Merge remote-tracking branch 'origin/T_ref300' into dynamic-C

python/damask/VERSION

@@ -1 +1 @@
-v3.0.0-alpha5-155-gbf76d9f3a
+v3.0.0-alpha5-164-gdc993bc6f

python/damask/_colormap.py

@@ -2,6 +2,9 @@ import os
 import json
 import functools
 import colorsys
+from pathlib import Path
+from typing import Sequence, Union, TextIO
+
 
 import numpy as np
 import matplotlib as mpl
@@ -39,20 +42,20 @@ class Colormap(mpl.colors.ListedColormap):
 
     """
 
-    def __add__(self,other):
+    def __add__(self, other: "Colormap") -> "Colormap":
         """Concatenate."""
         return Colormap(np.vstack((self.colors,other.colors)),
                         f'{self.name}+{other.name}')
 
-    def __iadd__(self,other):
+    def __iadd__(self, other: "Colormap") -> "Colormap":
         """Concatenate (in-place)."""
         return self.__add__(other)
 
-    def __invert__(self):
+    def __invert__(self) -> "Colormap":
         """Reverse."""
         return self.reversed()
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """Show as matplotlib figure."""
         fig = plt.figure(self.name,figsize=(5,.5))
         ax1 = fig.add_axes([0, 0, 1, 1])
@@ -64,7 +67,11 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def from_range(low,high,name='DAMASK colormap',N=256,model='rgb'):
+    def from_range(low: Sequence[float],
+                   high: Sequence[float],
+                   name: str = 'DAMASK colormap',
+                   N: int = 256,
+                   model: str = 'rgb') -> "Colormap":
         """
         Create a perceptually uniform colormap between given (inclusive) bounds.
 
@@ -145,7 +152,7 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def from_predefined(name,N=256):
+    def from_predefined(name: str, N: int = 256) -> "Colormap":
         """
         Select from a set of predefined colormaps.
 
@@ -185,7 +192,10 @@ class Colormap(mpl.colors.ListedColormap):
             return Colormap.from_range(definition['low'],definition['high'],name,N)
 
 
-    def shade(self,field,bounds=None,gap=None):
+    def shade(self,
+              field: np.ndarray,
+              bounds: Sequence[float] = None,
+              gap: float = None) -> Image:
         """
         Generate PIL image of 2D field using colormap.
 
@@ -226,7 +236,7 @@ class Colormap(mpl.colors.ListedColormap):
             mode='RGBA')
 
 
-    def reversed(self,name=None):
+    def reversed(self, name: str = None) -> "Colormap":
         """
         Reverse.
 
@@ -251,7 +261,7 @@ class Colormap(mpl.colors.ListedColormap):
         return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
 
 
-    def _get_file_handle(self,fname,extension):
+    def _get_file_handle(self, fname: Union[TextIO, str, Path, None], suffix: str) -> TextIO:
         """
         Provide file handle.
 
@@ -259,8 +269,7 @@ class Colormap(mpl.colors.ListedColormap):
         ----------
         fname : file, str, pathlib.Path, or None
             Filename or filehandle, will be name of the colormap+extension if None.
-
+        suffix: str
-        extension: str
             Extension of the filename.
 
         Returns
@@ -270,17 +279,14 @@ class Colormap(mpl.colors.ListedColormap):
 
         """
         if fname is None:
-            fhandle = open(self.name.replace(' ','_')+'.'+extension,'w',newline='\n')
+            return open(self.name.replace(' ','_')+suffix, 'w', newline='\n')
+        elif isinstance(fname, (str, Path)):
+            return open(fname, 'w', newline='\n')
         else:
-            try:
+            return fname
-                fhandle = open(fname,'w',newline='\n')
-            except TypeError:
-                fhandle = fname
-
-        return fhandle
 
 
-    def save_paraview(self,fname=None):
+    def save_paraview(self, fname: Union[TextIO, str, Path] = None):
         """
         Save as JSON file for use in Paraview.
 
@@ -303,10 +309,10 @@ class Colormap(mpl.colors.ListedColormap):
                 'RGBPoints':colors
                }]
 
-        json.dump(out,self._get_file_handle(fname,'json'),indent=4)
+        json.dump(out,self._get_file_handle(fname,'.json'),indent=4)
 
 
-    def save_ASCII(self,fname=None):
+    def save_ASCII(self, fname: Union[TextIO, str, Path] = None):
         """
         Save as ASCII file.
 
@@ -319,10 +325,10 @@ class Colormap(mpl.colors.ListedColormap):
         """
         labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
         t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
-        t.save(self._get_file_handle(fname,'txt'))
+        t.save(self._get_file_handle(fname,'.txt'))
 
 
-    def save_GOM(self,fname=None):
+    def save_GOM(self, fname: Union[TextIO, str, Path] = None):
         """
         Save as ASCII file for use in GOM Aramis.
 
@@ -340,10 +346,10 @@ class Colormap(mpl.colors.ListedColormap):
                 + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
                 + '\n'
 
-        self._get_file_handle(fname,'legend').write(GOM_str)
+        self._get_file_handle(fname,'.legend').write(GOM_str)
 
 
-    def save_gmsh(self,fname=None):
+    def save_gmsh(self, fname: Union[TextIO, str, Path] = None):
         """
         Save as ASCII file for use in gmsh.
 
@@ -358,11 +364,13 @@ class Colormap(mpl.colors.ListedColormap):
         gmsh_str = 'View.ColorTable = {\n' \
                  +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
                  +'\n}\n'
-        self._get_file_handle(fname,'msh').write(gmsh_str)
+        self._get_file_handle(fname,'.msh').write(gmsh_str)
 
 
     @staticmethod
-    def _interpolate_msh(frac,low,high):
+    def _interpolate_msh(frac,
+                         low: np.ndarray,
+                         high: np.ndarray) -> np.ndarray:
         """
         Interpolate in Msh color space.
 
@@ -439,31 +447,31 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def _hsv2rgb(hsv):
+    def _hsv2rgb(hsv: np.ndarray) -> np.ndarray:
         """H(ue) S(aturation) V(alue) to R(red) G(reen) B(lue)."""
         return np.array(colorsys.hsv_to_rgb(hsv[0]/360.,hsv[1],hsv[2]))
 
     @staticmethod
-    def _rgb2hsv(rgb):
+    def _rgb2hsv(rgb: np.ndarray) -> np.ndarray:
         """R(ed) G(reen) B(lue) to H(ue) S(aturation) V(alue)."""
         h,s,v = colorsys.rgb_to_hsv(rgb[0],rgb[1],rgb[2])
         return np.array([h*360,s,v])
 
 
     @staticmethod
-    def _hsl2rgb(hsl):
+    def _hsl2rgb(hsl: np.ndarray) -> np.ndarray:
         """H(ue) S(aturation) L(uminance) to R(red) G(reen) B(lue)."""
         return np.array(colorsys.hls_to_rgb(hsl[0]/360.,hsl[2],hsl[1]))
 
     @staticmethod
-    def _rgb2hsl(rgb):
+    def _rgb2hsl(rgb: np.ndarray) -> np.ndarray:
         """R(ed) G(reen) B(lue) to H(ue) S(aturation) L(uminance)."""
         h,l,s = colorsys.rgb_to_hls(rgb[0],rgb[1],rgb[2])
         return np.array([h*360,s,l])
 
 
     @staticmethod
-    def _xyz2rgb(xyz):
+    def _xyz2rgb(xyz: np.ndarray) -> np.ndarray:
         """
         CIE Xyz to R(ed) G(reen) B(lue).
 
@@ -483,7 +491,7 @@ class Colormap(mpl.colors.ListedColormap):
         return np.clip(rgb,0.,1.)
 
     @staticmethod
-    def _rgb2xyz(rgb):
+    def _rgb2xyz(rgb: np.ndarray) -> np.ndarray:
         """
         R(ed) G(reen) B(lue) to CIE Xyz.
 
@@ -501,7 +509,7 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def _lab2xyz(lab,ref_white=None):
+    def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
         """
         CIE Lab to CIE Xyz.
 
@@ -520,7 +528,7 @@ class Colormap(mpl.colors.ListedColormap):
                         ])*(ref_white if ref_white is not None else _ref_white)
 
     @staticmethod
-    def _xyz2lab(xyz,ref_white=None):
+    def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
         """
         CIE Xyz to CIE Lab.
 
@@ -540,7 +548,7 @@ class Colormap(mpl.colors.ListedColormap):
 
 
     @staticmethod
-    def _lab2msh(lab):
+    def _lab2msh(lab: np.ndarray) -> np.ndarray:
         """
         CIE Lab to Msh.
 
@@ -558,7 +566,7 @@ class Colormap(mpl.colors.ListedColormap):
                         ])
 
     @staticmethod
-    def _msh2lab(msh):
+    def _msh2lab(msh: np.ndarray) -> np.ndarray:
         """
         Msh to CIE Lab.
 
@@ -575,29 +583,29 @@ class Colormap(mpl.colors.ListedColormap):
                         ])
 
     @staticmethod
-    def _lab2rgb(lab):
+    def _lab2rgb(lab: np.ndarray) -> np.ndarray:
         return Colormap._xyz2rgb(Colormap._lab2xyz(lab))
 
     @staticmethod
-    def _rgb2lab(rgb):
+    def _rgb2lab(rgb: np.ndarray) -> np.ndarray:
         return Colormap._xyz2lab(Colormap._rgb2xyz(rgb))
 
     @staticmethod
-    def _msh2rgb(msh):
+    def _msh2rgb(msh: np.ndarray) -> np.ndarray:
         return Colormap._lab2rgb(Colormap._msh2lab(msh))
 
     @staticmethod
-    def _rgb2msh(rgb):
+    def _rgb2msh(rgb: np.ndarray) -> np.ndarray:
         return Colormap._lab2msh(Colormap._rgb2lab(rgb))
 
     @staticmethod
-    def _hsv2msh(hsv):
+    def _hsv2msh(hsv: np.ndarray) -> np.ndarray:
         return Colormap._rgb2msh(Colormap._hsv2rgb(hsv))
 
     @staticmethod
-    def _hsl2msh(hsl):
+    def _hsl2msh(hsl: np.ndarray) -> np.ndarray:
         return Colormap._rgb2msh(Colormap._hsl2rgb(hsl))
 
     @staticmethod
-    def _xyz2msh(xyz):
+    def _xyz2msh(xyz: np.ndarray) -> np.ndarray:
         return Colormap._lab2msh(Colormap._xyz2lab(xyz))

python/tests/test_Colormap.py

@@ -77,6 +77,12 @@ class TestColormap:
             # xyz2msh
             assert np.allclose(Colormap._xyz2msh(xyz),msh,atol=1.e-6,rtol=0)
 
+    @pytest.mark.parametrize('low,high',[((0,0,0),(1,1,1)),
+                                         ([0,0,0],[1,1,1])])
+    def test_from_range_types(self,low,high):
+        a = Colormap.from_range(low,high)
+        b = Colormap.from_range(np.array(low),np.array(high))
+        assert np.all(a.colors == b.colors) 
 
     @pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
     @pytest.mark.parametrize('model',['rgb','hsv','hsl','xyz','lab','msh'])

src/commercialFEM_fileList.f90

@@ -4,6 +4,7 @@
 !> @details List of files needed by MSC.Marc
 !--------------------------------------------------------------------------------------------------
 #include "parallelization.f90"
+#include "constants.f90"
 #include "IO.f90"
 #include "YAML_types.f90"
 #include "YAML_parse.f90"

src/constants.f90

@@ -0,0 +1,15 @@
+!--------------------------------------------------------------------------------------------------
+!> @author Martin Diehl, KU Leuven
+!> @brief  physical constants
+!--------------------------------------------------------------------------------------------------
+module constants
+  use prec
+
+  implicit none
+  public
+
+  real(pReal), parameter :: &
+    T_ROOM = 300.0_pReal, &                                                                         !< Room temperature in K
+    kB = 1.38e-23_pReal                                                                             !< Boltzmann constant in J/Kelvin
+
+end module constants

src/phase.f90

@@ -5,6 +5,7 @@
 !--------------------------------------------------------------------------------------------------
 module phase
   use prec
+  use constants
   use math
   use rotations
   use IO

src/phase_mechanical_eigen_thermalexpansion.f90

@@ -58,7 +58,7 @@ module function thermalexpansion_init(kinematics_length) result(myKinematics)
         associate(prm  => param(kinematics_thermal_expansion_instance(p)))
           kinematic_type => kinematics%get(k)
 
-          prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=0.0_pReal)
+          prm%T_ref = kinematic_type%get_asFloat('T_ref', defaultVal=T_ROOM)
 
           prm%A(1,1,1) = kinematic_type%get_asFloat('A_11')
           prm%A(1,1,2) = kinematic_type%get_asFloat('A_11,T',defaultVal=0.0_pReal)

src/phase_mechanical_plastic_dislotungsten.f90

@@ -7,9 +7,6 @@
 !--------------------------------------------------------------------------------------------------
 submodule(phase:plastic) dislotungsten
 
-  real(pReal), parameter :: &
-    kB = 1.38e-23_pReal                                                                             !< Boltzmann constant in J/Kelvin
-
   type :: tParameters
     real(pReal) :: &
       D    = 1.0_pReal, &                                                                           !< grain size

src/phase_mechanical_plastic_dislotwin.f90

@@ -9,9 +9,6 @@
 !--------------------------------------------------------------------------------------------------
 submodule(phase:plastic) dislotwin
 
-  real(pReal), parameter :: &
-    kB = 1.38e-23_pReal                                                                             !< Boltzmann constant in J/Kelvin
-
   type :: tParameters
     real(pReal) :: &
       Q_cl                = 1.0_pReal, &                                                            !< activation energy for dislocation climb
@@ -31,7 +28,7 @@ submodule(phase:plastic) dislotwin
       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
-      T_ref               = 0.0_pReal, &
+      T_ref               = T_ROOM, &
       a_cI                = 1.0_pReal, &
       a_cF                = 1.0_pReal
     real(pReal),                            dimension(2) :: &

src/phase_mechanical_plastic_nonlocal.f90

@@ -19,9 +19,6 @@ submodule(phase:plastic) nonlocal
 
   type(tGeometry), dimension(:), allocatable :: geom
 
-  real(pReal), parameter :: &
-    kB = 1.38e-23_pReal                                                                             !< Boltzmann constant in J/Kelvin
-
   ! storage order of dislocation types
   integer, dimension(*), parameter :: &
     sgl = [1,2,3,4,5,6,7,8]                                                                         !< signed (single)