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Merge remote-tracking branch 'origin/development' into MiscImprovements

This commit is contained in:
Martin Diehl 2020-03-01 07:32:00 +01:00
parent ed2489de9a be08af71d4
commit 08aef5531c
6 changed files with 375 additions and 484 deletions
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11
.gitlab-ci.yml
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@ -104,7 +104,7 @@ checkout:
- release - release
################################################################################################### ###################################################################################################
Pytest: Pytest_python:
stage: python stage: python
script: script:
- cd $DAMASKROOT/python - cd $DAMASKROOT/python
@ -385,6 +385,15 @@ Phenopowerlaw_singleSlip:
- master - master
- release - release
Pytest_grid:
stage: grid
script:
- cd pytest
- pytest
except:
- master
- release
################################################################################################### ###################################################################################################
Marc_compileIfort: Marc_compileIfort:
stage: compileMarc stage: compileMarc

2
PRIVATE

@ -1 +1 @@
Subproject commit 6db5f4666fc651b4de3b44ceaed3f2b848170ac9 Subproject commit 9573ce7bd2c1a7188c1aac5b83aa76d480c2bdb0

2
VERSION
View File

@ -1 +1 @@
v2.0.3-1747-ga2e8e5b1 v2.0.3-1808-g13c3ce00

49
examples/ConfigFiles/Phase_Phenopowerlaw_multiField.config
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@ -1,49 +0,0 @@
[Aluminum]
elasticity hooke
plasticity phenopowerlaw
(output) resistance_slip
(output) shearrate_slip
(output) resolvedstress_slip
(output) accumulated_shear_slip
(output) resistance_twin
(output) shearrate_twin
(output) resolvedstress_twin
(output) accumulated_shear_twin
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
gdot0_twin 0.001
n_twin 20
tau0_twin 31e6 # per family
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
atol_resistance 1
(stiffness_degradation) damage
(stiffness_degradation) porosity
{./Phase_Damage.config}
{./Phase_Thermal.config}
{./Phase_Vacancy.config}
{./Phase_Porosity.config}
{./Phase_Hydrogen.config}
{./Source_Damage_IsoBrittle.config}
{./Source_Thermal_Dissipation.config}
{./Source_Vacancy_PhenoPlasticity.config}
{./Source_Vacancy_Irradiation.config}
{./Kinematics_Thermal_Expansion.config}
{./Kinematics_Vacancy_Strain.config}
{./Kinematics_Hydrogen_Strain.config}

739
python/damask/dadf5.py
View File

@ -1,7 +1,8 @@
from queue import Queue import multiprocessing
import re import re
import glob import glob
import os import os
from functools import partial
import vtk import vtk
from vtk.util import numpy_support from vtk.util import numpy_support
@ -36,24 +37,23 @@ class DADF5():
with h5py.File(fname,'r') as f: with h5py.File(fname,'r') as f:
try: try:
self.version_major = f.attrs['DADF5_version_major'] self.version_major = f.attrs['DADF5_version_major']
self.version_minor = f.attrs['DADF5_version_minor'] self.version_minor = f.attrs['DADF5_version_minor']
except KeyError: except KeyError:
self.version_major = f.attrs['DADF5-major'] self.version_major = f.attrs['DADF5-major']
self.version_minor = f.attrs['DADF5-minor'] self.version_minor = f.attrs['DADF5-minor']
if self.version_major != 0 or not 2 <= self.version_minor <= 6: if self.version_major != 0 or not 2 <= self.version_minor <= 6:
raise TypeError('Unsupported DADF5 version {}.{} '.format(f.attrs['DADF5_version_major'], raise TypeError('Unsupported DADF5 version {}.{} '.format(self.version_major,
f.attrs['DADF5_version_minor'])) self.version_minor))
self.structured = 'grid' in f['geometry'].attrs.keys() self.structured = 'grid' in f['geometry'].attrs.keys()
if self.structured: if self.structured:
self.grid = f['geometry'].attrs['grid'] self.grid = f['geometry'].attrs['grid']
self.size = f['geometry'].attrs['size'] self.size = f['geometry'].attrs['size']
if self.version_major == 0 and self.version_minor >= 5: self.origin = f['geometry'].attrs['origin'] if self.version_major == 0 and self.version_minor >= 5 else \
self.origin = f['geometry'].attrs['origin'] np.zeros(3)
r=re.compile('inc[0-9]+') r=re.compile('inc[0-9]+')
increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)} increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)}
@ -66,12 +66,12 @@ class DADF5():
self.con_physics = [] self.con_physics = []
for c in self.constituents: for c in self.constituents:
self.con_physics += f['/'.join([self.increments[0],'constituent',c])].keys() self.con_physics += f['/'.join([self.increments[0],'constituent',c])].keys()
self.con_physics = list(set(self.con_physics)) # make unique self.con_physics = list(set(self.con_physics)) # make unique
self.mat_physics = [] self.mat_physics = []
for m in self.materialpoints: for m in self.materialpoints:
self.mat_physics += f['/'.join([self.increments[0],'materialpoint',m])].keys() self.mat_physics += f['/'.join([self.increments[0],'materialpoint',m])].keys()
self.mat_physics = list(set(self.mat_physics)) # make unique self.mat_physics = list(set(self.mat_physics)) # make unique
self.selection= {'increments': self.increments, self.selection= {'increments': self.increments,
@ -446,6 +446,17 @@ class DADF5():
return f['geometry/x_c'][()] return f['geometry/x_c'][()]
@staticmethod
def _add_absolute(x):
return {
'data': np.abs(x['data']),
'label': '|{}|'.format(x['label']),
'meta': {
'Unit': x['meta']['Unit'],
'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
'Creator': 'dadf5.py:add_abs v{}'.format(version)
}
}
def add_absolute(self,x): def add_absolute(self,x):
""" """
Add absolute value. Add absolute value.
@ -456,21 +467,24 @@ class DADF5():
Label of scalar, vector, or tensor dataset to take absolute value of. Label of scalar, vector, or tensor dataset to take absolute value of.
""" """
def _add_absolute(x): self._add_generic_pointwise(self._add_absolute,{'x':x})
return {
'data': np.abs(x['data']),
'label': '|{}|'.format(x['label']),
'meta': {
'Unit': x['meta']['Unit'],
'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
'Creator': 'dadf5.py:add_abs v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_absolute,{'x':x})
@staticmethod
def _add_calculation(**kwargs):
formula = kwargs['formula']
for d in re.findall(r'#(.*?)#',formula):
formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
return {
'data': eval(formula),
'label': kwargs['label'],
'meta': {
'Unit': kwargs['unit'],
'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
'Creator': 'dadf5.py:add_calculation v{}'.format(version)
}
}
def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True): def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True):
""" """
Add result of a general formula. Add result of a general formula.
@ -492,28 +506,24 @@ class DADF5():
if not vectorized: if not vectorized:
raise NotImplementedError raise NotImplementedError
def _add_calculation(**kwargs): dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
formula = kwargs['formula']
for d in re.findall(r'#(.*?)#',formula):
formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
return {
'data': eval(formula),
'label': kwargs['label'],
'meta': {
'Unit': kwargs['unit'],
'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
'Creator': 'dadf5.py:add_calculation v{}'.format(version)
}
}
dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
args = {'formula':formula,'label':label,'unit':unit,'description':description} args = {'formula':formula,'label':label,'unit':unit,'description':description}
self._add_generic_pointwise(self._add_calculation,dataset_mapping,args)
self.__add_generic_pointwise(_add_calculation,dataset_mapping,args)
@staticmethod
def _add_Cauchy(P,F):
return {
'data': mechanics.Cauchy(P['data'],F['data']),
'label': 'sigma',
'meta': {
'Unit': P['meta']['Unit'],
'Description': 'Cauchy stress calculated from {} ({}) '.format(P['label'],
P['meta']['Description'])+\
'and {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_Cauchy v{}'.format(version)
}
}
def add_Cauchy(self,P='P',F='F'): def add_Cauchy(self,P='P',F='F'):
""" """
Add Cauchy stress calculated from first Piola-Kirchhoff stress and deformation gradient. Add Cauchy stress calculated from first Piola-Kirchhoff stress and deformation gradient.
@ -526,23 +536,20 @@ class DADF5():
Label of the dataset containing the deformation gradient. Defaults to ‘F’. Label of the dataset containing the deformation gradient. Defaults to ‘F’.
""" """
def _add_Cauchy(P,F): self._add_generic_pointwise(self._add_Cauchy,{'P':P,'F':F})
return {
'data': mechanics.Cauchy(P['data'],F['data']),
'label': 'sigma',
'meta': {
'Unit': P['meta']['Unit'],
'Description': 'Cauchy stress calculated from {} ({}) '.format(P['label'],
P['meta']['Description'])+\
'and {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_Cauchy v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_Cauchy,{'P':P,'F':F})
@staticmethod
def _add_determinant(T):
return {
'data': np.linalg.det(T['data']),
'label': 'det({})'.format(T['label']),
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Determinant of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Creator': 'dadf5.py:add_determinant v{}'.format(version)
}
}
def add_determinant(self,T): def add_determinant(self,T):
""" """
Add the determinant of a tensor. Add the determinant of a tensor.
@ -553,21 +560,23 @@ class DADF5():
Label of tensor dataset. Label of tensor dataset.
""" """
def _add_determinant(T): self._add_generic_pointwise(self._add_determinant,{'T':T})
return {
'data': np.linalg.det(T['data']),
'label': 'det({})'.format(T['label']),
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Determinant of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Creator': 'dadf5.py:add_determinant v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_determinant,{'T':T})
@staticmethod
def _add_deviator(T):
if not T['data'].shape[1:] == (3,3):
raise ValueError
return {
'data': mechanics.deviatoric_part(T['data']),
'label': 's_{}'.format(T['label']),
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Deviator of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Creator': 'dadf5.py:add_deviator v{}'.format(version)
}
}
def add_deviator(self,T): def add_deviator(self,T):
""" """
Add the deviatoric part of a tensor. Add the deviatoric part of a tensor.
@ -578,24 +587,20 @@ class DADF5():
Label of tensor dataset. Label of tensor dataset.
""" """
def _add_deviator(T): self._add_generic_pointwise(self._add_deviator,{'T':T})
if not np.all(np.array(T['data'].shape[1:]) == np.array([3,3])):
raise ValueError
return {
'data': mechanics.deviatoric_part(T['data']),
'label': 's_{}'.format(T['label']),
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Deviator of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Creator': 'dadf5.py:add_deviator v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_deviator,{'T':T})
@staticmethod
def _add_eigenvalue(S):
return {
'data': mechanics.eigenvalues(S['data']),
'label': 'lambda({})'.format(S['label']),
'meta' : {
'Unit': S['meta']['Unit'],
'Description': 'Eigenvalues of {} ({})'.format(S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_eigenvalues v{}'.format(version)
}
}
def add_eigenvalues(self,S): def add_eigenvalues(self,S):
""" """
Add eigenvalues of symmetric tensor. Add eigenvalues of symmetric tensor.
@ -606,21 +611,20 @@ class DADF5():
Label of symmetric tensor dataset. Label of symmetric tensor dataset.
""" """
def _add_eigenvalue(S): self._add_generic_pointwise(self._add_eigenvalue,{'S':S})
return {
'data': mechanics.eigenvalues(S['data']),
'label': 'lambda({})'.format(S['label']),
'meta' : {
'Unit': S['meta']['Unit'],
'Description': 'Eigenvalues of {} ({})'.format(S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_eigenvalues v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_eigenvalue,{'S':S})
@staticmethod
def _add_eigenvector(S):
return {
'data': mechanics.eigenvectors(S['data']),
'label': 'v({})'.format(S['label']),
'meta' : {
'Unit': '1',
'Description': 'Eigenvectors of {} ({})'.format(S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_eigenvectors v{}'.format(version)
}
}
def add_eigenvectors(self,S): def add_eigenvectors(self,S):
""" """
Add eigenvectors of symmetric tensor. Add eigenvectors of symmetric tensor.
@ -631,21 +635,32 @@ class DADF5():
Label of symmetric tensor dataset. Label of symmetric tensor dataset.
""" """
def _add_eigenvector(S): self._add_generic_pointwise(self._add_eigenvector,{'S':S})
return {
'data': mechanics.eigenvectors(S['data']),
'label': 'v({})'.format(S['label']),
'meta' : {
'Unit': '1',
'Description': 'Eigenvectors of {} ({})'.format(S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_eigenvectors v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_eigenvector,{'S':S})
@staticmethod
def _add_IPFcolor(q,l):
d = np.array(l)
d_unit = d/np.linalg.norm(d)
m = util.scale_to_coprime(d)
colors = np.empty((len(q['data']),3),np.uint8)
lattice = q['meta']['Lattice']
for i,q in enumerate(q['data']):
o = Orientation(np.array([q['w'],q['x'],q['y'],q['z']]),lattice).reduced()
colors[i] = np.uint8(o.IPFcolor(d_unit)*255)
return {
'data': colors,
'label': 'IPFcolor_[{} {} {}]'.format(*m),
'meta' : {
'Unit': 'RGB (8bit)',
'Lattice': lattice,
'Description': 'Inverse Pole Figure (IPF) colors for direction/plane [{} {} {})'.format(*m),
'Creator': 'dadf5.py:add_IPFcolor v{}'.format(version)
}
}
def add_IPFcolor(self,q,l): def add_IPFcolor(self,q,l):
""" """
Add RGB color tuple of inverse pole figure (IPF) color. Add RGB color tuple of inverse pole figure (IPF) color.
@ -658,33 +673,20 @@ class DADF5():
Lab frame direction for inverse pole figure. Lab frame direction for inverse pole figure.
""" """
def _add_IPFcolor(q,l): self._add_generic_pointwise(self._add_IPFcolor,{'q':q},{'l':l})
d = np.array(l)
d_unit = d/np.linalg.norm(d)
m = util.scale_to_coprime(d)
colors = np.empty((len(q['data']),3),np.uint8)
lattice = q['meta']['Lattice'] @staticmethod
def _add_maximum_shear(S):
for i,q in enumerate(q['data']): return {
o = Orientation(np.array([q['w'],q['x'],q['y'],q['z']]),lattice).reduced() 'data': mechanics.maximum_shear(S['data']),
colors[i] = np.uint8(o.IPFcolor(d_unit)*255) 'label': 'max_shear({})'.format(S['label']),
'meta': {
return { 'Unit': S['meta']['Unit'],
'data': colors, 'Description': 'Maximum shear component of {} ({})'.format(S['label'],S['meta']['Description']),
'label': 'IPFcolor_[{} {} {}]'.format(*m), 'Creator': 'dadf5.py:add_maximum_shear v{}'.format(version)
'meta' : { }
'Unit': 'RGB (8bit)',
'Lattice': lattice,
'Description': 'Inverse Pole Figure (IPF) colors for direction/plane [{} {} {})'.format(*m),
'Creator': 'dadf5.py:add_IPFcolor v{}'.format(version)
}
} }
self.__add_generic_pointwise(_add_IPFcolor,{'q':q},{'l':l})
def add_maximum_shear(self,S): def add_maximum_shear(self,S):
""" """
Add maximum shear components of symmetric tensor. Add maximum shear components of symmetric tensor.
@ -695,21 +697,23 @@ class DADF5():
Label of symmetric tensor dataset. Label of symmetric tensor dataset.
""" """
def _add_maximum_shear(S): self._add_generic_pointwise(self._add_maximum_shear,{'S':S})
return {
'data': mechanics.maximum_shear(S['data']),
'label': 'max_shear({})'.format(S['label']),
'meta': {
'Unit': S['meta']['Unit'],
'Description': 'Maximum shear component of {} ({})'.format(S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_maximum_shear v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_maximum_shear,{'S':S})
@staticmethod
def _add_Mises(S):
t = 'strain' if S['meta']['Unit'] == '1' else \
'stress'
return {
'data': mechanics.Mises_strain(S['data']) if t=='strain' else mechanics.Mises_stress(S['data']),
'label': '{}_vM'.format(S['label']),
'meta': {
'Unit': S['meta']['Unit'],
'Description': 'Mises equivalent {} of {} ({})'.format(t,S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_Mises v{}'.format(version)
}
}
def add_Mises(self,S): def add_Mises(self,S):
""" """
Add the equivalent Mises stress or strain of a symmetric tensor. Add the equivalent Mises stress or strain of a symmetric tensor.
@ -720,23 +724,32 @@ class DADF5():
Label of symmetric tensorial stress or strain dataset. Label of symmetric tensorial stress or strain dataset.
""" """
def _add_Mises(S): self._add_generic_pointwise(self._add_Mises,{'S':S})
t = 'strain' if S['meta']['Unit'] == '1' else \
'stress'
return {
'data': mechanics.Mises_strain(S['data']) if t=='strain' else mechanics.Mises_stress(S['data']),
'label': '{}_vM'.format(S['label']),
'meta': {
'Unit': S['meta']['Unit'],
'Description': 'Mises equivalent {} of {} ({})'.format(t,S['label'],S['meta']['Description']),
'Creator': 'dadf5.py:add_Mises v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_Mises,{'S':S})
@staticmethod
def _add_norm(x,ord):
o = ord
if len(x['data'].shape) == 2:
axis = 1
t = 'vector'
if o is None: o = 2
elif len(x['data'].shape) == 3:
axis = (1,2)
t = 'tensor'
if o is None: o = 'fro'
else:
raise ValueError
return {
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
'label': '|{}|_{}'.format(x['label'],o),
'meta': {
'Unit': x['meta']['Unit'],
'Description': '{}-norm of {} {} ({})'.format(o,t,x['label'],x['meta']['Description']),
'Creator': 'dadf5.py:add_norm v{}'.format(version)
}
}
def add_norm(self,x,ord=None): def add_norm(self,x,ord=None):
""" """
Add the norm of vector or tensor. Add the norm of vector or tensor.
@ -749,36 +762,25 @@ class DADF5():
Order of the norm. inf means NumPy’s inf object. For details refer to numpy.linalg.norm. Order of the norm. inf means NumPy’s inf object. For details refer to numpy.linalg.norm.
""" """
def _add_norm(x,ord): self._add_generic_pointwise(self._add_norm,{'x':x},{'ord':ord})
o = ord
if len(x['data'].shape) == 2:
axis = 1
t = 'vector'
if o is None: o = 2
elif len(x['data'].shape) == 3:
axis = (1,2)
t = 'tensor'
if o is None: o = 'fro'
else:
raise ValueError
return {
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
'label': '|{}|_{}'.format(x['label'],o),
'meta': {
'Unit': x['meta']['Unit'],
'Description': '{}-norm of {} {} ({})'.format(ord,t,x['label'],x['meta']['Description']),
'Creator': 'dadf5.py:add_norm v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_norm,{'x':x},{'ord':ord})
@staticmethod
def _add_PK2(P,F):
return {
'data': mechanics.PK2(P['data'],F['data']),
'label': 'S',
'meta': {
'Unit': P['meta']['Unit'],
'Description': '2. Kirchhoff stress calculated from {} ({}) '.format(P['label'],
P['meta']['Description'])+\
'and {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_PK2 v{}'.format(version)
}
}
def add_PK2(self,P='P',F='F'): def add_PK2(self,P='P',F='F'):
""" """
Add 2. Piola-Kirchhoff calculated from first Piola-Kirchhoff stress and deformation gradient. Add second Piola-Kirchhoff calculated from first Piola-Kirchhoff stress and deformation gradient.
Parameters Parameters
---------- ----------
@ -788,23 +790,32 @@ class DADF5():
Label of deformation gradient dataset. Defaults to ‘F’. Label of deformation gradient dataset. Defaults to ‘F’.
""" """
def _add_PK2(P,F): self._add_generic_pointwise(self._add_PK2,{'P':P,'F':F})
return {
'data': mechanics.PK2(P['data'],F['data']),
'label': 'S',
'meta': {
'Unit': P['meta']['Unit'],
'Description': '2. Kirchhoff stress calculated from {} ({}) '.format(P['label'],
P['meta']['Description'])+\
'and {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_PK2 v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_PK2,{'P':P,'F':F})
@staticmethod
def _add_pole(q,p,polar):
pole = np.array(p)
unit_pole = pole/np.linalg.norm(pole)
m = util.scale_to_coprime(pole)
coords = np.empty((len(q['data']),2))
for i,q in enumerate(q['data']):
o = Rotation(np.array([q['w'],q['x'],q['y'],q['z']]))
rotatedPole = o*unit_pole # rotate pole according to crystal orientation
(x,y) = rotatedPole[0:2]/(1.+abs(unit_pole[2])) # stereographic projection
coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y]
return {
'data': coords,
'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
'meta' : {
'Unit': '1',
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
.format('Polar' if polar else 'Cartesian'),
'Creator' : 'dadf5.py:add_pole v{}'.format(version)
}
}
def add_pole(self,q,p,polar=False): def add_pole(self,q,p,polar=False):
""" """
Add coordinates of stereographic projection of given pole in crystal frame. Add coordinates of stereographic projection of given pole in crystal frame.
@ -819,33 +830,22 @@ class DADF5():
Give pole in polar coordinates. Defaults to False. Give pole in polar coordinates. Defaults to False.
""" """
def _add_pole(q,p,polar): self._add_generic_pointwise(self._add_pole,{'q':q},{'p':p,'polar':polar})
pole = np.array(p)
unit_pole = pole/np.linalg.norm(pole)
m = util.scale_to_coprime(pole)
coords = np.empty((len(q['data']),2))
for i,q in enumerate(q['data']): @staticmethod
o = Rotation(np.array([q['w'],q['x'],q['y'],q['z']])) def _add_rotational_part(F):
rotatedPole = o*unit_pole # rotate pole according to crystal orientation if not F['data'].shape[1:] == (3,3):
(x,y) = rotatedPole[0:2]/(1.+abs(unit_pole[2])) # stereographic projection raise ValueError
coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if polar else [x,y] return {
'data': mechanics.rotational_part(F['data']),
return { 'label': 'R({})'.format(F['label']),
'data': coords, 'meta': {
'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m), 'Unit': F['meta']['Unit'],
'meta' : { 'Description': 'Rotational part of {} ({})'.format(F['label'],F['meta']['Description']),
'Unit': '1', 'Creator': 'dadf5.py:add_rotational_part v{}'.format(version)
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\ }
.format('Polar' if polar else 'Cartesian'),
'Creator' : 'dadf5.py:add_pole v{}'.format(version)
}
} }
self.__add_generic_pointwise(_add_pole,{'q':q},{'p':p,'polar':polar})
def add_rotational_part(self,F): def add_rotational_part(self,F):
""" """
Add rotational part of a deformation gradient. Add rotational part of a deformation gradient.
@ -856,21 +856,23 @@ class DADF5():
Label of deformation gradient dataset. Label of deformation gradient dataset.
""" """
def _add_rotational_part(F): self._add_generic_pointwise(self._add_rotational_part,{'F':F})
return {
'data': mechanics.rotational_part(F['data']),
'label': 'R({})'.format(F['label']),
'meta': {
'Unit': F['meta']['Unit'],
'Description': 'Rotational part of {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_rotational_part v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_rotational_part,{'F':F})
@staticmethod
def _add_spherical(T):
if not T['data'].shape[1:] == (3,3):
raise ValueError
return {
'data': mechanics.spherical_part(T['data']),
'label': 'p_{}'.format(T['label']),
'meta': {
'Unit': T['meta']['Unit'],
'Description': 'Spherical component of tensor {} ({})'.format(T['label'],T['meta']['Description']),
'Creator': 'dadf5.py:add_spherical v{}'.format(version)
}
}
def add_spherical(self,T): def add_spherical(self,T):
""" """
Add the spherical (hydrostatic) part of a tensor. Add the spherical (hydrostatic) part of a tensor.
@ -881,24 +883,23 @@ class DADF5():
Label of tensor dataset. Label of tensor dataset.
""" """
def _add_spherical(T): self._add_generic_pointwise(self._add_spherical,{'T':T})
if not np.all(np.array(T['data'].shape[1:]) == np.array([3,3])):
@staticmethod
def _add_strain_tensor(F,t,m):
if not F['data'].shape[1:] == (3,3):
raise ValueError raise ValueError
return { return {
'data': mechanics.spherical_part(T['data']), 'data': mechanics.strain_tensor(F['data'],t,m),
'label': 'p_{}'.format(T['label']), 'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
'meta': { 'meta': {
'Unit': T['meta']['Unit'], 'Unit': F['meta']['Unit'],
'Description': 'Spherical component of tensor {} ({})'.format(T['label'],T['meta']['Description']), 'Description': 'Strain tensor of {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_spherical v{}'.format(version) 'Creator': 'dadf5.py:add_strain_tensor v{}'.format(version)
} }
} }
self.__add_generic_pointwise(_add_spherical,{'T':T})
def add_strain_tensor(self,F='F',t='V',m=0.0): def add_strain_tensor(self,F='F',t='V',m=0.0):
""" """
Add strain tensor of a deformation gradient. Add strain tensor of a deformation gradient.
@ -916,21 +917,24 @@ class DADF5():
Order of the strain calculation. Defaults to ‘0.0’. Order of the strain calculation. Defaults to ‘0.0’.
""" """
def _add_strain_tensor(F,t,m): self._add_generic_pointwise(self._add_strain_tensor,{'F':F},{'t':t,'m':m})
return {
'data': mechanics.strain_tensor(F['data'],t,m),
'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
'meta': {
'Unit': F['meta']['Unit'],
'Description': 'Strain tensor of {} ({})'.format(F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_strain_tensor v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_strain_tensor,{'F':F},{'t':t,'m':m})
@staticmethod
def _add_stretch_tensor(F,t):
if not F['data'].shape[1:] == (3,3):
raise ValueError
return {
'data': mechanics.left_stretch(F['data']) if t == 'V' else mechanics.right_stretch(F['data']),
'label': '{}({})'.format(t,F['label']),
'meta': {
'Unit': F['meta']['Unit'],
'Description': '{} stretch tensor of {} ({})'.format('Left' if t == 'V' else 'Right',
F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_stretch_tensor v{}'.format(version)
}
}
def add_stretch_tensor(self,F='F',t='V'): def add_stretch_tensor(self,F='F',t='V'):
""" """
Add stretch tensor of a deformation gradient. Add stretch tensor of a deformation gradient.
@ -944,77 +948,65 @@ class DADF5():
Defaults to ‘V’. Defaults to ‘V’.
""" """
def _add_stretch_tensor(F,t): self._add_generic_pointwise(self._add_stretch_tensor,{'F':F},{'t':t})
return {
'data': mechanics.left_stretch(F['data']) if t == 'V' else mechanics.right_stretch(F['data']),
'label': '{}({})'.format(t,F['label']),
'meta': {
'Unit': F['meta']['Unit'],
'Description': '{} stretch tensor of {} ({})'.format('Left' if t == 'V' else 'Right',
F['label'],F['meta']['Description']),
'Creator': 'dadf5.py:add_stretch_tensor v{}'.format(version)
}
}
self.__add_generic_pointwise(_add_stretch_tensor,{'F':F},{'t':t})
def __add_generic_pointwise(self,func,dataset_mapping,args={}): def _job(self,group,func,datasets,args,lock):
"""Execute job for _add_generic_pointwise."""
try:
datasets_in = {}
lock.acquire()
with h5py.File(self.fname,'r') as f:
for arg,label in datasets.items():
loc = f[group+'/'+label]
datasets_in[arg]={'data' :loc[()],
'label':label,
'meta': {k:v.decode() for k,v in loc.attrs.items()}}
lock.release()
r = func(**datasets_in,**args)
return [group,r]
except Exception as err:
print('Error during calculation: {}.'.format(err))
return None
def _add_generic_pointwise(self,func,datasets,args={}):
""" """
General function to add pointwise data. General function to add pointwise data.
Parameters Parameters
---------- ----------
func : function func : function
Function that calculates a new dataset from one or more datasets per HDF5 group. Callback function that calculates a new dataset from one or more datasets per HDF5 group.
dataset_mapping : dictionary datasets : dictionary
Mapping HDF5 data label to callback function argument Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func).
extra_args : dictionary, optional args : dictionary, optional
Any extra arguments parsed to func. Arguments parsed to func.
""" """
def job(args): N_threads = int(Environment().options['DAMASK_NUM_THREADS'])
"""Call function with input data + extra arguments, returns results + group.""" pool = multiprocessing.Pool(N_threads)
args['results'].put({**args['func'](**args['in']),'group':args['group']}) lock = multiprocessing.Manager().Lock()
env = Environment() groups = self.groups_with_datasets(datasets.values())
N_threads = int(env.options['DAMASK_NUM_THREADS']) default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock)
N_threads //=N_threads # disable for the moment
results = Queue(N_threads) util.progressBar(iteration=0,total=len(groups))
pool = util.ThreadPool(N_threads) for i,result in enumerate(pool.imap_unordered(default_arg,groups)):
N_added = N_threads + 1 util.progressBar(iteration=i+1,total=len(groups))
if not result: continue
lock.acquire()
with h5py.File(self.fname, 'a') as f:
try:
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
for l,v in result[1]['meta'].items():
dataset.attrs[l]=v.encode()
except OSError as err:
print('Could not add dataset: {}.'.format(err))
lock.release()
todo = [] pool.close()
# ToDo: It would be more memory efficient to read only from file when required, i.e. do to it in pool.add_task pool.join()
for group in self.groups_with_datasets(dataset_mapping.values()):
with h5py.File(self.fname,'r') as f:
datasets_in = {}
for arg,label in dataset_mapping.items():
loc = f[group+'/'+label]
data = loc[()]
meta = {k:loc.attrs[k].decode() for k in loc.attrs.keys()}
datasets_in[arg] = {'data': data, 'meta': meta, 'label': label}
todo.append({'in':{**datasets_in,**args},'func':func,'group':group,'results':results})
pool.map(job, todo[:N_added]) # initialize
N_not_calculated = len(todo)
while N_not_calculated > 0:
result = results.get()
with h5py.File(self.fname,'a') as f: # write to file
dataset_out = f[result['group']].create_dataset(result['label'],data=result['data'])
for k in result['meta'].keys():
dataset_out.attrs[k] = result['meta'][k].encode()
N_not_calculated-=1
if N_added < len(todo): # add more jobs
pool.add_task(job,todo[N_added])
N_added +=1
pool.wait_completion()
def to_vtk(self,labels,mode='cell'): def to_vtk(self,labels,mode='cell'):
@ -1098,29 +1090,27 @@ class DADF5():
for label in (labels if isinstance(labels,list) else [labels]): for label in (labels if isinstance(labels,list) else [labels]):
for p in self.iter_visible('con_physics'): for p in self.iter_visible('con_physics'):
if p != 'generic': if p != 'generic':
for c in self.iter_visible('constituents'): for c in self.iter_visible('constituents'):
x = self.get_dataset_location(label) x = self.get_dataset_location(label)
if len(x) == 0: if len(x) == 0:
continue continue
array = self.read_dataset(x,0) array = self.read_dataset(x,0)
shape = [array.shape[0],np.product(array.shape[1:])] shape = [array.shape[0],np.product(array.shape[1:])]
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape), vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True))
deep=True,array_type= vtk.VTK_DOUBLE)) vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1! vtk_geom.GetCellData().AddArray(vtk_data[-1])
vtk_geom.GetCellData().AddArray(vtk_data[-1])
else: else:
x = self.get_dataset_location(label) x = self.get_dataset_location(label)
if len(x) == 0: if len(x) == 0:
continue continue
array = self.read_dataset(x,0) array = self.read_dataset(x,0)
shape = [array.shape[0],np.product(array.shape[1:])] shape = [array.shape[0],np.product(array.shape[1:])]
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape), vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True))
deep=True,array_type= vtk.VTK_DOUBLE)) ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name
ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') # identify phase name dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name
dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) # removing phase name vtk_data[-1].SetName(dset_name)
vtk_data[-1].SetName(dset_name) vtk_geom.GetCellData().AddArray(vtk_data[-1])
vtk_geom.GetCellData().AddArray(vtk_data[-1])
self.set_visible('materialpoints',materialpoints_backup) self.set_visible('materialpoints',materialpoints_backup)
@ -1129,38 +1119,35 @@ class DADF5():
for label in (labels if isinstance(labels,list) else [labels]): for label in (labels if isinstance(labels,list) else [labels]):
for p in self.iter_visible('mat_physics'): for p in self.iter_visible('mat_physics'):
if p != 'generic': if p != 'generic':
for m in self.iter_visible('materialpoints'): for m in self.iter_visible('materialpoints'):
x = self.get_dataset_location(label)
if len(x) == 0:
continue
array = self.read_dataset(x,0)
shape = [array.shape[0],np.product(array.shape[1:])]
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True))
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
vtk_geom.GetCellData().AddArray(vtk_data[-1])
else:
x = self.get_dataset_location(label) x = self.get_dataset_location(label)
if len(x) == 0: if len(x) == 0:
continue continue
array = self.read_dataset(x,0) array = self.read_dataset(x,0)
shape = [array.shape[0],np.product(array.shape[1:])] shape = [array.shape[0],np.product(array.shape[1:])]
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape), vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True))
deep=True,array_type= vtk.VTK_DOUBLE)) vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
vtk_geom.GetCellData().AddArray(vtk_data[-1]) vtk_geom.GetCellData().AddArray(vtk_data[-1])
else:
x = self.get_dataset_location(label)
if len(x) == 0:
continue
array = self.read_dataset(x,0)
shape = [array.shape[0],np.product(array.shape[1:])]
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
deep=True,array_type= vtk.VTK_DOUBLE))
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
vtk_geom.GetCellData().AddArray(vtk_data[-1])
self.set_visible('constituents',constituents_backup) self.set_visible('constituents',constituents_backup)
if mode.lower()=='cell': if mode.lower()=='cell':
writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \ writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
vtk.vtkXMLUnstructuredGridWriter() vtk.vtkXMLUnstructuredGridWriter()
x = self.get_dataset_location('u_n') x = self.get_dataset_location('u_n')
vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0), vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0),deep=True))
deep=True,array_type=vtk.VTK_DOUBLE)) vtk_data[-1].SetName('u')
vtk_data[-1].SetName('u') vtk_geom.GetPointData().AddArray(vtk_data[-1])
vtk_geom.GetPointData().AddArray(vtk_data[-1])
elif mode.lower()=='point': elif mode.lower()=='point':
writer = vtk.vtkXMLPolyDataWriter() writer = vtk.vtkXMLPolyDataWriter()
file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0], file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0],

56
python/damask/util.py
View File

@ -6,8 +6,6 @@ import shlex
from fractions import Fraction from fractions import Fraction
from functools import reduce from functools import reduce
from optparse import Option from optparse import Option
from queue import Queue
from threading import Thread
import numpy as np import numpy as np
@ -201,57 +199,3 @@ class return_message():
def __repr__(self): def __repr__(self):
"""Return message suitable for interactive shells.""" """Return message suitable for interactive shells."""
return srepr(self.message) return srepr(self.message)
class ThreadPool:
"""Pool of threads consuming tasks from a queue."""
class Worker(Thread):
"""Thread executing tasks from a given tasks queue."""
def __init__(self, tasks):
"""Worker for tasks."""
Thread.__init__(self)
self.tasks = tasks
self.daemon = True
self.start()
def run(self):
while True:
func, args, kargs = self.tasks.get()
try:
func(*args, **kargs)
except Exception as e:
# An exception happened in this thread
print(e)
finally:
# Mark this task as done, whether an exception happened or not
self.tasks.task_done()
def __init__(self, num_threads):
"""
Thread pool.
Parameters
----------
num_threads : int
number of threads
"""
self.tasks = Queue(num_threads)
for _ in range(num_threads):
self.Worker(self.tasks)
def add_task(self, func, *args, **kargs):
"""Add a task to the queue."""
self.tasks.put((func, args, kargs))
def map(self, func, args_list):
"""Add a list of tasks to the queue."""
for args in args_list:
self.add_task(func, args)
def wait_completion(self):
"""Wait for completion of all the tasks in the queue."""
self.tasks.join()