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Merge remote-tracking branch 'origin/development' into vector-mechanics

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Martin Diehl 2020-11-14 15:10:52 +01:00
parent cf958d32b4 12140bb657
commit 6529613726
86 changed files with 3839 additions and 2337 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit e2301f7d12ff0ae12218d9b58e33a814eb5431c9 Subproject commit 281e7eb84f76a2974a50eb54faf35ea25ec89b20

2
VERSION
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@ -1 +1 @@
v3.0.0-alpha-633-g086b215d9 v3.0.0-alpha-726-g1f59f6301

7
cmake/Compiler-Intel.cmake
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@ -98,11 +98,12 @@ set (DEBUG_FLAGS "${DEBUG_FLAGS} -ftrapuv")
set (DEBUG_FLAGS "${DEBUG_FLAGS} -fpe-all=0") set (DEBUG_FLAGS "${DEBUG_FLAGS} -fpe-all=0")
# ... capture all floating-point exceptions, sets -ftz automatically # ... capture all floating-point exceptions, sets -ftz automatically
set (DEBUG_FLAGS "${DEBUG_FLAGS} -warn") # disable due to compiler bug https://community.intel.com/t5/Intel-Fortran-Compiler/false-positive-stand-f18-and-IEEE-SELECTED-REAL-KIND/m-p/1227336
#set (DEBUG_FLAGS "${DEBUG_FLAGS} -warn")
# enables warnings ... # enables warnings ...
set (DEBUG_FLAGS "${DEBUG_FLAGS} errors") #set (DEBUG_FLAGS "${DEBUG_FLAGS} errors")
# ... warnings are changed to errors # ... warnings are changed to errors
set (DEBUG_FLAGS "${DEBUG_FLAGS},stderrors") #set (DEBUG_FLAGS "${DEBUG_FLAGS},stderrors")
# ... warnings about Fortran standard violations are changed to errors # ... warnings about Fortran standard violations are changed to errors
set (DEBUG_FLAGS "${DEBUG_FLAGS} -debug-parameters all") set (DEBUG_FLAGS "${DEBUG_FLAGS} -debug-parameters all")

30
examples/SpectralMethod/Polycrystal/material.yaml
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@ -108,19 +108,19 @@ material:
phase: phase:
Aluminum: Aluminum:
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
generic:
output: [F, P, F_e, F_p, L_p, O]
lattice: fcc lattice: fcc
plasticity: mech:
N_sl: [12] output: [F, P, F_e, F_p, L_p, O]
a_sl: 2.25 elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
atol_xi: 1.0 plasticity:
dot_gamma_0_sl: 0.001 N_sl: [12]
h_0_sl_sl: 75e6 a_sl: 2.25
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4] atol_xi: 1.0
n_sl: 20 dot_gamma_0_sl: 0.001
output: [xi_sl] h_0_sl_sl: 75e6
type: phenopowerlaw h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
xi_0_sl: [31e6] n_sl: 20
xi_inf_sl: [63e6] output: [xi_sl]
type: phenopowerlaw
xi_0_sl: [31e6]
xi_inf_sl: [63e6]

6
python/damask/__init__.py
View File

@ -15,12 +15,12 @@ from . import seeds # noqa
from . import mechanics # noqa from . import mechanics # noqa
from . import solver # noqa from . import solver # noqa
from . import grid_filters # noqa from . import grid_filters # noqa
from ._lattice import Symmetry, Lattice# noqa from . import lattice # noqa
from ._table import Table # noqa
from ._rotation import Rotation # noqa from ._rotation import Rotation # noqa
from ._orientation import Orientation # noqa
from ._table import Table # noqa
from ._vtk import VTK # noqa from ._vtk import VTK # noqa
from ._colormap import Colormap # noqa from ._colormap import Colormap # noqa
from ._orientation import Orientation # noqa
from ._config import Config # noqa from ._config import Config # noqa
from ._configmaterial import ConfigMaterial # noqa from ._configmaterial import ConfigMaterial # noqa
from ._geom import Geom # noqa from ._geom import Geom # noqa

35
python/damask/_asciitable.py
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@ -385,38 +385,3 @@ class ASCIItable():
self.data = np.loadtxt(self.__IO__['in'],usecols=use,ndmin=2) self.data = np.loadtxt(self.__IO__['in'],usecols=use,ndmin=2)
return labels_missing return labels_missing
# ------------------------------------------------------------------
def data_write(self):
"""Write current data array and report alive output back."""
if len(self.data) == 0: return True
if isinstance(self.data[0],list):
return self.output_write(['\t'.join(map(self._quote,items)) for items in self.data])
else:
return self.output_write( '\t'.join(map(self._quote,self.data)))
# ------------------------------------------------------------------
def data_writeArray(self):
"""Write whole numpy array data."""
for row in self.data:
try:
output = list(map(repr,row))
except Exception:
output = [repr(row)]
try:
self.__IO__['out'].write('\t'.join(output) + '\n')
except Exception:
pass
# ------------------------------------------------------------------
def data_append(self,
what):
if isinstance(what, str):
self.data += [what]
else:
try:
for item in what: self.data_append(item)
except TypeError:
self.data += [str(what)]

18
python/damask/_configmaterial.py
View File

@ -3,8 +3,8 @@ import copy
import numpy as np import numpy as np
from . import Config from . import Config
from . import Lattice
from . import Rotation from . import Rotation
from . import Orientation
class ConfigMaterial(Config): class ConfigMaterial(Config):
"""Material configuration.""" """Material configuration."""
@ -24,6 +24,20 @@ class ConfigMaterial(Config):
super().save(fname,**kwargs) super().save(fname,**kwargs)
@classmethod
def load(cls,fname='material.yaml'):
"""
Load from yaml file.
Parameters
----------
fname : file, str, or pathlib.Path, optional
Filename or file for writing. Defaults to 'material.yaml'.
"""
return super(ConfigMaterial,cls).load(fname)
@staticmethod @staticmethod
def from_table(table,constituents={},**kwargs): def from_table(table,constituents={},**kwargs):
""" """
@ -138,7 +152,7 @@ class ConfigMaterial(Config):
for k,v in self['phase'].items(): for k,v in self['phase'].items():
if 'lattice' in v: if 'lattice' in v:
try: try:
Lattice(v['lattice']) Orientation(lattice=v['lattice'])
except KeyError: except KeyError:
s = v['lattice'] s = v['lattice']
print(f"Invalid lattice: '{s}' in phase '{k}'") print(f"Invalid lattice: '{s}' in phase '{k}'")

205
python/damask/_geom.py
View File

@ -20,7 +20,7 @@ class Geom:
def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]): def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
""" """
New geometry definition from array of material, size, and origin. New geometry definition from array of materials, size, and origin.
Parameters Parameters
---------- ----------
@ -34,28 +34,10 @@ class Geom:
Comment lines. Comment lines.
""" """
if len(material.shape) != 3: self.material = material
raise ValueError(f'Invalid material shape {material.shape}.') self.size = size
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']: self.origin = origin
raise TypeError(f'Invalid material data type {material.dtype}.') self.comments = comments
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)
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}.')
else:
self.size = np.array(size)
if len(origin) != 3:
raise ValueError(f'Invalid origin {origin}.')
else:
self.origin = np.array(origin)
self.comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
def __repr__(self): def __repr__(self):
@ -113,13 +95,68 @@ class Geom:
return util.return_message(message) return util.return_message(message)
@property
def material(self):
"""Material indices."""
return self._material
@material.setter
def material(self,material):
if len(material.shape) != 3:
raise ValueError(f'Invalid material shape {material.shape}.')
elif material.dtype not in np.sctypes['float'] + 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)
@property
def size(self):
"""Physical size of geometry in meter."""
return self._size
@size.setter
def size(self,size):
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):
"""Coordinates of geometry origin in meter."""
return self._origin
@origin.setter
def origin(self,origin):
if len(origin) != 3:
raise ValueError(f'Invalid origin {origin}.')
else:
self._origin = np.array(origin)
@property
def comments(self):
"""Comments/history of geometry."""
return self._comments
@comments.setter
def comments(self,comments):
self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@property @property
def grid(self): def grid(self):
"""Grid dimension of geometry."""
return np.asarray(self.material.shape) return np.asarray(self.material.shape)
@property @property
def N_materials(self): def N_materials(self):
"""Number of (unique) material indices within geometry."""
return np.unique(self.material).size return np.unique(self.material).size
@ -132,7 +169,7 @@ class Geom:
---------- ----------
fname : str or or pathlib.Path fname : str or or pathlib.Path
Geometry file to read. Geometry file to read.
Valid extension is .vtr, it will be appended if not given. Valid extension is .vtr, which will be appended if not given.
""" """
v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr') v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
@ -153,7 +190,7 @@ class Geom:
Parameters Parameters
---------- ----------
fname : str or file handle fname : str, pathlib.Path, or file handle
Geometry file to read. Geometry file to read.
""" """
@ -221,26 +258,26 @@ class Geom:
fname : str fname : str
Filename of the DREAM.3D file Filename of the DREAM.3D file
base_group : str base_group : str
Name of the group (folder) below 'DataContainers'. For example Name of the group (folder) below 'DataContainers',
'SyntheticVolumeDataContainer'. for example 'SyntheticVolumeDataContainer'.
point_data : str, optional point_data : str, optional
Name of the group (folder) containing the point wise material data, Name of the group (folder) containing the pointwise material data,
for example 'CellData'. Defaults to None, in which case points consecutively numbered. for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
material : str, optional material : str, optional
Name of the dataset containing the material ID. Defaults to Name of the dataset containing the material ID.
'FeatureIds'. Defaults to 'FeatureIds'.
""" """
root_dir ='DataContainers' root_dir ='DataContainers'
f = h5py.File(fname, 'r') f = h5py.File(fname, 'r')
g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY') g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
size = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
grid = f[path.join(g,'DIMENSIONS')][()] grid = f[path.join(g,'DIMENSIONS')][()]
size = f[path.join(g,'SPACING')][()] * grid
origin = f[path.join(g,'ORIGIN')][()] origin = f[path.join(g,'ORIGIN')][()]
group_pointwise = path.join(root_dir,base_group,point_data)
ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \ ma = np.arange(grid.prod(),dtype=int) \
np.reshape(f[path.join(group_pointwise,material)],grid.prod()) if point_data is None else \
np.reshape(f[path.join(root_dir,base_group,point_data,material)],grid.prod())
return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D')) return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
@ -248,18 +285,18 @@ class Geom:
@staticmethod @staticmethod
def from_table(table,coordinates,labels): def from_table(table,coordinates,labels):
""" """
Load an ASCII table. Derive geometry from an ASCII table.
Parameters Parameters
---------- ----------
table : damask.Table table : damask.Table
Table that contains material information. Table that contains material information.
coordinates : str coordinates : str
Label of the column containing the vector of spatial coordinates. Label of the vector column containing the spatial coordinates.
Need to be ordered (1./x fast, 3./z slow). Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str labels : str or list of str
Label(s) of the columns containing the material definition. Label(s) of the columns containing the material definition.
Each unique combintation of values results in a material. Each unique combintation of values results in one material ID.
""" """
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates)) grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
@ -293,8 +330,8 @@ class Geom:
weights : numpy.ndarray of shape (seeds.shape[0]) weights : numpy.ndarray of shape (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation. 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 : numpy.ndarray of shape (seeds.shape[0]), optional
Material ID of the seeds. Defaults to None, in which case materials are Material ID of the seeds.
consecutively numbered. Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional periodic : Boolean, optional
Perform a periodic tessellation. Defaults to True. Perform a periodic tessellation. Defaults to True.
@ -342,8 +379,8 @@ class Geom:
seeds : numpy.ndarray of shape (:,3) seeds : numpy.ndarray of shape (:,3)
Position of the seed points in meter. All points need to lay within the box. 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 : numpy.ndarray of shape (seeds.shape[0]), optional
Material ID of the seeds. Defaults to None, in which case materials are Material ID of the seeds.
consecutively numbered. Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional periodic : Boolean, optional
Perform a periodic tessellation. Defaults to True. Perform a periodic tessellation. Defaults to True.
@ -438,19 +475,19 @@ class Geom:
References References
---------- ----------
Surface curvature in triply-periodic minimal surface architectures as
a distinct design parameter in preparing advanced tissue engineering scaffolds
Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi, Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
10.1088/1758-5090/aa6553 Surface curvature in triply-periodic minimal surface architectures as
a distinct design parameter in preparing advanced tissue engineering scaffolds
https://doi.org/10.1088/1758-5090/aa6553
Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
10.1021/ma0019499 Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
https://doi.org/10.1021/ma0019499
Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
Meng-Ting Hsieh, Lorenzo Valdevit Meng-Ting Hsieh, Lorenzo Valdevit
10.1016/j.simpa.2020.100026 Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
https://doi.org/10.1016/j.simpa.2020.100026
""" """
x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(grid[0])+0.5)/grid[0], x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(grid[0])+0.5)/grid[0],
@ -465,7 +502,7 @@ class Geom:
def save(self,fname,compress=True): def save(self,fname,compress=True):
""" """
Store as vtk rectilinear grid. Store as VTK rectilinear grid.
Parameters Parameters
---------- ----------
@ -521,20 +558,20 @@ class Geom:
Parameters Parameters
---------- ----------
dimension : int or float numpy.ndarray of shape(3) dimension : int or float numpy.ndarray of shape (3)
Dimension (diameter/side length) of the primitive. If given as Dimension (diameter/side length) of the primitive. If given as
integers, grid point locations (cell centers) are addressed. integers, grid point locations (cell centers) are addressed.
If given as floats, coordinates are addressed. If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape(3) center : int or float numpy.ndarray of shape (3)
Center of the primitive. If given as integers, grid point Center of the primitive. If given as integers, grid point
locations (cell centers) are addressed. coordinates (cell centers) are addressed.
If given as floats, coordinates are addressed. If given as floats, coordinates in space are addressed.
exponent : numpy.ndarray of shape(3) or float exponent : numpy.ndarray of shape (3) or float
Exponents for the three axes. Exponents for the three axes.
0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1) 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) 1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
fill : int, optional fill : int, optional
Fill value for primitive. Defaults to material.max() + 1. Fill value for primitive. Defaults to material.max()+1.
R : damask.Rotation, optional R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation. Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional inverse : Boolean, optional
@ -544,25 +581,27 @@ class Geom:
Repeat primitive over boundaries. Defaults to True. Repeat primitive over boundaries. Defaults to True.
""" """
# normalized 'radius' and center # radius and center
r = np.array(dimension)/self.grid/2.0 if np.array(dimension).dtype in np.sctypes['int'] else \ r = np.array(dimension)/2.0*self.size/self.grid if np.array(dimension).dtype in np.sctypes['int'] else \
np.array(dimension)/self.size/2.0 np.array(dimension)/2.0
c = (np.array(center) + .5)/self.grid if np.array(center).dtype in np.sctypes['int'] else \ c = (np.array(center) + .5)*self.size/self.grid if np.array(center).dtype in np.sctypes['int'] else \
(np.array(center) - self.origin)/self.size (np.array(center) - self.origin)
coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \ coords = grid_filters.cell_coord0(self.grid,self.size,
- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG -(0.5*(self.size + (self.size/self.grid
if np.array(center).dtype in np.sctypes['int'] else
0)) if periodic else c))
coords_rot = R.broadcast_to(tuple(self.grid))@coords coords_rot = R.broadcast_to(tuple(self.grid))@coords
with np.errstate(all='ignore'): with np.errstate(all='ignore'):
mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0 mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
if periodic: # translate back to center if periodic: # translate back to center
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2)) mask = np.roll(mask,((c/self.size-0.5)*self.grid).round().astype(int),(0,1,2))
fill_ = np.full_like(self.material,np.nanmax(self.material)+1 if fill is None else fill) return Geom(material = np.where(np.logical_not(mask) if inverse else mask,
self.material,
return Geom(material = np.where(np.logical_not(mask) if inverse else mask, self.material,fill_), np.nanmax(self.material)+1 if fill is None else fill),
size = self.size, size = self.size,
origin = self.origin, origin = self.origin,
comments = self.comments+[util.execution_stamp('Geom','add_primitive')], comments = self.comments+[util.execution_stamp('Geom','add_primitive')],
@ -689,7 +728,7 @@ class Geom:
def renumber(self): def renumber(self):
"""Renumber sorted material indices to 0,...,N-1.""" """Renumber sorted material indices as 0,...,N-1."""
_,renumbered = np.unique(self.material,return_inverse=True) _,renumbered = np.unique(self.material,return_inverse=True)
return Geom(material = renumbered.reshape(self.grid), return Geom(material = renumbered.reshape(self.grid),
@ -785,7 +824,7 @@ class Geom:
""" """
def mp(entry,mapper): def mp(entry,mapper):
return mapper[entry] if entry in mapper else entry return mapper[entry] if entry in mapper else entry
mp = np.vectorize(mp) mp = np.vectorize(mp)
mapper = dict(zip(from_material,to_material)) mapper = dict(zip(from_material,to_material))
@ -796,6 +835,20 @@ class Geom:
) )
def sort(self):
"""Sort material indices such that min(material) is located at (0,0,0)."""
a = self.material.flatten(order='F')
from_ma = pd.unique(a)
sort_idx = np.argsort(from_ma)
ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]
return Geom(material = ma.reshape(self.grid,order='F'),
size = self.size,
origin = self.origin,
comments = self.comments+[util.execution_stamp('Geom','sort')],
)
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True): def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
""" """
Offset material index of points in the vicinity of xxx. Offset material index of points in the vicinity of xxx.
@ -811,7 +864,7 @@ class Geom:
Defaults to 1. Defaults to 1.
offset : int, optional offset : int, optional
Offset (positive or negative) to tag material indices, Offset (positive or negative) to tag material indices,
defaults to material.max() + 1. defaults to material.max()+1.
trigger : list of ints, optional trigger : list of ints, optional
List of material indices that trigger a change. List of material indices that trigger a change.
Defaults to [], meaning that any different neighbor triggers a change. Defaults to [], meaning that any different neighbor triggers a change.
@ -822,15 +875,11 @@ class Geom:
def tainted_neighborhood(stencil,trigger): def tainted_neighborhood(stencil,trigger):
me = stencil[stencil.shape[0]//2] me = stencil[stencil.shape[0]//2]
if len(trigger) == 0: return np.any(stencil != me
return np.any(stencil != me) if len(trigger) == 0 else
if me in trigger: np.in1d(stencil,np.array(list(set(trigger) - {me}))))
trigger = set(trigger)
trigger.remove(me)
trigger = list(trigger)
return np.any(np.in1d(stencil,np.array(trigger)))
offset_ = np.nanmax(self.material) if offset is None else offset offset_ = np.nanmax(self.material)+1 if offset is None else offset
mask = ndimage.filters.generic_filter(self.material, mask = ndimage.filters.generic_filter(self.material,
tainted_neighborhood, tainted_neighborhood,
size=1+2*vicinity, size=1+2*vicinity,

646
python/damask/_lattice.py
View File

@ -1,646 +0,0 @@
import numpy as np
class Symmetry:
"""
Symmetry-related operations for crystal systems.
References
----------
https://en.wikipedia.org/wiki/Crystal_system
"""
crystal_systems = [None,'orthorhombic','tetragonal','hexagonal','cubic']
def __init__(self, system = None):
"""
Symmetry Definition.
Parameters
----------
system : {None,'orthorhombic','tetragonal','hexagonal','cubic'}, optional
Name of the crystal system. Defaults to 'None'.
"""
if system is not None and system.lower() not in self.crystal_systems:
raise KeyError(f'Crystal system "{system}" is unknown')
self.system = system.lower() if isinstance(system,str) else system
def __copy__(self):
"""Copy."""
return self.__class__(self.system)
copy = __copy__
def __repr__(self):
"""Readable string."""
return f'{self.system}'
def __eq__(self, other):
"""
Equal to other.
Parameters
----------
other : Symmetry
Symmetry to check for equality.
"""
return self.system == other.system
def __neq__(self, other):
"""
Not Equal to other.
Parameters
----------
other : Symmetry
Symmetry to check for inequality.
"""
return not self.__eq__(other)
def __cmp__(self,other):
"""
Linear ordering.
Parameters
----------
other : Symmetry
Symmetry to check for for order.
"""
myOrder = self.crystal_systems.index(self.system)
otherOrder = self.crystal_systems.index(other.system)
return (myOrder > otherOrder) - (myOrder < otherOrder)
@property
def symmetry_operations(self):
"""Symmetry operations as quaternions."""
if self.system == 'cubic':
sym_quats = [
[ 1.0, 0.0, 0.0, 0.0 ],
[ 0.0, 1.0, 0.0, 0.0 ],
[ 0.0, 0.0, 1.0, 0.0 ],
[ 0.0, 0.0, 0.0, 1.0 ],
[ 0.0, 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2) ],
[ 0.0, 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2) ],
[ 0.0, 0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2) ],
[ 0.0, 0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2) ],
[ 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
[ 0.0, -0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
[ 0.5, 0.5, 0.5, 0.5 ],
[-0.5, 0.5, 0.5, 0.5 ],
[-0.5, 0.5, 0.5, -0.5 ],
[-0.5, 0.5, -0.5, 0.5 ],
[-0.5, -0.5, 0.5, 0.5 ],
[-0.5, -0.5, 0.5, -0.5 ],
[-0.5, -0.5, -0.5, 0.5 ],
[-0.5, 0.5, -0.5, -0.5 ],
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
[-0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2), 0.0 ],
[-0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2), 0.0 ],
[-0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0, 0.0 ],
[-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0, 0.0 ],
]
elif self.system == 'hexagonal':
sym_quats = [
[ 1.0, 0.0, 0.0, 0.0 ],
[-0.5*np.sqrt(3), 0.0, 0.0, -0.5 ],
[ 0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
[ 0.0, 0.0, 0.0, 1.0 ],
[-0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
[-0.5*np.sqrt(3), 0.0, 0.0, 0.5 ],
[ 0.0, 1.0, 0.0, 0.0 ],
[ 0.0, -0.5*np.sqrt(3), 0.5, 0.0 ],
[ 0.0, 0.5, -0.5*np.sqrt(3), 0.0 ],
[ 0.0, 0.0, 1.0, 0.0 ],
[ 0.0, -0.5, -0.5*np.sqrt(3), 0.0 ],
[ 0.0, 0.5*np.sqrt(3), 0.5, 0.0 ],
]
elif self.system == 'tetragonal':
sym_quats = [
[ 1.0, 0.0, 0.0, 0.0 ],
[ 0.0, 1.0, 0.0, 0.0 ],
[ 0.0, 0.0, 1.0, 0.0 ],
[ 0.0, 0.0, 0.0, 1.0 ],
[ 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
[ 0.0, -0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
]
elif self.system == 'orthorhombic':
sym_quats = [
[ 1.0,0.0,0.0,0.0 ],
[ 0.0,1.0,0.0,0.0 ],
[ 0.0,0.0,1.0,0.0 ],
[ 0.0,0.0,0.0,1.0 ],
]
else:
sym_quats = [
[ 1.0,0.0,0.0,0.0 ],
]
return np.array(sym_quats)
def in_FZ(self,rho):
"""
Check whether given Rodrigues-Frank vector falls into fundamental zone.
Fundamental zone in Rodrigues space is point symmetric around origin.
"""
if(rho.shape[-1] != 3):
raise ValueError('Input is not a Rodrigues-Frank vector field.')
rho_abs = np.abs(rho)
with np.errstate(invalid='ignore'):
# using '*'/prod for 'and'
if self.system == 'cubic':
return np.where(np.prod(np.sqrt(2)-1. >= rho_abs,axis=-1) *
(1. >= np.sum(rho_abs,axis=-1)),True,False)
elif self.system == 'hexagonal':
return np.where(np.prod(1. >= rho_abs,axis=-1) *
(2. >= np.sqrt(3)*rho_abs[...,0] + rho_abs[...,1]) *
(2. >= np.sqrt(3)*rho_abs[...,1] + rho_abs[...,0]) *
(2. >= np.sqrt(3) + rho_abs[...,2]),True,False)
elif self.system == 'tetragonal':
return np.where(np.prod(1. >= rho_abs[...,:2],axis=-1) *
(np.sqrt(2) >= rho_abs[...,0] + rho_abs[...,1]) *
(np.sqrt(2) >= rho_abs[...,2] + 1.),True,False)
elif self.system == 'orthorhombic':
return np.where(np.prod(1. >= rho_abs,axis=-1),True,False)
else:
return np.where(np.all(np.isfinite(rho_abs),axis=-1),True,False)
def in_disorientation_SST(self,rho):
"""
Check whether given Rodrigues-Frank vector (of misorientation) falls into standard stereographic triangle.
References
----------
A. Heinz and P. Neumann, Acta Crystallographica Section A 47:780-789, 1991
https://doi.org/10.1107/S0108767391006864
"""
if(rho.shape[-1] != 3):
raise ValueError('Input is not a Rodrigues-Frank vector field.')
with np.errstate(invalid='ignore'):
# using '*' for 'and'
if self.system == 'cubic':
return np.where((rho[...,0] >= rho[...,1]) * \
(rho[...,1] >= rho[...,2]) * \
(rho[...,2] >= 0),True,False)
elif self.system == 'hexagonal':
return np.where((rho[...,0] >= rho[...,1]*np.sqrt(3)) * \
(rho[...,1] >= 0) * \
(rho[...,2] >= 0),True,False)
elif self.system == 'tetragonal':
return np.where((rho[...,0] >= rho[...,1]) * \
(rho[...,1] >= 0) * \
(rho[...,2] >= 0),True,False)
elif self.system == 'orthorhombic':
return np.where((rho[...,0] >= 0) * \
(rho[...,1] >= 0) * \
(rho[...,2] >= 0),True,False)
else:
return np.ones_like(rho[...,0],dtype=bool)
#ToDo: IPF color in separate function
def in_SST(self,vector,proper=False,color=False):
"""
Check whether given vector falls into standard stereographic triangle of own symmetry.
proper considers only vectors with z >= 0, hence uses two neighboring SSTs.
Return inverse pole figure color if requested.
Bases are computed from
>>> basis = {'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
... [1.,0.,1.]/np.sqrt(2.), # direction of green
... [1.,1.,1.]/np.sqrt(3.)]).T), # direction of blue
... 'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
... [1.,0.,0.], # direction of green
... [np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # direction of blue
... 'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
... [1.,0.,0.], # direction of green
... [1.,1.,0.]/np.sqrt(2.)]).T), # direction of blue
... 'orthorhombic': np.linalg.inv(np.array([[0.,0.,1.], # direction of red
... [1.,0.,0.], # direction of green
... [0.,1.,0.]]).T), # direction of blue
... }
"""
if(vector.shape[-1] != 3):
raise ValueError('Input is not a 3D vector field.')
if self.system == 'cubic':
basis = {'improper':np.array([ [-1. , 0. , 1. ],
[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
[ 0. , np.sqrt(3.) , 0. ] ]),
'proper':np.array([ [ 0. , -1. , 1. ],
[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
[ np.sqrt(3.) , 0. , 0. ] ]),
}
elif self.system == 'hexagonal':
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
[ 1. , -np.sqrt(3.) , 0. ],
[ 0. , 2. , 0. ] ]),
'proper':np.array([ [ 0. , 0. , 1. ],
[-1. , np.sqrt(3.) , 0. ],
[ np.sqrt(3.) , -1. , 0. ] ]),
}
elif self.system == 'tetragonal':
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
[ 1. , -1. , 0. ],
[ 0. , np.sqrt(2.) , 0. ] ]),
'proper':np.array([ [ 0. , 0. , 1. ],
[-1. , 1. , 0. ],
[ np.sqrt(2.) , 0. , 0. ] ]),
}
elif self.system == 'orthorhombic':
basis = {'improper':np.array([ [ 0., 0., 1.],
[ 1., 0., 0.],
[ 0., 1., 0.] ]),
'proper':np.array([ [ 0., 0., 1.],
[-1., 0., 0.],
[ 0., 1., 0.] ]),
}
else: # direct exit for unspecified symmetry
if color:
return (np.ones_like(vector[...,0],bool),np.zeros_like(vector))
else:
return np.ones_like(vector[...,0],bool)
b_i = np.broadcast_to(basis['improper'],vector.shape+(3,))
if proper:
b_p = np.broadcast_to(basis['proper'], vector.shape+(3,))
improper = np.all(np.around(np.einsum('...ji,...i',b_i,vector),12)>=0.0,axis=-1,keepdims=True)
theComponents = np.where(np.broadcast_to(improper,vector.shape),
np.around(np.einsum('...ji,...i',b_i,vector),12),
np.around(np.einsum('...ji,...i',b_p,vector),12))
else:
vector_ = np.block([vector[...,0:2],np.abs(vector[...,2:3])]) # z component projects identical
theComponents = np.around(np.einsum('...ji,...i',b_i,vector_),12)
in_SST = np.all(theComponents >= 0.0,axis=-1)
if color: # have to return color array
with np.errstate(invalid='ignore',divide='ignore'):
rgb = (theComponents/np.linalg.norm(theComponents,axis=-1,keepdims=True))**0.5 # smoothen color ramps
rgb = np.minimum(1.,rgb) # limit to maximum intensity
rgb /= np.max(rgb,axis=-1,keepdims=True) # normalize to (HS)V = 1
rgb[np.broadcast_to(~in_SST.reshape(vector[...,0].shape+(1,)),vector.shape)] = 0.0
return (in_SST,rgb)
else:
return in_SST
# ******************************************************************************************
class Lattice: # ToDo: Make a subclass of Symmetry!
"""
Bravais lattice.
This contains only a mapping from Bravais lattice to symmetry
and orientation relationships. It could include twin and slip systems.
References
----------
https://en.wikipedia.org/wiki/Bravais_lattice
"""
lattices = {
'iso': {'system':None},
'triclinic':{'system':None},
'bct': {'system':'tetragonal'},
'hex': {'system':'hexagonal'},
'fcc': {'system':'cubic','c/a':1.0},
'bcc': {'system':'cubic','c/a':1.0},
}
def __init__(self,lattice,c_over_a=None):
"""
New lattice of given type.
Parameters
----------
lattice : str
Bravais lattice.
"""
self.lattice = lattice
self.symmetry = Symmetry(self.lattices[lattice]['system'])
# transition to subclass
self.system = self.symmetry.system
self.in_SST = self.symmetry.in_SST
self.in_FZ = self.symmetry.in_FZ
self.in_disorientation_SST = self.symmetry.in_disorientation_SST
def __repr__(self):
"""Report basic lattice information."""
return f'Bravais lattice {self.lattice} ({self.symmetry} crystal system)'
# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
# from S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
# also see K. Kitahara et al., Acta Materialia 54:1279-1288, 2006
_KS = {'mapping':{'fcc':0,'bcc':1},
'planes': np.array([
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]]],dtype='float'),
'directions': np.array([
[[ -1, 0, 1],[ -1, -1, 1]],
[[ -1, 0, 1],[ -1, 1, -1]],
[[ 0, 1, -1],[ -1, -1, 1]],
[[ 0, 1, -1],[ -1, 1, -1]],
[[ 1, -1, 0],[ -1, -1, 1]],
[[ 1, -1, 0],[ -1, 1, -1]],
[[ 1, 0, -1],[ -1, -1, 1]],
[[ 1, 0, -1],[ -1, 1, -1]],
[[ -1, -1, 0],[ -1, -1, 1]],
[[ -1, -1, 0],[ -1, 1, -1]],
[[ 0, 1, 1],[ -1, -1, 1]],
[[ 0, 1, 1],[ -1, 1, -1]],
[[ 0, -1, 1],[ -1, -1, 1]],
[[ 0, -1, 1],[ -1, 1, -1]],
[[ -1, 0, -1],[ -1, -1, 1]],
[[ -1, 0, -1],[ -1, 1, -1]],
[[ 1, 1, 0],[ -1, -1, 1]],
[[ 1, 1, 0],[ -1, 1, -1]],
[[ -1, 1, 0],[ -1, -1, 1]],
[[ -1, 1, 0],[ -1, 1, -1]],
[[ 0, -1, -1],[ -1, -1, 1]],
[[ 0, -1, -1],[ -1, 1, -1]],
[[ 1, 0, 1],[ -1, -1, 1]],
[[ 1, 0, 1],[ -1, 1, -1]]],dtype='float')}
# Greninger--Troiano orientation relationship for fcc <-> bcc transformation
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
_GT = {'mapping':{'fcc':0,'bcc':1},
'planes': np.array([
[[ 1, 1, 1],[ 1, 0, 1]],
[[ 1, 1, 1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ -1, -1, 1],[ -1, 0, 1]],
[[ -1, -1, 1],[ -1, -1, 0]],
[[ -1, -1, 1],[ 0, -1, 1]],
[[ -1, 1, 1],[ -1, 0, 1]],
[[ -1, 1, 1],[ -1, 1, 0]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 1, 0, 1]],
[[ 1, -1, 1],[ 1, -1, 0]],
[[ 1, -1, 1],[ 0, -1, 1]],
[[ 1, 1, 1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 1, 0, 1]],
[[ -1, -1, 1],[ -1, -1, 0]],
[[ -1, -1, 1],[ 0, -1, 1]],
[[ -1, -1, 1],[ -1, 0, 1]],
[[ -1, 1, 1],[ -1, 1, 0]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ -1, 0, 1]],
[[ 1, -1, 1],[ 1, -1, 0]],
[[ 1, -1, 1],[ 0, -1, 1]],
[[ 1, -1, 1],[ 1, 0, 1]]],dtype='float'),
'directions': np.array([
[[ -5,-12, 17],[-17, -7, 17]],
[[ 17, -5,-12],[ 17,-17, -7]],
[[-12, 17, -5],[ -7, 17,-17]],
[[ 5, 12, 17],[ 17, 7, 17]],
[[-17, 5,-12],[-17, 17, -7]],
[[ 12,-17, -5],[ 7,-17,-17]],
[[ -5, 12,-17],[-17, 7,-17]],
[[ 17, 5, 12],[ 17, 17, 7]],
[[-12,-17, 5],[ -7,-17, 17]],
[[ 5,-12,-17],[ 17, -7,-17]],
[[-17, -5, 12],[-17,-17, 7]],
[[ 12, 17, 5],[ 7, 17, 17]],
[[ -5, 17,-12],[-17, 17, -7]],
[[-12, -5, 17],[ -7,-17, 17]],
[[ 17,-12, -5],[ 17, -7,-17]],
[[ 5,-17,-12],[ 17,-17, -7]],
[[ 12, 5, 17],[ 7, 17, 17]],
[[-17, 12, -5],[-17, 7,-17]],
[[ -5,-17, 12],[-17,-17, 7]],
[[-12, 5,-17],[ -7, 17,-17]],
[[ 17, 12, 5],[ 17, 7, 17]],
[[ 5, 17, 12],[ 17, 17, 7]],
[[ 12, -5,-17],[ 7,-17,-17]],
[[-17,-12, 5],[-17,-7, 17]]],dtype='float')}
# Greninger--Troiano' orientation relationship for fcc <-> bcc transformation
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
_GTprime = {'mapping':{'fcc':0,'bcc':1},
'planes': np.array([
[[ 7, 17, 17],[ 12, 5, 17]],
[[ 17, 7, 17],[ 17, 12, 5]],
[[ 17, 17, 7],[ 5, 17, 12]],
[[ -7,-17, 17],[-12, -5, 17]],
[[-17, -7, 17],[-17,-12, 5]],
[[-17,-17, 7],[ -5,-17, 12]],
[[ 7,-17,-17],[ 12, -5,-17]],
[[ 17, -7,-17],[ 17,-12, -5]],
[[ 17,-17, -7],[ 5,-17,-12]],
[[ -7, 17,-17],[-12, 5,-17]],
[[-17, 7,-17],[-17, 12, -5]],
[[-17, 17, -7],[ -5, 17,-12]],
[[ 7, 17, 17],[ 12, 17, 5]],
[[ 17, 7, 17],[ 5, 12, 17]],
[[ 17, 17, 7],[ 17, 5, 12]],
[[ -7,-17, 17],[-12,-17, 5]],
[[-17, -7, 17],[ -5,-12, 17]],
[[-17,-17, 7],[-17, -5, 12]],
[[ 7,-17,-17],[ 12,-17, -5]],
[[ 17, -7,-17],[ 5, -12,-17]],
[[ 17,-17, -7],[ 17, -5,-12]],
[[ -7, 17,-17],[-12, 17, -5]],
[[-17, 7,-17],[ -5, 12,-17]],
[[-17, 17, -7],[-17, 5,-12]]],dtype='float'),
'directions': np.array([
[[ 0, 1, -1],[ 1, 1, -1]],
[[ -1, 0, 1],[ -1, 1, 1]],
[[ 1, -1, 0],[ 1, -1, 1]],
[[ 0, -1, -1],[ -1, -1, -1]],
[[ 1, 0, 1],[ 1, -1, 1]],
[[ 1, -1, 0],[ 1, -1, -1]],
[[ 0, 1, -1],[ -1, 1, -1]],
[[ 1, 0, 1],[ 1, 1, 1]],
[[ -1, -1, 0],[ -1, -1, 1]],
[[ 0, -1, -1],[ 1, -1, -1]],
[[ -1, 0, 1],[ -1, -1, 1]],
[[ -1, -1, 0],[ -1, -1, -1]],
[[ 0, -1, 1],[ 1, -1, 1]],
[[ 1, 0, -1],[ 1, 1, -1]],
[[ -1, 1, 0],[ -1, 1, 1]],
[[ 0, 1, 1],[ -1, 1, 1]],
[[ -1, 0, -1],[ -1, -1, -1]],
[[ -1, 1, 0],[ -1, 1, -1]],
[[ 0, -1, 1],[ -1, -1, 1]],
[[ -1, 0, -1],[ -1, 1, -1]],
[[ 1, 1, 0],[ 1, 1, 1]],
[[ 0, 1, 1],[ 1, 1, 1]],
[[ 1, 0, -1],[ 1, -1, -1]],
[[ 1, 1, 0],[ 1, 1, -1]]],dtype='float')}
# Nishiyama--Wassermann orientation relationship for fcc <-> bcc transformation
# from H. Kitahara et al., Materials Characterization 54:378-386, 2005
_NW = {'mapping':{'fcc':0,'bcc':1},
'planes': np.array([
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ 1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ 1, -1, 1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]]],dtype='float'),
'directions': np.array([
[[ 2, -1, -1],[ 0, -1, 1]],
[[ -1, 2, -1],[ 0, -1, 1]],
[[ -1, -1, 2],[ 0, -1, 1]],
[[ -2, -1, -1],[ 0, -1, 1]],
[[ 1, 2, -1],[ 0, -1, 1]],
[[ 1, -1, 2],[ 0, -1, 1]],
[[ 2, 1, -1],[ 0, -1, 1]],
[[ -1, -2, -1],[ 0, -1, 1]],
[[ -1, 1, 2],[ 0, -1, 1]],
[[ 2, -1, 1],[ 0, -1, 1]], #It is wrong in the paper, but matrix is correct
[[ -1, 2, 1],[ 0, -1, 1]],
[[ -1, -1, -2],[ 0, -1, 1]]],dtype='float')}
# Pitsch orientation relationship for fcc <-> bcc transformation
# from Y. He et al., Acta Materialia 53:1179-1190, 2005
_Pitsch = {'mapping':{'fcc':0,'bcc':1},
'planes': np.array([
[[ 0, 1, 0],[ -1, 0, 1]],
[[ 0, 0, 1],[ 1, -1, 0]],
[[ 1, 0, 0],[ 0, 1, -1]],
[[ 1, 0, 0],[ 0, -1, -1]],
[[ 0, 1, 0],[ -1, 0, -1]],
[[ 0, 0, 1],[ -1, -1, 0]],
[[ 0, 1, 0],[ -1, 0, -1]],
[[ 0, 0, 1],[ -1, -1, 0]],
[[ 1, 0, 0],[ 0, -1, -1]],
[[ 1, 0, 0],[ 0, -1, 1]],
[[ 0, 1, 0],[ 1, 0, -1]],
[[ 0, 0, 1],[ -1, 1, 0]]],dtype='float'),
'directions': np.array([
[[ 1, 0, 1],[ 1, -1, 1]],
[[ 1, 1, 0],[ 1, 1, -1]],
[[ 0, 1, 1],[ -1, 1, 1]],
[[ 0, 1, -1],[ -1, 1, -1]],
[[ -1, 0, 1],[ -1, -1, 1]],
[[ 1, -1, 0],[ 1, -1, -1]],
[[ 1, 0, -1],[ 1, -1, -1]],
[[ -1, 1, 0],[ -1, 1, -1]],
[[ 0, -1, 1],[ -1, -1, 1]],
[[ 0, 1, 1],[ -1, 1, 1]],
[[ 1, 0, 1],[ 1, -1, 1]],
[[ 1, 1, 0],[ 1, 1, -1]]],dtype='float')}
# Bain orientation relationship for fcc <-> bcc transformation
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
_Bain = {'mapping':{'fcc':0,'bcc':1},
'planes': np.array([
[[ 1, 0, 0],[ 1, 0, 0]],
[[ 0, 1, 0],[ 0, 1, 0]],
[[ 0, 0, 1],[ 0, 0, 1]]],dtype='float'),
'directions': np.array([
[[ 0, 1, 0],[ 0, 1, 1]],
[[ 0, 0, 1],[ 1, 0, 1]],
[[ 1, 0, 0],[ 1, 1, 0]]],dtype='float')}
def relation_operations(self,model):
"""
Crystallographic orientation relationships for phase transformations.
References
----------
S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
https://doi.org/10.1016/j.jallcom.2012.02.004
K. Kitahara et al., Acta Materialia 54(5):1279-1288, 2006
https://doi.org/10.1016/j.actamat.2005.11.001
Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
https://doi.org/10.1107/S0021889805038276
H. Kitahara et al., Materials Characterization 54(4-5):378-386, 2005
https://doi.org/10.1016/j.matchar.2004.12.015
Y. He et al., Acta Materialia 53(4):1179-1190, 2005
https://doi.org/10.1016/j.actamat.2004.11.021
"""
models={'KS':self._KS, 'GT':self._GT, 'GT_prime':self._GTprime,
'NW':self._NW, 'Pitsch': self._Pitsch, 'Bain':self._Bain}
try:
relationship = models[model]
except KeyError :
raise KeyError(f'Orientation relationship "{model}" is unknown')
if self.lattice not in relationship['mapping']:
raise ValueError(f'Relationship "{model}" not supported for lattice "{self.lattice}"')
r = {'lattice':Lattice((set(relationship['mapping'])-{self.lattice}).pop()), # target lattice
'rotations':[] }
myPlane_id = relationship['mapping'][self.lattice]
otherPlane_id = (myPlane_id+1)%2
myDir_id = myPlane_id +2
otherDir_id = otherPlane_id +2
for miller in np.hstack((relationship['planes'],relationship['directions'])):
myPlane = miller[myPlane_id]/ np.linalg.norm(miller[myPlane_id])
myDir = miller[myDir_id]/ np.linalg.norm(miller[myDir_id])
myMatrix = np.array([myDir,np.cross(myPlane,myDir),myPlane])
otherPlane = miller[otherPlane_id]/ np.linalg.norm(miller[otherPlane_id])
otherDir = miller[otherDir_id]/ np.linalg.norm(miller[otherDir_id])
otherMatrix = np.array([otherDir,np.cross(otherPlane,otherDir),otherPlane])
r['rotations'].append(np.dot(otherMatrix.T,myMatrix))
r['rotations'] = np.array(r['rotations'])
return r

1302
python/damask/_orientation.py
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File diff suppressed because it is too large Load Diff

141
python/damask/_result.py
View File

@ -15,12 +15,12 @@ from numpy.lib import recfunctions as rfn
import damask import damask
from . import VTK from . import VTK
from . import Table from . import Table
from . import Rotation
from . import Orientation from . import Orientation
from . import grid_filters from . import grid_filters
from . import mechanics from . import mechanics
from . import util from . import util
h5py3 = h5py.__version__[0] == '3'
class Result: class Result:
""" """
@ -93,7 +93,7 @@ class Result:
def __repr__(self): def __repr__(self):
"""Show selected data.""" """Show summary of file content."""
all_selected_increments = self.selection['increments'] all_selected_increments = self.selection['increments']
self.pick('increments',all_selected_increments[0:1]) self.pick('increments',all_selected_increments[0:1])
@ -280,7 +280,8 @@ class Result:
for path_old in self.get_dataset_location(name_old): for path_old in self.get_dataset_location(name_old):
path_new = os.path.join(os.path.dirname(path_old),name_new) path_new = os.path.join(os.path.dirname(path_old),name_new)
f[path_new] = f[path_old] f[path_new] = f[path_old]
f[path_new].attrs['Renamed'] = 'Original name: {}'.encode() f[path_new].attrs['Renamed'] = f'Original name: {name_old}' if h5py3 else \
f'Original name: {name_old}'.encode()
del f[path_old] del f[path_old]
else: else:
raise PermissionError('Rename operation not permitted') raise PermissionError('Rename operation not permitted')
@ -422,8 +423,13 @@ class Result:
for d in f[group].keys(): for d in f[group].keys():
try: try:
dataset = f['/'.join([group,d])] dataset = f['/'.join([group,d])]
unit = f" / {dataset.attrs['Unit'].decode()}" if 'Unit' in dataset.attrs else '' if 'Unit' in dataset.attrs:
description = dataset.attrs['Description'].decode() unit = f" / {dataset.attrs['Unit']}" if h5py3 else \
f" / {dataset.attrs['Unit'].decode()}"
else:
unit = ''
description = dataset.attrs['Description'] if h5py3 else \
dataset.attrs['Description'].decode()
message += f' {d}{unit}: {description}\n' message += f' {d}{unit}: {description}\n'
except KeyError: except KeyError:
pass pass
@ -463,7 +469,8 @@ class Result:
def get_crystal_structure(self): # ToDo: extension to multi constituents/phase def get_crystal_structure(self): # ToDo: extension to multi constituents/phase
"""Info about the crystal structure.""" """Info about the crystal structure."""
with h5py.File(self.fname,'r') as f: with h5py.File(self.fname,'r') as f:
return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string return f[self.get_dataset_location('O')[0]].attrs['Lattice'] if h5py3 else \
f[self.get_dataset_location('O')[0]].attrs['Lattice'].decode()
def enable_user_function(self,func): def enable_user_function(self,func):
@ -735,11 +742,13 @@ class Result:
def _add_IPF_color(q,l): def _add_IPF_color(q,l):
m = util.scale_to_coprime(np.array(l)) m = util.scale_to_coprime(np.array(l))
o = Orientation(Rotation(rfn.structured_to_unstructured(q['data'])), o = Orientation(rotation = (rfn.structured_to_unstructured(q['data'])),
lattice = q['meta']['Lattice']) lattice = {'fcc':'cF',
'bcc':'cI',
'hex':'hP'}[q['meta']['Lattice']])
return { return {
'data': np.uint8(o.IPF_color(l)*255), 'data': np.uint8(o.IPF_color(o.to_SST(l))*255),
'label': 'IPFcolor_[{} {} {}]'.format(*m), 'label': 'IPFcolor_[{} {} {}]'.format(*m),
'meta' : { 'meta' : {
'Unit': '8-bit RGB', 'Unit': '8-bit RGB',
@ -788,20 +797,26 @@ class Result:
@staticmethod @staticmethod
def _add_Mises(T_sym): def _add_Mises(T_sym,kind):
t = 'strain' if T_sym['meta']['Unit'] == '1' else \ k = kind
'stress' if k is None:
if T_sym['meta']['Unit'] == '1':
k = 'strain'
elif T_sym['meta']['Unit'] == 'Pa':
k = 'stress'
if k not in ['stress', 'strain']:
raise ValueError('invalid von Mises kind {kind}')
return { return {
'data': (mechanics.Mises_strain if t=='strain' else mechanics.Mises_stress)(T_sym['data']), 'data': (mechanics.Mises_strain if k=='strain' else mechanics.Mises_stress)(T_sym['data']),
'label': f"{T_sym['label']}_vM", 'label': f"{T_sym['label']}_vM",
'meta': { 'meta': {
'Unit': T_sym['meta']['Unit'], 'Unit': T_sym['meta']['Unit'],
'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})", 'Description': f"Mises equivalent {k} of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': 'add_Mises' 'Creator': 'add_Mises'
} }
} }
def add_Mises(self,T_sym): def add_Mises(self,T_sym,kind=None):
""" """
Add the equivalent Mises stress or strain of a symmetric tensor. Add the equivalent Mises stress or strain of a symmetric tensor.
@ -809,9 +824,12 @@ class Result:
---------- ----------
T_sym : str T_sym : str
Label of symmetric tensorial stress or strain dataset. Label of symmetric tensorial stress or strain dataset.
kind : {'stress', 'strain', None}, optional
Kind of the von Mises equivalent. Defaults to None, in which case
it is selected based on the unit of the dataset ('1' -> strain, 'Pa' -> stress').
""" """
self._add_generic_pointwise(self._add_Mises,{'T_sym':T_sym}) self._add_generic_pointwise(self._add_Mises,{'T_sym':T_sym},{'kind':kind})
@staticmethod @staticmethod
@ -880,42 +898,47 @@ class Result:
self._add_generic_pointwise(self._add_PK2,{'P':P,'F':F}) self._add_generic_pointwise(self._add_PK2,{'P':P,'F':F})
@staticmethod # The add_pole functionality needs discussion.
def _add_pole(q,p,polar): # The new Crystal object can perform such a calculation but the outcome depends on the lattice parameters
pole = np.array(p) # as well as on whether a direction or plane is concerned (see the DAMASK_examples/pole_figure notebook).
unit_pole = pole/np.linalg.norm(pole) # Below code appears to be too simplistic.
m = util.scale_to_coprime(pole)
rot = Rotation(q['data'].view(np.double).reshape(-1,4))
rotatedPole = rot @ np.broadcast_to(unit_pole,rot.shape+(3,)) # rotate pole according to crystal orientation # @staticmethod
xy = rotatedPole[:,0:2]/(1.+abs(unit_pole[2])) # stereographic projection # def _add_pole(q,p,polar):
coords = xy if not polar else \ # pole = np.array(p)
np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])]) # unit_pole = pole/np.linalg.norm(pole)
return { # m = util.scale_to_coprime(pole)
'data': coords, # rot = Rotation(q['data'].view(np.double).reshape(-1,4))
'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m), #
'meta' : { # rotatedPole = rot @ np.broadcast_to(unit_pole,rot.shape+(3,)) # rotate pole according to crystal orientation
'Unit': '1', # xy = rotatedPole[:,0:2]/(1.+abs(unit_pole[2])) # stereographic projection
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\ # coords = xy if not polar else \
.format('Polar' if polar else 'Cartesian'), # np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])])
'Creator': 'add_pole' # return {
} # 'data': coords,
} # 'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
def add_pole(self,q,p,polar=False): # 'meta' : {
""" # 'Unit': '1',
Add coordinates of stereographic projection of given pole in crystal frame. # 'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
# .format('Polar' if polar else 'Cartesian'),
Parameters # 'Creator': 'add_pole'
---------- # }
q : str # }
Label of the dataset containing the crystallographic orientation as quaternions. # def add_pole(self,q,p,polar=False):
p : numpy.array of shape (3) # """
Crystallographic direction or plane. # Add coordinates of stereographic projection of given pole in crystal frame.
polar : bool, optional #
Give pole in polar coordinates. Defaults to False. # Parameters
# ----------
""" # q : str
self._add_generic_pointwise(self._add_pole,{'q':q},{'p':p,'polar':polar}) # Label of the dataset containing the crystallographic orientation as quaternions.
# p : numpy.array of shape (3)
# Crystallographic direction or plane.
# polar : bool, optional
# Give pole in polar coordinates. Defaults to False.
#
# """
# self._add_generic_pointwise(self._add_pole,{'q':q},{'p':p,'polar':polar})
@staticmethod @staticmethod
@ -1035,7 +1058,7 @@ class Result:
loc = f[group+'/'+label] loc = f[group+'/'+label]
datasets_in[arg]={'data' :loc[()], datasets_in[arg]={'data' :loc[()],
'label':label, 'label':label,
'meta': {k:v.decode() for k,v in loc.attrs.items()}} 'meta': {k:(v if h5py3 else v.decode()) for k,v in loc.attrs.items()}}
lock.release() lock.release()
r = func(**datasets_in,**args) r = func(**datasets_in,**args)
return [group,r] return [group,r]
@ -1080,17 +1103,21 @@ class Result:
if self._allow_modification and result[0]+'/'+result[1]['label'] in f: if self._allow_modification and result[0]+'/'+result[1]['label'] in f:
dataset = f[result[0]+'/'+result[1]['label']] dataset = f[result[0]+'/'+result[1]['label']]
dataset[...] = result[1]['data'] dataset[...] = result[1]['data']
dataset.attrs['Overwritten'] = 'Yes'.encode() dataset.attrs['Overwritten'] = 'Yes' if h5py3 else \
'Yes'.encode()
else: else:
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data']) dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
now = datetime.datetime.now().astimezone() now = datetime.datetime.now().astimezone()
dataset.attrs['Created'] = now.strftime('%Y-%m-%d %H:%M:%S%z').encode() dataset.attrs['Created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
now.strftime('%Y-%m-%d %H:%M:%S%z').encode()
for l,v in result[1]['meta'].items(): for l,v in result[1]['meta'].items():
dataset.attrs[l]=v.encode() dataset.attrs[l]=v if h5py3 else v.encode()
creator = f"damask.Result.{dataset.attrs['Creator'].decode()} v{damask.version}" creator = dataset.attrs['Creator'] if h5py3 else \
dataset.attrs['Creator'] = creator.encode() dataset.attrs['Creator'].decode()
dataset.attrs['Creator'] = f"damask.Result.{creator} v{damask.version}" if h5py3 else \
f"damask.Result.{creator} v{damask.version}".encode()
except (OSError,RuntimeError) as err: except (OSError,RuntimeError) as err:
print(f'Could not add dataset: {err}.') print(f'Could not add dataset: {err}.')

414
python/damask/_rotation.py
View File

@ -13,18 +13,18 @@ _R1 = (3.*np.pi/4.)**(1./3.)
class Rotation: class Rotation:
u""" u"""
Orientation stored with functionality for conversion to different representations. Rotation with functionality for conversion between different representations.
The following conventions apply: The following conventions apply:
- coordinate frames are right-handed. - Coordinate frames are right-handed.
- a rotation angle ω is taken to be positive for a counterclockwise rotation - A rotation angle ω is taken to be positive for a counterclockwise rotation
when viewing from the end point of the rotation axis towards the origin. when viewing from the end point of the rotation axis towards the origin.
- rotations will be interpreted in the passive sense. - Rotations will be interpreted in the passive sense.
- Euler angle triplets are implemented using the Bunge convention, - Euler angle triplets are implemented using the Bunge convention,
with the angular ranges as [0,2π], [0,π], [0,2π]. with angular ranges of [0,2π], [0,π], [0,2π].
- the rotation angle ω is limited to the interval [0,π]. - The rotation angle ω is limited to the interval [0,π].
- the real part of a quaternion is positive, Re(q) > 0 - The real part of a quaternion is positive, Re(q) > 0
- P = -1 (as default). - P = -1 (as default).
Examples Examples
@ -33,7 +33,7 @@ class Rotation:
coordinates "b" expressed in system "B": coordinates "b" expressed in system "B":
- b = Q @ a - b = Q @ a
- b = np.dot(Q.asMatrix(),a) - b = np.dot(Q.as_matrix(),a)
References References
---------- ----------
@ -44,20 +44,83 @@ class Rotation:
__slots__ = ['quaternion'] __slots__ = ['quaternion']
def __init__(self,quaternion = np.array([1.0,0.0,0.0,0.0])): def __init__(self,rotation = np.array([1.0,0.0,0.0,0.0])):
""" """
Initializes to identity unless specified. Initialize rotation object.
Parameters Parameters
---------- ----------
quaternion : numpy.ndarray, optional rotation : list, numpy.ndarray, Rotation, optional
Unit quaternion in positive real hemisphere. Unit quaternion in positive real hemisphere.
Use .from_quaternion to perform a sanity check. Use .from_quaternion to perform a sanity check.
Defaults to no rotation.
""" """
if quaternion.shape[-1] != 4: if isinstance(rotation,Rotation):
raise ValueError('Not a quaternion') self.quaternion = rotation.quaternion.copy()
self.quaternion = quaternion.copy() elif np.array(rotation).shape[-1] == 4:
self.quaternion = np.array(rotation)
else:
raise ValueError('"rotation" is neither a Rotation nor a quaternion')
def __repr__(self):
"""Represent rotation as unit quaternion, rotation matrix, and Bunge-Euler angles."""
return 'Quaternions:\n'+str(self.quaternion) \
if self.quaternion.shape != (4,) else \
'\n'.join([
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
])
# ToDo: Check difference __copy__ vs __deepcopy__
def __copy__(self,**kwargs):
"""Copy."""
return self.__class__(rotation=kwargs['rotation'] if 'rotation' in kwargs else self.quaternion)
copy = __copy__
def __getitem__(self,item):
"""Return slice according to item."""
return self.copy() \
if self.shape == () else \
self.copy(rotation=self.quaternion[item+(slice(None),)] if isinstance(item,tuple) else self.quaternion[item])
def __eq__(self,other):
"""
Equal to other.
Equality is determined taking limited floating point precision into
account. See numpy.allclose for details.
Parameters
----------
other : Rotation
Rotation to check for equality.
"""
return np.prod(self.shape,dtype=int) == np.prod(other.shape,dtype=int) \
and np.allclose(self.quaternion,other.quaternion)
def __neq__(self,other):
"""
Not Equal to other.
Equality is determined taking limited floating point precision into
account. See numpy.allclose for details.
Parameters
----------
other : Rotation
Rotation to check for inequality.
"""
return not self.__eq__(other)
@property @property
@ -65,39 +128,36 @@ class Rotation:
return self.quaternion.shape[:-1] return self.quaternion.shape[:-1]
# ToDo: Check difference __copy__ vs __deepcopy__
def __copy__(self):
"""Copy."""
return self.__class__(self.quaternion)
copy = __copy__
def __repr__(self):
"""Orientation displayed as unit quaternion, rotation matrix, and Bunge-Euler angles."""
if self.quaternion.shape != (4,):
return 'Quaternions:\n'+str(self.quaternion) # ToDo: could be nicer ...
return '\n'.join([
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
])
def __getitem__(self,item):
"""Iterate over leading/leftmost dimension of Rotation array."""
if self.shape == (): return self.copy()
if isinstance(item,tuple) and len(item) >= len(self):
raise IndexError('Too many indices')
return self.__class__(self.quaternion[item])
def __len__(self): def __len__(self):
"""Length of leading/leftmost dimension of Rotation array.""" """Length of leading/leftmost dimension of Rotation array."""
return 0 if self.shape == () else self.shape[0] return 0 if self.shape == () else self.shape[0]
def __matmul__(self, other): def __invert__(self):
"""Inverse rotation (backward rotation)."""
dup = self.copy()
dup.quaternion[...,1:] *= -1
return dup
def __pow__(self,pwr):
"""
Raise quaternion to power.
Equivalent to performing the rotation 'pwr' times.
Parameters
----------
pwr : float
Power to raise quaternion to.
"""
phi = np.arccos(self.quaternion[...,0:1])
p = self.quaternion[...,1:]/np.linalg.norm(self.quaternion[...,1:],axis=-1,keepdims=True)
return self.copy(rotation=Rotation(np.block([np.cos(pwr*phi),np.sin(pwr*phi)*p]))._standardize())
def __matmul__(self,other):
""" """
Rotation of vector, second or fourth order tensor, or rotation object. Rotation of vector, second or fourth order tensor, or rotation object.
@ -112,14 +172,14 @@ class Rotation:
Rotated vector, second or fourth order tensor, or rotation object. Rotated vector, second or fourth order tensor, or rotation object.
""" """
if isinstance(other, Rotation): if isinstance(other,Rotation):
q_m = self.quaternion[...,0:1] q_m = self.quaternion[...,0:1]
p_m = self.quaternion[...,1:] p_m = self.quaternion[...,1:]
q_o = other.quaternion[...,0:1] q_o = other.quaternion[...,0:1]
p_o = other.quaternion[...,1:] p_o = other.quaternion[...,1:]
q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,))) q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,)))
p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o) p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
return self.__class__(np.block([q,p]))._standardize() return Rotation(np.block([q,p]))._standardize()
elif isinstance(other,np.ndarray): elif isinstance(other,np.ndarray):
if self.shape + (3,) == other.shape: if self.shape + (3,) == other.shape:
@ -146,27 +206,89 @@ class Rotation:
def _standardize(self): def _standardize(self):
"""Standardize (ensure positive real hemisphere).""" """Standardize quaternion (ensure positive real hemisphere)."""
self.quaternion[self.quaternion[...,0] < 0.0] *= -1 self.quaternion[self.quaternion[...,0] < 0.0] *= -1
return self return self
def inverse(self):
"""In-place inverse rotation (backward rotation)."""
self.quaternion[...,1:] *= -1
return self
def __invert__(self): def append(self,other):
"""Inverse rotation (backward rotation).""" """Extend rotation array along first dimension with other array."""
return self.copy().inverse() return self.copy(rotation=np.vstack((self.quaternion,other.quaternion)))
def inversed(self):
"""Inverse rotation (backward rotation).""" def flatten(self,order = 'C'):
return ~ self """Flatten quaternion array."""
return self.copy(rotation=self.quaternion.reshape((-1,4),order=order))
def reshape(self,shape,order = 'C'):
"""Reshape quaternion array."""
if isinstance(shape,(int,np.integer)): shape = (shape,)
return self.copy(rotation=self.quaternion.reshape(tuple(shape)+(4,),order=order))
def broadcast_to(self,shape,mode = 'right'):
"""
Broadcast quaternion array to shape.
Parameters
----------
shape : tuple
Shape of broadcasted array.
mode : str, optional
Where to preferentially locate missing dimensions.
Either 'left' or 'right' (default).
"""
if isinstance(shape,(int,np.integer)): shape = (shape,)
return self.copy(rotation=np.broadcast_to(self.quaternion.reshape(util.shapeshifter(self.shape,shape,mode)+(4,)),
shape+(4,)))
def average(self,weights = None):
"""
Average rotations along last dimension.
Parameters
----------
weights : list of floats, optional
Relative weight of each rotation.
Returns
-------
average : Rotation
Weighted average of original Rotation field.
References
----------
Quaternion averaging
F. Landis Markley, Yang Cheng, John L. Crassidis, Yaakov Oshman
Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
10.2514/1.28949
"""
def _M(quat):
"""Intermediate representation supporting quaternion averaging."""
return np.einsum('...i,...j',quat,quat)
if not weights:
weights = np.ones(self.shape,dtype=float)
eig, vec = np.linalg.eig(np.sum(_M(self.quaternion) * weights[...,np.newaxis,np.newaxis],axis=-3) \
/np.sum( weights[...,np.newaxis,np.newaxis],axis=-3))
return Rotation.from_quaternion(np.real(
np.squeeze(
np.take_along_axis(vec,
eig.argmax(axis=-1)[...,np.newaxis,np.newaxis],
axis=-1),
axis=-1)),
accept_homomorph = True)
def misorientation(self,other): def misorientation(self,other):
""" """
Get Misorientation. Calculate misorientation from self to other Rotation.
Parameters Parameters
---------- ----------
@ -177,33 +299,6 @@ class Rotation:
return other@~self return other@~self
def broadcast_to(self,shape):
if isinstance(shape,(int,np.integer)): shape = (shape,)
if self.shape == ():
q = np.broadcast_to(self.quaternion,shape+(4,))
else:
q = np.block([np.broadcast_to(self.quaternion[...,0:1],shape).reshape(shape+(1,)),
np.broadcast_to(self.quaternion[...,1:2],shape).reshape(shape+(1,)),
np.broadcast_to(self.quaternion[...,2:3],shape).reshape(shape+(1,)),
np.broadcast_to(self.quaternion[...,3:4],shape).reshape(shape+(1,))])
return self.__class__(q)
def average(self,other): #ToDo: discuss calling for vectors
"""
Calculate the average rotation.
Parameters
----------
other : Rotation
Rotation from which the average is rotated.
"""
if self.quaternion.shape != (4,) or other.quaternion.shape != (4,):
raise NotImplementedError('Support for multiple rotations missing')
return Rotation.from_average([self,other])
################################################################################################ ################################################################################################
# convert to different orientation representations (numpy arrays) # convert to different orientation representations (numpy arrays)
@ -326,20 +421,6 @@ class Rotation:
""" """
return Rotation._qu2cu(self.quaternion) return Rotation._qu2cu(self.quaternion)
@property
def M(self): # ToDo not sure about the name: as_M or M? we do not have a from_M
"""
Intermediate representation supporting quaternion averaging.
References
----------
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
https://doi.org/10.2514/1.28949
"""
return np.einsum('...i,...j',self.quaternion,self.quaternion)
################################################################################################ ################################################################################################
# Static constructors. The input data needs to follow the conventions, options allow to # Static constructors. The input data needs to follow the conventions, options allow to
# relax the conventions. # relax the conventions.
@ -347,7 +428,7 @@ class Rotation:
def from_quaternion(q, def from_quaternion(q,
accept_homomorph = False, accept_homomorph = False,
P = -1, P = -1,
acceptHomomorph = None): # old name (for compatibility) **kwargs):
""" """
Initialize from quaternion. Initialize from quaternion.
@ -363,15 +444,13 @@ class Rotation:
Convention used. Defaults to -1. Convention used. Defaults to -1.
""" """
if acceptHomomorph is not None:
accept_homomorph = acceptHomomorph # for compatibility
qu = np.array(q,dtype=float) qu = np.array(q,dtype=float)
if qu.shape[:-2:-1] != (4,): if qu.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.') raise ValueError('Invalid shape.')
if abs(P) != 1: if abs(P) != 1:
raise ValueError('P ∉ {-1,1}') raise ValueError('P ∉ {-1,1}')
if P == 1: qu[...,1:4] *= -1 qu[...,1:4] *= -P
if accept_homomorph: if accept_homomorph:
qu[qu[...,0] < 0.0] *= -1 qu[qu[...,0] < 0.0] *= -1
else: else:
@ -384,7 +463,8 @@ class Rotation:
@staticmethod @staticmethod
def from_Eulers(phi, def from_Eulers(phi,
degrees = False): degrees = False,
**kwargs):
""" """
Initialize from Bunge-Euler angles. Initialize from Bunge-Euler angles.
@ -411,7 +491,8 @@ class Rotation:
def from_axis_angle(axis_angle, def from_axis_angle(axis_angle,
degrees = False, degrees = False,
normalize = False, normalize = False,
P = -1): P = -1,
**kwargs):
""" """
Initialize from Axis angle pair. Initialize from Axis angle pair.
@ -434,7 +515,7 @@ class Rotation:
if abs(P) != 1: if abs(P) != 1:
raise ValueError('P ∉ {-1,1}') raise ValueError('P ∉ {-1,1}')
if P == 1: ax[...,0:3] *= -1 ax[...,0:3] *= -P
if degrees: ax[..., 3] = np.radians(ax[...,3]) if degrees: ax[..., 3] = np.radians(ax[...,3])
if normalize: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1,keepdims=True) if normalize: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1,keepdims=True)
if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi): if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
@ -448,14 +529,15 @@ class Rotation:
@staticmethod @staticmethod
def from_basis(basis, def from_basis(basis,
orthonormal = True, orthonormal = True,
reciprocal = False): reciprocal = False,
**kwargs):
""" """
Initialize from lattice basis vectors. Initialize from lattice basis vectors.
Parameters Parameters
---------- ----------
basis : numpy.ndarray of shape (...,3,3) basis : numpy.ndarray of shape (...,3,3)
Three lattice basis vectors in three dimensions. Three three-dimensional lattice basis vectors.
orthonormal : boolean, optional orthonormal : boolean, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True. Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional reciprocal : boolean, optional
@ -463,7 +545,7 @@ class Rotation:
""" """
om = np.array(basis,dtype=float) om = np.array(basis,dtype=float)
if om.shape[:-3:-1] != (3,3): if om.shape[-2:] != (3,3):
raise ValueError('Invalid shape.') raise ValueError('Invalid shape.')
if reciprocal: if reciprocal:
@ -482,7 +564,7 @@ class Rotation:
return Rotation(Rotation._om2qu(om)) return Rotation(Rotation._om2qu(om))
@staticmethod @staticmethod
def from_matrix(R): def from_matrix(R,**kwargs):
""" """
Initialize from rotation matrix. Initialize from rotation matrix.
@ -494,10 +576,40 @@ class Rotation:
""" """
return Rotation.from_basis(R) return Rotation.from_basis(R)
@staticmethod
def from_parallel(a,b,
**kwargs):
"""
Initialize from pairs of two orthogonal lattice basis vectors.
Parameters
----------
a : numpy.ndarray of shape (...,2,3)
Two three-dimensional lattice vectors of first orthogonal basis.
b : numpy.ndarray of shape (...,2,3)
Corresponding three-dimensional lattice vectors of second basis.
"""
a_ = np.array(a)
b_ = np.array(b)
if a_.shape[-2:] != (2,3) or b_.shape[-2:] != (2,3) or a_.shape != b_.shape:
raise ValueError('Invalid shape.')
am = np.stack([ a_[...,0,:],
a_[...,1,:],
np.cross(a_[...,0,:],a_[...,1,:]) ],axis=-2)
bm = np.stack([ b_[...,0,:],
b_[...,1,:],
np.cross(b_[...,0,:],b_[...,1,:]) ],axis=-2)
return Rotation.from_basis(np.swapaxes(am/np.linalg.norm(am,axis=-1,keepdims=True),-1,-2))\
.misorientation(Rotation.from_basis(np.swapaxes(bm/np.linalg.norm(bm,axis=-1,keepdims=True),-1,-2)))
@staticmethod @staticmethod
def from_Rodrigues(rho, def from_Rodrigues(rho,
normalize = False, normalize = False,
P = -1): P = -1,
**kwargs):
""" """
Initialize from Rodrigues-Frank vector. Initialize from Rodrigues-Frank vector.
@ -518,7 +630,7 @@ class Rotation:
if abs(P) != 1: if abs(P) != 1:
raise ValueError('P ∉ {-1,1}') raise ValueError('P ∉ {-1,1}')
if P == 1: ro[...,0:3] *= -1 ro[...,0:3] *= -P
if normalize: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1,keepdims=True) if normalize: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1,keepdims=True)
if np.any(ro[...,3] < 0.0): if np.any(ro[...,3] < 0.0):
raise ValueError('Rodrigues vector rotation angle not positive.') raise ValueError('Rodrigues vector rotation angle not positive.')
@ -529,7 +641,8 @@ class Rotation:
@staticmethod @staticmethod
def from_homochoric(h, def from_homochoric(h,
P = -1): P = -1,
**kwargs):
""" """
Initialize from homochoric vector. Initialize from homochoric vector.
@ -547,7 +660,7 @@ class Rotation:
if abs(P) != 1: if abs(P) != 1:
raise ValueError('P ∉ {-1,1}') raise ValueError('P ∉ {-1,1}')
if P == 1: ho *= -1 ho *= -P
if np.any(np.linalg.norm(ho,axis=-1) >_R1+1e-9): if np.any(np.linalg.norm(ho,axis=-1) >_R1+1e-9):
raise ValueError('Homochoric coordinate outside of the sphere.') raise ValueError('Homochoric coordinate outside of the sphere.')
@ -556,7 +669,8 @@ class Rotation:
@staticmethod @staticmethod
def from_cubochoric(c, def from_cubochoric(c,
P = -1): P = -1,
**kwargs):
""" """
Initialize from cubochoric vector. Initialize from cubochoric vector.
@ -577,46 +691,15 @@ class Rotation:
if np.abs(np.max(cu)) > np.pi**(2./3.) * 0.5+1e-9: if np.abs(np.max(cu)) > np.pi**(2./3.) * 0.5+1e-9:
raise ValueError('Cubochoric coordinate outside of the cube.') raise ValueError('Cubochoric coordinate outside of the cube.')
ho = Rotation._cu2ho(cu) ho = -P * Rotation._cu2ho(cu)
if P == 1: ho *= -1
return Rotation(Rotation._ho2qu(ho)) return Rotation(Rotation._ho2qu(ho))
@staticmethod @staticmethod
def from_average(rotations,weights = None): def from_random(shape = None,
""" seed = None,
Average rotation. **kwargs):
References
----------
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
https://doi.org/10.2514/1.28949
Parameters
----------
rotations : list of Rotations
Rotations to average from
weights : list of floats, optional
Weights for each rotation used for averaging
"""
if not all(isinstance(item, Rotation) for item in rotations):
raise TypeError('Only instances of Rotation can be averaged.')
N = len(rotations)
if not weights:
weights = np.ones(N,dtype='i')
for i,(r,n) in enumerate(zip(rotations,weights)):
M = r.M * n if i == 0 \
else M + r.M * n # noqa add (multiples) of this rotation to average noqa
eig, vec = np.linalg.eig(M/N)
return Rotation.from_quaternion(np.real(vec.T[eig.argmax()]),accept_homomorph = True)
@staticmethod
def from_random(shape=None,seed=None):
""" """
Draw random rotation. Draw random rotation.
@ -633,12 +716,7 @@ class Rotation:
""" """
rng = np.random.default_rng(seed) rng = np.random.default_rng(seed)
if shape is None: r = rng.random(3 if shape is None else tuple(shape)+(3,) if hasattr(shape, '__iter__') else (shape,3))
r = rng.random(3)
elif hasattr(shape, '__iter__'):
r = rng.random(tuple(shape)+(3,))
else:
r = rng.random((shape,3))
A = np.sqrt(r[...,2]) A = np.sqrt(r[...,2])
B = np.sqrt(1.0-r[...,2]) B = np.sqrt(1.0-r[...,2])
@ -647,14 +725,17 @@ class Rotation:
np.cos(2.0*np.pi*r[...,1])*B, np.cos(2.0*np.pi*r[...,1])*B,
np.sin(2.0*np.pi*r[...,0])*A],axis=-1) np.sin(2.0*np.pi*r[...,0])*A],axis=-1)
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q)._standardize() return Rotation(q if shape is None else q.reshape(r.shape[:-1]+(4,)))._standardize()
# for compatibility
__mul__ = __matmul__
@staticmethod @staticmethod
def from_ODF(weights,Eulers,N=500,degrees=True,fractions=True,seed=None): def from_ODF(weights,
Eulers,
N = 500,
degrees = True,
fractions = True,
seed = None,
**kwargs):
""" """
Sample discrete values from a binned ODF. Sample discrete values from a binned ODF.
@ -707,7 +788,12 @@ class Rotation:
@staticmethod @staticmethod
def from_spherical_component(center,sigma,N=500,degrees=True,seed=None): def from_spherical_component(center,
sigma,
N = 500,
degrees = True,
seed = None,
**kwargs):
""" """
Calculate set of rotations with Gaussian distribution around center. Calculate set of rotations with Gaussian distribution around center.
@ -738,7 +824,13 @@ class Rotation:
@staticmethod @staticmethod
def from_fiber_component(alpha,beta,sigma=0.0,N=500,degrees=True,seed=None): def from_fiber_component(alpha,
beta,
sigma = 0.0,
N = 500,
degrees = True,
seed = None,
**kwargs):
""" """
Calculate set of rotations with Gaussian distribution around direction. Calculate set of rotations with Gaussian distribution around direction.

2
python/damask/_table.py
View File

@ -175,7 +175,7 @@ class Table:
@property @property
def labels(self): def labels(self):
return list(self.shapes.keys()) return list(self.shapes)
def get(self,label): def get(self,label):

6
python/damask/_test.py
View File

@ -316,12 +316,6 @@ class Test:
return self.compare_Array(refName,curName) return self.compare_Array(refName,curName)
def compare_ArrayCurCur(self,cur0,cur1):
cur0Name = self.fileInCurrent(cur0)
cur1Name = self.fileInCurrent(cur1)
return self.compare_Array(cur0Name,cur1Name)
def compare_Table(self,headings0,file0, def compare_Table(self,headings0,file0,
headings1,file1, headings1,file1,
normHeadings='',normType=None, normHeadings='',normType=None,

7
python/damask/_vtk.py
View File

@ -197,11 +197,10 @@ class VTK:
elif isinstance(self.vtk_data,vtk.vtkPolyData): elif isinstance(self.vtk_data,vtk.vtkPolyData):
writer = vtk.vtkXMLPolyDataWriter() writer = vtk.vtkXMLPolyDataWriter()
default_ext = writer.GetDefaultFileExtension() default_ext = '.'+writer.GetDefaultFileExtension()
ext = Path(fname).suffix ext = Path(fname).suffix
if ext and ext != '.'+default_ext: writer.SetFileName(str(fname)+(default_ext if default_ext != ext else ''))
raise ValueError(f'Given extension "{ext}" does not match default ".{default_ext}"')
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
if compress: if compress:
writer.SetCompressorTypeToZLib() writer.SetCompressorTypeToZLib()
else: else:

420
python/damask/lattice.py Normal file
View File

@ -0,0 +1,420 @@
import numpy as _np
kinematics = {
'cF': {
'slip' : _np.array([
[+0,+1,-1 , +1,+1,+1],
[-1,+0,+1 , +1,+1,+1],
[+1,-1,+0 , +1,+1,+1],
[+0,-1,-1 , -1,-1,+1],
[+1,+0,+1 , -1,-1,+1],
[-1,+1,+0 , -1,-1,+1],
[+0,-1,+1 , +1,-1,-1],
[-1,+0,-1 , +1,-1,-1],
[+1,+1,+0 , +1,-1,-1],
[+0,+1,+1 , -1,+1,-1],
[+1,+0,-1 , -1,+1,-1],
[-1,-1,+0 , -1,+1,-1],
[+1,+1,+0 , +1,-1,+0],
[+1,-1,+0 , +1,+1,+0],
[+1,+0,+1 , +1,+0,-1],
[+1,+0,-1 , +1,+0,+1],
[+0,+1,+1 , +0,+1,-1],
[+0,+1,-1 , +0,+1,+1],
],'d'),
'twin' : _np.array([
[-2, 1, 1, 1, 1, 1],
[ 1,-2, 1, 1, 1, 1],
[ 1, 1,-2, 1, 1, 1],
[ 2,-1, 1, -1,-1, 1],
[-1, 2, 1, -1,-1, 1],
[-1,-1,-2, -1,-1, 1],
[-2,-1,-1, 1,-1,-1],
[ 1, 2,-1, 1,-1,-1],
[ 1,-1, 2, 1,-1,-1],
[ 2, 1,-1, -1, 1,-1],
[-1,-2,-1, -1, 1,-1],
[-1, 1, 2, -1, 1,-1],
],dtype=float),
},
'cI': {
'slip' : _np.array([
[+1,-1,+1 , +0,+1,+1],
[-1,-1,+1 , +0,+1,+1],
[+1,+1,+1 , +0,-1,+1],
[-1,+1,+1 , +0,-1,+1],
[-1,+1,+1 , +1,+0,+1],
[-1,-1,+1 , +1,+0,+1],
[+1,+1,+1 , -1,+0,+1],
[+1,-1,+1 , -1,+0,+1],
[-1,+1,+1 , +1,+1,+0],
[-1,+1,-1 , +1,+1,+0],
[+1,+1,+1 , -1,+1,+0],
[+1,+1,-1 , -1,+1,+0],
[-1,+1,+1 , +2,+1,+1],
[+1,+1,+1 , -2,+1,+1],
[+1,+1,-1 , +2,-1,+1],
[+1,-1,+1 , +2,+1,-1],
[+1,-1,+1 , +1,+2,+1],
[+1,+1,-1 , -1,+2,+1],
[+1,+1,+1 , +1,-2,+1],
[-1,+1,+1 , +1,+2,-1],
[+1,+1,-1 , +1,+1,+2],
[+1,-1,+1 , -1,+1,+2],
[-1,+1,+1 , +1,-1,+2],
[+1,+1,+1 , +1,+1,-2],
],'d'),
'twin' : _np.array([
[-1, 1, 1, 2, 1, 1],
[ 1, 1, 1, -2, 1, 1],
[ 1, 1,-1, 2,-1, 1],
[ 1,-1, 1, 2, 1,-1],
[ 1,-1, 1, 1, 2, 1],
[ 1, 1,-1, -1, 2, 1],
[ 1, 1, 1, 1,-2, 1],
[-1, 1, 1, 1, 2,-1],
[ 1, 1,-1, 1, 1, 2],
[ 1,-1, 1, -1, 1, 2],
[-1, 1, 1, 1,-1, 2],
[ 1, 1, 1, 1, 1,-2],
],dtype=float),
},
'hP': {
'slip' : _np.array([
[+2,-1,-1,+0 , +0,+0,+0,+1],
[-1,+2,-1,+0 , +0,+0,+0,+1],
[-1,-1,+2,+0 , +0,+0,+0,+1],
[+2,-1,-1,+0 , +0,+1,-1,+0],
[-1,+2,-1,+0 , -1,+0,+1,+0],
[-1,-1,+2,+0 , +1,-1,+0,+0],
[-1,+1,+0,+0 , +1,+1,-2,+0],
[+0,-1,+1,+0 , -2,+1,+1,+0],
[+1,+0,-1,+0 , +1,-2,+1,+0],
[-1,+2,-1,+0 , +1,+0,-1,+1],
[-2,+1,+1,+0 , +0,+1,-1,+1],
[-1,-1,+2,+0 , -1,+1,+0,+1],
[+1,-2,+1,+0 , -1,+0,+1,+1],
[+2,-1,-1,+0 , +0,-1,+1,+1],
[+1,+1,-2,+0 , +1,-1,+0,+1],
[-2,+1,+1,+3 , +1,+0,-1,+1],
[-1,-1,+2,+3 , +1,+0,-1,+1],
[-1,-1,+2,+3 , +0,+1,-1,+1],
[+1,-2,+1,+3 , +0,+1,-1,+1],
[+1,-2,+1,+3 , -1,+1,+0,+1],
[+2,-1,-1,+3 , -1,+1,+0,+1],
[+2,-1,-1,+3 , -1,+0,+1,+1],
[+1,+1,-2,+3 , -1,+0,+1,+1],
[+1,+1,-2,+3 , +0,-1,+1,+1],
[-1,+2,-1,+3 , +0,-1,+1,+1],
[-1,+2,-1,+3 , +1,-1,+0,+1],
[-2,+1,+1,+3 , +1,-1,+0,+1],
[-1,-1,+2,+3 , +1,+1,-2,+2],
[+1,-2,+1,+3 , -1,+2,-1,+2],
[+2,-1,-1,+3 , -2,+1,+1,+2],
[+1,+1,-2,+3 , -1,-1,+2,+2],
[-1,+2,-1,+3 , +1,-2,+1,+2],
[-2,+1,+1,+3 , +2,-1,-1,+2],
],'d'),
'twin' : _np.array([
[-1, 0, 1, 1, 1, 0, -1, 2], # shear = (3-(c/a)^2)/(sqrt(3) c/a) <-10.1>{10.2}
[ 0, -1, 1, 1, 0, 1, -1, 2],
[ 1, -1, 0, 1, -1, 1, 0, 2],
[ 1, 0, -1, 1, -1, 0, 1, 2],
[ 0, 1, -1, 1, 0, -1, 1, 2],
[-1, 1, 0, 1, 1, -1, 0, 2],
[-1, -1, 2, 6, 1, 1, -2, 1], # shear = 1/(c/a) <11.6>{-1-1.1}
[ 1, -2, 1, 6, -1, 2, -1, 1],
[ 2, -1, -1, 6, -2, 1, 1, 1],
[ 1, 1, -2, 6, -1, -1, 2, 1],
[-1, 2, -1, 6, 1, -2, 1, 1],
[-2, 1, 1, 6, 2, -1, -1, 1],
[ 1, 0, -1, -2, 1, 0, -1, 1], # shear = (4(c/a)^2-9)/(4 sqrt(3) c/a) <10.-2>{10.1}
[ 0, 1, -1, -2, 0, 1, -1, 1],
[-1, 1, 0, -2, -1, 1, 0, 1],
[-1, 0, 1, -2, -1, 0, 1, 1],
[ 0, -1, 1, -2, 0, -1, 1, 1],
[ 1, -1, 0, -2, 1, -1, 0, 1],
[ 1, 1, -2, -3, 1, 1, -2, 2], # shear = 2((c/a)^2-2)/(3 c/a) <11.-3>{11.2}
[-1, 2, -1, -3, -1, 2, -1, 2],
[-2, 1, 1, -3, -2, 1, 1, 2],
[-1, -1, 2, -3, -1, -1, 2, 2],
[ 1, -2, 1, -3, 1, -2, 1, 2],
[ 2, -1, -1, -3, 2, -1, -1, 2],
],dtype=float),
},
}
# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
# from S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
# also see K. Kitahara et al., Acta Materialia 54:1279-1288, 2006
relations = {
'KS': {
'cF' : _np.array([
[[ -1, 0, 1],[ 1, 1, 1]],
[[ -1, 0, 1],[ 1, 1, 1]],
[[ 0, 1, -1],[ 1, 1, 1]],
[[ 0, 1, -1],[ 1, 1, 1]],
[[ 1, -1, 0],[ 1, 1, 1]],
[[ 1, -1, 0],[ 1, 1, 1]],
[[ 1, 0, -1],[ 1, -1, 1]],
[[ 1, 0, -1],[ 1, -1, 1]],
[[ -1, -1, 0],[ 1, -1, 1]],
[[ -1, -1, 0],[ 1, -1, 1]],
[[ 0, 1, 1],[ 1, -1, 1]],
[[ 0, 1, 1],[ 1, -1, 1]],
[[ 0, -1, 1],[ -1, 1, 1]],
[[ 0, -1, 1],[ -1, 1, 1]],
[[ -1, 0, -1],[ -1, 1, 1]],
[[ -1, 0, -1],[ -1, 1, 1]],
[[ 1, 1, 0],[ -1, 1, 1]],
[[ 1, 1, 0],[ -1, 1, 1]],
[[ -1, 1, 0],[ 1, 1, -1]],
[[ -1, 1, 0],[ 1, 1, -1]],
[[ 0, -1, -1],[ 1, 1, -1]],
[[ 0, -1, -1],[ 1, 1, -1]],
[[ 1, 0, 1],[ 1, 1, -1]],
[[ 1, 0, 1],[ 1, 1, -1]],
],dtype=float),
'cI' : _np.array([
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ -1, -1, 1],[ 0, 1, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
],dtype=float),
},
'GT': {
'cF' : _np.array([
[[ -5,-12, 17],[ 1, 1, 1]],
[[ 17, -5,-12],[ 1, 1, 1]],
[[-12, 17, -5],[ 1, 1, 1]],
[[ 5, 12, 17],[ -1, -1, 1]],
[[-17, 5,-12],[ -1, -1, 1]],
[[ 12,-17, -5],[ -1, -1, 1]],
[[ -5, 12,-17],[ -1, 1, 1]],
[[ 17, 5, 12],[ -1, 1, 1]],
[[-12,-17, 5],[ -1, 1, 1]],
[[ 5,-12,-17],[ 1, -1, 1]],
[[-17, -5, 12],[ 1, -1, 1]],
[[ 12, 17, 5],[ 1, -1, 1]],
[[ -5, 17,-12],[ 1, 1, 1]],
[[-12, -5, 17],[ 1, 1, 1]],
[[ 17,-12, -5],[ 1, 1, 1]],
[[ 5,-17,-12],[ -1, -1, 1]],
[[ 12, 5, 17],[ -1, -1, 1]],
[[-17, 12, -5],[ -1, -1, 1]],
[[ -5,-17, 12],[ -1, 1, 1]],
[[-12, 5,-17],[ -1, 1, 1]],
[[ 17, 12, 5],[ -1, 1, 1]],
[[ 5, 17, 12],[ 1, -1, 1]],
[[ 12, -5,-17],[ 1, -1, 1]],
[[-17,-12, 5],[ 1, -1, 1]],
],dtype=float),
'cI' : _np.array([
[[-17, -7, 17],[ 1, 0, 1]],
[[ 17,-17, -7],[ 1, 1, 0]],
[[ -7, 17,-17],[ 0, 1, 1]],
[[ 17, 7, 17],[ -1, 0, 1]],
[[-17, 17, -7],[ -1, -1, 0]],
[[ 7,-17,-17],[ 0, -1, 1]],
[[-17, 7,-17],[ -1, 0, 1]],
[[ 17, 17, 7],[ -1, 1, 0]],
[[ -7,-17, 17],[ 0, 1, 1]],
[[ 17, -7,-17],[ 1, 0, 1]],
[[-17,-17, 7],[ 1, -1, 0]],
[[ 7, 17, 17],[ 0, -1, 1]],
[[-17, 17, -7],[ 1, 1, 0]],
[[ -7,-17, 17],[ 0, 1, 1]],
[[ 17, -7,-17],[ 1, 0, 1]],
[[ 17,-17, -7],[ -1, -1, 0]],
[[ 7, 17, 17],[ 0, -1, 1]],
[[-17, 7,-17],[ -1, 0, 1]],
[[-17,-17, 7],[ -1, 1, 0]],
[[ -7, 17,-17],[ 0, 1, 1]],
[[ 17, 7, 17],[ -1, 0, 1]],
[[ 17, 17, 7],[ 1, -1, 0]],
[[ 7,-17,-17],[ 0, -1, 1]],
[[-17, -7, 17],[ 1, 0, 1]],
],dtype=float),
},
'GT_prime': {
'cF' : _np.array([
[[ 0, 1, -1],[ 7, 17, 17]],
[[ -1, 0, 1],[ 17, 7, 17]],
[[ 1, -1, 0],[ 17, 17, 7]],
[[ 0, -1, -1],[ -7,-17, 17]],
[[ 1, 0, 1],[-17, -7, 17]],
[[ 1, -1, 0],[-17,-17, 7]],
[[ 0, 1, -1],[ 7,-17,-17]],
[[ 1, 0, 1],[ 17, -7,-17]],
[[ -1, -1, 0],[ 17,-17, -7]],
[[ 0, -1, -1],[ -7, 17,-17]],
[[ -1, 0, 1],[-17, 7,-17]],
[[ -1, -1, 0],[-17, 17, -7]],
[[ 0, -1, 1],[ 7, 17, 17]],
[[ 1, 0, -1],[ 17, 7, 17]],
[[ -1, 1, 0],[ 17, 17, 7]],
[[ 0, 1, 1],[ -7,-17, 17]],
[[ -1, 0, -1],[-17, -7, 17]],
[[ -1, 1, 0],[-17,-17, 7]],
[[ 0, -1, 1],[ 7,-17,-17]],
[[ -1, 0, -1],[ 17, -7,-17]],
[[ 1, 1, 0],[ 17,-17, -7]],
[[ 0, 1, 1],[ -7, 17,-17]],
[[ 1, 0, -1],[-17, 7,-17]],
[[ 1, 1, 0],[-17, 17, -7]],
],dtype=float),
'cI' : _np.array([
[[ 1, 1, -1],[ 12, 5, 17]],
[[ -1, 1, 1],[ 17, 12, 5]],
[[ 1, -1, 1],[ 5, 17, 12]],
[[ -1, -1, -1],[-12, -5, 17]],
[[ 1, -1, 1],[-17,-12, 5]],
[[ 1, -1, -1],[ -5,-17, 12]],
[[ -1, 1, -1],[ 12, -5,-17]],
[[ 1, 1, 1],[ 17,-12, -5]],
[[ -1, -1, 1],[ 5,-17,-12]],
[[ 1, -1, -1],[-12, 5,-17]],
[[ -1, -1, 1],[-17, 12, -5]],
[[ -1, -1, -1],[ -5, 17,-12]],
[[ 1, -1, 1],[ 12, 17, 5]],
[[ 1, 1, -1],[ 5, 12, 17]],
[[ -1, 1, 1],[ 17, 5, 12]],
[[ -1, 1, 1],[-12,-17, 5]],
[[ -1, -1, -1],[ -5,-12, 17]],
[[ -1, 1, -1],[-17, -5, 12]],
[[ -1, -1, 1],[ 12,-17, -5]],
[[ -1, 1, -1],[ 5,-12,-17]],
[[ 1, 1, 1],[ 17, -5,-12]],
[[ 1, 1, 1],[-12, 17, -5]],
[[ 1, -1, -1],[ -5, 12,-17]],
[[ 1, 1, -1],[-17, 5,-12]],
],dtype=float),
},
'NW': {
'cF' : _np.array([
[[ 2, -1, -1],[ 1, 1, 1]],
[[ -1, 2, -1],[ 1, 1, 1]],
[[ -1, -1, 2],[ 1, 1, 1]],
[[ -2, -1, -1],[ -1, 1, 1]],
[[ 1, 2, -1],[ -1, 1, 1]],
[[ 1, -1, 2],[ -1, 1, 1]],
[[ 2, 1, -1],[ 1, -1, 1]],
[[ -1, -2, -1],[ 1, -1, 1]],
[[ -1, 1, 2],[ 1, -1, 1]],
[[ 2, -1, 1],[ -1, -1, 1]],
[[ -1, 2, 1],[ -1, -1, 1]],
[[ -1, -1, -2],[ -1, -1, 1]],
],dtype=float),
'cI' : _np.array([
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
[[ 0, -1, 1],[ 0, 1, 1]],
],dtype=float),
},
'Pitsch': {
'cF' : _np.array([
[[ 1, 0, 1],[ 0, 1, 0]],
[[ 1, 1, 0],[ 0, 0, 1]],
[[ 0, 1, 1],[ 1, 0, 0]],
[[ 0, 1, -1],[ 1, 0, 0]],
[[ -1, 0, 1],[ 0, 1, 0]],
[[ 1, -1, 0],[ 0, 0, 1]],
[[ 1, 0, -1],[ 0, 1, 0]],
[[ -1, 1, 0],[ 0, 0, 1]],
[[ 0, -1, 1],[ 1, 0, 0]],
[[ 0, 1, 1],[ 1, 0, 0]],
[[ 1, 0, 1],[ 0, 1, 0]],
[[ 1, 1, 0],[ 0, 0, 1]],
],dtype=float),
'cI' : _np.array([
[[ 1, -1, 1],[ -1, 0, 1]],
[[ 1, 1, -1],[ 1, -1, 0]],
[[ -1, 1, 1],[ 0, 1, -1]],
[[ -1, 1, -1],[ 0, -1, -1]],
[[ -1, -1, 1],[ -1, 0, -1]],
[[ 1, -1, -1],[ -1, -1, 0]],
[[ 1, -1, -1],[ -1, 0, -1]],
[[ -1, 1, -1],[ -1, -1, 0]],
[[ -1, -1, 1],[ 0, -1, -1]],
[[ -1, 1, 1],[ 0, -1, 1]],
[[ 1, -1, 1],[ 1, 0, -1]],
[[ 1, 1, -1],[ -1, 1, 0]],
],dtype=float),
},
'Bain': {
'cF' : _np.array([
[[ 0, 1, 0],[ 1, 0, 0]],
[[ 0, 0, 1],[ 0, 1, 0]],
[[ 1, 0, 0],[ 0, 0, 1]],
],dtype=float),
'cI' : _np.array([
[[ 0, 1, 1],[ 1, 0, 0]],
[[ 1, 0, 1],[ 0, 1, 0]],
[[ 1, 1, 0],[ 0, 0, 1]],
],dtype=float),
},
'Burgers' : {
'cI' : _np.array([
[[ -1, 1, 1],[ 1, 1, 0]],
[[ -1, 1, -1],[ 1, 1, 0]],
[[ 1, 1, 1],[ 1, -1, 0]],
[[ 1, 1, -1],[ 1, -1, 0]],
[[ 1, 1, -1],[ 1, 0, 1]],
[[ -1, 1, 1],[ 1, 0, 1]],
[[ 1, 1, 1],[ -1, 0, 1]],
[[ 1, -1, 1],[ -1, 0, 1]],
[[ -1, 1, -1],[ 0, 1, 1]],
[[ 1, 1, -1],[ 0, 1, 1]],
[[ -1, 1, 1],[ 0, -1, 1]],
[[ 1, 1, 1],[ 0, -1, 1]],
],dtype=float),
'hP' : _np.array([
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
[[ -1, 2, -1, 0],[ 0, 0, 0, 1]],
[[ -1, -1, 2, 0],[ 0, 0, 0, 1]],
],dtype=float),
},
}

99
python/damask/util.py
View File

@ -3,6 +3,7 @@ import datetime
import os import os
import subprocess import subprocess
import shlex import shlex
import re
import fractions import fractions
from functools import reduce from functools import reduce
from optparse import Option from optparse import Option
@ -20,10 +21,13 @@ __all__=[
'execute', 'execute',
'show_progress', 'show_progress',
'scale_to_coprime', 'scale_to_coprime',
'project_stereographic',
'hybrid_IA', 'hybrid_IA',
'return_message', 'return_message',
'extendableOption', 'extendableOption',
'execution_stamp' 'execution_stamp',
'shapeshifter',
'shapeblender',
] ]
#################################################################################################### ####################################################################################################
@ -182,6 +186,28 @@ def scale_to_coprime(v):
return m return m
def project_stereographic(vector,normalize=False):
"""
Apply stereographic projection to vector.
Parameters
----------
vector : numpy.ndarray of shape (...,3)
Vector coordinates to be projected.
normalize : bool
Ensure unit length for vector. Defaults to False.
Returns
-------
coordinates : numpy.ndarray of shape (...,2)
Projected coordinates.
"""
v_ = vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector
return np.block([v_[...,:2]/(1+np.abs(v_[...,2:3])),
np.zeros_like(v_[...,2:3])])
def execution_stamp(class_name,function_name=None): def execution_stamp(class_name,function_name=None):
"""Timestamp the execution of a (function within a) class.""" """Timestamp the execution of a (function within a) class."""
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z') now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
@ -203,6 +229,77 @@ def hybrid_IA(dist,N,seed=None):
return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(seed).permutation(N_inv_samples)[:N]] return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(seed).permutation(N_inv_samples)[:N]]
def shapeshifter(fro,to,mode='left',keep_ones=False):
"""
Return a tuple that reshapes 'fro' to become broadcastable to 'to'.
Parameters
----------
fro : tuple
Original shape of array.
to : tuple
Target shape of array after broadcasting.
len(to) cannot be less than len(fro).
mode : str, optional
Indicates whether new axes are preferably added to
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.
Defaults to False.
"""
beg = dict(left ='(^.*\\b)',
right='(^.*?\\b)')
sep = dict(left ='(.*\\b)',
right='(.*?\\b)')
end = dict(left ='(.*?$)',
right='(.*$)')
fro = (1,) if not len(fro) else fro
to = (1,) if not len(to) else to
try:
grp = 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:
raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
fill = ()
for g,d in zip(grp,fro+(None,)):
fill += (1,)*g.count(',')+(d,)
return fill[:-1]
def shapeblender(a,b):
"""
Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
Parameters
----------
a : tuple
Shape of first array.
b : tuple
Shape of second array.
Examples
--------
>>> shapeblender((4,4,3),(3,2,1))
(4,4,3,2,1)
>>> shapeblender((1,2),(1,2,3))
(1,2,3)
>>> shapeblender((1,),(2,2,1))
(1,2,2,1)
>>> shapeblender((3,2),(3,2))
(3,2)
"""
i = min(len(a),len(b))
while i > 0 and a[-i:] != b[:i]: i -= 1
return a + b[i:]
#################################################################################################### ####################################################################################################
# Classes # Classes
#################################################################################################### ####################################################################################################

16
python/tests/reference/ConfigMaterial/material.yaml
View File

@ -33,12 +33,12 @@ material:
phase: phase:
Aluminum: Aluminum:
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke} lattice: cF
generic: mech:
output: [F, P, Fe, Fp, Lp] output: [F, P, F_e, F_p, L_p]
lattice: fcc elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
Steel: Steel:
elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke} lattice: cI
generic: mech:
output: [F, P, Fe, Fp, Lp] output: [F, P, F_e, F_p, L_p]
lattice: bcc elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}

5
python/tests/reference/Orientation/cF_Bain.txt Normal file
View File

@ -0,0 +1,5 @@
1 header
1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
180.0 45.00000000000001 180.0 1 1
270.0 45.00000000000001 90.0 1 2
315.0 0.0 0.0 1 3

26
python/tests/reference/Orientation/cF_GT.txt Normal file
View File

@ -0,0 +1,26 @@
1 header
1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
146.75362934444064 9.976439066337804 256.395594327347 1 1
356.59977719102034 43.39784965440254 12.173896584899929 1 2
75.92521636876346 43.82007387041961 277.8843642946069 1 3
326.75362934444064 9.976439066337806 76.39559432734703 1 4
176.59977719102034 43.397849654402556 192.17389658489986 1 5
255.92521636876344 43.82007387041961 97.88436429460687 1 6
213.24637065555936 9.976439066337804 103.604405672653 1 7
3.400222808979685 43.39784965440255 347.8261034151001 1 8
284.0747836312365 43.82007387041961 82.11563570539313 1 9
33.24637065555936 9.976439066337804 283.60440567265294 1 10
183.40022280897963 43.397849654402556 167.8261034151001 1 11
104.07478363123654 43.82007387041961 262.1156357053931 1 12
273.4002228089796 43.397849654402556 77.82610341510008 1 13
123.24637065555939 9.976439066337806 193.60440567265297 1 14
194.07478363123653 43.82007387041961 172.11563570539317 1 15
93.40022280897969 43.39784965440255 257.8261034151001 1 16
303.24637065555936 9.976439066337804 13.604405672652977 1 17
14.074783631236542 43.82007387041961 352.1156357053931 1 18
86.59977719102032 43.39784965440254 282.17389658489986 1 19
236.75362934444058 9.976439066337804 166.39559432734703 1 20
165.92521636876344 43.82007387041961 187.88436429460683 1 21
266.59977719102034 43.39784965440254 102.17389658489992 1 22
56.75362934444064 9.976439066337804 346.395594327347 1 23
345.9252163687635 43.82007387041961 7.884364294606862 1 24

26
python/tests/reference/Orientation/cF_GT_prime.txt Normal file
View File

@ -0,0 +1,26 @@
1 header
1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
166.39559432734697 9.976439066337804 236.75362934444058 1 1
352.1156357053931 43.82007387041961 14.074783631236542 1 2
77.82610341510008 43.397849654402556 273.4002228089796 1 3
346.395594327347 9.976439066337804 56.75362934444064 1 4
172.11563570539317 43.82007387041961 194.07478363123653 1 5
257.8261034151001 43.39784965440255 93.40022280897969 1 6
193.604405672653 9.976439066337804 123.24637065555939 1 7
7.884364294606862 43.82007387041961 345.9252163687635 1 8
282.17389658489986 43.39784965440254 86.59977719102032 1 9
13.604405672652977 9.976439066337804 303.24637065555936 1 10
187.88436429460683 43.82007387041961 165.92521636876344 1 11
102.17389658489992 43.39784965440254 266.59977719102034 1 12
277.8843642946069 43.82007387041961 75.92521636876346 1 13
103.604405672653 9.976439066337804 213.24637065555936 1 14
192.17389658489986 43.397849654402556 176.59977719102034 1 15
97.88436429460687 43.82007387041961 255.92521636876344 1 16
283.60440567265294 9.976439066337804 33.24637065555936 1 17
12.173896584899929 43.39784965440254 356.59977719102034 1 18
82.11563570539313 43.82007387041961 284.0747836312365 1 19
256.395594327347 9.976439066337804 146.75362934444064 1 20
167.8261034151001 43.397849654402556 183.40022280897963 1 21
262.1156357053931 43.82007387041961 104.07478363123654 1 22
76.39559432734703 9.976439066337806 326.75362934444064 1 23
347.8261034151001 43.39784965440255 3.400222808979685 1 24

26
python/tests/reference/Orientation/cF_KS.txt Normal file
View File

@ -0,0 +1,26 @@
1 header
1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
114.20342833932975 10.52877936550932 204.20342833932972 1 1
94.3573968784815 80.40593177313954 311.22729452432543 1 2
175.6426031215185 80.40593177313954 48.77270547567447 1 3
155.79657166067025 10.52877936550932 155.79657166067025 1 4
99.62136089109411 85.70366403943004 318.04510841542015 1 5
170.37863910890587 85.70366403943002 41.954891584579855 1 6
85.64260312151852 80.40593177313954 48.77270547567448 1 7
65.79657166067024 10.52877936550932 155.79657166067025 1 8
9.621360891094124 85.70366403943004 318.04510841542015 1 9
80.37863910890587 85.70366403943004 41.95489158457987 1 10
24.203428339329758 10.52877936550932 204.20342833932975 1 11
4.357396878481486 80.40593177313954 311.2272945243255 1 12
204.20342833932972 10.52877936550932 204.20342833932972 1 13
184.35739687848147 80.40593177313954 311.2272945243255 1 14
265.64260312151845 80.40593177313953 48.77270547567449 1 15
245.79657166067025 10.528779365509317 155.79657166067025 1 16
189.62136089109413 85.70366403943004 318.04510841542015 1 17
260.3786391089059 85.70366403943002 41.954891584579855 1 18
170.37863910890587 94.29633596056996 138.04510841542015 1 19
99.62136089109411 94.29633596056998 221.95489158457983 1 20
155.79657166067025 169.4712206344907 24.203428339329754 1 21
175.64260312151848 99.59406822686046 131.22729452432552 1 22
94.35739687848151 99.59406822686046 228.77270547567446 1 23
114.20342833932975 169.4712206344907 335.7965716606702 1 24

14
python/tests/reference/Orientation/cF_NW.txt Normal file
View File

@ -0,0 +1,14 @@
1 header
1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
96.91733794010702 83.13253115922213 314.5844440567886 1 1
173.082662059893 83.13253115922211 45.41555594321143 1 2
135.0 9.735610317245317 180.0 1 3
263.082662059893 83.13253115922213 45.415555943211444 1 4
186.91733794010702 83.13253115922211 314.5844440567886 1 5
224.99999999999997 9.735610317245317 180.0 1 6
83.082662059893 83.13253115922213 45.415555943211444 1 7
6.917337940106983 83.13253115922211 314.5844440567886 1 8
45.0 9.73561031724532 180.0 1 9
13.638707279476469 45.81931182053557 80.40196970123216 1 10
256.36129272052347 45.81931182053556 279.59803029876775 1 11
315.0 99.73561031724536 0.0 1 12

14
python/tests/reference/Orientation/cF_Pitsch.txt Normal file
View File

@ -0,0 +1,14 @@
1 header
1_Eulers 2_Eulers 3_Eulers 1_pos 2_pos
135.41555594321144 83.13253115922213 173.082662059893 1 1
260.26438968275465 90.0 135.0 1 2
260.40196970123213 45.81931182053557 13.638707279476478 1 3
314.5844440567886 83.13253115922213 96.91733794010702 1 4
350.40196970123213 45.81931182053557 283.6387072794765 1 5
170.26438968275465 90.0 224.99999999999997 1 6
315.4155559432114 83.13253115922213 353.08266205989304 1 7
99.73561031724536 90.0 225.0 1 8
279.59803029876787 45.819311820535574 166.36129272052352 1 9
134.58444405678856 83.13253115922213 276.91733794010696 1 10
9.598030298767851 45.819311820535574 76.36129272052355 1 11
9.735610317245369 90.0 315.0 1 12

19
python/tests/reference/Orientation/cF_slip.txt Normal file
View File

@ -0,0 +1,19 @@
3x3:1_Schmid 3x3:2_Schmid 3x3:3_Schmid 3x3:4_Schmid 3x3:5_Schmid 3x3:6_Schmid 3x3:7_Schmid 3x3:8_Schmid 3x3:9_Schmid
0.0 0.0 0.0 0.408248290463863 0.408248290463863 0.40824829046386296 -0.4082482904638631 -0.4082482904638631 -0.408248290463863
-0.408248290463863 -0.408248290463863 -0.40824829046386296 2.4997998108697446e-17 2.4997998108697446e-17 2.499799810869744e-17 0.4082482904638631 0.4082482904638631 0.408248290463863
0.408248290463863 0.408248290463863 0.40824829046386296 -0.4082482904638631 -0.4082482904638631 -0.408248290463863 0.0 0.0 0.0
4.999599621739488e-17 4.9995996217394874e-17 -4.999599621739488e-17 0.408248290463863 0.40824829046386296 -0.408248290463863 0.408248290463863 0.40824829046386296 -0.408248290463863
-0.408248290463863 -0.40824829046386296 0.408248290463863 -2.499799810869744e-17 -2.4997998108697437e-17 2.499799810869744e-17 -0.408248290463863 -0.40824829046386296 0.408248290463863
0.408248290463863 0.40824829046386296 -0.408248290463863 -0.4082482904638631 -0.408248290463863 0.4082482904638631 0.0 0.0 0.0
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13
python/tests/reference/Orientation/cF_twin.txt Normal file
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5
python/tests/reference/Orientation/cI_Bain.txt Normal file
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1 header
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26
python/tests/reference/Orientation/cI_GT.txt Normal file
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1 header
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26
python/tests/reference/Orientation/cI_GT_prime.txt Normal file
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1 header
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26
python/tests/reference/Orientation/cI_KS.txt Normal file
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1 header
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14
python/tests/reference/Orientation/cI_NW.txt Normal file
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1 header
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14
python/tests/reference/Orientation/cI_Pitsch.txt Normal file
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@ -0,0 +1,14 @@
1 header
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25
python/tests/reference/Orientation/cI_slip.txt Normal file
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@ -0,0 +1,25 @@
3x3:1_Schmid 3x3:2_Schmid 3x3:3_Schmid 3x3:4_Schmid 3x3:5_Schmid 3x3:6_Schmid 3x3:7_Schmid 3x3:8_Schmid 3x3:9_Schmid
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13
python/tests/reference/Orientation/cI_twin.txt Normal file
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0.23570226039551587 0.23570226039551584 0.47140452079103173 0.23570226039551587 0.23570226039551584 0.47140452079103173 -0.2357022603955159 -0.23570226039551587 -0.4714045207910318
-0.2357022603955159 0.2357022603955159 0.4714045207910318 0.23570226039551587 -0.23570226039551587 -0.47140452079103173 -0.2357022603955159 0.2357022603955159 0.4714045207910318
-0.2357022603955158 0.2357022603955158 -0.4714045207910316 0.2357022603955159 -0.2357022603955159 0.4714045207910318 0.2357022603955159 -0.2357022603955159 0.4714045207910318
0.2357022603955159 0.23570226039551587 -0.4714045207910318 0.2357022603955159 0.23570226039551587 -0.4714045207910318 0.2357022603955159 0.23570226039551587 -0.4714045207910318

34
python/tests/reference/Orientation/hP_slip.txt Normal file
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@ -0,0 +1,34 @@
3x3:1_Schmid 3x3:2_Schmid 3x3:3_Schmid 3x3:4_Schmid 3x3:5_Schmid 3x3:6_Schmid 3x3:7_Schmid 3x3:8_Schmid 3x3:9_Schmid
0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 -0.4999999999999998 0.0 0.0 0.8660254037844388 0.0 0.0 0.0
0.0 0.0 -0.5000000000000001 0.0 0.0 -0.8660254037844386 0.0 0.0 0.0
0.0 1.0 -5.914589856893347e-17 0.0 0.0 0.0 0.0 0.0 0.0
0.4330127018922192 0.24999999999999975 -3.102315069664884e-17 -0.7500000000000002 -0.4330127018922192 5.373367321746164e-17 0.0 0.0 0.0
-0.43301270189221935 0.25000000000000006 1.4502014121821253e-18 -0.7499999999999998 0.4330127018922193 2.5118225271075755e-18 0.0 0.0 0.0
-0.4330127018922194 -0.7499999999999999 6.059609998111558e-17 0.2500000000000001 0.4330127018922194 -3.498517463593857e-17 0.0 0.0 0.0
2.563950248511418e-16 -5.693113199781536e-32 -9.614043519462407e-33 1.0 -2.220446049250313e-16 -3.7496997163046135e-17 0.0 0.0 0.0
0.4330127018922194 -0.75 2.8122747872284606e-17 0.25000000000000006 -0.43301270189221935 1.6236676054415494e-17 0.0 0.0 0.0
-0.38254602783800284 -0.22086305214969287 -0.23426064283290896 0.6625891564490795 0.38254602783800284 0.40575133560034454 0.0 0.0 0.0
0.0 -0.8834522085987724 -0.4685212856658182 0.0 0.0 0.0 0.0 0.0 0.0
0.38254602783800307 -0.22086305214969315 -0.23426064283290912 0.6625891564490792 -0.38254602783800296 -0.40575133560034443 0.0 0.0 0.0
-0.38254602783800284 -0.22086305214969287 0.23426064283290904 0.6625891564490795 0.38254602783800284 -0.4057513356003447 0.0 0.0 0.0
0.0 -0.8834522085987724 0.46852128566581835 0.0 0.0 0.0 0.0 0.0 0.0
0.38254602783800307 -0.22086305214969315 0.23426064283290912 0.6625891564490792 -0.38254602783800296 0.40575133560034443 0.0 0.0 0.0
-0.39955629492721617 -0.23068393443263763 -0.24467726152216654 3.8591083978971935e-17 2.228057272357889e-17 2.3632116092343994e-17 0.6524726973924442 0.3767052874784087 0.39955629492721606
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0.0 -0.23068393443263785 -0.12233863076108334 0.0 -0.39955629492721617 -0.211896724206605 0.0 0.7534105749568177 0.3995562949272161
0.0 0.23068393443263768 0.12233863076108326 0.0 -0.3995562949272162 -0.21189672420660502 0.0 0.7534105749568178 0.39955629492721617
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-0.3995562949272161 0.23068393443263774 0.24467726152216654 -3.859108397897193e-17 2.22805727235789e-17 2.3632116092343994e-17 -0.6524726973924441 0.37670528747840887 0.39955629492721606
-0.39955629492721617 -0.23068393443263763 0.24467726152216662 -3.8591083978971935e-17 -2.228057272357889e-17 2.3632116092344003e-17 -0.6524726973924442 -0.3767052874784087 0.39955629492721617
-0.1997781474636082 -0.11534196721631888 0.1223386307610834 -0.3460259016489568 -0.19977814746360806 0.21189672420660513 -0.6524726973924442 -0.3767052874784087 0.39955629492721617
0.0 -0.23068393443263788 0.12233863076108341 0.0 -0.3995562949272163 0.21189672420660516 0.0 -0.7534105749568177 0.3995562949272162
0.0 0.2306839344326376 -0.12233863076108324 0.0 -0.3995562949272163 0.21189672420660516 0.0 -0.7534105749568177 0.3995562949272162
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-0.3995562949272161 0.23068393443263774 -0.24467726152216654 3.859108397897193e-17 -2.22805727235789e-17 2.3632116092343994e-17 0.6524726973924441 -0.37670528747840887 0.39955629492721606
-0.11134044285378089 -0.19284730395996755 -0.1363636363636364 -0.19284730395996755 -0.3340213285613424 -0.23618874648666507 0.36363636363636365 0.6298366572977734 0.44536177141512323
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-0.44536177141512323 9.889017858258314e-17 0.2727272727272727 -4.301519895922435e-17 9.551292858672588e-33 2.634132215859942e-17 -0.7272727272727272 1.6148698540002275e-16 0.44536177141512323
-0.1113404428537809 -0.1928473039599676 0.13636363636363644 -0.1928473039599676 -0.33402132856134253 0.23618874648666516 -0.36363636363636365 -0.6298366572977734 0.44536177141512323
-0.11134044285378074 0.19284730395996735 -0.13636363636363627 0.19284730395996758 -0.33402132856134253 0.23618874648666516 0.3636363636363636 -0.6298366572977734 0.44536177141512323
-0.44536177141512334 9.889017858258316e-17 -0.2727272727272727 4.3015198959224354e-17 -9.55129285867259e-33 2.634132215859942e-17 0.7272727272727273 -1.6148698540002277e-16 0.44536177141512323

25
python/tests/reference/Orientation/hP_twin.txt Normal file
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@ -0,0 +1,25 @@
3x3:1_Schmid 3x3:2_Schmid 3x3:3_Schmid 3x3:4_Schmid 3x3:5_Schmid 3x3:6_Schmid 3x3:7_Schmid 3x3:8_Schmid 3x3:9_Schmid
-0.3743506488634663 -0.21613144789263322 -0.4584840372976439 -0.21613144789263333 -0.12478354962115536 -0.2647058823529411 0.4075413664867946 0.23529411764705865 0.4991341984846217
0.0 -1.1032987950073291e-16 -1.1702250894369439e-16 0.0 -0.4991341984846217 -0.5294117647058824 0.0 0.47058823529411753 0.4991341984846218
-0.3743506488634663 0.2161314478926334 0.4584840372976439 0.2161314478926334 -0.1247835496211555 -0.2647058823529412 -0.4075413664867947 0.23529411764705888 0.4991341984846218
-0.3743506488634663 -0.21613144789263322 0.4584840372976439 -0.2161314478926334 -0.12478354962115538 0.2647058823529412 -0.4075413664867946 -0.23529411764705865 0.4991341984846217
0.0 -1.4562117094830577e-16 1.5445457619280876e-16 0.0 -0.4991341984846217 0.5294117647058824 0.0 -0.47058823529411753 0.4991341984846218
-0.3743506488634663 0.2161314478926334 -0.4584840372976439 0.21613144789263342 -0.12478354962115551 0.26470588235294124 0.4075413664867947 -0.23529411764705888 0.4991341984846218
-0.06998542122237655 -0.1212183053462653 -0.04285714285714286 -0.12121830534626532 -0.20995626366712955 -0.07423074889580901 0.45714285714285724 0.7917946548886295 0.279941684889506
-0.06998542122237653 0.12121830534626528 0.04285714285714286 0.12121830534626532 -0.20995626366712958 -0.07423074889580904 -0.45714285714285724 0.7917946548886297 0.2799416848895061
-0.27994168488950616 6.2159540823338e-17 0.08571428571428573 -5.407625012016776e-17 1.2007339593759827e-32 1.6557402499691063e-17 -0.9142857142857143 2.0301221021717148e-16 0.27994168488950605
-0.0699854212223766 -0.12121830534626538 0.04285714285714291 -0.12121830534626538 -0.20995626366712963 0.07423074889580909 -0.45714285714285724 -0.7917946548886295 0.2799416848895062
-0.06998542122237648 0.12121830534626521 -0.04285714285714283 0.12121830534626538 -0.20995626366712966 0.07423074889580906 0.45714285714285724 -0.7917946548886297 0.2799416848895061
-0.27994168488950605 6.215954082333798e-17 -0.08571428571428569 5.407625012016776e-17 -1.2007339593759827e-32 1.6557402499691063e-17 0.9142857142857143 -2.0301221021717148e-16 0.27994168488950605
0.3104371234477526 0.17923095678901296 0.19010313741609627 0.17923095678901305 0.1034790411492508 0.1097560975609756 -0.6759222663683424 -0.39024390243902424 -0.41391616459700337
0.0 7.68600963028337e-17 4.07612214737886e-17 0.0 0.4139161645970035 0.21951219512195125 0.0 -0.7804878048780488 -0.4139161645970034
0.31043712344775254 -0.17923095678901305 -0.19010313741609627 -0.17923095678901302 0.10347904114925086 0.1097560975609756 0.6759222663683423 -0.3902439024390244 -0.41391616459700337
0.3104371234477527 0.179230956789013 -0.19010313741609638 0.17923095678901313 0.10347904114925086 -0.10975609756097568 0.6759222663683424 0.3902439024390242 -0.4139161645970035
0.0 1.3539199431344235e-16 -7.180244797305419e-17 0.0 0.4139161645970036 -0.21951219512195136 0.0 0.7804878048780487 -0.41391616459700353
0.3104371234477525 -0.179230956789013 0.19010313741609622 -0.17923095678901313 0.10347904114925092 -0.10975609756097565 -0.6759222663683423 0.3902439024390244 -0.41391616459700337
0.11134044285378089 0.19284730395996755 0.1363636363636364 0.19284730395996755 0.3340213285613424 0.23618874648666507 -0.36363636363636365 -0.6298366572977734 -0.44536177141512323
0.11134044285378081 -0.1928473039599675 -0.13636363636363633 -0.19284730395996758 0.3340213285613426 0.2361887464866651 0.3636363636363637 -0.6298366572977737 -0.4453617714151233
0.44536177141512323 -9.889017858258314e-17 -0.2727272727272727 4.301519895922435e-17 -9.551292858672588e-33 -2.634132215859942e-17 0.7272727272727272 -1.6148698540002275e-16 -0.44536177141512323
0.1113404428537809 0.1928473039599676 -0.13636363636363644 0.1928473039599676 0.33402132856134253 -0.23618874648666516 0.36363636363636365 0.6298366572977734 -0.44536177141512323
0.11134044285378074 -0.19284730395996735 0.13636363636363627 -0.19284730395996758 0.33402132856134253 -0.23618874648666516 -0.3636363636363636 0.6298366572977734 -0.44536177141512323
0.44536177141512334 -9.889017858258316e-17 0.2727272727272727 -4.3015198959224354e-17 9.55129285867259e-33 -2.634132215859942e-17 -0.7272727272727273 1.6148698540002277e-16 -0.44536177141512323

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python/tests/reference/Result/material.config
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<homogenization>
[none]
mech none
ngrains 1
<texture>
[Grain1]
(gauss) phi1 358.98 Phi 65.62 phi2 24.48
[Grain2]
(gauss) phi1 121.05 Phi 176.11 phi2 295.73
[Grain3]
(gauss) phi1 43.79 Phi 113.76 phi2 345.90
[Grain4]
(gauss) phi1 265.15 Phi 62.52 phi2 299.71
[Grain5]
(gauss) phi1 221.23 Phi 26.54 phi2 207.05
[Grain6]
(gauss) phi1 249.81 Phi 61.47 phi2 152.14
[Grain7]
(gauss) phi1 332.45 Phi 99.16 phi2 345.34
[Grain8]
(gauss) phi1 312.27 Phi 118.27 phi2 181.59
[Grain9]
(gauss) phi1 303.10 Phi 48.21 phi2 358.03
[Grain10]
(gauss) phi1 338.26 Phi 48.11 phi2 176.78
[Grain11]
(gauss) phi1 115.17 Phi 56.54 phi2 223.84
[Grain12]
(gauss) phi1 281.04 Phi 97.48 phi2 27.94
<microstructure>
[Grain1]
crystallite 1
(constituent) phase 1 texture 1 fraction 1.0
[Grain2]
crystallite 1
(constituent) phase 1 texture 2 fraction 1.0
[Grain3]
crystallite 1
(constituent) phase 1 texture 3 fraction 1.0
[Grain4]
crystallite 1
(constituent) phase 1 texture 4 fraction 1.0
[Grain5]
crystallite 1
(constituent) phase 1 texture 5 fraction 1.0
[Grain6]
crystallite 1
(constituent) phase 1 texture 6 fraction 1.0
[Grain7]
crystallite 1
(constituent) phase 2 texture 7 fraction 1.0
[Grain8]
crystallite 1
(constituent) phase 2 texture 8 fraction 1.0
[Grain9]
crystallite 1
(constituent) phase 2 texture 9 fraction 1.0
[Grain10]
crystallite 1
(constituent) phase 2 texture 10 fraction 1.0
[Grain11]
crystallite 1
(constituent) phase 2 texture 11 fraction 1.0
[Grain12]
crystallite 1
(constituent) phase 2 texture 12 fraction 1.0
<phase>
[pheno_fcc]
elasticity hooke
plasticity phenopowerlaw
(output) orientation # quaternion
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor
lattice_structure fcc
Nslip 12 # per family
Ntwin 0 # per family
c11 106.75e9
c12 60.41e9
c44 28.34e9
gdot0_slip 0.001
n_slip 20
tau0_slip 31e6 # per family
tausat_slip 63e6 # per family
a_slip 2.25
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
atol_resistance 1
[pheno_bcc]
elasticity hooke
plasticity phenopowerlaw
(output) orientation # quaternion
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor
lattice_structure bcc
Nslip 12 # per family
c11 106.75e9
c12 60.41e9
c44 28.34e9
gdot0_slip 0.001
n_slip 20
tau0_slip 31e6 # per family
tausat_slip 63e6 # per family
a_slip 2.25
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
atol_resistance 1

103
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---
homogenization:
SX:
N_constituents: 1
mech: {type: none}
phase:
pheno_fcc:
lattice: fcc
mech:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
plasticity:
N_sl: [12]
a_sl: 2.25
atol_xi: 1.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
output: [xi_sl]
type: phenopowerlaw
xi_0_sl: [31e6]
xi_inf_sl: [63e6]
pheno_bcc:
lattice: bcc
mech:
output: [F, P, F_e, F_p, L_p, O]
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
plasticity:
N_sl: [12]
a_sl: 2.25
atol_xi: 1.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
output: [xi_sl]
type: phenopowerlaw
xi_0_sl: [31e6]
xi_inf_sl: [63e6]
material:
- constituents:
- fraction: 1.0
O: [0.8229200444892315, 0.5284940239127993, -0.11958598847729246, 0.17086795611292308]
phase: pheno_fcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.029934934533052786, -0.0463822071939717, 0.9983440440417412, 0.01617900728410769]
phase: pheno_fcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.5285808688806949, 0.7326575088838098, 0.4051997815944012, 0.1401013087924221]
phase: pheno_fcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.1839974517790312, 0.49550065903084944, -0.1541415483910751, -0.8347840545305227]
phase: pheno_fcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.8055693100147384, -0.22778497057116814, -0.028331746016454287, 0.5462320075864553]
phase: pheno_fcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.8025842700117737, -0.33640019337884963, -0.3847408071640489, 0.3076815085881779]
phase: pheno_fcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.6048933483394416, 0.7565005822419409, -0.08545681892422426, -0.2334695661144201]
phase: pheno_bcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.2012339360745425, -0.3580127491130033, -0.7798091137625135, 0.47247171400774884]
phase: pheno_bcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.7949688202267222, 0.3623793306926909, -0.18836147613310203, -0.4485819321629098]
phase: pheno_bcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.19733162113429173, -0.06559103894055797, -0.40230149937129567, 0.8915781236183501]
phase: pheno_bcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.8659916384140512, -0.2761459420825848, 0.38479354764225004, -0.1604238964779258]
phase: pheno_bcc
homogenization: SX
- constituents:
- fraction: 1.0
O: [0.5951846978175659, 0.4476701545571293, -0.6038886363266418, -0.2840160613735736]
phase: pheno_bcc
homogenization: SX

1
python/tests/reference/Result/tensionY.load
View File

@ -1 +0,0 @@
fdot * 0 0 0 1.0e-3 0 0 0 * stress 0 * * * * * * * 0 time 20 incs 40 freq 4

14
python/tests/reference/Result/tensionY.yaml Normal file
View File

@ -0,0 +1,14 @@
---
step:
- discretization:
t: 20
N: 40
f_out: 4
mech:
dot_F: [x, 0, 0,
0, 1.0e-3, 0,
0, 0, x]
P: [0, x, x,
x, x, x,
x, x, 0]

26
python/tests/test_Geom.py
View File

@ -6,6 +6,7 @@ from damask import Geom
from damask import Table from damask import Table
from damask import Rotation from damask import Rotation
from damask import util from damask import util
from damask import seeds
from damask import grid_filters from damask import grid_filters
@ -204,6 +205,11 @@ class TestGeom:
assert np.array_equiv(t,f) or (not geom_equal(modified,default)) assert np.array_equiv(t,f) or (not geom_equal(modified,default))
assert geom_equal(default, modified.substitute(t,f)) assert geom_equal(default, modified.substitute(t,f))
def test_sort(self):
grid = np.random.randint(5,20,3)
m = Geom(np.random.randint(1,20,grid)*3,np.ones(3)).sort().material.flatten(order='F')
for i,v in enumerate(m):
assert i==0 or v > m[:i].max() or v in m[:i]
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]), @pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])]) np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
@ -259,12 +265,12 @@ class TestGeom:
@pytest.mark.parametrize('inverse',[True,False]) @pytest.mark.parametrize('inverse',[True,False])
@pytest.mark.parametrize('periodic',[True,False]) @pytest.mark.parametrize('periodic',[True,False])
def test_add_primitive_rotation(self,center,inverse,periodic): def test_add_primitive_rotation(self,center,inverse,periodic):
"""Rotation should not change result for sphere (except for discretization errors).""" """Rotation should not change result for sphere."""
g = np.array([32,32,32]) g = np.random.randint(8,32,(3))
s = np.random.random(3)+.5
fill = np.random.randint(10)+2 fill = np.random.randint(10)+2
eu=np.array([np.random.randint(4),np.random.randint(2),np.random.randint(4)])*.5*np.pi G_1 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
G_1 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic) G_2 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,Rotation.from_random(),inverse,periodic=periodic)
G_2 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,Rotation.from_Eulers(eu),inverse,periodic=periodic)
assert geom_equal(G_1,G_2) assert geom_equal(G_1,G_2)
@ -384,3 +390,13 @@ class TestGeom:
t = Table(np.column_stack((coords,z)),{'coords':3,'z':1}) t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
g = Geom.from_table(t,'coords',['1_coords','z']) g = Geom.from_table(t,'coords',['1_coords','z'])
assert g.N_materials == g.grid[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == grid[0]).all() assert g.N_materials == g.grid[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == grid[0]).all()
def test_from_table_recover(self,tmp_path):
grid = np.random.randint(60,100,3)
size = np.ones(3)+np.random.rand(3)
s = seeds.from_random(size,np.random.randint(60,100))
geom = Geom.from_Voronoi_tessellation(grid,size,s)
coords = grid_filters.cell_coord0(grid,size)
t = Table(np.column_stack((coords.reshape(-1,3,order='F'),geom.material.flatten(order='F'))),{'c':3,'m':1})
assert geom_equal(geom.sort().renumber(),Geom.from_table(t,'c',['m']))

157
python/tests/test_Lattice.py
View File

@ -1,157 +0,0 @@
import random
import pytest
import numpy as np
from damask import Rotation
from damask import Symmetry
def in_FZ(system,rho):
"""Non-vectorized version of 'in_FZ'."""
rho_abs = abs(rho)
if system == 'cubic':
return np.sqrt(2.0)-1.0 >= rho_abs[0] \
and np.sqrt(2.0)-1.0 >= rho_abs[1] \
and np.sqrt(2.0)-1.0 >= rho_abs[2] \
and 1.0 >= rho_abs[0] + rho_abs[1] + rho_abs[2]
elif system == 'hexagonal':
return 1.0 >= rho_abs[0] and 1.0 >= rho_abs[1] and 1.0 >= rho_abs[2] \
and 2.0 >= np.sqrt(3)*rho_abs[0] + rho_abs[1] \
and 2.0 >= np.sqrt(3)*rho_abs[1] + rho_abs[0] \
and 2.0 >= np.sqrt(3) + rho_abs[2]
elif system == 'tetragonal':
return 1.0 >= rho_abs[0] and 1.0 >= rho_abs[1] \
and np.sqrt(2.0) >= rho_abs[0] + rho_abs[1] \
and np.sqrt(2.0) >= rho_abs[2] + 1.0
elif system == 'orthorhombic':
return 1.0 >= rho_abs[0] and 1.0 >= rho_abs[1] and 1.0 >= rho_abs[2]
else:
return np.all(np.isfinite(rho_abs))
def in_disorientation_SST(system,rho):
"""Non-vectorized version of 'in_Disorientation_SST'."""
epsilon = 0.0
if system == 'cubic':
return rho[0] >= rho[1]+epsilon and rho[1] >= rho[2]+epsilon and rho[2] >= epsilon
elif system == 'hexagonal':
return rho[0] >= np.sqrt(3)*(rho[1]-epsilon) and rho[1] >= epsilon and rho[2] >= epsilon
elif system == 'tetragonal':
return rho[0] >= rho[1]-epsilon and rho[1] >= epsilon and rho[2] >= epsilon
elif system == 'orthorhombic':
return rho[0] >= epsilon and rho[1] >= epsilon and rho[2] >= epsilon
else:
return True
def in_SST(system,vector,proper = False):
"""Non-vectorized version of 'in_SST'."""
if system == 'cubic':
basis = {'improper':np.array([ [-1. , 0. , 1. ],
[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
[ 0. , np.sqrt(3.) , 0. ] ]),
'proper':np.array([ [ 0. , -1. , 1. ],
[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
[ np.sqrt(3.) , 0. , 0. ] ]),
}
elif system == 'hexagonal':
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
[ 1. , -np.sqrt(3.) , 0. ],
[ 0. , 2. , 0. ] ]),
'proper':np.array([ [ 0. , 0. , 1. ],
[-1. , np.sqrt(3.) , 0. ],
[ np.sqrt(3.) , -1. , 0. ] ]),
}
elif system == 'tetragonal':
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
[ 1. , -1. , 0. ],
[ 0. , np.sqrt(2.) , 0. ] ]),
'proper':np.array([ [ 0. , 0. , 1. ],
[-1. , 1. , 0. ],
[ np.sqrt(2.) , 0. , 0. ] ]),
}
elif system == 'orthorhombic':
basis = {'improper':np.array([ [ 0., 0., 1.],
[ 1., 0., 0.],
[ 0., 1., 0.] ]),
'proper':np.array([ [ 0., 0., 1.],
[-1., 0., 0.],
[ 0., 1., 0.] ]),
}
else:
return True
v = np.array(vector,dtype=float)
if proper:
theComponents = np.around(np.dot(basis['improper'],v),12)
inSST = np.all(theComponents >= 0.0)
if not inSST:
theComponents = np.around(np.dot(basis['proper'],v),12)
inSST = np.all(theComponents >= 0.0)
else:
v[2] = abs(v[2])
theComponents = np.around(np.dot(basis['improper'],v),12)
inSST = np.all(theComponents >= 0.0)
return inSST
@pytest.fixture
def set_of_rodrigues(set_of_quaternions):
return Rotation(set_of_quaternions).as_Rodrigues(vector=True)[:200]
class TestSymmetry:
@pytest.mark.parametrize('system',Symmetry.crystal_systems)
def test_in_FZ_vectorize(self,set_of_rodrigues,system):
result = Symmetry(system).in_FZ(set_of_rodrigues.reshape(50,4,3)).reshape(200)
for i,r in enumerate(result):
assert r == in_FZ(system,set_of_rodrigues[i])
@pytest.mark.parametrize('system',Symmetry.crystal_systems)
def test_in_disorientation_SST_vectorize(self,set_of_rodrigues,system):
result = Symmetry(system).in_disorientation_SST(set_of_rodrigues.reshape(50,4,3)).reshape(200)
for i,r in enumerate(result):
assert r == in_disorientation_SST(system,set_of_rodrigues[i])
@pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('system',Symmetry.crystal_systems)
def test_in_SST_vectorize(self,system,proper):
vecs = np.random.rand(20,4,3)
result = Symmetry(system).in_SST(vecs,proper).reshape(20*4)
for i,r in enumerate(result):
assert r == in_SST(system,vecs.reshape(20*4,3)[i],proper)
@pytest.mark.parametrize('invalid_symmetry',['fcc','bcc','hello'])
def test_invalid_symmetry(self,invalid_symmetry):
with pytest.raises(KeyError):
s = Symmetry(invalid_symmetry) # noqa
def test_equal(self):
symmetry = random.choice(Symmetry.crystal_systems)
print(symmetry)
assert Symmetry(symmetry) == Symmetry(symmetry)
def test_not_equal(self):
symmetries = random.sample(Symmetry.crystal_systems,k=2)
assert Symmetry(symmetries[0]) != Symmetry(symmetries[1])
@pytest.mark.parametrize('system',Symmetry.crystal_systems)
def test_in_FZ(self,system):
assert Symmetry(system).in_FZ(np.zeros(3))
@pytest.mark.parametrize('system',Symmetry.crystal_systems)
def test_in_disorientation_SST(self,system):
assert Symmetry(system).in_disorientation_SST(np.zeros(3))
@pytest.mark.parametrize('system',Symmetry.crystal_systems)
@pytest.mark.parametrize('proper',[True,False])
def test_in_SST(self,system,proper):
assert Symmetry(system).in_SST(np.zeros(3),proper)
@pytest.mark.parametrize('function',['in_FZ','in_disorientation_SST','in_SST'])
def test_invalid_argument(self,function):
s = Symmetry() # noqa
with pytest.raises(ValueError):
eval(f's.{function}(np.ones(4))')

593
python/tests/test_Orientation.py
View File

@ -1,131 +1,536 @@
import os
from itertools import permutations
import pytest import pytest
import numpy as np import numpy as np
from itertools import permutations
from damask import Table
from damask import Rotation from damask import Rotation
from damask import Orientation from damask import Orientation
from damask import Lattice from damask import Table
from damask import lattice
n = 1000 from damask import util
def IPF_color(orientation,direction):
"""TSL color of inverse pole figure for given axis (non-vectorized)."""
for o in orientation.equivalent:
pole = o.rotation@direction
inSST,color = orientation.lattice.in_SST(pole,color=True)
if inSST: break
return color
def inverse_pole(orientation,axis,proper=False,SST=True):
if SST:
for eq in orientation.equivalent:
pole = eq.rotation @ axis/np.linalg.norm(axis)
if orientation.lattice.in_SST(pole,proper=proper):
return pole
else:
return orientation.rotation @ axis/np.linalg.norm(axis)
@pytest.fixture @pytest.fixture
def reference_dir(reference_dir_base): def reference_dir(reference_dir_base):
"""Directory containing reference results.""" """Directory containing reference results."""
return reference_dir_base/'Rotation' return reference_dir_base/'Orientation'
@pytest.fixture
def set_of_rodrigues(set_of_quaternions):
return Rotation(set_of_quaternions).as_Rodrigues()[:200]
class TestOrientation: class TestOrientation:
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch']) @pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('lattice',['fcc','bcc']) @pytest.mark.parametrize('shape',[None,5,(4,6)])
def test_relationship_vectorize(self,set_of_quaternions,lattice,model): def test_equal(self,lattice,shape):
result = Orientation(set_of_quaternions[:200].reshape(50,4,4),lattice).related(model) R = Rotation.from_random(shape)
ref_qu = result.rotation.quaternion.reshape(-1,200,4) assert Orientation(R,lattice) == Orientation(R,lattice)
for i in range(200):
single = Orientation(set_of_quaternions[i],lattice).related(model).rotation.quaternion
assert np.allclose(ref_qu[:,i,:],single)
@pytest.mark.parametrize('lattice',Lattice.lattices) @pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_IPF_vectorize(self,set_of_quaternions,lattice): @pytest.mark.parametrize('shape',[None,5,(4,6)])
direction = np.random.random(3)*2.0-1 def test_unequal(self,lattice,shape):
oris = Orientation(Rotation(set_of_quaternions),lattice)[:200] R = Rotation.from_random(shape)
for i,color in enumerate(oris.IPF_color(direction)): assert not(Orientation(R,lattice) != Orientation(R,lattice))
assert np.allclose(color,IPF_color(oris[i],direction))
@pytest.mark.parametrize('SST',[False,True]) @pytest.mark.parametrize('a,b',[
(dict(rotation=[1,0,0,0]),
dict(rotation=[0.5,0.5,0.5,0.5])),
(dict(rotation=[1,0,0,0],lattice='cubic'),
dict(rotation=[1,0,0,0],lattice='hexagonal')),
(dict(rotation=[1,0,0,0],lattice='cF',a=1),
dict(rotation=[1,0,0,0],lattice='cF',a=2)),
])
def test_nonequal(self,a,b):
assert Orientation(**a) != Orientation(**b)
@pytest.mark.parametrize('kwargs',[
dict(lattice='aP', alpha=np.pi/4,beta=np.pi/3, ),
dict(lattice='mP', c=1.2,alpha=np.pi/4, gamma=np.pi/2),
dict(lattice='oP', c=1.2,alpha=np.pi/4, ),
dict(lattice='oS',a=1.0, c=2.0,alpha=np.pi/2,beta=np.pi/3, ),
dict(lattice='tP',a=1.0,b=1.2, ),
dict(lattice='tI', alpha=np.pi/3, ),
dict(lattice='hP', gamma=np.pi/2),
dict(lattice='cI',a=1.0, c=2.0,alpha=np.pi/2,beta=np.pi/2, ),
dict(lattice='cF', beta=np.pi/3, ),
])
def test_invalid_init(self,kwargs):
with pytest.raises(ValueError):
Orientation(**kwargs).parameters # noqa
@pytest.mark.parametrize('kwargs',[
dict(lattice='aP',a=1.0,b=1.1,c=1.2,alpha=np.pi/4,beta=np.pi/3,gamma=np.pi/2),
dict(lattice='mP',a=1.0,b=1.1,c=1.2, beta=np.pi/3 ),
dict(lattice='oS',a=1.0,b=1.1,c=1.2, ),
dict(lattice='tI',a=1.0, c=1.2, ),
dict(lattice='hP',a=1.0 ),
dict(lattice='cI',a=1.0, ),
])
def test_repr(self,kwargs):
o = Orientation.from_random(**kwargs)
assert isinstance(o.__repr__(),str)
@pytest.mark.parametrize('kwargs',[
dict(lattice='aP',a=1.0,b=1.1,c=1.2,alpha=np.pi/4,beta=np.pi/3,gamma=np.pi/2),
dict(lattice='mP',a=1.0,b=1.1,c=1.2, beta=np.pi/3 ),
dict(lattice='oS',a=1.0,b=1.1,c=1.2, ),
dict(lattice='tI',a=1.0, c=1.2, ),
dict(lattice='hP',a=1.0 ),
dict(lattice='cI',a=1.0, ),
])
def test_copy(self,kwargs):
o = Orientation.from_random(**kwargs)
p = o.copy(rotation=Rotation.from_random())
assert o != p
def test_from_quaternion(self):
assert np.all(Orientation.from_quaternion(q=np.array([1,0,0,0]),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_Eulers(self):
assert np.all(Orientation.from_Eulers(phi=np.zeros(3),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_axis_angle(self):
assert np.all(Orientation.from_axis_angle(axis_angle=[1,0,0,0],lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_basis(self):
assert np.all(Orientation.from_basis(basis=np.eye(3),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_matrix(self):
assert np.all(Orientation.from_matrix(R=np.eye(3),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_Rodrigues(self):
assert np.all(Orientation.from_Rodrigues(rho=np.array([0,0,1,0]),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_homochoric(self):
assert np.all(Orientation.from_homochoric(h=np.zeros(3),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_cubochoric(self):
assert np.all(Orientation.from_cubochoric(c=np.zeros(3),lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_spherical_component(self):
assert np.all(Orientation.from_spherical_component(center=Rotation(),
sigma=0.0,N=1,lattice='triclinic').as_matrix()
== np.eye(3))
def test_from_fiber_component(self):
r = Rotation.from_fiber_component(alpha=np.zeros(2),beta=np.zeros(2),
sigma=0.0,N=1,seed=0)
assert np.all(Orientation.from_fiber_component(alpha=np.zeros(2),beta=np.zeros(2),
sigma=0.0,N=1,seed=0,lattice='triclinic').quaternion
== r.quaternion)
@pytest.mark.parametrize('kwargs',[
dict(lattice='aP',a=1.0,b=1.1,c=1.2,alpha=np.pi/4.5,beta=np.pi/3.5,gamma=np.pi/2.5),
dict(lattice='mP',a=1.0,b=1.1,c=1.2, beta=np.pi/3.5),
dict(lattice='oS',a=1.0,b=1.1,c=1.2,),
dict(lattice='tI',a=1.0, c=1.2,),
dict(lattice='hP',a=1.0 ),
dict(lattice='cI',a=1.0, ),
])
def test_from_direction(self,kwargs):
for a,b in np.random.random((10,2,3)):
c = np.cross(b,a)
if np.all(np.isclose(c,0)): continue
o = Orientation.from_directions(uvw=a,hkl=c,**kwargs)
x = o.to_pole(uvw=a)
z = o.to_pole(hkl=c)
assert np.isclose(np.dot(x/np.linalg.norm(x),np.array([1,0,0])),1) \
and np.isclose(np.dot(z/np.linalg.norm(z),np.array([0,0,1])),1)
def test_negative_angle(self):
with pytest.raises(ValueError):
Orientation(lattice='aP',a=1,b=2,c=3,alpha=45,beta=45,gamma=-45,degrees=True) # noqa
def test_excess_angle(self):
with pytest.raises(ValueError):
Orientation(lattice='aP',a=1,b=2,c=3,alpha=45,beta=45,gamma=90.0001,degrees=True) # noqa
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('angle',[10,20,30,40])
def test_average(self,angle,lattice):
o = Orientation.from_axis_angle(lattice=lattice,axis_angle=[[0,0,1,10],[0,0,1,angle]],degrees=True)
avg_angle = o.average().as_axis_angle(degrees=True,pair=True)[1]
assert np.isclose(avg_angle,10+(angle-10)/2.)
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_reduced_equivalent(self,lattice):
i = Orientation(lattice=lattice)
o = Orientation.from_random(lattice=lattice)
eq = o.equivalent
FZ = np.argmin(abs(eq.misorientation(i.broadcast_to(len(eq))).as_axis_angle(pair=True)[1]))
assert o.reduced == eq[FZ]
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('N',[1,8,32])
def test_disorientation(self,lattice,N):
o = Orientation.from_random(lattice=lattice,shape=N,seed=0)
p = Orientation.from_random(lattice=lattice,shape=N,seed=1)
d,ops = o.disorientation(p,return_operators=True)
for n in range(N):
assert np.allclose(d[n].as_quaternion(),
o[n].equivalent[ops[n][0]]
.misorientation(p[n].equivalent[ops[n][1]])
.as_quaternion()) \
or np.allclose((~d)[n].as_quaternion(),
o[n].equivalent[ops[n][0]]
.misorientation(p[n].equivalent[ops[n][1]])
.as_quaternion())
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('a,b',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,None),
])
def test_disorientation_blending(self,lattice,a,b):
o = Orientation.from_random(lattice=lattice,shape=a,seed=0)
p = Orientation.from_random(lattice=lattice,shape=b,seed=1)
blend = util.shapeblender(o.shape,p.shape)
for loc in np.random.randint(0,blend,(10,len(blend))):
assert o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]) \
== o.disorientation(p)[tuple(loc)]
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_disorientation360(self,lattice):
o_1 = Orientation(Rotation(),lattice)
o_2 = Orientation.from_Eulers(lattice=lattice,phi=[360,0,0],degrees=True)
assert np.allclose((o_1.disorientation(o_2)).as_matrix(),np.eye(3))
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
def test_reduced_vectorization(self,lattice,shape):
o = Orientation.from_random(lattice=lattice,shape=shape,seed=0)
for r, theO in zip(o.reduced.flatten(),o.flatten()):
assert r == theO.reduced
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False]) @pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('lattice',Lattice.lattices) def test_to_SST_vectorization(self,lattice,shape,vector,proper):
def test_inverse_pole_vectorize(self,set_of_quaternions,lattice,SST,proper): o = Orientation.from_random(lattice=lattice,shape=shape,seed=0)
axis = np.random.random(3)*2.0-1 for r, theO in zip(o.to_SST(vector=vector,proper=proper).reshape((-1,3)),o.flatten()):
oris = Orientation(Rotation(set_of_quaternions),lattice)[:200] assert np.allclose(r,theO.to_SST(vector=vector,proper=proper))
for i,pole in enumerate(oris.inverse_pole(axis,SST=SST)):
assert np.allclose(pole,inverse_pole(oris[i],axis,SST=SST)) @pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
def test_IPF_color_vectorization(self,lattice,shape,vector,proper):
o = Orientation.from_random(lattice=lattice,shape=shape,seed=0)
poles = o.to_SST(vector=vector,proper=proper)
for r, theO in zip(o.IPF_color(poles,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.IPF_color(theO.to_SST(vector=vector,proper=proper),proper=proper))
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('a,b',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,(3,)),
])
def test_to_SST_blending(self,lattice,a,b):
o = Orientation.from_random(lattice=lattice,shape=a,seed=0)
v = np.random.random(b+(3,))
blend = util.shapeblender(o.shape,b)
for loc in np.random.randint(0,blend,(10,len(blend))):
print(f'{a}/{b} @ {loc}')
print(o[tuple(loc[:len(o.shape)])].to_SST(v[tuple(loc[-len(b):])]))
print(o.to_SST(v)[tuple(loc)])
assert np.allclose(o[tuple(loc[:len(o.shape)])].to_SST(v[tuple(loc[-len(b):])]),
o.to_SST(v)[tuple(loc)])
@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]}, @pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
{'label':'green','RGB':[0,1,0],'direction':[0,1,1]}, {'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}]) {'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
@pytest.mark.parametrize('lattice',['fcc','bcc']) @pytest.mark.parametrize('proper',[True,False])
def test_IPF_cubic(self,color,lattice): def test_IPF_cubic(self,color,proper):
cube = Orientation(Rotation(),lattice) cube = Orientation(lattice='cubic')
for direction in set(permutations(np.array(color['direction']))): for direction in set(permutations(np.array(color['direction']))):
assert np.allclose(cube.IPF_color(np.array(direction)),np.array(color['RGB'])) assert np.allclose(np.array(color['RGB']),
cube.IPF_color(cube.to_SST(vector=np.array(direction),proper=proper),proper=proper))
@pytest.mark.parametrize('lattice',Lattice.lattices) @pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_IPF_equivalent(self,set_of_quaternions,lattice): @pytest.mark.parametrize('proper',[True,False])
direction = np.random.random(3)*2.0-1 def test_IPF_equivalent(self,set_of_quaternions,lattice,proper):
for ori in Orientation(Rotation(set_of_quaternions),lattice)[:200]: direction = np.random.random(3)*2.0-1.0
color = ori.IPF_color(direction) o = Orientation(rotation=set_of_quaternions,lattice=lattice).equivalent
for equivalent in ori.equivalent: color = o.IPF_color(o.to_SST(vector=direction,proper=proper),proper=proper)
assert np.allclose(color,equivalent.IPF_color(direction)) assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
@pytest.mark.parametrize('lattice',Lattice.lattices) @pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_reduced(self,set_of_quaternions,lattice): def test_in_FZ_vectorization(self,set_of_rodrigues,lattice):
oris = Orientation(Rotation(set_of_quaternions),lattice) result = Orientation.from_Rodrigues(rho=set_of_rodrigues.reshape((50,4,-1)),lattice=lattice).in_FZ.reshape(-1)
reduced = oris.reduced for r,rho in zip(result,set_of_rodrigues[:len(result)]):
assert np.all(reduced.in_FZ) and oris.rotation.shape == reduced.rotation.shape assert r == Orientation.from_Rodrigues(rho=rho,lattice=lattice).in_FZ
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_in_disorientation_FZ_vectorization(self,set_of_rodrigues,lattice):
result = Orientation.from_Rodrigues(rho=set_of_rodrigues.reshape((50,4,-1)),
lattice=lattice).in_disorientation_FZ.reshape(-1)
for r,rho in zip(result,set_of_rodrigues[:len(result)]):
assert r == Orientation.from_Rodrigues(rho=rho,lattice=lattice).in_disorientation_FZ
@pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_in_SST_vectorization(self,lattice,proper):
vecs = np.random.rand(20,4,3)
result = Orientation(lattice=lattice).in_SST(vecs,proper).flatten()
for r,v in zip(result,vecs.reshape((-1,3))):
assert np.all(r == Orientation(lattice=lattice).in_SST(v,proper))
@pytest.mark.parametrize('invalid_lattice',['fcc','bcc','hello'])
def test_invalid_lattice_init(self,invalid_lattice):
with pytest.raises(KeyError):
Orientation(lattice=invalid_lattice) # noqa
@pytest.mark.parametrize('invalid_family',[None,'fcc','bcc','hello'])
def test_invalid_symmetry_family(self,invalid_family):
with pytest.raises(KeyError):
o = Orientation(lattice='cubic')
o.family = invalid_family
o.symmetry_operations # noqa
def test_missing_symmetry_equivalent(self):
with pytest.raises(ValueError):
Orientation(lattice=None).equivalent # noqa
def test_missing_symmetry_reduced(self):
with pytest.raises(ValueError):
Orientation(lattice=None).reduced # noqa
def test_missing_symmetry_in_FZ(self):
with pytest.raises(ValueError):
Orientation(lattice=None).in_FZ # noqa
def test_missing_symmetry_in_disorientation_FZ(self):
with pytest.raises(ValueError):
Orientation(lattice=None).in_disorientation_FZ # noqa
def test_missing_symmetry_disorientation(self):
with pytest.raises(ValueError):
Orientation(lattice=None).disorientation(Orientation(lattice=None)) # noqa
def test_missing_symmetry_average(self):
with pytest.raises(ValueError):
Orientation(lattice=None).average() # noqa
def test_missing_symmetry_to_SST(self):
with pytest.raises(ValueError):
Orientation(lattice=None).to_SST(np.zeros(3)) # noqa
def test_missing_symmetry_immutable(self):
with pytest.raises(KeyError):
Orientation(lattice=None).immutable # noqa
def test_missing_symmetry_basis_real(self):
with pytest.raises(KeyError):
Orientation(lattice=None).basis_real # noqa
def test_missing_symmetry_basis_reciprocal(self):
with pytest.raises(KeyError):
Orientation(lattice=None).basis_reciprocal # noqa
def test_double_Bravais_to_Miller(self):
with pytest.raises(KeyError):
Orientation.Bravais_to_Miller(uvtw=np.ones(4),hkil=np.ones(4)) # noqa
def test_double_Miller_to_Bravais(self):
with pytest.raises(KeyError):
Orientation.Miller_to_Bravais(uvw=np.ones(4),hkl=np.ones(4)) # noqa
def test_double_to_lattice(self):
with pytest.raises(KeyError):
Orientation().to_lattice(direction=np.ones(3),plane=np.ones(3)) # noqa
def test_double_to_frame(self):
with pytest.raises(KeyError):
Orientation().to_frame(uvw=np.ones(3),hkl=np.ones(3)) # noqa
@pytest.mark.parametrize('relation',[None,'Peter','Paul'])
def test_unknown_relation(self,relation):
with pytest.raises(KeyError):
Orientation(lattice='cF').related(relation) # noqa
@pytest.mark.parametrize('relation,lattice,a,b,c,alpha,beta,gamma',
[
('Bain', 'aP',0.5,2.0,3.0,0.8,0.5,1.2),
('KS', 'mP',1.0,2.0,3.0,np.pi/2,0.5,np.pi/2),
('Pitsch', 'oI',0.5,1.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('Burgers','tP',0.5,0.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('GT', 'hP',1.0,None,1.6,np.pi/2,np.pi/2,2*np.pi/3),
('Burgers','cF',1.0,1.0,None,np.pi/2,np.pi/2,np.pi/2),
])
def test_unknown_relation_lattice(self,relation,lattice,a,b,c,alpha,beta,gamma):
with pytest.raises(KeyError):
Orientation(lattice=lattice,
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma).related(relation) # noqa
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('proper',[True,False])
def test_in_SST(self,lattice,proper):
assert Orientation(lattice=lattice).in_SST(np.zeros(3),proper)
@pytest.mark.parametrize('function',['in_SST','IPF_color'])
def test_invalid_argument(self,function):
o = Orientation(lattice='cubic') # noqa
with pytest.raises(ValueError):
eval(f'o.{function}(np.ones(4))')
@pytest.mark.parametrize('model',lattice.relations)
def test_relationship_definition(self,model):
m,o = list(lattice.relations[model])
assert lattice.relations[model][m].shape[:-1] == lattice.relations[model][o].shape[:-1]
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch']) @pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['fcc','bcc']) @pytest.mark.parametrize('lattice',['cF','cI'])
def test_relationship_vectorize(self,set_of_quaternions,lattice,model):
r = Orientation(rotation=set_of_quaternions[:200].reshape((50,4,4)),lattice=lattice).related(model)
for i in range(200):
assert r.reshape((-1,200))[:,i] == Orientation(set_of_quaternions[i],lattice).related(model)
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['cF','cI'])
def test_relationship_forward_backward(self,model,lattice): def test_relationship_forward_backward(self,model,lattice):
ori = Orientation(Rotation.from_random(),lattice) o = Orientation.from_random(lattice=lattice)
for i,r in enumerate(ori.related(model)): for i,r in enumerate(o.related(model)):
ori2 = r.related(model)[i] assert o.disorientation(r.related(model)[i]).as_axis_angle(degrees=True,pair=True)[1]<1.0e-5
misorientation = ori.rotation.misorientation(ori2.rotation)
assert misorientation.as_axis_angle(degrees=True)[3]<1.0e-5
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch']) @pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['fcc','bcc']) @pytest.mark.parametrize('lattice',['cF','cI'])
def test_relationship_reference(self,update,reference_dir,model,lattice): def test_relationship_reference(self,update,reference_dir,model,lattice):
reference = os.path.join(reference_dir,f'{lattice}_{model}.txt') reference = reference_dir/f'{lattice}_{model}.txt'
ori = Orientation(Rotation(),lattice) o = Orientation(lattice=lattice)
eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.related(model)]) eu = o.related(model).as_Eulers(degrees=True)
if update: if update:
coords = np.array([(1,i+1) for i,x in enumerate(eu)]) coords = np.array([(1,i+1) for i,x in enumerate(eu)])
table = Table(eu,{'Eulers':(3,)}) Table(eu,{'Eulers':(3,)})\
table = table.add('pos',coords) .add('pos',coords)\
table.save(reference) .save(reference)
assert np.allclose(eu,Table.load(reference).get('Eulers')) assert np.allclose(eu,Table.load(reference).get('Eulers'))
@pytest.mark.parametrize('lattice',Lattice.lattices) def test_basis_real(self):
def test_disorientation360(self,lattice): for gamma in np.random.random(2**8)*np.pi:
R_1 = Orientation(Rotation(),lattice) basis = np.tril(np.random.random((3,3))+1e-6)
R_2 = Orientation(Rotation.from_Eulers([360,0,0],degrees=True),lattice) basis[1,:2] = basis[1,1]*np.array([np.cos(gamma),np.sin(gamma)])
assert np.allclose(R_1.disorientation(R_2).as_matrix(),np.eye(3)) basis[2,:2] = basis[2,:2]*2-1
lengths = np.linalg.norm(basis,axis=-1)
cosines = np.roll(np.einsum('ij,ij->i',basis,np.roll(basis,1,axis=0))/lengths/np.roll(lengths,1),1)
o = Orientation.from_random(lattice='aP',
**dict(zip(['a','b','c'],lengths)),
**dict(zip(['alpha','beta','gamma'],np.arccos(cosines))),
)
assert np.allclose(o.to_frame(uvw=np.eye(3)),basis), 'Lattice basis disagrees with initialization'
@pytest.mark.parametrize('lattice',Lattice.lattices) @pytest.mark.parametrize('lattice,a,b,c,alpha,beta,gamma',
@pytest.mark.parametrize('angle',[10,20,30,40]) [
def test_average(self,angle,lattice): ('aP',0.5,2.0,3.0,0.8,0.5,1.2),
R_1 = Orientation(Rotation.from_axis_angle([0,0,1,10],degrees=True),lattice) ('mP',1.0,2.0,3.0,np.pi/2,0.5,np.pi/2),
R_2 = Orientation(Rotation.from_axis_angle([0,0,1,angle],degrees=True),lattice) ('oI',0.5,1.5,3.0,np.pi/2,np.pi/2,np.pi/2),
avg_angle = R_1.average(R_2).rotation.as_axis_angle(degrees=True,pair=True)[1] ('tP',0.5,0.5,3.0,np.pi/2,np.pi/2,np.pi/2),
assert np.isclose(avg_angle,10+(angle-10)/2.) ('hP',1.0,None,1.6,np.pi/2,np.pi/2,2*np.pi/3),
('cF',1.0,1.0,None,np.pi/2,np.pi/2,np.pi/2),
])
def test_bases_contraction(self,lattice,a,b,c,alpha,beta,gamma):
L = Orientation(lattice=lattice,
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma)
assert np.allclose(np.eye(3),np.einsum('ik,jk',L.basis_real,L.basis_reciprocal))
@pytest.mark.parametrize('lattice',Lattice.lattices) @pytest.mark.parametrize('keyFrame,keyLattice',[('uvw','direction'),('hkl','plane'),])
def test_from_average(self,lattice): @pytest.mark.parametrize('vector',np.array([
R_1 = Orientation(Rotation.from_random(),lattice) [1.,1.,1.],
eqs = [r for r in R_1.equivalent] [-2.,3.,0.5],
R_2 = Orientation.from_average(eqs) [0.,0.,1.],
assert np.allclose(R_1.rotation.quaternion,R_2.rotation.quaternion) [1.,1.,1.],
[2.,2.,2.],
[0.,1.,1.],
]))
@pytest.mark.parametrize('lattice,a,b,c,alpha,beta,gamma',
[
('aP',0.5,2.0,3.0,0.8,0.5,1.2),
('mP',1.0,2.0,3.0,np.pi/2,0.5,np.pi/2),
('oI',0.5,1.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('tP',0.5,0.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('hP',1.0,1.0,1.6,np.pi/2,np.pi/2,2*np.pi/3),
('cF',1.0,1.0,1.0,np.pi/2,np.pi/2,np.pi/2),
])
def test_to_frame_to_lattice(self,lattice,a,b,c,alpha,beta,gamma,vector,keyFrame,keyLattice):
L = Orientation(lattice=lattice,
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma)
assert np.allclose(vector,
L.to_frame(**{keyFrame:L.to_lattice(**{keyLattice:vector})}))
@pytest.mark.parametrize('vector',np.array([
[1,0,0],
[1,1,0],
[1,1,1],
[1,0,-2],
]))
@pytest.mark.parametrize('kw_Miller,kw_Bravais',[('uvw','uvtw'),('hkl','hkil')])
def test_Miller_Bravais_Miller(self,vector,kw_Miller,kw_Bravais):
assert np.all(vector == Orientation.Bravais_to_Miller(**{kw_Bravais:Orientation.Miller_to_Bravais(**{kw_Miller:vector})}))
@pytest.mark.parametrize('vector',np.array([
[1,0,-1,2],
[1,-1,0,3],
[1,1,-2,-3],
[0,0,0,1],
]))
@pytest.mark.parametrize('kw_Miller,kw_Bravais',[('uvw','uvtw'),('hkl','hkil')])
def test_Bravais_Miller_Bravais(self,vector,kw_Miller,kw_Bravais):
assert np.all(vector == Orientation.Miller_to_Bravais(**{kw_Miller:Orientation.Bravais_to_Miller(**{kw_Bravais:vector})}))
@pytest.mark.parametrize('lattice,a,b,c,alpha,beta,gamma',
[
('aP',0.5,2.0,3.0,0.8,0.5,1.2),
('mP',1.0,2.0,3.0,np.pi/2,0.5,np.pi/2),
('oI',0.5,1.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('tP',0.5,0.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('hP',1.0,1.0,1.6,np.pi/2,np.pi/2,2*np.pi/3),
('cF',1.0,1.0,1.0,np.pi/2,np.pi/2,np.pi/2),
])
@pytest.mark.parametrize('kw',['uvw','hkl'])
@pytest.mark.parametrize('with_symmetry',[False,True])
@pytest.mark.parametrize('shape',[None,1,(12,24)])
@pytest.mark.parametrize('vector',[
np.random.random( 3 ),
np.random.random( (4,3)),
np.random.random((4,8,3)),
])
def test_to_pole(self,shape,lattice,a,b,c,alpha,beta,gamma,vector,kw,with_symmetry):
o = Orientation.from_random(shape=shape,
lattice=lattice,
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma)
assert o.to_pole(**{kw:vector,'with_symmetry':with_symmetry}).shape \
== o.shape + (o.symmetry_operations.shape if with_symmetry else ()) + vector.shape
@pytest.mark.parametrize('lattice',['hP','cI','cF'])
def test_Schmid(self,update,reference_dir,lattice):
L = Orientation(lattice=lattice)
for mode in L.kinematics:
reference = reference_dir/f'{lattice}_{mode}.txt'
P = L.Schmid(mode)
if update:
table = Table(P.reshape(-1,9),{'Schmid':(3,3,)})
table.save(reference)
assert np.allclose(P,Table.load(reference).get('Schmid'))

69
python/tests/test_Result.py
View File

@ -94,11 +94,11 @@ class TestResult:
default.pick('invalid',True) default.pick('invalid',True)
def test_add_absolute(self,default): def test_add_absolute(self,default):
default.add_absolute('Fe') default.add_absolute('F_e')
loc = {'Fe': default.get_dataset_location('Fe'), loc = {'F_e': default.get_dataset_location('F_e'),
'|Fe|': default.get_dataset_location('|Fe|')} '|F_e|': default.get_dataset_location('|F_e|')}
in_memory = np.abs(default.read_dataset(loc['Fe'],0)) in_memory = np.abs(default.read_dataset(loc['F_e'],0))
in_file = default.read_dataset(loc['|Fe|'],0) in_file = default.read_dataset(loc['|F_e|'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.parametrize('mode',['direct','function']) @pytest.mark.parametrize('mode',['direct','function'])
@ -168,15 +168,16 @@ class TestResult:
@pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]]) @pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]])
def test_add_IPF_color(self,default,d): def test_add_IPF_color(self,default,d):
default.add_IPF_color('orientation',d) default.add_IPF_color('O',np.array(d))
loc = {'orientation': default.get_dataset_location('orientation'), loc = {'O': default.get_dataset_location('O'),
'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))} 'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))}
qu = default.read_dataset(loc['orientation']).view(np.double).reshape(-1,4) qu = default.read_dataset(loc['O']).view(np.double).squeeze()
crystal_structure = default.get_crystal_structure() crystal_structure = default.get_crystal_structure()
in_memory = np.empty((qu.shape[0],3),np.uint8) c = Orientation(rotation=qu,
for i,q in enumerate(qu): lattice={'fcc':'cF',
o = Orientation(q,crystal_structure).reduced 'bcc':'cI',
in_memory[i] = np.uint8(o.IPF_color(np.array(d))*255) 'hex':'hP'}[crystal_structure])
in_memory = np.uint8(c.IPF_color(c.to_SST(np.array(d)))*255)
in_file = default.read_dataset(loc['color']) in_file = default.read_dataset(loc['color'])
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@ -209,6 +210,22 @@ class TestResult:
in_memory = mechanics.Mises_stress(default.read_dataset(loc['sigma'],0)).reshape(-1,1) in_memory = mechanics.Mises_stress(default.read_dataset(loc['sigma'],0)).reshape(-1,1)
in_file = default.read_dataset(loc['sigma_vM'],0) in_file = default.read_dataset(loc['sigma_vM'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_Mises_invalid(self,default):
default.add_Cauchy('P','F')
default.add_calculation('sigma_y','#sigma#',unit='y')
default.add_Mises('sigma_y')
assert default.get_dataset_location('sigma_y_vM') == []
def test_add_Mises_stress_strain(self,default):
default.add_Cauchy('P','F')
default.add_calculation('sigma_y','#sigma#',unit='y')
default.add_calculation('sigma_x','#sigma#',unit='x')
default.add_Mises('sigma_y',kind='strain')
default.add_Mises('sigma_x',kind='stress')
loc = {'y' :default.get_dataset_location('sigma_y_vM'),
'x' :default.get_dataset_location('sigma_x_vM')}
assert not np.allclose(default.read_dataset(loc['y'],0),default.read_dataset(loc['x'],0))
def test_add_norm(self,default): def test_add_norm(self,default):
default.add_norm('F',1) default.add_norm('F',1)
@ -228,13 +245,14 @@ class TestResult:
in_file = default.read_dataset(loc['S'],0) in_file = default.read_dataset(loc['S'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.skip(reason='requires rework of lattice.f90')
@pytest.mark.parametrize('polar',[True,False]) @pytest.mark.parametrize('polar',[True,False])
def test_add_pole(self,default,polar): def test_add_pole(self,default,polar):
pole = np.array([1.,0.,0.]) pole = np.array([1.,0.,0.])
default.add_pole('orientation',pole,polar) default.add_pole('O',pole,polar)
loc = {'orientation': default.get_dataset_location('orientation'), loc = {'O': default.get_dataset_location('O'),
'pole': default.get_dataset_location('p^{}_[1 0 0)'.format(u'rφ' if polar else 'xy'))} 'pole': default.get_dataset_location('p^{}_[1 0 0)'.format(u'rφ' if polar else 'xy'))}
rot = Rotation(default.read_dataset(loc['orientation']).view(np.double)) rot = Rotation(default.read_dataset(loc['O']).view(np.double))
rotated_pole = rot * np.broadcast_to(pole,rot.shape+(3,)) rotated_pole = rot * np.broadcast_to(pole,rot.shape+(3,))
xy = rotated_pole[:,0:2]/(1.+abs(pole[2])) xy = rotated_pole[:,0:2]/(1.+abs(pole[2]))
in_memory = xy if not polar else \ in_memory = xy if not polar else \
@ -296,7 +314,11 @@ class TestResult:
default.add_Cauchy() default.add_Cauchy()
loc = default.get_dataset_location('sigma') loc = default.get_dataset_location('sigma')
with h5py.File(default.fname,'r') as f: with h5py.File(default.fname,'r') as f:
created_first = f[loc[0]].attrs['Created'].decode() # h5py3 compatibility
try:
created_first = f[loc[0]].attrs['Created'].decode()
except AttributeError:
created_first = f[loc[0]].attrs['Created']
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z') created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
@ -305,9 +327,16 @@ class TestResult:
default.disallow_modification() default.disallow_modification()
time.sleep(2.) time.sleep(2.)
default.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress') try:
default.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress')
except ValueError:
pass
with h5py.File(default.fname,'r') as f: with h5py.File(default.fname,'r') as f:
created_second = f[loc[0]].attrs['Created'].decode() # h5py3 compatibility
try:
created_second = f[loc[0]].attrs['Created'].decode()
except AttributeError:
created_second = f[loc[0]].attrs['Created']
created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z') created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
assert created_first < created_second and np.allclose(default.read_dataset(loc),311.) assert created_first < created_second and np.allclose(default.read_dataset(loc),311.)

69
python/tests/test_Rotation.py
View File

@ -771,6 +771,53 @@ class TestRotation:
def test_random(self,shape): def test_random(self,shape):
Rotation.from_random(shape) Rotation.from_random(shape)
def test_equal(self):
r = Rotation.from_random(seed=0)
assert r == r
def test_unequal(self):
r = Rotation.from_random(seed=0)
assert not (r != r)
def test_inversion(self):
r = Rotation.from_random(seed=0)
assert r == ~~r
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(1,1,1)])
def test_shape(self,shape):
r = Rotation.from_random(shape=shape)
assert r.shape == (shape if isinstance(shape,tuple) else (shape,) if shape else ())
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(3,3,2)])
def test_append(self,shape):
r = Rotation.from_random(shape=shape)
p = Rotation.from_random(shape=shape)
s = r.append(p)
print(f'append 2x {shape} --> {s.shape}')
assert s[0,...] == r[0,...] and s[-1,...] == p[-1,...]
@pytest.mark.parametrize('quat,standardized',[
([-1,0,0,0],[1,0,0,0]),
([-0.5,-0.5,-0.5,-0.5],[0.5,0.5,0.5,0.5]),
])
def test_standardization(self,quat,standardized):
assert Rotation(quat)._standardize() == Rotation(standardized)
@pytest.mark.parametrize('shape,length',[
((2,3,4),2),
(4,4),
((),0)
])
def test_len(self,shape,length):
r = Rotation.from_random(shape=shape)
assert len(r) == length
@pytest.mark.parametrize('shape',[(4,6),(2,3,4),(3,3,3)])
@pytest.mark.parametrize('order',['C','F'])
def test_flatten_reshape(self,shape,order):
r = Rotation.from_random(shape=shape)
assert r == r.flatten(order).reshape(shape,order)
@pytest.mark.parametrize('function',[Rotation.from_quaternion, @pytest.mark.parametrize('function',[Rotation.from_quaternion,
Rotation.from_Eulers, Rotation.from_Eulers,
Rotation.from_axis_angle, Rotation.from_axis_angle,
@ -848,7 +895,8 @@ class TestRotation:
np.random.rand(3,3,3,3)]) np.random.rand(3,3,3,3)])
def test_rotate_identity(self,data): def test_rotate_identity(self,data):
R = Rotation() R = Rotation()
assert np.allclose(data,R*data) print(R,data)
assert np.allclose(data,R@data)
@pytest.mark.parametrize('data',[np.random.rand(3), @pytest.mark.parametrize('data',[np.random.rand(3),
np.random.rand(3,3), np.random.rand(3,3),
@ -860,6 +908,16 @@ class TestRotation:
R_2 = Rotation.from_Eulers(np.array([0.,0.,phi_2])) R_2 = Rotation.from_Eulers(np.array([0.,0.,phi_2]))
assert np.allclose(data,R_2@(R_1@data)) assert np.allclose(data,R_2@(R_1@data))
@pytest.mark.parametrize('pwr',[-10,0,1,2.5,np.pi,np.random.random()])
def test_rotate_power(self,pwr):
R = Rotation.from_random()
axis_angle = R.as_axis_angle()
axis_angle[ 3] = (pwr*axis_angle[-1])%(2.*np.pi)
if axis_angle[3] > np.pi:
axis_angle[3] -= 2.*np.pi
axis_angle *= -1
assert R**pwr == Rotation.from_axis_angle(axis_angle)
def test_rotate_inverse(self): def test_rotate_inverse(self):
R = Rotation.from_random() R = Rotation.from_random()
assert np.allclose(np.eye(3),(~R@R).as_matrix()) assert np.allclose(np.eye(3),(~R@R).as_matrix())
@ -877,7 +935,7 @@ class TestRotation:
def test_rotate_invalid_shape(self,data): def test_rotate_invalid_shape(self,data):
R = Rotation.from_random() R = Rotation.from_random()
with pytest.raises(ValueError): with pytest.raises(ValueError):
R*data R@data
@pytest.mark.parametrize('data',['does_not_work', @pytest.mark.parametrize('data',['does_not_work',
(1,2), (1,2),
@ -885,7 +943,7 @@ class TestRotation:
def test_rotate_invalid_type(self,data): def test_rotate_invalid_type(self,data):
R = Rotation.from_random() R = Rotation.from_random()
with pytest.raises(TypeError): with pytest.raises(TypeError):
R*data R@data
def test_misorientation(self): def test_misorientation(self):
R = Rotation.from_random() R = Rotation.from_random()
@ -898,9 +956,8 @@ class TestRotation:
@pytest.mark.parametrize('angle',[10,20,30,40,50,60,70,80,90,100,120]) @pytest.mark.parametrize('angle',[10,20,30,40,50,60,70,80,90,100,120])
def test_average(self,angle): def test_average(self,angle):
R_1 = Rotation.from_axis_angle([0,0,1,10],degrees=True) R = Rotation.from_axis_angle([[0,0,1,10],[0,0,1,angle]],degrees=True)
R_2 = Rotation.from_axis_angle([0,0,1,angle],degrees=True) avg_angle = R.average().as_axis_angle(degrees=True,pair=True)[1]
avg_angle = R_1.average(R_2).as_axis_angle(degrees=True,pair=True)[1]
assert np.isclose(avg_angle,10+(angle-10)/2.) assert np.isclose(avg_angle,10+(angle-10)/2.)

13
python/tests/test_VTK.py
View File

@ -85,6 +85,12 @@ class TestVTK:
assert(False) assert(False)
@pytest.mark.parametrize('fname',['a','a.vtp','a.b','a.b.vtp'])
def test_filename_variations(self,tmp_path,fname):
points = np.random.rand(102,3)
v = VTK.from_poly_data(points)
v.save(tmp_path/fname)
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk', None), @pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk', None),
('this_file_does_not_exist.vtk','vtk'), ('this_file_does_not_exist.vtk','vtk'),
('this_file_does_not_exist.vtx', None)]) ('this_file_does_not_exist.vtx', None)])
@ -92,9 +98,10 @@ class TestVTK:
with pytest.raises(TypeError): with pytest.raises(TypeError):
VTK.load(name,dataset_type) VTK.load(name,dataset_type)
def test_invalid_extension_write(self,default): def test_add_extension(self,tmp_path,default):
with pytest.raises(ValueError): default.save(tmp_path/'default.txt',parallel=False)
default.save('default.txt') assert os.path.isfile(tmp_path/'default.txt.vtr')
def test_invalid_get(self,default): def test_invalid_get(self,default):
with pytest.raises(ValueError): with pytest.raises(ValueError):

49
python/tests/test_util.py
View File

@ -44,3 +44,52 @@ class TestUtil:
selected = util.hybrid_IA(dist,N_samples) selected = util.hybrid_IA(dist,N_samples)
dist_sampled = np.histogram(centers[selected],bins)[0]/N_samples*np.sum(dist) dist_sampled = np.histogram(centers[selected],bins)[0]/N_samples*np.sum(dist)
assert np.sqrt(((dist - dist_sampled) ** 2).mean()) < .025 and selected.shape[0]==N_samples assert np.sqrt(((dist - dist_sampled) ** 2).mean()) < .025 and selected.shape[0]==N_samples
@pytest.mark.parametrize('point,normalize,answer',
[
([1,0,0],False,[1,0,0]),
([1,0,0],True, [1,0,0]),
([0,1,1],False,[0,0.5,0]),
([0,1,1],True, [0,0.41421356,0]),
([1,1,1],False,[0.5,0.5,0]),
([1,1,1],True, [0.3660254, 0.3660254, 0]),
])
def test_project_stereographic(self,point,normalize,answer):
assert np.allclose(util.project_stereographic(np.array(point),normalize=normalize),answer)
@pytest.mark.parametrize('fro,to,mode,answer',
[
((),(1,),'left',(1,)),
((1,),(7,),'right',(1,)),
((1,2),(1,1,2,2),'right',(1,1,2,1)),
((1,2),(1,1,2,2),'left',(1,1,1,2)),
((1,2,3),(1,1,2,3,4),'right',(1,1,2,3,1)),
((10,2),(10,3,2,2,),'right',(10,1,2,1)),
((10,2),(10,3,2,2,),'left',(10,1,1,2)),
((2,2,3),(2,2,2,3,4),'left',(1,2,2,3,1)),
((2,2,3),(2,2,2,3,4),'right',(2,2,1,3,1)),
])
def test_shapeshifter(self,fro,to,mode,answer):
assert util.shapeshifter(fro,to,mode) == answer
@pytest.mark.parametrize('fro,to,mode',
[
((10,3,4),(10,3,2,2),'left'),
((2,3),(10,3,2,2),'right'),
])
def test_invalid_shapeshifter(self,fro,to,mode):
with pytest.raises(ValueError):
util.shapeshifter(fro,to,mode)
@pytest.mark.parametrize('a,b,answer',
[
((),(1,),(1,)),
((1,),(),(1,)),
((1,),(7,),(1,7)),
((2,),(2,2),(2,2)),
((1,2),(2,2),(1,2,2)),
((1,2,3),(2,3,4),(1,2,3,4)),
((1,2,3),(1,2,3),(1,2,3)),
])
def test_shapeblender(self,a,b,answer):
assert util.shapeblender(a,b) == answer

246
src/HDF5_utilities.f90
View File

@ -12,11 +12,10 @@ module HDF5_utilities
use prec use prec
use parallelization use parallelization
use IO
use rotations use rotations
implicit none implicit none
public public
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief reads integer or float data of defined shape from file ! ToDo: order of arguments wrong !> @brief reads integer or float data of defined shape from file ! ToDo: order of arguments wrong
@ -93,15 +92,15 @@ subroutine HDF5_utilities_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!initialize HDF5 library and check if integer and float type size match !initialize HDF5 library and check if integer and float type size match
call h5open_f(hdferr) call h5open_f(hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_Utilities_init: h5open_f') if(hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr) call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_Utilities_init: h5tget_size_f (int)') if(hdferr < 0) error stop 'HDF5 error'
if (int(bit_size(0),SIZE_T)/=typeSize*8) & if (int(bit_size(0),SIZE_T)/=typeSize*8) &
error stop 'Default integer size does not match H5T_NATIVE_INTEGER' error stop 'Default integer size does not match H5T_NATIVE_INTEGER'
call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr) call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_Utilities_init: h5tget_size_f (double)') if(hdferr < 0) error stop 'HDF5 error'
if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) & if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) &
error stop 'pReal does not match H5T_NATIVE_DOUBLE' error stop 'pReal does not match H5T_NATIVE_DOUBLE'
@ -128,30 +127,30 @@ integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
endif endif
call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr) call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5pcreate_f') if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSc #ifdef PETSc
if (present(parallel)) then; if (parallel) then if (present(parallel)) then; if (parallel) then
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr) call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5pset_fapl_mpio_f') if(hdferr < 0) error stop 'HDF5 error'
endif; endif endif; endif
#endif #endif
if (m == 'w') then if (m == 'w') then
call h5fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id) call h5fcreate_f(fileName,H5F_ACC_TRUNC_F,HDF5_openFile,hdferr,access_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5fcreate_f (w)') if(hdferr < 0) error stop 'HDF5 error'
elseif(m == 'a') then elseif(m == 'a') then
call h5fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id) call h5fopen_f(fileName,H5F_ACC_RDWR_F,HDF5_openFile,hdferr,access_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5fopen_f (a)') if(hdferr < 0) error stop 'HDF5 error'
elseif(m == 'r') then elseif(m == 'r') then
call h5fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id) call h5fopen_f(fileName,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr,access_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5fopen_f (r)') if(hdferr < 0) error stop 'HDF5 error'
else else
call IO_error(1,ext_msg='HDF5_openFile: h5fopen_f unknown access mode: '//trim(m)) error stop 'unknown access mode'
endif endif
call h5pclose_f(plist_id, hdferr) call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5pclose_f') if(hdferr < 0) error stop 'HDF5 error'
end function HDF5_openFile end function HDF5_openFile
@ -166,7 +165,7 @@ subroutine HDF5_closeFile(fileHandle)
integer :: hdferr integer :: hdferr
call h5fclose_f(fileHandle,hdferr) call h5fclose_f(fileHandle,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_closeFile: h5fclose_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_closeFile end subroutine HDF5_closeFile
@ -185,19 +184,19 @@ integer(HID_T) function HDF5_addGroup(fileHandle,groupName)
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_addGroup: h5pcreate_f ('//trim(groupName)//')') if(hdferr < 0) error stop 'HDF5 error'
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! setting I/O mode to collective ! setting I/O mode to collective
#ifdef PETSc #ifdef PETSc
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_addGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')') if(hdferr < 0) error stop 'HDF5 error'
#endif #endif
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! Create group ! Create group
call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id) call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_addGroup: h5gcreate_f ('//trim(groupName)//')') if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(aplist_id,hdferr) call h5pclose_f(aplist_id,hdferr)
@ -221,19 +220,19 @@ integer(HID_T) function HDF5_openGroup(fileHandle,groupName)
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for data access properties ! creating a property list for data access properties
call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_openGroup: h5pcreate_f ('//trim(groupName)//')') if(hdferr < 0) error stop 'HDF5 error'
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! setting I/O mode to collective ! setting I/O mode to collective
#ifdef PETSc #ifdef PETSc
call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr) call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_openGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')') if(hdferr < 0) error stop 'HDF5 error'
#endif #endif
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! opening the group ! opening the group
call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id) call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_openGroup: h5gopen_f ('//trim(groupName)//')') if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(aplist_id,hdferr) call h5pclose_f(aplist_id,hdferr)
@ -250,7 +249,7 @@ subroutine HDF5_closeGroup(group_id)
integer :: hdferr integer :: hdferr
call h5gclose_f(group_id, hdferr) call h5gclose_f(group_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = int(group_id)) if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_closeGroup end subroutine HDF5_closeGroup
@ -273,11 +272,11 @@ logical function HDF5_objectExists(loc_id,path)
endif endif
call h5lexists_f(loc_id, p, HDF5_objectExists, hdferr) call h5lexists_f(loc_id, p, HDF5_objectExists, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_objectExists: h5oexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
if(HDF5_objectExists) then if(HDF5_objectExists) then
call h5oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr) call h5oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_objectExists: h5oexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
end function HDF5_objectExists end function HDF5_objectExists
@ -296,6 +295,8 @@ subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path)
logical :: attrExists logical :: attrExists
integer :: hdferr integer :: hdferr
character(len=:), allocatable :: p character(len=:), allocatable :: p
character(len=:,kind=C_CHAR), allocatable,target :: attrValue_
type(c_ptr), target, dimension(1) :: ptr
if (present(path)) then if (present(path)) then
p = trim(path) p = trim(path)
@ -303,28 +304,29 @@ subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path)
p = '.' p = '.'
endif endif
attrValue_ = trim(attrValue)//C_NULL_CHAR
ptr(1) = c_loc(attrValue_)
call h5screate_f(H5S_SCALAR_F,space_id,hdferr) call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5screate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr) call h5tcopy_f(H5T_STRING, type_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5tcopy_f') if(hdferr < 0) error stop 'HDF5 error'
call h5tset_size_f(type_id, int(len_trim(attrValue),HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5tset_size_f')
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5aexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5adelete_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5acreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, type_id, trim(attrValue), int([1],HSIZE_T), hdferr) call h5awrite_f(attr_id, type_id, c_loc(ptr(1)), hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5awrite_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr) call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5aclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(type_id,hdferr) call h5tclose_f(type_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5tclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr) call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5sclose_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_str end subroutine HDF5_addAttribute_str
@ -351,21 +353,21 @@ subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path)
endif endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr) call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5screate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5aexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5adelete_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5acreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr) call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5awrite_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr) call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5tclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr) call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5sclose_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_int end subroutine HDF5_addAttribute_int
@ -392,21 +394,21 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path)
endif endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr) call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5screate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5aexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5adelete_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5acreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr) call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5awrite_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr) call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5tclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr) call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5sclose_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_real end subroutine HDF5_addAttribute_real
@ -436,21 +438,21 @@ subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path)
array_size = size(attrValue,kind=HSIZE_T) array_size = size(attrValue,kind=HSIZE_T)
call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) call h5screate_simple_f(1, array_size, space_id, hdferr, array_size)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5screate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5aexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5adelete_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5acreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr) call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5awrite_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr) call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5tclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr) call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5sclose_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_int_array end subroutine HDF5_addAttribute_int_array
@ -480,21 +482,21 @@ subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path)
array_size = size(attrValue,kind=HSIZE_T) array_size = size(attrValue,kind=HSIZE_T)
call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) call h5screate_simple_f(1, array_size, space_id, hdferr, array_size)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5screate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5aexists_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
if (attrExists) then if (attrExists) then
call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5adelete_by_name_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5acreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr) call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5awrite_f') if(hdferr < 0) error stop 'HDF5 error'
call h5aclose_f(attr_id,hdferr) call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5tclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(space_id,hdferr) call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int_array: h5sclose_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_addAttribute_real_array end subroutine HDF5_addAttribute_real_array
@ -510,13 +512,13 @@ subroutine HDF5_setLink(loc_id,target_name,link_name)
logical :: linkExists logical :: linkExists
call h5lexists_f(loc_id, link_name,linkExists, hdferr) call h5lexists_f(loc_id, link_name,linkExists, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_setLink: h5lexists_soft_f ('//trim(link_name)//')') if(hdferr < 0) error stop 'HDF5 error'
if (linkExists) then if (linkExists) then
call h5ldelete_f(loc_id,link_name, hdferr) call h5ldelete_f(loc_id,link_name, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_setLink: h5ldelete_soft_f ('//trim(link_name)//')') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call h5lcreate_soft_f(target_name, loc_id, link_name, hdferr) call h5lcreate_soft_f(target_name, loc_id, link_name, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_setLink: h5lcreate_soft_f ('//trim(target_name)//' '//trim(link_name)//')') if(hdferr < 0) error stop 'HDF5 error'
end subroutine HDF5_setLink end subroutine HDF5_setLink
@ -555,7 +557,7 @@ subroutine HDF5_read_real1(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real1: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -595,7 +597,7 @@ subroutine HDF5_read_real2(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real2: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -635,7 +637,7 @@ subroutine HDF5_read_real3(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real3: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -675,7 +677,7 @@ subroutine HDF5_read_real4(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real4: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -715,7 +717,7 @@ subroutine HDF5_read_real5(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real5: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -755,7 +757,7 @@ subroutine HDF5_read_real6(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real6: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -795,7 +797,7 @@ subroutine HDF5_read_real7(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real7: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -837,7 +839,7 @@ subroutine HDF5_read_int1(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int1: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -877,7 +879,7 @@ subroutine HDF5_read_int2(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int2: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -917,7 +919,7 @@ subroutine HDF5_read_int3(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int3: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -957,7 +959,7 @@ subroutine HDF5_read_int4(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int4: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -997,7 +999,7 @@ subroutine HDF5_read_int5(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int5: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -1037,7 +1039,7 @@ subroutine HDF5_read_int6(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int6: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -1077,7 +1079,7 @@ subroutine HDF5_read_int7(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,& call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id) file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int7: h5dread_f') if(hdferr < 0) error stop 'HDF5 error'
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id) call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
@ -1118,7 +1120,7 @@ subroutine HDF5_write_real1(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real1: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1159,7 +1161,7 @@ subroutine HDF5_write_real2(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real2: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1200,7 +1202,7 @@ subroutine HDF5_write_real3(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real3: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1241,7 +1243,7 @@ subroutine HDF5_write_real4(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real4: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1283,7 +1285,7 @@ subroutine HDF5_write_real5(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real5: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1324,7 +1326,7 @@ subroutine HDF5_write_real6(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real6: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1365,7 +1367,7 @@ subroutine HDF5_write_real7(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real7: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1407,7 +1409,7 @@ subroutine HDF5_write_int1(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int1: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1448,7 +1450,7 @@ subroutine HDF5_write_int2(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int2: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1489,7 +1491,7 @@ subroutine HDF5_write_int3(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int3: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1530,7 +1532,7 @@ subroutine HDF5_write_int4(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int4: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1571,7 +1573,7 @@ subroutine HDF5_write_int5(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int5: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1612,7 +1614,7 @@ subroutine HDF5_write_int6(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int6: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1653,7 +1655,7 @@ subroutine HDF5_write_int7(loc_id,dataset,datasetName,parallel)
if (product(totalShape) /= 0) then if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int7: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1729,7 +1731,7 @@ subroutine HDF5_write_rotation(loc_id,dataset,datasetName,parallel)
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
call h5dwrite_f(dset_id, z_id,dataset_asArray(4,:),int(totalShape,HSIZE_T), hdferr,& call h5dwrite_f(dset_id, z_id,dataset_asArray(4,:),int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_rotation: h5dwrite_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id) call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
@ -1762,7 +1764,7 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective for MPI) ! creating a property list for transfer properties (is collective for MPI)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f') if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
readSize = 0 readSize = 0
@ -1770,9 +1772,9 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
#ifdef PETSc #ifdef PETSc
if (parallel) then if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pset_dxpl_mpio_f') 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_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894,ext_msg='initialize_read: MPI_allreduce') if (ierr /= 0) error stop 'MPI error'
endif endif
#endif #endif
myStart = int(0,HSIZE_T) myStart = int(0,HSIZE_T)
@ -1782,28 +1784,28 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) ! create dataspace in memory (local shape)
call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape) call h5screate_simple_f(size(localShape), localShape, memspace_id, hdferr, localShape)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5screate_simple_f/memspace_id') if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! creating a property list for IO and set it to collective ! creating a property list for IO and set it to collective
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr) call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f') if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSc #ifdef PETSc
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr) call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pset_all_coll_metadata_ops_f') if(hdferr < 0) error stop 'HDF5 error'
#endif #endif
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! open the dataset in the file and get the space ID ! open the dataset in the file and get the space ID
call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id) call h5dopen_f(loc_id,datasetName,dset_id,hdferr, dapl_id = aplist_id)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5dopen_f') if(hdferr < 0) error stop 'HDF5 error'
call h5dget_space_f(dset_id, filespace_id, hdferr) call h5dget_space_f(dset_id, filespace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5dget_space_f') if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! select a hyperslab (the portion of the current process) in the file ! select a hyperslab (the portion of the current process) in the file
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, localShape, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5sselect_hyperslab_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine initialize_read end subroutine initialize_read
@ -1817,15 +1819,15 @@ subroutine finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer :: hdferr integer :: hdferr
call h5pclose_f(plist_id, hdferr) call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: plist_id') if(hdferr < 0) error stop 'HDF5 error'
call h5pclose_f(aplist_id, hdferr) call h5pclose_f(aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: aplist_id') if(hdferr < 0) error stop 'HDF5 error'
call h5dclose_f(dset_id, hdferr) call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5dclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(filespace_id, hdferr) call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5sclose_f/filespace_id') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(memspace_id, hdferr) call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_read: h5sclose_f/memspace_id') if(hdferr < 0) error stop 'HDF5 error'
end subroutine finalize_read end subroutine finalize_read
@ -1856,11 +1858,11 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective when reading in parallel) ! creating a property list for transfer properties (is collective when reading in parallel)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5pcreate_f') if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSc #ifdef PETSc
if (parallel) then if (parallel) then
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5pset_dxpl_mpio_f') if(hdferr < 0) error stop 'HDF5 error'
endif endif
#endif #endif
@ -1871,7 +1873,7 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
#ifdef PETSc #ifdef PETSc
if (parallel) then 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_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process
if (ierr /= 0) call IO_error(894,ext_msg='initialize_write: MPI_allreduce') if (ierr /= 0) error stop 'MPI error'
endif endif
#endif #endif
myStart = int(0,HSIZE_T) myStart = int(0,HSIZE_T)
@ -1881,16 +1883,16 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape) and in file (global shape) ! create dataspace in memory (local shape) and in file (global shape)
call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape) call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dopen_f') if(hdferr < 0) error stop 'HDF5 error'
call h5screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape) call h5screate_simple_f(size(totalShape), totalShape, filespace_id, hdferr, totalShape)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dget_space_f') if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataset in the file and select a hyperslab from it (the portion of the current process) ! create dataset in the file and select a hyperslab from it (the portion of the current process)
call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr) call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5dcreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_write: h5sselect_hyperslab_f') if(hdferr < 0) error stop 'HDF5 error'
end subroutine initialize_write end subroutine initialize_write
@ -1904,13 +1906,13 @@ subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id)
integer :: hdferr integer :: hdferr
call h5pclose_f(plist_id, hdferr) call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: plist_id') if(hdferr < 0) error stop 'HDF5 error'
call h5dclose_f(dset_id, hdferr) call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5dclose_f') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(filespace_id, hdferr) call h5sclose_f(filespace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5sclose_f/filespace_id') if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(memspace_id, hdferr) call h5sclose_f(memspace_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='finalize_write: h5sclose_f/memspace_id') if(hdferr < 0) error stop 'HDF5 error'
end subroutine finalize_write end subroutine finalize_write

43
src/IO.f90
View File

@ -367,12 +367,8 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
! file handling errors ! file handling errors
case (100) case (100)
msg = 'could not open file:' msg = 'could not open file:'
case (101)
msg = 'write error for file:'
case (102) case (102)
msg = 'could not read file:' msg = 'could not read file:'
case (106)
msg = 'working directory does not exist:'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! file parsing errors ! file parsing errors
@ -395,14 +391,10 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
msg = 'hex lattice structure with invalid c/a ratio' msg = 'hex lattice structure with invalid c/a ratio'
case (132) case (132)
msg = 'trans_lattice_structure not possible' msg = 'trans_lattice_structure not possible'
case (133)
msg = 'transformed hex lattice structure with invalid c/a ratio'
case (134) case (134)
msg = 'negative lattice parameter' msg = 'negative lattice parameter'
case (135) case (135)
msg = 'zero entry on stiffness diagonal' msg = 'zero entry on stiffness diagonal'
case (136)
msg = 'zero entry on stiffness diagonal for transformed phase'
case (137) case (137)
msg = 'not defined for lattice structure' msg = 'not defined for lattice structure'
case (138) case (138)
@ -431,8 +423,6 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
! material error messages and related messages in mesh ! material error messages and related messages in mesh
case (150) case (150)
msg = 'index out of bounds' msg = 'index out of bounds'
case (151)
msg = 'material has no constituents'
case (153) case (153)
msg = 'sum of phase fractions differs from 1' msg = 'sum of phase fractions differs from 1'
case (155) case (155)
@ -463,10 +453,6 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! math errors ! math errors
case (400)
msg = 'matrix inversion error'
case (401)
msg = 'error in Eigenvalue calculation'
case (402) case (402)
msg = 'invalid orientation specified' msg = 'invalid orientation specified'
@ -499,10 +485,6 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
!------------------------------------------------------------------------------------------------- !-------------------------------------------------------------------------------------------------
! errors related to the grid solver ! errors related to the grid solver
case (809)
msg = 'initializing FFTW'
case (810)
msg = 'FFTW plan creation'
case (831) case (831)
msg = 'mask consistency violated in grid load case' msg = 'mask consistency violated in grid load case'
case (832) case (832)
@ -587,45 +569,20 @@ subroutine IO_warning(warning_ID,el,ip,g,ext_msg)
character(len=pStringLen) :: formatString character(len=pStringLen) :: formatString
select case (warning_ID) select case (warning_ID)
case (1)
msg = 'unknown key'
case (34)
msg = 'invalid restart increment given'
case (35)
msg = 'could not get $DAMASK_NUM_THREADS'
case (40)
msg = 'found spectral solver parameter'
case (42) case (42)
msg = 'parameter has no effect' msg = 'parameter has no effect'
case (43)
msg = 'main diagonal of C66 close to zero'
case (47) case (47)
msg = 'no valid parameter for FFTW, using FFTW_PATIENT' msg = 'no valid parameter for FFTW, using FFTW_PATIENT'
case (50)
msg = 'not all available slip system families are defined'
case (51)
msg = 'not all available twin system families are defined'
case (52)
msg = 'not all available parameters are defined'
case (53)
msg = 'not all available transformation system families are defined'
case (101)
msg = 'crystallite debugging off'
case (201)
msg = 'position not found when parsing line'
case (207) case (207)
msg = 'line truncated' msg = 'line truncated'
case (600) case (600)
msg = 'crystallite responds elastically' msg = 'crystallite responds elastically'
case (601) case (601)
msg = 'stiffness close to zero' msg = 'stiffness close to zero'
case (650)
msg = 'polar decomposition failed'
case (700) case (700)
msg = 'unknown crystal symmetry' msg = 'unknown crystal symmetry'
case (709) case (709)
msg = 'read only the first document' msg = 'read only the first document'
case (850) case (850)
msg = 'max number of cut back exceeded, terminating' msg = 'max number of cut back exceeded, terminating'
case default case default

2
src/commercialFEM_fileList.f90
View File

@ -25,7 +25,7 @@
#include "material.f90" #include "material.f90"
#include "lattice.f90" #include "lattice.f90"
#include "constitutive.f90" #include "constitutive.f90"
#include "constitutive_plastic.f90" #include "constitutive_mech.f90"
#include "constitutive_plastic_none.f90" #include "constitutive_plastic_none.f90"
#include "constitutive_plastic_isotropic.f90" #include "constitutive_plastic_isotropic.f90"
#include "constitutive_plastic_phenopowerlaw.f90" #include "constitutive_plastic_phenopowerlaw.f90"

148
src/constitutive.f90
View File

@ -19,7 +19,7 @@ module constitutive
implicit none implicit none
private private
integer(kind(ELASTICITY_undefined_ID)), dimension(:), allocatable, protected :: & integer(kind(ELASTICITY_undefined_ID)), dimension(:), allocatable :: & !ToDo: old intel compiler complains about protected
phase_elasticity !< elasticity of each phase phase_elasticity !< elasticity of each phase
integer(kind(PLASTICITY_undefined_ID)), dimension(:), allocatable :: & !ToDo: old intel compiler complains about protected integer(kind(PLASTICITY_undefined_ID)), dimension(:), allocatable :: & !ToDo: old intel compiler complains about protected
@ -52,8 +52,8 @@ module constitutive
interface interface
module subroutine plastic_init module subroutine mech_init
end subroutine plastic_init end subroutine mech_init
module subroutine damage_init module subroutine damage_init
end subroutine damage_init end subroutine damage_init
@ -343,6 +343,25 @@ module constitutive
end interface constitutive_dependentState end interface constitutive_dependentState
interface constitutive_SandItsTangents
module subroutine constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, Fe, Fi, ipc, ip, el)
integer, intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), intent(in), dimension(3,3) :: &
Fe, & !< elastic deformation gradient
Fi !< intermediate deformation gradient
real(pReal), intent(out), dimension(3,3) :: &
S !< 2nd Piola-Kirchhoff stress tensor
real(pReal), intent(out), dimension(3,3,3,3) :: &
dS_dFe, & !< derivative of 2nd P-K stress with respect to elastic deformation gradient
dS_dFi !< derivative of 2nd P-K stress with respect to intermediate deformation gradient
end subroutine constitutive_hooke_SandItsTangents
end interface constitutive_SandItsTangents
type :: tDebugOptions type :: tDebugOptions
logical :: & logical :: &
@ -385,14 +404,10 @@ subroutine constitutive_init
integer :: & integer :: &
p, & !< counter in phase loop p, & !< counter in phase loop
s, & !< counter in source loop s !< counter in source loop
stiffDegradationCtr
class (tNode), pointer :: & class (tNode), pointer :: &
debug_constitutive, & debug_constitutive, &
phases, & phases
phase, &
elastic, &
stiffDegradation
debug_constitutive => config_debug%get('constitutive', defaultVal=emptyList) debug_constitutive => config_debug%get('constitutive', defaultVal=emptyList)
debugConstitutive%basic = debug_constitutive%contains('basic') debugConstitutive%basic = debug_constitutive%contains('basic')
@ -402,52 +417,15 @@ subroutine constitutive_init
debugConstitutive%ip = config_debug%get_asInt('integrationpoint',defaultVal = 1) debugConstitutive%ip = config_debug%get_asInt('integrationpoint',defaultVal = 1)
debugConstitutive%grain = config_debug%get_asInt('grain',defaultVal = 1) debugConstitutive%grain = config_debug%get_asInt('grain',defaultVal = 1)
!-------------------------------------------------------------------------------------------------
! initialize elasticity (hooke) !ToDO: Maybe move to elastic submodule along with function homogenizedC?
phases => config_material%get('phase')
allocate(phase_elasticity(phases%length), source = ELASTICITY_undefined_ID)
allocate(phase_elasticityInstance(phases%length), source = 0)
allocate(phase_NstiffnessDegradations(phases%length),source=0)
do p = 1, phases%length
phase => phases%get(p)
elastic => phase%get('elasticity')
if(elastic%get_asString('type') == 'hooke') then
phase_elasticity(p) = ELASTICITY_HOOKE_ID
else
call IO_error(200,ext_msg=elastic%get_asString('type'))
endif
stiffDegradation => phase%get('stiffness_degradation',defaultVal=emptyList) ! check for stiffness degradation mechanisms
phase_NstiffnessDegradations(p) = stiffDegradation%length
enddo
allocate(phase_stiffnessDegradation(maxval(phase_NstiffnessDegradations),phases%length), &
source=STIFFNESS_DEGRADATION_undefined_ID)
if(maxVal(phase_NstiffnessDegradations)/=0) then
do p = 1, phases%length
phase => phases%get(p)
stiffDegradation => phase%get('stiffness_degradation',defaultVal=emptyList)
do stiffDegradationCtr = 1, stiffDegradation%length
if(stiffDegradation%get_asString(stiffDegradationCtr) == 'damage') &
phase_stiffnessDegradation(stiffDegradationCtr,p) = STIFFNESS_DEGRADATION_damage_ID
enddo
enddo
endif
do p = 1, phases%length
phase_elasticityInstance(p) = count(phase_elasticity(1:p) == phase_elasticity(p))
enddo
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! initialize constitutive laws ! initialize constitutive laws
call plastic_init call mech_init
call damage_init call damage_init
call thermal_init call thermal_init
print'(/,a)', ' <<<+- constitutive init -+>>>'; flush(IO_STDOUT) print'(/,a)', ' <<<+- constitutive init -+>>>'; flush(IO_STDOUT)
phases => config_material%get('phase')
constitutive_source_maxSizeDotState = 0 constitutive_source_maxSizeDotState = 0
PhaseLoop2:do p = 1,phases%length PhaseLoop2:do p = 1,phases%length
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -666,80 +644,6 @@ pure function constitutive_initialFi(ipc, ip, el)
end function constitutive_initialFi end function constitutive_initialFi
!--------------------------------------------------------------------------------------------------
!> @brief returns the 2nd Piola-Kirchhoff stress tensor and its tangent with respect to
!> the elastic/intermediate deformation gradients depending on the selected elastic law
!! (so far no case switch because only Hooke is implemented)
!--------------------------------------------------------------------------------------------------
subroutine constitutive_SandItsTangents(S, dS_dFe, dS_dFi, Fe, Fi, ipc, ip, el)
integer, intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), intent(in), dimension(3,3) :: &
Fe, & !< elastic deformation gradient
Fi !< intermediate deformation gradient
real(pReal), intent(out), dimension(3,3) :: &
S !< 2nd Piola-Kirchhoff stress tensor
real(pReal), intent(out), dimension(3,3,3,3) :: &
dS_dFe, & !< derivative of 2nd P-K stress with respect to elastic deformation gradient
dS_dFi !< derivative of 2nd P-K stress with respect to intermediate deformation gradient
call constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, Fe, Fi, ipc, ip, el)
end subroutine constitutive_SandItsTangents
!--------------------------------------------------------------------------------------------------
!> @brief returns the 2nd Piola-Kirchhoff stress tensor and its tangent with respect to
!> the elastic and intermediate deformation gradients using Hooke's law
!--------------------------------------------------------------------------------------------------
subroutine constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, &
Fe, Fi, ipc, ip, el)
integer, intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), intent(in), dimension(3,3) :: &
Fe, & !< elastic deformation gradient
Fi !< intermediate deformation gradient
real(pReal), intent(out), dimension(3,3) :: &
S !< 2nd Piola-Kirchhoff stress tensor in lattice configuration
real(pReal), intent(out), dimension(3,3,3,3) :: &
dS_dFe, & !< derivative of 2nd P-K stress with respect to elastic deformation gradient
dS_dFi !< derivative of 2nd P-K stress with respect to intermediate deformation gradient
real(pReal), dimension(3,3) :: E
real(pReal), dimension(3,3,3,3) :: C
integer :: &
ho, & !< homogenization
d !< counter in degradation loop
integer :: &
i, j
ho = material_homogenizationAt(el)
C = math_66toSym3333(constitutive_homogenizedC(ipc,ip,el))
DegradationLoop: do d = 1, phase_NstiffnessDegradations(material_phaseAt(ipc,el))
degradationType: select case(phase_stiffnessDegradation(d,material_phaseAt(ipc,el)))
case (STIFFNESS_DEGRADATION_damage_ID) degradationType
C = C * damage(ho)%p(damageMapping(ho)%p(ip,el))**2
end select degradationType
enddo DegradationLoop
E = 0.5_pReal*(matmul(transpose(Fe),Fe)-math_I3) !< Green-Lagrange strain in unloaded configuration
S = math_mul3333xx33(C,matmul(matmul(transpose(Fi),E),Fi)) !< 2PK stress in lattice configuration in work conjugate with GL strain pulled back to lattice configuration
do i =1, 3;do j=1,3
dS_dFe(i,j,1:3,1:3) = matmul(Fe,matmul(matmul(Fi,C(i,j,1:3,1:3)),transpose(Fi))) !< dS_ij/dFe_kl = C_ijmn * Fi_lm * Fi_on * Fe_ko
dS_dFi(i,j,1:3,1:3) = 2.0_pReal*matmul(matmul(E,Fi),C(i,j,1:3,1:3)) !< dS_ij/dFi_kl = C_ijln * E_km * Fe_mn
enddo; enddo
end subroutine constitutive_hooke_SandItsTangents
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief contains the constitutive equation for calculating the rate of change of microstructure !> @brief contains the constitutive equation for calculating the rate of change of microstructure
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

114
src/constitutive_plastic.f90 → src/constitutive_mech.f90
View File

@ -1,7 +1,7 @@
!---------------------------------------------------------------------------------------------------- !----------------------------------------------------------------------------------------------------
!> @brief internal microstructure state for all plasticity constitutive models !> @brief internal microstructure state for all plasticity constitutive models
!---------------------------------------------------------------------------------------------------- !----------------------------------------------------------------------------------------------------
submodule(constitutive) constitutive_plastic submodule(constitutive) constitutive_mech
interface interface
@ -191,17 +191,60 @@ contains
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief Initialize constitutive models for plasticity !> @brief Initialize mechanical field related constitutive models
!> @details Initialize elasticity, plasticity and stiffness degradation models.
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
module subroutine plastic_init module subroutine mech_init
integer :: p integer :: &
class(tNode), pointer :: phases p, &
stiffDegradationCtr
class(tNode), pointer :: &
phases, &
phase, &
mech, &
elastic, &
stiffDegradation
print'(/,a)', ' <<<+- constitutive_plastic init -+>>>' print'(/,a)', ' <<<+- constitutive_mech init -+>>>'
!-------------------------------------------------------------------------------------------------
! initialize elasticity (hooke) !ToDO: Maybe move to elastic submodule along with function homogenizedC?
phases => config_material%get('phase') phases => config_material%get('phase')
allocate(phase_elasticity(phases%length), source = ELASTICITY_undefined_ID)
allocate(phase_elasticityInstance(phases%length), source = 0)
allocate(phase_NstiffnessDegradations(phases%length),source=0)
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
elastic => mech%get('elasticity')
if(elastic%get_asString('type') == 'hooke') then
phase_elasticity(p) = ELASTICITY_HOOKE_ID
else
call IO_error(200,ext_msg=elastic%get_asString('type'))
endif
stiffDegradation => mech%get('stiffness_degradation',defaultVal=emptyList) ! check for stiffness degradation mechanisms
phase_NstiffnessDegradations(p) = stiffDegradation%length
enddo
allocate(phase_stiffnessDegradation(maxval(phase_NstiffnessDegradations),phases%length), &
source=STIFFNESS_DEGRADATION_undefined_ID)
if(maxVal(phase_NstiffnessDegradations)/=0) then
do p = 1, phases%length
phase => phases%get(p)
mech => phase%get('mech')
stiffDegradation => mech%get('stiffness_degradation',defaultVal=emptyList)
do stiffDegradationCtr = 1, stiffDegradation%length
if(stiffDegradation%get_asString(stiffDegradationCtr) == 'damage') &
phase_stiffnessDegradation(stiffDegradationCtr,p) = STIFFNESS_DEGRADATION_damage_ID
enddo
enddo
endif
! initialize plasticity
allocate(plasticState(phases%length)) allocate(plasticState(phases%length))
allocate(phase_plasticity(phases%length),source = PLASTICITY_undefined_ID) allocate(phase_plasticity(phases%length),source = PLASTICITY_undefined_ID)
allocate(phase_plasticityInstance(phases%length),source = 0) allocate(phase_plasticityInstance(phases%length),source = 0)
@ -216,11 +259,11 @@ module subroutine plastic_init
where(plastic_nonlocal_init()) phase_plasticity = PLASTICITY_NONLOCAL_ID where(plastic_nonlocal_init()) phase_plasticity = PLASTICITY_NONLOCAL_ID
do p = 1, phases%length do p = 1, phases%length
phase_elasticityInstance(p) = count(phase_elasticity(1:p) == phase_elasticity(p))
phase_plasticityInstance(p) = count(phase_plasticity(1:p) == phase_plasticity(p)) phase_plasticityInstance(p) = count(phase_plasticity(1:p) == phase_plasticity(p))
enddo enddo
end subroutine mech_init
end subroutine plastic_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -234,6 +277,7 @@ module function plastic_active(plastic_label) result(active_plastic)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
integer :: p integer :: p
@ -241,13 +285,62 @@ module function plastic_active(plastic_label) result(active_plastic)
allocate(active_plastic(phases%length), source = .false. ) allocate(active_plastic(phases%length), source = .false. )
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
pl => phase%get('plasticity') mech => phase%get('mech')
pl => mech%get('plasticity')
if(pl%get_asString('type') == plastic_label) active_plastic(p) = .true. if(pl%get_asString('type') == plastic_label) active_plastic(p) = .true.
enddo enddo
end function plastic_active end function plastic_active
!--------------------------------------------------------------------------------------------------
!> @brief returns the 2nd Piola-Kirchhoff stress tensor and its tangent with respect to
!> the elastic and intermediate deformation gradients using Hooke's law
!--------------------------------------------------------------------------------------------------
module subroutine constitutive_hooke_SandItsTangents(S, dS_dFe, dS_dFi, &
Fe, Fi, ipc, ip, el)
integer, intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
real(pReal), intent(in), dimension(3,3) :: &
Fe, & !< elastic deformation gradient
Fi !< intermediate deformation gradient
real(pReal), intent(out), dimension(3,3) :: &
S !< 2nd Piola-Kirchhoff stress tensor in lattice configuration
real(pReal), intent(out), dimension(3,3,3,3) :: &
dS_dFe, & !< derivative of 2nd P-K stress with respect to elastic deformation gradient
dS_dFi !< derivative of 2nd P-K stress with respect to intermediate deformation gradient
real(pReal), dimension(3,3) :: E
real(pReal), dimension(3,3,3,3) :: C
integer :: &
ho, & !< homogenization
d !< counter in degradation loop
integer :: &
i, j
ho = material_homogenizationAt(el)
C = math_66toSym3333(constitutive_homogenizedC(ipc,ip,el))
DegradationLoop: do d = 1, phase_NstiffnessDegradations(material_phaseAt(ipc,el))
degradationType: select case(phase_stiffnessDegradation(d,material_phaseAt(ipc,el)))
case (STIFFNESS_DEGRADATION_damage_ID) degradationType
C = C * damage(ho)%p(damageMapping(ho)%p(ip,el))**2
end select degradationType
enddo DegradationLoop
E = 0.5_pReal*(matmul(transpose(Fe),Fe)-math_I3) !< Green-Lagrange strain in unloaded configuration
S = math_mul3333xx33(C,matmul(matmul(transpose(Fi),E),Fi)) !< 2PK stress in lattice configuration in work conjugate with GL strain pulled back to lattice configuration
do i =1, 3;do j=1,3
dS_dFe(i,j,1:3,1:3) = matmul(Fe,matmul(matmul(Fi,C(i,j,1:3,1:3)),transpose(Fi))) !< dS_ij/dFe_kl = C_ijmn * Fi_lm * Fi_on * Fe_ko
dS_dFi(i,j,1:3,1:3) = 2.0_pReal*matmul(matmul(E,Fi),C(i,j,1:3,1:3)) !< dS_ij/dFi_kl = C_ijln * E_km * Fe_mn
enddo; enddo
end subroutine constitutive_hooke_SandItsTangents
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief calls microstructure function of the different plasticity constitutive models !> @brief calls microstructure function of the different plasticity constitutive models
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
@ -395,6 +488,5 @@ module subroutine plastic_results
end subroutine plastic_results end subroutine plastic_results
end submodule constitutive_mech
end submodule constitutive_plastic

7
src/constitutive_plastic_disloTungsten.f90
View File

@ -5,7 +5,7 @@
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH !> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @brief crystal plasticity model for bcc metals, especially Tungsten !> @brief crystal plasticity model for bcc metals, especially Tungsten
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_disloTungsten submodule(constitutive:constitutive_mech) plastic_disloTungsten
real(pReal), parameter :: & real(pReal), parameter :: &
kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
@ -94,6 +94,7 @@ module function plastic_disloTungsten_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_dislotungsten init -+>>>' print'(/,a)', ' <<<+- plastic_dislotungsten init -+>>>'
@ -115,14 +116,14 @@ module function plastic_disloTungsten_init() result(myPlasticity)
i = 0 i = 0
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
mech => phase%get('mech')
if(.not. myPlasticity(p)) cycle if(.not. myPlasticity(p)) cycle
i = i + 1 i = i + 1
associate(prm => param(i), & associate(prm => param(i), &
dot => dotState(i), & dot => dotState(i), &
stt => state(i), & stt => state(i), &
dst => dependentState(i)) dst => dependentState(i))
pl => phase%get('plasticity') pl => mech%get('plasticity')
#if defined (__GFORTRAN__) #if defined (__GFORTRAN__)
prm%output = output_asStrings(pl) prm%output = output_asStrings(pl)

7
src/constitutive_plastic_dislotwin.f90
View File

@ -7,7 +7,7 @@
!> @brief material subroutine incoprorating dislocation and twinning physics !> @brief material subroutine incoprorating dislocation and twinning physics
!> @details to be done !> @details to be done
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_dislotwin submodule(constitutive:constitutive_mech) plastic_dislotwin
real(pReal), parameter :: & real(pReal), parameter :: &
kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin kB = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
@ -141,6 +141,7 @@ module function plastic_dislotwin_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_dislotwin init -+>>>' print'(/,a)', ' <<<+- plastic_dislotwin init -+>>>'
@ -168,14 +169,14 @@ module function plastic_dislotwin_init() result(myPlasticity)
i = 0 i = 0
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
mech => phase%get('mech')
if(.not. myPlasticity(p)) cycle if(.not. myPlasticity(p)) cycle
i = i + 1 i = i + 1
associate(prm => param(i), & associate(prm => param(i), &
dot => dotState(i), & dot => dotState(i), &
stt => state(i), & stt => state(i), &
dst => dependentState(i)) dst => dependentState(i))
pl => phase%get('plasticity') pl => mech%get('plasticity')
#if defined (__GFORTRAN__) #if defined (__GFORTRAN__)
prm%output = output_asStrings(pl) prm%output = output_asStrings(pl)

7
src/constitutive_plastic_isotropic.f90
View File

@ -7,7 +7,7 @@
!! resolving the stress on the slip systems. Will give the response of phenopowerlaw for an !! resolving the stress on the slip systems. Will give the response of phenopowerlaw for an
!! untextured polycrystal !! untextured polycrystal
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_isotropic submodule(constitutive:constitutive_mech) plastic_isotropic
type :: tParameters type :: tParameters
real(pReal) :: & real(pReal) :: &
@ -65,6 +65,7 @@ module function plastic_isotropic_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_isotropic init -+>>>' print'(/,a)', ' <<<+- plastic_isotropic init -+>>>'
@ -85,13 +86,13 @@ module function plastic_isotropic_init() result(myPlasticity)
i = 0 i = 0
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
mech => phase%get('mech')
if(.not. myPlasticity(p)) cycle if(.not. myPlasticity(p)) cycle
i = i + 1 i = i + 1
associate(prm => param(i), & associate(prm => param(i), &
dot => dotState(i), & dot => dotState(i), &
stt => state(i)) stt => state(i))
pl => phase%get('plasticity') pl => mech%get('plasticity')
#if defined (__GFORTRAN__) #if defined (__GFORTRAN__)

7
src/constitutive_plastic_kinehardening.f90
View File

@ -5,7 +5,7 @@
!> @brief Phenomenological crystal plasticity using a power law formulation for the shear rates !> @brief Phenomenological crystal plasticity using a power law formulation for the shear rates
!! and a Voce-type kinematic hardening rule !! and a Voce-type kinematic hardening rule
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_kinehardening submodule(constitutive:constitutive_mech) plastic_kinehardening
type :: tParameters type :: tParameters
real(pReal) :: & real(pReal) :: &
@ -77,6 +77,7 @@ module function plastic_kinehardening_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_kinehardening init -+>>>' print'(/,a)', ' <<<+- plastic_kinehardening init -+>>>'
@ -95,14 +96,14 @@ module function plastic_kinehardening_init() result(myPlasticity)
i = 0 i = 0
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
mech => phase%get('mech')
if(.not. myPlasticity(p)) cycle if(.not. myPlasticity(p)) cycle
i = i + 1 i = i + 1
associate(prm => param(i), & associate(prm => param(i), &
dot => dotState(i), & dot => dotState(i), &
dlt => deltaState(i), & dlt => deltaState(i), &
stt => state(i)) stt => state(i))
pl => phase%get('plasticity') pl => mech%get('plasticity')
#if defined (__GFORTRAN__) #if defined (__GFORTRAN__)
prm%output = output_asStrings(pl) prm%output = output_asStrings(pl)

6
src/constitutive_plastic_none.f90
View File

@ -4,7 +4,7 @@
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH !> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @brief Dummy plasticity for purely elastic material !> @brief Dummy plasticity for purely elastic material
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_none submodule(constitutive:constitutive_mech) plastic_none
contains contains
@ -22,6 +22,7 @@ module function plastic_none_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_none init -+>>>' print'(/,a)', ' <<<+- plastic_none init -+>>>'
@ -30,7 +31,8 @@ module function plastic_none_init() result(myPlasticity)
allocate(myPlasticity(phases%length), source = .false.) allocate(myPlasticity(phases%length), source = .false.)
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
pl => phase%get('plasticity') mech => phase%get('mech')
pl => mech%get ('plasticity')
if(pl%get_asString('type') == 'none') myPlasticity(p) = .true. if(pl%get_asString('type') == 'none') myPlasticity(p) = .true.
enddo enddo

7
src/constitutive_plastic_nonlocal.f90
View File

@ -4,7 +4,7 @@
!> @author Philip Eisenlohr, Max-Planck-Institut für Eisenforschung GmbH !> @author Philip Eisenlohr, Max-Planck-Institut für Eisenforschung GmbH
!> @brief material subroutine for plasticity including dislocation flux !> @brief material subroutine for plasticity including dislocation flux
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_nonlocal submodule(constitutive:constitutive_mech) plastic_nonlocal
use geometry_plastic_nonlocal, only: & use geometry_plastic_nonlocal, only: &
nIPneighbors => geometry_plastic_nonlocal_nIPneighbors, & nIPneighbors => geometry_plastic_nonlocal_nIPneighbors, &
IPneighborhood => geometry_plastic_nonlocal_IPneighborhood, & IPneighborhood => geometry_plastic_nonlocal_IPneighborhood, &
@ -183,6 +183,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_nonlocal init -+>>>' print'(/,a)', ' <<<+- plastic_nonlocal init -+>>>'
@ -212,7 +213,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
i = 0 i = 0
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
mech => phase%get('mech')
if(.not. myPlasticity(p)) cycle if(.not. myPlasticity(p)) cycle
i = i + 1 i = i + 1
associate(prm => param(i), & associate(prm => param(i), &
@ -221,7 +222,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
st0 => state0(i), & st0 => state0(i), &
del => deltaState(i), & del => deltaState(i), &
dst => microstructure(i)) dst => microstructure(i))
pl => phase%get('plasticity') pl => mech%get('plasticity')
phase_localPlasticity(p) = .not. pl%contains('nonlocal') phase_localPlasticity(p) = .not. pl%contains('nonlocal')

7
src/constitutive_plastic_phenopowerlaw.f90
View File

@ -4,7 +4,7 @@
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH !> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @brief phenomenological crystal plasticity formulation using a powerlaw fitting !> @brief phenomenological crystal plasticity formulation using a powerlaw fitting
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
submodule(constitutive:constitutive_plastic) plastic_phenopowerlaw submodule(constitutive:constitutive_mech) plastic_phenopowerlaw
type :: tParameters type :: tParameters
real(pReal) :: & real(pReal) :: &
@ -86,6 +86,7 @@ module function plastic_phenopowerlaw_init() result(myPlasticity)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl pl
print'(/,a)', ' <<<+- plastic_phenopowerlaw init -+>>>' print'(/,a)', ' <<<+- plastic_phenopowerlaw init -+>>>'
@ -103,13 +104,13 @@ module function plastic_phenopowerlaw_init() result(myPlasticity)
i = 0 i = 0
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
mech => phase%get('mech')
if(.not. myPlasticity(p)) cycle if(.not. myPlasticity(p)) cycle
i = i + 1 i = i + 1
associate(prm => param(i), & associate(prm => param(i), &
dot => dotState(i), & dot => dotState(i), &
stt => state(i)) stt => state(i))
pl => phase%get('plasticity') pl => mech%get('plasticity')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! slip related parameters ! slip related parameters

10
src/crystallite.f90
View File

@ -150,7 +150,7 @@ subroutine crystallite_init
debug_crystallite, & ! pointer to debug options for crystallite debug_crystallite, & ! pointer to debug options for crystallite
phases, & phases, &
phase, & phase, &
generic_param mech
print'(/,a)', ' <<<+- crystallite init -+>>>' print'(/,a)', ' <<<+- crystallite init -+>>>'
@ -240,11 +240,11 @@ subroutine crystallite_init
allocate(output_constituent(phases%length)) allocate(output_constituent(phases%length))
do c = 1, phases%length do c = 1, phases%length
phase => phases%get(c) phase => phases%get(c)
generic_param => phase%get('generic',defaultVal = emptyDict) mech => phase%get('mech',defaultVal = emptyDict)
#if defined(__GFORTRAN__) #if defined(__GFORTRAN__)
output_constituent(c)%label = output_asStrings(generic_param) output_constituent(c)%label = output_asStrings(mech)
#else #else
output_constituent(c)%label = generic_param%get_asStrings('output',defaultVal=emptyStringArray) output_constituent(c)%label = mech%get_asStrings('output',defaultVal=emptyStringArray)
#endif #endif
enddo enddo
@ -736,7 +736,7 @@ subroutine crystallite_results
integer :: p,o integer :: p,o
real(pReal), allocatable, dimension(:,:,:) :: selected_tensors real(pReal), allocatable, dimension(:,:,:) :: selected_tensors
type(rotation), allocatable, dimension(:) :: selected_rotations type(rotation), allocatable, dimension(:) :: selected_rotations
character(len=pStringLen) :: group,structureLabel character(len=:), allocatable :: group,structureLabel
do p=1,size(material_name_phase) do p=1,size(material_name_phase)
group = trim('current/constituent')//'/'//trim(material_name_phase(p))//'/generic' group = trim('current/constituent')//'/'//trim(material_name_phase(p))//'/generic'

2
src/grid/discretization_grid.f90
View File

@ -84,6 +84,8 @@ subroutine discretization_grid_init(restart)
PETSC_COMM_WORLD, & PETSC_COMM_WORLD, &
z, & ! domain grid size along z z, & ! domain grid size along z
z_offset) ! domain grid offset along z z_offset) ! domain grid offset along z
if(z==0_C_INTPTR_T) call IO_error(894, ext_msg='Cannot distribute MPI processes')
grid3 = int(z) grid3 = int(z)
grid3Offset = int(z_offset) grid3Offset = int(z_offset)
size3 = geomSize(3)*real(grid3,pReal) /real(grid(3),pReal) size3 = geomSize(3)*real(grid3,pReal) /real(grid(3),pReal)

4
src/grid/grid_damage_spectral.f90
View File

@ -95,10 +95,10 @@ subroutine grid_damage_spectral_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc ! set default and user defined options for PETSc
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,'-damage_snes_type newtonls -damage_snes_mf & call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-damage_snes_type newtonls -damage_snes_mf &
&-damage_snes_ksp_ew -damage_ksp_type fgmres',ierr) &-damage_snes_ksp_ew -damage_ksp_type fgmres',ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

5
src/grid/grid_mech_FEM.f90
View File

@ -13,6 +13,7 @@ module grid_mech_FEM
use prec use prec
use parallelization use parallelization
use DAMASK_interface use DAMASK_interface
use IO
use HDF5_utilities use HDF5_utilities
use math use math
use spectral_utilities use spectral_utilities
@ -141,10 +142,10 @@ subroutine grid_mech_FEM_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc ! set default and user defined options for PETSc
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type newtonls -mech_ksp_type fgmres & call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type newtonls -mech_ksp_type fgmres &
&-mech_ksp_max_it 25 -mech_pc_type ml -mech_mg_levels_ksp_type chebyshev',ierr) &-mech_ksp_max_it 25 -mech_pc_type ml -mech_mg_levels_ksp_type chebyshev',ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

5
src/grid/grid_mech_spectral_basic.f90
View File

@ -13,6 +13,7 @@ module grid_mech_spectral_basic
use prec use prec
use parallelization use parallelization
use DAMASK_interface use DAMASK_interface
use IO
use HDF5_utilities use HDF5_utilities
use math use math
use spectral_utilities use spectral_utilities
@ -140,9 +141,9 @@ subroutine grid_mech_spectral_basic_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc ! set default and user defined options for PETSc
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type ngmres',ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type ngmres',ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

5
src/grid/grid_mech_spectral_polarisation.f90
View File

@ -13,6 +13,7 @@ module grid_mech_spectral_polarisation
use prec use prec
use parallelization use parallelization
use DAMASK_interface use DAMASK_interface
use IO
use HDF5_utilities use HDF5_utilities
use math use math
use spectral_utilities use spectral_utilities
@ -158,9 +159,9 @@ subroutine grid_mech_spectral_polarisation_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc ! set default and user defined options for PETSc
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type ngmres',ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type ngmres',ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

4
src/grid/grid_thermal_spectral.f90
View File

@ -89,9 +89,9 @@ subroutine grid_thermal_spectral_init
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! set default and user defined options for PETSc ! set default and user defined options for PETSc
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,'-thermal_snes_type ngmres',ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-thermal_snes_type ngmres',ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------

49
src/grid/spectral_utilities.f90
View File

@ -214,11 +214,11 @@ subroutine spectral_utilities_init
num_grid => config_numerics%get('grid',defaultVal=emptyDict) num_grid => config_numerics%get('grid',defaultVal=emptyDict)
call PETScOptionsClear(PETSC_NULL_OPTIONS,ierr) call PetscOptionsClear(PETSC_NULL_OPTIONS,ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
if(debugPETSc) call PETScOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),ierr) if(debugPETSc) call PetscOptionsInsertString(PETSC_NULL_OPTIONS,trim(PETSCDEBUG),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
call PETScOptionsInsertString(PETSC_NULL_OPTIONS,& call PetscOptionsInsertString(PETSC_NULL_OPTIONS,&
num_grid%get_asString('petsc_options',defaultVal=''),ierr) num_grid%get_asString('petsc_options',defaultVal=''),ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
@ -313,12 +313,12 @@ subroutine spectral_utilities_init
tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
tensorField_real, tensorField_fourier, & ! input data, output data tensorField_real, tensorField_fourier, & ! input data, output data
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
if (.not. C_ASSOCIATED(planTensorForth)) call IO_error(810, ext_msg='planTensorForth') 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 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 tensorSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
tensorField_fourier,tensorField_real, & ! input data, output data tensorField_fourier,tensorField_real, & ! input data, output data
PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
if (.not. C_ASSOCIATED(planTensorBack)) call IO_error(810, ext_msg='planTensorBack') if (.not. C_ASSOCIATED(planTensorBack)) error stop 'FFTW error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! vector MPI fftw plans ! vector MPI fftw plans
@ -326,12 +326,12 @@ subroutine spectral_utilities_init
vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK,&! no. of transforms, default iblock and oblock vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK,&! no. of transforms, default iblock and oblock
vectorField_real, vectorField_fourier, & ! input data, output data vectorField_real, vectorField_fourier, & ! input data, output data
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
if (.not. C_ASSOCIATED(planVectorForth)) call IO_error(810, ext_msg='planVectorForth') 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 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 vecSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, & ! no. of transforms, default iblock and oblock
vectorField_fourier,vectorField_real, & ! input data, output data vectorField_fourier,vectorField_real, & ! input data, output data
PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision PETSC_COMM_WORLD, FFTW_planner_flag) ! all processors, planer precision
if (.not. C_ASSOCIATED(planVectorBack)) call IO_error(810, ext_msg='planVectorBack') if (.not. C_ASSOCIATED(planVectorBack)) error stop 'FFTW error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! scalar MPI fftw plans ! scalar MPI fftw plans
@ -339,12 +339,12 @@ subroutine spectral_utilities_init
scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
scalarField_real, scalarField_fourier, & ! input data, output data scalarField_real, scalarField_fourier, & ! input data, output data
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
if (.not. C_ASSOCIATED(planScalarForth)) call IO_error(810, ext_msg='planScalarForth') 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 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 scalarSize, FFTW_MPI_DEFAULT_BLOCK, FFTW_MPI_DEFAULT_BLOCK, &! no. of transforms, default iblock and oblock
scalarField_fourier,scalarField_real, & ! input data, output data scalarField_fourier,scalarField_real, & ! input data, output data
PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision PETSC_COMM_WORLD, FFTW_planner_flag) ! use all processors, planer precision
if (.not. C_ASSOCIATED(planScalarBack)) call IO_error(810, ext_msg='planScalarBack') if (.not. C_ASSOCIATED(planScalarBack)) error stop 'FFTW error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! calculation of discrete angular frequencies, ordered as in FFTW (wrap around) ! calculation of discrete angular frequencies, ordered as in FFTW (wrap around)
@ -603,10 +603,9 @@ real(pReal) function utilities_divergenceRMS()
enddo; enddo enddo; enddo
if(grid(1) == 1) utilities_divergenceRMS = utilities_divergenceRMS * 0.5_pReal ! counted twice in case of grid(1) == 1 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,PETSC_COMM_WORLD,ierr) call MPI_Allreduce(MPI_IN_PLACE,utilities_divergenceRMS,1,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr)
if(ierr /=0) call IO_error(894, ext_msg='utilities_divergenceRMS') if(ierr /=0) error stop 'MPI error'
utilities_divergenceRMS = sqrt(utilities_divergenceRMS) * wgt ! RMS in real space calculated with Parsevals theorem from Fourier space utilities_divergenceRMS = sqrt(utilities_divergenceRMS) * wgt ! RMS in real space calculated with Parsevals theorem from Fourier space
end function utilities_divergenceRMS end function utilities_divergenceRMS
@ -664,7 +663,7 @@ real(pReal) function utilities_curlRMS()
enddo; enddo enddo; enddo
call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr) call MPI_Allreduce(MPI_IN_PLACE,utilities_curlRMS,1,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr)
if(ierr /=0) call IO_error(894, ext_msg='utilities_curlRMS') if(ierr /=0) error stop 'MPI error'
utilities_curlRMS = sqrt(utilities_curlRMS) * wgt 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 if(grid(1) == 1) utilities_curlRMS = utilities_curlRMS * 0.5_pReal ! counted twice in case of grid(1) == 1
@ -713,7 +712,6 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
allocate(s_reduced,mold = c_reduced) allocate(s_reduced,mold = c_reduced)
call math_invert(s_reduced, errmatinv, c_reduced) ! invert reduced stiffness call math_invert(s_reduced, errmatinv, c_reduced) ! invert reduced stiffness
if (any(IEEE_is_NaN(s_reduced))) errmatinv = .true. if (any(IEEE_is_NaN(s_reduced))) errmatinv = .true.
if (errmatinv) call IO_error(error_ID=400,ext_msg='utilities_maskedCompliance')
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! check if inversion was successful ! check if inversion was successful
@ -725,7 +723,7 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
write(IO_STDOUT,trim(formatString),advance='no') ' C * S (load) ', & write(IO_STDOUT,trim(formatString),advance='no') ' C * S (load) ', &
transpose(matmul(c_reduced,s_reduced)) transpose(matmul(c_reduced,s_reduced))
write(IO_STDOUT,trim(formatString),advance='no') ' S (load) ', transpose(s_reduced) write(IO_STDOUT,trim(formatString),advance='no') ' S (load) ', transpose(s_reduced)
if(errmatinv) call IO_error(error_ID=400,ext_msg='utilities_maskedCompliance') if(errmatinv) error stop 'matrix inversion error'
endif endif
temp99_real = reshape(unpack(reshape(s_reduced,[size_reduced**2]),reshape(mask,[81]),0.0_pReal),[9,9]) temp99_real = reshape(unpack(reshape(s_reduced,[size_reduced**2]),reshape(mask,[81]),0.0_pReal),[9,9])
else else
@ -857,20 +855,21 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
valueAndRank = [dPdF_norm_max,real(worldrank,pReal)] valueAndRank = [dPdF_norm_max,real(worldrank,pReal)]
call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MAXLOC, PETSC_COMM_WORLD, ierr) call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MAXLOC, PETSC_COMM_WORLD, ierr)
if (ierr /= 0) call IO_error(894, ext_msg='MPI_Allreduce max') if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(dPdF_max,81,MPI_DOUBLE,int(valueAndRank(2)),PETSC_COMM_WORLD, ierr) call MPI_Bcast(dPdF_max,81,MPI_DOUBLE,int(valueAndRank(2)),PETSC_COMM_WORLD, ierr)
if (ierr /= 0) call IO_error(894, ext_msg='MPI_Bcast max') if (ierr /= 0) error stop 'MPI error'
valueAndRank = [dPdF_norm_min,real(worldrank,pReal)] valueAndRank = [dPdF_norm_min,real(worldrank,pReal)]
call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MINLOC, PETSC_COMM_WORLD, ierr) call MPI_Allreduce(MPI_IN_PLACE,valueAndRank,1, MPI_2DOUBLE_PRECISION, MPI_MINLOC, PETSC_COMM_WORLD, ierr)
if (ierr /= 0) call IO_error(894, ext_msg='MPI_Allreduce min') if (ierr /= 0) error stop 'MPI error'
call MPI_Bcast(dPdF_min,81,MPI_DOUBLE,int(valueAndRank(2)),PETSC_COMM_WORLD, ierr) call MPI_Bcast(dPdF_min,81,MPI_DOUBLE,int(valueAndRank(2)),PETSC_COMM_WORLD, ierr)
if (ierr /= 0) call IO_error(894, ext_msg='MPI_Bcast min') if (ierr /= 0) error stop 'MPI error'
C_minmaxAvg = 0.5_pReal*(dPdF_max + dPdF_min) C_minmaxAvg = 0.5_pReal*(dPdF_max + dPdF_min)
C_volAvg = sum(sum(homogenization_dPdF,dim=6),dim=5) C_volAvg = sum(sum(homogenization_dPdF,dim=6),dim=5)
call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr) call MPI_Allreduce(MPI_IN_PLACE,C_volAvg,81,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr)
if (ierr /= 0) error stop 'MPI error'
C_volAvg = C_volAvg * wgt C_volAvg = C_volAvg * wgt
@ -1035,7 +1034,7 @@ subroutine utilities_updateCoords(F)
! average F ! average F
if (grid3Offset == 0) Favg = real(tensorField_fourier(1:3,1:3,1,1,1),pReal)*wgt if (grid3Offset == 0) Favg = real(tensorField_fourier(1:3,1:3,1,1,1),pReal)*wgt
call MPI_Bcast(Favg,9,MPI_DOUBLE,0,PETSC_COMM_WORLD,ierr) call MPI_Bcast(Favg,9,MPI_DOUBLE,0,PETSC_COMM_WORLD,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Bcast') if(ierr /=0) error stop 'MPI error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! pad cell center fluctuations along z-direction (needed when running MPI simulation) ! pad cell center fluctuations along z-direction (needed when running MPI simulation)
@ -1046,19 +1045,19 @@ subroutine utilities_updateCoords(F)
! send bottom layer to process below ! send bottom layer to process below
call MPI_Isend(IPfluct_padded(:,:,:,2), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,r,ierr) call MPI_Isend(IPfluct_padded(:,:,:,2), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,r,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Isend') if(ierr /=0) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,r,ierr) call MPI_Irecv(IPfluct_padded(:,:,:,grid3+2),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,r,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Irecv') if(ierr /=0) error stop 'MPI error'
call MPI_Wait(r,s,ierr) call MPI_Wait(r,s,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Wait') if(ierr /=0) error stop 'MPI error'
! send top layer to process above ! send top layer to process above
call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,r,ierr) call MPI_Isend(IPfluct_padded(:,:,:,grid3+1),c,MPI_DOUBLE,rank_t,0,PETSC_COMM_WORLD,r,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Isend') if(ierr /=0) error stop 'MPI error'
call MPI_Irecv(IPfluct_padded(:,:,:,1), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,r,ierr) call MPI_Irecv(IPfluct_padded(:,:,:,1), c,MPI_DOUBLE,rank_b,0,PETSC_COMM_WORLD,r,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Irecv') if(ierr /=0) error stop 'MPI error'
call MPI_Wait(r,s,ierr) call MPI_Wait(r,s,ierr)
if(ierr /=0) call IO_error(894, ext_msg='update_IPcoords/MPI_Wait') if(ierr /=0) error stop 'MPI error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! calculate nodal displacements ! calculate nodal displacements

2
src/homogenization.f90
View File

@ -529,7 +529,7 @@ subroutine homogenization_results
material_homogenization_type => homogenization_type material_homogenization_type => homogenization_type
integer :: p integer :: p
character(len=pStringLen) :: group_base,group character(len=:), allocatable :: group_base,group
!real(pReal), dimension(:,:,:), allocatable :: temp !real(pReal), dimension(:,:,:), allocatable :: temp

4
src/kinematics_cleavage_opening.f90
View File

@ -41,7 +41,6 @@ module function kinematics_cleavage_opening_init(kinematics_length) result(myKin
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
pl, &
kinematics, & kinematics, &
kinematic_type kinematic_type
@ -58,8 +57,7 @@ module function kinematics_cleavage_opening_init(kinematics_length) result(myKin
do p = 1, phases%length do p = 1, phases%length
if(any(myKinematics(:,p))) kinematics_cleavage_opening_instance(p) = count(myKinematics(:,1:p)) if(any(myKinematics(:,p))) kinematics_cleavage_opening_instance(p) = count(myKinematics(:,1:p))
phase => phases%get(p) phase => phases%get(p)
pl => phase%get('plasticity')
if(count(myKinematics(:,p)) == 0) cycle if(count(myKinematics(:,p)) == 0) cycle
kinematics => phase%get('kinematics') kinematics => phase%get('kinematics')
do k = 1, kinematics%length do k = 1, kinematics%length

6
src/kinematics_slipplane_opening.f90
View File

@ -44,6 +44,7 @@ module function kinematics_slipplane_opening_init(kinematics_length) result(myKi
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl, & pl, &
kinematics, & kinematics, &
kinematic_type kinematic_type
@ -61,8 +62,9 @@ module function kinematics_slipplane_opening_init(kinematics_length) result(myKi
do p = 1, phases%length do p = 1, phases%length
if(any(myKinematics(:,p))) kinematics_slipplane_opening_instance(p) = count(myKinematics(:,1:p)) if(any(myKinematics(:,p))) kinematics_slipplane_opening_instance(p) = count(myKinematics(:,1:p))
phase => phases%get(p) phase => phases%get(p)
pl => phase%get('plasticity') mech => phase%get('mech')
pl => mech%get('plasticity')
if(count(myKinematics(:,p)) == 0) cycle if(count(myKinematics(:,p)) == 0) cycle
kinematics => phase%get('kinematics') kinematics => phase%get('kinematics')
do k = 1, kinematics%length do k = 1, kinematics%length

2
src/kinematics_thermal_expansion.f90
View File

@ -34,7 +34,6 @@ module function kinematics_thermal_expansion_init(kinematics_length) result(myKi
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
pl, &
kinematics, & kinematics, &
kinematic_type kinematic_type
@ -52,7 +51,6 @@ module function kinematics_thermal_expansion_init(kinematics_length) result(myKi
do p = 1, phases%length do p = 1, phases%length
if(any(myKinematics(:,p))) kinematics_thermal_expansion_instance(p) = count(myKinematics(:,1:p)) if(any(myKinematics(:,p))) kinematics_thermal_expansion_instance(p) = count(myKinematics(:,1:p))
phase => phases%get(p) phase => phases%get(p)
pl => phase%get('plasticity')
if(count(myKinematics(:,p)) == 0) cycle if(count(myKinematics(:,p)) == 0) cycle
kinematics => phase%get('kinematics') kinematics => phase%get('kinematics')
do k = 1, kinematics%length do k = 1, kinematics%length

60
src/lattice.f90
View File

@ -455,6 +455,7 @@ subroutine lattice_init
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
elasticity elasticity
print'(/,a)', ' <<<+- lattice init -+>>>'; flush(IO_STDOUT) print'(/,a)', ' <<<+- lattice init -+>>>'; flush(IO_STDOUT)
@ -475,7 +476,8 @@ subroutine lattice_init
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
elasticity => phase%get('elasticity') mech => phase%get('mech')
elasticity => mech%get('elasticity')
lattice_C66(1,1,p) = elasticity%get_asFloat('C_11') lattice_C66(1,1,p) = elasticity%get_asFloat('C_11')
lattice_C66(1,2,p) = elasticity%get_asFloat('C_12') lattice_C66(1,2,p) = elasticity%get_asFloat('C_12')
@ -586,9 +588,6 @@ function lattice_characteristicShear_Twin(Ntwin,structure,CoverA) result(charact
4 & 4 &
],[HEX_NTWIN]) ! indicator to formulas below ],[HEX_NTWIN]) ! indicator to formulas below
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_characteristicShear_Twin: '//trim(structure))
a = 0 a = 0
myFamilies: do f = 1,size(Ntwin,1) myFamilies: do f = 1,size(Ntwin,1)
mySystems: do s = 1,Ntwin(f) mySystems: do s = 1,Ntwin(f)
@ -634,9 +633,6 @@ function lattice_C66_twin(Ntwin,C66,structure,CoverA)
type(rotation) :: R type(rotation) :: R
integer :: i integer :: i
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_C66_twin: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
coordinateSystem = buildCoordinateSystem(Ntwin,FCC_NSLIPSYSTEM,FCC_SYSTEMTWIN,& coordinateSystem = buildCoordinateSystem(Ntwin,FCC_NSLIPSYSTEM,FCC_SYSTEMTWIN,&
@ -964,9 +960,6 @@ function lattice_interaction_SlipBySlip(Nslip,interactionValues,structure) resul
],shape(BCT_INTERACTIONSLIPSLIP)) ],shape(BCT_INTERACTIONSLIPSLIP))
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_interaction_SlipBySlip: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
interactionTypes = FCC_INTERACTIONSLIPSLIP interactionTypes = FCC_INTERACTIONSLIPSLIP
@ -1068,9 +1061,6 @@ function lattice_interaction_TwinByTwin(Ntwin,interactionValues,structure) resul
20,20,20,20,20,20, 19,19,19,19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,16 & 20,20,20,20,20,20, 19,19,19,19,19,19, 18,18,18,18,18,18, 17,17,17,17,17,16 &
],shape(HEX_INTERACTIONTWINTWIN)) !< Twin-twin interaction types for hex ],shape(HEX_INTERACTIONTWINTWIN)) !< Twin-twin interaction types for hex
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_interaction_TwinByTwin: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
interactionTypes = FCC_INTERACTIONTWINTWIN interactionTypes = FCC_INTERACTIONTWINTWIN
@ -1120,9 +1110,6 @@ function lattice_interaction_TransByTrans(Ntrans,interactionValues,structure) re
2,2,2,2,2,2,2,2,2,1,1,1 & 2,2,2,2,2,2,2,2,2,1,1,1 &
],shape(FCC_INTERACTIONTRANSTRANS)) !< Trans-trans interaction types for fcc ],shape(FCC_INTERACTIONTRANSTRANS)) !< Trans-trans interaction types for fcc
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_interaction_TransByTrans: '//trim(structure))
if(structure == 'fcc') then if(structure == 'fcc') then
interactionTypes = FCC_INTERACTIONTRANSTRANS interactionTypes = FCC_INTERACTIONTRANSTRANS
NtransMax = FCC_NTRANSSYSTEM NtransMax = FCC_NTRANSSYSTEM
@ -1250,9 +1237,6 @@ function lattice_interaction_SlipByTwin(Nslip,Ntwin,interactionValues,structure)
! !
],shape(HEX_INTERACTIONSLIPTWIN)) !< Slip-twin interaction types for hex ],shape(HEX_INTERACTIONSLIPTWIN)) !< Slip-twin interaction types for hex
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_interaction_SlipByTwin: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
interactionTypes = FCC_INTERACTIONSLIPTWIN interactionTypes = FCC_INTERACTIONSLIPTWIN
@ -1314,9 +1298,6 @@ function lattice_interaction_SlipByTrans(Nslip,Ntrans,interactionValues,structur
4,4,4,4,4,4,4,4,4,4,4,4 & 4,4,4,4,4,4,4,4,4,4,4,4 &
],shape(FCC_INTERACTIONSLIPTRANS)) !< Slip-trans interaction types for fcc ],shape(FCC_INTERACTIONSLIPTRANS)) !< Slip-trans interaction types for fcc
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_interaction_SlipByTrans: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
interactionTypes = FCC_INTERACTIONSLIPTRANS interactionTypes = FCC_INTERACTIONSLIPTRANS
@ -1384,9 +1365,6 @@ function lattice_interaction_TwinBySlip(Ntwin,Nslip,interactionValues,structure)
4, 4, 4, 8, 8, 8, 12,12,12, 16,16,16,16,16,16, 20,20,20,20,20,20,20,20,20,20,20,20, 24,24,24,24,24,24 & 4, 4, 4, 8, 8, 8, 12,12,12, 16,16,16,16,16,16, 20,20,20,20,20,20,20,20,20,20,20,20, 24,24,24,24,24,24 &
],shape(HEX_INTERACTIONTWINSLIP)) !< Twin-slip interaction types for hex ],shape(HEX_INTERACTIONTWINSLIP)) !< Twin-slip interaction types for hex
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_interaction_TwinBySlip: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
interactionTypes = FCC_INTERACTIONTWINSLIP interactionTypes = FCC_INTERACTIONTWINSLIP
@ -1425,9 +1403,6 @@ function lattice_SchmidMatrix_slip(Nslip,structure,cOverA) result(SchmidMatrix)
integer, dimension(:), allocatable :: NslipMax integer, dimension(:), allocatable :: NslipMax
integer :: i integer :: i
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_SchmidMatrix_slip: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
NslipMax = FCC_NSLIPSYSTEM NslipMax = FCC_NSLIPSYSTEM
@ -1478,9 +1453,6 @@ function lattice_SchmidMatrix_twin(Ntwin,structure,cOverA) result(SchmidMatrix)
integer, dimension(:), allocatable :: NtwinMax integer, dimension(:), allocatable :: NtwinMax
integer :: i integer :: i
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_SchmidMatrix_twin: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
NtwinMax = FCC_NTWINSYSTEM NtwinMax = FCC_NTWINSYSTEM
@ -1558,9 +1530,6 @@ function lattice_SchmidMatrix_cleavage(Ncleavage,structure,cOverA) result(Schmid
integer, dimension(:), allocatable :: NcleavageMax integer, dimension(:), allocatable :: NcleavageMax
integer :: i integer :: i
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_SchmidMatrix_cleavage: '//trim(structure))
select case(structure) select case(structure)
case('ort') case('ort')
NcleavageMax = ORT_NCLEAVAGESYSTEM NcleavageMax = ORT_NCLEAVAGESYSTEM
@ -1660,9 +1629,6 @@ function lattice_labels_slip(Nslip,structure) result(labels)
real(pReal), dimension(:,:), allocatable :: slipSystems real(pReal), dimension(:,:), allocatable :: slipSystems
integer, dimension(:), allocatable :: NslipMax integer, dimension(:), allocatable :: NslipMax
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_labels_slip: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
NslipMax = FCC_NSLIPSYSTEM NslipMax = FCC_NSLIPSYSTEM
@ -1704,9 +1670,6 @@ function lattice_applyLatticeSymmetry33(T,structure) result(T_sym)
T_sym = 0.0_pReal T_sym = 0.0_pReal
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_applyLatticeSymmetry33: '//trim(structure))
select case(structure) select case(structure)
case('iso','fcc','bcc') case('iso','fcc','bcc')
do k=1,3 do k=1,3
@ -1742,9 +1705,6 @@ function applyLatticeSymmetryC66(C66,structure) result(C66_sym)
C66_sym = 0.0_pReal C66_sym = 0.0_pReal
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='applyLatticeSymmetryC66: '//trim(structure))
select case(structure) select case(structure)
case ('iso') case ('iso')
do k=1,3 do k=1,3
@ -1822,9 +1782,6 @@ function lattice_labels_twin(Ntwin,structure) result(labels)
real(pReal), dimension(:,:), allocatable :: twinSystems real(pReal), dimension(:,:), allocatable :: twinSystems
integer, dimension(:), allocatable :: NtwinMax integer, dimension(:), allocatable :: NtwinMax
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='lattice_labels_twin: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
NtwinMax = FCC_NTWINSYSTEM NtwinMax = FCC_NTWINSYSTEM
@ -1911,9 +1868,6 @@ function coordinateSystem_slip(Nslip,structure,cOverA) result(coordinateSystem)
real(pReal), dimension(:,:), allocatable :: slipSystems real(pReal), dimension(:,:), allocatable :: slipSystems
integer, dimension(:), allocatable :: NslipMax integer, dimension(:), allocatable :: NslipMax
if (len_trim(structure) /= 3) &
call IO_error(137,ext_msg='coordinateSystem_slip: '//trim(structure))
select case(structure) select case(structure)
case('fcc') case('fcc')
NslipMax = FCC_NSLIPSYSTEM NslipMax = FCC_NSLIPSYSTEM
@ -2255,11 +2209,11 @@ function equivalent_nu(C,assumption) result(nu)
/ 9.0_pReal / 9.0_pReal
elseif(IO_lc(assumption) == 'reuss') then elseif(IO_lc(assumption) == 'reuss') then
call math_invert(S,error,C) call math_invert(S,error,C)
if(error) call IO_error(0) if(error) error stop 'matrix inversion failed'
K = 1.0_pReal & K = 1.0_pReal &
/ (S(1,1)+S(2,2)+S(3,3) +2.0_pReal*(S(1,2)+S(2,3)+S(1,3))) / (S(1,1)+S(2,2)+S(3,3) +2.0_pReal*(S(1,2)+S(2,3)+S(1,3)))
else else
call IO_error(0) error stop 'invalid assumption'
K = 0.0_pReal K = 0.0_pReal
endif endif
@ -2287,11 +2241,11 @@ function equivalent_mu(C,assumption) result(mu)
/ 15.0_pReal / 15.0_pReal
elseif(IO_lc(assumption) == 'reuss') then elseif(IO_lc(assumption) == 'reuss') then
call math_invert(S,error,C) call math_invert(S,error,C)
if(error) call IO_error(0) if(error) error stop 'matrix inversion failed'
mu = 15.0_pReal & mu = 15.0_pReal &
/ (4.0_pReal*(S(1,1)+S(2,2)+S(3,3)) -4.0_pReal*(S(1,2)+S(2,3)+S(1,3)) +3.0_pReal*(S(4,4)+S(5,5)+S(6,6))) / (4.0_pReal*(S(1,1)+S(2,2)+S(3,3)) -4.0_pReal*(S(1,2)+S(2,3)+S(1,3)) +3.0_pReal*(S(4,4)+S(5,5)+S(6,6)))
else else
call IO_error(0) error stop 'invalid assumption'
mu = 0.0_pReal mu = 0.0_pReal
endif endif

6
src/math.f90
View File

@ -499,7 +499,7 @@ function math_invSym3333(A)
call dgetrf(6,6,temp66,6,ipiv6,ierr_i) call dgetrf(6,6,temp66,6,ipiv6,ierr_i)
call dgetri(6,temp66,6,ipiv6,work,size(work,1),ierr_f) call dgetri(6,temp66,6,ipiv6,work,size(work,1),ierr_f)
if (ierr_i /= 0 .or. ierr_f /= 0) then if (ierr_i /= 0 .or. ierr_f /= 0) then
call IO_error(400, ext_msg = 'math_invSym3333') error stop 'matrix inversion error'
else else
math_invSym3333 = math_66toSym3333(temp66) math_invSym3333 = math_66toSym3333(temp66)
endif endif
@ -1200,8 +1200,8 @@ subroutine selfTest
if(any(dNeq(math_exp33(math_I3,0),math_I3))) & if(any(dNeq(math_exp33(math_I3,0),math_I3))) &
error stop 'math_exp33(math_I3,1)' error stop 'math_exp33(math_I3,1)'
if(any(dNeq(math_exp33(math_I3,256),exp(1.0_pReal)*math_I3))) & if(any(dNeq(math_exp33(math_I3,128),exp(1.0_pReal)*math_I3))) &
error stop 'math_exp33(math_I3,256)' error stop 'math_exp33(math_I3,128)'
call random_number(v9) call random_number(v9)
if(any(dNeq(math_33to9(math_9to33(v9)),v9))) & if(any(dNeq(math_33to9(math_9to33(v9)),v9))) &

11
src/parallelization.f90
View File

@ -50,10 +50,17 @@ subroutine parallelization_init
if (threadLevel<MPI_THREAD_FUNNELED) error stop 'MPI library does not support OpenMP' if (threadLevel<MPI_THREAD_FUNNELED) error stop 'MPI library does not support OpenMP'
#endif #endif
call PETScInitializeNoArguments(petsc_err) ! first line in the code according to PETSc manual call PetscInitializeNoArguments(petsc_err) ! first line in the code according to PETSc manual
CHKERRQ(petsc_err) CHKERRQ(petsc_err)
call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,err) #if defined(DEBUG) && defined(__INTEL_COMPILER)
call PetscSetFPTrap(PETSC_FP_TRAP_ON,petsc_err)
#else
call PetscSetFPTrap(PETSC_FP_TRAP_OFF,petsc_err)
#endif
CHKERRQ(petsc_err)
call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,err)
if (err /= 0) error stop 'Could not determine worldrank' if (err /= 0) error stop 'Could not determine worldrank'
if (worldrank == 0) print'(/,a)', ' <<<+- parallelization init -+>>>' if (worldrank == 0) print'(/,a)', ' <<<+- parallelization init -+>>>'

3
src/prec.f90
View File

@ -93,7 +93,8 @@ subroutine prec_init
print'(a,i19)', ' Maximum value: ',huge(0) print'(a,i19)', ' Maximum value: ',huge(0)
print'(/,a,i3)', ' Size of float in bit: ',storage_size(0.0_pReal) print'(/,a,i3)', ' Size of float in bit: ',storage_size(0.0_pReal)
print'(a,e10.3)', ' Maximum value: ',huge(0.0_pReal) print'(a,e10.3)', ' Maximum value: ',huge(0.0_pReal)
print'(a,e10.3)', ' Minimum value: ',tiny(0.0_pReal) print'(a,e10.3)', ' Minimum value: ',PREAL_MIN
print'(a,e10.3)', ' Epsilon value: ',PREAL_EPSILON
print'(a,i3)', ' Decimal precision: ',precision(0.0_pReal) print'(a,i3)', ' Decimal precision: ',precision(0.0_pReal)
call selfTest call selfTest

2
src/quit.f90
View File

@ -23,7 +23,7 @@ subroutine quit(stop_id)
call h5close_f(error) call h5close_f(error)
if (error /= 0) write(6,'(a,i5)') ' Error in h5close_f ',error if (error /= 0) write(6,'(a,i5)') ' Error in h5close_f ',error
call PETScFinalize(ierr) call PetscFinalize(ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
#ifdef _OPENMP #ifdef _OPENMP

456
src/results.f90
View File

@ -7,6 +7,7 @@
module results module results
use DAMASK_interface use DAMASK_interface
use parallelization use parallelization
use IO
use rotations use rotations
use HDF5_utilities use HDF5_utilities
#ifdef PETSc #ifdef PETSc
@ -535,33 +536,46 @@ subroutine results_mapping_constituent(phaseAt,memberAtLocal,label)
integer(SIZE_T) :: type_size_string, type_size_int integer(SIZE_T) :: type_size_string, type_size_int
integer :: ierr, i integer :: hdferr, ierr, i
!--------------------------------------------------------------------------------------------------- !---------------------------------------------------------------------------------------------------
! compound type: name of phase section + position/index within results array ! compound type: name of phase section + position/index within results array
call h5tcopy_f(H5T_NATIVE_CHARACTER, dt_id, ierr) call h5tcopy_f(H5T_NATIVE_CHARACTER, dt_id, hdferr)
call h5tset_size_f(dt_id, int(len(label(1)),SIZE_T), ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(dt_id, type_size_string, ierr) call h5tset_size_f(dt_id, int(len(label(1)),SIZE_T), hdferr)
if(hdferr < 0) error stop 'HDF5 error'
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, ierr) call h5tget_size_f(H5T_NATIVE_INTEGER, 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, ierr) call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt_id,ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, "Position", type_size_string, H5T_NATIVE_INTEGER, ierr) call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, "Position", type_size_string, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create memory types for each component of the compound type ! create memory types for each component of the compound type
call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, ierr) call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, hdferr)
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, ierr) call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, hdferr)
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_NATIVE_INTEGER, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dt_id, ierr) call h5tclose_f(dt_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! prepare MPI communication (transparent for non-MPI runs) ! prepare MPI communication (transparent for non-MPI runs)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, ierr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
memberOffset = 0 memberOffset = 0
do i=1, size(label) do i=1, size(label)
memberOffset(i,worldrank) = count(phaseAt == i)*size(memberAtLocal,2) ! number of points/instance of this process memberOffset(i,worldrank) = count(phaseAt == i)*size(memberAtLocal,2) ! number of points/instance of this process
@ -572,14 +586,14 @@ subroutine results_mapping_constituent(phaseAt,memberAtLocal,label)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! MPI settings and communication ! MPI settings and communication
#ifdef PETSc #ifdef PETSc
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, ierr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5pset_dxpl_mpio_f') if(hdferr < 0) error stop 'HDF5 error'
call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get output at each process call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get output at each process
if (ierr /= 0) call IO_error(894,ext_msg='results_mapping_constituent: MPI_allreduce/writeSize') if(ierr /= 0) error stop 'MPI error'
call MPI_allreduce(MPI_IN_PLACE,memberOffset,size(memberOffset),MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)! get offset at each process call MPI_allreduce(MPI_IN_PLACE,memberOffset,size(memberOffset),MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)! get offset at each process
if (ierr /= 0) call IO_error(894,ext_msg='results_mapping_constituent: MPI_allreduce/memberOffset') if(ierr /= 0) error stop 'MPI error'
#endif #endif
myShape = int([size(phaseAt,1),writeSize(worldrank)], HSIZE_T) myShape = int([size(phaseAt,1),writeSize(worldrank)], HSIZE_T)
@ -588,14 +602,14 @@ subroutine results_mapping_constituent(phaseAt,memberAtLocal,label)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape = hyperslab) and in file (global shape) ! create dataspace in memory (local shape = hyperslab) and in file (global shape)
call h5screate_simple_f(2,myShape,memspace_id,ierr,myShape) call h5screate_simple_f(2,myShape,memspace_id,hdferr,myShape)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5screate_simple_f/memspace_id') if(hdferr < 0) error stop 'HDF5 error'
call h5screate_simple_f(2,totalShape,filespace_id,ierr,totalShape) call h5screate_simple_f(2,totalShape,filespace_id,hdferr,totalShape)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5screate_simple_f/filespace_id') if(hdferr < 0) error stop 'HDF5 error'
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myOffset, myShape, ierr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myOffset, myShape, hdferr)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5sselect_hyperslab_f') if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------- !---------------------------------------------------------------------------------------------------
! expand phaseAt to consider IPs (is not stored per IP) ! expand phaseAt to consider IPs (is not stored per IP)
@ -611,29 +625,36 @@ subroutine results_mapping_constituent(phaseAt,memberAtLocal,label)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! write the components of the compound type individually ! write the components of the compound type individually
call h5pset_preserve_f(plist_id, .TRUE., ierr) call h5pset_preserve_f(plist_id, .TRUE., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping') loc_id = results_openGroup('/mapping')
call h5dcreate_f(loc_id, 'phase', dtype_id, filespace_id, dset_id, ierr) call h5dcreate_f(loc_id, 'phase', dtype_id, filespace_id, dset_id, hdferr)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5dcreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, name_id, reshape(label(pack(phaseAtMaterialpoint,.true.)),myShape), & call h5dwrite_f(dset_id, name_id, reshape(label(pack(phaseAtMaterialpoint,.true.)),myShape), &
myShape, ierr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5dwrite_f/name_id') if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), & call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), &
myShape, ierr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_constituent: h5dwrite_f/position_id') if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! close all ! close all
call HDF5_closeGroup(loc_id) call HDF5_closeGroup(loc_id)
call h5pclose_f(plist_id, ierr) call h5pclose_f(plist_id, hdferr)
call h5sclose_f(filespace_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(memspace_id, ierr) call h5sclose_f(filespace_id, hdferr)
call h5dclose_f(dset_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dtype_id, ierr) call h5sclose_f(memspace_id, hdferr)
call h5tclose_f(name_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(position_id, ierr) call h5dclose_f(dset_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(name_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(position_id, hdferr)
! for backward compatibility ! for backward compatibility
call results_setLink('/mapping/phase','/mapping/cellResults/constituent') call results_setLink('/mapping/phase','/mapping/cellResults/constituent')
@ -673,51 +694,64 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
integer(SIZE_T) :: type_size_string, type_size_int integer(SIZE_T) :: type_size_string, type_size_int
integer :: ierr, i integer :: hdferr, ierr, i
!--------------------------------------------------------------------------------------------------- !---------------------------------------------------------------------------------------------------
! compound type: name of phase section + position/index within results array ! compound type: name of phase section + position/index within results array
call h5tcopy_f(H5T_NATIVE_CHARACTER, dt_id, ierr) call h5tcopy_f(H5T_NATIVE_CHARACTER, dt_id, hdferr)
call h5tset_size_f(dt_id, int(len(label(1)),SIZE_T), ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tget_size_f(dt_id, type_size_string, ierr) call h5tset_size_f(dt_id, int(len(label(1)),SIZE_T), hdferr)
if(hdferr < 0) error stop 'HDF5 error'
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, ierr) call h5tget_size_f(H5T_NATIVE_INTEGER, 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, ierr) call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt_id,ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, "Position", type_size_string, H5T_NATIVE_INTEGER, ierr) call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, "Position", type_size_string, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create memory types for each component of the compound type ! create memory types for each component of the compound type
call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, ierr) call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, hdferr)
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, ierr) call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, hdferr)
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_NATIVE_INTEGER, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dt_id, ierr) call h5tclose_f(dt_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! prepare MPI communication (transparent for non-MPI runs) ! prepare MPI communication (transparent for non-MPI runs)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, ierr) call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
memberOffset = 0 memberOffset = 0
do i=1, size(label) do i=1, size(label)
memberOffset(i,worldrank) = count(homogenizationAt == i)*size(memberAtLocal,1) ! number of points/instance of this process memberOffset(i,worldrank) = count(homogenizationAt == i)*size(memberAtLocal,1) ! number of points/instance of this process
enddo enddo
writeSize = 0 writeSize = 0
writeSize(worldrank) = size(memberAtLocal) ! total number of points by this process writeSize(worldrank) = size(memberAtLocal) ! total number of points by this process
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! MPI settings and communication ! MPI settings and communication
#ifdef PETSc #ifdef PETSc
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, ierr) call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5pset_dxpl_mpio_f') if(hdferr < 0) error stop 'HDF5 error'
call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get output at each process call MPI_allreduce(MPI_IN_PLACE,writeSize,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get output at each process
if (ierr /= 0) call IO_error(894,ext_msg='results_mapping_homogenization: MPI_allreduce/writeSize') if(ierr /= 0) error stop 'MPI error'
call MPI_allreduce(MPI_IN_PLACE,memberOffset,size(memberOffset),MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)! get offset at each process call MPI_allreduce(MPI_IN_PLACE,memberOffset,size(memberOffset),MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)! get offset at each process
if (ierr /= 0) call IO_error(894,ext_msg='results_mapping_homogenization: MPI_allreduce/memberOffset') if(ierr /= 0) error stop 'MPI error'
#endif #endif
myShape = int([writeSize(worldrank)], HSIZE_T) myShape = int([writeSize(worldrank)], HSIZE_T)
@ -726,14 +760,14 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! create dataspace in memory (local shape = hyperslab) and in file (global shape) ! create dataspace in memory (local shape = hyperslab) and in file (global shape)
call h5screate_simple_f(1,myShape,memspace_id,ierr,myShape) call h5screate_simple_f(1,myShape,memspace_id,hdferr,myShape)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5screate_simple_f/memspace_id') if(hdferr < 0) error stop 'HDF5 error'
call h5screate_simple_f(1,totalShape,filespace_id,ierr,totalShape) call h5screate_simple_f(1,totalShape,filespace_id,hdferr,totalShape)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5screate_simple_f/filespace_id') if(hdferr < 0) error stop 'HDF5 error'
call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myOffset, myShape, ierr) call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myOffset, myShape, hdferr)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5sselect_hyperslab_f') if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------- !---------------------------------------------------------------------------------------------------
! expand phaseAt to consider IPs (is not stored per IP) ! expand phaseAt to consider IPs (is not stored per IP)
@ -749,29 +783,36 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! write the components of the compound type individually ! write the components of the compound type individually
call h5pset_preserve_f(plist_id, .TRUE., ierr) call h5pset_preserve_f(plist_id, .TRUE., hdferr)
loc_id = results_openGroup('/mapping') loc_id = results_openGroup('/mapping')
call h5dcreate_f(loc_id, 'homogenization', dtype_id, filespace_id, dset_id, ierr) call h5dcreate_f(loc_id, 'homogenization', dtype_id, filespace_id, dset_id, hdferr)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5dcreate_f') if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, name_id, reshape(label(pack(homogenizationAtMaterialpoint,.true.)),myShape), & call h5dwrite_f(dset_id, name_id, reshape(label(pack(homogenizationAtMaterialpoint,.true.)),myShape), &
myShape, ierr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5dwrite_f/name_id') if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), & call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), &
myShape, ierr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id) myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (ierr < 0) call IO_error(1,ext_msg='results_mapping_homogenization: h5dwrite_f/position_id') if(hdferr < 0) error stop 'HDF5 error'
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
! close all ! close all
call HDF5_closeGroup(loc_id) call HDF5_closeGroup(loc_id)
call h5pclose_f(plist_id, ierr) call h5pclose_f(plist_id, hdferr)
call h5sclose_f(filespace_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5sclose_f(memspace_id, ierr) call h5sclose_f(filespace_id, hdferr)
call h5dclose_f(dset_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dtype_id, ierr) call h5sclose_f(memspace_id, hdferr)
call h5tclose_f(name_id, ierr) if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(position_id, ierr) call h5dclose_f(dset_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(name_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(position_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
! for backward compatibility ! for backward compatibility
call results_setLink('/mapping/homogenization','/mapping/cellResults/materialpoint') call results_setLink('/mapping/homogenization','/mapping/cellResults/materialpoint')
@ -793,263 +834,4 @@ character(len=24) function now()
end function now end function now
!!--------------------------------------------------------------------------------------------------
!!> @brief adds the backward mapping from spatial position and constituent ID to results
!!--------------------------------------------------------------------------------------------------
!subroutine HDF5_backwardMappingPhase(material_phase,phasememberat,phase_name,dataspace_size,mpiOffset,mpiOffset_phase)
! integer(pInt), intent(in), dimension(:,:,:) :: material_phase, phasememberat
! character(len=*), intent(in), dimension(:) :: phase_name
! integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_phase
! integer(pInt), intent(in) :: mpiOffset
! integer(pInt) :: hdferr, NmatPoints, Nconstituents, i, j
! integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace
! integer(SIZE_T) :: type_size
! integer(pInt), dimension(:,:), allocatable :: arr
! integer(HSIZE_T), dimension(1) :: counter
! integer(HSSIZE_T), dimension(1) :: fileOffset
! character(len=64) :: phaseID
! Nconstituents = size(phasememberat,1)
! NmatPoints = count(material_phase /=0)/Nconstituents
! allocate(arr(2,NmatPoints*Nconstituents))
! do i=1, NmatPoints
! do j=Nconstituents-1, 0, -1
! arr(1,Nconstituents*i-j) = i-1
! enddo
! enddo
! arr(2,:) = pack(material_phase,material_phase/=0)
! do i=1, size(phase_name)
! write(phaseID, '(i0)') i
! mapping_ID = results_openGroup('/current/constitutive/'//trim(phaseID)//'_'//phase_name(i))
! NmatPoints = count(material_phase == i)
!!--------------------------------------------------------------------------------------------------
! ! create dataspace
! call h5screate_simple_f(1, int([dataspace_size(i)],HSIZE_T), space_id, hdferr, &
! int([dataspace_size(i)],HSIZE_T))
! if (hdferr < 0) call IO_error(1,ext_msg='HDF5_writeBackwardMapping')
!!--------------------------------------------------------------------------------------------------
! ! compound type
! call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr)
! call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id')
! call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5tinsert_f 0')
!!--------------------------------------------------------------------------------------------------
! ! create Dataset
! call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase')
!!--------------------------------------------------------------------------------------------------
! ! Create memory types (one compound datatype for each member)
! call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5tcreate_f position_id')
! call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5tinsert_f position_id')
!!--------------------------------------------------------------------------------------------------
! ! Define and select hyperslabs
! counter = NmatPoints ! how big i am
! fileOffset = mpiOffset_phase(i) ! where i start to write my data
! call h5screate_simple_f(1, counter, memspace, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5screate_simple_f')
! call h5dget_space_f(dset_id, space_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5dget_space_f')
! call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5sselect_hyperslab_f')
!!--------------------------------------------------------------------------------------------------
! ! Create property list for collective dataset write
!#ifdef PETSc
! call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5pcreate_f')
! call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5pset_dxpl_mpio_f')
!#endif
!!--------------------------------------------------------------------------------------------------
! ! write data by fields in the datatype. Fields order is not important.
! call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i)+mpiOffset, int([dataspace_size(i)],HSIZE_T),&
! hdferr, file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5dwrite_f instance_id')
!!--------------------------------------------------------------------------------------------------
! !close types, dataspaces
! call h5tclose_f(dtype_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5tclose_f dtype_id')
! call h5tclose_f(position_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5tclose_f position_id')
! call h5dclose_f(dset_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5dclose_f')
! call h5sclose_f(space_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5sclose_f space_id')
! call h5sclose_f(memspace, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5sclose_f memspace')
! call h5pclose_f(plist_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingPhase: h5pclose_f')
! call HDF5_closeGroup(mapping_ID)
! enddo
!end subroutine HDF5_backwardMappingPhase
!!--------------------------------------------------------------------------------------------------
!!> @brief adds the backward mapping from spatial position and constituent ID to results
!!--------------------------------------------------------------------------------------------------
!subroutine HDF5_backwardMappingHomog(material_homog,homogmemberat,homogenization_name,dataspace_size,mpiOffset,mpiOffset_homog)
! integer(pInt), intent(in), dimension(:,:) :: material_homog, homogmemberat
! character(len=*), intent(in), dimension(:) :: homogenization_name
! integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_homog
! integer(pInt), intent(in) :: mpiOffset
! integer(pInt) :: hdferr, NmatPoints, i
! integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace
! integer(SIZE_T) :: type_size
! integer(pInt), dimension(:,:), allocatable :: arr
! integer(HSIZE_T), dimension(1) :: counter
! integer(HSSIZE_T), dimension(1) :: fileOffset
! character(len=64) :: homogID
! NmatPoints = count(material_homog /=0)
! allocate(arr(2,NmatPoints))
! arr(1,:) = (/(i, i=0,NmatPoints-1)/)
! arr(2,:) = pack(material_homog,material_homog/=0)
! do i=1, size(homogenization_name)
! write(homogID, '(i0)') i
! mapping_ID = results_openGroup('/current/homogenization/'//trim(homogID)//'_'//homogenization_name(i))
!!--------------------------------------------------------------------------------------------------
! ! create dataspace
! call h5screate_simple_f(1, int([dataspace_size(i)],HSIZE_T), space_id, hdferr, &
! int([dataspace_size(i)],HSIZE_T))
! if (hdferr < 0) call IO_error(1,ext_msg='HDF5_writeBackwardMapping')
!!--------------------------------------------------------------------------------------------------
! ! compound type
! call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr)
! call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id')
! call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5tinsert_f 0')
!!--------------------------------------------------------------------------------------------------
! ! create Dataset
! call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog')
!!--------------------------------------------------------------------------------------------------
! ! Create memory types (one compound datatype for each member)
! call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5tcreate_f position_id')
! call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5tinsert_f position_id')
!!--------------------------------------------------------------------------------------------------
! ! Define and select hyperslabs
! counter = NmatPoints ! how big i am
! fileOffset = mpiOffset_homog(i) ! where i start to write my data
! call h5screate_simple_f(1, counter, memspace, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5screate_simple_f')
! call h5dget_space_f(dset_id, space_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5dget_space_f')
! call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5sselect_hyperslab_f')
!!--------------------------------------------------------------------------------------------------
! ! Create property list for collective dataset write
!#ifdef PETSc
! call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5pcreate_f')
! call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5pset_dxpl_mpio_f')
!#endif
!!--------------------------------------------------------------------------------------------------
! ! write data by fields in the datatype. Fields order is not important.
! call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i)+mpiOffset,int([dataspace_size(i)],HSIZE_T),&
! hdferr, file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5dwrite_f instance_id')
!!--------------------------------------------------------------------------------------------------
! !close types, dataspaces
! call h5tclose_f(dtype_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5tclose_f dtype_id')
! call h5tclose_f(position_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5tclose_f position_id')
! call h5dclose_f(dset_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5dclose_f')
! call h5sclose_f(space_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5sclose_f space_id')
! call h5sclose_f(memspace, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5sclose_f memspace')
! call h5pclose_f(plist_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_backwardMappingHomog: h5pclose_f')
! call HDF5_closeGroup(mapping_ID)
! enddo
!end subroutine HDF5_backwardMappingHomog
!!--------------------------------------------------------------------------------------------------
!!> @brief adds the unique cell to node mapping
!!--------------------------------------------------------------------------------------------------
!subroutine HDF5_mappingCells(mapping)
! integer(pInt), intent(in), dimension(:) :: mapping
! integer :: hdferr, Nnodes
! integer(HID_T) :: mapping_id, dset_id, space_id
! Nnodes=size(mapping)
! mapping_ID = results_openGroup("mapping")
!!--------------------------------------------------------------------------------------------------
!! create dataspace
! call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, &
! int([Nnodes],HSIZE_T))
! if (hdferr < 0) call IO_error(1,ext_msg='IO_mappingCells: h5screate_simple_f')
!!--------------------------------------------------------------------------------------------------
!! create Dataset
! call h5dcreate_f(mapping_id, "Cell",H5T_NATIVE_INTEGER, space_id, dset_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_mappingCells')
!!--------------------------------------------------------------------------------------------------
!! write data by fields in the datatype. Fields order is not important.
! call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, mapping, int([Nnodes],HSIZE_T), hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_mappingCells: h5dwrite_f instance_id')
!!--------------------------------------------------------------------------------------------------
!!close types, dataspaces
! call h5dclose_f(dset_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_mappingConstitutive: h5dclose_f')
! call h5sclose_f(space_id, hdferr)
! if (hdferr < 0) call IO_error(1,ext_msg='IO_mappingConstitutive: h5sclose_f')
! call HDF5_closeGroup(mapping_ID)
!end subroutine HDF5_mappingCells
end module results end module results

4
src/rotations.f90
View File

@ -640,13 +640,13 @@ function om2ax(om) result(ax)
ax(1:3) = [ 0.0_pReal, 0.0_pReal, 1.0_pReal ] ax(1:3) = [ 0.0_pReal, 0.0_pReal, 1.0_pReal ]
else else
call dgeev('N','V',3,om_,3,Wr,Wi,devNull,3,VR,3,work,size(work,1),ierr) call dgeev('N','V',3,om_,3,Wr,Wi,devNull,3,VR,3,work,size(work,1),ierr)
if (ierr /= 0) call IO_error(401,ext_msg='Error in om2ax: DGEEV return not zero') if (ierr /= 0) error stop 'LAPACK error'
#if defined(__GFORTRAN__) && __GNUC__<9 || defined(__INTEL_COMPILER) && INTEL_COMPILER<1800 || defined(__PGI) #if defined(__GFORTRAN__) && __GNUC__<9 || defined(__INTEL_COMPILER) && INTEL_COMPILER<1800 || defined(__PGI)
i = maxloc(merge(1,0,cEq(cmplx(Wr,Wi,pReal),cmplx(1.0_pReal,0.0_pReal,pReal),tol=1.0e-14_pReal)),dim=1) i = maxloc(merge(1,0,cEq(cmplx(Wr,Wi,pReal),cmplx(1.0_pReal,0.0_pReal,pReal),tol=1.0e-14_pReal)),dim=1)
#else #else
i = findloc(cEq(cmplx(Wr,Wi,pReal),cmplx(1.0_pReal,0.0_pReal,pReal),tol=1.0e-14_pReal),.true.,dim=1) !find eigenvalue (1,0) i = findloc(cEq(cmplx(Wr,Wi,pReal),cmplx(1.0_pReal,0.0_pReal,pReal),tol=1.0e-14_pReal),.true.,dim=1) !find eigenvalue (1,0)
#endif #endif
if (i == 0) call IO_error(401,ext_msg='Error in om2ax Real: eigenvalue not found') if (i == 0) error stop 'om2ax conversion failed'
ax(1:3) = VR(1:3,i) ax(1:3) = VR(1:3,i)
where ( dNeq0([om(2,3)-om(3,2), om(3,1)-om(1,3), om(1,2)-om(2,1)])) & where ( dNeq0([om(2,3)-om(3,2), om(3,1)-om(1,3), om(1,2)-om(2,1)])) &
ax(1:3) = sign(ax(1:3),-P *[om(2,3)-om(3,2), om(3,1)-om(1,3), om(1,2)-om(2,1)]) ax(1:3) = sign(ax(1:3),-P *[om(2,3)-om(3,2), om(3,1)-om(1,3), om(1,2)-om(2,1)])

6
src/source_damage_anisoDuctile.f90
View File

@ -36,6 +36,7 @@ module function source_damage_anisoDuctile_init(source_length) result(mySources)
class(tNode), pointer :: & class(tNode), pointer :: &
phases, & phases, &
phase, & phase, &
mech, &
pl, & pl, &
sources, & sources, &
src src
@ -56,11 +57,12 @@ module function source_damage_anisoDuctile_init(source_length) result(mySources)
allocate(source_damage_anisoDuctile_instance(phases%length), source=0) allocate(source_damage_anisoDuctile_instance(phases%length), source=0)
do p = 1, phases%length do p = 1, phases%length
phase => phases%get(p) phase => phases%get(p)
if(any(mySources(:,p))) source_damage_anisoDuctile_instance(p) = count(mySources(:,1:p)) if(any(mySources(:,p))) source_damage_anisoDuctile_instance(p) = count(mySources(:,1:p))
if(count(mySources(:,p)) == 0) cycle if(count(mySources(:,p)) == 0) cycle
mech => phase%get('mech')
pl => mech%get('plasticity')
sources => phase%get('source') sources => phase%get('source')
pl => phase%get('plasticity')
do sourceOffset = 1, sources%length do sourceOffset = 1, sources%length
if(mySources(sourceOffset,p)) then if(mySources(sourceOffset,p)) then
source_damage_anisoDuctile_offset(p) = sourceOffset source_damage_anisoDuctile_offset(p) = sourceOffset