mu_ref = mu_ref*wgt
-  call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 end subroutine updateReference
 
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 548fa4b3c..edc703858 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -71,7 +71,8 @@ subroutine grid_thermal_spectral_init(T_0)
   integer :: i, j, k, ce
   DM :: thermal_grid
   PetscScalar, dimension(:,:,:), pointer :: T_PETSc
-  PetscErrorCode :: ierr
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  PetscErrorCode :: err_PETSc
   class(tNode), pointer :: &
     num_grid
 
@@ -94,18 +95,19 @@ subroutine grid_thermal_spectral_init(T_0)
 !--------------------------------------------------------------------------------------------------
 ! set default and user defined options for PETSc
  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-thermal_snes_type newtonls -thermal_snes_mf &
-                               &-thermal_snes_ksp_ew -thermal_ksp_type fgmres',ierr)
- CHKERRQ(ierr)
- call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
- CHKERRQ(ierr)
+                               &-thermal_snes_ksp_ew -thermal_ksp_type fgmres',err_PETSc)
+ CHKERRQ(err_PETSc)
+ call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
+ CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,thermal_snes,ierr); CHKERRQ(ierr)
-  call SNESSetOptionsPrefix(thermal_snes,'thermal_',ierr);CHKERRQ(ierr)
+  call SNESCreate(PETSC_COMM_WORLD,thermal_snes,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(thermal_snes,'thermal_',err_PETSc);CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
-  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   call DMDACreate3D(PETSC_COMM_WORLD, &
          DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &                                    ! cut off stencil at boundary
          DMDA_STENCIL_BOX, &                                                                        ! Moore (26) neighborhood around central point
@@ -113,20 +115,21 @@ subroutine grid_thermal_spectral_init(T_0)
          1_pPetscInt, 1_pPetscInt, int(worldsize,pPetscInt), &
          1_pPetscInt, 0_pPetscInt, &                                                                ! #dof (T, scalar), ghost boundary width (domain overlap)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
-         thermal_grid,ierr)                                                                         ! handle, error
-  CHKERRQ(ierr)
-  call SNESSetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr)                                     ! connect snes to da
-  call DMsetFromOptions(thermal_grid,ierr); CHKERRQ(ierr)
-  call DMsetUp(thermal_grid,ierr); CHKERRQ(ierr)
-  call DMCreateGlobalVector(thermal_grid,solution_vec,ierr); CHKERRQ(ierr)                          ! global solution vector (grid x 1, i.e. every def grad tensor)
-  call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,ierr)       ! residual vector of same shape as solution vector
-  CHKERRQ(ierr)
-  call SNESSetFromOptions(thermal_snes,ierr); CHKERRQ(ierr)                                         ! pull it all together with additional CLI arguments
+         thermal_grid,err_PETSc)                                                                    ! handle, error
+  CHKERRQ(err_PETSc)
+  call SNESSetDM(thermal_snes,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)                           ! connect snes to da
+  call DMsetFromOptions(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
+  call DMsetUp(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(thermal_grid,solution_vec,err_PETSc)                                    ! global solution vector (grid x 1, i.e. every def grad tensor)
+  CHKERRQ(err_PETSc)
+  call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)  ! residual vector of same shape as solution vector
+  CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(thermal_snes,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
-  CHKERRQ(ierr)
+  call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)
+  CHKERRQ(err_PETSc)
   xend = xstart + xend - 1
   yend = ystart + yend - 1
   zend = zstart + zend - 1
@@ -143,9 +146,11 @@ subroutine grid_thermal_spectral_init(T_0)
     call homogenization_thermal_setField(T_0,0.0_pReal,ce)
   end do; end do; end do
 
-  call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,ierr); CHKERRQ(ierr)
+  call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
+  CHKERRQ(err_PETSc)
   T_PETSc(xstart:xend,ystart:yend,zstart:zend) = T_current
-  call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,ierr); CHKERRQ(ierr)
+  call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   call updateReference
 
@@ -164,7 +169,8 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
   PetscInt  :: devNull
   PetscReal :: T_min, T_max, stagNorm
 
-  PetscErrorCode :: ierr
+  integer(MPI_INTEGER_KIND) :: err_MPI
+  PetscErrorCode :: err_PETSc
   SNESConvergedReason :: reason
 
   solution%converged =.false.
@@ -173,8 +179,10 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
 ! set module wide availabe data
   params%Delta_t = Delta_t
 
-  call SNESSolve(thermal_snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
-  call SNESGetConvergedReason(thermal_snes,reason,ierr); CHKERRQ(ierr)
+  call SNESSolve(thermal_snes,PETSC_NULL_VEC,solution_vec,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetConvergedReason(thermal_snes,reason,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (reason < 1) then
     solution%converged = .false.
@@ -184,9 +192,11 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
     solution%iterationsNeeded = totalIter
   end if
   stagNorm = maxval(abs(T_current - T_stagInc))
-  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   solution%stagConverged = stagNorm < max(num%eps_thermal_atol, num%eps_thermal_rtol*maxval(T_current))
-  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   T_stagInc = T_current
 
 !--------------------------------------------------------------------------------------------------
@@ -197,8 +207,8 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
     call homogenization_thermal_setField(T_current(i,j,k),(T_current(i,j,k)-T_lastInc(i,j,k))/params%Delta_t,ce)
   end do; end do; end do
 
-  call VecMin(solution_vec,devNull,T_min,ierr); CHKERRQ(ierr)
-  call VecMax(solution_vec,devNull,T_max,ierr); CHKERRQ(ierr)
+  call VecMin(solution_vec,devNull,T_min,err_PETSc); CHKERRQ(err_PETSc)
+  call VecMax(solution_vec,devNull,T_max,err_PETSc); CHKERRQ(err_PETSc)
   if (solution%converged) &
     print'(/,1x,a)', '... thermal conduction converged ..................................'
   print'(/,1x,a,f8.4,2x,f8.4,2x,f8.4)', 'Minimum|Maximum|Delta Temperature / K = ', T_min, T_max, stagNorm
@@ -217,7 +227,7 @@ subroutine grid_thermal_spectral_forward(cutBack)
   integer :: i, j, k, ce
   DM :: dm_local
   PetscScalar,  dimension(:,:,:), pointer :: x_scal
-  PetscErrorCode :: ierr
+  PetscErrorCode :: err_PETSc
 
   if (cutBack) then
     T_current = T_lastInc
@@ -225,10 +235,13 @@ subroutine grid_thermal_spectral_forward(cutBack)
 
 !--------------------------------------------------------------------------------------------------
 ! reverting thermal field state
-    call SNESGetDM(thermal_snes,dm_local,ierr); CHKERRQ(ierr)
-    call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr)                       !< get the data out of PETSc to work with
+    call SNESGetDM(thermal_snes,dm_local,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
+    CHKERRQ(err_PETSc)
     x_scal(xstart:xend,ystart:yend,zstart:zend) = T_current
-    call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,ierr); CHKERRQ(ierr)
+    call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
+    CHKERRQ(err_PETSc)
     ce = 0
     do k = 1, grid3;  do j = 1, grid(2);  do i = 1,grid(1)
       ce = ce + 1
@@ -245,7 +258,7 @@ end subroutine grid_thermal_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the spectral thermal residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
+subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
     in
@@ -256,7 +269,7 @@ subroutine formResidual(in,x_scal,f_scal,dummy,ierr)
     X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
     f_scal
   PetscObject :: dummy
-  PetscErrorCode :: ierr
+  PetscErrorCode :: dummy_err
   integer :: i, j, k, ce
 
   T_current = x_scal
@@ -301,7 +314,8 @@ end subroutine formResidual
 !--------------------------------------------------------------------------------------------------
 subroutine updateReference()
 
-  integer :: ce,ierr
+  integer :: ce
+  integer(MPI_INTEGER_KIND) :: err_MPI
 
 
   K_ref = 0.0_pReal
@@ -312,9 +326,11 @@ subroutine updateReference()
   end do
 
   K_ref = K_ref*wgt
-  call MPI_Allreduce(MPI_IN_PLACE,K_ref,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,K_ref,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   mu_ref = mu_ref*wgt
-  call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 end subroutine updateReference
 
diff --git a/src/quit.f90 b/src/quit.f90
index 3f9aabdf5..3c5f5e6f2 100644
--- a/src/quit.f90
+++ b/src/quit.f90
@@ -20,16 +20,18 @@ subroutine quit(stop_id)
   PetscErrorCode :: err_PETSc
  
   call h5open_f(err_HDF5)
-  if (err_HDF5 /= 0) write(6,'(a,i5)') ' Error in h5open_f ',err_HDF5                               ! prevents error if not opened yet
+  if (err_HDF5 /= 0_MPI_INTEGER_KIND) write(6,'(a,i5)') ' Error in h5open_f ',err_HDF5                               ! prevents error if not opened yet
   call h5close_f(err_HDF5)
-  if (err_HDF5 /= 0) write(6,'(a,i5)') ' Error in h5close_f ',err_HDF5
+  if (err_HDF5 /= 0_MPI_INTEGER_KIND) write(6,'(a,i5)') ' Error in h5close_f ',err_HDF5
  
   call PetscFinalize(err_PETSc)
   CHKERRQ(err_PETSc)
  
 #ifdef _OPENMP
   call MPI_finalize(err_MPI)
-  if (err_MPI /= 0) write(6,'(a,i5)') ' Error in MPI_finalize',err_MPI
+  if (err_MPI /= 0_MPI_INTEGER_KIND) write(6,'(a,i5)') ' Error in MPI_finalize',err_MPI
+#else
+  err_MPI = 0_MPI_INTEGER_KIND
 #endif
   
   call date_and_time(values = dateAndTime)

From b4088b666e5c8031dab9a66967a765deb7ff856b Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Thu, 13 Jan 2022 13:27:50 +0100
Subject: [PATCH 047/133] adjusted filehandle conditional type

---
 python/damask/_table.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index 04ab426ce..ed7c80460 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -1,13 +1,15 @@
 import re
 import copy
-from typing import Union, Optional, Tuple, List, TextIO, Set
 import pathlib
+from typing import Union, Optional, Tuple, List, TextIO, Set
+from _io import TextIOWrapper
 
 import pandas as pd
 import numpy as np
 
 from . import util
 
+
 class Table:
     """Manipulate multi-dimensional spreadsheet-like data."""
 
@@ -239,7 +241,7 @@ class Table:
             Table data from file.
 
         """
-        if isinstance(fname, TextIO):
+        if isinstance(fname, TextIOWrapper):
             f = fname
             f.seek(0)
         elif isinstance(fname, (str, pathlib.Path)):
@@ -298,7 +300,7 @@ class Table:
             Table data from file.
 
         """
-        if isinstance(fname, TextIO):
+        if isinstance(fname, TextIOWrapper):
             f = fname
             f.seek(0)
         elif isinstance(fname, (str, pathlib.Path)):
@@ -569,7 +571,7 @@ class Table:
                 labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                           for i in range(np.prod(self.shapes[l]))]
 
-        if isinstance(fname, TextIO):
+        if isinstance(fname, TextIOWrapper):
             fhandle = fname
         elif isinstance(fname, (str, pathlib.Path)):
             fhandle = open(fname,'w',newline='\n')

From 29530da579ec1ec28b4c75ca8fff88ac2def098e Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 13:50:30 +0100
Subject: [PATCH 048/133] use correct kind of constants for calls to MPI/PETSc

---
 src/grid/discretization_grid.f90             |  6 ++--
 src/grid/grid_damage_spectral.f90            |  4 +--
 src/grid/grid_mech_FEM.f90                   |  8 ++---
 src/grid/grid_mech_spectral_basic.f90        | 16 ++++-----
 src/grid/grid_mech_spectral_polarisation.f90 | 18 +++++-----
 src/grid/grid_thermal_spectral.f90           |  8 ++---
 src/grid/spectral_utilities.f90              | 35 ++++++++++----------
 src/mesh/FEM_utilities.f90                   |  2 +-
 src/mesh/discretization_mesh.f90             | 16 ++++-----
 9 files changed, 57 insertions(+), 56 deletions(-)

diff --git a/src/grid/discretization_grid.f90 b/src/grid/discretization_grid.f90
index 93b3cbc91..738206f9a 100644
--- a/src/grid/discretization_grid.f90
+++ b/src/grid/discretization_grid.f90
@@ -88,12 +88,12 @@ subroutine discretization_grid_init(restart)
   end if
 
 
-  call MPI_Bcast(grid,3,MPI_INTEGER,0,MPI_COMM_WORLD, err_MPI)
+  call MPI_Bcast(grid,3_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   if (grid(1) < 2) call IO_error(844, ext_msg='cells(1) must be larger than 1')
-  call MPI_Bcast(geomSize,3,MPI_DOUBLE,0,MPI_COMM_WORLD, err_MPI)
+  call MPI_Bcast(geomSize,3_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Bcast(origin,3,MPI_DOUBLE,0,MPI_COMM_WORLD, err_MPI)
+  call MPI_Bcast(origin,3_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD, err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   print'(/,1x,a,3(i12,1x))',    'cells  a b c: ', grid
diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 480f3c944..8955f9d66 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -194,10 +194,10 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
     solution%iterationsNeeded = totalIter
   end if
   stagNorm = maxval(abs(phi_current - phi_stagInc))
-  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   solution%stagConverged = stagNorm < max(num%eps_damage_atol, num%eps_damage_rtol*maxval(phi_current))
-  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   phi_stagInc = phi_current
 
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index dbb87440b..010f11cea 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -241,16 +241,16 @@ subroutine grid_mechanical_FEM_init
     groupHandle = HDF5_openGroup(fileHandle,'solver')
 
     call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
-    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(P_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
-    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aim_lastInc,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
-    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aimDot,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if(err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F,groupHandle,'F')
     call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 2d5376781..74400f160 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -194,16 +194,16 @@ subroutine grid_mechanical_spectral_basic_init
     groupHandle = HDF5_openGroup(fileHandle,'solver')
 
     call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
-    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(P_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
-    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aim_lastInc,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
-    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aimDot,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F,groupHandle,'F')
     call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
@@ -223,10 +223,10 @@ subroutine grid_mechanical_spectral_basic_init
   restartRead2: if (interface_restartInc > 0) then
     print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
     call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
-    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
@@ -235,7 +235,7 @@ subroutine grid_mechanical_spectral_basic_init
     call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
                        MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-    call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
+    call MPI_File_read(fileUnit,C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call MPI_File_close(fileUnit,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
@@ -503,7 +503,7 @@ subroutine formResidual(in, F, &
   call utilities_constitutiveResponse(residuum, &                                                   ! "residuum" gets field of first PK stress (to save memory)
                                       P_av,C_volAvg,C_minMaxAvg, &
                                       F,params%Delta_t,params%rotation_BC)
-  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 !--------------------------------------------------------------------------------------------------
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index a6ce8d173..765a1a5a7 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -216,16 +216,16 @@ subroutine grid_mechanical_spectral_polarisation_init
     groupHandle = HDF5_openGroup(fileHandle,'solver')
 
     call HDF5_read(P_aim,groupHandle,'P_aim',.false.)
-    call MPI_Bcast(P_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(P_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim,groupHandle,'F_aim',.false.)
-    call MPI_Bcast(F_aim,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aim,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-    call MPI_Bcast(F_aim_lastInc,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aim_lastInc,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F_aimDot,groupHandle,'F_aimDot',.false.)
-    call MPI_Bcast(F_aimDot,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(F_aimDot,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(F,groupHandle,'F')
     call HDF5_read(F_lastInc,groupHandle,'F_lastInc')
@@ -250,10 +250,10 @@ subroutine grid_mechanical_spectral_polarisation_init
   restartRead2: if (interface_restartInc > 0) then
     print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
     call HDF5_read(C_volAvg,groupHandle,'C_volAvg',.false.)
-    call MPI_Bcast(C_volAvg,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call HDF5_read(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-    call MPI_Bcast(C_volAvgLastInc,81,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+    call MPI_Bcast(C_volAvgLastInc,81_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
     call HDF5_closeGroup(groupHandle)
@@ -262,7 +262,7 @@ subroutine grid_mechanical_spectral_polarisation_init
     call MPI_File_open(MPI_COMM_WORLD, trim(getSolverJobName())//'.C_ref', &
                        MPI_MODE_RDONLY,MPI_INFO_NULL,fileUnit,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-    call MPI_File_read(fileUnit,C_minMaxAvg,81,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
+    call MPI_File_read(fileUnit,C_minMaxAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_STATUS_IGNORE,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     call MPI_File_close(fileUnit,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
@@ -564,7 +564,7 @@ subroutine formResidual(in, FandF_tau, &
                              X_RANGE, Y_RANGE, Z_RANGE)
 
   F_av = sum(sum(sum(F,dim=5),dim=4),dim=3) * wgt
-  call MPI_Allreduce(MPI_IN_PLACE,F_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,F_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   call SNESGetNumberFunctionEvals(snes,nfuncs,err_PETSc); CHKERRQ(err_PETSc)
@@ -609,7 +609,7 @@ subroutine formResidual(in, FandF_tau, &
   call utilities_constitutiveResponse(residual_F, &                                                 ! "residuum" gets field of first PK stress (to save memory)
                                       P_av,C_volAvg,C_minMaxAvg, &
                                       F - residual_F_tau/num%beta,params%Delta_t,params%rotation_BC)
-  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
 
 !--------------------------------------------------------------------------------------------------
 ! stress BC handling
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index edc703858..8862df725 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -192,10 +192,10 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
     solution%iterationsNeeded = totalIter
   end if
   stagNorm = maxval(abs(T_current - T_stagInc))
-  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,stagNorm,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_MAX,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   solution%stagConverged = stagNorm < max(num%eps_thermal_atol, num%eps_thermal_rtol*maxval(T_current))
-  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,solution%stagConverged,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LAND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   T_stagInc = T_current
 
@@ -326,10 +326,10 @@ subroutine updateReference()
   end do
 
   K_ref = K_ref*wgt
-  call MPI_Allreduce(MPI_IN_PLACE,K_ref,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,K_ref,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   mu_ref = mu_ref*wgt
-  call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,mu_ref,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 end subroutine updateReference
diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index 35803481c..80cde388f 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -590,7 +590,7 @@ real(pReal) function utilities_divergenceRMS()
                                   conjg(-xi1st(1:3,grid1Red,j,k))*rescaledGeom))**2)
   enddo; enddo
   if (grid(1) == 1) utilities_divergenceRMS = utilities_divergenceRMS * 0.5_pReal                   ! counted twice in case of grid(1) == 1
-  call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   utilities_divergenceRMS = sqrt(utilities_divergenceRMS) * wgt                                     ! RMS in real space calculated with Parsevals theorem from Fourier space
 
@@ -651,7 +651,7 @@ real(pReal) function utilities_curlRMS()
                       + sum(curl_fourier%re**2 + curl_fourier%im**2)                                ! this layer (Nyquist) does not have a conjugate complex counterpart (if grid(1) /= 1)
   enddo; enddo
 
-  call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   utilities_curlRMS = sqrt(utilities_curlRMS) * wgt
   if (grid(1) == 1) utilities_curlRMS = utilities_curlRMS * 0.5_pReal                               ! counted twice in case of grid(1) == 1
@@ -820,7 +820,7 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
 
   P = reshape(homogenization_P, [3,3,grid(1),grid(2),grid3])
   P_av = sum(sum(sum(P,dim=5),dim=4),dim=3) * wgt
-  call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,P_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   if (debugRotation) print'(/,1x,a,/,2(3(2x,f12.4,1x)/),3(2x,f12.4,1x))', &
     'Piola--Kirchhoff stress (lab) / MPa =', transpose(P_av)*1.e-6_pReal
@@ -845,21 +845,21 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
   enddo
 
   valueAndRank = [dPdF_norm_max,real(worldrank,pReal)]
-  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MAXLOC, MPI_COMM_WORLD, err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1_MPI_INTEGER_KIND,MPI_2DOUBLE_PRECISION,MPI_MAXLOC,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Bcast(dPdF_max,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, err_MPI)
+  call MPI_Bcast(dPdF_max,81_MPI_INTEGER_KIND,MPI_DOUBLE,int(valueAndRank(2),MPI_INTEGER_KIND),MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   valueAndRank = [dPdF_norm_min,real(worldrank,pReal)]
-  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MINLOC, MPI_COMM_WORLD, err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1_MPI_INTEGER_KIND,MPI_2DOUBLE_PRECISION,MPI_MINLOC,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Bcast(dPdF_min,81,MPI_DOUBLE,int(valueAndRank(2)),MPI_COMM_WORLD, err_MPI)
+  call MPI_Bcast(dPdF_min,81_MPI_INTEGER_KIND,MPI_DOUBLE,int(valueAndRank(2),MPI_INTEGER_KIND),MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   C_minmaxAvg = 0.5_pReal*(dPdF_max + dPdF_min)
 
   C_volAvg = sum(homogenization_dPdF,dim=5)
-  call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   C_volAvg = C_volAvg * wgt
 
@@ -914,7 +914,7 @@ function utilities_forwardField(Delta_t,field_lastInc,rate,aim)
   utilities_forwardField = field_lastInc + rate*Delta_t
   if (present(aim)) then                                                                            !< correct to match average
     fieldDiff = sum(sum(sum(utilities_forwardField,dim=5),dim=4),dim=3)*wgt
-    call MPI_Allreduce(MPI_IN_PLACE,fieldDiff,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+    call MPI_Allreduce(MPI_IN_PLACE,fieldDiff,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
     if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
     fieldDiff = fieldDiff - aim
     utilities_forwardField = utilities_forwardField - &
@@ -985,8 +985,9 @@ subroutine utilities_updateCoords(F)
   real(pReal),   dimension(3,  grid(1)+1,grid(2)+1,grid3+1)       :: nodeCoords
   integer :: &
     i,j,k,n, &
-    rank_t, rank_b, &
     c
+  integer(MPI_INTEGER_KIND) :: &
+    rank_t, rank_b
   integer(MPI_INTEGER_KIND) :: err_MPI
 #if (PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>14) && !defined(PETSC_HAVE_MPI_F90MODULE_VISIBILITY)
   type(MPI_Request), dimension(4) :: request
@@ -1029,26 +1030,26 @@ subroutine utilities_updateCoords(F)
  !--------------------------------------------------------------------------------------------------
  ! average F
   if (grid3Offset == 0) Favg = real(tensorField_fourier(1:3,1:3,1,1,1),pReal)*wgt
-  call MPI_Bcast(Favg,9,MPI_DOUBLE,0,MPI_COMM_WORLD,err_MPI)
+  call MPI_Bcast(Favg,9_MPI_INTEGER_KIND,MPI_DOUBLE,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
  !--------------------------------------------------------------------------------------------------
  ! pad cell center fluctuations along z-direction (needed when running MPI simulation)
   IPfluct_padded(1:3,1:grid(1),1:grid(2),2:grid3+1) = vectorField_real(1:3,1:grid(1),1:grid(2),1:grid3)
   c = product(shape(IPfluct_padded(:,:,:,1)))                                                        !< amount of data to transfer
-  rank_t = modulo(worldrank+1,worldsize)
-  rank_b = modulo(worldrank-1,worldsize)
+  rank_t = modulo(worldrank+1_MPI_INTEGER_KIND,worldsize)
+  rank_b = modulo(worldrank-1_MPI_INTEGER_KIND,worldsize)
 
   ! send bottom layer to process below
-  call MPI_Isend(IPfluct_padded(:,:,:,2),      c,MPI_DOUBLE,rank_b,0,MPI_COMM_WORLD,request(1),err_MPI)
+  call MPI_Isend(IPfluct_padded(:,:,:,2),      c,MPI_DOUBLE,rank_b,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(1),err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,MPI_COMM_WORLD,request(2),err_MPI)
+  call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(2),err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   ! send top layer to process above
-  call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1,MPI_COMM_WORLD,request(3),err_MPI)
+  call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,1_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(3),err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Irecv(IPfluct_padded(:,:,:,1),      c,MPI_DOUBLE,rank_b,1,MPI_COMM_WORLD,request(4),err_MPI)
+  call MPI_Irecv(IPfluct_padded(:,:,:,1),      c,MPI_DOUBLE,rank_b,1_MPI_INTEGER_KIND,MPI_COMM_WORLD,request(4),err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   call MPI_Waitall(4,request,status,err_MPI)
diff --git a/src/mesh/FEM_utilities.f90 b/src/mesh/FEM_utilities.f90
index ce97e7776..724a5520e 100644
--- a/src/mesh/FEM_utilities.f90
+++ b/src/mesh/FEM_utilities.f90
@@ -156,7 +156,7 @@ subroutine utilities_constitutiveResponse(timeinc,P_av,forwardData)
   cutBack = .false.
 
   P_av = sum(homogenization_P,dim=3) * wgt
-  call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
+  call MPI_Allreduce(MPI_IN_PLACE,P_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
 
diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90
index 172101976..7e12cfd7e 100644
--- a/src/mesh/discretization_mesh.f90
+++ b/src/mesh/discretization_mesh.f90
@@ -114,17 +114,17 @@ subroutine discretization_mesh_init(restart)
   ! get number of IDs in face sets (for boundary conditions?)
   call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,err_PETSc)
   CHKERRQ(err_PETSc)
-  call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  call MPI_Bcast(mesh_Nboundaries,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  call MPI_Bcast(mesh_NcpElemsGlobal,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  call MPI_Bcast(dimPlex,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   if (worldrank == 0) then
     call DMClone(globalMesh,geomMesh,err_PETSc)
   else
-    call DMPlexDistribute(globalMesh,0,sf,geomMesh,err_PETSc)
+    call DMPlexDistribute(globalMesh,0_pPETSCINT,sf,geomMesh,err_PETSc)
   endif
   CHKERRQ(err_PETSc)
 
@@ -140,14 +140,14 @@ subroutine discretization_mesh_init(restart)
     CHKERRQ(err_PETSc)
     call ISRestoreIndicesF90(faceSetIS,pFaceSets,err_PETSc)
   endif
-  call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0,MPI_COMM_WORLD,err_MPI)
+  call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   call DMDestroy(globalMesh,err_PETSc); CHKERRQ(err_PETSc)
 
   call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,err_PETSc)
+  call DMGetStratumSize(geomMesh,'depth',0_pPETSCINT,mesh_Nnodes,err_PETSc)
   CHKERRQ(err_PETSc)
 
 ! Get initial nodal coordinates
@@ -197,7 +197,7 @@ subroutine mesh_FEM_build_ipVolumes(dimPlex)
 
   allocate(mesh_ipVolume(mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
 
-  call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,err_PETSc)
+  call DMPlexGetHeightStratum(geomMesh,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
   CHKERRQ(err_PETSc)
   allocate(pCent(dimPlex))
   allocate(pNorm(dimPlex))
@@ -229,7 +229,7 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
   allocate(pV0(dimPlex))
   allocatE(pCellJ(dimPlex**2))
   allocatE(pinvCellJ(dimPlex**2))
-  call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,err_PETSc)
+  call DMPlexGetHeightStratum(geomMesh,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
   CHKERRQ(err_PETSc)
   do cell = cellStart, cellEnd-1                                                                     !< loop over all elements
     call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,err_PETSc)

From 4562f4262cb85a08f4b89e53cab6273d6f7480c4 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Thu, 13 Jan 2022 10:14:10 -0500
Subject: [PATCH 049/133] add documentation to source code

---
 src/lattice.f90 | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/lattice.f90 b/src/lattice.f90
index 469bfa556..1f824cc98 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -788,7 +788,26 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
       68,68,69,  66,66,67,  64,64,65,64,64,65,  60,63,63,60,62,62,60,61,61,60,62,62,  59,58,58,57,58,58, & ! 2. pyr<c+a>
       68,69,68,  66,67,66,  65,64,64,65,64,64,  62,62,60,63,63,60,62,62,60,61,61,60,  58,59,58,58,57,58, &
       69,68,68,  67,66,66,  64,65,64,64,65,64,  61,60,62,62,60,63,63,60,62,62,60,61,  58,58,59,58,58,57  &
-      ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme)
+      ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme and 10.1016/j.ijplas.2014.06.010 table 3)
+                                                                                                    !<  1: S1 basal self-interaction
+                                                                                                    !<  2:  1 coplanar basal/basal
+                                                                                                    !<  3:  3 collinear basal/prismatic
+                                                                                                    !<  4:  4 non-collinear basal prismatic
+                                                                                                    !<  5: S2 prismatic self-interaction
+                                                                                                    !<  6:  2 prismatic/prismatic
+                                                                                                    !<  7:  5 collinear prismatic/basal
+                                                                                                    !<  8:  6 non-collinear prismatic/basal
+                                                                                                    !< 47:  8 non-collinear basal/pyramidal
+                                                                                                    !< 48:  7 collinear basal/pyramidal
+                                                                                                    !< 49: 10 non-collinear prismatic/pyramidal
+                                                                                                    !< 50:  9 collinear prismatic/pyramidal
+                                                                                                    !< 57: S3 pyramidal c+a self-interaction
+                                                                                                    !< 58: 16 non-collinear pyramidal/pyramidal
+                                                                                                    !< 59: 15 collinear pyramidal/pyramidal
+                                                                                                    !< 66: 14 non-collienar pyramidal/prismatic
+                                                                                                    !< 67: 13 semi-collienar pyramidal/prismatic
+                                                                                                    !< 68: 12 non-collinear pyramidal/basal
+                                                                                                    !< 69: 11 semi-collinear pyramidal/basal
 
   integer, dimension(BCT_NSLIP,BCT_NSLIP), parameter :: &
     BCT_INTERACTIONSLIPSLIP = reshape( [&

From 82dabe29c149072b3abf306eabcfdc622a05f2aa Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 13 Jan 2022 16:01:06 +0100
Subject: [PATCH 050/133] mesh: separate kind for DAMASK and PETSc integers

---
 .gitlab-ci.yml                   |  7 ++++
 src/mesh/FEM_utilities.f90       |  2 +-
 src/mesh/discretization_mesh.f90 | 28 +++++++------
 src/mesh/mesh_mech_FEM.f90       | 72 +++++++++++++++++---------------
 4 files changed, 62 insertions(+), 47 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 001c326a4..959cc961a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -100,6 +100,13 @@ test_grid_GNU-64bit:
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU-64bit
 
+test_mesh_GNU-64bit:
+  stage: compile
+  script:
+    - module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
+    - cd PRIVATE/testing/pytest
+    - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU-64bit
+
 test_grid_IntelLLVM:
   stage: compile
   script:
diff --git a/src/mesh/FEM_utilities.f90 b/src/mesh/FEM_utilities.f90
index 724a5520e..703c6c818 100644
--- a/src/mesh/FEM_utilities.f90
+++ b/src/mesh/FEM_utilities.f90
@@ -50,7 +50,7 @@ module FEM_utilities
   type, public :: tSolutionState                                                                    !< return type of solution from FEM solver variants
     logical :: converged        = .true.
     logical :: stagConverged    = .true.
-    integer :: iterationsNeeded = 0
+    PetscInt :: iterationsNeeded = 0_pPETSCINT
   end type tSolutionState
 
   type, public :: tComponentBC
diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90
index 7e12cfd7e..8623ebee4 100644
--- a/src/mesh/discretization_mesh.f90
+++ b/src/mesh/discretization_mesh.f90
@@ -71,22 +71,22 @@ subroutine discretization_mesh_init(restart)
 
   logical, intent(in) :: restart
 
-  integer :: dimPlex, &
+  PetscInt :: dimPlex, &
     mesh_Nnodes, &                                                                                  !< total number of nodes in mesh
     j, &
     debug_element, debug_ip
   PetscSF :: sf
   DM :: globalMesh
-  PetscInt :: nFaceSets
+  PetscInt :: nFaceSets, Nboundaries, NelemsGlobal, Nelems
   PetscInt, pointer, dimension(:) :: pFaceSets
   IS :: faceSetIS
   PetscErrorCode :: err_PETSc
   integer(MPI_INTEGER_KIND) :: err_MPI
-  integer, dimension(:), allocatable :: &
+  PetscInt, dimension(:), allocatable :: &
     materialAt
   class(tNode), pointer :: &
     num_mesh
-  integer :: p_i                                                                                    !< integration order (quadrature rule)
+  integer :: p_i, dim                                                                               !< integration order (quadrature rule)
   type(tvec) :: coords_node0
 
   print'(/,1x,a)',   '<<<+-  discretization_mesh init  -+>>>'
@@ -105,20 +105,23 @@ subroutine discretization_mesh_init(restart)
   CHKERRQ(err_PETSc)
   call DMGetDimension(globalMesh,dimPlex,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,err_PETSc)
+  call DMGetStratumSize(globalMesh,'depth',dimPlex,NelemsGlobal,err_PETSc)
   CHKERRQ(err_PETSc)
-  print'()'
+  mesh_NcpElemsGlobal = int(NelemsGlobal)
   call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,err_PETSc)
   CHKERRQ(err_PETSc)
 
   ! get number of IDs in face sets (for boundary conditions?)
-  call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,err_PETSc)
+  call DMGetLabelSize(globalMesh,'Face Sets',Nboundaries,err_PETSc)
   CHKERRQ(err_PETSc)
+  mesh_Nboundaries = int(Nboundaries)
   call MPI_Bcast(mesh_Nboundaries,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
   call MPI_Bcast(mesh_NcpElemsGlobal,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
-  call MPI_Bcast(dimPlex,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+  dim = int(dimPlex)
+  call MPI_Bcast(dim,1_MPI_INTEGER_KIND,MPI_INTEGER,0_MPI_INTEGER_KIND,MPI_COMM_WORLD,err_MPI)
+  dimPlex = int(dim,pPETSCINT)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
   if (worldrank == 0) then
@@ -128,7 +131,7 @@ subroutine discretization_mesh_init(restart)
   endif
   CHKERRQ(err_PETSc)
 
-  allocate(mesh_boundaries(mesh_Nboundaries), source = 0)
+  allocate(mesh_boundaries(mesh_Nboundaries), source = 0_pPETSCINT)
   call DMGetLabelSize(globalMesh,'Face Sets',nFaceSets,err_PETSc)
   CHKERRQ(err_PETSc)
   call DMGetLabelIdIS(globalMesh,'Face Sets',faceSetIS,err_PETSc)
@@ -145,8 +148,9 @@ subroutine discretization_mesh_init(restart)
 
   call DMDestroy(globalMesh,err_PETSc); CHKERRQ(err_PETSc)
 
-  call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,err_PETSc)
+  call DMGetStratumSize(geomMesh,'depth',dimPlex,Nelems,err_PETSc)
   CHKERRQ(err_PETSc)
+  mesh_NcpElems = int(Nelems)
   call DMGetStratumSize(geomMesh,'depth',0_pPETSCINT,mesh_Nnodes,err_PETSc)
   CHKERRQ(err_PETSc)
 
@@ -166,7 +170,7 @@ subroutine discretization_mesh_init(restart)
     call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),err_PETSc)
     CHKERRQ(err_PETSc)
   enddo
-  materialAt = materialAt + 1
+  materialAt = materialAt + 1_pPETSCINT
 
   if (debug_element < 1 .or. debug_element > mesh_NcpElems) call IO_error(602,ext_msg='element')
   if (debug_ip < 1 .or. debug_ip > mesh_maxNips)            call IO_error(602,ext_msg='IP')
@@ -175,7 +179,7 @@ subroutine discretization_mesh_init(restart)
   mesh_node0(1:dimPlex,:) = reshape(mesh_node0_temp,[dimPlex,mesh_Nnodes])
 
 
-  call discretization_init(materialAt,&
+  call discretization_init(int(materialAt),&
                            reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
                            mesh_node0)
 
diff --git a/src/mesh/mesh_mech_FEM.f90 b/src/mesh/mesh_mech_FEM.f90
index bb7bfaece..8cf9dbfa1 100644
--- a/src/mesh/mesh_mech_FEM.f90
+++ b/src/mesh/mesh_mech_FEM.f90
@@ -40,7 +40,7 @@ module mesh_mechanical_FEM
   type(tSolutionParams)  :: params
 
   type, private :: tNumerics
-    integer :: &
+    PetscInt :: &
       p_i, &                                                                                        !< integration order (quadrature rule)
       itmax
     logical :: &
@@ -55,7 +55,8 @@ module mesh_mechanical_FEM
 ! PETSc data
   SNES                           :: mechanical_snes
   Vec                            :: solution, solution_rate, solution_local
-  PetscInt                       :: dimPlex, cellDof, nQuadrature, nBasis
+  PetscInt                       :: dimPlex, cellDof, nBasis
+  integer                        :: nQuadrature
   PetscReal, allocatable, target :: qPoints(:), qWeights(:)
   MatNullSpace                   :: matnull
 
@@ -104,8 +105,8 @@ subroutine FEM_mechanical_init(fieldBC)
   PetscReal                              :: detJ
   PetscReal,         allocatable, target :: cellJMat(:,:)
 
-  PetscScalar,                   pointer :: px_scal(:)
-  PetscScalar,       allocatable, target ::  x_scal(:)
+  PetscScalar,                   pointer, dimension(:) :: px_scal
+  PetscScalar,       allocatable, target, dimension(:) ::  x_scal
 
   character(len=*), parameter            :: prefix = 'mechFE_'
   PetscErrorCode                         :: err_PETSc
@@ -118,8 +119,8 @@ subroutine FEM_mechanical_init(fieldBC)
 !-----------------------------------------------------------------------------
 ! read numerical parametes and do sanity checks
   num_mesh => config_numerics%get('mesh',defaultVal=emptyDict)
-  num%p_i               = num_mesh%get_asInt('p_i',defaultVal = 2)
-  num%itmax             = num_mesh%get_asInt('itmax',defaultVal=250)
+  num%p_i               = int(num_mesh%get_asInt('p_i',defaultVal = 2),pPETSCINT)
+  num%itmax             = int(num_mesh%get_asInt('itmax',defaultVal=250),pPETSCINT)
   num%BBarStabilisation = num_mesh%get_asBool('bbarstabilisation',defaultVal = .false.)
   num%eps_struct_atol   = num_mesh%get_asFloat('eps_struct_atol', defaultVal = 1.0e-10_pReal)
   num%eps_struct_rtol   = num_mesh%get_asFloat('eps_struct_rtol', defaultVal = 1.0e-4_pReal)
@@ -143,7 +144,7 @@ subroutine FEM_mechanical_init(fieldBC)
   call PetscQuadratureCreate(PETSC_COMM_SELF,mechQuad,err_PETSc)
   CHKERRQ(err_PETSc)
   nc = dimPlex
-  call PetscQuadratureSetData(mechQuad,dimPlex,nc,nQuadrature,qPointsP,qWeightsP,err_PETSc)
+  call PetscQuadratureSetData(mechQuad,dimPlex,nc,int(nQuadrature,pPETSCINT),qPointsP,qWeightsP,err_PETSc)
   CHKERRQ(err_PETSc)
   call PetscFECreateDefault(PETSC_COMM_SELF,dimPlex,nc,PETSC_TRUE,prefix, &
                             num%p_i,mechFE,err_PETSc); CHKERRQ(err_PETSc)
@@ -165,7 +166,7 @@ subroutine FEM_mechanical_init(fieldBC)
   call DMPlexLabelComplete(mechanical_mesh,BCLabel,err_PETSc); CHKERRQ(err_PETSc)
   call DMGetLocalSection(mechanical_mesh,section,err_PETSc); CHKERRQ(err_PETSc)
   allocate(pnumComp(1), source=dimPlex)
-  allocate(pnumDof(0:dimPlex), source = 0)
+  allocate(pnumDof(0:dimPlex), source = 0_pPETSCINT)
   do topologDim = 0, dimPlex
     call DMPlexGetDepthStratum(mechanical_mesh,topologDim,cellStart,cellEnd,err_PETSc)
     CHKERRQ(err_PETSc)
@@ -176,14 +177,14 @@ subroutine FEM_mechanical_init(fieldBC)
   do field = 1, dimPlex; do faceSet = 1, mesh_Nboundaries
     if (fieldBC%componentBC(field)%Mask(faceSet)) numBC = numBC + 1
   enddo; enddo
-  allocate(pbcField(numBC), source=0)
+  allocate(pbcField(numBC), source=0_pPETSCINT)
   allocate(pbcComps(numBC))
   allocate(pbcPoints(numBC))
   numBC = 0
   do field = 1, dimPlex; do faceSet = 1, mesh_Nboundaries
     if (fieldBC%componentBC(field)%Mask(faceSet)) then
       numBC = numBC + 1
-      call ISCreateGeneral(PETSC_COMM_WORLD,1,[field-1],PETSC_COPY_VALUES,pbcComps(numBC),err_PETSc)
+      call ISCreateGeneral(PETSC_COMM_WORLD,1_pPETSCINT,[field-1],PETSC_COPY_VALUES,pbcComps(numBC),err_PETSc)
       CHKERRQ(err_PETSc)
       call DMGetStratumSize(mechanical_mesh,'Face Sets',mesh_boundaries(faceSet),bcSize,err_PETSc)
       CHKERRQ(err_PETSc)
@@ -196,7 +197,7 @@ subroutine FEM_mechanical_init(fieldBC)
         call ISRestoreIndicesF90(bcPoint,pBcPoint,err_PETSc); CHKERRQ(err_PETSc)
         call ISDestroy(bcPoint,err_PETSc); CHKERRQ(err_PETSc)
       else
-        call ISCreateGeneral(PETSC_COMM_WORLD,0,[0],PETSC_COPY_VALUES,pbcPoints(numBC),err_PETSc)
+        call ISCreateGeneral(PETSC_COMM_WORLD,0_pPETSCINT,[0_pPETSCINT],PETSC_COPY_VALUES,pbcPoints(numBC),err_PETSc)
         CHKERRQ(err_PETSc)
       endif
     endif
@@ -226,7 +227,7 @@ subroutine FEM_mechanical_init(fieldBC)
   CHKERRQ(err_PETSc)
   call DMSNESSetJacobianLocal(mechanical_mesh,FEM_mechanical_formJacobian,PETSC_NULL_VEC,err_PETSc) ! function to evaluate stiffness matrix
   CHKERRQ(err_PETSc)
-  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1), err_PETSc)                           ! ignore linear solve failures CHKERRQ(err_PETSc)                                                                                !< ignore linear solve failures
+  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPETSCINT), err_PETSc)                 ! ignore linear solve failures
   CHKERRQ(err_PETSc)
   call SNESSetConvergenceTest(mechanical_snes,FEM_mechanical_converged,PETSC_NULL_VEC,PETSC_NULL_FUNCTION,err_PETSc)
   CHKERRQ(err_PETSc)
@@ -245,10 +246,10 @@ subroutine FEM_mechanical_init(fieldBC)
   allocate(pcellJ(dimPlex**2))
   allocate(pinvcellJ(dimPlex**2))
   allocate(cellJMat(dimPlex,dimPlex))
-  call PetscDSGetDiscretization(mechDS,0,mechFE,err_PETSc)
+  call PetscDSGetDiscretization(mechDS,0_pPETSCINT,mechFE,err_PETSc)
   CHKERRQ(err_PETSc)
   call PetscFEGetDualSpace(mechFE,mechDualSpace,err_PETSc); CHKERRQ(err_PETSc)
-  call DMPlexGetHeightStratum(mechanical_mesh,0,cellStart,cellEnd,err_PETSc)
+  call DMPlexGetHeightStratum(mechanical_mesh,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
   CHKERRQ(err_PETSc)
   do cell = cellStart, cellEnd-1                                                                    !< loop over all elements
     x_scal = 0.0_pReal
@@ -352,19 +353,21 @@ subroutine FEM_mechanical_formResidual(dm_local,xx_local,f_local,dummy,err_PETSc
 
   call DMGetLocalSection(dm_local,section,err_PETSc); CHKERRQ(err_PETSc)
   call DMGetDS(dm_local,prob,err_PETSc); CHKERRQ(err_PETSc)
-  call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,err_PETSc)
+  call PetscDSGetTabulation(prob,0_pPETSCINT,basisField,basisFieldDer,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMPlexGetHeightStratum(dm_local,0,cellStart,cellEnd,err_PETSc)
+  call DMPlexGetHeightStratum(dm_local,0_pPETSCINT,cellStart,cellEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMGetLocalVector(dm_local,x_local,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecWAXPY(x_local,1.0,xx_local,solution_local,err_PETSc)
   CHKERRQ(err_PETSc)
-  call DMGetLocalVector(dm_local,x_local,err_PETSc); CHKERRQ(err_PETSc)
-  call VecWAXPY(x_local,1.0,xx_local,solution_local,err_PETSc); CHKERRQ(err_PETSc)
   do field = 1, dimPlex; do face = 1, mesh_Nboundaries
     if (params%fieldBC%componentBC(field)%Mask(face)) then
       call DMGetStratumSize(dm_local,'Face Sets',mesh_boundaries(face),bcSize,err_PETSc)
       if (bcSize > 0) then
         call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
         CHKERRQ(err_PETSc)
-        call utilities_projectBCValues(x_local,section,0,field-1,bcPoints, &
+        call utilities_projectBCValues(x_local,section,0_pPETSCINT,field-1,bcPoints, &
                                        0.0_pReal,params%fieldBC%componentBC(field)%Value(face),params%timeinc)
         call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
       endif
@@ -515,7 +518,7 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,err_P
       if (bcSize > 0) then
         call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
         CHKERRQ(err_PETSc)
-        call utilities_projectBCValues(x_local,section,0,field-1,bcPoints, &
+        call utilities_projectBCValues(x_local,section,0_pPETSCINT,field-1,bcPoints, &
                                        0.0_pReal,params%fieldBC%componentBC(field)%Value(face),params%timeinc)
         call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
       endif
@@ -553,11 +556,11 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,err_P
         FInv = math_inv33(F)
         K_eA = K_eA + matmul(transpose(BMat),MatA)*math_det33(FInv)**(1.0/real(dimPlex))
         K_eB = K_eB - &
-               matmul(transpose(matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[dimPlex*dimPlex,1]), &
+               matmul(transpose(matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[dimPlex**2,1_pPETSCINT]), &
                                        matmul(reshape(FInv(1:dimPlex,1:dimPlex), &
-                                                      shape=[1,dimPlex*dimPlex],order=[2,1]),BMat))),MatA)
+                                                      shape=[1_pPETSCINT,dimPlex**2],order=[2,1]),BMat))),MatA)
         MatB = MatB &
-             + matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[1,dimPlex*dimPlex]),MatA)
+             + matmul(reshape(homogenization_F(1:dimPlex,1:dimPlex,m),shape=[1_pPETSCINT,dimPlex**2]),MatA)
         FAvg = FAvg + F
         BMatAvg = BMatAvg + BMat
       else
@@ -568,12 +571,12 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,err_P
       FInv = math_inv33(FAvg)
       K_e = K_eA*math_det33(FAvg/real(nQuadrature))**(1.0/real(dimPlex)) + &
             (matmul(matmul(transpose(BMatAvg), &
-                           reshape(FInv(1:dimPlex,1:dimPlex),shape=[dimPlex*dimPlex,1],order=[2,1])),MatB) + &
+                           reshape(FInv(1:dimPlex,1:dimPlex),shape=[dimPlex**2,1_pPETSCINT],order=[2,1])),MatB) + &
              K_eB)/real(dimPlex)
     else
       K_e = K_eA
     endif
-    K_e = (K_e + eps*math_eye(cellDof)) * abs(detJ)
+    K_e = (K_e + eps*math_eye(int(cellDof))) * abs(detJ)
 #ifndef __INTEL_COMPILER
     pK_e(1:cellDOF**2) => K_e
 #else
@@ -596,7 +599,8 @@ subroutine FEM_mechanical_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,err_P
 #if (PETSC_VERSION_MINOR < 14)
   call DMPlexCreateRigidBody(dm_local,matnull,err_PETSc); CHKERRQ(err_PETSc)
 #else
-  call DMPlexCreateRigidBody(dm_local,0,matnull,err_PETSc); CHKERRQ(err_PETSc)
+  call DMPlexCreateRigidBody(dm_local,0_pPETSCINT,matnull,err_PETSc)
+  CHKERRQ(err_PETSc)
 #endif
   call MatSetNullSpace(Jac,matnull,err_PETSc); CHKERRQ(err_PETSc)
   call MatSetNearNullSpace(Jac,matnull,err_PETSc); CHKERRQ(err_PETSc)
@@ -645,7 +649,7 @@ subroutine FEM_mechanical_forward(guess,timeinc,timeinc_old,fieldBC)
         if (bcSize > 0) then
           call DMGetStratumIS(dm_local,'Face Sets',mesh_boundaries(face),bcPoints,err_PETSc)
           CHKERRQ(err_PETSc)
-          call utilities_projectBCValues(solution_local,section,0,field-1,bcPoints, &
+          call utilities_projectBCValues(solution_local,section,0_pPETSCINT,field-1,bcPoints, &
                                          0.0_pReal,fieldBC%componentBC(field)%Value(face),timeinc_old)
           call ISDestroy(bcPoints,err_PETSc); CHKERRQ(err_PETSc)
         endif
@@ -684,7 +688,7 @@ subroutine FEM_mechanical_converged(snes_local,PETScIter,xnorm,snorm,fnorm,reaso
   if (terminallyIll) reason = SNES_DIVERGED_FUNCTION_DOMAIN
   print'(/,1x,a,a,i0,a,i0,f0.3)', trim(incInfo), &
                   ' @ Iteration ',PETScIter,' mechanical residual norm = ', &
-                                                  int(fnorm/divTol),fnorm/divTol-int(fnorm/divTol)
+                                                  int(fnorm/divTol),fnorm/divTol-int(fnorm/divTol)  ! ToDo: int casting?
   print'(/,1x,a,/,2(3(2x,f12.4,1x)/),3(2x,f12.4,1x))', &
     'Piola--Kirchhoff stress / MPa =',transpose(P_av)*1.e-6_pReal
   flush(IO_STDOUT)
@@ -697,9 +701,7 @@ end subroutine FEM_mechanical_converged
 !--------------------------------------------------------------------------------------------------
 subroutine FEM_mechanical_updateCoords()
 
-  real(pReal), pointer, dimension(:) :: &
-    nodeCoords_linear                                                                               !< nodal coordinates (dimPlex*Nnodes)
-  real(pReal), pointer, dimension(:,:) :: &
+  PetscReal, pointer, dimension(:,:) :: &
     nodeCoords                                                                                      !< nodal coordinates (3,Nnodes)
   real(pReal), pointer, dimension(:,:,:) :: &
     ipCoords                                                                                        !< ip coordinates (3,nQuadrature,mesh_NcpElems)
@@ -717,8 +719,9 @@ subroutine FEM_mechanical_updateCoords()
               cellStart, cellEnd, c, n
   PetscSection :: section
   PetscQuadrature :: mechQuad
-  PetscReal,      dimension(:),  pointer :: basisField, basisFieldDer
-  PetscScalar, dimension(:),   pointer :: x_scal
+  PetscReal, dimension(:), pointer :: basisField, basisFieldDer, &
+    nodeCoords_linear                                                                               !< nodal coordinates (dimPlex*Nnodes)
+  PetscScalar, dimension(:), pointer :: x_scal
 
   call SNESGetDM(mechanical_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
   call DMGetDS(dm_local,mechQuad,err_PETSc); CHKERRQ(err_PETSc)
@@ -727,7 +730,8 @@ subroutine FEM_mechanical_updateCoords()
   call DMGetDimension(dm_local,dimPlex,err_PETSc); CHKERRQ(err_PETSc)
 
   ! write cell vertex displacements
-  call DMPlexGetDepthStratum(dm_local,0,pStart,pEnd,err_PETSc); CHKERRQ(err_PETSc)
+  call DMPlexGetDepthStratum(dm_local,0_pPETSCINT,pStart,pEnd,err_PETSc)
+  CHKERRQ(err_PETSc)
   allocate(nodeCoords(3,pStart:pEnd-1),source=0.0_pReal)
   call VecGetArrayF90(x_local,nodeCoords_linear,err_PETSc); CHKERRQ(err_PETSc)
   do p=pStart, pEnd-1

From 45e33782e4e7ffaa1447adb78d76a3294f289968 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Thu, 13 Jan 2022 10:42:05 -0500
Subject: [PATCH 051/133] documentating more hex interactions

---
 src/lattice.f90 | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/lattice.f90 b/src/lattice.f90
index 1f824cc98..c5a237baf 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -788,15 +788,25 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
       68,68,69,  66,66,67,  64,64,65,64,64,65,  60,63,63,60,62,62,60,61,61,60,62,62,  59,58,58,57,58,58, & ! 2. pyr<c+a>
       68,69,68,  66,67,66,  65,64,64,65,64,64,  62,62,60,63,63,60,62,62,60,61,61,60,  58,59,58,58,57,58, &
       69,68,68,  67,66,66,  64,65,64,64,65,64,  61,60,62,62,60,63,63,60,62,62,60,61,  58,58,59,58,58,57  &
-      ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme and 10.1016/j.ijplas.2014.06.010 table 3)
+      ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme)
+                                                                                                    !< 10.1016/j.ijplas.2014.06.010 table 3
+                                                                                                    !< 10.1080/14786435.2012.699689 table 2 and 3
                                                                                                     !<  1: S1 basal self-interaction
                                                                                                     !<  2:  1 coplanar basal/basal
                                                                                                     !<  3:  3 collinear basal/prismatic
-                                                                                                    !<  4:  4 non-collinear basal prismatic
+                                                                                                    !<  4:  4 non-collinear basal/prismatic
                                                                                                     !<  5: S2 prismatic self-interaction
                                                                                                     !<  6:  2 prismatic/prismatic
                                                                                                     !<  7:  5 collinear prismatic/basal
                                                                                                     !<  8:  6 non-collinear prismatic/basal
+                                                                                                    !<  9:    non-collinear basal/pyr a
+                                                                                                    !< 10:    collinear basal/pyr a
+                                                                                                    !< 11:    non-collinear prismatic/pyr a
+                                                                                                    !< 12:    collinear prismatic/pyr a
+                                                                                                    !< 16:    non-collinear pyr a/prismatic
+                                                                                                    !< 17:    collinear pyr a/prismatic
+                                                                                                    !< 18:    non-collinear pyr a/basal
+                                                                                                    !< 19:    collinear pyr a/basal
                                                                                                     !< 47:  8 non-collinear basal/pyramidal
                                                                                                     !< 48:  7 collinear basal/pyramidal
                                                                                                     !< 49: 10 non-collinear prismatic/pyramidal

From db21e82fe3315bfc0f744099437a864277e3e8ca Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Thu, 13 Jan 2022 17:15:54 +0100
Subject: [PATCH 052/133] adjusted data.column retrieval in save method

---
 python/damask/_table.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index ed7c80460..0610e3140 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -1,7 +1,7 @@
 import re
 import copy
 import pathlib
-from typing import Union, Optional, Tuple, List, TextIO, Set
+from typing import Union, Optional, Tuple, List, TextIO
 from _io import TextIOWrapper
 
 import pandas as pd
@@ -9,7 +9,6 @@ import numpy as np
 
 from . import util
 
-
 class Table:
     """Manipulate multi-dimensional spreadsheet-like data."""
 
@@ -372,7 +371,7 @@ class Table:
 
         """
         dup = self.copy()
-        dup._add_comment(label, data.shape[1:],info)
+        dup._add_comment(label, data.shape[1:], info)
         m = re.match(r'(.*)\[((\d+,)*(\d+))\]',label)
         if m:
             key = m.group(1)
@@ -559,9 +558,12 @@ class Table:
             Filename or file for writing.
 
         """
-        seen: Set = set()
+        data_column_items = []
+        for col in self.data.columns:
+            if col not in data_column_items:
+                data_column_items.append(col)
         labels = []
-        for l in [x for x in self.data.columns if x not in seen]:
+        for l in data_column_items:
             if self.shapes[l] == (1,):
                 labels.append(f'{l}')
             elif len(self.shapes[l]) == 1:

From 2c054f2b38af36e8a40ac049bb355a9e3b84f816 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Thu, 13 Jan 2022 11:23:09 -0500
Subject: [PATCH 053/133] use same hex-hex interaction documentation as webpage

---
 src/lattice.f90 | 97 +++++++++++++++++++++++++++++++++++--------------
 1 file changed, 70 insertions(+), 27 deletions(-)

diff --git a/src/lattice.f90 b/src/lattice.f90
index c5a237baf..e18c71edf 100644
--- a/src/lattice.f90
+++ b/src/lattice.f90
@@ -791,33 +791,76 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,lattice) result(
       ],shape(HEX_INTERACTIONSLIPSLIP))                                                             !< Slip-slip interaction types for hex (onion peel naming scheme)
                                                                                                     !< 10.1016/j.ijplas.2014.06.010 table 3
                                                                                                     !< 10.1080/14786435.2012.699689 table 2 and 3
-                                                                                                    !<  1: S1 basal self-interaction
-                                                                                                    !<  2:  1 coplanar basal/basal
-                                                                                                    !<  3:  3 collinear basal/prismatic
-                                                                                                    !<  4:  4 non-collinear basal/prismatic
-                                                                                                    !<  5: S2 prismatic self-interaction
-                                                                                                    !<  6:  2 prismatic/prismatic
-                                                                                                    !<  7:  5 collinear prismatic/basal
-                                                                                                    !<  8:  6 non-collinear prismatic/basal
-                                                                                                    !<  9:    non-collinear basal/pyr a
-                                                                                                    !< 10:    collinear basal/pyr a
-                                                                                                    !< 11:    non-collinear prismatic/pyr a
-                                                                                                    !< 12:    collinear prismatic/pyr a
-                                                                                                    !< 16:    non-collinear pyr a/prismatic
-                                                                                                    !< 17:    collinear pyr a/prismatic
-                                                                                                    !< 18:    non-collinear pyr a/basal
-                                                                                                    !< 19:    collinear pyr a/basal
-                                                                                                    !< 47:  8 non-collinear basal/pyramidal
-                                                                                                    !< 48:  7 collinear basal/pyramidal
-                                                                                                    !< 49: 10 non-collinear prismatic/pyramidal
-                                                                                                    !< 50:  9 collinear prismatic/pyramidal
-                                                                                                    !< 57: S3 pyramidal c+a self-interaction
-                                                                                                    !< 58: 16 non-collinear pyramidal/pyramidal
-                                                                                                    !< 59: 15 collinear pyramidal/pyramidal
-                                                                                                    !< 66: 14 non-collienar pyramidal/prismatic
-                                                                                                    !< 67: 13 semi-collienar pyramidal/prismatic
-                                                                                                    !< 68: 12 non-collinear pyramidal/basal
-                                                                                                    !< 69: 11 semi-collinear pyramidal/basal
+                                                                                                    !< index & label & description
+                                                                                                    !<  1 & S1 & basal self-interaction
+                                                                                                    !<  2 &  1 & basal/basal coplanar
+                                                                                                    !<  3 &  3 & basal/prismatic collinear
+                                                                                                    !<  4 &  4 & basal/prismatic non-collinear
+                                                                                                    !<  5 & S2 & prismatic self-interaction
+                                                                                                    !<  6 &  2 & prismatic/prismatic
+                                                                                                    !<  7 &  5 & prismatic/basal collinear
+                                                                                                    !<  8 &  6 & prismatic/basal non-collinear
+                                                                                                    !<  9 &  - & basal/pyramidal <a> non-collinear
+                                                                                                    !< 10 &  - & basal/pyramidal <a> collinear
+                                                                                                    !< 11 &  - & prismatic/pyramidal <a> non-collinear
+                                                                                                    !< 12 &  - & prismatic/pyramidal <a> collinear
+                                                                                                    !< 13 &  - & pyramidal <a> self-interaction
+                                                                                                    !< 14 &  - & pyramidal <a> non-collinear
+                                                                                                    !< 15 &  - & pyramidal <a> collinear
+                                                                                                    !< 16 &  - & pyramidal <a>/prismatic non-collinear
+                                                                                                    !< 17 &  - & pyramidal <a>/prismatic collinear
+                                                                                                    !< 18 &  - & pyramidal <a>/basal non-collinear
+                                                                                                    !< 19 &  - & pyramidal <a>/basal collinear
+                                                                                                    !< 20 &  - & basal/1. order pyramidal <c+a> semi-collinear
+                                                                                                    !< 21 &  - & basal/1. order pyramidal <c+a>
+                                                                                                    !< 22 &  - & basal/1. order pyramidal <c+a>
+                                                                                                    !< 23 &  - & prismatic/1. order pyramidal <c+a> semi-collinear
+                                                                                                    !< 24 &  - & prismatic/1. order pyramidal <c+a>
+                                                                                                    !< 25 &  - & prismatic/1. order pyramidal <c+a> semi-coplanar?
+                                                                                                    !< 26 &  - & pyramidal <a>/1. order pyramidal <c+a> coplanar
+                                                                                                    !< 27 &  - & pyramidal <a>/1. order pyramidal <c+a>
+                                                                                                    !< 28 &  - & pyramidal <a>/1. order pyramidal <c+a> semi-collinear
+                                                                                                    !< 29 &  - & pyramidal <a>/1. order pyramidal <c+a> semi-coplanar
+                                                                                                    !< 30 &  - & 1. order pyramidal <c+a> self-interaction
+                                                                                                    !< 31 &  - & 1. order pyramidal <c+a> coplanar
+                                                                                                    !< 32 &  - & 1. order pyramidal <c+a>
+                                                                                                    !< 33 &  - & 1. order pyramidal <c+a>
+                                                                                                    !< 34 &  - & 1. order pyramidal <c+a> semi-coplanar
+                                                                                                    !< 35 &  - & 1. order pyramidal <c+a> semi-coplanar
+                                                                                                    !< 36 &  - & 1. order pyramidal <c+a> collinear
+                                                                                                    !< 37 &  - & 1. order pyramidal <c+a>/pyramidal <a> coplanar
+                                                                                                    !< 38 &  - & 1. order pyramidal <c+a>/pyramidal <a> semi-collinear
+                                                                                                    !< 39 &  - & 1. order pyramidal <c+a>/pyramidal <a>
+                                                                                                    !< 40 &  - & 1. order pyramidal <c+a>/pyramidal <a> semi-coplanar
+                                                                                                    !< 41 &  - & 1. order pyramidal <c+a>/prismatic semi-collinear
+                                                                                                    !< 42 &  - & 1. order pyramidal <c+a>/prismatic semi-coplanar
+                                                                                                    !< 43 &  - & 1. order pyramidal <c+a>/prismatic
+                                                                                                    !< 44 &  - & 1. order pyramidal <c+a>/basal semi-collinear
+                                                                                                    !< 45 &  - & 1. order pyramidal <c+a>/basal
+                                                                                                    !< 46 &  - & 1. order pyramidal <c+a>/basal
+                                                                                                    !< 47 &  8 & basal/2. order pyramidal <c+a> non-collinear
+                                                                                                    !< 48 &  7 & basal/2. order pyramidal <c+a> semi-collinear
+                                                                                                    !< 49 & 10 & prismatic/2. order pyramidal <c+a>
+                                                                                                    !< 50 &  9 & prismatic/2. order pyramidal <c+a> semi-collinear
+                                                                                                    !< 51 &  - & pyramidal <a>/2. order pyramidal <c+a>
+                                                                                                    !< 52 &  - & pyramidal <a>/2. order pyramidal <c+a> semi collinear
+                                                                                                    !< 53 &  - & 1. order pyramidal <c+a>/2. order pyramidal <c+a>
+                                                                                                    !< 54 &  - & 1. order pyramidal <c+a>/2. order pyramidal <c+a>
+                                                                                                    !< 55 &  - & 1. order pyramidal <c+a>/2. order pyramidal <c+a>
+                                                                                                    !< 56 &  - & 1. order pyramidal <c+a>/2. order pyramidal <c+a> collinear
+                                                                                                    !< 57 & S3 & 2. order pyramidal <c+a> self-interaction
+                                                                                                    !< 58 & 16 & 2. order pyramidal <c+a> non-collinear
+                                                                                                    !< 59 & 15 & 2. order pyramidal <c+a> semi-collinear
+                                                                                                    !< 60 &  - & 2. order pyramidal <c+a>/1. order pyramidal <c+a>
+                                                                                                    !< 61 &  - & 2. order pyramidal <c+a>/1. order pyramidal <c+a> collinear
+                                                                                                    !< 62 &  - & 2. order pyramidal <c+a>/1. order pyramidal <c+a>
+                                                                                                    !< 63 &  - & 2. order pyramidal <c+a>/1. order pyramidal <c+a>
+                                                                                                    !< 64 &  - & 2. order pyramidal <c+a>/pyramidal <a> non-collinear
+                                                                                                    !< 65 &  - & 2. order pyramidal <c+a>/pyramidal <a> semi-collinear
+                                                                                                    !< 66 & 14 & 2. order pyramidal <c+a>/prismatic non-collinear
+                                                                                                    !< 67 & 13 & 2. order pyramidal <c+a>/prismatic semi-collinear
+                                                                                                    !< 68 & 12 & 2. order pyramidal <c+a>/basal non-collinear
+                                                                                                    !< 69 & 11 & 2. order pyramidal <c+a>/basal semi-collinear
 
   integer, dimension(BCT_NSLIP,BCT_NSLIP), parameter :: &
     BCT_INTERACTIONSLIPSLIP = reshape( [&

From 6da3f0fa51a77b2a5b1351e07acdec6aba41f3d9 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 14 Jan 2022 07:24:12 +0100
Subject: [PATCH 054/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-389-ga000e477c

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index fe2ec0531..11b9d06bd 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-379-g731222d09
+v3.0.0-alpha5-389-ga000e477c

From dd82c3c8f07add648ddac84c9295dbd94704ee38 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Fri, 14 Jan 2022 15:08:40 +0100
Subject: [PATCH 055/133] rewrote table module adjustments to not make use of
 _io module

---
 python/damask/_table.py | 25 +++++++++----------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index 0610e3140..2221ab318 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -2,7 +2,6 @@ import re
 import copy
 import pathlib
 from typing import Union, Optional, Tuple, List, TextIO
-from _io import TextIOWrapper
 
 import pandas as pd
 import numpy as np
@@ -238,15 +237,13 @@ class Table:
         -------
         loaded : damask.Table
             Table data from file.
-
+            
         """
-        if isinstance(fname, TextIOWrapper):
-            f = fname
-            f.seek(0)
-        elif isinstance(fname, (str, pathlib.Path)):
+        if isinstance(fname, (str, pathlib.Path)):
             f = open(fname)
         else:
-            raise TypeError
+            f = fname
+            f.seek(0)
 
         comments = []
         line = f.readline().strip()
@@ -299,13 +296,11 @@ class Table:
             Table data from file.
 
         """
-        if isinstance(fname, TextIOWrapper):
-            f = fname
-            f.seek(0)
-        elif isinstance(fname, (str, pathlib.Path)):
+        if isinstance(fname, (str, pathlib.Path)):
             f = open(fname)
         else:
-            raise TypeError
+            f = fname
+            f.seek(0)
 
         content = f.readlines()
 
@@ -573,12 +568,10 @@ class Table:
                 labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                           for i in range(np.prod(self.shapes[l]))]
 
-        if isinstance(fname, TextIOWrapper):
-            fhandle = fname
-        elif isinstance(fname, (str, pathlib.Path)):
+        if isinstance(fname, (str, pathlib.Path)):
             fhandle = open(fname,'w',newline='\n')
         else:
-            raise TypeError
+            fhandle = fname
 
         fhandle.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
         self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)

From 6324ffcb9e9d2abe11764f4c98f4b7ba5302ccd5 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 14 Jan 2022 15:51:02 +0100
Subject: [PATCH 056/133] more robust update of VERSION file

update version only if no push to development has occured in the
meantime.

Less error prone.  Very small change for race condition remains
---
 .gitlab-ci.yml | 25 ++++++++-----------------
 1 file changed, 8 insertions(+), 17 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1bf5cf8b1..c27c90bce 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -172,6 +172,10 @@ Marc:
 ###################################################################################################
 grid_runtime:
   stage: performance
+  before_script:
+    - ${LOCAL_HOME}/bin/queue ${CI_JOB_ID} --blocking
+    - source env/DAMASK.sh
+    - echo Job start:" $(date)"
   script:
     - module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
     - cd $(mktemp -d)
@@ -186,10 +190,6 @@ grid_runtime:
         --output_dir ./
         --tag ${CI_COMMIT_SHA}
     - if [ ${CI_COMMIT_BRANCH} == development ]; then git commit -am ${CI_PIPELINE_ID}_${CI_COMMIT_SHA}; git push; fi
-  before_script:
-    - ${LOCAL_HOME}/bin/queue ${CI_JOB_ID} --blocking
-    - source env/DAMASK.sh
-    - echo Job start:" $(date)"
 
 
 ###################################################################################################
@@ -209,19 +209,10 @@ update_revision:
   script:
     - cd $(mktemp -d)
     - git clone -q git@git.damask.mpie.de:damask/DAMASK.git .
-    - git checkout ${CI_COMMIT_SHA}
-    - export VERSION=$(git describe)
+    - git pull
+    - export VERSION=$(git describe ${CI_COMMIT_SHA})
     - echo ${VERSION} > python/damask/VERSION
-    - git add python/damask/VERSION
-    - git commit -m "[skip ci] updated version information after successful test of $VERSION"
-    - export UPDATEDREV=$(git describe)                                                             # tested state + 1 commit
-    - git checkout master
-    - git pull
-    - git merge $UPDATEDREV -s recursive -X ours                                                    # conflicts occur only for inconsistent state
-    - git push
-    - git checkout development
-    - git pull
-    - git merge master -s recursive -X ours -m "[skip ci] Merge branch 'master' into development"   # only possible conflict is in VERSION file
-    - git push origin development                                                                   # development is unchanged (as master is based on it) but has updated VERSION file
+    - git commit python/damask/VERSION -m "[skip ci] updated version information after successful test of $VERSION"
+    - if [ ${CI_COMMIT_SHA} == $(git rev-parse HEAD^) ]; then git push origin HEAD:master HEAD:development; fi
   only:
     - development

From 01cc6ffd2c0df6e9ffba8e00c9f3b05353a124bc Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Fri, 14 Jan 2022 17:56:58 +0100
Subject: [PATCH 057/133] added minor grid adjustments after initial merge of
 typehints_grid branch

---
 python/damask/_grid.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 5006e1b40..ed1b2b57f 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -4,7 +4,7 @@ import warnings
 import multiprocessing as mp
 from functools import partial
 import typing
-from typing import Union, Optional, TextIO, List, Sequence
+from typing import Union, Optional, TextIO, List, Sequence, Literal, Dict, Callable
 from pathlib import Path
 
 import numpy as np
@@ -422,6 +422,7 @@ class Grid:
             Grid-based geometry from tessellation.
 
         """
+        weights_p: FloatSequence
         if periodic:
             weights_p = np.tile(weights,27)                                                         # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
             seeds_p = np.vstack((seeds  -np.array([size[0],0.,0.]),seeds,  seeds  +np.array([size[0],0.,0.])))
@@ -821,7 +822,7 @@ class Grid:
                    )
 
 
-    def flip(self, directions: Sequence[str]) -> "Grid":
+    def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> "Grid":
         """
         Flip grid along given directions.
 
@@ -841,7 +842,8 @@ class Grid:
         if not set(directions).issubset(valid):
             raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
 
-        mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
+
+        mat = np.flip(self.material, [valid.index(d) for d in directions if d in valid])
 
         return Grid(material = mat,
                     size     = self.size,
@@ -1034,7 +1036,7 @@ class Grid:
         if fill is None: fill = np.nanmax(self.material) + 1
         dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
 
-        canvas = np.full(cells_,fill,dtype)
+        canvas: np.ndarray = np.full(cells_,fill,dtype)
 
         LL = np.clip( offset_,           0,np.minimum(self.cells,     cells_+offset_))
         UR = np.clip( offset_+cells_,    0,np.minimum(self.cells,     cells_+offset_))
@@ -1067,13 +1069,13 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def mp(entry, mapper):
+        def mp(entry: np.ndarray, mapper:Dict[np.ndarray, np.ndarray]) -> np.ndarray:
             return mapper[entry] if entry in mapper else entry
 
-        mp = np.vectorize(mp)
+        mp_: Callable = np.vectorize(mp)
         mapper = dict(zip(from_material,to_material))
 
-        return Grid(material = mp(self.material,mapper).reshape(self.cells),
+        return Grid(material = mp_(self.material,mapper).reshape(self.cells),
                     size     = self.size,
                     origin   = self.origin,
                     comments = self.comments+[util.execution_stamp('Grid','substitute')],

From b796bc0697edf9978ae461e433eb6fe7b8ea78ef Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 14 Jan 2022 20:44:34 +0100
Subject: [PATCH 058/133] simplified

---
 python/damask/_grid.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index ed1b2b57f..9b24e5600 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -4,7 +4,7 @@ import warnings
 import multiprocessing as mp
 from functools import partial
 import typing
-from typing import Union, Optional, TextIO, List, Sequence, Literal, Dict, Callable
+from typing import Union, Optional, TextIO, List, Sequence, Literal
 from pathlib import Path
 
 import numpy as np
@@ -1069,13 +1069,11 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def mp(entry: np.ndarray, mapper:Dict[np.ndarray, np.ndarray]) -> np.ndarray:
-            return mapper[entry] if entry in mapper else entry
+        material = self.material.copy()
+        for f,t in zip(from_material,to_material):        # ToDo Python 3.10 has strict mode for zip
+            material[self.material==f] = t
 
-        mp_: Callable = np.vectorize(mp)
-        mapper = dict(zip(from_material,to_material))
-
-        return Grid(material = mp_(self.material,mapper).reshape(self.cells),
+        return Grid(material = material,
                     size     = self.size,
                     origin   = self.origin,
                     comments = self.comments+[util.execution_stamp('Grid','substitute')],

From 8a17cef28cdfe323bc72a72041281705616f351a Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 15 Jan 2022 00:20:29 +0100
Subject: [PATCH 059/133] using AGPL instead of GPL

ensures back-contributions for cloud-based services
---
 COPYING | 110 ++++++++++++++++++++++++++++----------------------------
 LICENSE |  10 +++---
 2 files changed, 59 insertions(+), 61 deletions(-)

diff --git a/COPYING b/COPYING
index bc08fe2e4..bbba84b05 100644
--- a/COPYING
+++ b/COPYING
@@ -1,23 +1,21 @@
-                    GNU GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
                             Preamble
 
-  The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
+  The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
 
   The licenses for most software and other practical works are designed
 to take away your freedom to share and change the works.  By contrast,
-the GNU General Public License is intended to guarantee your freedom to
+our General Public Licenses are intended to guarantee your freedom to
 share and change all versions of a program--to make sure it remains free
-software for all its users.  We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors.  You can apply it to
-your programs, too.
+software for all its users.
 
   When we speak of free software, we are referring to freedom, not
 price.  Our General Public Licenses are designed to make sure that you
@@ -26,44 +24,34 @@ them if you wish), that you receive source code or can get it if you
 want it, that you can change the software or use pieces of it in new
 free programs, and that you know you can do these things.
 
-  To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights.  Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
+  Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
 
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received.  You must make sure that they, too, receive
-or can get the source code.  And you must show them these terms so they
-know their rights.
+  A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate.  Many developers of free software are heartened and
+encouraged by the resulting cooperation.  However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
 
-  Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
+  The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community.  It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server.  Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
 
-  For the developers' and authors' protection, the GPL clearly explains
-that there is no warranty for this free software.  For both users' and
-authors' sake, the GPL requires that modified versions be marked as
-changed, so that their problems will not be attributed erroneously to
-authors of previous versions.
-
-  Some devices are designed to deny users access to install or run
-modified versions of the software inside them, although the manufacturer
-can do so.  This is fundamentally incompatible with the aim of
-protecting users' freedom to change the software.  The systematic
-pattern of such abuse occurs in the area of products for individuals to
-use, which is precisely where it is most unacceptable.  Therefore, we
-have designed this version of the GPL to prohibit the practice for those
-products.  If such problems arise substantially in other domains, we
-stand ready to extend this provision to those domains in future versions
-of the GPL, as needed to protect the freedom of users.
-
-  Finally, every program is threatened constantly by software patents.
-States should not allow patents to restrict development and use of
-software on general-purpose computers, but in those that do, we wish to
-avoid the special danger that patents applied to a free program could
-make it effectively proprietary.  To prevent this, the GPL assures that
-patents cannot be used to render the program non-free.
+  An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals.  This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
 
   The precise terms and conditions for copying, distribution and
 modification follow.
@@ -72,7 +60,7 @@ modification follow.
 
   0. Definitions.
 
-  "This License" refers to version 3 of the GNU General Public License.
+  "This License" refers to version 3 of the GNU Affero General Public License.
 
   "Copyright" also means copyright-like laws that apply to other kinds of
 works, such as semiconductor masks.
@@ -549,35 +537,45 @@ to collect a royalty for further conveying from those to whom you convey
 the Program, the only way you could satisfy both those terms and this
 License would be to refrain entirely from conveying the Program.
 
-  13. Use with the GNU Affero General Public License.
+  13. Remote Network Interaction; Use with the GNU General Public License.
+
+  Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software.  This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
 
   Notwithstanding any other provision of this License, you have
 permission to link or combine any covered work with a work licensed
-under version 3 of the GNU Affero General Public License into a single
+under version 3 of the GNU General Public License into a single
 combined work, and to convey the resulting work.  The terms of this
 License will continue to apply to the part which is the covered work,
-but the special requirements of the GNU Affero General Public License,
-section 13, concerning interaction through a network will apply to the
-combination as such.
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
 
   14. Revised Versions of this License.
 
   The Free Software Foundation may publish revised and/or new versions of
-the GNU General Public License from time to time.  Such new versions will
-be similar in spirit to the present version, but may differ in detail to
+the GNU Affero General Public License from time to time.  Such new versions
+will be similar in spirit to the present version, but may differ in detail to
 address new problems or concerns.
 
   Each version is given a distinguishing version number.  If the
-Program specifies that a certain numbered version of the GNU General
+Program specifies that a certain numbered version of the GNU Affero General
 Public License "or any later version" applies to it, you have the
 option of following the terms and conditions either of that numbered
 version or of any later version published by the Free Software
 Foundation.  If the Program does not specify a version number of the
-GNU General Public License, you may choose any version ever published
+GNU Affero General Public License, you may choose any version ever published
 by the Free Software Foundation.
 
   If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
+versions of the GNU Affero General Public License can be used, that proxy's
 public statement of acceptance of a version permanently authorizes you
 to choose that version for the Program.
 
diff --git a/LICENSE b/LICENSE
index 0aaac06e9..b4318ac92 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,14 +1,14 @@
 Copyright 2011-2021 Max-Planck-Institut für Eisenforschung GmbH
 
 DAMASK is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
+it under the terms of the GNU Affero General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
 
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.

From d1cd125a5bda0ce92a52979676fb06a1efabec1b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 15 Jan 2022 12:19:53 +0100
Subject: [PATCH 060/133] direct array reversal, don't duplicate FFTW manual

---
 src/grid/spectral_utilities.f90 | 66 ++++++++++++++++-----------------
 1 file changed, 33 insertions(+), 33 deletions(-)

diff --git a/src/grid/spectral_utilities.f90 b/src/grid/spectral_utilities.f90
index f40025039..3dfb87243 100644
--- a/src/grid/spectral_utilities.f90
+++ b/src/grid/spectral_utilities.f90
@@ -37,7 +37,7 @@ module spectral_utilities
 !--------------------------------------------------------------------------------------------------
 ! variables storing information for spectral method and FFTW
 
-  real   (C_DOUBLE),        public,  dimension(:,:,:,:,:),     pointer     :: tensorField_real      !< real representation (some stress or deformation) of field_fourier
+  real(C_DOUBLE),           public,  dimension(:,:,:,:,:),     pointer     :: tensorField_real      !< real representation (some stress or deformation) of field_fourier
   complex(C_DOUBLE_COMPLEX),public,  dimension(:,:,:,:,:),     pointer     :: tensorField_fourier   !< field on which the Fourier transform operates
   real(C_DOUBLE),           public,  dimension(:,:,:,:),       pointer     :: vectorField_real      !< vector field real representation for fftw
   complex(C_DOUBLE_COMPLEX),public,  dimension(:,:,:,:),       pointer     :: vectorField_fourier   !< vector field fourier representation for fftw
@@ -156,7 +156,7 @@ subroutine spectral_utilities_init
   integer(C_INTPTR_T) :: alloc_local, local_K, local_K_offset
   integer(C_INTPTR_T), parameter :: &
     scalarSize = 1_C_INTPTR_T, &
-    vecSize    = 3_C_INTPTR_T, &
+    vectorSize = 3_C_INTPTR_T, &
     tensorSize = 9_C_INTPTR_T
   character(len=*), parameter :: &
     PETSCDEBUG = ' -snes_view -snes_monitor '
@@ -274,7 +274,7 @@ subroutine spectral_utilities_init
   call c_f_pointer(tensorField, tensorField_fourier, [3_C_INTPTR_T,3_C_INTPTR_T, &
                    gridFFTW(1)/2_C_INTPTR_T + 1_C_INTPTR_T ,              gridFFTW(2),local_K])     ! place a pointer for a fourier tensor representation
 
-  vectorField = fftw_alloc_complex(vecSize*alloc_local)
+  vectorField = fftw_alloc_complex(vectorSize*alloc_local)
   call c_f_pointer(vectorField, vectorField_real,   [3_C_INTPTR_T,&
                    2_C_INTPTR_T*(gridFFTW(1)/2_C_INTPTR_T + 1_C_INTPTR_T),gridFFTW(2),local_K])     ! place a pointer for a real vector representation
   call c_f_pointer(vectorField, vectorField_fourier,[3_C_INTPTR_T,&
@@ -288,42 +288,42 @@ subroutine spectral_utilities_init
 
 !--------------------------------------------------------------------------------------------------
 ! tensor MPI fftw plans
-  planTensorForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], &          ! dimension, logical length in each dimension in reversed order
-                                        tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
-                                                       tensorField_real, tensorField_fourier, &     ! input data, output data
-                                                               PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
-  if (.not. C_ASSOCIATED(planTensorForth)) error stop 'FFTW error'
-  planTensorBack  = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], &          ! dimension, logical length in each dimension in reversed order
-                                       tensorSize,  FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
-                                                        tensorField_fourier,tensorField_real, &     ! input data, output data
-                                                               PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
-  if (.not. C_ASSOCIATED(planTensorBack)) error stop 'FFTW error'
+  planTensorForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),tensorSize, &
+                                               FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
+                                               tensorField_real,tensorField_fourier, &
+                                               PETSC_COMM_WORLD,FFTW_planner_flag)
+  if (.not. c_associated(planTensorForth)) error stop 'FFTW error'
+  planTensorBack  = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),tensorSize, &
+                                               FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
+                                               tensorField_fourier,tensorField_real, &
+                                               PETSC_COMM_WORLD, FFTW_planner_flag)
+  if (.not. c_associated(planTensorBack)) error stop 'FFTW error'
 
 !--------------------------------------------------------------------------------------------------
 ! vector MPI fftw plans
-  planVectorForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], &          ! dimension, logical length in each dimension in reversed order
-                                           vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK,&! no. of transforms, default iblock and oblock
-                                                       vectorField_real, vectorField_fourier, &     ! input data, output data
-                                                               PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
-  if (.not. C_ASSOCIATED(planVectorForth)) error stop 'FFTW error'
-  planVectorBack  = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)],  &         ! dimension, logical length in each dimension in reversed order
-                                         vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, & ! no. of transforms, default iblock and oblock
-                                                      vectorField_fourier,vectorField_real, &       ! input data, output data
-                                                               PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
-  if (.not. C_ASSOCIATED(planVectorBack)) error stop 'FFTW error'
+  planVectorForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),vectorSize, &
+                                               FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
+                                               vectorField_real,vectorField_fourier, &
+                                               PETSC_COMM_WORLD,FFTW_planner_flag)
+  if (.not. c_associated(planVectorForth)) error stop 'FFTW error'
+  planVectorBack  = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),vectorSize, &
+                                               FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
+                                               vectorField_fourier,vectorField_real, &
+                                               PETSC_COMM_WORLD, FFTW_planner_flag)
+  if (.not. c_associated(planVectorBack)) error stop 'FFTW error'
 
 !--------------------------------------------------------------------------------------------------
 ! scalar MPI fftw plans
-  planScalarForth = fftw_mpi_plan_many_dft_r2c(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], &          ! dimension, logical length in each dimension in reversed order
-                                       scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
-                                                       scalarField_real, scalarField_fourier, &     ! input data, output data
-                                                               PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
-  if (.not. C_ASSOCIATED(planScalarForth)) error stop 'FFTW error'
-  planScalarBack  = fftw_mpi_plan_many_dft_c2r(3, [gridFFTW(3),gridFFTW(2),gridFFTW(1)], &          ! dimension, logical length in each dimension in reversed order, no. of transforms
-                                       scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
-                                                       scalarField_fourier,scalarField_real, &      ! input data, output data
-                                                               PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
-  if (.not. C_ASSOCIATED(planScalarBack)) error stop 'FFTW error'
+  planScalarForth = fftw_mpi_plan_many_dft_r2c(3,gridFFTW(3:1:-1),scalarSize, &
+                                               FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK, &
+                                               scalarField_real,scalarField_fourier, &
+                                               PETSC_COMM_WORLD,FFTW_planner_flag)
+  if (.not. c_associated(planScalarForth)) error stop 'FFTW error'
+  planScalarBack  = fftw_mpi_plan_many_dft_c2r(3,gridFFTW(3:1:-1),scalarSize, &
+                                               FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &
+                                               scalarField_fourier,scalarField_real, &
+                                               PETSC_COMM_WORLD, FFTW_planner_flag)
+  if (.not. c_associated(planScalarBack)) error stop 'FFTW error'
 
 !--------------------------------------------------------------------------------------------------
 ! calculation of discrete angular frequencies, ordered as in FFTW (wrap around)

From a37178ddeea46c8f4ab44dadcd1d1c0c22a12eb0 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 15 Jan 2022 12:28:39 +0100
Subject: [PATCH 061/133] handle case of -0.0

-0.0 < 0.0 ! false
so need sign to change direction for also for the corner case of -0.0
---
 src/rotations.f90 | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/rotations.f90 b/src/rotations.f90
index b4728e38b..7629060cb 100644
--- a/src/rotations.f90
+++ b/src/rotations.f90
@@ -270,7 +270,7 @@ pure elemental subroutine standardize(self)
 
   class(rotation), intent(inout) :: self
 
-  if (self%q(1) < 0.0_pReal) self%q = - self%q
+  if (sign(1.0_pReal,self%q(1)) < 0.0_pReal) self%q = - self%q
 
 end subroutine standardize
 
@@ -450,7 +450,7 @@ pure function qu2om(qu) result(om)
   om(3,2) = 2.0_pReal*(qu(4)*qu(3)+qu(1)*qu(2))
   om(1,3) = 2.0_pReal*(qu(2)*qu(4)+qu(1)*qu(3))
 
-  if (P < 0.0_pReal) om = transpose(om)
+  if (sign(1.0_pReal,P) < 0.0_pReal) om = transpose(om)
 
 end function qu2om
 
@@ -480,7 +480,7 @@ pure function qu2eu(qu) result(eu)
           atan2( 2.0_pReal*chi, q03-q12 ), &
           atan2(( P*qu(1)*qu(3)+qu(2)*qu(4))*chi, (-P*qu(1)*qu(2)+qu(3)*qu(4))*chi )]
   endif degenerated
-  where(eu<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
+  where(sign(1.0_pReal,eu)<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
 
 end function qu2eu
 
@@ -602,7 +602,7 @@ pure function om2qu(om) result(qu)
           qu = [ (om(2,1) - om(1,2)) /s,(om(1,3) + om(3,1)) / s,(om(2,3) + om(3,2)) / s,0.25_pReal * s]
       endif
   endif
-  if(qu(1)<0._pReal) qu =-1.0_pReal * qu
+  if(sign(1.0_pReal,qu(1))<0.0_pReal) qu =-1.0_pReal * qu
   qu = qu*[1.0_pReal,P,P,P]
 
 end function om2qu
@@ -628,7 +628,7 @@ pure function om2eu(om) result(eu)
     eu = [atan2(om(1,2),om(1,1)), 0.5_pReal*PI*(1.0_pReal-om(3,3)),0.0_pReal ]
   end if
   where(abs(eu) < 1.e-8_pReal) eu = 0.0_pReal
-  where(eu<0.0_pReal)          eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
+  where(sign(1.0_pReal,eu)<0.0_pReal) eu = mod(eu+2.0_pReal*PI,[2.0_pReal*PI,PI,2.0_pReal*PI])
 
 end function om2eu
 
@@ -735,7 +735,7 @@ pure function eu2qu(eu) result(qu)
         -P*sPhi*cos(ee(1)-ee(3)), &
         -P*sPhi*sin(ee(1)-ee(3)), &
         -P*cPhi*sin(ee(1)+ee(3))]
-  if(qu(1) < 0.0_pReal) qu = qu * (-1.0_pReal)
+  if(sign(1.0_pReal,qu(1)) < 0.0_pReal) qu = qu * (-1.0_pReal)
 
 end function eu2qu
 
@@ -792,7 +792,7 @@ pure function eu2ax(eu) result(ax)
   else
     ax(1:3) = -P/tau * [ t*cos(delta), t*sin(delta), sin(sigma) ]                                   ! passive axis-angle pair so a minus sign in front
     ax(4) = alpha
-    if (alpha < 0.0_pReal) ax = -ax                                                                 ! ensure alpha is positive
+    if (sign(1.0_pReal,alpha) < 0.0_pReal) ax = -ax                                                                 ! ensure alpha is positive
   end if
 
 end function eu2ax

From 6657e5c4ebbbfa997cbbf6a5a121dbba90abc4b4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 15 Jan 2022 13:22:15 +0100
Subject: [PATCH 062/133] testing a few corner cases

behavior for __eq__ is now following python standard, comparing to wrong
class gives False
---
 python/damask/_result.py         | 2 +-
 python/tests/test_Colormap.py    | 1 +
 python/tests/test_Crystal.py     | 3 +++
 python/tests/test_Grid.py        | 1 +
 python/tests/test_Orientation.py | 9 +++++++++
 python/tests/test_Result.py      | 3 +++
 python/tests/test_Rotation.py    | 9 +++++++++
 7 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/python/damask/_result.py b/python/damask/_result.py
index c87b51a89..02d4174c9 100644
--- a/python/damask/_result.py
+++ b/python/damask/_result.py
@@ -981,7 +981,7 @@ class Result:
             t = 'tensor'
             if o is None: o = 'fro'
         else:
-            raise ValueError(f'invalid norm order {ord}')
+            raise ValueError(f'invalid shape of {x["label"]}')
 
         return {
                 'data':  np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
diff --git a/python/tests/test_Colormap.py b/python/tests/test_Colormap.py
index 156907670..2321745aa 100644
--- a/python/tests/test_Colormap.py
+++ b/python/tests/test_Colormap.py
@@ -81,6 +81,7 @@ class TestColormap:
         assert Colormap.from_predefined('strain') == Colormap.from_predefined('strain')
         assert Colormap.from_predefined('strain') != Colormap.from_predefined('stress')
         assert Colormap.from_predefined('strain',N=128) != Colormap.from_predefined('strain',N=64)
+        assert not Colormap.from_predefined('strain',N=128) == 1
 
     @pytest.mark.parametrize('low,high',[((0,0,0),(1,1,1)),
                                          ([0,0,0],[1,1,1])])
diff --git a/python/tests/test_Crystal.py b/python/tests/test_Crystal.py
index 9c6de965d..235ed554a 100644
--- a/python/tests/test_Crystal.py
+++ b/python/tests/test_Crystal.py
@@ -40,6 +40,9 @@ class TestCrystal:
                     alpha=alpha,beta=beta,gamma=gamma)
         assert np.allclose(np.eye(3),np.einsum('ik,jk',c.basis_real,c.basis_reciprocal))
 
+    def test_basis_invalid(self):
+        with pytest.raises(KeyError):
+            Crystal(family='cubic').basis_real
 
     @pytest.mark.parametrize('keyFrame,keyLattice',[('uvw','direction'),('hkl','plane'),])
     @pytest.mark.parametrize('vector',np.array([
diff --git a/python/tests/test_Grid.py b/python/tests/test_Grid.py
index 2b9ca22f4..6dd94f4bb 100644
--- a/python/tests/test_Grid.py
+++ b/python/tests/test_Grid.py
@@ -44,6 +44,7 @@ class TestGrid:
 
     def test_equal(self,default):
         assert default == default
+        assert not default == 42
 
     def test_repr(self,default):
         print(default)
diff --git a/python/tests/test_Orientation.py b/python/tests/test_Orientation.py
index 9f623fc6c..2a32adea4 100644
--- a/python/tests/test_Orientation.py
+++ b/python/tests/test_Orientation.py
@@ -364,6 +364,11 @@ class TestOrientation:
                 table.save(reference)
             assert np.allclose(P,Table.load(reference).get('Schmid'))
 
+    def test_Schmid_invalid(self):
+        with pytest.raises(KeyError):
+            Orientation(lattice='fcc').Schmid()
+
+
 ### vectorization tests ###
 
     @pytest.mark.parametrize('lattice',['hP','cI','cF']) # tI not included yet
@@ -505,3 +510,7 @@ class TestOrientation:
         for loc in np.random.randint(0,blend,(10,len(blend))):
             assert np.allclose(o[tuple(loc[:len(o.shape)])].to_pole(uvw=v[tuple(loc[-len(v.shape[:-1]):])]),
                                o.to_pole(uvw=v)[tuple(loc)])
+
+    def test_mul_invalid(self):
+        with pytest.raises(TypeError):
+            Orientation.from_random(lattice='cF')*np.ones(3)
diff --git a/python/tests/test_Result.py b/python/tests/test_Result.py
index 4fea08eb3..1da56dedf 100644
--- a/python/tests/test_Result.py
+++ b/python/tests/test_Result.py
@@ -102,6 +102,9 @@ class TestResult:
         with pytest.raises(AttributeError):
             default.view('invalid',True)
 
+    def test_add_invalid(self,default):
+        default.add_absolute('xxxx')
+
     def test_add_absolute(self,default):
         default.add_absolute('F_e')
         in_memory = np.abs(default.place('F_e'))
diff --git a/python/tests/test_Rotation.py b/python/tests/test_Rotation.py
index 2d623adf5..a431bc64b 100644
--- a/python/tests/test_Rotation.py
+++ b/python/tests/test_Rotation.py
@@ -792,6 +792,11 @@ class TestRotation:
         R = Rotation.from_random(shape,rng_seed=1)
         assert R == R if shape is None else (R == R).all()
 
+    @pytest.mark.parametrize('shape',[None,5,(4,6)])
+    def test_allclose(self,shape):
+        R = Rotation.from_random(shape,rng_seed=1)
+        assert R.allclose(R)
+
     @pytest.mark.parametrize('shape',[None,5,(4,6)])
     def test_unequal(self,shape):
         R = Rotation.from_random(shape,rng_seed=1)
@@ -1124,3 +1129,7 @@ class TestRotation:
         weights_r = np.histogramdd(Eulers_r,steps,rng)[0].flatten(order='F')/N * np.sum(weights)
 
         assert np.sqrt(((weights_r - weights) ** 2).mean()) < 5
+
+    def test_mul_invalid(self):
+        with pytest.raises(TypeError):
+            Rotation.from_random()*np.ones(3)

From a545baebbf07fd53e2b3a5db3bd7d3a827d90faa Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 16 Jan 2022 08:18:06 +0100
Subject: [PATCH 063/133] VTK polishing

avoid segmentation fault (also allows testing)
---
 python/damask/__init__.py |  2 +-
 python/damask/_grid.py    |  2 +-
 python/damask/_vtk.py     | 18 ++++++++++--------
 python/tests/test_VTK.py  |  4 ++++
 4 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/python/damask/__init__.py b/python/damask/__init__.py
index 584a97e87..aa3c36b07 100644
--- a/python/damask/__init__.py
+++ b/python/damask/__init__.py
@@ -21,8 +21,8 @@ from ._rotation        import Rotation         # noqa
 from ._crystal         import Crystal          # noqa
 from ._orientation     import Orientation      # noqa
 from ._table           import Table            # noqa
-from ._vtk             import VTK              # noqa
 from ._colormap        import Colormap         # noqa
+from ._vtk             import VTK              # noqa
 from ._config          import Config           # noqa
 from ._configmaterial  import ConfigMaterial   # noqa
 from ._grid            import Grid             # noqa
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 5006e1b40..002d00259 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -674,7 +674,7 @@ class Grid:
 
     def show(self) -> None:
         """Show on screen."""
-        VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
+        VTK.from_image_data(self.cells,self.size,self.origin).show()
 
 
     def add_primitive(self,
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index dbbfb1b10..6bb7a5d1c 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -442,22 +442,24 @@ class VTK:
 
         mapper = vtk.vtkDataSetMapper()
         mapper.SetInputData(self.vtk_data)
+
         actor = vtk.vtkActor()
         actor.SetMapper(mapper)
+        actor.GetProperty().SetColor(230/255,150/255,68/255)
 
         ren = vtk.vtkRenderer()
+        ren.AddActor(actor)
+        ren.SetBackground(67/255,128/255,208/255)
 
         window = vtk.vtkRenderWindow()
         window.AddRenderer(ren)
-
-        ren.AddActor(actor)
-        ren.SetBackground(0.2,0.2,0.2)
-
         window.SetSize(width,height)
+        window.SetWindowName(util.execution_stamp('VTK','show'))
 
         iren = vtk.vtkRenderWindowInteractor()
         iren.SetRenderWindow(window)
-
-        iren.Initialize()
-        window.Render()
-        iren.Start()
+        if os.name == 'posix' and 'DISPLAY' not in os.environ:
+            print('Found no rendering device')
+        else:
+            window.Render()
+            iren.Start()
diff --git a/python/tests/test_VTK.py b/python/tests/test_VTK.py
index 68224ff33..e59409a20 100644
--- a/python/tests/test_VTK.py
+++ b/python/tests/test_VTK.py
@@ -28,6 +28,10 @@ class TestVTK:
     def _patch_execution_stamp(self, patch_execution_stamp):
         print('patched damask.util.execution_stamp')
 
+    def test_show(sef,default,monkeypatch):
+        monkeypatch.delenv('DISPLAY',raising=False)
+        default.show()
+
     def test_rectilinearGrid(self,tmp_path):
         cells  = np.random.randint(5,10,3)*2
         size   = np.random.random(3) + 1.0

From adf7abbda62be655b04b69fea18119b8a0a29800 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Mon, 17 Jan 2022 14:58:08 +0100
Subject: [PATCH 064/133] added typehints for util module

---
 python/damask/util.py | 75 +++++++++++++++++++++++++------------------
 1 file changed, 43 insertions(+), 32 deletions(-)

diff --git a/python/damask/util.py b/python/damask/util.py
index 0581302db..a28a9e2eb 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -8,6 +8,8 @@ import shlex
 import re
 import fractions
 from functools import reduce
+from typing import Union, Tuple, Sequence, Callable, Dict, List, Any, Literal
+import pathlib
 
 import numpy as np
 import h5py
@@ -50,7 +52,7 @@ _colors = {
 ####################################################################################################
 # Functions
 ####################################################################################################
-def srepr(arg,glue = '\n'):
+def srepr(arg: Union[np.ndarray, Sequence[Any]], glue: str = '\n') -> str:
     r"""
     Join items with glue string.
 
@@ -75,7 +77,7 @@ def srepr(arg,glue = '\n'):
        return arg if isinstance(arg,str) else repr(arg)
 
 
-def emph(what):
+def emph(what: Any) -> str:
     """
     Format with emphasis.
 
@@ -92,7 +94,7 @@ def emph(what):
     """
     return _colors['bold']+srepr(what)+_colors['end_color']
 
-def deemph(what):
+def deemph(what: Any) -> str:
     """
     Format with deemphasis.
 
@@ -109,7 +111,7 @@ def deemph(what):
     """
     return _colors['dim']+srepr(what)+_colors['end_color']
 
-def warn(what):
+def warn(what: Any) -> str:
     """
     Format for warning.
 
@@ -126,7 +128,7 @@ def warn(what):
     """
     return _colors['warning']+emph(what)+_colors['end_color']
 
-def strikeout(what):
+def strikeout(what: Any) -> str:
     """
     Format as strikeout.
 
@@ -144,7 +146,7 @@ def strikeout(what):
     return _colors['crossout']+srepr(what)+_colors['end_color']
 
 
-def run(cmd,wd='./',env=None,timeout=None):
+def run(cmd: str, wd: str = './', env: Dict[str, Any] = None, timeout: int = None) -> Tuple[str, str]:
     """
     Run a command.
 
@@ -185,7 +187,7 @@ def run(cmd,wd='./',env=None,timeout=None):
 execute = run
 
 
-def natural_sort(key):
+def natural_sort(key: str) -> List[Union[int, str]]:
     """
     Natural sort.
 
@@ -200,7 +202,10 @@ def natural_sort(key):
     return [ convert(c) for c in re.split('([0-9]+)', key) ]
 
 
-def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
+def show_progress(iterable: Sequence[Any],
+                  N_iter: int = None,
+                  prefix: str = '',
+                  bar_length: int = 50) -> Any:
     """
     Decorate a loop with a progress bar.
 
@@ -229,7 +234,7 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
             status.update(i)
 
 
-def scale_to_coprime(v):
+def scale_to_coprime(v: np.ndarray) -> np.ndarray:
     """
     Scale vector to co-prime (relatively prime) integers.
 
@@ -267,13 +272,13 @@ def scale_to_coprime(v):
     return m
 
 
-def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
+def project_equal_angle(vector: np.ndarray, direction: str  = 'z', normalize: bool = True, keepdims: bool = False) -> np.ndarray:
     """
     Apply equal-angle projection to vector.
 
     Parameters
     ----------
-    vector : numpy.ndarray, shape (...,3)
+    vector : numpy.ndarray of shape (...,3)
         Vector coordinates to be projected.
     direction : str
         Projection direction 'x', 'y', or 'z'.
@@ -309,7 +314,10 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
     return np.roll(np.block([v[...,:2]/(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
                    -shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
 
-def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
+def project_equal_area(vector: np.ndarray,
+                       direction: Literal['x', 'y', 'z'] = 'z',
+                       normalize: bool = True,
+                       keepdims: bool = False) -> np.ndarray:
     """
     Apply equal-area projection to vector.
 
@@ -351,15 +359,14 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
     return np.roll(np.block([v[...,:2]/np.sqrt(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
                    -shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
 
-
-def execution_stamp(class_name,function_name=None):
+def execution_stamp(class_name: str, function_name: str = None) -> str:
     """Timestamp the execution of a (function within a) class."""
     now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
     _function_name = '' if function_name is None else f'.{function_name}'
     return f'damask.{class_name}{_function_name} v{version} ({now})'
 
 
-def hybrid_IA(dist,N,rng_seed=None):
+def hybrid_IA(dist: np.ndarray, N: int, rng_seed: Union[int, np.ndarray] = None) -> np.ndarray:
     """
     Hybrid integer approximation.
 
@@ -387,7 +394,10 @@ def hybrid_IA(dist,N,rng_seed=None):
     return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]]
 
 
-def shapeshifter(fro,to,mode='left',keep_ones=False):
+def shapeshifter(fro: Tuple[int, ...],
+                 to: Tuple[int, ...],
+                 mode: Literal['left','right'] = 'left',
+                 keep_ones: bool = False) -> Tuple[int, ...]:
     """
     Return dimensions that reshape 'fro' to become broadcastable to 'to'.
 
@@ -434,21 +444,22 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
     fro = (1,) if not len(fro) else fro
     to  = (1,) if not len(to)  else to
     try:
-        grp = re.match(beg[mode]
+        match = re.match((beg[mode]
                       +f',{sep[mode]}'.join(map(lambda x: f'{x}'
                                                           if x>1 or (keep_ones and len(fro)>1) else
                                                           '\\d+',fro))
-                      +f',{end[mode]}',
-                       ','.join(map(str,to))+',').groups()
-    except AttributeError:
+                      +f',{end[mode]}'),','.join(map(str,to))+',')
+        assert match
+    except AssertionError:
         raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
-    fill = ()
+    grp: Sequence[str] = match.groups()
+    fill: Tuple[int, ...] = ()
     for g,d in zip(grp,fro+(None,)):
         fill += (1,)*g.count(',')+(d,)
     return fill[:-1]
 
 
-def shapeblender(a,b):
+def shapeblender(a: Tuple[int, ...], b: Tuple[int, ...]) -> Tuple[int, ...]:
     """
     Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
 
@@ -476,7 +487,7 @@ def shapeblender(a,b):
     return a + b[i:]
 
 
-def extend_docstring(extra_docstring):
+def extend_docstring(extra_docstring: str) -> Callable:
     """
     Decorator: Append to function's docstring.
 
@@ -492,7 +503,7 @@ def extend_docstring(extra_docstring):
     return _decorator
 
 
-def extended_docstring(f,extra_docstring):
+def extended_docstring(f: Callable, extra_docstring: str) -> Callable:
     """
     Decorator: Combine another function's docstring with a given docstring.
 
@@ -510,7 +521,7 @@ def extended_docstring(f,extra_docstring):
     return _decorator
 
 
-def DREAM3D_base_group(fname):
+def DREAM3D_base_group(fname: Union[str, pathlib.Path]) -> str:
     """
     Determine the base group of a DREAM.3D file.
 
@@ -536,7 +547,7 @@ def DREAM3D_base_group(fname):
 
     return base_group
 
-def DREAM3D_cell_data_group(fname):
+def DREAM3D_cell_data_group(fname: Union[str, pathlib.Path]) -> str:
     """
     Determine the cell data group of a DREAM.3D file.
 
@@ -568,7 +579,7 @@ def DREAM3D_cell_data_group(fname):
     return cell_data_group
 
 
-def Bravais_to_Miller(*,uvtw=None,hkil=None):
+def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np.ndarray:
     """
     Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
 
@@ -595,7 +606,7 @@ def Bravais_to_Miller(*,uvtw=None,hkil=None):
     return np.einsum('il,...l',basis,axis)
 
 
-def Miller_to_Bravais(*,uvw=None,hkl=None):
+def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
     """
     Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
 
@@ -624,7 +635,7 @@ def Miller_to_Bravais(*,uvw=None,hkl=None):
     return np.einsum('il,...l',basis,axis)
 
 
-def dict_prune(d):
+def dict_prune(d: Dict[Any, Any]) -> Dict[Any, Any]:
     """
     Recursively remove empty dictionaries.
 
@@ -650,7 +661,7 @@ def dict_prune(d):
     return new
 
 
-def dict_flatten(d):
+def dict_flatten(d: Dict[Any, Any]) -> Dict[Any, Any]:
     """
     Recursively remove keys of single-entry dictionaries.
 
@@ -685,7 +696,7 @@ class _ProgressBar:
     Works for 0-based loops, ETA is estimated by linear extrapolation.
     """
 
-    def __init__(self,total,prefix,bar_length):
+    def __init__(self, total: int, prefix: str, bar_length: int):
         """
         Set current time as basis for ETA estimation.
 
@@ -708,7 +719,7 @@ class _ProgressBar:
         sys.stderr.write(f"{self.prefix} {'░'*self.bar_length}   0% ETA n/a")
         sys.stderr.flush()
 
-    def update(self,iteration):
+    def update(self, iteration: int) -> None:
 
         fraction = (iteration+1) / self.total
         filled_length = int(self.bar_length * fraction)

From 7b158ba10899de258a48142b6737faea9596a946 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Mon, 17 Jan 2022 15:00:25 +0100
Subject: [PATCH 065/133] added typehints for vtk module

---
 python/damask/_vtk.py | 31 +++++++++++++++++--------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index dbbfb1b10..561726153 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -2,6 +2,7 @@ import os
 import warnings
 import multiprocessing as mp
 from pathlib import Path
+from typing import Union, Optional, Literal, List
 
 import numpy as np
 import vtk
@@ -20,7 +21,7 @@ class VTK:
     High-level interface to VTK.
     """
 
-    def __init__(self,vtk_data):
+    def __init__(self, vtk_data: vtk.vtkImageData):
         """
         New spatial visualization.
 
@@ -36,7 +37,8 @@ class VTK:
 
 
     @staticmethod
-    def from_image_data(cells,size,origin=np.zeros(3)):
+    #ITERABLES PROPER
+    def from_image_data(cells: np.ndarray, size: np.ndarray, origin: Optional[np.ndarray] = np.zeros(3)) -> "VTK":
         """
         Create VTK of type vtk.vtkImageData.
 
@@ -66,7 +68,7 @@ class VTK:
 
 
     @staticmethod
-    def from_rectilinear_grid(grid,size,origin=np.zeros(3)):
+    def from_rectilinear_grid(grid: np.ndarray, size: np.ndarray, origin: np.ndarray = np.zeros(3)) -> "VTK":
         """
         Create VTK of type vtk.vtkRectilinearGrid.
 
@@ -98,7 +100,7 @@ class VTK:
 
 
     @staticmethod
-    def from_unstructured_grid(nodes,connectivity,cell_type):
+    def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> "VTK":
         """
         Create VTK of type vtk.vtkUnstructuredGrid.
 
@@ -138,7 +140,7 @@ class VTK:
 
 
     @staticmethod
-    def from_poly_data(points):
+    def from_poly_data(points: np.ndarray) -> "VTK":
         """
         Create VTK of type vtk.polyData.
 
@@ -172,7 +174,8 @@ class VTK:
 
 
     @staticmethod
-    def load(fname,dataset_type=None):
+    def load(fname: Union[str, Path],
+             dataset_type: Literal['vtkImageData', 'vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'] = None) -> "VTK":
         """
         Load from VTK file.
 
@@ -189,7 +192,7 @@ class VTK:
             VTK-based geometry from file.
 
         """
-        if not os.path.isfile(fname):                                                               # vtk has a strange error handling
+        if not os.path.isfile(fname):                                                  # vtk has a strange error handling
             raise FileNotFoundError(f'No such file: {fname}')
         ext = Path(fname).suffix
         if ext == '.vtk' or dataset_type is not None:
@@ -234,7 +237,7 @@ class VTK:
     def _write(writer):
         """Wrapper for parallel writing."""
         writer.Write()
-    def save(self,fname,parallel=True,compress=True):
+    def save(self, fname: Union[str, Path], parallel: bool = True, compress: bool = True):
         """
         Save as VTK file.
 
@@ -280,7 +283,7 @@ class VTK:
 
     # Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
     # Needs support for damask.Table
-    def add(self,data,label=None):
+    def add(self, data: Union[np.ndarray, np.ma.MaskedArray], label: str = None):
         """
         Add data to either cells or points.
 
@@ -327,7 +330,7 @@ class VTK:
             raise TypeError
 
 
-    def get(self,label):
+    def get(self, label: str) -> np.ndarray:
         """
         Get either cell or point data.
 
@@ -369,7 +372,7 @@ class VTK:
             raise ValueError(f'Array "{label}" not found.')
 
 
-    def get_comments(self):
+    def get_comments(self) -> List[str]:
         """Return the comments."""
         fielddata = self.vtk_data.GetFieldData()
         for a in range(fielddata.GetNumberOfArrays()):
@@ -379,7 +382,7 @@ class VTK:
         return []
 
 
-    def set_comments(self,comments):
+    def set_comments(self, comments: Union[str, List[str]]):
         """
         Set comments.
 
@@ -396,7 +399,7 @@ class VTK:
         self.vtk_data.GetFieldData().AddArray(s)
 
 
-    def add_comments(self,comments):
+    def add_comments(self, comments: Union[str, List[str]]):
         """
         Add comments.
 
@@ -409,7 +412,7 @@ class VTK:
         self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
 
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """ASCII representation of the VTK data."""
         writer = vtk.vtkDataSetWriter()
         writer.SetHeader(f'# {util.execution_stamp("VTK")}')

From 4cd260881aa7c7a2b5eb64b700ca49770b4b45e6 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Mon, 17 Jan 2022 23:52:17 +0100
Subject: [PATCH 066/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-441-g8b5122f52

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 11b9d06bd..278b0bc78 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-389-ga000e477c
+v3.0.0-alpha5-441-g8b5122f52

From c5fd6a36777e68013ba6d7839d720bc99db90193 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 17 Jan 2022 07:41:17 +0100
Subject: [PATCH 067/133] random seed should contain some entropy

setting all elements to the same value does not make sense. Moreover,
negative values are allowed
---
 PRIVATE      |  2 +-
 src/math.f90 | 32 ++++++++++++++------------------
 2 files changed, 15 insertions(+), 19 deletions(-)

diff --git a/PRIVATE b/PRIVATE
index b898a8b55..d570b4a1f 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit b898a8b5552bd9d1c555edc3d8134564dd32fe53
+Subproject commit d570b4a1fac5b9b99d026d3ff9bf593615e22ce5
diff --git a/src/math.f90 b/src/math.f90
index 3ea4d6a08..db0666ab0 100644
--- a/src/math.f90
+++ b/src/math.f90
@@ -84,38 +84,34 @@ contains
 subroutine math_init
 
   real(pReal), dimension(4) :: randTest
-  integer :: &
-    randSize, &
-    randomSeed                                                                                      !< fixed seeding for pseudo-random number generator, Default 0: use random seed
-  integer, dimension(:), allocatable :: randInit
+  integer :: randSize
+  integer, dimension(:), allocatable :: seed
   class(tNode), pointer :: &
     num_generic
 
+
   print'(/,1x,a)', '<<<+-  math init  -+>>>'; flush(IO_STDOUT)
 
   num_generic => config_numerics%get('generic',defaultVal=emptyDict)
-  randomSeed  = num_generic%get_asInt('random_seed', defaultVal = 0)
 
   call random_seed(size=randSize)
-  allocate(randInit(randSize))
-  if (randomSeed > 0) then
-    randInit = randomSeed
+  allocate(seed(randSize))
+
+  if (num_generic%contains('random_seed')) then
+    seed = num_generic%get_as1dInt('random_seed',requiredSize=randSize)
   else
     call random_seed()
-    call random_seed(get = randInit)
-    randInit(2:randSize) = randInit(1)
-  endif
+    call random_seed(get = seed)
+  end if
 
-  call random_seed(put = randInit)
+  call random_seed(put = seed)
   call random_number(randTest)
 
-  print'(/,a,i2)',                ' size  of random seed:     ', randSize
-  print'(  a,i0)',                ' value of random seed:     ', randInit(1)
-  print'(  a,4(/,26x,f17.14),/)', ' start of random sequence: ', randTest
+  print'(/,a,i2)',              ' size  of random seed:     ', randSize
+  print*,                       'value of random seed:     ', seed
+  print'(  a,4(/,26x,f17.14))', ' start of random sequence: ', randTest
 
-  call random_seed(put = randInit)
-
-  call selfTest
+  call selfTest()
 
 end subroutine math_init
 

From 632180d67e347225eaba26f7e03d5380cc30242b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 18 Jan 2022 14:27:47 +0100
Subject: [PATCH 068/133] not needed

---
 python/damask/_rotation.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/python/damask/_rotation.py b/python/damask/_rotation.py
index fd19ec31b..8e5f7f7f9 100644
--- a/python/damask/_rotation.py
+++ b/python/damask/_rotation.py
@@ -812,8 +812,7 @@ class Rotation:
         return Rotation.from_basis(R)
 
     @staticmethod
-    def from_parallel(a,b,
-                      **kwargs):
+    def from_parallel(a,b):
         """
         Initialize from pairs of two orthogonal lattice basis vectors.
 
@@ -963,8 +962,7 @@ class Rotation:
                  N = 500,
                  degrees = True,
                  fractions = True,
-                 rng_seed = None,
-                 **kwargs):
+                 rng_seed = None):
         """
         Sample discrete values from a binned orientation distribution function (ODF).
 

From c3b492c5da9b3ca75dd4b0c8c8235270563b193c Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 18 Jan 2022 21:06:39 +0100
Subject: [PATCH 069/133] new PETSc version with backported fix for ML

---
 .gitlab-ci.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6da114938..f3e74e030 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -46,7 +46,7 @@ variables:
   # ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   PETSC_GNU:       "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
   PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
-  PETSC_INTEL:    "Libraries/PETSc/3.16.2/Intel-2022.0.1-IntelMPI-2021.5.0"
+  PETSC_INTEL:    "Libraries/PETSc/3.16.3/Intel-2022.0.1-IntelMPI-2021.5.0"
   # ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   MSC:            "FEM/MSC/2021.3.1"
   IntelMarc:      "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
@@ -79,63 +79,63 @@ mypy:
 
 
 ###################################################################################################
-test_grid_GNU:
+grid_GNU:
   stage: compile
   script:
     - module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU
 
-test_mesh_GNU:
+mesh_GNU:
   stage: compile
   script:
     - module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU
 
-test_grid_GNU-64bit:
+grid_GNU-64bit:
   stage: compile
   script:
     - module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU-64bit
 
-test_mesh_GNU-64bit:
+mesh_GNU-64bit:
   stage: compile
   script:
     - module load Compiler/GNU/10 Libraries/PETSc/3.16.2/64bit
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU-64bit
 
-test_grid_IntelLLVM:
+grid_IntelLLVM:
   stage: compile
   script:
     - module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_IntelLLVM
 
-test_mesh_IntelLLVM:
+mesh_IntelLLVM:
   stage: compile
   script:
     - module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_IntelLLVM
 
-test_grid_Intel:
+grid_Intel:
   stage: compile
   script:
     - module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_Intel
 
-test_mesh_Intel:
+mesh_Intel:
   stage: compile
   script:
     - module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
     - cd PRIVATE/testing/pytest
     - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_Intel
 
-test_Marc:
+Marc_Intel:
   stage: compile
   script:
     - module load $IntelMarc $HDF5Marc $MSC
@@ -158,7 +158,7 @@ setup_mesh:
     - cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
     - make -j2 all install
 
-compile_Marc:
+setup_Marc:
   stage: compile
   script:
     - module load $IntelMarc $HDF5Marc $MSC

From 23743c73d47fe9631c3c35e966a484d469f6ff2a Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Wed, 19 Jan 2022 10:37:22 +0100
Subject: [PATCH 070/133] adjusted util.hybrid_IA function argument

---
 python/damask/util.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/damask/util.py b/python/damask/util.py
index a28a9e2eb..053ca9a2e 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -14,6 +14,7 @@ import pathlib
 import numpy as np
 import h5py
 
+from ._typehints import IntSequence
 from . import version
 
 # limit visibility
@@ -366,7 +367,7 @@ def execution_stamp(class_name: str, function_name: str = None) -> str:
     return f'damask.{class_name}{_function_name} v{version} ({now})'
 
 
-def hybrid_IA(dist: np.ndarray, N: int, rng_seed: Union[int, np.ndarray] = None) -> np.ndarray:
+def hybrid_IA(dist: np.ndarray, N: int, rng_seed: Union[int, IntSequence] = None) -> np.ndarray:
     """
     Hybrid integer approximation.
 

From 5d8fff423e40f1d945ca42871397e980d363d619 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Wed, 19 Jan 2022 10:40:29 +0100
Subject: [PATCH 071/133] replaced vtk.init argument type with vtkDataSet

---
 python/damask/_vtk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index 561726153..ab2cc5270 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -21,7 +21,7 @@ class VTK:
     High-level interface to VTK.
     """
 
-    def __init__(self, vtk_data: vtk.vtkImageData):
+    def __init__(self, vtk_data: vtk.vtkDataSet):
         """
         New spatial visualization.
 

From f9f0972e3e0a7d83d661a8cf02700da178931d00 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Wed, 19 Jan 2022 10:58:33 +0100
Subject: [PATCH 072/133] added FloatSequence type to
 vtk.from_rectilinear_gridfunction

---
 python/damask/_vtk.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index ab2cc5270..1ebf0c684 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -10,6 +10,7 @@ from vtk.util.numpy_support import numpy_to_vtk            as np_to_vtk
 from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
 from vtk.util.numpy_support import vtk_to_numpy            as vtk_to_np
 
+from ._typehints import FloatSequence
 from . import util
 from . import Table
 
@@ -68,7 +69,7 @@ class VTK:
 
 
     @staticmethod
-    def from_rectilinear_grid(grid: np.ndarray, size: np.ndarray, origin: np.ndarray = np.zeros(3)) -> "VTK":
+    def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> "VTK":
         """
         Create VTK of type vtk.vtkRectilinearGrid.
 

From b18483cc6ede226ed5b9e500b8c42f5f19e58825 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 16:31:19 +0100
Subject: [PATCH 073/133] simplify MPI debugging

needs manual modification in the source code
---
 src/grid/discretization_grid.f90 | 8 ++++----
 src/parallelization.f90          | 2 ++
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/grid/discretization_grid.f90 b/src/grid/discretization_grid.f90
index 738206f9a..8de2de6ef 100644
--- a/src/grid/discretization_grid.f90
+++ b/src/grid/discretization_grid.f90
@@ -27,14 +27,14 @@ module discretization_grid
   private
 
   integer,     dimension(3), public, protected :: &
-    grid                                                                                           !< (global) grid
+    grid                                                                                            !< (global) grid
   integer,                   public, protected :: &
-    grid3, &                                                                                       !< (local) grid in 3rd direction
+    grid3, &                                                                                        !< (local) grid in 3rd direction
     grid3Offset                                                                                     !< (local) grid offset in 3rd direction
   real(pReal), dimension(3), public, protected :: &
-    geomSize                                                                                       !< (global) physical size
+    geomSize                                                                                        !< (global) physical size
   real(pReal),               public, protected :: &
-    size3, &                                                                                       !< (local) size in 3rd direction
+    size3, &                                                                                        !< (local) size in 3rd direction
     size3offset                                                                                     !< (local) size offset in 3rd direction
 
   public :: &
diff --git a/src/parallelization.f90 b/src/parallelization.f90
index d9ca15981..29deaf724 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -53,6 +53,7 @@ contains
 subroutine parallelization_init
 
   integer(MPI_INTEGER_KIND) :: err_MPI, typeSize
+  character(len=4) :: rank_str
 !$ integer :: got_env, threadLevel
 !$ integer(pI32) :: OMP_NUM_THREADS
 !$ character(len=6) NumThreadsString
@@ -112,6 +113,7 @@ subroutine parallelization_init
 
   if (worldrank /= 0) then
     close(OUTPUT_UNIT)                                                                              ! disable output
+    write(rank_str,'(i4.4)') worldrank                                                              ! use for MPI debug filenames
     open(OUTPUT_UNIT,file='/dev/null',status='replace')                                             ! close() alone will leave some temp files in cwd
   endif
 

From 1ad537b60cf06623c42361f75f0b7ab203fc3efe Mon Sep 17 00:00:00 2001
From: Sharan Roongta <s.roongta@mpie.de>
Date: Wed, 19 Jan 2022 16:46:13 +0100
Subject: [PATCH 074/133] better to use global grid dimensions

also checking early allocation of Temperature field
---
 src/grid/grid_thermal_spectral.f90 | 36 ++++++++++++------------------
 1 file changed, 14 insertions(+), 22 deletions(-)

diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 8862df725..5b92d6054 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -40,7 +40,6 @@ module grid_thermal_spectral
 ! PETSc data
   SNES     :: thermal_snes
   Vec      :: solution_vec
-  PetscInt :: xstart, xend, ystart, yend, zstart, zend
   real(pReal), dimension(:,:,:), allocatable :: &
     T_current, &                                                                                    !< field of current temperature
     T_lastInc, &                                                                                    !< field of previous temperature
@@ -100,6 +99,18 @@ subroutine grid_thermal_spectral_init(T_0)
  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
  CHKERRQ(err_PETSc)
 
+!--------------------------------------------------------------------------------------------------
+! init fields
+  allocate(T_current(grid(1),grid(2),grid3), source=T_0)
+  allocate(T_lastInc(grid(1),grid(2),grid3), source=T_0)
+  allocate(T_stagInc(grid(1),grid(2),grid3), source=T_0)
+
+  ce = 0
+  do k = 1, grid3; do j = 1, grid(2); do i = 1,grid(1)
+    ce = ce + 1
+    call homogenization_thermal_setField(T_0,0.0_pReal,ce)
+  end do; end do; end do
+
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
   call SNESCreate(PETSC_COMM_WORLD,thermal_snes,err_PETSc); CHKERRQ(err_PETSc)
@@ -127,28 +138,9 @@ subroutine grid_thermal_spectral_init(T_0)
   call SNESSetFromOptions(thermal_snes,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
-! init fields
-  call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)
-  CHKERRQ(err_PETSc)
-  xend = xstart + xend - 1
-  yend = ystart + yend - 1
-  zend = zstart + zend - 1
-  allocate(T_current(grid(1),grid(2),grid3), source=0.0_pReal)
-  allocate(T_lastInc(grid(1),grid(2),grid3), source=0.0_pReal)
-  allocate(T_stagInc(grid(1),grid(2),grid3), source=0.0_pReal)
-
-  ce = 0
-  do k = 1, grid3; do j = 1, grid(2); do i = 1,grid(1)
-    ce = ce + 1
-    T_current(i,j,k) = T_0
-    T_lastInc(i,j,k) = T_current(i,j,k)
-    T_stagInc(i,j,k) = T_current(i,j,k)
-    call homogenization_thermal_setField(T_0,0.0_pReal,ce)
-  end do; end do; end do
-
   call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
-  T_PETSc(xstart:xend,ystart:yend,zstart:zend) = T_current
+  T_PETSc = T_current
   call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
 
@@ -239,7 +231,7 @@ subroutine grid_thermal_spectral_forward(cutBack)
     CHKERRQ(err_PETSc)
     call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
-    x_scal(xstart:xend,ystart:yend,zstart:zend) = T_current
+    x_scal = T_current
     call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
     CHKERRQ(err_PETSc)
     ce = 0

From 642df406342d29e02a8137fd687db92dc7553bfc Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 16:55:37 +0100
Subject: [PATCH 075/133] one-based counting

---
 src/grid/grid_mech_FEM.f90 | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 010f11cea..9a200044b 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -560,13 +560,13 @@ subroutine formResidual(da_local,x_local, &
 !--------------------------------------------------------------------------------------------------
 ! get deformation gradient
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
-  do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
+  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
     ctr = 0
-    do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
+    do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
     enddo; enddo; enddo
-    ii = i-xstart+1; jj = j-ystart+1; kk = k-zstart+1
+    ii = i-xstart; jj = j-ystart; kk = k-zstart
     F(1:3,1:3,ii,jj,kk) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
@@ -590,20 +590,20 @@ subroutine formResidual(da_local,x_local, &
   call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
+  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
     ctr = 0
-    do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
+    do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
     enddo; enddo; enddo
-    ii = i-xstart+1; jj = j-ystart+1; kk = k-zstart+1
+    ii = i-xstart; jj = j-ystart; kk = k-zstart
     ele = ele + 1
     f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,ii,jj,kk)))*detJ + &
              matmul(HGMat,x_elem)*(homogenization_dPdF(1,1,1,1,ele) + &
                                    homogenization_dPdF(2,2,2,2,ele) + &
                                    homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
     ctr = 0
-    do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
+    do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       f_scal(0:2,i+ii,j+jj,k+kk) = f_scal(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
     enddo; enddo; enddo
@@ -660,9 +660,9 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   CHKERRQ(err_PETSc)
   call MatZeroEntries(Jac,err_PETSc); CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
+  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
     ctr = 0
-    do kk = 0, 1; do jj = 0, 1; do ii = 0, 1
+    do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       col(MatStencil_i,ctr   ) = i+ii
       col(MatStencil_j,ctr   ) = j+jj
@@ -713,14 +713,14 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   call DMDAVecGetArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart, zend; do j = ystart, yend; do i = xstart, xend
+  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
     ele = ele + 1
-    x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ele)
+    x_scal(0:2,i-1,j-1,k-1) = discretization_IPcoords(1:3,ele)
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,err_PETSc)
-  CHKERRQ(err_PETSc)                                                                          ! initialize to undeformed coordinates (ToDo: use ip coordinates)
+  CHKERRQ(err_PETSc)                                                                                ! initialize to undeformed coordinates (ToDo: use ip coordinates)
   call MatNullSpaceCreateRigidBody(coordinates,matnull,err_PETSc)
-  CHKERRQ(err_PETSc)                                                                          ! get rigid body deformation modes
+  CHKERRQ(err_PETSc)                                                                                ! get rigid body deformation modes
   call DMRestoreGlobalVector(da_local,coordinates,err_PETSc)
   CHKERRQ(err_PETSc)
   call MatSetNullSpace(Jac,matnull,err_PETSc)

From 6fb4320fc29078f287e65ffcbf05eec4cb1a6de8 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Wed, 19 Jan 2022 17:02:22 +0100
Subject: [PATCH 076/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-451-g3fbf1459d

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 278b0bc78..75b174809 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-441-g8b5122f52
+v3.0.0-alpha5-451-g3fbf1459d

From 96ff3314a37562e5690cf9367ec1dfd3fa347428 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 17:10:47 +0100
Subject: [PATCH 077/133] simplified

---
 src/grid/grid_mech_FEM.f90 | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 9a200044b..df57d30ab 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -703,9 +703,8 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
-  diag = (C_volAvg(1,1,1,1)/delta(1)**2 + &
-          C_volAvg(2,2,2,2)/delta(2)**2 + &
-          C_volAvg(3,3,3,3)/delta(3)**2)*detJ
+  diag = (C_volAvg(1,1,1,1)/delta(1)**2 + C_volAvg(2,2,2,2)/delta(2)**2 + C_volAvg(3,3,3,3)/delta(3)**2) &
+       * detJ
   call MatZeroRowsColumns(Jac,size(rows,kind=pPetscInt),rows,diag,PETSC_NULL_VEC,PETSC_NULL_VEC,err_PETSc)
   CHKERRQ(err_PETSc)
   call DMGetGlobalVector(da_local,coordinates,err_PETSc)

From 25ddec76e7627834c6b1053c449db251bacaee47 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 17:28:24 +0100
Subject: [PATCH 078/133] avoid (x/y/z)end and (x/y/z)start, same information
 is in grid

---
 src/grid/grid_damage_spectral.f90  |  8 +-------
 src/grid/grid_mech_FEM.f90         | 16 ++++++++--------
 src/grid/grid_thermal_spectral.f90 | 10 ++--------
 src/parallelization.f90            |  2 +-
 4 files changed, 12 insertions(+), 24 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 8955f9d66..17c6ab435 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -41,7 +41,6 @@ module grid_damage_spectral
 ! PETSc data
   SNES :: damage_snes
   Vec  :: solution_vec
-  PetscInt :: xstart, xend, ystart, yend, zstart, zend
   real(pReal), dimension(:,:,:), allocatable :: &
     phi_current, &                                                                                  !< field of current damage
     phi_lastInc, &                                                                                  !< field of previous damage
@@ -143,11 +142,6 @@ subroutine grid_damage_spectral_init()
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAGetCorners(damage_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)
-  CHKERRQ(err_PETSc)
-  xend = xstart + xend - 1
-  yend = ystart + yend - 1
-  zend = zstart + zend - 1
   allocate(phi_current(grid(1),grid(2),grid3), source=1.0_pReal)
   allocate(phi_lastInc(grid(1),grid(2),grid3), source=1.0_pReal)
   allocate(phi_stagInc(grid(1),grid(2),grid3), source=1.0_pReal)
@@ -239,7 +233,7 @@ subroutine grid_damage_spectral_forward(cutBack)
     call SNESGetDM(damage_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
     call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
-    x_scal(xstart:xend,ystart:yend,zstart:zend) = phi_current
+    x_scal = phi_current
     call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
     CHKERRQ(err_PETSc)
     ce = 0
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index df57d30ab..a0a7d4a47 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -560,14 +560,14 @@ subroutine formResidual(da_local,x_local, &
 !--------------------------------------------------------------------------------------------------
 ! get deformation gradient
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
-  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
+  do k = zstart+1, zend+1; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
     enddo; enddo; enddo
-    ii = i-xstart; jj = j-ystart; kk = k-zstart
-    F(1:3,1:3,ii,jj,kk) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
+    kk = k-zstart
+    F(1:3,1:3,i,j,kk) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
 
@@ -590,15 +590,15 @@ subroutine formResidual(da_local,x_local, &
   call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
+  do k = zstart+1, zend+1; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
     enddo; enddo; enddo
-    ii = i-xstart; jj = j-ystart; kk = k-zstart
+    kk = k-zstart
     ele = ele + 1
-    f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,ii,jj,kk)))*detJ + &
+    f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,i,j,kk)))*detJ + &
              matmul(HGMat,x_elem)*(homogenization_dPdF(1,1,1,1,ele) + &
                                    homogenization_dPdF(2,2,2,2,ele) + &
                                    homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
@@ -712,9 +712,9 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   call DMDAVecGetArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
+  do k = grid3offset, grid3offset+grid3-1; do j = 0, grid(2)-1; do i = 0, grid(1)-1
     ele = ele + 1
-    x_scal(0:2,i-1,j-1,k-1) = discretization_IPcoords(1:3,ele)
+    x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ele)
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)                                                                                ! initialize to undeformed coordinates (ToDo: use ip coordinates)
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 8862df725..c0a7e3940 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -40,7 +40,6 @@ module grid_thermal_spectral
 ! PETSc data
   SNES     :: thermal_snes
   Vec      :: solution_vec
-  PetscInt :: xstart, xend, ystart, yend, zstart, zend
   real(pReal), dimension(:,:,:), allocatable :: &
     T_current, &                                                                                    !< field of current temperature
     T_lastInc, &                                                                                    !< field of previous temperature
@@ -128,11 +127,6 @@ subroutine grid_thermal_spectral_init(T_0)
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)
-  CHKERRQ(err_PETSc)
-  xend = xstart + xend - 1
-  yend = ystart + yend - 1
-  zend = zstart + zend - 1
   allocate(T_current(grid(1),grid(2),grid3), source=0.0_pReal)
   allocate(T_lastInc(grid(1),grid(2),grid3), source=0.0_pReal)
   allocate(T_stagInc(grid(1),grid(2),grid3), source=0.0_pReal)
@@ -148,7 +142,7 @@ subroutine grid_thermal_spectral_init(T_0)
 
   call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
-  T_PETSc(xstart:xend,ystart:yend,zstart:zend) = T_current
+  T_PETSc = T_current
   call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
 
@@ -239,7 +233,7 @@ subroutine grid_thermal_spectral_forward(cutBack)
     CHKERRQ(err_PETSc)
     call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
-    x_scal(xstart:xend,ystart:yend,zstart:zend) = T_current
+    x_scal = T_current
     call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
     CHKERRQ(err_PETSc)
     ce = 0
diff --git a/src/parallelization.f90 b/src/parallelization.f90
index 29deaf724..d1e1576bb 100644
--- a/src/parallelization.f90
+++ b/src/parallelization.f90
@@ -114,7 +114,7 @@ subroutine parallelization_init
   if (worldrank /= 0) then
     close(OUTPUT_UNIT)                                                                              ! disable output
     write(rank_str,'(i4.4)') worldrank                                                              ! use for MPI debug filenames
-    open(OUTPUT_UNIT,file='/dev/null',status='replace')                                             ! close() alone will leave some temp files in cwd
+    open(OUTPUT_UNIT,file='./log.'//rank_str,status='replace')                                             ! close() alone will leave some temp files in cwd
   endif
 
 !$ call get_environment_variable(name='OMP_NUM_THREADS',value=NumThreadsString,STATUS=got_env)

From 89cb018189f376f4fc3a7cdb2468e89f3eec42dc Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 18:58:46 +0100
Subject: [PATCH 079/133] polishing

---
 src/grid/grid_damage_spectral.f90  | 33 +++++++++++++++---------------
 src/grid/grid_thermal_spectral.f90 | 18 ++++++++--------
 2 files changed, 26 insertions(+), 25 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 17c6ab435..263272bd3 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -39,7 +39,7 @@ module grid_damage_spectral
   type(tSolutionParams) :: params
 !--------------------------------------------------------------------------------------------------
 ! PETSc data
-  SNES :: damage_snes
+  SNES :: SNES_damage
   Vec  :: solution_vec
   real(pReal), dimension(:,:,:), allocatable :: &
     phi_current, &                                                                                  !< field of current damage
@@ -104,10 +104,16 @@ subroutine grid_damage_spectral_init()
  call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
  CHKERRQ(err_PETSc)
 
+!--------------------------------------------------------------------------------------------------
+! init fields
+  allocate(phi_current(grid(1),grid(2),grid3), source=1.0_pReal)
+  allocate(phi_lastInc(grid(1),grid(2),grid3), source=1.0_pReal)
+  allocate(phi_stagInc(grid(1),grid(2),grid3), source=1.0_pReal)
+
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,damage_snes,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(damage_snes,'damage_',err_PETSc);CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_damage,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(SNES_damage,'damage_',err_PETSc);CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
@@ -121,34 +127,29 @@ subroutine grid_damage_spectral_init()
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          damage_grid,err_PETSc)                                                                     ! handle, error
   CHKERRQ(err_PETSc)
-  call SNESSetDM(damage_snes,damage_grid,err_PETSc); CHKERRQ(err_PETSc)                             ! connect snes to da
+  call SNESSetDM(SNES_damage,damage_grid,err_PETSc); CHKERRQ(err_PETSc)                             ! connect snes to da
   call DMsetFromOptions(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMsetUp(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                 ! global solution vector (grid x 1, i.e. every def grad tensor)
   call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)   ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESSetFromOptions(damage_snes,err_PETSc); CHKERRQ(err_PETSc)                                ! pull it all together with additional CLI arguments
-  call SNESGetType(damage_snes,snes_type,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(SNES_damage,err_PETSc); CHKERRQ(err_PETSc)                                ! pull it all together with additional CLI arguments
+  call SNESGetType(SNES_damage,snes_type,err_PETSc); CHKERRQ(err_PETSc)
   if (trim(snes_type) == 'vinewtonrsls' .or. &
       trim(snes_type) == 'vinewtonssls') then
     call DMGetGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
     call DMGetGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
     call VecSet(lBound,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
     call VecSet(uBound,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
-    call SNESVISetVariableBounds(damage_snes,lBound,uBound,err_PETSc)                                ! variable bounds for variational inequalities like contact mechanics, damage etc.
+    call SNESVISetVariableBounds(SNES_damage,lBound,uBound,err_PETSc)                                ! variable bounds for variational inequalities like contact mechanics, damage etc.
     call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
     call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
   end if
 
 !--------------------------------------------------------------------------------------------------
-! init fields
-  allocate(phi_current(grid(1),grid(2),grid3), source=1.0_pReal)
-  allocate(phi_lastInc(grid(1),grid(2),grid3), source=1.0_pReal)
-  allocate(phi_stagInc(grid(1),grid(2),grid3), source=1.0_pReal)
-
   call VecSet(solution_vec,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
 
-  call updateReference
+  call updateReference()
 
 end subroutine grid_damage_spectral_init
 
@@ -175,9 +176,9 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
 ! set module wide availabe data
   params%Delta_t = Delta_t
 
-  call SNESSolve(damage_snes,PETSC_NULL_VEC,solution_vec,err_PETSc)
+  call SNESSolve(SNES_damage,PETSC_NULL_VEC,solution_vec,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESGetConvergedReason(damage_snes,reason,err_PETSc)
+  call SNESGetConvergedReason(SNES_damage,reason,err_PETSc)
   CHKERRQ(err_PETSc)
 
   if (reason < 1) then
@@ -230,7 +231,7 @@ subroutine grid_damage_spectral_forward(cutBack)
     phi_stagInc = phi_lastInc
 !--------------------------------------------------------------------------------------------------
 ! reverting damage field state
-    call SNESGetDM(damage_snes,dm_local,err_PETSc); CHKERRQ(err_PETSc)
+    call SNESGetDM(SNES_damage,dm_local,err_PETSc); CHKERRQ(err_PETSc)
     call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
     x_scal = phi_current
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index bfc9fa52a..a207ebd99 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -38,7 +38,7 @@ module grid_thermal_spectral
   type(tSolutionParams) :: params
 !--------------------------------------------------------------------------------------------------
 ! PETSc data
-  SNES :: thermal_snes
+  SNES :: SNES_thermal
   Vec :: solution_vec
   real(pReal), dimension(:,:,:), allocatable :: &
     T_current, &                                                                                    !< field of current temperature
@@ -113,8 +113,8 @@ subroutine grid_thermal_spectral_init(T_0)
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,thermal_snes,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(thermal_snes,'thermal_',err_PETSc);CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(SNES_thermal,'thermal_',err_PETSc);CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
@@ -128,14 +128,14 @@ subroutine grid_thermal_spectral_init(T_0)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          thermal_grid,err_PETSc)                                                                    ! handle, error
   CHKERRQ(err_PETSc)
-  call SNESSetDM(thermal_snes,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)                           ! connect snes to da
+  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)                           ! connect snes to da
   call DMsetFromOptions(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMsetUp(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMCreateGlobalVector(thermal_grid,solution_vec,err_PETSc)                                    ! global solution vector (grid x 1, i.e. every def grad tensor)
   CHKERRQ(err_PETSc)
   call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)  ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESSetFromOptions(thermal_snes,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
+  call SNESSetFromOptions(SNES_thermal,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
   call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
@@ -144,7 +144,7 @@ subroutine grid_thermal_spectral_init(T_0)
   call DMDAVecRestoreArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
 
-  call updateReference
+  call updateReference()
 
 end subroutine grid_thermal_spectral_init
 
@@ -171,9 +171,9 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
 ! set module wide availabe data
   params%Delta_t = Delta_t
 
-  call SNESSolve(thermal_snes,PETSC_NULL_VEC,solution_vec,err_PETSc)
+  call SNESSolve(SNES_thermal,PETSC_NULL_VEC,solution_vec,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESGetConvergedReason(thermal_snes,reason,err_PETSc)
+  call SNESGetConvergedReason(SNES_thermal,reason,err_PETSc)
   CHKERRQ(err_PETSc)
 
   if (reason < 1) then
@@ -227,7 +227,7 @@ subroutine grid_thermal_spectral_forward(cutBack)
 
 !--------------------------------------------------------------------------------------------------
 ! reverting thermal field state
-    call SNESGetDM(thermal_snes,dm_local,err_PETSc)
+    call SNESGetDM(SNES_thermal,dm_local,err_PETSc)
     CHKERRQ(err_PETSc)
     call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)

From 0f4f2b67174ba756497f636d4da5e4133d179c66 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 19:38:07 +0100
Subject: [PATCH 080/133] use only grid, not (x/y/z) start and end

---
 src/grid/grid_mech_FEM.f90 | 44 ++++++++++++++++----------------------
 1 file changed, 18 insertions(+), 26 deletions(-)

diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index a0a7d4a47..681de0860 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -60,7 +60,6 @@ module grid_mechanical_FEM
   real(pReal), dimension(3)   :: delta
   real(pReal), dimension(3,8) :: BMat
   real(pReal), dimension(8,8) :: HGMat
-  PetscInt :: xstart,ystart,zstart,xend,yend,zend
 
 !--------------------------------------------------------------------------------------------------
 ! stress, stiffness and compliance average etc.
@@ -146,7 +145,7 @@ subroutine grid_mechanical_FEM_init
 ! set default and user defined options for PETSc
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS, &
                                 '-mechanical_snes_type newtonls -mechanical_ksp_type fgmres &
-                                &-mechanical_ksp_max_it 25 -mechanical_mg_levels_ksp_type chebyshev', &
+                                &-mechanical_ksp_max_it 25', &
                                 err_PETSc)
   CHKERRQ(err_PETSc)
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),err_PETSc)
@@ -212,11 +211,6 @@ subroutine grid_mechanical_FEM_init
   call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
   CHKERRQ(err_PETSc)
 
-  call DMDAGetCorners(mechanical_grid,xstart,ystart,zstart,xend,yend,zend,err_PETSc)                ! local grid extent
-  CHKERRQ(err_PETSc)
-  xend = xstart+xend-1
-  yend = ystart+yend-1
-  zend = zstart+zend-1
   delta = geomSize/real(grid,pReal)                                                                 ! grid spacing
   detJ = product(delta)                                                                             ! cell volume
 
@@ -560,14 +554,13 @@ subroutine formResidual(da_local,x_local, &
 !--------------------------------------------------------------------------------------------------
 ! get deformation gradient
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
-  do k = zstart+1, zend+1; do j = 1, grid(2); do i = 1, grid(1)
+  do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
     enddo; enddo; enddo
-    kk = k-zstart
-    F(1:3,1:3,i,j,kk) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
+    F(1:3,1:3,i,j,k-grid3offset) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
 
@@ -590,15 +583,14 @@ subroutine formResidual(da_local,x_local, &
   call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart+1, zend+1; do j = 1, grid(2); do i = 1, grid(1)
+  do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
       x_elem(ctr,1:3) = x_scal(0:2,i+ii,j+jj,k+kk)
     enddo; enddo; enddo
-    kk = k-zstart
     ele = ele + 1
-    f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,i,j,kk)))*detJ + &
+    f_elem = matmul(transpose(BMat),transpose(P_current(1:3,1:3,i,j,k-grid3offset)))*detJ + &
              matmul(HGMat,x_elem)*(homogenization_dPdF(1,1,1,1,ele) + &
                                    homogenization_dPdF(2,2,2,2,ele) + &
                                    homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
@@ -614,18 +606,18 @@ subroutine formResidual(da_local,x_local, &
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
   call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
-  if (zstart == 0) then
-    f_scal(0:2,xstart,ystart,zstart) = 0.0
-    f_scal(0:2,xend+1,ystart,zstart) = 0.0
-    f_scal(0:2,xstart,yend+1,zstart) = 0.0
-    f_scal(0:2,xend+1,yend+1,zstart) = 0.0
-  endif
-  if (zend + 1 == grid(3)) then
-    f_scal(0:2,xstart,ystart,zend+1) = 0.0
-    f_scal(0:2,xend+1,ystart,zend+1) = 0.0
-    f_scal(0:2,xstart,yend+1,zend+1) = 0.0
-    f_scal(0:2,xend+1,yend+1,zend+1) = 0.0
-  endif
+  if (grid3offset == 0) then
+    f_scal(0:2,0,      0,      0) = 0.0_pReal
+    f_scal(0:2,grid(1),0,      0) = 0.0_pReal
+    f_scal(0:2,0,      grid(2),0) = 0.0_pReal
+    f_scal(0:2,grid(1),grid(2),0) = 0.0_pReal
+  end if
+  if (grid3+grid3offset == grid(3)) then
+    f_scal(0:2,0,      0,      grid(3)) = 0.0_pReal
+    f_scal(0:2,grid(1),0,      grid(3)) = 0.0_pReal
+    f_scal(0:2,0,      grid(2),grid(3)) = 0.0_pReal
+    f_scal(0:2,grid(1),grid(2),grid(3)) = 0.0_pReal
+  end if
   call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
 
 end subroutine formResidual
@@ -660,7 +652,7 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   CHKERRQ(err_PETSc)
   call MatZeroEntries(Jac,err_PETSc); CHKERRQ(err_PETSc)
   ele = 0
-  do k = zstart+1, zend+1; do j = ystart+1, yend+1; do i = xstart+1, xend+1
+  do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1

From fe094939e625fb561fa048ddc8a1b2e582599e63 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 19:43:54 +0100
Subject: [PATCH 081/133] better to understand

---
 src/grid/grid_damage_spectral.f90  | 8 ++++----
 src/grid/grid_thermal_spectral.f90 | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 263272bd3..5c4f357eb 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -223,7 +223,7 @@ subroutine grid_damage_spectral_forward(cutBack)
   logical, intent(in) :: cutBack
   integer :: i, j, k, ce
   DM :: dm_local
-  PetscScalar,  dimension(:,:,:), pointer :: x_scal
+  PetscScalar,  dimension(:,:,:), pointer :: phi_PETSc
   PetscErrorCode :: err_PETSc
 
   if (cutBack) then
@@ -232,10 +232,10 @@ subroutine grid_damage_spectral_forward(cutBack)
 !--------------------------------------------------------------------------------------------------
 ! reverting damage field state
     call SNESGetDM(SNES_damage,dm_local,err_PETSc); CHKERRQ(err_PETSc)
-    call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
+    call DMDAVecGetArrayF90(dm_local,solution_vec,phi_PETSc,err_PETSc)                              !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
-    x_scal = phi_current
-    call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
+    phi_PETSc = phi_current
+    call DMDAVecRestoreArrayF90(dm_local,solution_vec,phi_PETSc,err_PETSc)
     CHKERRQ(err_PETSc)
     ce = 0
     do k = 1, grid3;  do j = 1, grid(2);  do i = 1,grid(1)
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index a207ebd99..86acf7c30 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -218,7 +218,7 @@ subroutine grid_thermal_spectral_forward(cutBack)
   logical, intent(in) :: cutBack
   integer :: i, j, k, ce
   DM :: dm_local
-  PetscScalar,  dimension(:,:,:), pointer :: x_scal
+  PetscScalar,  dimension(:,:,:), pointer :: T_PETSc
   PetscErrorCode :: err_PETSc
 
   if (cutBack) then
@@ -229,10 +229,10 @@ subroutine grid_thermal_spectral_forward(cutBack)
 ! reverting thermal field state
     call SNESGetDM(SNES_thermal,dm_local,err_PETSc)
     CHKERRQ(err_PETSc)
-    call DMDAVecGetArrayF90(dm_local,solution_vec,x_scal,err_PETSc)                                 !< get the data out of PETSc to work with
+    call DMDAVecGetArrayF90(dm_local,solution_vec,T_PETSc,err_PETSc)                                 !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
-    x_scal = T_current
-    call DMDAVecRestoreArrayF90(dm_local,solution_vec,x_scal,err_PETSc)
+    T_PETSc = T_current
+    call DMDAVecRestoreArrayF90(dm_local,solution_vec,T_PETSc,err_PETSc)
     CHKERRQ(err_PETSc)
     ce = 0
     do k = 1, grid3;  do j = 1, grid(2);  do i = 1,grid(1)

From 1f86111f57513fc00714bae219d359464a1965bd Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 19 Jan 2022 22:57:22 +0100
Subject: [PATCH 082/133] call SNESSetDM after DMDASNESSetFunctionLocal

following example ex5f.F90, seems to resolve segmentation fault
---
 src/grid/grid_damage_spectral.f90            | 2 +-
 src/grid/grid_mech_FEM.f90                   | 4 ++--
 src/grid/grid_mech_spectral_basic.f90        | 2 +-
 src/grid/grid_mech_spectral_polarisation.f90 | 2 +-
 src/grid/grid_thermal_spectral.f90           | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 5c4f357eb..9ed1dd051 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -127,12 +127,12 @@ subroutine grid_damage_spectral_init()
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          damage_grid,err_PETSc)                                                                     ! handle, error
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_damage,damage_grid,err_PETSc); CHKERRQ(err_PETSc)                             ! connect snes to da
   call DMsetFromOptions(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMsetUp(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                 ! global solution vector (grid x 1, i.e. every def grad tensor)
   call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)   ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
+  call SNESSetDM(SNES_damage,damage_grid,err_PETSc); CHKERRQ(err_PETSc)                             ! connect snes to da
   call SNESSetFromOptions(SNES_damage,err_PETSc); CHKERRQ(err_PETSc)                                ! pull it all together with additional CLI arguments
   call SNESGetType(SNES_damage,snes_type,err_PETSc); CHKERRQ(err_PETSc)
   if (trim(snes_type) == 'vinewtonrsls' .or. &
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 681de0860..ed0d01810 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -176,8 +176,6 @@ subroutine grid_mechanical_FEM_init
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          mechanical_grid,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESSetDM(mechanical_snes,mechanical_grid,err_PETSc)
-  CHKERRQ(err_PETSc)
   call DMsetFromOptions(mechanical_grid,err_PETSc)
   CHKERRQ(err_PETSc)
   call DMsetUp(mechanical_grid,err_PETSc)
@@ -198,6 +196,8 @@ subroutine grid_mechanical_FEM_init
   CHKERRQ(err_PETSc)
   call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPetscInt), err_PETSc)                 ! ignore linear solve failures
   CHKERRQ(err_PETSc)
+  call SNESSetDM(mechanical_snes,mechanical_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
   call SNESSetFromOptions(mechanical_snes,err_PETSc)                                                ! pull it all together with additional cli arguments
   CHKERRQ(err_PETSc)
 
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 74400f160..56c619b7e 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -173,7 +173,6 @@ subroutine grid_mechanical_spectral_basic_init
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          da,err_PETSc)                                                                              ! handle, error
   CHKERRQ(err_PETSc)
-  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
   call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
   call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
   call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 9, i.e. every def grad tensor)
@@ -181,6 +180,7 @@ subroutine grid_mechanical_spectral_basic_init
   CHKERRQ(err_PETSc)
   call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)         ! specify custom convergence check function "converged"
   CHKERRQ(err_PETSc)
+  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
   call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc)                                       ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index 765a1a5a7..ccd26f451 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -193,7 +193,6 @@ subroutine grid_mechanical_spectral_polarisation_init
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          da,err_PETSc)                                                                              ! handle, error
   CHKERRQ(err_PETSc)
-  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
   call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
   call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
   call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 18, i.e. every def grad tensor)
@@ -201,6 +200,7 @@ subroutine grid_mechanical_spectral_polarisation_init
   CHKERRQ(err_PETSc)
   call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)         ! specify custom convergence check function "converged"
   CHKERRQ(err_PETSc)
+  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
   call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc)                                       ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 86acf7c30..ea32f3b68 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -128,13 +128,13 @@ subroutine grid_thermal_spectral_init(T_0)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          thermal_grid,err_PETSc)                                                                    ! handle, error
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)                           ! connect snes to da
   call DMsetFromOptions(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMsetUp(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
   call DMCreateGlobalVector(thermal_grid,solution_vec,err_PETSc)                                    ! global solution vector (grid x 1, i.e. every def grad tensor)
   CHKERRQ(err_PETSc)
   call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)  ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
+  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)                           ! connect snes to da
   call SNESSetFromOptions(SNES_thermal,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------

From 7b1080fdb72f7c43ac40b63f108dbbbef83f84dd Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 20 Jan 2022 07:42:16 +0100
Subject: [PATCH 083/133] better and consistent variable name

---
 src/grid/grid_damage_spectral.f90            |  6 ++---
 src/grid/grid_mech_FEM.f90                   | 28 ++++++++++----------
 src/grid/grid_mech_spectral_basic.f90        | 10 +++----
 src/grid/grid_mech_spectral_polarisation.f90 | 12 ++++-----
 src/grid/grid_thermal_spectral.f90           |  6 ++---
 5 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 9ed1dd051..c8029b5a9 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -253,7 +253,7 @@ end subroutine grid_damage_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the spectral damage residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
+subroutine formResidual(in,x_scal,r,dummy,dummy_err)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
     in
@@ -262,7 +262,7 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
     x_scal
   PetscScalar, dimension( &
     X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
-    f_scal
+    r
   PetscObject :: dummy
   PetscErrorCode :: dummy_err
   integer :: i, j, k, ce
@@ -305,7 +305,7 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  f_scal = scalarField_real(1:grid(1),1:grid(2),1:grid3) - phi_current
+  r = scalarField_real(1:grid(1),1:grid(2),1:grid3) - phi_current
 
 end subroutine formResidual
 
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index ed0d01810..565cde36d 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -521,7 +521,7 @@ subroutine formResidual(da_local,x_local, &
 
   DM                   :: da_local
   Vec                  :: x_local, f_local
-  PetscScalar, pointer,dimension(:,:,:,:) :: x_scal, f_scal
+  PetscScalar, pointer,dimension(:,:,:,:) :: x_scal, r
   PetscScalar, dimension(8,3) :: x_elem,  f_elem
   PetscInt             :: i, ii, j, jj, k, kk, ctr, ele
   PetscInt :: &
@@ -580,7 +580,7 @@ subroutine formResidual(da_local,x_local, &
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
   call VecSet(f_local,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
   ele = 0
   do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
@@ -597,28 +597,28 @@ subroutine formResidual(da_local,x_local, &
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
       ctr = ctr + 1
-      f_scal(0:2,i+ii,j+jj,k+kk) = f_scal(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
+      r(0:2,i+ii,j+jj,k+kk) = r(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
     enddo; enddo; enddo
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
-  call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
-  call DMDAVecGetArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
   if (grid3offset == 0) then
-    f_scal(0:2,0,      0,      0) = 0.0_pReal
-    f_scal(0:2,grid(1),0,      0) = 0.0_pReal
-    f_scal(0:2,0,      grid(2),0) = 0.0_pReal
-    f_scal(0:2,grid(1),grid(2),0) = 0.0_pReal
+    r(0:2,0,      0,      0) = 0.0_pReal
+    r(0:2,grid(1),0,      0) = 0.0_pReal
+    r(0:2,0,      grid(2),0) = 0.0_pReal
+    r(0:2,grid(1),grid(2),0) = 0.0_pReal
   end if
   if (grid3+grid3offset == grid(3)) then
-    f_scal(0:2,0,      0,      grid(3)) = 0.0_pReal
-    f_scal(0:2,grid(1),0,      grid(3)) = 0.0_pReal
-    f_scal(0:2,0,      grid(2),grid(3)) = 0.0_pReal
-    f_scal(0:2,grid(1),grid(2),grid(3)) = 0.0_pReal
+    r(0:2,0,      0,      grid(3)) = 0.0_pReal
+    r(0:2,grid(1),0,      grid(3)) = 0.0_pReal
+    r(0:2,0,      grid(2),grid(3)) = 0.0_pReal
+    r(0:2,grid(1),grid(2),grid(3)) = 0.0_pReal
   end if
-  call DMDAVecRestoreArrayF90(da_local,f_local,f_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
 
 end subroutine formResidual
 
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 56c619b7e..6486e22f1 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -465,13 +465,13 @@ end subroutine converged
 !> @brief forms the residual vector
 !--------------------------------------------------------------------------------------------------
 subroutine formResidual(in, F, &
-                        residuum, dummy, err_PETSc)
+                        r, dummy, err_PETSc)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: in                                              !< DMDA info (needs to be named "in" for macros like XRANGE to work)
   PetscScalar, dimension(3,3,XG_RANGE,YG_RANGE,ZG_RANGE), &
     intent(in) :: F                                                                                 !< deformation gradient field
   PetscScalar, dimension(3,3,X_RANGE,Y_RANGE,Z_RANGE), &
-    intent(out) :: residuum                                                                         !< residuum field
+    intent(out) :: r                                                                                !< residuum field
   real(pReal),  dimension(3,3) :: &
     deltaF_aim
   PetscInt :: &
@@ -500,7 +500,7 @@ subroutine formResidual(in, F, &
 
 !--------------------------------------------------------------------------------------------------
 ! evaluate constitutive response
-  call utilities_constitutiveResponse(residuum, &                                                   ! "residuum" gets field of first PK stress (to save memory)
+  call utilities_constitutiveResponse(r, &                                                          ! residuum gets field of first PK stress (to save memory)
                                       P_av,C_volAvg,C_minMaxAvg, &
                                       F,params%Delta_t,params%rotation_BC)
   call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
@@ -515,7 +515,7 @@ subroutine formResidual(in, F, &
 !--------------------------------------------------------------------------------------------------
 ! updated deformation gradient using fix point algorithm of basic scheme
   tensorField_real = 0.0_pReal
-  tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = residuum                                  ! store fPK field for subsequent FFT forward transform
+  tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = r                                         ! store fPK field for subsequent FFT forward transform
   call utilities_FFTtensorForward                                                                   ! FFT forward of global "tensorField_real"
   err_div = utilities_divergenceRMS()                                                               ! divRMS of tensorField_fourier for later use
   call utilities_fourierGammaConvolution(params%rotation_BC%rotate(deltaF_aim,active=.true.))       ! convolution of Gamma and tensorField_fourier
@@ -523,7 +523,7 @@ subroutine formResidual(in, F, &
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  residuum = tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)                                   ! Gamma*P gives correction towards div(P) = 0, so needs to be zero, too
+  r = tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)                                         ! Gamma*P gives correction towards div(P) = 0, so needs to be zero, too
 
 end subroutine formResidual
 
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index ccd26f451..a541f2882 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -531,13 +531,13 @@ end subroutine converged
 !> @brief forms the residual vector
 !--------------------------------------------------------------------------------------------------
 subroutine formResidual(in, FandF_tau, &
-                        residuum, dummy,err_PETSc)
+                        r, dummy,err_PETSc)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: in                                              !< DMDA info (needs to be named "in" for macros like XRANGE to work)
   PetscScalar, dimension(3,3,2,XG_RANGE,YG_RANGE,ZG_RANGE), &
     target, intent(in) :: FandF_tau
   PetscScalar, dimension(3,3,2,X_RANGE,Y_RANGE,Z_RANGE),&
-    target,  intent(out) :: residuum                                                                !< residuum field
+    target, intent(out) :: r                                                                        !< residuum field
   PetscScalar, pointer, dimension(:,:,:,:,:) :: &
     F, &
     F_tau, &
@@ -558,10 +558,10 @@ subroutine formResidual(in, FandF_tau, &
                               XG_RANGE,YG_RANGE,ZG_RANGE)
   F_tau          => FandF_tau(1:3,1:3,2,&
                               XG_RANGE,YG_RANGE,ZG_RANGE)
-  residual_F     => residuum(1:3,1:3,1,&
-                             X_RANGE, Y_RANGE, Z_RANGE)
-  residual_F_tau => residuum(1:3,1:3,2,&
-                             X_RANGE, Y_RANGE, Z_RANGE)
+  residual_F     => r(1:3,1:3,1,&
+                      X_RANGE, Y_RANGE, Z_RANGE)
+  residual_F_tau => r(1:3,1:3,2,&
+                      X_RANGE, Y_RANGE, Z_RANGE)
 
   F_av = sum(sum(sum(F,dim=5),dim=4),dim=3) * wgt
   call MPI_Allreduce(MPI_IN_PLACE,F_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index ea32f3b68..389ff10f4 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -250,7 +250,7 @@ end subroutine grid_thermal_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the spectral thermal residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
+subroutine formResidual(in,x_scal,r,dummy,dummy_err)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
     in
@@ -259,7 +259,7 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
     x_scal
   PetscScalar, dimension( &
     X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
-    f_scal
+    r
   PetscObject :: dummy
   PetscErrorCode :: dummy_err
   integer :: i, j, k, ce
@@ -296,7 +296,7 @@ subroutine formResidual(in,x_scal,f_scal,dummy,dummy_err)
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  f_scal = T_current - scalarField_real(1:grid(1),1:grid(2),1:grid3)
+  r = T_current - scalarField_real(1:grid(1),1:grid(2),1:grid3)
 
 end subroutine formResidual
 

From 7bd8452bf8a9d4bd9f4ccd48df73e4120cbda0fa Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 20 Jan 2022 07:56:45 +0100
Subject: [PATCH 084/133] set return value

---
 src/grid/grid_damage_spectral.f90            | 5 +++--
 src/grid/grid_mech_FEM.f90                   | 1 +
 src/grid/grid_mech_spectral_basic.f90        | 1 +
 src/grid/grid_mech_spectral_polarisation.f90 | 1 +
 src/grid/grid_thermal_spectral.f90           | 5 +++--
 5 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index c8029b5a9..f699ee7de 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -253,7 +253,7 @@ end subroutine grid_damage_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the spectral damage residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,r,dummy,dummy_err)
+subroutine formResidual(in,x_scal,r,dummy,err_PETSc)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
     in
@@ -264,7 +264,7 @@ subroutine formResidual(in,x_scal,r,dummy,dummy_err)
     X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
     r
   PetscObject :: dummy
-  PetscErrorCode :: dummy_err
+  PetscErrorCode :: err_PETSc
   integer :: i, j, k, ce
 
 
@@ -306,6 +306,7 @@ subroutine formResidual(in,x_scal,r,dummy,dummy_err)
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
   r = scalarField_real(1:grid(1),1:grid(2),1:grid3) - phi_current
+  err_PETSc = 0
 
 end subroutine formResidual
 
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 565cde36d..de0935d2e 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -509,6 +509,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,e
           err_BC/BCTol,    ' (',err_BC, ' Pa,  tol = ',BCTol,')'
   print'(/,1x,a)', '==========================================================================='
   flush(IO_STDOUT)
+  err_PETSc = 0
 
 end subroutine converged
 
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 6486e22f1..bf72d1d08 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -457,6 +457,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
           err_BC/BCTol,    ' (',err_BC, ' Pa,  tol = ',BCTol,')'
   print'(/,1x,a)', '==========================================================================='
   flush(IO_STDOUT)
+  err_PETSc = 0
 
 end subroutine converged
 
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index a541f2882..9a258e13e 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -523,6 +523,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
             err_BC/BCTol,    ' (',err_BC,  ' Pa,  tol = ',BCTol,')'
   print'(/,1x,a)', '==========================================================================='
   flush(IO_STDOUT)
+  err_PETSc = 0
 
 end subroutine converged
 
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 389ff10f4..d1d165b83 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -250,7 +250,7 @@ end subroutine grid_thermal_spectral_forward
 !--------------------------------------------------------------------------------------------------
 !> @brief forms the spectral thermal residual vector
 !--------------------------------------------------------------------------------------------------
-subroutine formResidual(in,x_scal,r,dummy,dummy_err)
+subroutine formResidual(in,x_scal,r,dummy,err_PETSc)
 
   DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
     in
@@ -261,7 +261,7 @@ subroutine formResidual(in,x_scal,r,dummy,dummy_err)
     X_RANGE,Y_RANGE,Z_RANGE), intent(out) :: &
     r
   PetscObject :: dummy
-  PetscErrorCode :: dummy_err
+  PetscErrorCode :: err_PETSc
   integer :: i, j, k, ce
 
   T_current = x_scal
@@ -297,6 +297,7 @@ subroutine formResidual(in,x_scal,r,dummy,dummy_err)
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
   r = T_current - scalarField_real(1:grid(1),1:grid(2),1:grid3)
+  err_PETSc = 0
 
 end subroutine formResidual
 

From 77f22318a885cdf2f564b054530b0f6bd7a1f29d Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Thu, 20 Jan 2022 11:52:56 +0000
Subject: [PATCH 085/133] Typehint improvements

---
 python/damask/_colormap.py |  2 +-
 python/damask/_grid.py     | 26 +++++++++++---------------
 2 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 2c7f01d94..1ccc292e6 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -250,7 +250,7 @@ class Colormap(mpl.colors.ListedColormap):
                np.logical_or (np.isnan(field), field == gap))                                       # mask NaN (and gap if present)
 
         l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
-              np.array(bounds,float)[:2]
+              (bounds[0],bounds[1])
 
         delta,avg = r-l,0.5*abs(r+l)
 
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 002d00259..eefd1e0be 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -428,7 +428,7 @@ class Grid:
             seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
             seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
         else:
-            weights_p = weights
+            weights_p = np.array(weights,float)
             seeds_p   = seeds
 
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
@@ -841,7 +841,8 @@ class Grid:
         if not set(directions).issubset(valid):
             raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
 
-        mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
+
+        mat = np.flip(self.material, [valid.index(d) for d in directions if d in valid])
 
         return Grid(material = mat,
                     size     = self.size,
@@ -973,14 +974,13 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        if fill is None: fill = np.nanmax(self.material) + 1
-        dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
-
         material = self.material
         # These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
         # see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
         for angle,axes in zip(R.as_Euler_angles(degrees=True)[::-1], [(0,1),(1,2),(0,1)]):
-            material_temp = ndimage.rotate(material,angle,axes,order=0,prefilter=False,output=dtype,cval=fill)
+            material_temp = ndimage.rotate(material,angle,axes,order=0,prefilter=False,
+                                           output=self.material.dtype,
+                                           cval=np.nanmax(self.material) + 1 if fill is None else fill)
             # avoid scipy interpolation errors for rotations close to multiples of 90°
             material = material_temp if np.prod(material_temp.shape) != np.prod(material.shape) else \
                        np.rot90(material,k=np.rint(angle/90.).astype(int),axes=axes)
@@ -1031,10 +1031,8 @@ class Grid:
         """
         offset_ = np.array(offset,int) if offset is not None else np.zeros(3,int)
         cells_ = np.array(cells,int) if cells is not None else self.cells
-        if fill is None: fill = np.nanmax(self.material) + 1
-        dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
 
-        canvas = np.full(cells_,fill,dtype)
+        canvas = np.full(cells_,np.nanmax(self.material) + 1 if fill is None else fill,self.material.dtype)
 
         LL = np.clip( offset_,           0,np.minimum(self.cells,     cells_+offset_))
         UR = np.clip( offset_+cells_,    0,np.minimum(self.cells,     cells_+offset_))
@@ -1067,13 +1065,11 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        def mp(entry, mapper):
-            return mapper[entry] if entry in mapper else entry
+        material = self.material.copy()
+        for f,t in zip(from_material,to_material):        # ToDo Python 3.10 has strict mode for zip
+            material[self.material==f] = t
 
-        mp = np.vectorize(mp)
-        mapper = dict(zip(from_material,to_material))
-
-        return Grid(material = mp(self.material,mapper).reshape(self.cells),
+        return Grid(material = material,
                     size     = self.size,
                     origin   = self.origin,
                     comments = self.comments+[util.execution_stamp('Grid','substitute')],

From 292cbdee30104d1eff07351d77bb3f1d12a3ca19 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 20 Jan 2022 14:56:21 +0100
Subject: [PATCH 086/133] consistent name

---
 src/grid/grid_mech_FEM.f90 | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index de0935d2e..a697ce14a 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -636,7 +636,7 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   PetscScalar,pointer,dimension(:,:,:,:) :: x_scal
   PetscScalar,dimension(24,24)         :: K_ele
   PetscScalar,dimension(9,24)          :: BMatFull
-  PetscInt                             :: i, ii, j, jj, k, kk, ctr, ele
+  PetscInt                             :: i, ii, j, jj, k, kk, ctr, ce
   PetscInt,dimension(3),parameter      :: rows = [0, 1, 2]
   PetscScalar                          :: diag
   PetscObject                          :: dummy
@@ -652,7 +652,7 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,err_PETSc)
   CHKERRQ(err_PETSc)
   call MatZeroEntries(Jac,err_PETSc); CHKERRQ(err_PETSc)
-  ele = 0
+  ce = 0
   do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
@@ -671,20 +671,20 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
       col(MatStencil_c,ctr+16) = 2
     enddo; enddo; enddo
     row = col
-    ele = ele + 1
+    ce = ce + 1
     K_ele = 0.0
-    K_ele(1 :8 ,1 :8 ) = HGMat*(homogenization_dPdF(1,1,1,1,ele) + &
-                                homogenization_dPdF(2,2,2,2,ele) + &
-                                homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
-    K_ele(9 :16,9 :16) = HGMat*(homogenization_dPdF(1,1,1,1,ele) + &
-                                homogenization_dPdF(2,2,2,2,ele) + &
-                                homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
-    K_ele(17:24,17:24) = HGMat*(homogenization_dPdF(1,1,1,1,ele) + &
-                                homogenization_dPdF(2,2,2,2,ele) + &
-                                homogenization_dPdF(3,3,3,3,ele))/3.0_pReal
+    K_ele(1 :8 ,1 :8 ) = HGMat*(homogenization_dPdF(1,1,1,1,ce) + &
+                                homogenization_dPdF(2,2,2,2,ce) + &
+                                homogenization_dPdF(3,3,3,3,ce))/3.0_pReal
+    K_ele(9 :16,9 :16) = HGMat*(homogenization_dPdF(1,1,1,1,ce) + &
+                                homogenization_dPdF(2,2,2,2,ce) + &
+                                homogenization_dPdF(3,3,3,3,ce))/3.0_pReal
+    K_ele(17:24,17:24) = HGMat*(homogenization_dPdF(1,1,1,1,ce) + &
+                                homogenization_dPdF(2,2,2,2,ce) + &
+                                homogenization_dPdF(3,3,3,3,ce))/3.0_pReal
     K_ele = K_ele + &
             matmul(transpose(BMatFull), &
-                   matmul(reshape(reshape(homogenization_dPdF(1:3,1:3,1:3,1:3,ele), &
+                   matmul(reshape(reshape(homogenization_dPdF(1:3,1:3,1:3,1:3,ce), &
                                           shape=[3,3,3,3], order=[2,1,4,3]),shape=[9,9]),BMatFull))*detJ
     call MatSetValuesStencil(Jac,24_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,err_PETSc)
     CHKERRQ(err_PETSc)
@@ -704,10 +704,10 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
-  ele = 0
+  ce = 0
   do k = grid3offset, grid3offset+grid3-1; do j = 0, grid(2)-1; do i = 0, grid(1)-1
-    ele = ele + 1
-    x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ele)
+    ce = ce + 1
+    x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ce)
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)                                                                                ! initialize to undeformed coordinates (ToDo: use ip coordinates)

From 48f38e74d71c0d259fa99d70d6f00a1ed0b43693 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Thu, 20 Jan 2022 15:11:14 +0100
Subject: [PATCH 087/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-454-gb64a603ef

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 75b174809..208571663 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-451-g3fbf1459d
+v3.0.0-alpha5-454-gb64a603ef

From c2a822d8fd36a17f67e1d0fc31b9c514a7a633a1 Mon Sep 17 00:00:00 2001
From: Sharan Roongta <s.roongta@mpie.de>
Date: Thu, 20 Jan 2022 23:45:47 +0000
Subject: [PATCH 088/133] keys() function for dictionary as in Python. Does not
 work for gfortran which fails with an ICE.

---
 src/YAML_types.f90 | 28 ++++++++++++++++++++++++++++
 src/material.f90   | 11 +++++++++--
 2 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/src/YAML_types.f90 b/src/YAML_types.f90
index 5884c2850..6e926b39e 100644
--- a/src/YAML_types.f90
+++ b/src/YAML_types.f90
@@ -62,6 +62,8 @@ module YAML_types
       tNode_get_byKey_as1dString   => tNode_get_byKey_as1dString
     procedure :: &
       getKey                       => tNode_get_byIndex_asKey
+    procedure :: &
+      Keys                         => tNode_getKeys
     procedure :: &
       getIndex                     => tNode_get_byKey_asIndex
     procedure :: &
@@ -625,6 +627,32 @@ function tNode_get_byIndex_asKey(self,i)  result(key)
 end function tNode_get_byIndex_asKey
 
 
+!--------------------------------------------------------------------------------------------------
+!> @brief Get all keys from a dictionary
+!--------------------------------------------------------------------------------------------------
+function tNode_getKeys(self) result(keys)
+
+  class(tNode), intent(in) :: self
+  character(len=:), dimension(:), allocatable :: keys
+
+  character(len=pStringLen), dimension(:), allocatable :: temp
+  integer :: j, l
+
+  allocate(temp(self%length))
+  l = 0
+  do j = 1, self%length
+    temp(j) = self%getKey(j)
+    l = max(len_trim(temp(j)),l)
+  end do
+
+  allocate(character(l)::keys(self%length))
+  do j = 1, self%length
+    keys(j) = trim(temp(j))
+  end do
+
+end function tNode_getKeys
+
+
 !-------------------------------------------------------------------------------------------------
 !> @brief Checks if a given key/item is present in the dict/list
 !-------------------------------------------------------------------------------------------------
diff --git a/src/material.f90 b/src/material.f90
index 52940ee4a..1e3a4b4ec 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -108,8 +108,14 @@ subroutine parse()
   homogenizations => config_material%get('homogenization')
 
   call sanityCheck(materials, homogenizations)
+
+#if defined (__GFORTRAN__)
   material_name_phase          = getKeys(phases)
   material_name_homogenization = getKeys(homogenizations)
+#else
+  material_name_phase          = phases%Keys()
+  material_name_homogenization = homogenizations%Keys()
+#endif
 
   allocate(homogenization_Nconstituents(homogenizations%length))
   do h=1, homogenizations%length
@@ -203,9 +209,9 @@ subroutine sanityCheck(materials,homogenizations)
 
 end subroutine sanityCheck
 
-
+#if defined (__GFORTRAN__)
 !--------------------------------------------------------------------------------------------------
-!> @brief Get all keys from a dictionary
+!> @brief %keys() is broken on gfortran
 !--------------------------------------------------------------------------------------------------
 function getKeys(dict)
 
@@ -228,5 +234,6 @@ function getKeys(dict)
   end do
 
 end function getKeys
+#endif
 
 end module material

From 4b601a38e7f2904f95f3550c511b94627c1d58bc Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Fri, 21 Jan 2022 03:05:10 +0100
Subject: [PATCH 089/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-457-g75040047c

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 208571663..beee5f0d7 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-454-gb64a603ef
+v3.0.0-alpha5-457-g75040047c

From 76ccd4aaaa7f83b286779a5eb85f57c22ea23441 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@matesting.mpie.de>
Date: Fri, 21 Jan 2022 11:45:14 +0100
Subject: [PATCH 090/133] replaced typehint in shapeshifter function

---
 python/damask/util.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/damask/util.py b/python/damask/util.py
index 053ca9a2e..37d10a7ad 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -8,7 +8,7 @@ import shlex
 import re
 import fractions
 from functools import reduce
-from typing import Union, Tuple, Sequence, Callable, Dict, List, Any, Literal
+from typing import Union, Tuple, Sequence, Callable, Dict, List, Any, Literal, Optional
 import pathlib
 
 import numpy as np
@@ -398,7 +398,7 @@ def hybrid_IA(dist: np.ndarray, N: int, rng_seed: Union[int, IntSequence] = None
 def shapeshifter(fro: Tuple[int, ...],
                  to: Tuple[int, ...],
                  mode: Literal['left','right'] = 'left',
-                 keep_ones: bool = False) -> Tuple[int, ...]:
+                 keep_ones: bool = False) -> Tuple[Optional[int], ...]:
     """
     Return dimensions that reshape 'fro' to become broadcastable to 'to'.
 
@@ -454,7 +454,7 @@ def shapeshifter(fro: Tuple[int, ...],
     except AssertionError:
         raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
     grp: Sequence[str] = match.groups()
-    fill: Tuple[int, ...] = ()
+    fill: Tuple[Optional[int], ...] = ()
     for g,d in zip(grp,fro+(None,)):
         fill += (1,)*g.count(',')+(d,)
     return fill[:-1]

From 96fed368adfa97968d313f3fce0ecd134535ec50 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 21 Jan 2022 08:09:00 +0100
Subject: [PATCH 091/133] name adjustments

---
 src/grid/grid_damage_spectral.f90            |  6 +-
 src/grid/grid_mech_FEM.f90                   | 27 ++++----
 src/grid/grid_mech_spectral_basic.f90        | 31 ++++-----
 src/grid/grid_mech_spectral_polarisation.f90 | 66 ++++++++++----------
 src/grid/grid_thermal_spectral.f90           |  4 +-
 5 files changed, 63 insertions(+), 71 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index f699ee7de..48994ec15 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -132,7 +132,7 @@ subroutine grid_damage_spectral_init()
   call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                 ! global solution vector (grid x 1, i.e. every def grad tensor)
   call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)   ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_damage,damage_grid,err_PETSc); CHKERRQ(err_PETSc)                             ! connect snes to da
+  call SNESSetDM(SNES_damage,damage_grid,err_PETSc); CHKERRQ(err_PETSc)
   call SNESSetFromOptions(SNES_damage,err_PETSc); CHKERRQ(err_PETSc)                                ! pull it all together with additional CLI arguments
   call SNESGetType(SNES_damage,snes_type,err_PETSc); CHKERRQ(err_PETSc)
   if (trim(snes_type) == 'vinewtonrsls' .or. &
@@ -141,12 +141,10 @@ subroutine grid_damage_spectral_init()
     call DMGetGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
     call VecSet(lBound,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
     call VecSet(uBound,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
-    call SNESVISetVariableBounds(SNES_damage,lBound,uBound,err_PETSc)                                ! variable bounds for variational inequalities like contact mechanics, damage etc.
+    call SNESVISetVariableBounds(SNES_damage,lBound,uBound,err_PETSc)                               ! variable bounds for variational inequalities
     call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
     call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
   end if
-
-!--------------------------------------------------------------------------------------------------
   call VecSet(solution_vec,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
 
   call updateReference()
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index a697ce14a..fb3ec85f6 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -50,7 +50,7 @@ module grid_mechanical_FEM
 !--------------------------------------------------------------------------------------------------
 ! PETSc data
   DM   :: mechanical_grid
-  SNES :: mechanical_snes
+  SNES :: SNES_mechanical
   Vec  :: solution_current, solution_lastInc, solution_rate
 
 !--------------------------------------------------------------------------------------------------
@@ -159,9 +159,9 @@ subroutine grid_mechanical_FEM_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,mechanical_snes,err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(mechanical_snes,'mechanical_',err_PETSc)
+  call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
   CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
@@ -192,13 +192,13 @@ subroutine grid_mechanical_FEM_init
   CHKERRQ(err_PETSc)
   call DMSNESSetJacobianLocal(mechanical_grid,formJacobian,PETSC_NULL_SNES,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESSetConvergenceTest(mechanical_snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "_converged"
+  call SNESSetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "_converged"
   CHKERRQ(err_PETSc)
-  call SNESSetMaxLinearSolveFailures(mechanical_snes, huge(1_pPetscInt), err_PETSc)                 ! ignore linear solve failures
+  call SNESSetMaxLinearSolveFailures(SNES_mechanical, huge(1_pPetscInt), err_PETSc)                 ! ignore linear solve failures
   CHKERRQ(err_PETSc)
-  call SNESSetDM(mechanical_snes,mechanical_grid,err_PETSc)
+  call SNESSetDM(SNES_mechanical,mechanical_grid,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESSetFromOptions(mechanical_snes,err_PETSc)                                                ! pull it all together with additional cli arguments
+  call SNESSetFromOptions(SNES_mechanical,err_PETSc)                                                ! pull it all together with additional cli arguments
   CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
@@ -305,14 +305,9 @@ function grid_mechanical_FEM_solution(incInfoIn) result(solution)
 ! update stiffness (and gamma operator)
   S = utilities_maskedCompliance(params%rotation_BC,params%stress_mask,C_volAvg)
 
-!--------------------------------------------------------------------------------------------------
-! solve BVP
-  call SNESsolve(mechanical_snes,PETSC_NULL_VEC,solution_current,err_PETSc)
+  call SNESsolve(SNES_mechanical,PETSC_NULL_VEC,solution_current,err_PETSc)
   CHKERRQ(err_PETSc)
-
-!--------------------------------------------------------------------------------------------------
-! check convergence
-  call SNESGetConvergedReason(mechanical_snes,reason,err_PETSc)
+  call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
   CHKERRQ(err_PETSc)
 
   solution%converged = reason > 0
@@ -533,9 +528,9 @@ subroutine formResidual(da_local,x_local, &
   integer(MPI_INTEGER_KIND) :: err_MPI
   real(pReal), dimension(3,3,3,3) :: devNull
 
-  call SNESGetNumberFunctionEvals(mechanical_snes,nfuncs,err_PETSc)
+  call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
   CHKERRQ(err_PETSc)
-  call SNESGetIterationNumber(mechanical_snes,PETScIter,err_PETSc)
+  call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
   CHKERRQ(err_PETSc)
 
   if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1                                              ! new increment
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index bf72d1d08..00ff756ec 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -50,7 +50,7 @@ module grid_mechanical_spectral_basic
 !--------------------------------------------------------------------------------------------------
 ! PETSc data
   DM   :: da
-  SNES :: snes
+  SNES :: SNES_mechanical
   Vec  :: solution_vec
 
 !--------------------------------------------------------------------------------------------------
@@ -158,8 +158,10 @@ subroutine grid_mechanical_spectral_basic_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,snes,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(snes,'mechanical_',err_PETSc);CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
+  CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
@@ -178,10 +180,10 @@ subroutine grid_mechanical_spectral_basic_init
   call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 9, i.e. every def grad tensor)
   call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)            ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)         ! specify custom convergence check function "converged"
+  call SNESsetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
   CHKERRQ(err_PETSc)
-  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
-  call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc)                                       ! pull it all together with additional CLI arguments
+  call SNESSetDM(SNES_mechanical,da,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESsetFromOptions(SNES_mechanical,err_PETSc); CHKERRQ(err_PETSc)                            ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
@@ -270,13 +272,10 @@ function grid_mechanical_spectral_basic_solution(incInfoIn) result(solution)
   S = utilities_maskedCompliance(params%rotation_BC,params%stress_mask,C_volAvg)
   if (num%update_gamma) call utilities_updateGamma(C_minMaxAvg)
 
-!--------------------------------------------------------------------------------------------------
-! solve BVP
-  call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,err_PETSc); CHKERRQ(err_PETSc)
-
-!--------------------------------------------------------------------------------------------------
-! check convergence
-  call SNESGetConvergedReason(snes,reason,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESsolve(SNES_mechanical,PETSC_NULL_VEC,solution_vec,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   solution%converged = reason > 0
   solution%iterationsNeeded = totalIter
@@ -482,8 +481,10 @@ subroutine formResidual(in, F, &
   PetscErrorCode :: err_PETSc
   integer(MPI_INTEGER_KIND) :: err_MPI
 
-  call SNESGetNumberFunctionEvals(snes,nfuncs,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESGetIterationNumber(snes,PETScIter,err_PETSc);  CHKERRQ(err_PETSc)
+  call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1                                              ! new increment
 
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index 9a258e13e..52c308ae9 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -55,7 +55,7 @@ module grid_mechanical_spectral_polarisation
 !--------------------------------------------------------------------------------------------------
 ! PETSc data
   DM   :: da
-  SNES :: snes
+  SNES :: SNES_mechanical
   Vec  :: solution_vec
 
 !--------------------------------------------------------------------------------------------------
@@ -178,8 +178,9 @@ subroutine grid_mechanical_spectral_polarisation_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,snes,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(snes,'mechanical_',err_PETSc);CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
+  CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
@@ -198,10 +199,10 @@ subroutine grid_mechanical_spectral_polarisation_init
   call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 18, i.e. every def grad tensor)
   call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)            ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESsetConvergenceTest(snes,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)         ! specify custom convergence check function "converged"
+  call SNESsetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
   CHKERRQ(err_PETSc)
-  call SNESSetDM(snes,da,err_PETSc); CHKERRQ(err_PETSc)                                             ! connect snes to da
-  call SNESsetFromOptions(snes,err_PETSc); CHKERRQ(err_PETSc)                                       ! pull it all together with additional CLI arguments
+  call SNESSetDM(SNES_mechanical,da,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESsetFromOptions(SNES_mechanical,err_PETSc); CHKERRQ(err_PETSc)                            ! pull it all together with additional CLI arguments
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
@@ -285,7 +286,7 @@ function grid_mechanical_spectral_polarisation_solution(incInfoIn) result(soluti
 ! input data for solution
   character(len=*), intent(in) :: &
     incInfoIn
-  type(tSolutionState)                    :: &
+  type(tSolutionState) :: &
     solution
 !--------------------------------------------------------------------------------------------------
 ! PETSc Data
@@ -303,13 +304,10 @@ function grid_mechanical_spectral_polarisation_solution(incInfoIn) result(soluti
     S_scale = math_invSym3333(C_minMaxAvg)
   end if
 
-!--------------------------------------------------------------------------------------------------
-! solve BVP
-  call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,err_PETSc); CHKERRQ(err_PETSc)
-
-!--------------------------------------------------------------------------------------------------
-! check convergence
-  call SNESGetConvergedReason(snes,reason,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSolve(SNES_mechanical,PETSC_NULL_VEC,solution_vec,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetConvergedReason(SNES_mechanical,reason,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   solution%converged = reason > 0
   solution%iterationsNeeded = totalIter
@@ -542,8 +540,8 @@ subroutine formResidual(in, FandF_tau, &
   PetscScalar, pointer, dimension(:,:,:,:,:) :: &
     F, &
     F_tau, &
-    residual_F, &
-    residual_F_tau
+    r_F, &
+    r_F_tau
   PetscInt :: &
     PETScIter, &
     nfuncs
@@ -555,21 +553,23 @@ subroutine formResidual(in, FandF_tau, &
 
 !---------------------------------------------------------------------------------------------------
 
-  F              => FandF_tau(1:3,1:3,1,&
-                              XG_RANGE,YG_RANGE,ZG_RANGE)
-  F_tau          => FandF_tau(1:3,1:3,2,&
-                              XG_RANGE,YG_RANGE,ZG_RANGE)
-  residual_F     => r(1:3,1:3,1,&
-                      X_RANGE, Y_RANGE, Z_RANGE)
-  residual_F_tau => r(1:3,1:3,2,&
-                      X_RANGE, Y_RANGE, Z_RANGE)
+  F       => FandF_tau(1:3,1:3,1,&
+                       XG_RANGE,YG_RANGE,ZG_RANGE)
+  F_tau   => FandF_tau(1:3,1:3,2,&
+                       XG_RANGE,YG_RANGE,ZG_RANGE)
+  r_F     => r(1:3,1:3,1,&
+               X_RANGE, Y_RANGE, Z_RANGE)
+  r_F_tau => r(1:3,1:3,2,&
+               X_RANGE, Y_RANGE, Z_RANGE)
 
   F_av = sum(sum(sum(F,dim=5),dim=4),dim=3) * wgt
   call MPI_Allreduce(MPI_IN_PLACE,F_av,9_MPI_INTEGER_KIND,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD,err_MPI)
   if (err_MPI /= 0_MPI_INTEGER_KIND) error stop 'MPI error'
 
-  call SNESGetNumberFunctionEvals(snes,nfuncs,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESGetIterationNumber(snes,PETScIter,err_PETSc);  CHKERRQ(err_PETSc)
+  call SNESGetNumberFunctionEvals(SNES_mechanical,nfuncs,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESGetIterationNumber(SNES_mechanical,PETScIter,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (nfuncs == 0 .and. PETScIter == 0) totalIter = -1                                              ! new increment
 
@@ -603,13 +603,13 @@ subroutine formResidual(in, FandF_tau, &
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  residual_F_tau = num%beta*F - tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)
+  r_F_tau = num%beta*F - tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)
 
 !--------------------------------------------------------------------------------------------------
 ! evaluate constitutive response
-  call utilities_constitutiveResponse(residual_F, &                                                 ! "residuum" gets field of first PK stress (to save memory)
+  call utilities_constitutiveResponse(r_F, &                                                        ! "residuum" gets field of first PK stress (to save memory)
                                       P_av,C_volAvg,C_minMaxAvg, &
-                                      F - residual_F_tau/num%beta,params%Delta_t,params%rotation_BC)
+                                      F - r_F_tau/num%beta,params%Delta_t,params%rotation_BC)
   call MPI_Allreduce(MPI_IN_PLACE,terminallyIll,1_MPI_INTEGER_KIND,MPI_LOGICAL,MPI_LOR,MPI_COMM_WORLD,err_MPI)
 
 !--------------------------------------------------------------------------------------------------
@@ -620,7 +620,7 @@ subroutine formResidual(in, FandF_tau, &
                             params%stress_mask)))
 ! calculate divergence
   tensorField_real = 0.0_pReal
-  tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = residual_F                                !< stress field in disguise
+  tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3) = r_F                                       !< stress field in disguise
   call utilities_FFTtensorForward
   err_div = utilities_divergenceRMS()                                                               !< root mean squared error in divergence of stress
 
@@ -629,11 +629,11 @@ subroutine formResidual(in, FandF_tau, &
   e = 0
   do k = 1, grid3; do j = 1, grid(2); do i = 1, grid(1)
     e = e + 1
-    residual_F(1:3,1:3,i,j,k) = &
+    r_F(1:3,1:3,i,j,k) = &
       math_mul3333xx33(math_invSym3333(homogenization_dPdF(1:3,1:3,1:3,1:3,e) + C_scale), &
-                       residual_F(1:3,1:3,i,j,k) - matmul(F(1:3,1:3,i,j,k), &
+                       r_F(1:3,1:3,i,j,k) - matmul(F(1:3,1:3,i,j,k), &
                        math_mul3333xx33(C_scale,F_tau(1:3,1:3,i,j,k) - F(1:3,1:3,i,j,k) - math_I3))) &
-                       + residual_F_tau(1:3,1:3,i,j,k)
+                       + r_F_tau(1:3,1:3,i,j,k)
   end do; end do; end do
 
 !--------------------------------------------------------------------------------------------------
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index d1d165b83..9c6d10cca 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -134,10 +134,8 @@ subroutine grid_thermal_spectral_init(T_0)
   CHKERRQ(err_PETSc)
   call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)  ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)                           ! connect snes to da
+  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
   call SNESSetFromOptions(SNES_thermal,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
-
-!--------------------------------------------------------------------------------------------------
   call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
   T_PETSc = T_current

From f1051ec28f58723c73bbef8b45090d1fc02e63f3 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 21 Jan 2022 23:34:42 +0000
Subject: [PATCH 092/133] polishing

---
 src/YAML_types.f90 | 258 ++++++++++++++++++++++-----------------------
 1 file changed, 129 insertions(+), 129 deletions(-)

diff --git a/src/YAML_types.f90 b/src/YAML_types.f90
index 6e926b39e..c57f602cf 100644
--- a/src/YAML_types.f90
+++ b/src/YAML_types.f90
@@ -119,7 +119,7 @@ module YAML_types
 
   type, extends(tNode), public :: tList
 
-    class(tItem), pointer  :: first => null()
+    class(tItem), pointer  :: first => NULL()
 
     contains
     procedure :: asFormattedString => tList_asFormattedString
@@ -146,8 +146,8 @@ module YAML_types
 
   type :: tItem
     character(len=:), allocatable :: key
-    class(tNode),     pointer     :: node => null()
-    class(tItem),     pointer     :: next => null()
+    class(tNode),     pointer     :: node => NULL()
+    class(tItem),     pointer     :: next => NULL()
 
     contains
     final :: tItem_finalize
@@ -223,22 +223,22 @@ subroutine selfTest
     select type(s1)
       class is(tScalar)
         s1 = '2'
-    endselect
+    end select
 
     select type(s2)
       class is(tScalar)
         s2 = '3'
-    endselect
+    end select
 
     select type(s3)
       class is(tScalar)
         s3 = '4'
-    endselect
+    end select
 
     select type(s4)
       class is(tScalar)
         s4 = '5'
-    endselect
+    end select
 
 
     allocate(tList::l1)
@@ -251,14 +251,14 @@ subroutine selfTest
         if (any(dNeq(l1%as1dFloat(),[2.0_pReal,3.0_pReal]))) error stop 'tList_as1dFloat'
         if (n%get_asInt(1) /= 2)                             error stop 'byIndex_asInt'
         if (dNeq(n%get_asFloat(2),3.0_pReal))                error stop 'byIndex_asFloat'
-    endselect
+    end select
 
     allocate(tList::l3)
     select type(l3)
       class is(tList)
         call l3%append(s3)
         call l3%append(s4)
-    endselect
+    end select
 
     allocate(tList::l2)
     select type(l2)
@@ -334,9 +334,12 @@ function tNode_asScalar(self) result(scalar)
   class(tNode),   intent(in), target :: self
   class(tScalar), pointer            :: scalar
 
+
   select type(self)
     class is(tScalar)
       scalar => self
+    class default
+      nullify(scalar)
   end select
 
 end function tNode_asScalar
@@ -350,9 +353,12 @@ function tNode_asList(self) result(list)
   class(tNode), intent(in), target :: self
   class(tList), pointer            :: list
 
+
   select type(self)
     class is(tList)
       list => self
+    class default
+      nullify(list)
   end select
 
 end function tNode_asList
@@ -366,9 +372,12 @@ function tNode_asDict(self) result(dict)
   class(tNode), intent(in), target :: self
   class(tDict), pointer            :: dict
 
+
   select type(self)
     class is(tDict)
       dict => self
+    class default
+      nullify(dict)
   end select
 
 end function tNode_asDict
@@ -387,12 +396,13 @@ function tNode_get_byIndex(self,i) result(node)
   class(tItem),  pointer :: item
   integer :: j
 
+
   select type(self)
     class is(tList)
       self_ => self%asList()
     class default
       call IO_error(706,ext_msg='Expected list')
-  endselect
+  end select
 
   item => self_%first
 
@@ -411,15 +421,14 @@ end function tNode_get_byIndex
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_asFloat(self,i) result(nodeAsFloat)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   real(pReal) :: nodeAsFloat
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
-  node   => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tScalar)
       scalar => node%asScalar()
       nodeAsFloat = scalar%asFloat()
@@ -435,15 +444,15 @@ end function tNode_get_byIndex_asFloat
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_asInt(self,i) result(nodeAsInt)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   integer :: nodeAsInt
 
   class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
-  node   => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tScalar)
       scalar => node%asScalar()
       nodeAsInt = scalar%asInt()
@@ -459,21 +468,20 @@ end function tNode_get_byIndex_asInt
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_asBool(self,i) result(nodeAsBool)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   logical :: nodeAsBool
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
-  node   => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tScalar)
       scalar => node%asScalar()
       nodeAsBool = scalar%asBool()
     class default
       call IO_error(706,ext_msg='Expected scalar Boolean')
-  endselect
+  end select
 
 end function tNode_get_byIndex_asBool
 
@@ -483,21 +491,20 @@ end function tNode_get_byIndex_asBool
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_asString(self,i) result(nodeAsString)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   character(len=:), allocatable :: nodeAsString
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
-  node   => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tScalar)
       scalar => node%asScalar()
       nodeAsString = scalar%asString()
     class default
       call IO_error(706,ext_msg='Expected scalar string')
-  endselect
+  end select
 
 end function tNode_get_byIndex_asString
 
@@ -507,21 +514,20 @@ end function tNode_get_byIndex_asString
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_as1dFloat(self,i) result(nodeAs1dFloat)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   real(pReal), dimension(:), allocatable :: nodeAs1dFloat
 
-  class(tNode), pointer  :: node
   class(tList),  pointer :: list
 
-  node => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tList)
       list => node%asList()
       nodeAs1dFloat = list%as1dFloat()
     class default
       call IO_error(706,ext_msg='Expected list of floats')
-  endselect
+  end select
 
 end function tNode_get_byIndex_as1dFloat
 
@@ -531,21 +537,20 @@ end function tNode_get_byIndex_as1dFloat
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_as1dInt(self,i) result(nodeAs1dInt)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   integer, dimension(:), allocatable :: nodeAs1dInt
 
-  class(tNode), pointer :: node
   class(tList), pointer :: list
 
-  node => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tList)
       list => node%asList()
       nodeAs1dInt = list%as1dInt()
     class default
       call IO_error(706,ext_msg='Expected list of integers')
-  endselect
+  end select
 
 end function tNode_get_byIndex_as1dInt
 
@@ -555,21 +560,20 @@ end function tNode_get_byIndex_as1dInt
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_as1dBool(self,i) result(nodeAs1dBool)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   logical, dimension(:), allocatable :: nodeAs1dBool
 
-  class(tNode), pointer :: node
   class(tList), pointer :: list
 
-  node => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tList)
       list => node%asList()
       nodeAs1dBool = list%as1dBool()
     class default
       call IO_error(706,ext_msg='Expected list of Booleans')
-  endselect
+  end select
 
 end function tNode_get_byIndex_as1dBool
 
@@ -579,21 +583,20 @@ end function tNode_get_byIndex_as1dBool
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byIndex_as1dString(self,i) result(nodeAs1dString)
 
-  class(tNode), intent(in), target :: self
-  integer,      intent(in)         :: i
+  class(tNode), intent(in) :: self
+  integer,      intent(in) :: i
   character(len=:), allocatable, dimension(:) :: nodeAs1dString
 
-  class(tNode), pointer :: node
   type(tList),  pointer :: list
 
-  node => self%get(i)
-  select type(node)
+
+  select type(node => self%get(i))
     class is(tList)
       list => node%asList()
       nodeAs1dString = list%as1dString()
     class default
       call IO_error(706,ext_msg='Expected list of strings')
-  endselect
+  end select
 
 end function tNode_get_byIndex_as1dString
 
@@ -611,16 +614,17 @@ function tNode_get_byIndex_asKey(self,i)  result(key)
   type(tDict), pointer :: dict
   type(tItem), pointer :: item
 
+
   select type(self)
     class is(tDict)
       dict => self%asDict()
       item => dict%first
       do j = 1, min(i,dict%length)-1
         item => item%next
-      enddo
+      end do
     class default
       call IO_error(706,ext_msg='Expected dict')
-  endselect
+  end select
 
   key = item%key
 
@@ -638,6 +642,7 @@ function tNode_getKeys(self) result(keys)
   character(len=pStringLen), dimension(:), allocatable :: temp
   integer :: j, l
 
+
   allocate(temp(self%length))
   l = 0
   do j = 1, self%length
@@ -686,7 +691,7 @@ function tNode_contains(self,k)  result(exists)
       enddo
     class default
       call IO_error(706,ext_msg='Expected list or dict')
-  endselect
+  end select
 
 end function tNode_contains
 
@@ -714,7 +719,7 @@ function tNode_get_byKey(self,k,defaultVal) result(node)
       self_ => self%asDict()
     class default
       call IO_error(706,ext_msg='Expected dict for key '//k)
-  endselect
+  end select
 
   j = 1
   item => self_%first
@@ -741,23 +746,22 @@ end function tNode_get_byKey
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_asFloat(self,k,defaultVal) result(nodeAsFloat)
 
-  class(tNode),     intent(in), target  :: self
-  character(len=*), intent(in)          :: k
-  real(pReal),      intent(in),optional :: defaultVal
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
+  real(pReal),      intent(in), optional :: defaultVal
   real(pReal) :: nodeAsFloat
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tScalar)
         scalar => node%asScalar()
         nodeAsFloat = scalar%asFloat()
       class default
         call IO_error(706,ext_msg='Expected scalar float for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAsFloat = defaultVal
   else
@@ -772,23 +776,22 @@ end function tNode_get_byKey_asFloat
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_asInt(self,k,defaultVal) result(nodeAsInt)
 
-  class(tNode),     intent(in), target  :: self
-  character(len=*), intent(in)          :: k
-  integer,          intent(in),optional :: defaultVal
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
+  integer,          intent(in), optional :: defaultVal
   integer :: nodeAsInt
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tScalar)
         scalar => node%asScalar()
         nodeAsInt = scalar%asInt()
       class default
         call IO_error(706,ext_msg='Expected scalar integer for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAsInt = defaultVal
   else
@@ -803,23 +806,22 @@ end function tNode_get_byKey_asInt
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_asBool(self,k,defaultVal) result(nodeAsBool)
 
-  class(tNode),     intent(in), target  :: self
-  character(len=*), intent(in)          :: k
-  logical,          intent(in),optional :: defaultVal
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
+  logical,          intent(in), optional :: defaultVal
   logical :: nodeAsBool
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tScalar)
         scalar => node%asScalar()
         nodeAsBool = scalar%asBool()
       class default
         call IO_error(706,ext_msg='Expected scalar Boolean for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAsBool = defaultVal
   else
@@ -834,23 +836,22 @@ end function tNode_get_byKey_asBool
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_asString(self,k,defaultVal) result(nodeAsString)
 
-  class(tNode),     intent(in), target  :: self
-  character(len=*), intent(in)          :: k
-  character(len=*), intent(in),optional :: defaultVal
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
+  character(len=*), intent(in), optional :: defaultVal
   character(len=:), allocatable :: nodeAsString
 
-  class(tNode),  pointer :: node
   type(tScalar), pointer :: scalar
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tScalar)
         scalar => node%asScalar()
         nodeAsString = scalar%asString()
       class default
         call IO_error(706,ext_msg='Expected scalar string for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAsString = defaultVal
   else
@@ -865,25 +866,24 @@ end function tNode_get_byKey_asString
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_as1dFloat(self,k,defaultVal,requiredSize) result(nodeAs1dFloat)
 
-  class(tNode),     intent(in), target                 :: self
-  character(len=*), intent(in)                         :: k
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
   real(pReal),      intent(in), dimension(:), optional :: defaultVal
   integer,          intent(in),               optional :: requiredSize
 
   real(pReal), dimension(:), allocatable :: nodeAs1dFloat
 
-  class(tNode), pointer :: node
   type(tList),  pointer :: list
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tList)
         list => node%asList()
         nodeAs1dFloat = list%as1dFloat()
       class default
         call IO_error(706,ext_msg='Expected 1D float array for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAs1dFloat = defaultVal
   else
@@ -902,25 +902,24 @@ end function tNode_get_byKey_as1dFloat
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_as2dFloat(self,k,defaultVal,requiredShape) result(nodeAs2dFloat)
 
-  class(tNode),     intent(in), target                   :: self
-  character(len=*), intent(in)                           :: k
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
   real(pReal),      intent(in), dimension(:,:), optional :: defaultVal
   integer,          intent(in), dimension(2),   optional :: requiredShape
 
   real(pReal), dimension(:,:), allocatable :: nodeAs2dFloat
 
-  class(tNode), pointer :: node
   type(tList),  pointer :: rows
 
+
   if(self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tList)
         rows => node%asList()
         nodeAs2dFloat = rows%as2dFloat()
       class default
         call IO_error(706,ext_msg='Expected 2D float array for key '//k)
-    endselect
+    end select
   elseif(present(defaultVal)) then
     nodeAs2dFloat = defaultVal
   else
@@ -939,24 +938,22 @@ end function tNode_get_byKey_as2dFloat
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_as1dInt(self,k,defaultVal,requiredSize) result(nodeAs1dInt)
 
-  class(tNode),          intent(in), target   :: self
-  character(len=*),      intent(in)           :: k
+  class(tNode),          intent(in) :: self
+  character(len=*),      intent(in) :: k
   integer, dimension(:), intent(in), optional :: defaultVal
   integer,               intent(in), optional :: requiredSize
   integer, dimension(:), allocatable :: nodeAs1dInt
 
-  class(tNode), pointer :: node
   type(tList),  pointer :: list
 
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tList)
         list => node%asList()
         nodeAs1dInt = list%as1dInt()
       class default
         call IO_error(706,ext_msg='Expected 1D integer array for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAs1dInt = defaultVal
   else
@@ -975,23 +972,22 @@ end function tNode_get_byKey_as1dInt
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_as1dBool(self,k,defaultVal) result(nodeAs1dBool)
 
-  class(tNode),          intent(in), target   :: self
-  character(len=*),      intent(in)           :: k
+  class(tNode),          intent(in) :: self
+  character(len=*),      intent(in) :: k
   logical, dimension(:), intent(in), optional :: defaultVal
   logical, dimension(:), allocatable          :: nodeAs1dBool
 
-  class(tNode), pointer :: node
   type(tList),  pointer :: list
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tList)
         list => node%asList()
         nodeAs1dBool = list%as1dBool()
       class default
         call IO_error(706,ext_msg='Expected 1D Boolean array for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAs1dBool = defaultVal
   else
@@ -1006,23 +1002,22 @@ end function tNode_get_byKey_as1dBool
 !--------------------------------------------------------------------------------------------------
 function tNode_get_byKey_as1dString(self,k,defaultVal) result(nodeAs1dString)
 
-  class(tNode),     intent(in), target                 :: self
-  character(len=*), intent(in)                         :: k
+  class(tNode),     intent(in) :: self
+  character(len=*), intent(in) :: k
   character(len=*), intent(in), dimension(:), optional :: defaultVal
   character(len=:), allocatable, dimension(:)          :: nodeAs1dString
 
-  class(tNode), pointer :: node
   type(tList),  pointer :: list
 
+
   if (self%contains(k)) then
-    node => self%get(k)
-    select type(node)
+    select type(node => self%get(k))
       class is(tList)
         list => node%asList()
         nodeAs1dString = list%as1dString()
       class default
         call IO_error(706,ext_msg='Expected 1D string array for key '//k)
-    endselect
+    end select
   elseif (present(defaultVal)) then
     nodeAs1dString = defaultVal
   else
@@ -1043,11 +1038,11 @@ function output_as1dString(self)  result(output)                   !ToDo: SR: Re
   class(tNode), pointer :: output_list
   integer :: o
 
-  output_list   => self%get('output',defaultVal=emptyList)
+  output_list => self%get('output',defaultVal=emptyList)
   allocate(output(output_list%length))
   do o = 1, output_list%length
     output(o) = output_list%get_asString(o)
-  enddo
+  end do
 
 end function output_as1dString
 
@@ -1070,7 +1065,7 @@ function tNode_get_byKey_asIndex(self,key)  result(keyIndex)
   do while (associated(item%next) .and. item%key /= key)
     item => item%next
     keyIndex = keyIndex+1
-  enddo
+  end do
 
   if (item%key /= key) call IO_error(140,ext_msg=key)
 
@@ -1115,7 +1110,7 @@ recursive function tList_asFormattedString(self,indent) result(str)
     if (i /= 1) str = str//repeat(' ',indent_)
     str = str//'- '//item%node%asFormattedString(indent_+2)
     item => item%next
-  enddo
+  end do
 
 end function tList_asFormattedString
 
@@ -1147,9 +1142,9 @@ recursive function tDict_asFormattedString(self,indent) result(str)
         str = str//trim(item%key)//': '//item%node%asFormattedString(indent_+len_trim(item%key)+2)
       class default
         str = str//trim(item%key)//':'//IO_EOL//repeat(' ',indent_+2)//item%node%asFormattedString(indent_+2)
-    endselect
+    end select
     item => item%next
-  enddo
+  end do
 
 end function tDict_asFormattedString
 
@@ -1218,13 +1213,14 @@ function tList_as1dFloat(self)
   type(tItem),   pointer :: item
   type(tScalar), pointer :: scalar
 
+
   allocate(tList_as1dFloat(self%length))
   item => self%first
   do i = 1, self%length
     scalar => item%node%asScalar()
     tList_as1dFloat(i) = scalar%asFloat()
     item => item%next
-  enddo
+  end do
 
 end function tList_as1dFloat
 
@@ -1241,6 +1237,7 @@ function tList_as2dFloat(self)
   class(tNode), pointer :: row
   type(tList),  pointer :: row_data
 
+
   row => self%get(1)
   row_data => row%asList()
   allocate(tList_as2dFloat(self%length,row_data%length))
@@ -1248,9 +1245,9 @@ function tList_as2dFloat(self)
   do i=1,self%length
     row => self%get(i)
     row_data => row%asList()
-    if(row_data%length /= size(tList_as2dFloat,2)) call IO_error(709,ext_msg='Varying number of columns')
+    if (row_data%length /= size(tList_as2dFloat,2)) call IO_error(709,ext_msg='Varying number of columns')
     tList_as2dFloat(i,:) = self%get_as1dFloat(i)
-  enddo
+  end do
 
 end function tList_as2dFloat
 
@@ -1267,13 +1264,14 @@ function tList_as1dInt(self)
   type(tItem),   pointer :: item
   type(tScalar), pointer :: scalar
 
+
   allocate(tList_as1dInt(self%length))
   item => self%first
   do i = 1, self%length
     scalar => item%node%asScalar()
     tList_as1dInt(i) = scalar%asInt()
     item => item%next
-  enddo
+  end do
 
 end function tList_as1dInt
 
@@ -1290,13 +1288,14 @@ function tList_as1dBool(self)
   type(tItem),   pointer :: item
   type(tScalar), pointer :: scalar
 
+
   allocate(tList_as1dBool(self%length))
   item => self%first
   do i = 1, self%length
     scalar => item%node%asScalar()
     tList_as1dBool(i) = scalar%asBool()
     item => item%next
-  enddo
+  end do
 
 end function tList_as1dBool
 
@@ -1313,13 +1312,14 @@ function tList_as1dString(self)
   type(tItem),   pointer :: item
   type(tScalar), pointer :: scalar
 
+
   len_max = 0
   item => self%first
   do i = 1, self%length
     scalar => item%node%asScalar()
     len_max = max(len_max, len_trim(scalar%asString()))
     item => item%next
-  enddo
+  end do
 
   allocate(character(len=len_max) :: tList_as1dString(self%length))
   item => self%first

From beb62e1c0aa237eb08f1e5bb3e27b9b376891a11 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Sat, 22 Jan 2022 02:46:29 +0100
Subject: [PATCH 093/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-460-gfc7c165af

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index beee5f0d7..189f07735 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-457-g75040047c
+v3.0.0-alpha5-460-gfc7c165af

From 7e9ce682e7403c3f064da1aeee31a7d381af5fb3 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Fri, 21 Jan 2022 23:50:16 +0100
Subject: [PATCH 094/133] correcting types

Not really sure if srepr and friends take really 'Any'. They take
everything that can be casted (piecewise) to a string. So keep it open
at the moment and leave out a typehint
---
 python/damask/util.py | 106 +++++++++++++++++++++---------------------
 1 file changed, 54 insertions(+), 52 deletions(-)

diff --git a/python/damask/util.py b/python/damask/util.py
index 37d10a7ad..8ae83014c 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -9,13 +9,13 @@ import re
 import fractions
 from functools import reduce
 from typing import Union, Tuple, Sequence, Callable, Dict, List, Any, Literal, Optional
-import pathlib
+from pathlib import Path
 
 import numpy as np
 import h5py
 
-from ._typehints import IntSequence
 from . import version
+from ._typehints import FloatSequence, IntSequence
 
 # limit visibility
 __all__=[
@@ -53,16 +53,16 @@ _colors = {
 ####################################################################################################
 # Functions
 ####################################################################################################
-def srepr(arg: Union[np.ndarray, Sequence[Any]], glue: str = '\n') -> str:
+def srepr(msg, glue: str = '\n') -> str:
     r"""
     Join items with glue string.
 
     Parameters
     ----------
-    arg : iterable
+    msg : object with __repr__ or sequence of objects with __repr__
         Items to join.
     glue : str, optional
-        Glue used for joining operation. Defaults to \n.
+        Glue used for joining operation. Defaults to '\n'.
 
     Returns
     -------
@@ -70,21 +70,21 @@ def srepr(arg: Union[np.ndarray, Sequence[Any]], glue: str = '\n') -> str:
         String representation of the joined items.
 
     """
-    if (not hasattr(arg, 'strip') and
-           (hasattr(arg, '__getitem__') or
-            hasattr(arg, '__iter__'))):
-        return glue.join(str(x) for x in arg)
+    if (not hasattr(msg, 'strip') and
+           (hasattr(msg, '__getitem__') or
+            hasattr(msg, '__iter__'))):
+        return glue.join(str(x) for x in msg)
     else:
-       return arg if isinstance(arg,str) else repr(arg)
+       return msg if isinstance(msg,str) else repr(msg)
 
 
-def emph(what: Any) -> str:
+def emph(msg) -> str:
     """
     Format with emphasis.
 
     Parameters
     ----------
-    what : object with __repr__ or iterable of objects with __repr__.
+    msg : object with __repr__ or sequence of objects with __repr__
         Message to format.
 
     Returns
@@ -93,15 +93,15 @@ def emph(what: Any) -> str:
         Formatted string representation of the joined items.
 
     """
-    return _colors['bold']+srepr(what)+_colors['end_color']
+    return _colors['bold']+srepr(msg)+_colors['end_color']
 
-def deemph(what: Any) -> str:
+def deemph(msg) -> str:
     """
     Format with deemphasis.
 
     Parameters
     ----------
-    what : object with __repr__ or iterable of objects with __repr__.
+    msg : object with __repr__ or sequence of objects with __repr__
         Message to format.
 
     Returns
@@ -110,15 +110,15 @@ def deemph(what: Any) -> str:
         Formatted string representation of the joined items.
 
     """
-    return _colors['dim']+srepr(what)+_colors['end_color']
+    return _colors['dim']+srepr(msg)+_colors['end_color']
 
-def warn(what: Any) -> str:
+def warn(msg) -> str:
     """
     Format for warning.
 
     Parameters
     ----------
-    what : object with __repr__ or iterable of objects with __repr__.
+    msg : object with __repr__ or sequence of objects with __repr__
         Message to format.
 
     Returns
@@ -127,15 +127,15 @@ def warn(what: Any) -> str:
         Formatted string representation of the joined items.
 
     """
-    return _colors['warning']+emph(what)+_colors['end_color']
+    return _colors['warning']+emph(msg)+_colors['end_color']
 
-def strikeout(what: Any) -> str:
+def strikeout(msg) -> str:
     """
     Format as strikeout.
 
     Parameters
     ----------
-    what : object with __repr__ or iterable of objects with __repr__.
+    msg : object with __repr__ or iterable of objects with __repr__
         Message to format.
 
     Returns
@@ -144,10 +144,10 @@ def strikeout(what: Any) -> str:
         Formatted string representation of the joined items.
 
     """
-    return _colors['crossout']+srepr(what)+_colors['end_color']
+    return _colors['crossout']+srepr(msg)+_colors['end_color']
 
 
-def run(cmd: str, wd: str = './', env: Dict[str, Any] = None, timeout: int = None) -> Tuple[str, str]:
+def run(cmd: str, wd: str = './', env: Dict[str, str] = None, timeout: int = None) -> Tuple[str, str]:
     """
     Run a command.
 
@@ -156,7 +156,7 @@ def run(cmd: str, wd: str = './', env: Dict[str, Any] = None, timeout: int = Non
     cmd : str
         Command to be executed.
     wd : str, optional
-        Working directory of process. Defaults to ./ .
+        Working directory of process. Defaults to './'.
     env : dict, optional
         Environment for execution.
     timeout : integer, optional
@@ -235,18 +235,18 @@ def show_progress(iterable: Sequence[Any],
             status.update(i)
 
 
-def scale_to_coprime(v: np.ndarray) -> np.ndarray:
+def scale_to_coprime(v: FloatSequence) -> np.ndarray:
     """
     Scale vector to co-prime (relatively prime) integers.
 
     Parameters
     ----------
-    v : numpy.ndarray of shape (:)
+    v : sequence of float, len (:)
         Vector to scale.
 
     Returns
     -------
-    m : numpy.ndarray of shape (:)
+    m : numpy.ndarray, shape (:)
         Vector scaled to co-prime numbers.
 
     """
@@ -263,27 +263,30 @@ def scale_to_coprime(v: np.ndarray) -> np.ndarray:
         except AttributeError:
             return a * b // np.gcd(a, b)
 
-    m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
+    v_ = np.array(v)
+    m = (v_ * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v_))**0.5).astype(int)
     m = m//reduce(np.gcd,m)
 
     with np.errstate(invalid='ignore'):
-        if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
-            raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
+        if not np.allclose(np.ma.masked_invalid(v_/m),v_[np.argmax(abs(v_))]/m[np.argmax(abs(v_))]):
+            raise ValueError(f'Invalid result {m} for input {v_}. Insufficient precision?')
 
     return m
 
 
-def project_equal_angle(vector: np.ndarray, direction: str  = 'z', normalize: bool = True, keepdims: bool = False) -> np.ndarray:
+def project_equal_angle(vector: np.ndarray,
+                        direction: Literal['x', 'y', 'z'] = 'z',
+                        normalize: bool = True,
+                        keepdims: bool = False) -> np.ndarray:
     """
     Apply equal-angle projection to vector.
 
     Parameters
     ----------
-    vector : numpy.ndarray of shape (...,3)
+    vector : numpy.ndarray, shape (...,3)
         Vector coordinates to be projected.
-    direction : str
-        Projection direction 'x', 'y', or 'z'.
-        Defaults to 'z'.
+    direction : {'x', 'y', 'z'}
+        Projection direction. Defaults to 'z'.
     normalize : bool
         Ensure unit length of input vector. Defaults to True.
     keepdims : bool
@@ -326,9 +329,8 @@ def project_equal_area(vector: np.ndarray,
     ----------
     vector : numpy.ndarray, shape (...,3)
         Vector coordinates to be projected.
-    direction : str
-        Projection direction 'x', 'y', or 'z'.
-        Defaults to 'z'.
+    direction : {'x', 'y', 'z'}
+        Projection direction. Defaults to 'z'.
     normalize : bool
         Ensure unit length of input vector. Defaults to True.
     keepdims : bool
@@ -367,7 +369,7 @@ def execution_stamp(class_name: str, function_name: str = None) -> str:
     return f'damask.{class_name}{_function_name} v{version} ({now})'
 
 
-def hybrid_IA(dist: np.ndarray, N: int, rng_seed: Union[int, IntSequence] = None) -> np.ndarray:
+def hybrid_IA(dist: np.ndarray, N: int, rng_seed = None) -> np.ndarray:
     """
     Hybrid integer approximation.
 
@@ -409,9 +411,9 @@ def shapeshifter(fro: Tuple[int, ...],
     to : tuple
         Target shape of array after broadcasting.
         len(to) cannot be less than len(fro).
-    mode : str, optional
+    mode : {'left', 'right'}, optional
         Indicates whether new axes are preferably added to
-        either 'left' or 'right' of the original shape.
+        either left or right of the original shape.
         Defaults to 'left'.
     keep_ones : bool, optional
         Treat '1' in fro as literal value instead of dimensional placeholder.
@@ -445,15 +447,15 @@ def shapeshifter(fro: Tuple[int, ...],
     fro = (1,) if not len(fro) else fro
     to  = (1,) if not len(to)  else to
     try:
-        match = re.match((beg[mode]
+        match = re.match(beg[mode]
                       +f',{sep[mode]}'.join(map(lambda x: f'{x}'
                                                           if x>1 or (keep_ones and len(fro)>1) else
                                                           '\\d+',fro))
-                      +f',{end[mode]}'),','.join(map(str,to))+',')
+                      +f',{end[mode]}',','.join(map(str,to))+',')
         assert match
+        grp = match.groups()
     except AssertionError:
         raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
-    grp: Sequence[str] = match.groups()
     fill: Tuple[Optional[int], ...] = ()
     for g,d in zip(grp,fro+(None,)):
         fill += (1,)*g.count(',')+(d,)
@@ -522,7 +524,7 @@ def extended_docstring(f: Callable, extra_docstring: str) -> Callable:
     return _decorator
 
 
-def DREAM3D_base_group(fname: Union[str, pathlib.Path]) -> str:
+def DREAM3D_base_group(fname: Union[str, Path]) -> str:
     """
     Determine the base group of a DREAM.3D file.
 
@@ -548,7 +550,7 @@ def DREAM3D_base_group(fname: Union[str, pathlib.Path]) -> str:
 
     return base_group
 
-def DREAM3D_cell_data_group(fname: Union[str, pathlib.Path]) -> str:
+def DREAM3D_cell_data_group(fname: Union[str, Path]) -> str:
     """
     Determine the cell data group of a DREAM.3D file.
 
@@ -586,12 +588,12 @@ def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np
 
     Parameters
     ----------
-    uvtw|hkil : numpy.ndarray of shape (...,4)
+    uvtw|hkil : numpy.ndarray, shape (...,4)
         Miller–Bravais indices of crystallographic direction [uvtw] or plane normal (hkil).
 
     Returns
     -------
-    uvw|hkl : numpy.ndarray of shape (...,3)
+    uvw|hkl : numpy.ndarray, shape (...,3)
         Miller indices of [uvw] direction or (hkl) plane normal.
 
     """
@@ -613,12 +615,12 @@ def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.n
 
     Parameters
     ----------
-    uvw|hkl : numpy.ndarray of shape (...,3)
+    uvw|hkl : numpy.ndarray, shape (...,3)
         Miller indices of crystallographic direction [uvw] or plane normal (hkl).
 
     Returns
     -------
-    uvtw|hkil : numpy.ndarray of shape (...,4)
+    uvtw|hkil : numpy.ndarray, shape (...,4)
         Miller–Bravais indices of [uvtw] direction or (hkil) plane normal.
 
     """
@@ -636,7 +638,7 @@ def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.n
     return np.einsum('il,...l',basis,axis)
 
 
-def dict_prune(d: Dict[Any, Any]) -> Dict[Any, Any]:
+def dict_prune(d: Dict) -> Dict:
     """
     Recursively remove empty dictionaries.
 
@@ -662,7 +664,7 @@ def dict_prune(d: Dict[Any, Any]) -> Dict[Any, Any]:
     return new
 
 
-def dict_flatten(d: Dict[Any, Any]) -> Dict[Any, Any]:
+def dict_flatten(d: Dict) -> Dict:
     """
     Recursively remove keys of single-entry dictionaries.
 

From a35a01d41b443f205bc224f589758b736a247dbf Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 22 Jan 2022 07:50:52 +0100
Subject: [PATCH 095/133] iterable can be any Iterable, not just a Sequence

need to give N_iter only in cases when iterable is not a Sequence
---
 python/damask/seeds.py |  2 +-
 python/damask/util.py  | 29 ++++++++++++++++++++---------
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index 6ff150df3..e6d1f9613 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -79,7 +79,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
 
     s = 1
     i = 0
-    progress = _util._ProgressBar(N_seeds+1,'',50)
+    progress = _util.ProgressBar(N_seeds+1,'',50)
     while s < N_seeds:
         i += 1
         candidates = rng.random((N_candidates,3))*_np.broadcast_to(size,(N_candidates,3))
diff --git a/python/damask/util.py b/python/damask/util.py
index 8ae83014c..d7f674a1c 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -7,8 +7,9 @@ import subprocess
 import shlex
 import re
 import fractions
+import collections.abc as abc
 from functools import reduce
-from typing import Union, Tuple, Sequence, Callable, Dict, List, Any, Literal, Optional
+from typing import Union, Tuple, Iterable, Sequence, Callable, Dict, List, Any, Literal, Optional
 from pathlib import Path
 
 import numpy as np
@@ -203,7 +204,7 @@ def natural_sort(key: str) -> List[Union[int, str]]:
     return [ convert(c) for c in re.split('([0-9]+)', key) ]
 
 
-def show_progress(iterable: Sequence[Any],
+def show_progress(iterable: Iterable,
                   N_iter: int = None,
                   prefix: str = '',
                   bar_length: int = 50) -> Any:
@@ -214,22 +215,32 @@ def show_progress(iterable: Sequence[Any],
 
     Parameters
     ----------
-    iterable : iterable or function with yield statement
-        Iterable (or function with yield statement) to be decorated.
+    iterable : iterable
+        Iterable to be decorated.
     N_iter : int, optional
-        Total number of iterations. Required unless obtainable as len(iterable).
+        Total number of iterations. Required if iterable is not a sequence.
     prefix : str, optional
         Prefix string.
     bar_length : int, optional
         Length of progress bar in characters. Defaults to 50.
 
     """
-    if N_iter in [0,1] or (hasattr(iterable,'__len__') and len(iterable) <= 1):
+    if isinstance(iterable,abc.Sequence):
+       if N_iter is None:
+          N = len(iterable)
+       else:
+          raise ValueError('N_iter given for sequence')
+    else:
+       if N_iter is None:
+          raise ValueError('N_iter not given')
+       else:
+          N = N_iter
+
+    if N <= 1:
         for item in iterable:
             yield item
     else:
-        status = _ProgressBar(N_iter if N_iter is not None else len(iterable),prefix,bar_length)
-
+        status = ProgressBar(N,prefix,bar_length)
         for i,item in enumerate(iterable):
             yield item
             status.update(i)
@@ -692,7 +703,7 @@ def dict_flatten(d: Dict) -> Dict:
 ####################################################################################################
 # Classes
 ####################################################################################################
-class _ProgressBar:
+class ProgressBar:
     """
     Report progress of an interation as a status bar.
 

From 2bbc4c4e4609f5dd36dadc152d7214ae6a3164ad Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 22 Jan 2022 08:05:49 +0100
Subject: [PATCH 096/133] polishing

---
 python/damask/_grid.py | 40 ++++++++++++++++++++--------------------
 python/damask/_vtk.py  | 26 +++++++++++++-------------
 python/damask/util.py  |  4 ++--
 3 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 53b0bd5dc..94f7eefd0 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -70,7 +70,7 @@ class Grid:
               ])
 
 
-    def __copy__(self) -> "Grid":
+    def __copy__(self) -> 'Grid':
         """Create deep copy."""
         return copy.deepcopy(self)
 
@@ -161,7 +161,7 @@ class Grid:
 
 
     @staticmethod
-    def load(fname: Union[str, Path]) -> "Grid":
+    def load(fname: Union[str, Path]) -> 'Grid':
         """
         Load from VTK image data file.
 
@@ -190,7 +190,7 @@ class Grid:
 
     @typing. no_type_check
     @staticmethod
-    def load_ASCII(fname)-> "Grid":
+    def load_ASCII(fname)-> 'Grid':
         """
         Load from geom file.
 
@@ -264,7 +264,7 @@ class Grid:
 
 
     @staticmethod
-    def load_Neper(fname: Union[str, Path]) -> "Grid":
+    def load_Neper(fname: Union[str, Path]) -> 'Grid':
         """
         Load from Neper VTK file.
 
@@ -279,7 +279,7 @@ class Grid:
             Grid-based geometry from file.
 
         """
-        v = VTK.load(fname,'vtkImageData')
+        v = VTK.load(fname,'ImageData')
         cells = np.array(v.vtk_data.GetDimensions())-1
         bbox  = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
 
@@ -292,7 +292,7 @@ class Grid:
     def load_DREAM3D(fname: Union[str, Path],
                      feature_IDs: str = None, cell_data: str = None,
                      phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
-                     base_group: str = None) -> "Grid":
+                     base_group: str = None) -> 'Grid':
         """
         Load DREAM.3D (HDF5) file.
 
@@ -354,7 +354,7 @@ class Grid:
     @staticmethod
     def from_table(table: Table,
                    coordinates: str,
-                   labels: Union[str, Sequence[str]]) -> "Grid":
+                   labels: Union[str, Sequence[str]]) -> 'Grid':
         """
         Create grid from ASCII table.
 
@@ -453,7 +453,7 @@ class Grid:
                                   size: FloatSequence,
                                   seeds: np.ndarray,
                                   material: IntSequence = None,
-                                  periodic: bool = True) -> "Grid":
+                                  periodic: bool = True) -> 'Grid':
         """
         Create grid from Voronoi tessellation.
 
@@ -539,7 +539,7 @@ class Grid:
                              surface: str,
                              threshold: float = 0.0,
                              periods: int = 1,
-                             materials: IntSequence = (0,1)) -> "Grid":
+                             materials: IntSequence = (0,1)) -> 'Grid':
         """
         Create grid from definition of triply periodic minimal surface.
 
@@ -685,7 +685,7 @@ class Grid:
                       fill: int = None,
                       R: Rotation = Rotation(),
                       inverse: bool = False,
-                      periodic: bool = True) -> "Grid":
+                      periodic: bool = True) -> 'Grid':
         """
         Insert a primitive geometric object at a given position.
 
@@ -770,7 +770,7 @@ class Grid:
                    )
 
 
-    def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
+    def mirror(self, directions: Sequence[str], reflect: bool = False) -> 'Grid':
         """
         Mirror grid along given directions.
 
@@ -822,7 +822,7 @@ class Grid:
                    )
 
 
-    def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> "Grid":
+    def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
         """
         Flip grid along given directions.
 
@@ -852,7 +852,7 @@ class Grid:
                    )
 
 
-    def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
+    def scale(self, cells: IntSequence, periodic: bool = True) -> 'Grid':
         """
         Scale grid to new cells.
 
@@ -899,7 +899,7 @@ class Grid:
     def clean(self,
               stencil: int = 3,
               selection: IntSequence = None,
-              periodic: bool = True) -> "Grid":
+              periodic: bool = True) -> 'Grid':
         """
         Smooth grid by selecting most frequent material index within given stencil at each location.
 
@@ -939,7 +939,7 @@ class Grid:
                    )
 
 
-    def renumber(self) -> "Grid":
+    def renumber(self) -> 'Grid':
         """
         Renumber sorted material indices as 0,...,N-1.
 
@@ -958,7 +958,7 @@ class Grid:
                    )
 
 
-    def rotate(self, R: Rotation, fill: int = None) -> "Grid":
+    def rotate(self, R: Rotation, fill: int = None) -> 'Grid':
         """
         Rotate grid (pad if required).
 
@@ -998,7 +998,7 @@ class Grid:
     def canvas(self,
                cells: IntSequence = None,
                offset: IntSequence = None,
-               fill: int = None) -> "Grid":
+               fill: int = None) -> 'Grid':
         """
         Crop or enlarge/pad grid.
 
@@ -1049,7 +1049,7 @@ class Grid:
                    )
 
 
-    def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
+    def substitute(self, from_material: IntSequence, to_material: IntSequence) -> 'Grid':
         """
         Substitute material indices.
 
@@ -1077,7 +1077,7 @@ class Grid:
                    )
 
 
-    def sort(self) -> "Grid":
+    def sort(self) -> 'Grid':
         """
         Sort material indices such that min(material) is located at (0,0,0).
 
@@ -1103,7 +1103,7 @@ class Grid:
                         vicinity: int = 1,
                         offset: int = None,
                         trigger: IntSequence = [],
-                        periodic: bool = True) -> "Grid":
+                        periodic: bool = True) -> 'Grid':
         """
         Offset material index of points in the vicinity of xxx.
 
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index 787aa3c72..4e3f27e0e 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -2,7 +2,7 @@ import os
 import warnings
 import multiprocessing as mp
 from pathlib import Path
-from typing import Union, Optional, Literal, List
+from typing import Union, Literal, List
 
 import numpy as np
 import vtk
@@ -10,7 +10,7 @@ from vtk.util.numpy_support import numpy_to_vtk            as np_to_vtk
 from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
 from vtk.util.numpy_support import vtk_to_numpy            as vtk_to_np
 
-from ._typehints import FloatSequence
+from ._typehints import FloatSequence, IntSequence
 from . import util
 from . import Table
 
@@ -38,8 +38,7 @@ class VTK:
 
 
     @staticmethod
-    #ITERABLES PROPER
-    def from_image_data(cells: np.ndarray, size: np.ndarray, origin: Optional[np.ndarray] = np.zeros(3)) -> "VTK":
+    def from_image_data(cells: IntSequence, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
         """
         Create VTK of type vtk.vtkImageData.
 
@@ -63,13 +62,13 @@ class VTK:
         vtk_data = vtk.vtkImageData()
         vtk_data.SetDimensions(*(np.array(cells)+1))
         vtk_data.SetOrigin(*(np.array(origin)))
-        vtk_data.SetSpacing(*(size/cells))
+        vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
 
         return VTK(vtk_data)
 
 
     @staticmethod
-    def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> "VTK":
+    def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
         """
         Create VTK of type vtk.vtkRectilinearGrid.
 
@@ -101,7 +100,7 @@ class VTK:
 
 
     @staticmethod
-    def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> "VTK":
+    def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> 'VTK':
         """
         Create VTK of type vtk.vtkUnstructuredGrid.
 
@@ -141,7 +140,7 @@ class VTK:
 
 
     @staticmethod
-    def from_poly_data(points: np.ndarray) -> "VTK":
+    def from_poly_data(points: np.ndarray) -> 'VTK':
         """
         Create VTK of type vtk.polyData.
 
@@ -176,15 +175,16 @@ class VTK:
 
     @staticmethod
     def load(fname: Union[str, Path],
-             dataset_type: Literal['vtkImageData', 'vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'] = None) -> "VTK":
+             dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData'] = None) -> 'VTK':
         """
         Load from VTK file.
 
         Parameters
         ----------
         fname : str or pathlib.Path
-            Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
-        dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
+            Filename for reading.
+            Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
+        dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData'}, optional
             Name of the vtk.vtkDataSet subclass when opening a .vtk file.
 
         Returns
@@ -193,7 +193,7 @@ class VTK:
             VTK-based geometry from file.
 
         """
-        if not os.path.isfile(fname):                                                  # vtk has a strange error handling
+        if not os.path.isfile(fname):                                                               # vtk has a strange error handling
             raise FileNotFoundError(f'No such file: {fname}')
         ext = Path(fname).suffix
         if ext == '.vtk' or dataset_type is not None:
@@ -423,7 +423,7 @@ class VTK:
         return writer.GetOutputString()
 
 
-    def show(self) -> None:
+    def show(self):
         """
         Render.
 
diff --git a/python/damask/util.py b/python/damask/util.py
index d7f674a1c..2872762b9 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -9,14 +9,14 @@ import re
 import fractions
 import collections.abc as abc
 from functools import reduce
-from typing import Union, Tuple, Iterable, Sequence, Callable, Dict, List, Any, Literal, Optional
+from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, Optional
 from pathlib import Path
 
 import numpy as np
 import h5py
 
 from . import version
-from ._typehints import FloatSequence, IntSequence
+from ._typehints import FloatSequence
 
 # limit visibility
 __all__=[

From 87ea3dcd1c426a8d37d3089e91afb0eec60ee10d Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 22 Jan 2022 11:54:24 +0100
Subject: [PATCH 097/133] updated license for packages

---
 PRIVATE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PRIVATE b/PRIVATE
index d570b4a1f..2495e15d0 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit d570b4a1fac5b9b99d026d3ff9bf593615e22ce5
+Subproject commit 2495e15d064dea61e0faf078f817e32a637d6eda

From efd9b37235136e87041884c5715975153cac0fb9 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Sun, 23 Jan 2022 12:43:29 +0100
Subject: [PATCH 098/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-475-g160eb1c60

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 189f07735..808f9b405 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-460-gfc7c165af
+v3.0.0-alpha5-475-g160eb1c60

From 3e584570b287f9c98e2aaf68922f8cae859ed20b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 23 Jan 2022 14:15:25 +0100
Subject: [PATCH 099/133] polishing

---
 python/damask/_table.py | 58 ++++++++++++++++++-----------------------
 1 file changed, 25 insertions(+), 33 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index 2221ab318..418549cbb 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -1,11 +1,12 @@
 import re
 import copy
-import pathlib
-from typing import Union, Optional, Tuple, List, TextIO
+from pathlib import Path
+from typing import Union, Optional, Tuple, List
 
 import pandas as pd
 import numpy as np
 
+from ._typehints import FileHandle
 from . import util
 
 class Table:
@@ -40,7 +41,7 @@ class Table:
         return '\n'.join(['# '+c for c in self.comments])+'\n'+data_repr
 
 
-    def __getitem__(self, item: Union[slice, Tuple[slice, ...]]) -> "Table":
+    def __getitem__(self, item: Union[slice, Tuple[slice, ...]]) -> 'Table':
         """
         Slice the Table according to item.
 
@@ -92,7 +93,7 @@ class Table:
         return len(self.data)
 
 
-    def __copy__(self) -> "Table":
+    def __copy__(self) -> 'Table':
         """Create deep copy."""
         return copy.deepcopy(self)
 
@@ -154,7 +155,7 @@ class Table:
 
 
     def isclose(self,
-                    other: "Table",
+                    other: 'Table',
                     rtol: float = 1e-5,
                     atol: float = 1e-8,
                     equal_nan: bool = True) -> np.ndarray:
@@ -186,7 +187,7 @@ class Table:
 
 
     def allclose(self,
-                 other: "Table",
+                 other: 'Table',
                  rtol: float = 1e-5,
                  atol: float = 1e-8,
                  equal_nan: bool = True) -> bool:
@@ -218,7 +219,7 @@ class Table:
 
 
     @staticmethod
-    def load(fname: Union[TextIO, str, pathlib.Path]) -> "Table":
+    def load(fname: FileHandle) -> 'Table':
         """
         Load from ASCII table file.
 
@@ -237,13 +238,10 @@ class Table:
         -------
         loaded : damask.Table
             Table data from file.
-            
+
         """
-        if isinstance(fname, (str, pathlib.Path)):
-            f = open(fname)
-        else:
-            f = fname
-            f.seek(0)
+        f = open(fname) if isinstance(fname, (str, Path)) else fname
+        f.seek(0)
 
         comments = []
         line = f.readline().strip()
@@ -271,7 +269,7 @@ class Table:
 
 
     @staticmethod
-    def load_ang(fname: Union[TextIO, str, pathlib.Path]) -> "Table":
+    def load_ang(fname: FileHandle) -> 'Table':
         """
         Load from ang file.
 
@@ -296,11 +294,8 @@ class Table:
             Table data from file.
 
         """
-        if isinstance(fname, (str, pathlib.Path)):
-            f = open(fname)
-        else:
-            f = fname
-            f.seek(0)
+        f = open(fname) if isinstance(fname, (str, Path)) else fname
+        f.seek(0)
 
         content = f.readlines()
 
@@ -346,7 +341,7 @@ class Table:
         return data.astype(type(data.flatten()[0]))
 
 
-    def set(self, label: str, data: np.ndarray, info: str = None) -> "Table":
+    def set(self, label: str, data: np.ndarray, info: str = None) -> 'Table':
         """
         Set column data.
 
@@ -379,7 +374,7 @@ class Table:
         return dup
 
 
-    def add(self, label: str, data: np.ndarray, info: str = None) -> "Table":
+    def add(self, label: str, data: np.ndarray, info: str = None) -> 'Table':
         """
         Add column data.
 
@@ -411,7 +406,7 @@ class Table:
         return dup
 
 
-    def delete(self, label: str) -> "Table":
+    def delete(self, label: str) -> 'Table':
         """
         Delete column data.
 
@@ -432,7 +427,7 @@ class Table:
         return dup
 
 
-    def rename(self, old: Union[str, List[str]], new: Union[str, List[str]], info: str = None) -> "Table":
+    def rename(self, old: Union[str, List[str]], new: Union[str, List[str]], info: str = None) -> 'Table':
         """
         Rename column data.
 
@@ -458,7 +453,7 @@ class Table:
         return dup
 
 
-    def sort_by(self, labels: Union[str, List[str]], ascending: Union[bool, List[bool]] = True) -> "Table":
+    def sort_by(self, labels: Union[str, List[str]], ascending: Union[bool, List[bool]] = True) -> 'Table':
         """
         Sort table by values of given labels.
 
@@ -491,7 +486,7 @@ class Table:
         return dup
 
 
-    def append(self, other: "Table") -> "Table":
+    def append(self, other: 'Table') -> 'Table':
         """
         Append other table vertically (similar to numpy.vstack).
 
@@ -516,7 +511,7 @@ class Table:
             return dup
 
 
-    def join(self, other: "Table") -> "Table":
+    def join(self, other: 'Table') -> 'Table':
         """
         Append other table horizontally (similar to numpy.hstack).
 
@@ -543,7 +538,7 @@ class Table:
             return dup
 
 
-    def save(self, fname: Union[TextIO, str, pathlib.Path]):
+    def save(self, fname: FileHandle):
         """
         Save as plain text file.
 
@@ -568,10 +563,7 @@ class Table:
                 labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
                           for i in range(np.prod(self.shapes[l]))]
 
-        if isinstance(fname, (str, pathlib.Path)):
-            fhandle = open(fname,'w',newline='\n')
-        else:
-            fhandle = fname
+        f = open(fname,'w',newline='\n') if isinstance(fname, (str, Path)) else fname
 
-        fhandle.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
-        self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)
+        f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
+        self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)

From e320623a40c30b611eaa2907884e337d360c4d19 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 23 Jan 2022 14:22:36 +0100
Subject: [PATCH 100/133] simplified

dict keeps order since Python 3.6
---
 python/damask/_table.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index 418549cbb..68ed869c3 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -548,12 +548,8 @@ class Table:
             Filename or file for writing.
 
         """
-        data_column_items = []
-        for col in self.data.columns:
-            if col not in data_column_items:
-                data_column_items.append(col)
         labels = []
-        for l in data_column_items:
+        for l in list(dict.fromkeys(self.data.columns)):
             if self.shapes[l] == (1,):
                 labels.append(f'{l}')
             elif len(self.shapes[l]) == 1:

From 6bd23715b822c49aa1202c8cea626905ba6102d2 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Mon, 24 Jan 2022 11:53:33 +0100
Subject: [PATCH 101/133] added multiplication as color repeat functionality

---
 python/damask/_colormap.py    | 10 ++++++++++
 python/tests/test_Colormap.py |  5 +++++
 2 files changed, 15 insertions(+)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 1ccc292e6..36f9e2d1b 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -63,6 +63,16 @@ class Colormap(mpl.colors.ListedColormap):
         """Concatenate (in-place)."""
         return self.__add__(other)
 
+    def __mul__(self, factor: int) -> 'Colormap':
+        """Repeat."""
+        return Colormap(np.broadcast_to(self.colors,(factor,)+self.colors.shape)
+                          .reshape((factor*self.colors.shape[0],)+self.colors.shape[1:]),
+                        f'{self.name}*{factor}')
+
+    def __imul__(self, factor: int) -> 'Colormap':
+        """Repeat (in-place)."""
+        return self.__mul__(factor)
+
     def __invert__(self) -> 'Colormap':
         """Reverse."""
         return self.reversed()
diff --git a/python/tests/test_Colormap.py b/python/tests/test_Colormap.py
index 2321745aa..12a26e550 100644
--- a/python/tests/test_Colormap.py
+++ b/python/tests/test_Colormap.py
@@ -140,6 +140,11 @@ class TestColormap:
         c += c
         assert (np.allclose(c.colors[:len(c.colors)//2],c.colors[len(c.colors)//2:]))
 
+    def test_mul(self):
+        c = o = Colormap.from_predefined('jet')
+        o *= 2
+        assert c+c == o
+
     @pytest.mark.parametrize('N,cmap,at,result',[
            (8,'gray',0.5,[0.5,0.5,0.5]),
            (17,'gray',0.5,[0.5,0.5,0.5]),

From 7c72bd48fb5092a0f8bbaee275b3fbb505a5af90 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 24 Jan 2022 15:07:47 +0100
Subject: [PATCH 102/133] simplified

---
 python/damask/_colormap.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 36f9e2d1b..93bd83cdc 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -65,9 +65,7 @@ class Colormap(mpl.colors.ListedColormap):
 
     def __mul__(self, factor: int) -> 'Colormap':
         """Repeat."""
-        return Colormap(np.broadcast_to(self.colors,(factor,)+self.colors.shape)
-                          .reshape((factor*self.colors.shape[0],)+self.colors.shape[1:]),
-                        f'{self.name}*{factor}')
+        return Colormap(np.vstack([self.colors]*factor),f'{self.name}*{factor}')
 
     def __imul__(self, factor: int) -> 'Colormap':
         """Repeat (in-place)."""

From 2f07d88bc7fbd8ed12b7deca259822030adf7ea3 Mon Sep 17 00:00:00 2001
From: Philip Eisenlohr <eisenlohr@egr.msu.edu>
Date: Mon, 24 Jan 2022 21:09:13 +0000
Subject: [PATCH 103/133] clarified set of option values

---
 python/damask/_table.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index 68ed869c3..fed309439 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -108,7 +108,7 @@ class Table:
         ----------
         what : str or list
             Labels to expand.
-        how : str
+        how : {'uniform, 'shapes', 'linear'}
             Mode of labeling.
             'uniform' ==> v v v
             'shapes'  ==> 3:v v v
@@ -137,7 +137,7 @@ class Table:
 
         Parameters
         ----------
-        how : str
+        how : {'uniform, 'shapes', 'linear'}
             Mode of labeling.
             'uniform' ==> v v v
             'shapes'  ==> 3:v v v
@@ -155,10 +155,10 @@ class Table:
 
 
     def isclose(self,
-                    other: 'Table',
-                    rtol: float = 1e-5,
-                    atol: float = 1e-8,
-                    equal_nan: bool = True) -> np.ndarray:
+                other: 'Table',
+                rtol: float = 1e-5,
+                atol: float = 1e-8,
+                equal_nan: bool = True) -> np.ndarray:
         """
         Report where values are approximately equal to corresponding ones of other Table.
 

From 53a34be4fb760a86c0b38f9768ad49f7847da024 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 25 Jan 2022 04:08:56 +0100
Subject: [PATCH 104/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-489-g80526967c

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 808f9b405..76ac47312 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-475-g160eb1c60
+v3.0.0-alpha5-489-g80526967c

From 4c3702215a491d492ed1eb403f6f9f65db522170 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Tue, 25 Jan 2022 08:33:53 +0100
Subject: [PATCH 105/133] nicer formatting (official plain text download)

---
 img/COPYING | 358 ++++++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 288 insertions(+), 70 deletions(-)

diff --git a/img/COPYING b/img/COPYING
index 55872ace2..2aef54637 100644
--- a/img/COPYING
+++ b/img/COPYING
@@ -1,94 +1,312 @@
-Creative Commons Attribution-NoDerivatives 4.0 International Public License
+Creative Commons Attribution-NoDerivatives 4.0 International Public
+License
 
-By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NoDerivatives 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution-NoDerivatives 4.0 International Public License ("Public
+License"). To the extent this Public License may be interpreted as a
+contract, You are granted the Licensed Rights in consideration of Your
+acceptance of these terms and conditions, and the Licensor grants You
+such rights in consideration of benefits the Licensor receives from
+making the Licensed Material available under these terms and
+conditions.
 
-Section 1 – Definitions.
 
-    Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
-    Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
-    Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
-    Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
-    Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
-    Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
-    Licensor means the individual(s) or entity(ies) granting rights under this Public License.
-    Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
-    Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
-    You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
+Section 1 -- Definitions.
 
-Section 2 – Scope.
+  a. Adapted Material means material subject to Copyright and Similar
+     Rights that is derived from or based upon the Licensed Material
+     and in which the Licensed Material is translated, altered,
+     arranged, transformed, or otherwise modified in a manner requiring
+     permission under the Copyright and Similar Rights held by the
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+Section 8 -- Interpretation.
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+     shall not be interpreted to, reduce, limit, restrict, or impose
+     conditions on any use of the Licensed Material that could lawfully
+     be made without permission under this Public License.
+
+  b. To the extent possible, if any provision of this Public License is
+     deemed unenforceable, it shall be automatically reformed to the
+     minimum extent necessary to make it enforceable. If the provision
+     cannot be reformed, it shall be severed from this Public License
+     without affecting the enforceability of the remaining terms and
+     conditions.
+
+  c. No term or condition of this Public License will be waived and no
+     failure to comply consented to unless expressly agreed to by the
+     Licensor.
+
+  d. Nothing in this Public License constitutes or may be interpreted
+     as a limitation upon, or waiver of, any privileges and immunities
+     that apply to the Licensor or You, including from the legal
+     processes of any jurisdiction or authority.

From 4f926b968691a9b06e84d16c88835cdb972dbe11 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 25 Jan 2022 10:47:22 +0100
Subject: [PATCH 106/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-495-g814d89532

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 76ac47312..663e61aee 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-489-g80526967c
+v3.0.0-alpha5-495-g814d89532

From e8c39077df2c0cdda72987756ea712224b6b69aa Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 06:26:37 +0100
Subject: [PATCH 107/133] optional is usually not needed

---
 python/damask/_table.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/python/damask/_table.py b/python/damask/_table.py
index fed309439..d20372d2e 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -1,7 +1,7 @@
 import re
 import copy
 from pathlib import Path
-from typing import Union, Optional, Tuple, List
+from typing import Union, Tuple, List
 
 import pandas as pd
 import numpy as np
@@ -12,7 +12,7 @@ from . import util
 class Table:
     """Manipulate multi-dimensional spreadsheet-like data."""
 
-    def __init__(self, data: np.ndarray, shapes: dict, comments: Optional[Union[str, list]] = None):
+    def __init__(self, data: np.ndarray, shapes: dict, comments: Union[str, list] = None):
         """
         New spreadsheet.
 
@@ -147,7 +147,7 @@ class Table:
         self.data.columns = self._label(self.shapes,how) #type: ignore
 
 
-    def _add_comment(self, label: str, shape: Tuple[int, ...], info: Optional[str]):
+    def _add_comment(self, label: str, shape: Tuple[int, ...], info: str = None):
         if info is not None:
             specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
             general  = util.execution_stamp('Table')

From a86dc322fb113eb08e5b4a848ab1d93d22f04049 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 12:18:26 +0100
Subject: [PATCH 108/133] consistently put the check on the next line

---
 src/grid/grid_damage_spectral.f90            | 55 ++++++++++++-------
 src/grid/grid_mech_FEM.f90                   | 57 +++++++++++++-------
 src/grid/grid_mech_spectral_basic.f90        | 39 +++++++++-----
 src/grid/grid_mech_spectral_polarisation.f90 | 27 ++++++----
 src/grid/grid_thermal_spectral.f90           | 24 ++++++---
 5 files changed, 135 insertions(+), 67 deletions(-)

diff --git a/src/grid/grid_damage_spectral.f90 b/src/grid/grid_damage_spectral.f90
index 48994ec15..96b72dbcc 100644
--- a/src/grid/grid_damage_spectral.f90
+++ b/src/grid/grid_damage_spectral.f90
@@ -112,8 +112,10 @@ subroutine grid_damage_spectral_init()
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,SNES_damage,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(SNES_damage,'damage_',err_PETSc);CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_damage,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(SNES_damage,'damage_',err_PETSc)
+  CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
@@ -127,25 +129,39 @@ subroutine grid_damage_spectral_init()
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          damage_grid,err_PETSc)                                                                     ! handle, error
   CHKERRQ(err_PETSc)
-  call DMsetFromOptions(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
-  call DMsetUp(damage_grid,err_PETSc); CHKERRQ(err_PETSc)
-  call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                 ! global solution vector (grid x 1, i.e. every def grad tensor)
+  call DMsetFromOptions(damage_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMsetUp(damage_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMCreateGlobalVector(damage_grid,solution_vec,err_PETSc)                                     ! global solution vector (grid x 1, i.e. every def grad tensor)
+  CHKERRQ(err_PETSc)
   call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)   ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_damage,damage_grid,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetFromOptions(SNES_damage,err_PETSc); CHKERRQ(err_PETSc)                                ! pull it all together with additional CLI arguments
-  call SNESGetType(SNES_damage,snes_type,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESSetDM(SNES_damage,damage_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(SNES_damage,err_PETSc)                                                    ! pull it all together with additional CLI arguments
+  CHKERRQ(err_PETSc)
+  call SNESGetType(SNES_damage,snes_type,err_PETSc)
+  CHKERRQ(err_PETSc)
   if (trim(snes_type) == 'vinewtonrsls' .or. &
       trim(snes_type) == 'vinewtonssls') then
-    call DMGetGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
-    call DMGetGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
-    call VecSet(lBound,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
-    call VecSet(uBound,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+    call DMGetGlobalVector(damage_grid,lBound,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMGetGlobalVector(damage_grid,uBound,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call VecSet(lBound,0.0_pReal,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call VecSet(uBound,1.0_pReal,err_PETSc)
+    CHKERRQ(err_PETSc)
     call SNESVISetVariableBounds(SNES_damage,lBound,uBound,err_PETSc)                               ! variable bounds for variational inequalities
-    call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc); CHKERRQ(err_PETSc)
-    call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc); CHKERRQ(err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMRestoreGlobalVector(damage_grid,lBound,err_PETSc)
+    CHKERRQ(err_PETSc)
+    call DMRestoreGlobalVector(damage_grid,uBound,err_PETSc)
+    CHKERRQ(err_PETSc)
   end if
-  call VecSet(solution_vec,1.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+  call VecSet(solution_vec,1.0_pReal,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   call updateReference()
 
@@ -202,8 +218,10 @@ function grid_damage_spectral_solution(Delta_t) result(solution)
     call homogenization_set_phi(phi_current(i,j,k),ce)
   end do; end do; end do
 
-  call VecMin(solution_vec,devNull,phi_min,err_PETSc); CHKERRQ(err_PETSc)
-  call VecMax(solution_vec,devNull,phi_max,err_PETSc); CHKERRQ(err_PETSc)
+  call VecMin(solution_vec,devNull,phi_min,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecMax(solution_vec,devNull,phi_max,err_PETSc)
+  CHKERRQ(err_PETSc)
   if (solution%converged) &
     print'(/,1x,a)', '... nonlocal damage converged .....................................'
   print'(/,1x,a,f8.6,2x,f8.6,2x,e11.4)', 'Minimum|Maximum|Delta Damage      = ', phi_min, phi_max, stagNorm
@@ -229,7 +247,8 @@ subroutine grid_damage_spectral_forward(cutBack)
     phi_stagInc = phi_lastInc
 !--------------------------------------------------------------------------------------------------
 ! reverting damage field state
-    call SNESGetDM(SNES_damage,dm_local,err_PETSc); CHKERRQ(err_PETSc)
+    call SNESGetDM(SNES_damage,dm_local,err_PETSc)
+    CHKERRQ(err_PETSc)
     call DMDAVecGetArrayF90(dm_local,solution_vec,phi_PETSc,err_PETSc)                              !< get the data out of PETSc to work with
     CHKERRQ(err_PETSc)
     phi_PETSc = phi_current
diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index fb3ec85f6..1dc421f09 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -203,9 +203,12 @@ subroutine grid_mechanical_FEM_init
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call VecSet(solution_current,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
-  call VecSet(solution_lastInc,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
-  call VecSet(solution_rate   ,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
+  call VecSet(solution_current,0.0_pReal,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecSet(solution_lastInc,0.0_pReal,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecSet(solution_rate   ,0.0_pReal,err_PETSc)
+  CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,err_PETSc)
   CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(mechanical_grid,solution_lastInc,u_lastInc,err_PETSc)
@@ -375,9 +378,11 @@ subroutine grid_mechanical_FEM_forward(cutBack,guess,Delta_t,Delta_t_old,t_remai
       call VecScale(solution_rate,1.0_pReal/Delta_t_old,err_PETSc)
       CHKERRQ(err_PETSc)
     else
-      call VecSet(solution_rate,0.0_pReal,err_PETSc); CHKERRQ(err_PETSc)
+      call VecSet(solution_rate,0.0_pReal,err_PETSc)
+      CHKERRQ(err_PETSc)
     endif
-    call VecCopy(solution_current,solution_lastInc,err_PETSc); CHKERRQ(err_PETSc)
+    call VecCopy(solution_current,solution_lastInc,err_PETSc)
+    CHKERRQ(err_PETSc)
 
     F_lastInc = F
 
@@ -549,7 +554,8 @@ subroutine formResidual(da_local,x_local, &
 
 !--------------------------------------------------------------------------------------------------
 ! get deformation gradient
-  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc)
+  CHKERRQ(err_PETSc)
   do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
     do kk = -1, 0; do jj = -1, 0; do ii = -1, 0
@@ -558,7 +564,8 @@ subroutine formResidual(da_local,x_local, &
     enddo; enddo; enddo
     F(1:3,1:3,i,j,k-grid3offset) = params%rotation_BC%rotate(F_aim,active=.true.) + transpose(matmul(BMat,x_elem))
   enddo; enddo; enddo
-  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! evaluate constitutive response
@@ -575,9 +582,12 @@ subroutine formResidual(da_local,x_local, &
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  call VecSet(f_local,0.0_pReal,err_PETSc);CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
-  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
+  call VecSet(f_local,0.0_pReal,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,x_local,x_scal,err_PETSc)
+  CHKERRQ(err_PETSc)
   ele = 0
   do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
@@ -596,12 +606,15 @@ subroutine formResidual(da_local,x_local, &
       r(0:2,i+ii,j+jj,k+kk) = r(0:2,i+ii,j+jj,k+kk) + f_elem(ctr,1:3)
     enddo; enddo; enddo
   enddo; enddo; enddo
-  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc);CHKERRQ(err_PETSc)
-  call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,x_local,x_scal,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
-  call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da_local,f_local,r,err_PETSc)
+  CHKERRQ(err_PETSc)
   if (grid3offset == 0) then
     r(0:2,0,      0,      0) = 0.0_pReal
     r(0:2,grid(1),0,      0) = 0.0_pReal
@@ -614,7 +627,8 @@ subroutine formResidual(da_local,x_local, &
     r(0:2,0,      grid(2),grid(3)) = 0.0_pReal
     r(0:2,grid(1),grid(2),grid(3)) = 0.0_pReal
   end if
-  call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc);CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da_local,f_local,r,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine formResidual
 
@@ -646,7 +660,8 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   CHKERRQ(err_PETSc)
   call MatSetOption(Jac,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE,err_PETSc)
   CHKERRQ(err_PETSc)
-  call MatZeroEntries(Jac,err_PETSc); CHKERRQ(err_PETSc)
+  call MatZeroEntries(Jac,err_PETSc)
+  CHKERRQ(err_PETSc)
   ce = 0
   do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ctr = 0
@@ -684,10 +699,14 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
     call MatSetValuesStencil(Jac,24_pPETScInt,row,24_pPetscInt,col,K_ele,ADD_VALUES,err_PETSc)
     CHKERRQ(err_PETSc)
   enddo; enddo; enddo
-  call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
-  call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
-  call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
-  call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc); CHKERRQ(err_PETSc)
+  call MatAssemblyBegin(Jac,MAT_FINAL_ASSEMBLY,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatAssemblyEnd(Jac,MAT_FINAL_ASSEMBLY,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatAssemblyBegin(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call MatAssemblyEnd(Jac_pre,MAT_FINAL_ASSEMBLY,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! applying boundary conditions
diff --git a/src/grid/grid_mech_spectral_basic.f90 b/src/grid/grid_mech_spectral_basic.f90
index 00ff756ec..c60c542d0 100644
--- a/src/grid/grid_mech_spectral_basic.f90
+++ b/src/grid/grid_mech_spectral_basic.f90
@@ -175,19 +175,25 @@ subroutine grid_mechanical_spectral_basic_init
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          da,err_PETSc)                                                                              ! handle, error
   CHKERRQ(err_PETSc)
-  call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
-  call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
-  call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 9, i.e. every def grad tensor)
+  call DMsetFromOptions(da,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMsetUp(da,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMcreateGlobalVector(da,solution_vec,err_PETSc)                                              ! global solution vector (grid x 9, i.e. every def grad tensor)
+  CHKERRQ(err_PETSc)
   call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)            ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
   call SNESsetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_mechanical,da,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESsetFromOptions(SNES_mechanical,err_PETSc); CHKERRQ(err_PETSc)                            ! pull it all together with additional CLI arguments
+  call SNESSetDM(SNES_mechanical,da,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESsetFromOptions(SNES_mechanical,err_PETSc)                                                ! pull it all together with additional CLI arguments
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)                          ! places pointer on PETSc data
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)                                              ! places pointer on PETSc data
+  CHKERRQ(err_PETSc)
 
   restartRead: if (interface_restartInc > 0) then
     print'(/,1x,a,i0,a)', 'reading restart data of increment ', interface_restartInc, ' from file'
@@ -220,7 +226,8 @@ subroutine grid_mechanical_spectral_basic_init
   call utilities_constitutiveResponse(P,P_av,C_volAvg,C_minMaxAvg, &                                ! stress field, stress avg, global average of stiffness and (min+max)/2
                                       reshape(F,shape(F_lastInc)), &                                ! target F
                                       0.0_pReal)                                                    ! time increment
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)                      ! deassociate pointer
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)                                          ! deassociate pointer
+  CHKERRQ(err_PETSc)
 
   restartRead2: if (interface_restartInc > 0) then
     print'(1x,a,i0,a)', 'reading more restart data of increment ', interface_restartInc, ' from file'
@@ -309,7 +316,8 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
   PetscScalar, pointer, dimension(:,:,:,:) :: F
 
 
-  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   if (cutBack) then
     C_volAvg    = C_volAvgLastInc
@@ -352,7 +360,8 @@ subroutine grid_mechanical_spectral_basic_forward(cutBack,guess,Delta_t,Delta_t_
 
   F = reshape(utilities_forwardField(Delta_t,F_lastInc,Fdot, &                                      ! estimate of F at end of time+Delta_t that matches rotated F_aim on average
               rotation_BC%rotate(F_aim,active=.true.)),[9,grid(1),grid(2),grid3])
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! set module wide available data
@@ -371,9 +380,11 @@ subroutine grid_mechanical_spectral_basic_updateCoords
   PetscErrorCode :: err_PETSc
   PetscScalar, dimension(:,:,:,:), pointer :: F
 
-  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
+  CHKERRQ(err_PETSc)
   call utilities_updateCoords(F)
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_basic_updateCoords
 
@@ -387,7 +398,8 @@ subroutine grid_mechanical_spectral_basic_restartWrite
   integer(HID_T) :: fileHandle, groupHandle
   PetscScalar, dimension(:,:,:,:), pointer :: F
 
-  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da,solution_vec,F,err_PETSc)
+  CHKERRQ(err_PETSc)
 
   print'(1x,a)', 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
@@ -414,7 +426,8 @@ subroutine grid_mechanical_spectral_basic_restartWrite
 
   if (num%update_gamma) call utilities_saveReferenceStiffness
 
-  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecRestoreArrayF90(da,solution_vec,F,err_PETSc)
+  CHKERRQ(err_PETSc)
 
 end subroutine grid_mechanical_spectral_basic_restartWrite
 
diff --git a/src/grid/grid_mech_spectral_polarisation.f90 b/src/grid/grid_mech_spectral_polarisation.f90
index 52c308ae9..810047403 100644
--- a/src/grid/grid_mech_spectral_polarisation.f90
+++ b/src/grid/grid_mech_spectral_polarisation.f90
@@ -178,7 +178,8 @@ subroutine grid_mechanical_spectral_polarisation_init
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc); CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_mechanical,err_PETSc)
+  CHKERRQ(err_PETSc)
   call SNESSetOptionsPrefix(SNES_mechanical,'mechanical_',err_PETSc)
   CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
@@ -194,19 +195,25 @@ subroutine grid_mechanical_spectral_polarisation_init
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          da,err_PETSc)                                                                              ! handle, error
   CHKERRQ(err_PETSc)
-  call DMsetFromOptions(da,err_PETSc); CHKERRQ(err_PETSc)
-  call DMsetUp(da,err_PETSc); CHKERRQ(err_PETSc)
-  call DMcreateGlobalVector(da,solution_vec,err_PETSc); CHKERRQ(err_PETSc)                          ! global solution vector (grid x 18, i.e. every def grad tensor)
+  call DMsetFromOptions(da,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMsetUp(da,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMcreateGlobalVector(da,solution_vec,err_PETSc)                                              ! global solution vector (grid x 18, i.e. every def grad tensor)
+  CHKERRQ(err_PETSc)
   call DMDASNESsetFunctionLocal(da,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)            ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
   call SNESsetConvergenceTest(SNES_mechanical,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc) ! specify custom convergence check function "converged"
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_mechanical,da,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESsetFromOptions(SNES_mechanical,err_PETSc); CHKERRQ(err_PETSc)                            ! pull it all together with additional CLI arguments
+  call SNESSetDM(SNES_mechanical,da,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESsetFromOptions(SNES_mechanical,err_PETSc)                                                ! pull it all together with additional CLI arguments
+  CHKERRQ(err_PETSc)
 
 !--------------------------------------------------------------------------------------------------
 ! init fields
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)                  ! places pointer on PETSc data
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)                                      ! places pointer on PETSc data
+  CHKERRQ(err_PETSc)
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
@@ -343,7 +350,8 @@ subroutine grid_mechanical_spectral_polarisation_forward(cutBack,guess,Delta_t,D
   real(pReal), dimension(3,3) :: F_lambda33
 
 
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  CHKERRQ(err_PETSc)
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
@@ -444,7 +452,8 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
   integer(HID_T) :: fileHandle, groupHandle
   PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
 
-  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc); CHKERRQ(err_PETSc)
+  call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,err_PETSc)
+  CHKERRQ(err_PETSc)
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
diff --git a/src/grid/grid_thermal_spectral.f90 b/src/grid/grid_thermal_spectral.f90
index 9c6d10cca..f102cf2c1 100644
--- a/src/grid/grid_thermal_spectral.f90
+++ b/src/grid/grid_thermal_spectral.f90
@@ -113,8 +113,10 @@ subroutine grid_thermal_spectral_init(T_0)
 
 !--------------------------------------------------------------------------------------------------
 ! initialize solver specific parts of PETSc
-  call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetOptionsPrefix(SNES_thermal,'thermal_',err_PETSc);CHKERRQ(err_PETSc)
+  call SNESCreate(PETSC_COMM_WORLD,SNES_thermal,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetOptionsPrefix(SNES_thermal,'thermal_',err_PETSc)
+  CHKERRQ(err_PETSc)
   localK            = 0_pPetscInt
   localK(worldrank) = int(grid3,pPetscInt)
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,MPI_COMM_WORLD,err_MPI)
@@ -128,14 +130,18 @@ subroutine grid_thermal_spectral_init(T_0)
          [int(grid(1),pPetscInt)],[int(grid(2),pPetscInt)],localK, &                                ! local grid
          thermal_grid,err_PETSc)                                                                    ! handle, error
   CHKERRQ(err_PETSc)
-  call DMsetFromOptions(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
-  call DMsetUp(thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
+  call DMsetFromOptions(thermal_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call DMsetUp(thermal_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
   call DMCreateGlobalVector(thermal_grid,solution_vec,err_PETSc)                                    ! global solution vector (grid x 1, i.e. every def grad tensor)
   CHKERRQ(err_PETSc)
   call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)  ! residual vector of same shape as solution vector
   CHKERRQ(err_PETSc)
-  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc); CHKERRQ(err_PETSc)
-  call SNESSetFromOptions(SNES_thermal,err_PETSc); CHKERRQ(err_PETSc)                               ! pull it all together with additional CLI arguments
+  call SNESSetDM(SNES_thermal,thermal_grid,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call SNESSetFromOptions(SNES_thermal,err_PETSc)                                                   ! pull it all together with additional CLI arguments
+  CHKERRQ(err_PETSc)
   call DMDAVecGetArrayF90(thermal_grid,solution_vec,T_PETSc,err_PETSc)
   CHKERRQ(err_PETSc)
   T_PETSc = T_current
@@ -197,8 +203,10 @@ function grid_thermal_spectral_solution(Delta_t) result(solution)
     call homogenization_thermal_setField(T_current(i,j,k),(T_current(i,j,k)-T_lastInc(i,j,k))/params%Delta_t,ce)
   end do; end do; end do
 
-  call VecMin(solution_vec,devNull,T_min,err_PETSc); CHKERRQ(err_PETSc)
-  call VecMax(solution_vec,devNull,T_max,err_PETSc); CHKERRQ(err_PETSc)
+  call VecMin(solution_vec,devNull,T_min,err_PETSc)
+  CHKERRQ(err_PETSc)
+  call VecMax(solution_vec,devNull,T_max,err_PETSc)
+  CHKERRQ(err_PETSc)
   if (solution%converged) &
     print'(/,1x,a)', '... thermal conduction converged ..................................'
   print'(/,1x,a,f8.4,2x,f8.4,2x,f8.4)', 'Minimum|Maximum|Delta Temperature / K = ', T_min, T_max, stagNorm

From 68ea33c591423cf919f616a273ca11cb47dedb73 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 12:21:08 +0100
Subject: [PATCH 109/133] start at 1 for the same loop pattern

---
 src/grid/grid_mech_FEM.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/grid/grid_mech_FEM.f90 b/src/grid/grid_mech_FEM.f90
index 1dc421f09..6a3f1323d 100644
--- a/src/grid/grid_mech_FEM.f90
+++ b/src/grid/grid_mech_FEM.f90
@@ -719,9 +719,9 @@ subroutine formJacobian(da_local,x_local,Jac_pre,Jac,dummy,err_PETSc)
   call DMDAVecGetArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)
   ce = 0
-  do k = grid3offset, grid3offset+grid3-1; do j = 0, grid(2)-1; do i = 0, grid(1)-1
+  do k = grid3offset+1, grid3offset+grid3; do j = 1, grid(2); do i = 1, grid(1)
     ce = ce + 1
-    x_scal(0:2,i,j,k) = discretization_IPcoords(1:3,ce)
+    x_scal(0:2,i-1,j-1,k-1) = discretization_IPcoords(1:3,ce)
   enddo; enddo; enddo
   call DMDAVecRestoreArrayF90(da_local,coordinates,x_scal,err_PETSc)
   CHKERRQ(err_PETSc)                                                                                ! initialize to undeformed coordinates (ToDo: use ip coordinates)

From 03d1a14801c93c836096f650c4036d870f37ea9c Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 14:10:21 +0100
Subject: [PATCH 110/133] drop support for Python 3.7

does not support Literal from typing and is in maintenance mode
---
 .github/workflows/Python.yml | 2 +-
 LICENSE                      | 2 +-
 python/setup.py              | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/Python.yml b/.github/workflows/Python.yml
index 4c199b81c..b3d714f92 100644
--- a/.github/workflows/Python.yml
+++ b/.github/workflows/Python.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9'] #, '3.10']
+        python-version: ['3.8', '3.9'] #, '3.10']
         os: [ubuntu-latest, macos-latest]
 
     steps:
diff --git a/LICENSE b/LICENSE
index b4318ac92..8f9664407 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,4 @@
-Copyright 2011-2021 Max-Planck-Institut für Eisenforschung GmbH
+Copyright 2011-2022 Max-Planck-Institut für Eisenforschung GmbH
 
 DAMASK is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as published by
diff --git a/python/setup.py b/python/setup.py
index 1740b54a5..abb8053a9 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -16,7 +16,7 @@ setuptools.setup(
     url='https://damask.mpie.de',
     packages=setuptools.find_packages(),
     include_package_data=True,
-    python_requires = '>=3.7',
+    python_requires = '>=3.8',
     install_requires = [
         'pandas>=0.24',                                                                             # requires numpy
         'numpy>=1.17',                                                                              # needed for default_rng
@@ -30,7 +30,7 @@ setuptools.setup(
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering',
         'Programming Language :: Python :: 3',
-        'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
+        'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
         'Operating System :: OS Independent',
     ],
 )

From 0c21b6a8e0aa7a221e29908560be4590f4ffe5f3 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Wed, 26 Jan 2022 16:25:27 +0100
Subject: [PATCH 111/133] [skip ci] changed almost all function definition
 lines to multiline for colormap, grid, table, vtk and util modules

---
 python/damask/_colormap.py |  3 ++-
 python/damask/_grid.py     | 47 +++++++++++++++++++++++++----------
 python/damask/_table.py    | 51 ++++++++++++++++++++++++++++----------
 python/damask/_vtk.py      | 34 ++++++++++++++++++-------
 python/damask/util.py      | 37 +++++++++++++++++++--------
 5 files changed, 126 insertions(+), 46 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 93bd83cdc..30ae2677e 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -161,7 +161,8 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def from_predefined(name: str, N: int = 256) -> 'Colormap':
+    def from_predefined(name: str,
+                        N: int = 256) -> 'Colormap':
         """
         Select from a set of predefined colormaps.
 
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 94f7eefd0..c62d00cbb 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -101,7 +101,8 @@ class Grid:
         return self._material
 
     @material.setter
-    def material(self, material: np.ndarray):
+    def material(self,
+                 material: np.ndarray):
         if len(material.shape) != 3:
             raise ValueError(f'invalid material shape {material.shape}')
         elif material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
@@ -120,7 +121,8 @@ class Grid:
         return self._size
 
     @size.setter
-    def size(self, size: FloatSequence):
+    def size(self,
+             size: FloatSequence):
         if len(size) != 3 or any(np.array(size) < 0):
             raise ValueError(f'invalid size {size}')
         else:
@@ -132,7 +134,8 @@ class Grid:
         return self._origin
 
     @origin.setter
-    def origin(self, origin: FloatSequence):
+    def origin(self,
+               origin: FloatSequence):
         if len(origin) != 3:
             raise ValueError(f'invalid origin {origin}')
         else:
@@ -144,7 +147,8 @@ class Grid:
         return self._comments
 
     @comments.setter
-    def comments(self, comments: Union[str, Sequence[str]]):
+    def comments(self,
+                 comments: Union[str, Sequence[str]]):
         self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
 
 
@@ -387,7 +391,9 @@ class Grid:
 
 
     @staticmethod
-    def _find_closest_seed(seeds: np.ndarray, weights: np.ndarray, point: np.ndarray) -> np.integer:
+    def _find_closest_seed(seeds: np.ndarray,
+                           weights: np.ndarray,
+                           point: np.ndarray) -> np.integer:
         return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
 
     @staticmethod
@@ -624,7 +630,9 @@ class Grid:
                    )
 
 
-    def save(self, fname: Union[str, Path], compress: bool = True):
+    def save(self,
+             fname: Union[str, Path],
+             compress: bool = True):
         """
         Save as VTK image data file.
 
@@ -643,7 +651,8 @@ class Grid:
         v.save(fname,parallel=False,compress=compress)
 
 
-    def save_ASCII(self, fname: Union[str, TextIO]):
+    def save_ASCII(self,
+                   fname: Union[str, TextIO]):
         """
         Save as geom file.
 
@@ -770,7 +779,9 @@ class Grid:
                    )
 
 
-    def mirror(self, directions: Sequence[str], reflect: bool = False) -> 'Grid':
+    def mirror(self,
+               directions: Sequence[str],
+               reflect: bool = False) -> 'Grid':
         """
         Mirror grid along given directions.
 
@@ -822,7 +833,9 @@ class Grid:
                    )
 
 
-    def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
+    def flip(self,
+             directions: Union[Literal['x', 'y', 'z'],
+             Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
         """
         Flip grid along given directions.
 
@@ -852,7 +865,9 @@ class Grid:
                    )
 
 
-    def scale(self, cells: IntSequence, periodic: bool = True) -> 'Grid':
+    def scale(self,
+              cells: IntSequence,
+              periodic: bool = True) -> 'Grid':
         """
         Scale grid to new cells.
 
@@ -958,7 +973,9 @@ class Grid:
                    )
 
 
-    def rotate(self, R: Rotation, fill: int = None) -> 'Grid':
+    def rotate(self,
+               R: Rotation,
+               fill: int = None) -> 'Grid':
         """
         Rotate grid (pad if required).
 
@@ -1049,7 +1066,9 @@ class Grid:
                    )
 
 
-    def substitute(self, from_material: IntSequence, to_material: IntSequence) -> 'Grid':
+    def substitute(self,
+                   from_material: IntSequence,
+                   to_material: IntSequence) -> 'Grid':
         """
         Substitute material indices.
 
@@ -1150,7 +1169,9 @@ class Grid:
                    )
 
 
-    def get_grain_boundaries(self, periodic: bool = True, directions: Sequence[str] = 'xyz'):
+    def get_grain_boundaries(self,
+                             periodic: bool = True,
+                             directions: Sequence[str] = 'xyz'):
         """
         Create VTK unstructured grid containing grain boundaries.
 
diff --git a/python/damask/_table.py b/python/damask/_table.py
index d20372d2e..16779b83d 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -12,7 +12,10 @@ from . import util
 class Table:
     """Manipulate multi-dimensional spreadsheet-like data."""
 
-    def __init__(self, data: np.ndarray, shapes: dict, comments: Union[str, list] = None):
+    def __init__(self,
+                 data: np.ndarray,
+                 shapes: dict, 
+                 comments: Union[str, list] = None):
         """
         New spreadsheet.
 
@@ -41,7 +44,8 @@ class Table:
         return '\n'.join(['# '+c for c in self.comments])+'\n'+data_repr
 
 
-    def __getitem__(self, item: Union[slice, Tuple[slice, ...]]) -> 'Table':
+    def __getitem__(self,
+                    item: Union[slice, Tuple[slice, ...]]) -> 'Table':
         """
         Slice the Table according to item.
 
@@ -100,7 +104,9 @@ class Table:
     copy = __copy__
 
 
-    def _label(self, what: Union[str, List[str]], how: str) -> List[str]:
+    def _label(self,
+               what: Union[str, List[str]],
+               how: str) -> List[str]:
         """
         Expand labels according to data shape.
 
@@ -147,7 +153,10 @@ class Table:
         self.data.columns = self._label(self.shapes,how) #type: ignore
 
 
-    def _add_comment(self, label: str, shape: Tuple[int, ...], info: str = None):
+    def _add_comment(self,
+                     label: str,
+                     shape: Tuple[int, ...],
+                     info: str = None):
         if info is not None:
             specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
             general  = util.execution_stamp('Table')
@@ -321,7 +330,8 @@ class Table:
         return list(self.shapes)
 
 
-    def get(self, label: str) -> np.ndarray:
+    def get(self,
+            label: str) -> np.ndarray:
         """
         Get column data.
 
@@ -341,7 +351,10 @@ class Table:
         return data.astype(type(data.flatten()[0]))
 
 
-    def set(self, label: str, data: np.ndarray, info: str = None) -> 'Table':
+    def set(self,
+            label: str,
+            data: np.ndarray,
+            info: str = None) -> 'Table':
         """
         Set column data.
 
@@ -374,7 +387,10 @@ class Table:
         return dup
 
 
-    def add(self, label: str, data: np.ndarray, info: str = None) -> 'Table':
+    def add(self,
+            label: str,
+            data: np.ndarray,
+            info: str = None) -> 'Table':
         """
         Add column data.
 
@@ -406,7 +422,8 @@ class Table:
         return dup
 
 
-    def delete(self, label: str) -> 'Table':
+    def delete(self,
+               label: str) -> 'Table':
         """
         Delete column data.
 
@@ -427,7 +444,10 @@ class Table:
         return dup
 
 
-    def rename(self, old: Union[str, List[str]], new: Union[str, List[str]], info: str = None) -> 'Table':
+    def rename(self,
+               old: Union[str, List[str]],
+               new: Union[str, List[str]],
+               info: str = None) -> 'Table':
         """
         Rename column data.
 
@@ -453,7 +473,9 @@ class Table:
         return dup
 
 
-    def sort_by(self, labels: Union[str, List[str]], ascending: Union[bool, List[bool]] = True) -> 'Table':
+    def sort_by(self,
+                labels: Union[str, List[str]],
+                ascending: Union[bool, List[bool]] = True) -> 'Table':
         """
         Sort table by values of given labels.
 
@@ -486,7 +508,8 @@ class Table:
         return dup
 
 
-    def append(self, other: 'Table') -> 'Table':
+    def append(self,
+               other: 'Table') -> 'Table':
         """
         Append other table vertically (similar to numpy.vstack).
 
@@ -511,7 +534,8 @@ class Table:
             return dup
 
 
-    def join(self, other: 'Table') -> 'Table':
+    def join(self,
+             other: 'Table') -> 'Table':
         """
         Append other table horizontally (similar to numpy.hstack).
 
@@ -538,7 +562,8 @@ class Table:
             return dup
 
 
-    def save(self, fname: FileHandle):
+    def save(self,
+             fname: FileHandle):
         """
         Save as plain text file.
 
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index 4e3f27e0e..601608520 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -22,7 +22,8 @@ class VTK:
     High-level interface to VTK.
     """
 
-    def __init__(self, vtk_data: vtk.vtkDataSet):
+    def __init__(self, 
+                 vtk_data: vtk.vtkDataSet):
         """
         New spatial visualization.
 
@@ -38,7 +39,9 @@ class VTK:
 
 
     @staticmethod
-    def from_image_data(cells: IntSequence, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
+    def from_image_data(cells: IntSequence,
+                        size: FloatSequence,
+                        origin: FloatSequence = np.zeros(3)) -> 'VTK':
         """
         Create VTK of type vtk.vtkImageData.
 
@@ -68,7 +71,9 @@ class VTK:
 
 
     @staticmethod
-    def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
+    def from_rectilinear_grid(grid: np.ndarray,
+                              size: FloatSequence,
+                              origin: FloatSequence = np.zeros(3)) -> 'VTK':
         """
         Create VTK of type vtk.vtkRectilinearGrid.
 
@@ -100,7 +105,9 @@ class VTK:
 
 
     @staticmethod
-    def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> 'VTK':
+    def from_unstructured_grid(nodes: np.ndarray,
+                               connectivity: np.ndarray,
+                               cell_type: str) -> 'VTK':
         """
         Create VTK of type vtk.vtkUnstructuredGrid.
 
@@ -238,7 +245,11 @@ class VTK:
     def _write(writer):
         """Wrapper for parallel writing."""
         writer.Write()
-    def save(self, fname: Union[str, Path], parallel: bool = True, compress: bool = True):
+
+    def save(self,
+             fname: Union[str, Path],
+             parallel: bool = True,
+             compress: bool = True):
         """
         Save as VTK file.
 
@@ -284,7 +295,9 @@ class VTK:
 
     # Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
     # Needs support for damask.Table
-    def add(self, data: Union[np.ndarray, np.ma.MaskedArray], label: str = None):
+    def add(self,
+            data: Union[np.ndarray, np.ma.MaskedArray],
+            label: str = None):
         """
         Add data to either cells or points.
 
@@ -331,7 +344,8 @@ class VTK:
             raise TypeError
 
 
-    def get(self, label: str) -> np.ndarray:
+    def get(self,
+            label: str) -> np.ndarray:
         """
         Get either cell or point data.
 
@@ -383,7 +397,8 @@ class VTK:
         return []
 
 
-    def set_comments(self, comments: Union[str, List[str]]):
+    def set_comments(self,
+                     comments: Union[str, List[str]]):
         """
         Set comments.
 
@@ -400,7 +415,8 @@ class VTK:
         self.vtk_data.GetFieldData().AddArray(s)
 
 
-    def add_comments(self, comments: Union[str, List[str]]):
+    def add_comments(self,
+                     comments: Union[str, List[str]]):
         """
         Add comments.
 
diff --git a/python/damask/util.py b/python/damask/util.py
index 2872762b9..7c1803e80 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -54,7 +54,8 @@ _colors = {
 ####################################################################################################
 # Functions
 ####################################################################################################
-def srepr(msg, glue: str = '\n') -> str:
+def srepr(msg,
+          glue: str = '\n') -> str:
     r"""
     Join items with glue string.
 
@@ -148,7 +149,10 @@ def strikeout(msg) -> str:
     return _colors['crossout']+srepr(msg)+_colors['end_color']
 
 
-def run(cmd: str, wd: str = './', env: Dict[str, str] = None, timeout: int = None) -> Tuple[str, str]:
+def run(cmd: str,
+        wd: str = './',
+        env: Dict[str, str] = None,
+        timeout: int = None) -> Tuple[str, str]:
     """
     Run a command.
 
@@ -373,14 +377,17 @@ def project_equal_area(vector: np.ndarray,
     return np.roll(np.block([v[...,:2]/np.sqrt(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
                    -shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
 
-def execution_stamp(class_name: str, function_name: str = None) -> str:
+def execution_stamp(class_name: str,
+                    function_name: str = None) -> str:
     """Timestamp the execution of a (function within a) class."""
     now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
     _function_name = '' if function_name is None else f'.{function_name}'
     return f'damask.{class_name}{_function_name} v{version} ({now})'
 
 
-def hybrid_IA(dist: np.ndarray, N: int, rng_seed = None) -> np.ndarray:
+def hybrid_IA(dist: np.ndarray,
+              N: int,
+              rng_seed = None) -> np.ndarray:
     """
     Hybrid integer approximation.
 
@@ -473,7 +480,8 @@ def shapeshifter(fro: Tuple[int, ...],
     return fill[:-1]
 
 
-def shapeblender(a: Tuple[int, ...], b: Tuple[int, ...]) -> Tuple[int, ...]:
+def shapeblender(a: Tuple[int, ...],
+                 b: Tuple[int, ...]) -> Tuple[int, ...]:
     """
     Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
 
@@ -517,7 +525,8 @@ def extend_docstring(extra_docstring: str) -> Callable:
     return _decorator
 
 
-def extended_docstring(f: Callable, extra_docstring: str) -> Callable:
+def extended_docstring(f: Callable,
+                       extra_docstring: str) -> Callable:
     """
     Decorator: Combine another function's docstring with a given docstring.
 
@@ -593,7 +602,9 @@ def DREAM3D_cell_data_group(fname: Union[str, Path]) -> str:
     return cell_data_group
 
 
-def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np.ndarray:
+def Bravais_to_Miller(*,
+                      uvtw: np.ndarray = None,
+                      hkil: np.ndarray = None) -> np.ndarray:
     """
     Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
 
@@ -620,7 +631,9 @@ def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np
     return np.einsum('il,...l',basis,axis)
 
 
-def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
+def Miller_to_Bravais(*,
+                      uvw: np.ndarray = None,
+                      hkl: np.ndarray = None) -> np.ndarray:
     """
     Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
 
@@ -710,7 +723,10 @@ class ProgressBar:
     Works for 0-based loops, ETA is estimated by linear extrapolation.
     """
 
-    def __init__(self, total: int, prefix: str, bar_length: int):
+    def __init__(self,
+                 total: int,
+                 prefix: str,
+                 bar_length: int):
         """
         Set current time as basis for ETA estimation.
 
@@ -733,7 +749,8 @@ class ProgressBar:
         sys.stderr.write(f"{self.prefix} {'░'*self.bar_length}   0% ETA n/a")
         sys.stderr.flush()
 
-    def update(self, iteration: int) -> None:
+    def update(self,
+               iteration: int) -> None:
 
         fraction = (iteration+1) / self.total
         filled_length = int(self.bar_length * fraction)

From 8e514bf6f42dae2b012ba2cad432d28bbbd10dde Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Wed, 26 Jan 2022 16:36:26 +0100
Subject: [PATCH 112/133] added missing utils typehint

---
 python/damask/util.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/damask/util.py b/python/damask/util.py
index 7c1803e80..e1db35007 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -16,7 +16,7 @@ import numpy as np
 import h5py
 
 from . import version
-from ._typehints import FloatSequence
+from ._typehints import IntSequence, FloatSequence
 
 # limit visibility
 __all__=[
@@ -387,7 +387,7 @@ def execution_stamp(class_name: str,
 
 def hybrid_IA(dist: np.ndarray,
               N: int,
-              rng_seed = None) -> np.ndarray:
+              rng_seed: Union[int, IntSequence] = None) -> np.ndarray:
     """
     Hybrid integer approximation.
 

From a2ad146c3ea7f691a66b1e3ecbbcc45fc5eac190 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 21:47:07 +0100
Subject: [PATCH 113/133] TWIP/TRIP is broken, skip testing at the moment

---
 PRIVATE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PRIVATE b/PRIVATE
index 2495e15d0..5598ec489 160000
--- a/PRIVATE
+++ b/PRIVATE
@@ -1 +1 @@
-Subproject commit 2495e15d064dea61e0faf078f817e32a637d6eda
+Subproject commit 5598ec4892b0921fccf63e8570f9fcd8e0365716

From c5fd467b448c09db261ef104176fe978eeafd2df Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 07:21:56 +0100
Subject: [PATCH 114/133] power to one not needed

---
 src/phase_mechanical_eigen_thermalexpansion.f90 |  4 ++--
 src/phase_mechanical_elastic.f90                | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/phase_mechanical_eigen_thermalexpansion.f90 b/src/phase_mechanical_eigen_thermalexpansion.f90
index 087cf7d3d..70bf84cd8 100644
--- a/src/phase_mechanical_eigen_thermalexpansion.f90
+++ b/src/phase_mechanical_eigen_thermalexpansion.f90
@@ -99,11 +99,11 @@ module subroutine thermalexpansion_LiAndItsTangent(Li, dLi_dTstar, ph,me)
   associate(prm => param(kinematics_thermal_expansion_instance(ph)))
     Li = dot_T * ( &
                   prm%A(1:3,1:3,1) &                                                                ! constant  coefficient
-                + prm%A(1:3,1:3,2)*(T - prm%T_ref)**1 &                                             ! linear    coefficient
+                + prm%A(1:3,1:3,2)*(T - prm%T_ref) &                                                ! linear    coefficient
                 + prm%A(1:3,1:3,3)*(T - prm%T_ref)**2 &                                             ! quadratic coefficient
                 ) / &
          (1.0_pReal &
-               + prm%A(1:3,1:3,1)*(T - prm%T_ref)**1 / 1.0_pReal &
+               + prm%A(1:3,1:3,1)*(T - prm%T_ref)    / 1.0_pReal &
                + prm%A(1:3,1:3,2)*(T - prm%T_ref)**2 / 2.0_pReal &
                + prm%A(1:3,1:3,3)*(T - prm%T_ref)**3 / 3.0_pReal &
          )
diff --git a/src/phase_mechanical_elastic.f90 b/src/phase_mechanical_elastic.f90
index bb530747b..8972367d5 100644
--- a/src/phase_mechanical_elastic.f90
+++ b/src/phase_mechanical_elastic.f90
@@ -101,32 +101,32 @@ pure module function elastic_C66(ph,en) result(C66)
     T = thermal_T(ph,en)
 
     C66(1,1) = prm%C_11(1) &
-             + prm%C_11(2)*(T - prm%T_ref)**1 &
+             + prm%C_11(2)*(T - prm%T_ref) &
              + prm%C_11(3)*(T - prm%T_ref)**2
 
     C66(1,2) = prm%C_12(1) &
-             + prm%C_12(2)*(T - prm%T_ref)**1 &
+             + prm%C_12(2)*(T - prm%T_ref) &
              + prm%C_12(3)*(T - prm%T_ref)**2
 
     C66(4,4) = prm%C_44(1) &
-             + prm%C_44(2)*(T - prm%T_ref)**1 &
+             + prm%C_44(2)*(T - prm%T_ref) &
              + prm%C_44(3)*(T - prm%T_ref)**2
 
 
     if (any(phase_lattice(ph) == ['hP','tI'])) then
       C66(1,3) = prm%C_13(1) &
-               + prm%C_13(2)*(T - prm%T_ref)**1 &
+               + prm%C_13(2)*(T - prm%T_ref) &
                + prm%C_13(3)*(T - prm%T_ref)**2
 
       C66(3,3) = prm%C_33(1) &
-               + prm%C_33(2)*(T - prm%T_ref)**1 &
+               + prm%C_33(2)*(T - prm%T_ref) &
                + prm%C_33(3)*(T - prm%T_ref)**2
 
     end if
 
     if (phase_lattice(ph) == 'tI') then
       C66(6,6) = prm%C_66(1) &
-               + prm%C_66(2)*(T - prm%T_ref)**1 &
+               + prm%C_66(2)*(T - prm%T_ref) &
                + prm%C_66(3)*(T - prm%T_ref)**2
     end if
 

From bc667888ce196586f6b9588e7d50a186af0a5c1b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Wed, 26 Jan 2022 23:37:07 +0100
Subject: [PATCH 115/133] consistent style

---
 python/damask/_colormap.py | 33 ++++++++++++++++++++++-----------
 python/damask/_grid.py     |  3 ++-
 python/damask/_table.py    |  3 ++-
 3 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 30ae2677e..5c77cf61e 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -47,27 +47,32 @@ class Colormap(mpl.colors.ListedColormap):
 
     """
 
-    def __eq__(self, other: object) -> bool:
+    def __eq__(self,
+               other: object) -> bool:
         """Test equality of colormaps."""
         if not isinstance(other, Colormap):
             return NotImplemented
         return         len(self.colors) == len(other.colors) \
            and bool(np.all(self.colors  ==     other.colors))
 
-    def __add__(self, other: 'Colormap') -> 'Colormap':
+    def __add__(self,
+                other: 'Colormap') -> 'Colormap':
         """Concatenate."""
         return Colormap(np.vstack((self.colors,other.colors)),
                         f'{self.name}+{other.name}')
 
-    def __iadd__(self, other: 'Colormap') -> 'Colormap':
+    def __iadd__(self,
+                 other: 'Colormap') -> 'Colormap':
         """Concatenate (in-place)."""
         return self.__add__(other)
 
-    def __mul__(self, factor: int) -> 'Colormap':
+    def __mul__(self,
+                factor: int) -> 'Colormap':
         """Repeat."""
         return Colormap(np.vstack([self.colors]*factor),f'{self.name}*{factor}')
 
-    def __imul__(self, factor: int) -> 'Colormap':
+    def __imul__(self,
+                 factor: int) -> 'Colormap':
         """Repeat (in-place)."""
         return self.__mul__(factor)
 
@@ -276,7 +281,8 @@ class Colormap(mpl.colors.ListedColormap):
             mode='RGBA')
 
 
-    def reversed(self, name: str = None) -> 'Colormap':
+    def reversed(self,
+                 name: str = None) -> 'Colormap':
         """
         Reverse.
 
@@ -329,7 +335,8 @@ class Colormap(mpl.colors.ListedColormap):
             return fname
 
 
-    def save_paraview(self, fname: FileHandle = None):
+    def save_paraview(self,
+                      fname: FileHandle = None):
         """
         Save as JSON file for use in Paraview.
 
@@ -356,7 +363,8 @@ class Colormap(mpl.colors.ListedColormap):
         fhandle.write('\n')
 
 
-    def save_ASCII(self, fname: FileHandle = None):
+    def save_ASCII(self,
+                   fname: FileHandle = None):
         """
         Save as ASCII file.
 
@@ -391,7 +399,8 @@ class Colormap(mpl.colors.ListedColormap):
         self._get_file_handle(fname,'.legend').write(GOM_str)
 
 
-    def save_gmsh(self, fname: FileHandle = None):
+    def save_gmsh(self,
+                  fname: FileHandle = None):
         """
         Save as ASCII file for use in gmsh.
 
@@ -622,7 +631,8 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
+    def _lab2xyz(lab: np.ndarray,
+                 ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
         """
         CIE Lab to CIE Xyz.
 
@@ -653,7 +663,8 @@ class Colormap(mpl.colors.ListedColormap):
                         ])*ref_white
 
     @staticmethod
-    def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
+    def _xyz2lab(xyz: np.ndarray,
+                 ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
         """
         CIE Xyz to CIE Lab.
 
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index c62d00cbb..b188873a4 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -77,7 +77,8 @@ class Grid:
     copy = __copy__
 
 
-    def __eq__(self, other: object) -> bool:
+    def __eq__(self,
+               other: object) -> bool:
         """
         Test equality of other.
 
diff --git a/python/damask/_table.py b/python/damask/_table.py
index 16779b83d..44a04b40a 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -137,7 +137,8 @@ class Table:
         return labels
 
 
-    def _relabel(self, how: str):
+    def _relabel(self,
+                 how: str):
         """
         Modify labeling of data in-place.
 

From 4ca501c73f221924729d695cd0e73dae004e200e Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 27 Jan 2022 08:53:27 +0100
Subject: [PATCH 116/133] small changes in logic for type hints

---
 python/damask/_crystal.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/python/damask/_crystal.py b/python/damask/_crystal.py
index 7a21f9245..a8b2ccf79 100644
--- a/python/damask/_crystal.py
+++ b/python/damask/_crystal.py
@@ -33,9 +33,9 @@ class Crystal():
     def __init__(self,*,
                  family = None,
                  lattice = None,
-                 a = None,b = None,c = None,
-                 alpha = None,beta = None,gamma = None,
-                 degrees = False):
+                 a: float = None, b: float = None, c: float = None,
+                 alpha: float = None, beta: float = None, gamma: float = None,
+                 degrees: bool = False):
         """
         Representation of crystal in terms of crystal family or Bravais lattice.
 
@@ -62,7 +62,7 @@ class Crystal():
             Angles are given in degrees. Defaults to False.
 
         """
-        if family not in [None] + list(lattice_symmetries.values()):
+        if family is not None and family not in list(lattice_symmetries.values()):
             raise KeyError(f'invalid crystal family "{family}"')
         if lattice is not None and family is not None and family != lattice_symmetries[lattice]:
             raise KeyError(f'incompatible family "{family}" for lattice "{lattice}"')
@@ -107,9 +107,6 @@ class Crystal():
             if np.any([np.roll([self.alpha,self.beta,self.gamma],r)[0]
               >= np.sum(np.roll([self.alpha,self.beta,self.gamma],r)[1:]) for r in range(3)]):
                 raise ValueError ('each lattice angle must be less than sum of others')
-        else:
-            self.a = self.b = self.c = None
-            self.alpha = self.beta = self.gamma = None
 
 
     def __repr__(self):
@@ -139,8 +136,7 @@ class Crystal():
     @property
     def parameters(self):
         """Return lattice parameters a, b, c, alpha, beta, gamma."""
-        return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
-
+        if hasattr(self,'a'): return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
 
     @property
     def immutable(self):
@@ -269,7 +265,7 @@ class Crystal():
         https://doi.org/10.1063/1.1661333
 
         """
-        if None in self.parameters:
+        if self.parameters is None:
             raise KeyError('missing crystal lattice parameters')
         return np.array([
                           [1,0,0],

From a12135fe7786b2ca0ca90a9bf2c7cb48a801f1c0 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Thu, 27 Jan 2022 10:45:14 +0100
Subject: [PATCH 117/133] [skip ci] changed function definition to multiline
 layout for crystal, seeds and tensor module

---
 python/damask/_crystal.py | 15 +++++++++++----
 python/damask/seeds.py    | 19 ++++++++++++++-----
 python/damask/tensor.py   |  6 ++++--
 3 files changed, 29 insertions(+), 11 deletions(-)

diff --git a/python/damask/_crystal.py b/python/damask/_crystal.py
index a8b2ccf79..c97f75d01 100644
--- a/python/damask/_crystal.py
+++ b/python/damask/_crystal.py
@@ -311,7 +311,9 @@ class Crystal():
                         + _lattice_points.get(self.lattice if self.lattice == 'hP' else \
                                               self.lattice[-1],None),dtype=float)
 
-    def to_lattice(self, *, direction: np.ndarray = None, plane: np.ndarray = None) -> np.ndarray:
+    def to_lattice(self,
+                   *, direction: np.ndarray = None,
+                   plane: np.ndarray = None) -> np.ndarray:
         """
         Calculate lattice vector corresponding to crystal frame direction or plane normal.
 
@@ -335,7 +337,10 @@ class Crystal():
         return np.einsum('il,...l',basis,axis)
 
 
-    def to_frame(self, *, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
+    def to_frame(self,
+                 *,
+                 uvw: np.ndarray = None,
+                 hkl: np.ndarray = None) -> np.ndarray:
         """
         Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
 
@@ -358,7 +363,8 @@ class Crystal():
         return np.einsum('il,...l',basis,axis)
 
 
-    def kinematics(self, mode: str) -> Dict[str, List[np.ndarray]]:
+    def kinematics(self,
+                   mode: str) -> Dict[str, List[np.ndarray]]:
         """
         Return crystal kinematics systems.
 
@@ -617,7 +623,8 @@ class Crystal():
                     'plane':    [m[:,3:6] for m in master]}
 
 
-    def relation_operations(self, model: str) -> Tuple[str, Rotation]:
+    def relation_operations(self,
+                            model: str) -> Tuple[str, Rotation]:
         """
         Crystallographic orientation relationships for phase transformations.
 
diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index e6d1f9613..1a3af7a64 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -10,7 +10,9 @@ from . import util as _util
 from . import grid_filters as _grid_filters
 
 
-def from_random(size: _FloatSequence, N_seeds: int, cells: _IntSequence = None,
+def from_random(size: _FloatSequence,
+                N_seeds: int,
+                cells: _IntSequence = None,
                 rng_seed=None) -> _np.ndarray:
     """
     Place seeds randomly in space.
@@ -46,8 +48,12 @@ def from_random(size: _FloatSequence, N_seeds: int, cells: _IntSequence = None,
     return coords
 
 
-def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, distance: float,
-                      periodic: bool = True, rng_seed=None) -> _np.ndarray:
+def from_Poisson_disc(size: _FloatSequence,
+                      N_seeds: int,
+                      N_candidates: int,
+                      distance: float,
+                      periodic: bool = True,
+                      rng_seed=None) -> _np.ndarray:
     """
     Place seeds according to a Poisson disc distribution.
 
@@ -99,8 +105,11 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
     return coords
 
 
-def from_grid(grid, selection: _IntSequence = None, invert_selection: bool = False,
-              average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
+def from_grid(grid,
+              selection: _IntSequence = None,
+              invert_selection: bool = False,
+              average: bool = False,
+              periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
     """
     Create seeds from grid description.
 
diff --git a/python/damask/tensor.py b/python/damask/tensor.py
index 4f6cb36ea..73cdd7400 100644
--- a/python/damask/tensor.py
+++ b/python/damask/tensor.py
@@ -45,7 +45,8 @@ def eigenvalues(T_sym: _np.ndarray) -> _np.ndarray:
     return _np.linalg.eigvalsh(symmetric(T_sym))
 
 
-def eigenvectors(T_sym: _np.ndarray, RHS: bool = False) -> _np.ndarray:
+def eigenvectors(T_sym: _np.ndarray,
+                 RHS: bool = False) -> _np.ndarray:
     """
     Eigenvectors of a symmetric tensor.
 
@@ -70,7 +71,8 @@ def eigenvectors(T_sym: _np.ndarray, RHS: bool = False) -> _np.ndarray:
     return v
 
 
-def spherical(T: _np.ndarray, tensor: bool = True) -> _np.ndarray:
+def spherical(T: _np.ndarray,
+              tensor: bool = True) -> _np.ndarray:
     """
     Calculate spherical part of a tensor.
 

From 19a73bbf3b50a61ca866c8a9d3d805eb6df36bf5 Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Thu, 27 Jan 2022 12:14:54 +0100
Subject: [PATCH 118/133] [skip ci] adjusted function argument alignment with
 asterisk

---
 python/damask/_crystal.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/python/damask/_crystal.py b/python/damask/_crystal.py
index c97f75d01..e42622210 100644
--- a/python/damask/_crystal.py
+++ b/python/damask/_crystal.py
@@ -311,8 +311,8 @@ class Crystal():
                         + _lattice_points.get(self.lattice if self.lattice == 'hP' else \
                                               self.lattice[-1],None),dtype=float)
 
-    def to_lattice(self,
-                   *, direction: np.ndarray = None,
+    def to_lattice(self, *,
+                   direction: np.ndarray = None,
                    plane: np.ndarray = None) -> np.ndarray:
         """
         Calculate lattice vector corresponding to crystal frame direction or plane normal.
@@ -337,8 +337,7 @@ class Crystal():
         return np.einsum('il,...l',basis,axis)
 
 
-    def to_frame(self,
-                 *,
+    def to_frame(self, *,
                  uvw: np.ndarray = None,
                  hkl: np.ndarray = None) -> np.ndarray:
         """

From 79864818df78e336752cba455f65d903227d7e54 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Thu, 27 Jan 2022 15:13:59 +0100
Subject: [PATCH 119/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-518-g4fa97b9a3

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 663e61aee..750043c40 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-495-g814d89532
+v3.0.0-alpha5-518-g4fa97b9a3

From e2437ee9b556b72fbed947b9f908a5b38f4164a0 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Thu, 27 Jan 2022 15:29:33 +0100
Subject: [PATCH 120/133] adjusting style + documentation

---
 python/damask/_crystal.py  |  5 ++++-
 python/damask/mechanics.py | 18 ++++++++++++------
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/python/damask/_crystal.py b/python/damask/_crystal.py
index e42622210..0b1c00458 100644
--- a/python/damask/_crystal.py
+++ b/python/damask/_crystal.py
@@ -119,7 +119,8 @@ class Crystal():
                           'α={:.5g}°, β={:.5g}°, γ={:.5g}°'.format(*np.degrees(self.parameters[3:]))])
 
 
-    def __eq__(self,other):
+    def __eq__(self,
+               other: object) -> bool:
         """
         Equal to other.
 
@@ -129,6 +130,8 @@ class Crystal():
             Crystal to check for equality.
 
         """
+        if not isinstance(other, Crystal):
+            return NotImplemented
         return self.lattice == other.lattice and \
                self.parameters == other.parameters and \
                self.family == other.family
diff --git a/python/damask/mechanics.py b/python/damask/mechanics.py
index 7c1af6c5f..65ec1ef3b 100644
--- a/python/damask/mechanics.py
+++ b/python/damask/mechanics.py
@@ -122,7 +122,9 @@ def rotation(T: _np.ndarray) -> _rotation.Rotation:
     return _rotation.Rotation.from_matrix(_polar_decomposition(T,'R')[0])
 
 
-def strain(F: _np.ndarray, t: str, m: float) -> _np.ndarray:
+def strain(F: _np.ndarray,
+           t: str,
+           m: float) -> _np.ndarray:
     """
     Calculate strain tensor (Seth–Hill family).
 
@@ -162,7 +164,8 @@ def strain(F: _np.ndarray, t: str, m: float) -> _np.ndarray:
     return eps
 
 
-def stress_Cauchy(P: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def stress_Cauchy(P: _np.ndarray,
+                  F: _np.ndarray) -> _np.ndarray:
     """
     Calculate the Cauchy stress (true stress).
 
@@ -184,7 +187,8 @@ def stress_Cauchy(P: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
     return _tensor.symmetric(_np.einsum('...,...ij,...kj',1.0/_np.linalg.det(F),P,F))
 
 
-def stress_second_Piola_Kirchhoff(P: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
+def stress_second_Piola_Kirchhoff(P: _np.ndarray,
+                                  F: _np.ndarray) -> _np.ndarray:
     """
     Calculate the second Piola-Kirchhoff stress.
 
@@ -243,7 +247,8 @@ def stretch_right(T: _np.ndarray) -> _np.ndarray:
     return _polar_decomposition(T,'U')[0]
 
 
-def _polar_decomposition(T: _np.ndarray, requested: _Sequence[str]) -> tuple:
+def _polar_decomposition(T: _np.ndarray,
+                         requested: _Sequence[str]) -> tuple:
     """
     Perform singular value decomposition.
 
@@ -251,7 +256,7 @@ def _polar_decomposition(T: _np.ndarray, requested: _Sequence[str]) -> tuple:
     ----------
     T : numpy.ndarray, shape (...,3,3)
         Tensor of which the singular values are computed.
-    requested : iterable of str
+    requested : sequence of {'R', 'U', 'V'}
         Requested outputs: ‘R’ for the rotation tensor,
         ‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
 
@@ -273,7 +278,8 @@ def _polar_decomposition(T: _np.ndarray, requested: _Sequence[str]) -> tuple:
     return tuple(output)
 
 
-def _equivalent_Mises(T_sym: _np.ndarray, s: float) -> _np.ndarray:
+def _equivalent_Mises(T_sym: _np.ndarray,
+                      s: float) -> _np.ndarray:
     """
     Base equation for Mises equivalent of a stress or strain tensor.
 

From 609f13c590ea29c0ce835e023d468767be94b8cb Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 29 Jan 2022 18:16:19 +0100
Subject: [PATCH 121/133] Python 3.8 magic: The walrus operator ":="

---
 python/damask/_colormap.py |  4 +---
 python/damask/_grid.py     | 15 +++++----------
 python/damask/_table.py    |  9 +++------
 python/damask/_vtk.py      |  5 ++---
 python/damask/seeds.py     |  5 ++---
 python/damask/tensor.py    |  3 +--
 python/damask/util.py      |  3 +--
 7 files changed, 15 insertions(+), 29 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 5c77cf61e..e7982ec52 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -266,9 +266,7 @@ class Colormap(mpl.colors.ListedColormap):
         l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
               (bounds[0],bounds[1])
 
-        delta,avg = r-l,0.5*abs(r+l)
-
-        if abs(delta) * 1e8 <= avg:                                                                 # delta is similar to numerical noise
+        if abs(delta := r-l) * 1e8 <= (avg := 0.5*abs(r+l)):                                        # delta is similar to numerical noise
             l,r = l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta),                                # extend range to have actual data centered within
 
         return Image.fromarray(
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index b188873a4..639b4e91f 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -234,8 +234,7 @@ class Grid:
         content = f.readlines()
         for i,line in enumerate(content[:header_length]):
             items = line.split('#')[0].lower().strip().split()
-            key = items[0] if items else ''
-            if   key == 'grid':
+            if (key := items[0] if items else '') ==  'grid':
                 cells  = np.array([  int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
             elif key == 'size':
                 size   = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
@@ -247,8 +246,7 @@ class Grid:
         material = np.empty(int(cells.prod()))                                                      # initialize as flat array
         i = 0
         for line in content[header_length:]:
-            items = line.split('#')[0].split()
-            if len(items) == 3:
+            if len(items := line.split('#')[0].split()) == 3:
                 if items[1].lower() == 'of':
                     material_entry = np.ones(int(items[0]))*float(items[2])
                 elif items[1].lower() == 'to':
@@ -813,8 +811,7 @@ class Grid:
         # materials: 1
 
         """
-        valid = ['x','y','z']
-        if not set(directions).issubset(valid):
+        if not set(directions).issubset(valid := ['x', 'y', 'z']):
             raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
 
         limits: Sequence[Optional[int]] = [None,None] if reflect else [-2,0]
@@ -852,8 +849,7 @@ class Grid:
             Updated grid-based geometry.
 
         """
-        valid = ['x','y','z']
-        if not set(directions).issubset(valid):
+        if not set(directions).issubset(valid := ['x', 'y', 'z']):
             raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
 
 
@@ -1190,8 +1186,7 @@ class Grid:
             VTK-based geometry of grain boundary network.
 
         """
-        valid = ['x','y','z']
-        if not set(directions).issubset(valid):
+        if not set(directions).issubset(valid := ['x', 'y', 'z']):
             raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
 
         o = [[0, self.cells[0]+1,           np.prod(self.cells[:2]+1)+self.cells[0]+1, np.prod(self.cells[:2]+1)],
diff --git a/python/damask/_table.py b/python/damask/_table.py
index 44a04b40a..bd82dc134 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -319,8 +319,7 @@ class Table:
         data = np.loadtxt(content)
 
         shapes = {'eu':3, 'pos':2, 'IQ':1, 'CI':1, 'ID':1, 'intensity':1, 'fit':1}
-        remainder = data.shape[1]-sum(shapes.values())
-        if remainder > 0:                                                       # 3.8 can do: if (remainder := data.shape[1]-sum(shapes.values())) > 0
+        if (remainder := data.shape[1]-sum(shapes.values())) > 0:
             shapes['unknown'] = remainder
 
         return Table(data,shapes,comments)
@@ -376,8 +375,7 @@ class Table:
         """
         dup = self.copy()
         dup._add_comment(label, data.shape[1:], info)
-        m = re.match(r'(.*)\[((\d+,)*(\d+))\]',label)
-        if m:
+        if m := re.match(r'(.*)\[((\d+,)*(\d+))\]',label):
             key = m.group(1)
             idx = np.ravel_multi_index(tuple(map(int,m.group(2).split(","))),
                                        self.shapes[key])
@@ -495,8 +493,7 @@ class Table:
         """
         labels_ = [labels] if isinstance(labels,str) else labels.copy()
         for i,l in enumerate(labels_):
-            m = re.match(r'(.*)\[((\d+,)*(\d+))\]',l)
-            if m:
+            if m := re.match(r'(.*)\[((\d+,)*(\d+))\]',l):
                 idx = np.ravel_multi_index(tuple(map(int,m.group(2).split(','))),
                                            self.shapes[m.group(1)])
                 labels_[i] = f'{1+idx}_{m.group(1)}'
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index 601608520..8247bb6c8 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -22,7 +22,7 @@ class VTK:
     High-level interface to VTK.
     """
 
-    def __init__(self, 
+    def __init__(self,
                  vtk_data: vtk.vtkDataSet):
         """
         New spatial visualization.
@@ -202,8 +202,7 @@ class VTK:
         """
         if not os.path.isfile(fname):                                                               # vtk has a strange error handling
             raise FileNotFoundError(f'No such file: {fname}')
-        ext = Path(fname).suffix
-        if ext == '.vtk' or dataset_type is not None:
+        if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None:
             reader = vtk.vtkGenericDataObjectReader()
             reader.SetFileName(str(fname))
             if dataset_type is None:
diff --git a/python/damask/seeds.py b/python/damask/seeds.py
index 1a3af7a64..47e34d871 100644
--- a/python/damask/seeds.py
+++ b/python/damask/seeds.py
@@ -92,10 +92,9 @@ def from_Poisson_disc(size: _FloatSequence,
         tree = _spatial.cKDTree(coords[:s],boxsize=size) if periodic else \
                _spatial.cKDTree(coords[:s])
         distances = tree.query(candidates)[0]
-        best = distances.argmax()
-        if distances[best] > distance:                                                              # require minimum separation
+        if distances.max() > distance:                                                              # require minimum separation
             i = 0
-            coords[s] = candidates[best]                                                            # maximum separation to existing point cloud
+            coords[s] = candidates[distances.argmax()]                                              # maximum separation to existing point cloud
             s += 1
             progress.update(s)
 
diff --git a/python/damask/tensor.py b/python/damask/tensor.py
index 73cdd7400..0e2118002 100644
--- a/python/damask/tensor.py
+++ b/python/damask/tensor.py
@@ -66,8 +66,7 @@ def eigenvectors(T_sym: _np.ndarray,
     """
     (u,v) = _np.linalg.eigh(symmetric(T_sym))
 
-    if RHS:
-        v[_np.linalg.det(v) < 0.0,:,2] *= -1.0
+    if RHS: v[_np.linalg.det(v) < 0.0,:,2] *= -1.0
     return v
 
 
diff --git a/python/damask/util.py b/python/damask/util.py
index e1db35007..c042e4dd4 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -753,9 +753,8 @@ class ProgressBar:
                iteration: int) -> None:
 
         fraction = (iteration+1) / self.total
-        filled_length = int(self.bar_length * fraction)
 
-        if filled_length > int(self.bar_length * self.fraction_last) or \
+        if filled_length := int(self.bar_length * fraction) > int(self.bar_length * self.fraction_last) or \
             datetime.datetime.now() - self.time_last_update > datetime.timedelta(seconds=10):
             self.time_last_update = datetime.datetime.now()
             bar = '█' * filled_length + '░' * (self.bar_length - filled_length)

From 03b0decfcfe6d0fa35f7b1222d77ba202af4d402 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 29 Jan 2022 18:32:04 +0100
Subject: [PATCH 122/133] starting to configure mypy

---
 python/mypy.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/python/mypy.ini b/python/mypy.ini
index 01001daa6..5ef04daee 100644
--- a/python/mypy.ini
+++ b/python/mypy.ini
@@ -1,3 +1,5 @@
+[mypy]
+warn_redundant_casts = True
 [mypy-scipy.*]
 ignore_missing_imports = True
 [mypy-h5py.*]

From ce4591fa29f4066451d6b3e3cde4e5a5ff1c28a3 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 29 Jan 2022 19:10:12 +0100
Subject: [PATCH 123/133] silence prospector on Python 3.9

---
 python/damask/_colormap.py | 2 +-
 python/damask/_vtk.py      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index e7982ec52..9d9776821 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -484,7 +484,7 @@ class Colormap(mpl.colors.ListedColormap):
                          'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg',
                          'gist_rainbow', 'rainbow', 'jet', 'nipy_spectral', 'gist_ncar']}
 
-    _predefined_DAMASK = {'orientation':   {'low':  [0.933334,0.878432,0.878431],
+    _predefined_DAMASK = {'orientation':   {'low':  [0.933334,0.878432,0.878431],                   # noqa
                                             'high': [0.250980,0.007843,0.000000]},
                           'strain':        {'low':  [0.941177,0.941177,0.870588],
                                             'high': [0.266667,0.266667,0.000000]},
diff --git a/python/damask/_vtk.py b/python/damask/_vtk.py
index 8247bb6c8..3d9e5011c 100644
--- a/python/damask/_vtk.py
+++ b/python/damask/_vtk.py
@@ -455,7 +455,7 @@ class VTK:
                 width  = tk.winfo_screenwidth()
                 height = tk.winfo_screenheight()
                 tk.destroy()
-            except Exception as e:
+            except Exception:
                 width  = 1024
                 height =  768
 

From df96110733c85da52615c8f1b05794c0ac95e2cc Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 29 Jan 2022 22:38:17 +0100
Subject: [PATCH 124/133] some suggestions from prospector/pylint

---
 python/damask/_colormap.py | 18 +++++++++---------
 python/damask/_grid.py     | 24 ++++++++++++------------
 python/damask/_table.py    | 22 +++++++++++-----------
 python/damask/tensor.py    |  2 +-
 python/damask/util.py      | 26 +++++++++++++-------------
 5 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/python/damask/_colormap.py b/python/damask/_colormap.py
index 9d9776821..005cf80d6 100644
--- a/python/damask/_colormap.py
+++ b/python/damask/_colormap.py
@@ -267,7 +267,7 @@ class Colormap(mpl.colors.ListedColormap):
               (bounds[0],bounds[1])
 
         if abs(delta := r-l) * 1e8 <= (avg := 0.5*abs(r+l)):                                        # delta is similar to numerical noise
-            l,r = l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta),                                # extend range to have actual data centered within
+            l,r = (l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta))                               # extend range to have actual data centered within
 
         return Image.fromarray(
             (np.dstack((
@@ -301,7 +301,7 @@ class Colormap(mpl.colors.ListedColormap):
         >>> damask.Colormap.from_predefined('stress').reversed()
 
         """
-        rev = super(Colormap,self).reversed(name)
+        rev = super().reversed(name)
         return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
 
 
@@ -436,11 +436,11 @@ class Colormap(mpl.colors.ListedColormap):
         def adjust_hue(msh_sat, msh_unsat):
             """If saturation of one of the two colors is much less than the other, hue of the less."""
             if msh_sat[0] >= msh_unsat[0]:
-               return msh_sat[2]
-            else:
-                hSpin = msh_sat[1]/np.sin(msh_sat[1])*np.sqrt(msh_unsat[0]**2.0-msh_sat[0]**2)/msh_sat[0]
-                if msh_sat[2] < - np.pi/3.0: hSpin *= -1.0
-                return msh_sat[2] + hSpin
+                return msh_sat[2]
+
+            hSpin = msh_sat[1]/np.sin(msh_sat[1])*np.sqrt(msh_unsat[0]**2.0-msh_sat[0]**2)/msh_sat[0]
+            if msh_sat[2] < - np.pi/3.0: hSpin *= -1.0
+            return msh_sat[2] + hSpin
 
         lo = np.array(low)
         hi = np.array(high)
@@ -453,9 +453,9 @@ class Colormap(mpl.colors.ListedColormap):
             else:
                 lo = np.array([M_mid,0.0,0.0])
                 frac = 2.0*frac - 1.0
-        if   lo[1] < 0.05 and hi[1] > 0.05:
+        if   lo[1] < 0.05 < hi[1]:
             lo[2] = adjust_hue(hi,lo)
-        elif lo[1] > 0.05 and hi[1] < 0.05:
+        elif hi[1] < 0.05 < lo[1]:
             hi[2] = adjust_hue(lo,hi)
 
         return (1.0 - frac) * lo + frac * hi
diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 639b4e91f..0b3a067e2 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -33,7 +33,7 @@ class Grid:
                  material: np.ndarray,
                  size: FloatSequence,
                  origin: FloatSequence = np.zeros(3),
-                 comments: Union[str, Sequence[str]] = []):
+                 comments: Union[str, Sequence[str]] = None):
         """
         New geometry definition for grid solvers.
 
@@ -53,7 +53,7 @@ class Grid:
         self.material = material
         self.size = size                                                                            # type: ignore
         self.origin = origin                                                                        # type: ignore
-        self.comments = comments                                                                    # type: ignore
+        self.comments = [] if comments is None else comments                                        # type: ignore
 
 
     def __repr__(self) -> str:
@@ -106,14 +106,14 @@ class Grid:
                  material: np.ndarray):
         if len(material.shape) != 3:
             raise ValueError(f'invalid material shape {material.shape}')
-        elif material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
+        if material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
             raise TypeError(f'invalid material data type {material.dtype}')
-        else:
-            self._material = np.copy(material)
 
-            if self.material.dtype in np.sctypes['float'] and \
-               np.all(self.material == self.material.astype(int).astype(float)):
-                self._material = self.material.astype(int)
+        self._material = np.copy(material)
+
+        if self.material.dtype in np.sctypes['float'] and \
+           np.all(self.material == self.material.astype(int).astype(float)):
+            self._material = self.material.astype(int)
 
 
     @property
@@ -126,8 +126,8 @@ class Grid:
              size: FloatSequence):
         if len(size) != 3 or any(np.array(size) < 0):
             raise ValueError(f'invalid size {size}')
-        else:
-            self._size = np.array(size)
+
+        self._size = np.array(size)
 
     @property
     def origin(self) -> np.ndarray:
@@ -139,8 +139,8 @@ class Grid:
                origin: FloatSequence):
         if len(origin) != 3:
             raise ValueError(f'invalid origin {origin}')
-        else:
-            self._origin = np.array(origin)
+
+        self._origin = np.array(origin)
 
     @property
     def comments(self) -> List[str]:
diff --git a/python/damask/_table.py b/python/damask/_table.py
index bd82dc134..1572c4f76 100644
--- a/python/damask/_table.py
+++ b/python/damask/_table.py
@@ -14,7 +14,7 @@ class Table:
 
     def __init__(self,
                  data: np.ndarray,
-                 shapes: dict, 
+                 shapes: dict,
                  comments: Union[str, list] = None):
         """
         New spreadsheet.
@@ -526,10 +526,10 @@ class Table:
         """
         if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns):
             raise KeyError('Labels or shapes or order do not match')
-        else:
-            dup = self.copy()
-            dup.data = dup.data.append(other.data,ignore_index=True)
-            return dup
+
+        dup = self.copy()
+        dup.data = dup.data.append(other.data,ignore_index=True)
+        return dup
 
 
     def join(self,
@@ -552,12 +552,12 @@ class Table:
         """
         if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]:
             raise KeyError('Duplicated keys or row count mismatch')
-        else:
-            dup = self.copy()
-            dup.data = dup.data.join(other.data)
-            for key in other.shapes:
-                dup.shapes[key] = other.shapes[key]
-            return dup
+
+        dup = self.copy()
+        dup.data = dup.data.join(other.data)
+        for key in other.shapes:
+            dup.shapes[key] = other.shapes[key]
+        return dup
 
 
     def save(self,
diff --git a/python/damask/tensor.py b/python/damask/tensor.py
index 0e2118002..63eb15b99 100644
--- a/python/damask/tensor.py
+++ b/python/damask/tensor.py
@@ -64,7 +64,7 @@ def eigenvectors(T_sym: _np.ndarray,
         associated eigenvalues.
 
     """
-    (u,v) = _np.linalg.eigh(symmetric(T_sym))
+    _,v = _np.linalg.eigh(symmetric(T_sym))
 
     if RHS: v[_np.linalg.det(v) < 0.0,:,2] *= -1.0
     return v
diff --git a/python/damask/util.py b/python/damask/util.py
index c042e4dd4..0cf6606fb 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -7,7 +7,7 @@ import subprocess
 import shlex
 import re
 import fractions
-import collections.abc as abc
+from collections import abc
 from functools import reduce
 from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, Optional
 from pathlib import Path
@@ -77,7 +77,7 @@ def srepr(msg,
             hasattr(msg, '__iter__'))):
         return glue.join(str(x) for x in msg)
     else:
-       return msg if isinstance(msg,str) else repr(msg)
+        return msg if isinstance(msg,str) else repr(msg)
 
 
 def emph(msg) -> str:
@@ -230,15 +230,15 @@ def show_progress(iterable: Iterable,
 
     """
     if isinstance(iterable,abc.Sequence):
-       if N_iter is None:
-          N = len(iterable)
-       else:
-          raise ValueError('N_iter given for sequence')
+        if N_iter is None:
+            N = len(iterable)
+        else:
+            raise ValueError('N_iter given for sequence')
     else:
-       if N_iter is None:
-          raise ValueError('N_iter not given')
-       else:
-          N = N_iter
+        if N_iter is None:
+            raise ValueError('N_iter not given')
+
+        N = N_iter
 
     if N <= 1:
         for item in iterable:
@@ -454,7 +454,7 @@ def shapeshifter(fro: Tuple[int, ...],
 
 
     """
-    if not len(fro) and not len(to): return ()
+    if len(fro) == 0 and len(to) == 0: return ()
 
     beg = dict(left ='(^.*\\b)',
                right='(^.*?\\b)')
@@ -462,8 +462,8 @@ def shapeshifter(fro: Tuple[int, ...],
                right='(.*?\\b)')
     end = dict(left ='(.*?$)',
                right='(.*$)')
-    fro = (1,) if not len(fro) else fro
-    to  = (1,) if not len(to)  else to
+    fro = (1,) if len(fro) == 0 else fro
+    to  = (1,) if len(to) == 0 else to
     try:
         match = re.match(beg[mode]
                       +f',{sep[mode]}'.join(map(lambda x: f'{x}'

From 9ce4573b12660fcbcb7be092df4fe829ccfff3b8 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 29 Jan 2022 23:16:57 +0100
Subject: [PATCH 125/133] docstring polishing

---
 python/damask/_grid.py | 13 +++++--------
 python/damask/util.py  | 25 +++++++++++++++++--------
 2 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index 0b3a067e2..b08f99757 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -786,9 +786,8 @@ class Grid:
 
         Parameters
         ----------
-        directions : (sequence of) str
+        directions : (sequence of) {'x', 'y', 'z'}
             Direction(s) along which the grid is mirrored.
-            Valid entries are 'x', 'y', 'z'.
         reflect : bool, optional
             Reflect (include) outermost layers. Defaults to False.
 
@@ -832,16 +831,14 @@ class Grid:
 
 
     def flip(self,
-             directions: Union[Literal['x', 'y', 'z'],
-             Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
+             directions: Sequence[str]) -> 'Grid':
         """
         Flip grid along given directions.
 
         Parameters
         ----------
-        directions : (sequence of) str
+        directions : (sequence of) {'x', 'y', 'z'}
             Direction(s) along which the grid is flipped.
-            Valid entries are 'x', 'y', 'z'.
 
         Returns
         -------
@@ -1176,9 +1173,9 @@ class Grid:
         ----------
         periodic : bool, optional
             Assume grid to be periodic. Defaults to True.
-        directions : (sequence of) string, optional
+        directions : (sequence of) {'x', 'y', 'z'}, optional
             Direction(s) along which the boundaries are determined.
-            Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.
+            Defaults to 'xyz'.
 
         Returns
         -------
diff --git a/python/damask/util.py b/python/damask/util.py
index 0cf6606fb..0bbc1e7b5 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -305,16 +305,20 @@ def project_equal_angle(vector: np.ndarray,
     normalize : bool
         Ensure unit length of input vector. Defaults to True.
     keepdims : bool
-        Maintain three-dimensional output coordinates. Defaults to False.
-        Two-dimensional output uses right-handed frame spanned by
-        the next and next-next axis relative to the projection direction,
-        e.g. x-y when projecting along z and z-x when projecting along y.
+        Maintain three-dimensional output coordinates.
+        Defaults to False.
 
     Returns
     -------
     coordinates : numpy.ndarray, shape (...,2 | 3)
         Projected coordinates.
 
+    Notes
+    -----
+    Two-dimensional output uses right-handed frame spanned by
+    the next and next-next axis relative to the projection direction,
+    e.g. x-y when projecting along z and z-x when projecting along y.
+
     Examples
     --------
     >>> import damask
@@ -349,16 +353,21 @@ def project_equal_area(vector: np.ndarray,
     normalize : bool
         Ensure unit length of input vector. Defaults to True.
     keepdims : bool
-        Maintain three-dimensional output coordinates. Defaults to False.
-        Two-dimensional output uses right-handed frame spanned by
-        the next and next-next axis relative to the projection direction,
-        e.g. x-y when projecting along z and z-x when projecting along y.
+        Maintain three-dimensional output coordinates.
+        Defaults to False.
 
     Returns
     -------
     coordinates : numpy.ndarray, shape (...,2 | 3)
         Projected coordinates.
 
+    Notes
+    -----
+    Two-dimensional output uses right-handed frame spanned by
+    the next and next-next axis relative to the projection direction,
+    e.g. x-y when projecting along z and z-x when projecting along y.
+
+
     Examples
     --------
     >>> import damask

From a479c2971478325b2677c2000f40e6d7a30f5c5b Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 30 Jan 2022 15:46:26 +0100
Subject: [PATCH 126/133] not used

---
 python/damask/_grid.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index b08f99757..f5c06df1b 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -4,7 +4,7 @@ import warnings
 import multiprocessing as mp
 from functools import partial
 import typing
-from typing import Union, Optional, TextIO, List, Sequence, Literal
+from typing import Union, Optional, TextIO, List, Sequence
 from pathlib import Path
 
 import numpy as np

From 26cd8a46c2e10e6416705713a4ea273a4fd0eb30 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sun, 30 Jan 2022 22:36:30 +0100
Subject: [PATCH 127/133] consistent style

---
 python/damask/grid_filters.py | 43 ++++++++++++++++++++++++-----------
 1 file changed, 30 insertions(+), 13 deletions(-)

diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py
index d9d658d0b..e2178a4b6 100644
--- a/python/damask/grid_filters.py
+++ b/python/damask/grid_filters.py
@@ -20,7 +20,9 @@ import numpy as _np
 from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
 
 
-def _ks(size: _FloatSequence, cells: _IntSequence, first_order: bool = False) -> _np.ndarray:
+def _ks(size: _FloatSequence,
+        cells: _IntSequence,
+        first_order: bool = False) -> _np.ndarray:
     """
     Get wave numbers operator.
 
@@ -47,7 +49,8 @@ def _ks(size: _FloatSequence, cells: _IntSequence, first_order: bool = False) ->
     return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
 
 
-def curl(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
+def curl(size: _FloatSequence,
+         f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate curl of a vector or tensor field in Fourier space.
 
@@ -78,7 +81,8 @@ def curl(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(curl_,axes=(0,1,2),s=f.shape[:3])
 
 
-def divergence(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
+def divergence(size: _FloatSequence,
+               f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate divergence of a vector or tensor field in Fourier space.
 
@@ -105,7 +109,8 @@ def divergence(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
     return _np.fft.irfftn(div_,axes=(0,1,2),s=f.shape[:3])
 
 
-def gradient(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
+def gradient(size: _FloatSequence,
+             f: _np.ndarray) -> _np.ndarray:
     u"""
     Calculate gradient of a scalar or vector field in Fourier space.
 
@@ -163,7 +168,8 @@ def coordinates0_point(cells: _IntSequence,
                      axis = -1)
 
 
-def displacement_fluct_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
+def displacement_fluct_point(size: _FloatSequence,
+                             F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from fluctuation part of the deformation gradient field.
 
@@ -195,7 +201,8 @@ def displacement_fluct_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarra
     return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
 
 
-def displacement_avg_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
+def displacement_avg_point(size: _FloatSequence,
+                           F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from average part of the deformation gradient field.
 
@@ -216,7 +223,8 @@ def displacement_avg_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
 
 
-def displacement_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
+def displacement_point(size: _FloatSequence,
+                       F: _np.ndarray) -> _np.ndarray:
     """
     Cell center displacement field from deformation gradient field.
 
@@ -236,7 +244,9 @@ def displacement_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
 
 
-def coordinates_point(size: _FloatSequence, F: _np.ndarray, origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
+def coordinates_point(size: _FloatSequence,
+                      F: _np.ndarray,
+                      origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
     """
     Cell center positions.
 
@@ -335,7 +345,8 @@ def coordinates0_node(cells: _IntSequence,
                      axis = -1)
 
 
-def displacement_fluct_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
+def displacement_fluct_node(size: _FloatSequence,
+                            F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from fluctuation part of the deformation gradient field.
 
@@ -355,7 +366,8 @@ def displacement_fluct_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray
     return point_to_node(displacement_fluct_point(size,F))
 
 
-def displacement_avg_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
+def displacement_avg_node(size: _FloatSequence,
+                          F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from average part of the deformation gradient field.
 
@@ -376,7 +388,8 @@ def displacement_avg_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
 
 
-def displacement_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
+def displacement_node(size: _FloatSequence,
+                      F: _np.ndarray) -> _np.ndarray:
     """
     Nodal displacement field from deformation gradient field.
 
@@ -396,7 +409,9 @@ def displacement_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
     return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
 
 
-def coordinates_node(size: _FloatSequence, F: _np.ndarray, origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
+def coordinates_node(size: _FloatSequence,
+                     F: _np.ndarray,
+                     origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
     """
     Nodal positions.
 
@@ -526,7 +541,9 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
         return False
 
 
-def regrid(size: _FloatSequence, F: _np.ndarray, cells: _IntSequence) -> _np.ndarray:
+def regrid(size: _FloatSequence,
+           F: _np.ndarray,
+           cells: _IntSequence) -> _np.ndarray:
     """
     Return mapping from coordinates in deformed configuration to a regular grid.
 

From 3105b2c978548eb0965a8cd4b814c2927ddca1ec Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Mon, 31 Jan 2022 12:40:29 +0100
Subject: [PATCH 128/133] added missing return type to
 grid.get_grain_boundaries function

---
 python/damask/_grid.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/_grid.py b/python/damask/_grid.py
index f5c06df1b..8a9a4bbd9 100644
--- a/python/damask/_grid.py
+++ b/python/damask/_grid.py
@@ -1165,7 +1165,7 @@ class Grid:
 
     def get_grain_boundaries(self,
                              periodic: bool = True,
-                             directions: Sequence[str] = 'xyz'):
+                             directions: Sequence[str] = 'xyz') -> VTK:
         """
         Create VTK unstructured grid containing grain boundaries.
 

From 39aa24369547616fddca666b56fa9248ffe411e4 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Mon, 31 Jan 2022 14:05:15 +0000
Subject: [PATCH 129/133] Polynomial Class

---
 src/CPFEM.f90                    |   2 +
 src/CPFEM2.f90                   |   2 +
 src/YAML_parse.f90               |   6 +-
 src/commercialFEM_fileList.f90   |   1 +
 src/material.f90                 |   2 +-
 src/phase.f90                    |   1 +
 src/phase_mechanical_elastic.f90 |  80 ++++----------
 src/polynomials.f90              | 179 +++++++++++++++++++++++++++++++
 8 files changed, 211 insertions(+), 62 deletions(-)
 create mode 100644 src/polynomials.f90

diff --git a/src/CPFEM.f90 b/src/CPFEM.f90
index 8ee26ffe7..0f7590782 100644
--- a/src/CPFEM.f90
+++ b/src/CPFEM.f90
@@ -14,6 +14,7 @@ module CPFEM
   use config
   use math
   use rotations
+  use polynomials
   use lattice
   use material
   use phase
@@ -83,6 +84,7 @@ subroutine CPFEM_initAll
   call config_init
   call math_init
   call rotations_init
+  call polynomials_init
   call lattice_init
   call discretization_marc_init
   call material_init(.false.)
diff --git a/src/CPFEM2.f90 b/src/CPFEM2.f90
index 647befd30..ed8fb611b 100644
--- a/src/CPFEM2.f90
+++ b/src/CPFEM2.f90
@@ -16,6 +16,7 @@ module CPFEM2
   use config
   use math
   use rotations
+  use polynomials
   use lattice
   use material
   use phase
@@ -57,6 +58,7 @@ subroutine CPFEM_initAll
   call config_init
   call math_init
   call rotations_init
+  call polynomials_init
   call lattice_init
 #if   defined(MESH)
   call discretization_mesh_init(restart=interface_restartInc>0)
diff --git a/src/YAML_parse.f90 b/src/YAML_parse.f90
index 9ebde963b..8a3264cff 100644
--- a/src/YAML_parse.f90
+++ b/src/YAML_parse.f90
@@ -191,8 +191,10 @@ logical function isScalar(line)
 
   character(len=*), intent(in) :: line
 
-  isScalar = (.not.isKeyValue(line) .and. .not.isKey(line) .and. .not.isListItem(line) &
-                                                            .and. .not.isFlow(line))
+  isScalar = (.not. isKeyValue(line) .and. &
+              .not. isKey(line) .and. &
+              .not. isListItem(line) .and. &
+              .not. isFlow(line))
 
 end function isScalar
 
diff --git a/src/commercialFEM_fileList.f90 b/src/commercialFEM_fileList.f90
index e67149dea..8dbbea706 100644
--- a/src/commercialFEM_fileList.f90
+++ b/src/commercialFEM_fileList.f90
@@ -14,6 +14,7 @@
 #include "LAPACK_interface.f90"
 #include "math.f90"
 #include "rotations.f90"
+#include "polynomials.f90"
 #include "lattice.f90"
 #include "element.f90"
 #include "geometry_plastic_nonlocal.f90"
diff --git a/src/material.f90 b/src/material.f90
index 1e3a4b4ec..31eeef5e1 100644
--- a/src/material.f90
+++ b/src/material.f90
@@ -66,7 +66,7 @@ subroutine material_init(restart)
   print'(/,1x,a)', '<<<+-  material init  -+>>>'; flush(IO_STDOUT)
 
 
-  call parse
+  call parse()
   print'(/,1x,a)', 'parsed material.yaml'
 
 
diff --git a/src/phase.f90 b/src/phase.f90
index 6035b4491..df7557a0b 100644
--- a/src/phase.f90
+++ b/src/phase.f90
@@ -8,6 +8,7 @@ module phase
   use constants
   use math
   use rotations
+  use polynomials
   use IO
   use config
   use material
diff --git a/src/phase_mechanical_elastic.f90 b/src/phase_mechanical_elastic.f90
index 8972367d5..c57849b1f 100644
--- a/src/phase_mechanical_elastic.f90
+++ b/src/phase_mechanical_elastic.f90
@@ -1,15 +1,13 @@
 submodule(phase:mechanical) elastic
 
   type :: tParameters
-    real(pReal),dimension(3) :: &
-      C_11 = 0.0_pReal, &
-      C_12 = 0.0_pReal, &
-      C_13 = 0.0_pReal, &
-      C_33 = 0.0_pReal, &
-      C_44 = 0.0_pReal, &
-      C_66 = 0.0_pReal
-    real(pReal) :: &
-      T_ref
+    type(tPolynomial) :: &
+      C_11, &
+      C_12, &
+      C_13, &
+      C_33, &
+      C_44, &
+      C_66
   end type tParameters
 
   type(tParameters), allocatable, dimension(:) :: param
@@ -47,35 +45,17 @@ module subroutine elastic_init(phases)
 
     associate(prm => param(ph))
 
-      prm%T_ref = elastic%get_asFloat('T_ref', defaultVal=T_ROOM)
-
-      prm%C_11(1) = elastic%get_asFloat('C_11')
-      prm%C_11(2) = elastic%get_asFloat('C_11,T',  defaultVal=0.0_pReal)
-      prm%C_11(3) = elastic%get_asFloat('C_11,T^2',defaultVal=0.0_pReal)
- 
-      prm%C_12(1) = elastic%get_asFloat('C_12')
-      prm%C_12(2) = elastic%get_asFloat('C_12,T',  defaultVal=0.0_pReal)
-      prm%C_12(3) = elastic%get_asFloat('C_12,T^2',defaultVal=0.0_pReal)
- 
-      prm%C_44(1) = elastic%get_asFloat('C_44')
-      prm%C_44(2) = elastic%get_asFloat('C_44,T',  defaultVal=0.0_pReal)
-      prm%C_44(3) = elastic%get_asFloat('C_44,T^2',defaultVal=0.0_pReal)
+      prm%C_11 = polynomial(elastic%asDict(),'C_11','T')
+      prm%C_12 = polynomial(elastic%asDict(),'C_12','T')
+      prm%C_44 = polynomial(elastic%asDict(),'C_44','T')
  
       if (any(phase_lattice(ph) == ['hP','tI'])) then
-        prm%C_13(1) = elastic%get_asFloat('C_13')
-        prm%C_13(2) = elastic%get_asFloat('C_13,T',  defaultVal=0.0_pReal)
-        prm%C_13(3) = elastic%get_asFloat('C_13,T^2',defaultVal=0.0_pReal)
- 
-        prm%C_33(1) = elastic%get_asFloat('C_33')
-        prm%C_33(2) = elastic%get_asFloat('C_33,T',  defaultVal=0.0_pReal)
-        prm%C_33(3) = elastic%get_asFloat('C_33,T^2',defaultVal=0.0_pReal)
+        prm%C_13 = polynomial(elastic%asDict(),'C_13','T')
+        prm%C_33 = polynomial(elastic%asDict(),'C_33','T')
       end if
 
-      if (phase_lattice(ph) == 'tI') then
-        prm%C_66(1) = elastic%get_asFloat('C_66')
-        prm%C_66(2) = elastic%get_asFloat('C_66,T',  defaultVal=0.0_pReal)
-        prm%C_66(3) = elastic%get_asFloat('C_66,T^2',defaultVal=0.0_pReal)
-      end if
+      if (phase_lattice(ph) == 'tI') &
+        prm%C_66 = polynomial(elastic%asDict(),'C_66','T')
 
     end associate
   end do
@@ -97,38 +77,20 @@ pure module function elastic_C66(ph,en) result(C66)
 
 
   associate(prm => param(ph))
+    
     C66 = 0.0_pReal
     T = thermal_T(ph,en)
 
-    C66(1,1) = prm%C_11(1) &
-             + prm%C_11(2)*(T - prm%T_ref) &
-             + prm%C_11(3)*(T - prm%T_ref)**2
-
-    C66(1,2) = prm%C_12(1) &
-             + prm%C_12(2)*(T - prm%T_ref) &
-             + prm%C_12(3)*(T - prm%T_ref)**2
-
-    C66(4,4) = prm%C_44(1) &
-             + prm%C_44(2)*(T - prm%T_ref) &
-             + prm%C_44(3)*(T - prm%T_ref)**2
-
+    C66(1,1) = prm%C_11%at(T)
+    C66(1,2) = prm%C_12%at(T)
+    C66(4,4) = prm%C_44%at(T)
 
     if (any(phase_lattice(ph) == ['hP','tI'])) then
-      C66(1,3) = prm%C_13(1) &
-               + prm%C_13(2)*(T - prm%T_ref) &
-               + prm%C_13(3)*(T - prm%T_ref)**2
-
-      C66(3,3) = prm%C_33(1) &
-               + prm%C_33(2)*(T - prm%T_ref) &
-               + prm%C_33(3)*(T - prm%T_ref)**2
-
+      C66(1,3) = prm%C_13%at(T)
+      C66(3,3) = prm%C_33%at(T)
     end if
 
-    if (phase_lattice(ph) == 'tI') then
-      C66(6,6) = prm%C_66(1) &
-               + prm%C_66(2)*(T - prm%T_ref) &
-               + prm%C_66(3)*(T - prm%T_ref)**2
-    end if
+    if (phase_lattice(ph) == 'tI') C66(6,6) = prm%C_66%at(T)
 
     C66 = lattice_symmetrize_C66(C66,phase_lattice(ph))
 
diff --git a/src/polynomials.f90 b/src/polynomials.f90
new file mode 100644
index 000000000..49a46e2e4
--- /dev/null
+++ b/src/polynomials.f90
@@ -0,0 +1,179 @@
+!--------------------------------------------------------------------------------------------------
+!> @author Martin Diehl, KU Leuven
+!> @brief Polynomial representation for variable data
+!--------------------------------------------------------------------------------------------------
+module polynomials
+  use prec
+  use IO
+  use YAML_parse
+  use YAML_types
+
+  implicit none
+  private
+
+  type, public :: tPolynomial
+    real(pReal), dimension(:), allocatable :: coef
+    real(pReal) :: x_ref
+    contains
+    procedure, public :: at => eval
+    procedure, public :: der1_at => eval_der1
+  end type tPolynomial
+
+  interface polynomial
+    module procedure polynomial_from_dict
+    module procedure polynomial_from_coef
+  end interface polynomial
+
+  public :: &
+    polynomial, &
+    polynomials_init
+
+contains
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Run self-test.
+!--------------------------------------------------------------------------------------------------
+subroutine polynomials_init()
+
+  print'(/,1x,a)', '<<<+-  polynomials init  -+>>>'; flush(IO_STDOUT)
+
+  call selfTest()
+
+end subroutine polynomials_init
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Initialize a Polynomial from Coefficients.
+!--------------------------------------------------------------------------------------------------
+function polynomial_from_coef(coef,x_ref) result(p)
+
+  real(pReal), dimension(:), intent(in) :: coef
+  real(pReal), intent(in) :: x_ref
+  type(tPolynomial) :: p
+
+
+  allocate(p%coef(0:size(coef)-1),source=coef)                                                      ! should be zero based
+  p%x_ref = x_ref
+
+end function polynomial_from_coef
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Initialize a Polynomial from a Dictionary with Coefficients.
+!--------------------------------------------------------------------------------------------------
+function polynomial_from_dict(dict,y,x) result(p)
+
+  type(tDict), intent(in) :: dict
+  character(len=*), intent(in) :: y, x
+  type(tPolynomial) :: p
+
+  real(pReal), dimension(:), allocatable :: coef
+  real(pReal) :: x_ref
+
+
+  allocate(coef(1),source=dict%get_asFloat(y))
+
+  if (dict%contains(y//','//x)) then
+    x_ref = dict%get_asFloat(x//'_ref')
+    coef = [coef,dict%get_asFloat(y//','//x)]
+    if (dict%contains(y//','//x//'^2')) then
+      coef = [coef,dict%get_asFloat(y//','//x//'^2')]
+    end if
+  else
+    x_ref = huge(0.0_pReal)                                                                         ! Simplify debugging
+  end if
+
+  p = Polynomial(coef,x_ref)
+
+end function polynomial_from_dict
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Evaluate a Polynomial.
+!--------------------------------------------------------------------------------------------------
+pure function eval(self,x) result(y)
+
+  class(tPolynomial), intent(in) :: self
+  real(pReal), intent(in) :: x
+  real(pReal) :: y
+
+  integer :: i
+
+
+  y = self%coef(0)
+  do i = 1, ubound(self%coef,1)
+    y = y + self%coef(i) * (x-self%x_ref)**i
+  enddo
+
+end function eval
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Evaluate a first derivative of Polynomial.
+!--------------------------------------------------------------------------------------------------
+pure function eval_der1(self,x) result(y)
+
+  class(tPolynomial), intent(in) :: self
+  real(pReal), intent(in) :: x
+  real(pReal) :: y
+
+  integer :: i
+
+
+  y = 0.0_pReal
+  do i = 1, ubound(self%coef,1)
+    y = y + real(i,pReal)*self%coef(i) * (x-self%x_ref)**(i-1)
+  enddo
+
+end function eval_der1
+
+
+!--------------------------------------------------------------------------------------------------
+!> @brief Check correctness of polynomical functionality.
+!--------------------------------------------------------------------------------------------------
+subroutine selfTest
+
+  type(tPolynomial) :: p1, p2
+  real(pReal), dimension(3) :: coef
+  real(pReal) :: x_ref, x
+  class(tNode), pointer :: dict
+  character(len=pStringLen), dimension(3) :: coef_s
+  character(len=pStringLen) :: x_ref_s, x_s, YAML_s
+
+  call random_number(coef)
+  call random_number(x_ref)
+  call random_number(x)
+
+  coef = coef*10_pReal -0.5_pReal
+  x_ref = x_ref*10_pReal -0.5_pReal
+  x = x*10_pReal -0.5_pReal
+
+  p1 = polynomial(coef,x_ref)
+  if (dNeq(p1%at(x_ref),coef(1)))  error stop 'polynomial: @ref'
+
+  write(coef_s(1),*) coef(1)
+  write(coef_s(2),*) coef(2)
+  write(coef_s(3),*) coef(3)
+  write(x_ref_s,*) x_ref
+  write(x_s,*) x
+  YAML_s = 'C: '//trim(adjustl(coef_s(1)))//IO_EOL//&
+           'C,T: '//trim(adjustl(coef_s(2)))//IO_EOL//&
+           'C,T^2: '//trim(adjustl(coef_s(3)))//IO_EOL//&
+           'T_ref: '//trim(adjustl(x_ref_s))//IO_EOL
+  Dict => YAML_parse_str(trim(YAML_s))
+  p2 = polynomial(dict%asDict(),'C','T')
+  if (dNeq(p1%at(x),p2%at(x),1.0e-12_pReal))                      error stop 'polynomials: init'
+
+  p1 = polynomial(coef*[0.0_pReal,1.0_pReal,0.0_pReal],x_ref)
+  if (dNeq(p1%at(x_ref+x),-p1%at(x_ref-x),1.0e-10_pReal))         error stop 'polynomials: eval(odd)'
+  if (dNeq(p1%der1_at(x),p1%der1_at(5.0_pReal*x),1.0e-10_pReal))  error stop 'polynomials: eval_der(odd)'
+
+  p1 = polynomial(coef*[0.0_pReal,0.0_pReal,1.0_pReal],x_ref)
+  if (dNeq(p1%at(x_ref+x),p1%at(x_ref-x),1e-10_pReal))            error stop 'polynomials: eval(even)'
+  if (dNeq(p1%der1_at(x_ref+x),-p1%der1_at(x_ref-x),1e-10_pReal)) error stop 'polynomials: eval_der(even)'
+
+
+end subroutine selfTest
+
+end module polynomials

From 90b6b0e164a7cda9d5b27f82f672b9bc8dcebe2e Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Mon, 31 Jan 2022 17:16:01 +0100
Subject: [PATCH 130/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-521-g30bf38641

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 750043c40..9c785bbbc 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-518-g4fa97b9a3
+v3.0.0-alpha5-521-g30bf38641

From 98381bff2a1515e7a33a47c4977d65affb74a0ee Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Mon, 31 Jan 2022 20:14:24 +0100
Subject: [PATCH 131/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-542-g225a5d908

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 9c785bbbc..92cb9dcb3 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-521-g30bf38641
+v3.0.0-alpha5-542-g225a5d908

From 086ff42be58447056ed99480e2733029bf5f402a Mon Sep 17 00:00:00 2001
From: Daniel Otto de Mentock <d.mentock@mpie.de>
Date: Tue, 1 Feb 2022 07:30:00 +0000
Subject: [PATCH 132/133] 05 Typehints config configmaterial

---
 python/damask/_config.py         | 55 ++++++++++++++++++++++----------
 python/damask/_configmaterial.py | 54 +++++++++++++++++++++----------
 python/damask/util.py            |  8 ++---
 3 files changed, 79 insertions(+), 38 deletions(-)

diff --git a/python/damask/_config.py b/python/damask/_config.py
index 2f5904cc6..5f7453b11 100644
--- a/python/damask/_config.py
+++ b/python/damask/_config.py
@@ -2,25 +2,34 @@ import copy
 from io import StringIO
 from collections.abc import Iterable
 import abc
+from pathlib import Path
+from typing import Union, Dict, Any, Type, TypeVar
 
 import numpy as np
 import yaml
 
+from ._typehints import FileHandle
 from . import Rotation
 
+MyType = TypeVar('MyType', bound='Config')
+
 class NiceDumper(yaml.SafeDumper):
     """Make YAML readable for humans."""
 
-    def write_line_break(self, data=None):
+    def write_line_break(self,
+                         data: str = None):
         super().write_line_break(data)
 
         if len(self.indents) == 1:
             super().write_line_break()
 
-    def increase_indent(self, flow=False, indentless=False):
+    def increase_indent(self,
+                        flow: bool = False,
+                        indentless: bool = False):
         return super().increase_indent(flow, False)
 
-    def represent_data(self, data):
+    def represent_data(self,
+                       data: Any):
         """Cast Config objects and its subclasses to dict."""
         if isinstance(data, dict) and type(data) != dict:
             return self.represent_data(dict(data))
@@ -31,14 +40,17 @@ class NiceDumper(yaml.SafeDumper):
         else:
             return super().represent_data(data)
 
-    def ignore_aliases(self, data):
+    def ignore_aliases(self,
+                       data: Any) -> bool:
         """Do not use references to existing objects."""
         return True
 
 class Config(dict):
     """YAML-based configuration."""
 
-    def __init__(self,yml=None,**kwargs):
+    def __init__(self,
+                 yml: Union[str, Dict[str, Any]] = None,
+                 **kwargs):
         """Initialize from YAML, dict, or key=value pairs."""
         if isinstance(yml,str):
             kwargs.update(yaml.safe_load(yml))
@@ -47,7 +59,7 @@ class Config(dict):
 
         super().__init__(**kwargs)
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """Show as in file."""
         output = StringIO()
         self.save(output)
@@ -55,14 +67,15 @@ class Config(dict):
         return ''.join(output.readlines())
 
 
-    def __copy__(self):
+    def __copy__(self: MyType) -> MyType:
         """Create deep copy."""
         return copy.deepcopy(self)
 
     copy = __copy__
 
 
-    def __or__(self,other):
+    def __or__(self: MyType,
+               other) -> MyType:
         """
         Update configuration with contents of other.
 
@@ -76,18 +89,24 @@ class Config(dict):
         updated : damask.Config
             Updated configuration.
 
+        Note
+        ----
+        This functionality is a backport for Python 3.8
+
         """
         duplicate = self.copy()
         duplicate.update(other)
         return duplicate
 
 
-    def __ior__(self,other):
+    def __ior__(self: MyType,
+                other) -> MyType:
         """Update configuration with contents of other."""
         return self.__or__(other)
 
 
-    def delete(self,keys):
+    def delete(self: MyType,
+               keys: Union[Iterable, str]) -> MyType:
         """
         Remove configuration keys.
 
@@ -109,7 +128,8 @@ class Config(dict):
 
 
     @classmethod
-    def load(cls,fname):
+    def load(cls: Type[MyType],
+             fname: FileHandle) -> MyType:
         """
         Load from yaml file.
 
@@ -124,14 +144,15 @@ class Config(dict):
             Configuration from file.
 
         """
-        try:
+        if isinstance(fname, (str, Path)):
             fhandle = open(fname)
-        except TypeError:
+        else:
             fhandle = fname
         return cls(yaml.safe_load(fhandle))
 
-
-    def save(self,fname,**kwargs):
+    def save(self,
+             fname: FileHandle,
+             **kwargs):
         """
         Save to yaml file.
 
@@ -143,9 +164,9 @@ class Config(dict):
             Keyword arguments parsed to yaml.dump.
 
         """
-        try:
+        if isinstance(fname, (str, Path)):
             fhandle = open(fname,'w',newline='\n')
-        except TypeError:
+        else:
             fhandle = fname
 
         if 'width' not in kwargs:
diff --git a/python/damask/_configmaterial.py b/python/damask/_configmaterial.py
index 1b4d4439c..01d85f6a4 100644
--- a/python/damask/_configmaterial.py
+++ b/python/damask/_configmaterial.py
@@ -1,10 +1,14 @@
 import numpy as np
 import h5py
+from typing import Sequence, Dict, Any, Collection
 
+from ._typehints import FileHandle
 from . import Config
 from . import Rotation
 from . import Orientation
 from . import util
+from . import Table
+
 
 class ConfigMaterial(Config):
     """
@@ -17,7 +21,9 @@ class ConfigMaterial(Config):
 
     """
 
-    def __init__(self,d=None,**kwargs):
+    def __init__(self,
+                 d: Dict[str, Any] = None,
+                 **kwargs):
         """
         New material configuration.
 
@@ -30,14 +36,17 @@ class ConfigMaterial(Config):
             Initial content specified as pairs of key=value.
 
         """
+        default: Collection
         if d is None:
-            for section,default in {'material':[],'homogenization':{},'phase':{}}.items():
+            for section, default in {'material':[],'homogenization':{},'phase':{}}.items():
                 if section not in kwargs: kwargs.update({section:default})
 
         super().__init__(d,**kwargs)
 
 
-    def save(self,fname='material.yaml',**kwargs):
+    def save(self,
+             fname: FileHandle = 'material.yaml',
+             **kwargs):
         """
         Save to yaml file.
 
@@ -53,7 +62,8 @@ class ConfigMaterial(Config):
 
 
     @classmethod
-    def load(cls,fname='material.yaml'):
+    def load(cls,
+             fname: FileHandle = 'material.yaml') -> 'ConfigMaterial':
         """
         Load from yaml file.
 
@@ -72,10 +82,14 @@ class ConfigMaterial(Config):
 
 
     @staticmethod
-    def load_DREAM3D(fname,
-                     grain_data=None,cell_data=None,cell_ensemble_data='CellEnsembleData',
-                     phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
-                     base_group=None):
+    def load_DREAM3D(fname: str,
+                     grain_data: str = None,
+                     cell_data: str = None,
+                     cell_ensemble_data: str = 'CellEnsembleData',
+                     phases: str = 'Phases',
+                     Euler_angles: str = 'EulerAngles',
+                     phase_names: str = 'PhaseName',
+                     base_group: str = None) -> 'ConfigMaterial':
         """
         Load DREAM.3D (HDF5) file.
 
@@ -154,7 +168,8 @@ class ConfigMaterial(Config):
 
 
     @staticmethod
-    def from_table(table,**kwargs):
+    def from_table(table: Table,
+                   **kwargs) -> 'ConfigMaterial':
         """
         Generate from an ASCII table.
 
@@ -207,7 +222,7 @@ class ConfigMaterial(Config):
 
 
     @property
-    def is_complete(self):
+    def is_complete(self) -> bool:
         """
         Check for completeness.
 
@@ -267,12 +282,11 @@ class ConfigMaterial(Config):
             if homogenization - set(self['homogenization']):
                 print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
                 ok = False
-
         return ok
 
 
     @property
-    def is_valid(self):
+    def is_valid(self) -> bool:
         """
         Check for valid content.
 
@@ -316,7 +330,10 @@ class ConfigMaterial(Config):
         return ok
 
 
-    def material_rename_phase(self,mapping,ID=None,constituent=None):
+    def material_rename_phase(self,
+                              mapping: Dict[str, str],
+                              ID: Sequence[int] = None,
+                              constituent: Sequence[int] = None) -> 'ConfigMaterial':
         """
         Change phase name in material.
 
@@ -347,7 +364,9 @@ class ConfigMaterial(Config):
         return dup
 
 
-    def material_rename_homogenization(self,mapping,ID=None):
+    def material_rename_homogenization(self,
+                                       mapping: Dict[str, str],
+                                       ID: Sequence[int] = None) -> 'ConfigMaterial':
         """
         Change homogenization name in material.
 
@@ -374,7 +393,8 @@ class ConfigMaterial(Config):
         return dup
 
 
-    def material_add(self,**kwargs):
+    def material_add(self,
+                     **kwargs: Any) -> 'ConfigMaterial':
         """
         Add material entries.
 
@@ -453,7 +473,7 @@ class ConfigMaterial(Config):
             N = max(N,s[0]) if len(s)>0 else N
             n = max(n,s[1]) if len(s)>1 else n
 
-        mat = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
+        mat: Sequence[dict] = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
 
         if 'v' not in kwargs:
             shaped['v'] = np.broadcast_to(1/n,(N,n))
@@ -461,7 +481,7 @@ class ConfigMaterial(Config):
         map_shape = {'O':(N,n,4),'F_i':(N,n,3,3)}
         for k,v in shaped.items():
             target = map_shape.get(k,(N,n))
-            obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape,target,mode='right')),target)
+            obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape, target, mode = 'right')), target)
             for i in range(N):
                 if k in ['phase','O','v','F_i']:
                     for j in range(n):
diff --git a/python/damask/util.py b/python/damask/util.py
index 0bbc1e7b5..b4c287884 100644
--- a/python/damask/util.py
+++ b/python/damask/util.py
@@ -9,7 +9,7 @@ import re
 import fractions
 from collections import abc
 from functools import reduce
-from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, Optional
+from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, SupportsIndex, Sequence
 from pathlib import Path
 
 import numpy as np
@@ -427,7 +427,7 @@ def hybrid_IA(dist: np.ndarray,
 def shapeshifter(fro: Tuple[int, ...],
                  to: Tuple[int, ...],
                  mode: Literal['left','right'] = 'left',
-                 keep_ones: bool = False) -> Tuple[Optional[int], ...]:
+                 keep_ones: bool = False) -> Sequence[SupportsIndex]:
     """
     Return dimensions that reshape 'fro' to become broadcastable to 'to'.
 
@@ -483,14 +483,14 @@ def shapeshifter(fro: Tuple[int, ...],
         grp = match.groups()
     except AssertionError:
         raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
-    fill: Tuple[Optional[int], ...] = ()
+    fill: Any = ()
     for g,d in zip(grp,fro+(None,)):
         fill += (1,)*g.count(',')+(d,)
     return fill[:-1]
 
 
 def shapeblender(a: Tuple[int, ...],
-                 b: Tuple[int, ...]) -> Tuple[int, ...]:
+                 b: Tuple[int, ...]) -> Sequence[SupportsIndex]:
     """
     Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
 

From dc5ab9aee9f935e03e463fc13eb9d857f873c007 Mon Sep 17 00:00:00 2001
From: Test User <damask_user@mpie.de>
Date: Tue, 1 Feb 2022 11:55:34 +0100
Subject: [PATCH 133/133] [skip ci] updated version information after
 successful test of v3.0.0-alpha5-545-gad74f5dbe

---
 python/damask/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/damask/VERSION b/python/damask/VERSION
index 92cb9dcb3..8d2c8c56d 100644
--- a/python/damask/VERSION
+++ b/python/damask/VERSION
@@ -1 +1 @@
-v3.0.0-alpha5-542-g225a5d908
+v3.0.0-alpha5-545-gad74f5dbe