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DAMASK_EICMD
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Merge branch 'development' into YAML-Prerequisites

This commit is contained in:
Martin Diehl 2020-05-07 23:11:38 +02:00
parent 1610a6e12a 58537c478d
commit 4f8c7ea2d5
67 changed files with 1011 additions and 2053 deletions
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1
.gitlab-ci.yml
View File

@ -203,7 +203,6 @@ Post_OrientationConversion:
stage: postprocessing
script:
- OrientationConversion/test.py
- OrientationConversion/test2.py
except:
- master
- release

2
PRIVATE

@ -1 +1 @@
Subproject commit 232a094c715bcbbd1c6652c4dc4a4a50d402b82f
Subproject commit c595994cd8880acadf50b5dedb79156d04d35b91

2
VERSION
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@ -1 +1 @@
v2.0.3-2311-gf1afc159
v2.0.3-2412-g0d03c469

6
installation/symlink_Processing.py
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@ -16,10 +16,6 @@ if not os.path.isdir(binDir):
#define ToDo list
processing_subDirs = ['pre',
'post',
'misc',
]
processing_extensions = ['.py',
'.sh',
]
sys.stdout.write('\nsymbolic linking...\n')
@ -31,7 +27,7 @@ for subDir in processing_subDirs:
for theFile in os.listdir(theDir):
theName,theExt = os.path.splitext(theFile)
if theExt in processing_extensions: # only consider files with proper extensions
if theExt in ['.py']:
src = os.path.abspath(os.path.join(theDir,theFile))
sym_link = os.path.abspath(os.path.join(binDir,theName))

30
processing/misc/ang_toTable.py
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@ -1,30 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [angfile[s]]', description = """
Convert TSL/EDAX *.ang file to ASCIItable
""", version = scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ang(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.txt')

2
processing/post/DADF5_postResults.py
View File

@ -33,7 +33,7 @@ for filename in options.filenames:
results = damask.Result(filename)
if not results.structured: continue
coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin)
coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin).reshape(-1,3,order='F')
N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
N_digits = 5 # hack to keep test intact

49
processing/post/addCauchy.py
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@ -1,49 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column containing Cauchy stress based on deformation gradient and first Piola--Kirchhoff stress.
""", version = scriptID)
parser.add_option('-f','--defgrad',
dest = 'defgrad',
type = 'string', metavar = 'string',
help = 'heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress',
dest = 'stress',
type = 'string', metavar = 'string',
help = 'heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.set_defaults(defgrad = 'f',
stress = 'p',
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.add('Cauchy',
damask.mechanics.Cauchy(table.get(options.stress ).reshape(-1,3,3),
table.get(options.defgrad).reshape(-1,3,3)).reshape(-1,9),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

55
processing/post/addCompatibilityMismatch.py
View File

@ -17,7 +17,7 @@ def volTetrahedron(coords):
"""
Return the volume of the tetrahedron with given vertices or sides.
Ifvertices are given they must be in a NumPy array with shape (4,3): the
If vertices are given they must be in a NumPy array with shape (4,3): the
position vectors of the 4 vertices in 3 dimensions; if the six sides are
given, they must be an array of length 6. If both are given, the sides
will be used in the calculation.
@ -67,14 +67,13 @@ def volumeMismatch(size,F,nodes):
(compatible) cube and determinant of deformation gradient at Fourier point.
"""
coords = np.empty([8,3])
vMismatch = np.empty(grid[::-1])
volInitial = size.prod()/grid.prod()
vMismatch = np.empty(F.shape[:3])
#--------------------------------------------------------------------------------------------------
# calculate actual volume and volume resulting from deformation gradient
for k in range(grid[2]):
for k in range(grid[0]):
for j in range(grid[1]):
for i in range(grid[0]):
for i in range(grid[2]):
coords[0,0:3] = nodes[k, j, i ,0:3]
coords[1,0:3] = nodes[k ,j, i+1,0:3]
coords[2,0:3] = nodes[k ,j+1,i+1,0:3]
@ -91,8 +90,7 @@ def volumeMismatch(size,F,nodes):
+ abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[5,0:3]])) \
+ abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[0,0:3]]))) \
/np.linalg.det(F[k,j,i,0:3,0:3])
return vMismatch/volInitial
return vMismatch/(size.prod()/grid.prod())
def shapeMismatch(size,F,nodes,centres):
@ -103,35 +101,34 @@ def shapeMismatch(size,F,nodes,centres):
the corners of reconstructed (combatible) volume element and the vectors calculated by deforming
the initial volume element with the current deformation gradient.
"""
coordsInitial = np.empty([8,3])
sMismatch = np.empty(grid[::-1])
sMismatch = np.empty(F.shape[:3])
#--------------------------------------------------------------------------------------------------
# initial positions
coordsInitial[0,0:3] = [-size[0]/grid[0],-size[1]/grid[1],-size[2]/grid[2]]
coordsInitial[1,0:3] = [+size[0]/grid[0],-size[1]/grid[1],-size[2]/grid[2]]
coordsInitial[2,0:3] = [+size[0]/grid[0],+size[1]/grid[1],-size[2]/grid[2]]
coordsInitial[3,0:3] = [-size[0]/grid[0],+size[1]/grid[1],-size[2]/grid[2]]
coordsInitial[4,0:3] = [-size[0]/grid[0],-size[1]/grid[1],+size[2]/grid[2]]
coordsInitial[5,0:3] = [+size[0]/grid[0],-size[1]/grid[1],+size[2]/grid[2]]
coordsInitial[6,0:3] = [+size[0]/grid[0],+size[1]/grid[1],+size[2]/grid[2]]
coordsInitial[7,0:3] = [-size[0]/grid[0],+size[1]/grid[1],+size[2]/grid[2]]
coordsInitial = coordsInitial/2.0
delta = size/grid*.5
coordsInitial = np.vstack((delta * np.array((-1,-1,-1)),
delta * np.array((+1,-1,-1)),
delta * np.array((+1,+1,-1)),
delta * np.array((-1,+1,-1)),
delta * np.array((-1,-1,+1)),
delta * np.array((+1,-1,+1)),
delta * np.array((+1,+1,+1)),
delta * np.array((-1,+1,+1))))
#--------------------------------------------------------------------------------------------------
# compare deformed original and deformed positions to actual positions
for k in range(grid[2]):
for k in range(grid[0]):
for j in range(grid[1]):
for i in range(grid[0]):
for i in range(grid[2]):
sMismatch[k,j,i] = \
+ np.linalg.norm(nodes[k, j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[0,0:3]))\
+ np.linalg.norm(nodes[k, j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[1,0:3]))\
+ np.linalg.norm(nodes[k, j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[2,0:3]))\
+ np.linalg.norm(nodes[k+1,j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[1,0:3]))\
+ np.linalg.norm(nodes[k+1,j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[2,0:3]))\
+ np.linalg.norm(nodes[k, j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[3,0:3]))\
+ np.linalg.norm(nodes[k+1,j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[4,0:3]))\
+ np.linalg.norm(nodes[k, j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[4,0:3]))\
+ np.linalg.norm(nodes[k+1,j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[5,0:3]))\
+ np.linalg.norm(nodes[k+1,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[6,0:3]))\
+ np.linalg.norm(nodes[k+1,j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[7,0:3]))
+ np.linalg.norm(nodes[k ,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[7,0:3]))
return sMismatch
@ -178,20 +175,20 @@ for name in filenames:
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
F = table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3)
F = table.get(options.defgrad).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
nodes = damask.grid_filters.node_coord(size,F)
if options.shape:
centers = damask.grid_filters.cell_coord(size,F)
shapeMismatch = shapeMismatch( size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes,centers)
shapeMismatch = shapeMismatch(size,F,nodes,centers)
table.add('shapeMismatch(({}))'.format(options.defgrad),
shapeMismatch.reshape(-1,1),
shapeMismatch.reshape(-1,1,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
if options.volume:
volumeMismatch = volumeMismatch(size,table.get(options.defgrad).reshape(grid[2],grid[1],grid[0],3,3),nodes)
volumeMismatch = volumeMismatch(size,F,nodes)
table.add('volMismatch(({}))'.format(options.defgrad),
volumeMismatch.reshape(-1,1),
volumeMismatch.reshape(-1,1,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

5
processing/post/addCurl.py
View File

@ -49,9 +49,10 @@ for name in filenames:
for label in options.labels:
field = table.get(label)
shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3) # vector or tensor
field = field.reshape(np.append(grid[::-1],shape))
field = field.reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+shape)
curl = damask.grid_filters.curl(size,field)
table.add('curlFFT({})'.format(label),
damask.grid_filters.curl(size[::-1],field).reshape(-1,np.prod(shape)),
curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

45
processing/post/addDeterminant.py
View File

@ -1,45 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing determinant of requested tensor column(s).
""", version = scriptID)
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing tensor field values')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.tensor is None:
parser.error('no data column specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for tensor in options.tensor:
table.add('det({})'.format(tensor),
np.linalg.det(table.get(tensor).reshape(-1,3,3)),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

51
processing/post/addDeviator.py
View File

@ -1,51 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(2)]', description = """
Add column(s) containing deviator of requested tensor column(s).
""", version = scriptID)
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar='<string LIST>',
help = 'heading of columns containing tensor field values')
parser.add_option('-s','--spherical',
dest = 'spherical',
action = 'store_true',
help = 'report spherical part of tensor (hydrostatic component, pressure)')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.tensor is None:
parser.error('no data column specified...')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for tensor in options.tensor:
table.add('dev({})'.format(tensor),
damask.mechanics.deviatoric_part(table.get(tensor).reshape(-1,3,3)).reshape(-1,9),
scriptID+' '+' '.join(sys.argv[1:]))
if options.spherical:
table.add('sph({})'.format(tensor),
damask.mechanics.spherical_part(table.get(tensor).reshape(-1,3,3)),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

14
processing/post/addDisplacement.py
View File

@ -5,8 +5,6 @@ import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
@ -52,22 +50,22 @@ for name in filenames:
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
F = table.get(options.f).reshape(np.append(grid[::-1],(3,3)))
F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
if options.nodal:
table = damask.Table(damask.grid_filters.node_coord0(grid[::-1],size[::-1]).reshape(-1,3),
table = damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'),
{'pos':(3,)})
table.add('avg({}).{}'.format(options.f,options.pos),
damask.grid_filters.node_displacement_avg(size[::-1],F).reshape(-1,3),
damask.grid_filters.node_displacement_avg(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.add('fluct({}).{}'.format(options.f,options.pos),
damask.grid_filters.node_displacement_fluct(size[::-1],F).reshape(-1,3),
damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
else:
table.add('avg({}).{}'.format(options.f,options.pos),
damask.grid_filters.cell_displacement_avg(size[::-1],F).reshape(-1,3),
damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.add('fluct({}).{}'.format(options.f,options.pos),
damask.grid_filters.cell_displacement_fluct(size[::-1],F).reshape(-1,3),
damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

5
processing/post/addDivergence.py
View File

@ -49,9 +49,10 @@ for name in filenames:
for label in options.labels:
field = table.get(label)
shape = (3,) if np.prod(field.shape)//np.prod(grid) == 3 else (3,3) # vector or tensor
field = field.reshape(np.append(grid[::-1],shape))
field = field.reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+shape)
div = damask.grid_filters.divergence(size,field)
table.add('divFFT({})'.format(label),
damask.grid_filters.divergence(size[::-1],field).reshape(-1,np.prod(shape)//3),
div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

5
processing/post/addGradient.py
View File

@ -49,9 +49,10 @@ for name in filenames:
for label in options.labels:
field = table.get(label)
shape = (1,) if np.prod(field.shape)//np.prod(grid) == 1 else (3,) # scalar or vector
field = field.reshape(np.append(grid[::-1],shape))
field = field.reshape(tuple(grid)+(-1,),order='F')
grad = damask.grid_filters.gradient(size,field)
table.add('gradFFT({})'.format(label),
damask.grid_filters.gradient(size[::-1],field).reshape(-1,np.prod(shape)*3),
grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

41
processing/post/addInfo.py
View File

@ -1,41 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add info lines to ASCIItable header.
""", version = scriptID)
parser.add_option('-i',
'--info',
dest = 'info', action = 'extend', metavar = '<string LIST>',
help = 'items to add')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.info is None:
parser.error('no info specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.comments += options.info
table.to_ASCII(sys.stdout if name is None else name)

56
processing/post/addMises.py
View File

@ -1,56 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add vonMises equivalent values for symmetric part of requested strains and/or stresses.
""", version = scriptID)
parser.add_option('-e','--strain',
dest = 'strain',
action = 'extend', metavar = '<string LIST>',
help = 'heading(s) of columns containing strain tensors')
parser.add_option('-s','--stress',
dest = 'stress',
action = 'extend', metavar = '<string LIST>',
help = 'heading(s) of columns containing stress tensors')
parser.set_defaults(strain = [],
stress = [],
)
(options,filenames) = parser.parse_args()
if options.stress is [] and options.strain is []:
parser.error('no data column specified...')
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for strain in options.strain:
table.add('Mises({})'.format(strain),
damask.mechanics.Mises_strain(damask.mechanics.symmetric(table.get(strain).reshape(-1,3,3))),
scriptID+' '+' '.join(sys.argv[1:]))
for stress in options.stress:
table.add('Mises({})'.format(stress),
damask.mechanics.Mises_stress(damask.mechanics.symmetric(table.get(stress).reshape(-1,3,3))),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

2
processing/post/addOrientations.py
View File

@ -172,7 +172,7 @@ for name in filenames:
elif inputtype == 'matrix':
d = representations['matrix'][1]
o = damask.Rotation.fromMatrix(list(map(float,table.data[column:column+d])))
o = damask.Rotation.fromMatrix(np.array(list(map(float,table.data[column:column+d]))).reshape(3,3))
elif inputtype == 'frame':
M = np.array(list(map(float,table.data[column[0]:column[0]+3] + \

2
processing/post/addSchmidfactors.py
View File

@ -214,7 +214,7 @@ for name in filenames:
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
o = damask.Rotation(list(map(float,table.data[column:column+4])))
o = damask.Rotation(np.array(list(map(float,table.data[column:column+4]))))
table.data_append( np.abs( np.sum(slip_direction * (o * force) ,axis=1) \
* np.sum(slip_normal * (o * normal),axis=1)))

44
processing/post/addTable.py
View File

@ -1,44 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Append data of ASCIItable(s) column-wise.
""", version = scriptID)
parser.add_option('-a', '--add','--table',
dest = 'table',
action = 'extend', metavar = '<string LIST>',
help = 'tables to add')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.table is None:
parser.error('no table specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for addTable in options.table:
table2 = damask.Table.from_ASCII(addTable)
table2.data = table2.data[:table.data.shape[0]]
table.join(table2)
table.to_ASCII(sys.stdout if name is None else name)

2
processing/post/averageDown.py
View File

@ -91,7 +91,7 @@ for name in filenames:
table = damask.Table(averagedDown,table.shapes,table.comments)
coords = damask.grid_filters.cell_coord0(packedGrid,size,shift/packedGrid*size+origin)
table.set(options.pos, coords.reshape(-1,3))
table.set(options.pos, coords.reshape(-1,3,order='F'))
outname = os.path.join(os.path.dirname(name),prefix+os.path.basename(name))

6
processing/post/blowUp.py
View File

@ -59,13 +59,13 @@ for name in filenames:
packing = np.array(options.packing,'i')
outSize = grid*packing
data = table.data.values.reshape(tuple(grid)+(-1,))
blownUp = ndimage.interpolation.zoom(data,tuple(packing)+(1,),order=0,mode='nearest').reshape(outSize.prod(),-1)
data = table.data.values.reshape(tuple(grid)+(-1,),order='F')
blownUp = ndimage.interpolation.zoom(data,tuple(packing)+(1,),order=0,mode='nearest').reshape(outSize.prod(),-1,order='F')
table = damask.Table(blownUp,table.shapes,table.comments)
coords = damask.grid_filters.cell_coord0(outSize,size,origin)
table.set(options.pos,coords.reshape(-1,3))
table.set(options.pos,coords.reshape(-1,3,order='F'))
table.set('elem',np.arange(1,outSize.prod()+1))
outname = os.path.join(os.path.dirname(name),prefix+os.path.basename(name))

43
processing/post/growTable.py
View File

@ -1,43 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Append data of ASCIItable(s) row-wise.
""", version = scriptID)
parser.add_option('-a', '--add','--table',
dest = 'table',
action = 'extend', metavar = '<string LIST>',
help = 'tables to add')
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.table is None:
parser.error('no table specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for growTable in options.table:
table2 = damask.Table.from_ASCII(growTable)
table.append(table2)
table.to_ASCII(sys.stdout if name is None else name)

74
processing/post/permuteData.py
View File

@ -2,6 +2,7 @@
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
@ -41,73 +42,20 @@ parser.set_defaults(label = [],
)
(options,filenames) = parser.parse_args()
if len(options.label) == 0:
parser.error('no labels specified.')
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name)
except IOError:
continue
damask.util.report(scriptName,name)
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
randomSeed = int(os.urandom(4).hex(), 16) if options.randomSeed is None else options.randomSeed # random seed per file
rng = np.random.default_rng(randomSeed)
# ------------------------------------------ process labels ---------------------------------------
for label in options.label:
data = table.get(label)
uniques,inverse = np.unique(data,return_inverse=True,axis=0) if options.unique else (data,np.arange(len(data)))
rng.shuffle(uniques)
table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:]))
errors = []
remarks = []
columns = []
dims = []
indices = table.label_index (options.label)
dimensions = table.label_dimension(options.label)
for i,index in enumerate(indices):
if index == -1: remarks.append('label "{}" not present...'.format(options.label[i]))
else:
columns.append(index)
dims.append(dimensions[i])
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header ---------------------------------------
randomSeed = int(os.urandom(4).hex(), 16) if options.randomSeed is None else options.randomSeed # random seed per file
np.random.seed(randomSeed)
table.info_append([scriptID + '\t' + ' '.join(sys.argv[1:]),
'random seed {}'.format(randomSeed),
])
table.head_write()
# ------------------------------------------ process data ------------------------------------------
table.data_readArray() # read all data at once
for col,dim in zip(columns,dims):
if options.unique:
s = set(map(tuple,table.data[:,col:col+dim])) # generate set of (unique) values
uniques = np.array(map(np.array,s)) # translate set to np.array
shuffler = dict(zip(s,np.random.permutation(len(s)))) # random permutation
table.data[:,col:col+dim] = uniques[np.array(map(lambda x: shuffler[tuple(x)],
table.data[:,col:col+dim]))] # fill table with mapped uniques
else:
np.random.shuffle(table.data[:,col:col+dim]) # independently shuffle every row
# ------------------------------------------ output result -----------------------------------------
table.data_writeArray()
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables
table.to_ASCII(sys.stdout if name is None else name)

50
processing/post/reLabel.py
View File

@ -1,50 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Rename scalar, vectorial, and/or tensorial data header labels.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'label',
action = 'extend', metavar='<string LIST>',
help = 'column(s) to rename')
parser.add_option('-s','--substitute',
dest = 'substitute',
action = 'extend', metavar='<string LIST>',
help = 'new column label(s)')
parser.set_defaults(label = [],
substitute = [],
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if len(options.label) != len(options.substitute):
parser.error('number of column labels and substitutes do not match.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for label,substitute in zip(options.label,options.substitute):
table.rename(label,substitute,scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

49
processing/post/scaleData.py
View File

@ -1,49 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Uniformly scale column values by given factor.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'labels',
action = 'extend', metavar = '<string LIST>',
help ='column(s) to scale')
parser.add_option('-f','--factor',
dest = 'factor',
action = 'extend', metavar='<float LIST>',
help = 'factor(s) per column')
parser.set_defaults(label = [],
factor = [])
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if len(options.labels) != len(options.factor):
parser.error('number of column labels and factors do not match.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for label,factor in zip(options.labels,options.factor):
table.set(label,table.get(label)*float(factor),scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

49
processing/post/shiftData.py
View File

@ -1,49 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Uniformly shift column values by given offset.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'labels',
action = 'extend', metavar = '<string LIST>',
help ='column(s) to shift')
parser.add_option('-o','--offset',
dest = 'offset',
action = 'extend', metavar='<float LIST>',
help = 'offset(s) per column')
parser.set_defaults(label = [],
offset = [])
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if len(options.labels) != len(options.offset):
parser.error('number of column labels and offsets do not match.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for label,offset in zip(options.labels,options.offset):
table.set(label,table.get(label)+float(offset),scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

50
processing/post/sortTable.py
View File

@ -1,50 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Sort rows by given (or all) column label(s).
Examples:
With coordinates in columns "x", "y", and "z"; sorting with x slowest and z fastest varying index: --label x,y,z.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'labels',
action = 'extend', metavar = '<string LIST>',
help = 'list of column labels (a,b,c,...)')
parser.add_option('-r','--reverse',
dest = 'reverse',
action = 'store_true',
help = 'sort in reverse')
parser.set_defaults(reverse = False,
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.labels is None:
parser.error('no labels specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.sort_by(options.labels,not options.reverse)
table.to_ASCII(sys.stdout if name is None else name)

42
processing/pre/geom_clean.py
View File

@ -1,42 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Smooth microstructure by selecting most frequent index within given stencil at each location.
""", version=scriptID)
parser.add_option('-s','--stencil',
dest = 'stencil',
type = 'int', metavar = 'int',
help = 'size of smoothing stencil [%default]')
parser.set_defaults(stencil = 3)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom.clean(options.stencil))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

66
processing/pre/geom_fromScratch.py
View File

@ -1,66 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Generate homogeneous geometry.
""", version = scriptID)
parser.add_option('-g','--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c grid of hexahedral box %default')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'x,y,z of geometry size')
parser.add_option('-o','--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'x,y,z of geometry origin %default')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index [%default]')
parser.add_option('-f','--fill',
dest = 'fill',
type = 'float', metavar = 'int',
help = 'microstructure index [%default]')
parser.set_defaults(grid = (16,16,16),
origin = (0.,0.,0.),
homogenization = 1,
fill = 1,
)
(options, filename) = parser.parse_args()
name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)
dtype = float if np.isnan(options.fill) or int(options.fill) != options.fill else int
geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype),
size=options.size,
origin=options.origin,
homogenization=options.homogenization,
comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak(geom)
geom.to_file(sys.stdout if name is None else name,pack=False)

12
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -24,22 +24,22 @@ def findClosestSeed(seeds, weights, point):
def Laguerre_tessellation(grid, size, seeds, weights, origin = np.zeros(3), periodic = True, cpus = 2):
if periodic:
weights_p = np.tile(weights,27).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
weights_p = np.tile(weights.squeeze(),27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.])))
seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
coords = damask.grid_filters.cell_coord0(grid*3,size*3,-origin-size).reshape(-1,3,order='F')
coords = damask.grid_filters.cell_coord0(grid*3,size*3,-origin-size).reshape(-1,3)
else:
weights_p = weights.flatten()
weights_p = weights.squeeze()
seeds_p = seeds
coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3,order='F')
coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3)
if cpus > 1:
pool = multiprocessing.Pool(processes = cpus)
result = pool.map_async(partial(findClosestSeed,seeds_p,weights_p), [coord for coord in coords])
pool.close()
pool.join()
closest_seed = np.array(result.get())
closest_seed = np.array(result.get()).reshape(-1,3)
else:
closest_seed= np.array([findClosestSeed(seeds_p,weights_p,coord) for coord in coords])
@ -52,7 +52,7 @@ def Laguerre_tessellation(grid, size, seeds, weights, origin = np.zeros(3), peri
def Voronoi_tessellation(grid, size, seeds, origin = np.zeros(3), periodic = True):
coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3,order='F')
coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3)
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,closest_seed = KDTree.query(coords)

47
processing/pre/geom_mirror.py
View File

@ -1,47 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Mirror along given directions.
""", version=scriptID)
validDirections = ['x','y','z']
parser.add_option('-d','--direction',
dest = 'directions',
action = 'extend', metavar = '<string LIST>',
help = "directions in which to mirror {{{}}}".format(','.join(validDirections)))
parser.add_option( '--reflect',
dest = 'reflect',
action = 'store_true',
help = 'reflect (include) outermost layers')
parser.set_defaults(reflect = False)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom.mirror(options.directions,options.reflect))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

37
processing/pre/geom_pack.py
View File

@ -1,37 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Pack ranges to "a to b" and/or multiples to "n of x".
""", version = scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=True)

60
processing/pre/geom_rescale.py
View File

@ -1,60 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Scales independently in x, y, and z direction in terms of grid and/or size.
Either absolute values or relative factors (like "0.25x") can be used.
""", version = scriptID)
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'string', nargs = 3, metavar = 'string string string',
help = 'a,b,c grid of hexahedral box')
parser.add_option('-s', '--size',
dest = 'size',
type = 'string', nargs = 3, metavar = 'string string string',
help = 'x,y,z size of hexahedral box')
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid = geom.get_grid()
size = geom.get_size()
new_grid = grid if options.grid is None else \
np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
else int(n) for o,n in zip(grid,options.grid)],dtype=int)
new_size = size if options.size is None else \
np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \
else float(n) for o,n in zip(size,options.size)],dtype=float)
geom.scale(new_grid)
damask.util.croak(geom.update(microstructure = None,size = new_size))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

45
processing/pre/geom_toTable.py
View File

@ -1,45 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Translate geom description into ASCIItable containing position and microstructure.
""", version = scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom)
coord0 = damask.grid_filters.cell_coord0(geom.grid,geom.size,geom.origin).reshape(-1,3)
comments = geom.comments \
+ [scriptID + ' ' + ' '.join(sys.argv[1:]),
'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
'size\tx {}\ty {}\tz {}'.format(*geom.size),
'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
'homogenization\t{}'.format(geom.homogenization)]
table = damask.Table(coord0,{'pos':(3,)},comments)
table.add('microstructure',geom.microstructure.reshape((-1,1),order='F'))
table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.txt')

37
processing/pre/geom_unpack.py
View File

@ -1,37 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Unpack ranges "a to b" and/or "n of x" multiples (exclusively in one line).
""", version = scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

2
processing/pre/seeds_fromGeom.py
View File

@ -54,7 +54,7 @@ for name in filenames:
np.in1d(microstructure,options.blacklist,invert=True) if options.blacklist else \
np.full(geom.grid.prod(),True,dtype=bool))
seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3)
seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3,order='F')
comments = geom.comments \
+ [scriptID + ' ' + ' '.join(sys.argv[1:]),

2
processing/pre/seeds_fromRandom.py
View File

@ -128,7 +128,7 @@ for name in filenames:
if not options.selective:
coords = damask.grid_filters.cell_coord0(grid,size).reshape(-1,3)
coords = damask.grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
seeds = coords[np.random.choice(np.prod(grid), options.N, replace=False)] \
+ np.broadcast_to(size/grid,(options.N,3))*(np.random.rand(options.N,3)*.5-.25) # wobble without leaving grid
else:

3
python/.coveragerc
View File

@ -1,2 +1,5 @@
[run]
omit = tests/*
damask/_asciitable.py
damask/_test.py
damask/config/*

16
python/damask/_geom.py
View File

@ -322,11 +322,10 @@ class Geom:
if i != grid.prod():
raise TypeError('Invalid file: expected {} entries, found {}'.format(grid.prod(),i))
microstructure = microstructure.reshape(grid,order='F')
if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present
if not np.any(np.mod(microstructure,1) != 0.0): # no float present
microstructure = microstructure.astype('int')
return Geom(microstructure.reshape(grid),size,origin,homogenization,comments)
return Geom(microstructure.reshape(grid,order='F'),size,origin,homogenization,comments)
@staticmethod
@ -352,16 +351,15 @@ class Geom:
"""
if periodic:
weights_p = np.tile(weights,27).flatten(order='F') # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
weights_p = np.tile(weights,27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.])))
seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
coords = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3,order='F')
coords = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3)
else:
weights_p = weights.flatten()
weights_p = weights
seeds_p = seeds
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
pool = multiprocessing.Pool(processes = int(Environment().options['DAMASK_NUM_THREADS']))
result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
@ -396,7 +394,7 @@ class Geom:
perform a periodic tessellation. Defaults to True.
"""
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,microstructure = KDTree.query(coords)

3
python/damask/_orientation.py
View File

@ -38,6 +38,9 @@ class Orientation:
else:
self.rotation = Rotation.fromQuaternion(rotation) # assume quaternion
if self.rotation.quaternion.shape != (4,):
raise NotImplementedError('Support for multiple rotations missing')
def disorientation(self,
other,
SST = True,

24
python/damask/_result.py
View File

@ -111,7 +111,7 @@ class Result:
select from 'set', 'add', and 'del'
what : str
attribute to change (must be from self.selection)
datasets : list of str or Boolean
datasets : list of str or bool
name of datasets as list, supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []
@ -203,7 +203,7 @@ class Result:
----------
what : str
attribute to change (must be from self.selection)
datasets : list of str or Boolean
datasets : list of str or bool
name of datasets as list, supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []
@ -219,7 +219,7 @@ class Result:
----------
what : str
attribute to change (must be from self.selection)
datasets : list of str or Boolean
datasets : list of str or bool
name of datasets as list, supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []
@ -235,7 +235,7 @@ class Result:
----------
what : str
attribute to change (must be from self.selection)
datasets : list of str or Boolean
datasets : list of str or bool
name of datasets as list, supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []
@ -262,10 +262,10 @@ class Result:
datasets : iterable or str
component : int
homogenization component to consider for constituent data
tagged : Boolean
tagged : bool
tag Table.column name with '#component'
defaults to False
split : Boolean
split : bool
split Table by increment and return dictionary of Tables
defaults to True
@ -326,7 +326,7 @@ class Result:
Parameters
----------
datasets : iterable or str or Boolean
datasets : iterable or str or bool
Examples
--------
@ -460,11 +460,19 @@ class Result:
def cell_coordinates(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
return grid_filters.cell_coord0(self.grid,self.size,self.origin).reshape(-1,3)
return grid_filters.cell_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F')
else:
with h5py.File(self.fname,'r') as f:
return f['geometry/x_c'][()]
def node_coordinates(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
return grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F')
else:
with h5py.File(self.fname,'r') as f:
return f['geometry/x_n'][()]
@staticmethod
def _add_absolute(x):

259
python/damask/_rotation.py
View File

@ -1,6 +1,7 @@
import numpy as np
from ._Lambert import ball_to_cube, cube_to_ball
from . import mechanics
_P = -1
@ -61,6 +62,8 @@ class Rotation:
def __repr__(self):
"""Orientation displayed as unit quaternion, rotation matrix, and Bunge-Euler angles."""
if self.quaternion.shape != (4,):
raise NotImplementedError('Support for multiple rotations missing')
return '\n'.join([
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
'Matrix:\n{}'.format(self.asMatrix()),
@ -83,6 +86,8 @@ class Rotation:
considere rotation of (3,3,3,3)-matrix
"""
if self.quaternion.shape != (4,):
raise NotImplementedError('Support for multiple rotations missing')
if isinstance(other, Rotation): # rotate a rotation
self_q = self.quaternion[0]
self_p = self.quaternion[1:]
@ -107,7 +112,7 @@ class Rotation:
elif other.shape == (3,3,): # rotate a single (3x3)-matrix
return np.dot(self.asMatrix(),np.dot(other,self.asMatrix().T))
elif other.shape == (3,3,3,3,):
raise NotImplementedError
raise NotImplementedError('Support for rotation of 4th order tensors missing')
else:
return NotImplemented
else:
@ -116,7 +121,7 @@ class Rotation:
def inverse(self):
"""In-place inverse rotation/backward rotation."""
self.quaternion[1:] *= -1
self.quaternion[...,1:] *= -1
return self
def inversed(self):
@ -125,12 +130,12 @@ class Rotation:
def standardize(self):
"""In-place quaternion representation with positive q."""
if self.quaternion[0] < 0.0: self.quaternion*=-1
"""In-place quaternion representation with positive real part."""
self.quaternion[self.quaternion[...,0] < 0.0] *= -1
return self
def standardized(self):
"""Quaternion representation with positive q."""
"""Quaternion representation with positive real part."""
return self.copy().standardize()
@ -157,15 +162,17 @@ class 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.fromAverage([self,other])
################################################################################################
# convert to different orientation representations (numpy arrays)
def asQuaternion(self):
def as_quaternion(self):
"""
Unit quaternion [q, p_1, p_2, p_3] unless quaternion == True: damask.quaternion object.
Unit quaternion [q, p_1, p_2, p_3].
Parameters
----------
@ -175,8 +182,8 @@ class Rotation:
"""
return self.quaternion
def asEulers(self,
degrees = False):
def as_Eulers(self,
degrees = False):
"""
Bunge-Euler angles: (φ_1, ϕ, φ_2).
@ -190,9 +197,9 @@ class Rotation:
if degrees: eu = np.degrees(eu)
return eu
def asAxisAngle(self,
degrees = False,
pair = False):
def as_axis_angle(self,
degrees = False,
pair = False):
"""
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
@ -205,15 +212,15 @@ class Rotation:
"""
ax = Rotation.qu2ax(self.quaternion)
if degrees: ax[3] = np.degrees(ax[3])
return (ax[:3],ax[3]) if pair else ax
if degrees: ax[...,3] = np.degrees(ax[...,3])
return (ax[...,:3],ax[...,3]) if pair else ax
def asMatrix(self):
def as_matrix(self):
"""Rotation matrix."""
return Rotation.qu2om(self.quaternion)
def asRodrigues(self,
vector = False):
def as_Rodrigues(self,
vector = False):
"""
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
@ -224,9 +231,9 @@ class Rotation:
"""
ro = Rotation.qu2ro(self.quaternion)
return ro[:3]*ro[3] if vector else ro
return ro[...,:3]*ro[...,3] if vector else ro
def asHomochoric(self):
def as_homochoric(self):
"""Homochoric vector: (h_1, h_2, h_3)."""
return Rotation.qu2ho(self.quaternion)
@ -234,7 +241,7 @@ class Rotation:
"""Cubochoric vector: (c_1, c_2, c_3)."""
return Rotation.qu2cu(self.quaternion)
def asM(self):
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.
@ -244,114 +251,133 @@ class Rotation:
https://doi.org/10.2514/1.28949
"""
return np.outer(self.quaternion,self.quaternion)
return np.einsum('...i,...j',self.quaternion,self.quaternion)
# for compatibility (old names do not follow convention)
asM = M
asQuaternion = as_quaternion
asEulers = as_Eulers
asAxisAngle = as_axis_angle
asMatrix = as_matrix
asRodrigues = as_Rodrigues
asHomochoric = as_homochoric
################################################################################################
# static constructors. The input data needs to follow the convention, options allow to
# relax these convections
# Static constructors. The input data needs to follow the conventions, options allow to
# relax the conventions.
@staticmethod
def fromQuaternion(quaternion,
acceptHomomorph = False,
P = -1):
def from_quaternion(quaternion,
acceptHomomorph = False,
P = -1):
qu = quaternion if isinstance(quaternion,np.ndarray) and quaternion.dtype == np.dtype(float) \
else np.array(quaternion,dtype=float)
if P > 0: qu[1:4] *= -1 # convert from P=1 to P=-1
if qu[0] < 0.0:
if acceptHomomorph:
qu *= -1.
else:
raise ValueError('Quaternion has negative first component: {}.'.format(qu[0]))
if not np.isclose(np.linalg.norm(qu), 1.0):
raise ValueError('Quaternion is not of unit length: {} {} {} {}.'.format(*qu))
qu = np.array(quaternion,dtype=float)
if qu.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if P > 0: qu[...,1:4] *= -1 # convert from P=1 to P=-1
if acceptHomomorph:
qu[qu[...,0] < 0.0] *= -1
else:
if np.any(qu[...,0] < 0.0):
raise ValueError('Quaternion with negative first (real) component.')
if not np.all(np.isclose(np.linalg.norm(qu,axis=-1), 1.0)):
raise ValueError('Quaternion is not of unit length.')
return Rotation(qu)
@staticmethod
def fromEulers(eulers,
degrees = False):
def from_Eulers(eulers,
degrees = False):
eu = np.array(eulers,dtype=float)
if eu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
eu = eulers if isinstance(eulers, np.ndarray) and eulers.dtype == np.dtype(float) \
else np.array(eulers,dtype=float)
eu = np.radians(eu) if degrees else eu
if np.any(eu < 0.0) or np.any(eu > 2.0*np.pi) or eu[1] > np.pi:
raise ValueError('Euler angles outside of [0..2π],[0..π],[0..2π]: {} {} {}.'.format(*eu))
if np.any(eu < 0.0) or np.any(eu > 2.0*np.pi) or np.any(eu[...,1] > np.pi): # ToDo: No separate check for PHI
raise ValueError('Euler angles outside of [0..2π],[0..π],[0..2π].')
return Rotation(Rotation.eu2qu(eu))
@staticmethod
def fromAxisAngle(angleAxis,
degrees = False,
normalise = False,
P = -1):
def from_axis_angle(axis_angle,
degrees = False,
normalise = False,
P = -1):
ax = angleAxis if isinstance(angleAxis, np.ndarray) and angleAxis.dtype == np.dtype(float) \
else np.array(angleAxis,dtype=float)
if P > 0: ax[0:3] *= -1 # convert from P=1 to P=-1
if degrees: ax[ 3] = np.radians(ax[3])
if normalise: ax[0:3] /= np.linalg.norm(ax[0:3])
if ax[3] < 0.0 or ax[3] > np.pi:
raise ValueError('Axis angle rotation angle outside of [0..π]: {}.'.format(ax[3]))
if not np.isclose(np.linalg.norm(ax[0:3]), 1.0):
raise ValueError('Axis angle rotation axis is not of unit length: {} {} {}.'.format(*ax[0:3]))
ax = np.array(axis_angle,dtype=float)
if ax.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if P > 0: ax[...,0:3] *= -1 # convert from P=1 to P=-1
if degrees: ax[..., 3] = np.radians(ax[...,3])
if normalise: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1)
if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
raise ValueError('Axis angle rotation angle outside of [0..π].')
if not np.all(np.isclose(np.linalg.norm(ax[...,0:3],axis=-1), 1.0)):
raise ValueError('Axis angle rotation axis is not of unit length.')
return Rotation(Rotation.ax2qu(ax))
@staticmethod
def fromBasis(basis,
orthonormal = True,
reciprocal = False,
):
def from_basis(basis,
orthonormal = True,
reciprocal = False):
om = np.array(basis,dtype=float)
if om.shape[:-3:-1] != (3,3):
raise ValueError('Invalid shape.')
om = basis if isinstance(basis, np.ndarray) else np.array(basis).reshape(3,3)
if reciprocal:
om = np.linalg.inv(om.T/np.pi) # transform reciprocal basis set
om = np.linalg.inv(mechanics.transpose(om)/np.pi) # transform reciprocal basis set
orthonormal = False # contains stretch
if not orthonormal:
(U,S,Vh) = np.linalg.svd(om) # singular value decomposition
om = np.dot(U,Vh)
if not np.isclose(np.linalg.det(om),1.0):
raise ValueError('matrix is not a proper rotation: {}.'.format(om))
if not np.isclose(np.dot(om[0],om[1]), 0.0) \
or not np.isclose(np.dot(om[1],om[2]), 0.0) \
or not np.isclose(np.dot(om[2],om[0]), 0.0):
raise ValueError('matrix is not orthogonal: {}.'.format(om))
om = np.einsum('...ij,...jl->...il',U,Vh)
if not np.all(np.isclose(np.linalg.det(om),1.0)):
raise ValueError('Orientation matrix has determinant ≠ 1.')
if not np.all(np.isclose(np.einsum('...i,...i',om[...,0],om[...,1]), 0.0)) \
or not np.all(np.isclose(np.einsum('...i,...i',om[...,1],om[...,2]), 0.0)) \
or not np.all(np.isclose(np.einsum('...i,...i',om[...,2],om[...,0]), 0.0)):
raise ValueError('Orientation matrix is not orthogonal.')
return Rotation(Rotation.om2qu(om))
@staticmethod
def fromMatrix(om,
):
def from_matrix(om):
return Rotation.fromBasis(om)
return Rotation.from_basis(om)
@staticmethod
def fromRodrigues(rodrigues,
normalise = False,
P = -1):
def from_Rodrigues(rodrigues,
normalise = False,
P = -1):
ro = rodrigues if isinstance(rodrigues, np.ndarray) and rodrigues.dtype == np.dtype(float) \
else np.array(rodrigues,dtype=float)
if P > 0: ro[0:3] *= -1 # convert from P=1 to P=-1
if normalise: ro[0:3] /= np.linalg.norm(ro[0:3])
if not np.isclose(np.linalg.norm(ro[0:3]), 1.0):
raise ValueError('Rodrigues rotation axis is not of unit length: {} {} {}.'.format(*ro[0:3]))
if ro[3] < 0.0:
raise ValueError('Rodrigues rotation angle not positive: {}.'.format(ro[3]))
ro = np.array(rodrigues,dtype=float)
if ro.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if P > 0: ro[...,0:3] *= -1 # convert from P=1 to P=-1
if normalise: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1)
if np.any(ro[...,3] < 0.0):
raise ValueError('Rodrigues vector rotation angle not positive.')
if not np.all(np.isclose(np.linalg.norm(ro[...,0:3],axis=-1), 1.0)):
raise ValueError('Rodrigues vector rotation axis is not of unit length.')
return Rotation(Rotation.ro2qu(ro))
@staticmethod
def fromHomochoric(homochoric,
P = -1):
def from_homochoric(homochoric,
P = -1):
ho = np.array(homochoric,dtype=float)
if ho.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
ho = homochoric if isinstance(homochoric, np.ndarray) and homochoric.dtype == np.dtype(float) \
else np.array(homochoric,dtype=float)
if P > 0: ho *= -1 # convert from P=1 to P=-1
if np.linalg.norm(ho) > (3.*np.pi/4.)**(1./3.)+1e-9:
raise ValueError('Coordinate outside of the sphere: {} {} {}.'.format(ho))
if np.any(np.linalg.norm(ho,axis=-1) > (3.*np.pi/4.)**(1./3.)+1e-9):
raise ValueError('Homochoric coordinate outside of the sphere.')
return Rotation(Rotation.ho2qu(ho))
@ -359,11 +385,12 @@ class Rotation:
def fromCubochoric(cubochoric,
P = -1):
cu = cubochoric if isinstance(cubochoric, np.ndarray) and cubochoric.dtype == np.dtype(float) \
else np.array(cubochoric,dtype=float)
cu = np.array(cubochoric,dtype=float)
if cu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
if np.abs(np.max(cu))>np.pi**(2./3.) * 0.5+1e-9:
raise ValueError('Coordinate outside of the cube: {} {} {}.'.format(*cu))
raise ValueError('Cubochoric coordinate outside of the cube: {} {} {}.'.format(*cu))
ho = Rotation.cu2ho(cu)
if P > 0: ho *= -1 # convert from P=1 to P=-1
@ -403,17 +430,34 @@ class Rotation:
return Rotation.fromQuaternion(np.real(vec.T[eig.argmax()]),acceptHomomorph = True)
@staticmethod
def fromRandom():
r = np.random.random(3)
A = np.sqrt(r[2])
B = np.sqrt(1.0-r[2])
return Rotation(np.array([np.cos(2.0*np.pi*r[0])*A,
np.sin(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])).standardize()
def from_random(shape=None):
if shape is None:
r = np.random.random(3)
elif hasattr(shape, '__iter__'):
r = np.random.random(tuple(shape)+(3,))
else:
r = np.random.random((shape,3))
A = np.sqrt(r[...,2])
B = np.sqrt(1.0-r[...,2])
q = np.stack([np.cos(2.0*np.pi*r[...,0])*A,
np.sin(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)
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q).standardize()
# for compatibility (old names do not follow convention)
fromQuaternion = from_quaternion
fromEulers = from_Eulers
fromAxisAngle = from_axis_angle
fromBasis = from_basis
fromMatrix = from_matrix
fromRodrigues = from_Rodrigues
fromHomochoric = from_homochoric
fromRandom = from_random
####################################################################################################
# Code below available according to the following conditions on https://github.com/MarDiehl/3Drotations
@ -808,12 +852,11 @@ class Rotation:
c = np.cos(ax[3]*0.5)
s = np.sin(ax[3]*0.5)
qu = np.array([ c, ax[0]*s, ax[1]*s, ax[2]*s ])
return qu
else:
c = np.cos(ax[...,3:4]*.5)
s = np.sin(ax[...,3:4]*.5)
qu = np.where(np.abs(ax[...,3:4])<1.e-6,[1.0, 0.0, 0.0, 0.0],np.block([c, ax[...,:3]*s]))
return qu
return qu
@staticmethod
def ax2om(ax):
@ -859,7 +902,7 @@ class Rotation:
# 180 degree case
ro += [np.inf] if np.isclose(ax[3],np.pi,atol=1.0e-15,rtol=0.0) else \
[np.tan(ax[3]*0.5)]
return np.array(ro)
ro = np.array(ro)
else:
ro = np.block([ax[...,:3],
np.where(np.isclose(ax[...,3:4],np.pi,atol=1.e-15,rtol=.0),
@ -867,7 +910,7 @@ class Rotation:
np.tan(ax[...,3:4]*0.5))
])
ro[np.abs(ax[...,3])<1.e-6] = [.0,.0,_P,.0]
return ro
return ro
@staticmethod
def ax2ho(ax):
@ -875,11 +918,10 @@ class Rotation:
if len(ax.shape) == 1:
f = (0.75 * ( ax[3] - np.sin(ax[3]) ))**(1.0/3.0)
ho = ax[0:3] * f
return ho
else:
f = (0.75 * ( ax[...,3:4] - np.sin(ax[...,3:4]) ))**(1.0/3.0)
ho = ax[...,:3] * f
return ho
return ho
@staticmethod
def ax2cu(ax):
@ -936,7 +978,6 @@ class Rotation:
f = np.where(np.isfinite(ro[...,3:4]),2.0*np.arctan(ro[...,3:4]) -np.sin(2.0*np.arctan(ro[...,3:4])),np.pi)
ho = np.where(np.broadcast_to(np.sum(ro[...,0:3]**2.0,axis=-1,keepdims=True) < 1.e-6,ro[...,0:3].shape),
np.zeros(3), ro[...,0:3]* (0.75*f)**(1.0/3.0))
return ho
@staticmethod
@ -1010,7 +1051,7 @@ class Rotation:
if len(ho.shape) == 1:
return ball_to_cube(ho)
else:
raise NotImplementedError
raise NotImplementedError('Support for multiple rotations missing')
#---------- Cubochoric ----------
@ -1045,4 +1086,4 @@ class Rotation:
if len(cu.shape) == 1:
return cube_to_ball(cu)
else:
raise NotImplementedError
raise NotImplementedError('Support for multiple rotations missing')

130
python/damask/grid_filters.py
View File

@ -1,3 +1,17 @@
"""
Filters for operations on regular grids.
Notes
-----
The grids are defined as (x,y,z,...) where x is fastest and z is slowest.
This convention is consistent with the geom file format.
When converting to/from a plain list (e.g. storage in ASCII table),
the following operations are required for tensorial data:
D3 = D1.reshape(grid+(-1,),order='F').reshape(grid+(3,3))
D1 = D3.reshape(grid+(-1,)).reshape(-1,9,order='F')
"""
from scipy import spatial as _spatial
import numpy as _np
@ -7,8 +21,12 @@ def _ks(size,grid,first_order=False):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
grid : numpy.ndarray of shape (3)
number of grid points.
first_order : bool, optional
correction for first order derivatives, defaults to False.
"""
k_sk = _np.where(_np.arange(grid[0])>grid[0]//2,_np.arange(grid[0])-grid[0],_np.arange(grid[0]))/size[0]
@ -19,8 +37,7 @@ def _ks(size,grid,first_order=False):
k_si = _np.arange(grid[2]//2+1)/size[2]
kk, kj, ki = _np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
return _np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3)
return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
def curl(size,field):
@ -29,8 +46,10 @@ def curl(size,field):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
periodic field of which the curl is calculated.
"""
n = _np.prod(field.shape[3:])
@ -53,8 +72,10 @@ def divergence(size,field):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
periodic field of which the divergence is calculated.
"""
n = _np.prod(field.shape[3:])
@ -69,12 +90,14 @@ def divergence(size,field):
def gradient(size,field):
"""
Calculate gradient of a vector or scalar field in Fourier space.
Calculate gradient of a scalar or vector field in Fourier space.
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
field : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
periodic field of which the gradient is calculated.
"""
n = _np.prod(field.shape[3:])
@ -93,9 +116,9 @@ def cell_coord0(grid,size,origin=_np.zeros(3)):
Parameters
----------
grid : numpy.ndarray
grid : numpy.ndarray of shape (3)
number of grid points.
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
origin : numpy.ndarray, optional
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
@ -103,7 +126,11 @@ def cell_coord0(grid,size,origin=_np.zeros(3)):
"""
start = origin + size/grid*.5
end = origin + size - size/grid*.5
return _np.mgrid[start[0]:end[0]:grid[0]*1j,start[1]:end[1]:grid[1]*1j,start[2]:end[2]:grid[2]*1j].T
return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],grid[0]),
_np.linspace(start[1],end[1],grid[1]),
_np.linspace(start[2],end[2],grid[2]),indexing = 'ij'),
axis = -1)
def cell_displacement_fluct(size,F):
@ -112,7 +139,7 @@ def cell_displacement_fluct(size,F):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
@ -139,14 +166,14 @@ def cell_displacement_avg(size,F):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
"""
F_avg = _np.average(F,axis=(0,1,2))
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),cell_coord0(F.shape[:3][::-1],size))
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),cell_coord0(F.shape[:3],size))
def cell_displacement(size,F):
@ -155,7 +182,7 @@ def cell_displacement(size,F):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
@ -170,25 +197,25 @@ def cell_coord(size,F,origin=_np.zeros(3)):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
origin : numpy.ndarray, optional
origin : numpy.ndarray of shape (3), optional
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
"""
return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
return cell_coord0(F.shape[:3],size,origin) + cell_displacement(size,F)
def cell_coord0_gridSizeOrigin(coord0,ordered=True):
"""
Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
Return grid 'DNA', i.e. grid, size, and origin from 1D array of cell positions.
Parameters
----------
coord0 : numpy.ndarray
array of undeformed cell coordinates.
coord0 : numpy.ndarray of shape (:,3)
undeformed cell coordinates.
ordered : bool, optional
expect coord0 data to be ordered (x fast, z slow).
@ -211,13 +238,13 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
start = origin + delta*.5
end = origin - delta*.5 + size
if not _np.allclose(coords[0],_np.linspace(start[0],end[0],grid[0])) and \
_np.allclose(coords[1],_np.linspace(start[1],end[1],grid[1])) and \
_np.allclose(coords[2],_np.linspace(start[2],end[2],grid[2])):
if not (_np.allclose(coords[0],_np.linspace(start[0],end[0],grid[0])) and \
_np.allclose(coords[1],_np.linspace(start[1],end[1],grid[1])) and \
_np.allclose(coords[2],_np.linspace(start[2],end[2],grid[2]))):
raise ValueError('Regular grid spacing violated.')
if ordered and not _np.allclose(coord0.reshape(tuple(grid[::-1])+(3,)),cell_coord0(grid,size,origin)):
raise ValueError('Input data is not a regular grid.')
if ordered and not _np.allclose(coord0.reshape(tuple(grid)+(3,),order='F'),cell_coord0(grid,size,origin)):
raise ValueError('Input data is not ordered (x fast, z slow).')
return (grid,size,origin)
@ -241,17 +268,18 @@ def node_coord0(grid,size,origin=_np.zeros(3)):
Parameters
----------
grid : numpy.ndarray
grid : numpy.ndarray of shape (3)
number of grid points.
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
origin : numpy.ndarray, optional
origin : numpy.ndarray of shape (3), optional
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
"""
return _np.mgrid[origin[0]:size[0]+origin[0]:(grid[0]+1)*1j,
origin[1]:size[1]+origin[1]:(grid[1]+1)*1j,
origin[2]:size[2]+origin[2]:(grid[2]+1)*1j].T
return _np.stack(_np.meshgrid(_np.linspace(origin[0],size[0]+origin[0],grid[0]+1),
_np.linspace(origin[1],size[1]+origin[1],grid[1]+1),
_np.linspace(origin[2],size[2]+origin[2],grid[2]+1),indexing = 'ij'),
axis = -1)
def node_displacement_fluct(size,F):
@ -260,7 +288,7 @@ def node_displacement_fluct(size,F):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
@ -275,14 +303,14 @@ def node_displacement_avg(size,F):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
"""
F_avg = _np.average(F,axis=(0,1,2))
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),node_coord0(F.shape[:3][::-1],size))
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),node_coord0(F.shape[:3],size))
def node_displacement(size,F):
@ -291,7 +319,7 @@ def node_displacement(size,F):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
@ -306,15 +334,15 @@ def node_coord(size,F,origin=_np.zeros(3)):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size of the periodic field.
F : numpy.ndarray
deformation gradient field.
origin : numpy.ndarray, optional
origin : numpy.ndarray of shape (3), optional
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
"""
return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F)
return node_coord0(F.shape[:3],size,origin) + node_displacement(size,F)
def cell_2_node(cell_data):
@ -335,14 +363,14 @@ def node_2_cell(node_data):
return c[:-1,:-1,:-1]
def node_coord0_gridSizeOrigin(coord0,ordered=False):
def node_coord0_gridSizeOrigin(coord0,ordered=True):
"""
Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
Return grid 'DNA', i.e. grid, size, and origin from 1D array of nodal positions.
Parameters
----------
coord0 : numpy.ndarray
array of undeformed nodal coordinates.
coord0 : numpy.ndarray of shape (:,3)
undeformed nodal coordinates.
ordered : bool, optional
expect coord0 data to be ordered (x fast, z slow).
@ -357,13 +385,13 @@ def node_coord0_gridSizeOrigin(coord0,ordered=False):
if (grid+1).prod() != len(coord0):
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
if not _np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \
_np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \
_np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],grid[2]+1)):
if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \
_np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \
_np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],grid[2]+1))):
raise ValueError('Regular grid spacing violated.')
if ordered and not _np.allclose(coord0.reshape(tuple((grid+1)[::-1])+(3,)),node_coord0(grid,size,origin)):
raise ValueError('Input data is not a regular grid.')
if ordered and not _np.allclose(coord0.reshape(tuple(grid+1)+(3,),order='F'),node_coord0(grid,size,origin)):
raise ValueError('Input data is not ordered (x fast, z slow).')
return (grid,size,origin)
@ -374,15 +402,15 @@ def regrid(size,F,new_grid):
Parameters
----------
size : numpy.ndarray
size : numpy.ndarray of shape (3)
physical size
F : numpy.ndarray
F : numpy.ndarray of shape (:,:,:,3,3)
deformation gradient field
new_grid : numpy.ndarray
new_grid : numpy.ndarray of shape (3)
new grid for undeformed coordinates
"""
c = cell_coord0(F.shape[:3][::-1],size) \
c = cell_coord0(F.shape[:3],size) \
+ cell_displacement_avg(size,F) \
+ cell_displacement_fluct(size,F)

12
python/damask/mechanics.py
View File

@ -135,16 +135,16 @@ def PK2(P,F):
Parameters
----------
P : numpy.ndarray of shape (:,3,3) or (3,3)
P : numpy.ndarray of shape (...,3,3) or (3,3)
First Piola-Kirchhoff stress.
F : numpy.ndarray of shape (:,3,3) or (3,3)
F : numpy.ndarray of shape (...,3,3) or (3,3)
Deformation gradient.
"""
if _np.shape(F) == _np.shape(P) == (3,3):
S = _np.dot(_np.linalg.inv(F),P)
else:
S = _np.einsum('ijk,ikl->ijl',_np.linalg.inv(F),P)
S = _np.einsum('...jk,...kl->...jl',_np.linalg.inv(F),P)
return symmetric(S)
@ -241,7 +241,7 @@ def symmetric(T):
Parameters
----------
T : numpy.ndarray of shape (:,3,3) or (3,3)
T : numpy.ndarray of shape (...,3,3) or (3,3)
Tensor of which the symmetrized values are computed.
"""
@ -254,12 +254,12 @@ def transpose(T):
Parameters
----------
T : numpy.ndarray of shape (:,3,3) or (3,3)
T : numpy.ndarray of shape (...,3,3) or (3,3)
Tensor of which the transpose is computed.
"""
return T.T if _np.shape(T) == (3,3) else \
_np.transpose(T,(0,2,1))
_np.swapaxes(T,axis2=-2,axis1=-1)
def _polar_decomposition(T,requested):

24
python/tests/test_Rotation.py
View File

@ -157,6 +157,30 @@ class TestRotation:
print(m,o,rot.asQuaternion())
assert ok and o.max() < np.pi**(2./3.)*0.5+1.e-9
@pytest.mark.parametrize('function',[Rotation.from_quaternion,
Rotation.from_Eulers,
Rotation.from_axis_angle,
Rotation.from_matrix,
Rotation.from_Rodrigues,
Rotation.from_homochoric])
def test_invalid_shape(self,function):
invalid_shape = np.random.random(np.random.randint(8,32,(3)))
with pytest.raises(ValueError):
function(invalid_shape)
@pytest.mark.parametrize('function,invalid',[(Rotation.from_quaternion, np.array([-1,0,0,0])),
(Rotation.from_quaternion, np.array([1,1,1,0])),
(Rotation.from_Eulers, np.array([1,4,0])),
(Rotation.from_axis_angle, np.array([1,0,0,4])),
(Rotation.from_axis_angle, np.array([1,1,0,1])),
(Rotation.from_matrix, np.random.rand(3,3)),
(Rotation.from_Rodrigues, np.array([1,0,0,-1])),
(Rotation.from_Rodrigues, np.array([1,1,0,1])),
(Rotation.from_homochoric, np.array([2,2,2])) ])
def test_invalid(self,function,invalid):
with pytest.raises(ValueError):
function(invalid)
@pytest.mark.parametrize('conversion',[Rotation.qu2om,
Rotation.qu2eu,
Rotation.qu2ax,

47
python/tests/test_grid_filters.py
View File

@ -9,13 +9,13 @@ class TestGridFilters:
size = np.random.random(3)
grid = np.random.randint(8,32,(3))
coord = grid_filters.cell_coord0(grid,size)
assert np.allclose(coord[0,0,0],size/grid*.5) and coord.shape == tuple(grid[::-1]) + (3,)
assert np.allclose(coord[0,0,0],size/grid*.5) and coord.shape == tuple(grid) + (3,)
def test_node_coord0(self):
size = np.random.random(3)
grid = np.random.randint(8,32,(3))
coord = grid_filters.node_coord0(grid,size)
assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(grid[::-1]+1) + (3,)
assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(grid+1) + (3,)
def test_coord0(self):
size = np.random.random(3)
@ -31,7 +31,7 @@ class TestGridFilters:
size = np.random.random(3)
origin = np.random.random(3)
coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa
_grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape(-1,3))'.format(mode))
_grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))'.format(mode))
assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
def test_displacement_fluct_equivalence(self):
@ -57,9 +57,9 @@ class TestGridFilters:
shifted = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode))
unshifted = eval('grid_filters.{}_coord0(grid,size)'.format(mode))
if mode == 'cell':
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid[::-1]) +(3,)))
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid) +(3,)))
elif mode == 'node':
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid[::-1]+1)+(3,)))
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid+1)+(3,)))
@pytest.mark.parametrize('function',[grid_filters.cell_displacement_avg,
grid_filters.node_displacement_avg])
@ -80,8 +80,43 @@ class TestGridFilters:
F = np.broadcast_to(np.random.random((3,3)), tuple(grid)+(3,3))
assert np.allclose(function(size,F),0.0)
@pytest.mark.parametrize('function',[grid_filters.coord0_check,
grid_filters.node_coord0_gridSizeOrigin,
grid_filters.cell_coord0_gridSizeOrigin])
def test_invalid_coordinates(self,function):
invalid_coordinates = np.random.random((np.random.randint(12,52),3))
with pytest.raises(ValueError):
function(invalid_coordinates)
@pytest.mark.parametrize('function',[grid_filters.node_coord0_gridSizeOrigin,
grid_filters.cell_coord0_gridSizeOrigin])
def test_uneven_spaced_coordinates(self,function):
start = np.random.random(3)
end = np.random.random(3)*10. + start
grid = np.random.randint(8,32,(3))
uneven = np.stack(np.meshgrid(np.logspace(start[0],end[0],grid[0]),
np.logspace(start[1],end[1],grid[1]),
np.logspace(start[2],end[2],grid[2]),indexing = 'ij'),
axis = -1).reshape((grid.prod(),3),order='F')
with pytest.raises(ValueError):
function(uneven)
@pytest.mark.parametrize('mode',[True,False])
@pytest.mark.parametrize('function',[grid_filters.node_coord0_gridSizeOrigin,
grid_filters.cell_coord0_gridSizeOrigin])
def test_unordered_coordinates(self,function,mode):
origin = np.random.random(3)
size = np.random.random(3)*10.+origin
grid = np.random.randint(8,32,(3))
unordered = grid_filters.node_coord0(grid,size,origin).reshape(-1,3)
if mode:
with pytest.raises(ValueError):
function(unordered,mode)
else:
function(unordered,mode)
def test_regrid(self):
size = np.random.random(3)
grid = np.random.randint(8,32,(3))
F = np.broadcast_to(np.eye(3), tuple(grid[::-1])+(3,3))
F = np.broadcast_to(np.eye(3), tuple(grid)+(3,3))
assert all(grid_filters.regrid(size,F,grid) == np.arange(grid.prod()))

158
python/tests/test_mechanics.py
View File

@ -1,4 +1,6 @@
import pytest
import numpy as np
from damask import mechanics
class TestMechanics:
@ -7,127 +9,77 @@ class TestMechanics:
c = np.random.randint(n)
def test_vectorize_Cauchy(self):
P = np.random.random((self.n,3,3))
F = np.random.random((self.n,3,3))
assert np.allclose(mechanics.Cauchy(P,F)[self.c],
mechanics.Cauchy(P[self.c],F[self.c]))
@pytest.mark.parametrize('function',[mechanics.deviatoric_part,
mechanics.eigenvalues,
mechanics.eigenvectors,
mechanics.left_stretch,
mechanics.maximum_shear,
mechanics.Mises_strain,
mechanics.Mises_stress,
mechanics.right_stretch,
mechanics.rotational_part,
mechanics.spherical_part,
mechanics.symmetric,
mechanics.transpose,
])
def test_vectorize_1_arg(self,function):
epsilon = np.random.rand(self.n,3,3)
assert np.allclose(function(epsilon)[self.c],function(epsilon[self.c]))
def test_vectorize_deviatoric_part(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.deviatoric_part(x)[self.c],
mechanics.deviatoric_part(x[self.c]))
def test_vectorize_eigenvalues(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.eigenvalues(x)[self.c],
mechanics.eigenvalues(x[self.c]))
def test_vectorize_eigenvectors(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.eigenvectors(x)[self.c],
mechanics.eigenvectors(x[self.c]))
def test_vectorize_left_stretch(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.left_stretch(x)[self.c],
mechanics.left_stretch(x[self.c]))
def test_vectorize_maximum_shear(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.maximum_shear(x)[self.c],
mechanics.maximum_shear(x[self.c]))
def test_vectorize_Mises_strain(self):
epsilon = np.random.random((self.n,3,3))
assert np.allclose(mechanics.Mises_strain(epsilon)[self.c],
mechanics.Mises_strain(epsilon[self.c]))
def test_vectorize_Mises_stress(self):
sigma = np.random.random((self.n,3,3))
assert np.allclose(mechanics.Mises_stress(sigma)[self.c],
mechanics.Mises_stress(sigma[self.c]))
def test_vectorize_PK2(self):
F = np.random.random((self.n,3,3))
P = np.random.random((self.n,3,3))
assert np.allclose(mechanics.PK2(P,F)[self.c],
mechanics.PK2(P[self.c],F[self.c]))
def test_vectorize_right_stretch(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.right_stretch(x)[self.c],
mechanics.right_stretch(x[self.c]))
def test_vectorize_rotational_part(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.rotational_part(x)[self.c],
mechanics.rotational_part(x[self.c]))
def test_vectorize_spherical_part(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.spherical_part(x,True)[self.c],
mechanics.spherical_part(x[self.c],True))
@pytest.mark.parametrize('function',[mechanics.Cauchy,
mechanics.PK2,
])
def test_vectorize_2_arg(self,function):
P = np.random.rand(self.n,3,3)
F = np.random.rand(self.n,3,3)
assert np.allclose(function(P,F)[self.c],function(P[self.c],F[self.c]))
def test_vectorize_strain_tensor(self):
F = np.random.random((self.n,3,3))
F = np.random.rand(self.n,3,3)
t = ['V','U'][np.random.randint(0,2)]
m = np.random.random()*10. -5.0
assert np.allclose(mechanics.strain_tensor(F,t,m)[self.c],
mechanics.strain_tensor(F[self.c],t,m))
def test_vectorize_symmetric(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.symmetric(x)[self.c],
mechanics.symmetric(x[self.c]))
def test_vectorize_transpose(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.transpose(x)[self.c],
mechanics.transpose(x[self.c]))
def test_Cauchy(self):
"""Ensure Cauchy stress is symmetrized 1. Piola-Kirchhoff stress for no deformation."""
P = np.random.random((self.n,3,3))
assert np.allclose(mechanics.Cauchy(P,np.broadcast_to(np.eye(3),(self.n,3,3))),
mechanics.symmetric(P))
@pytest.mark.parametrize('function',[mechanics.Cauchy,
mechanics.PK2,
])
def test_stress_measures(self,function):
"""Ensure that all stress measures are equivalent for no deformation."""
P = np.random.rand(self.n,3,3)
assert np.allclose(function(P,np.broadcast_to(np.eye(3),(self.n,3,3))),mechanics.symmetric(P))
def test_deviatoric_part(self):
I_n = np.broadcast_to(np.eye(3),(self.n,3,3))
r = np.logical_not(I_n)*np.random.rand(self.n,3,3)
assert np.allclose(mechanics.deviatoric_part(I_n+r),r)
def test_polar_decomposition(self):
"""F = RU = VR."""
F = np.broadcast_to(np.eye(3),[self.n,3,3])*np.random.random((self.n,3,3))
F = np.broadcast_to(np.eye(3),[self.n,3,3])*np.random.rand(self.n,3,3)
R = mechanics.rotational_part(F)
V = mechanics.left_stretch(F)
U = mechanics.right_stretch(F)
assert np.allclose(np.matmul(R,U),
np.matmul(V,R))
def test_PK2(self):
"""Ensure 2. Piola-Kirchhoff stress is symmetrized 1. Piola-Kirchhoff stress for no deformation."""
P = np.random.random((self.n,3,3))
assert np.allclose(mechanics.PK2(P,np.broadcast_to(np.eye(3),(self.n,3,3))),
mechanics.symmetric(P))
def test_strain_tensor_no_rotation(self):
"""Ensure that left and right stretch give same results for no rotation."""
F = np.broadcast_to(np.eye(3),[self.n,3,3])*np.random.random((self.n,3,3))
F = np.broadcast_to(np.eye(3),[self.n,3,3])*np.random.rand(self.n,3,3)
m = np.random.random()*20.0-10.0
assert np.allclose(mechanics.strain_tensor(F,'U',m),
mechanics.strain_tensor(F,'V',m))
def test_strain_tensor_rotation_equivalence(self):
"""Ensure that left and right strain differ only by a rotation."""
F = np.broadcast_to(np.eye(3),[self.n,3,3]) + (np.random.random((self.n,3,3))*0.5 - 0.25)
F = np.broadcast_to(np.eye(3),[self.n,3,3]) + (np.random.rand(self.n,3,3)*0.5 - 0.25)
m = np.random.random()*5.0-2.5
assert np.allclose(np.linalg.det(mechanics.strain_tensor(F,'U',m)),
np.linalg.det(mechanics.strain_tensor(F,'V',m)))
def test_strain_tensor_rotation(self):
"""Ensure that pure rotation results in no strain."""
F = mechanics.rotational_part(np.random.random((self.n,3,3)))
F = mechanics.rotational_part(np.random.rand(self.n,3,3))
t = ['V','U'][np.random.randint(0,2)]
m = np.random.random()*2.0 - 1.0
assert np.allclose(mechanics.strain_tensor(F,t,m),
@ -139,21 +91,20 @@ class TestMechanics:
Should be +1, but random F might contain a reflection.
"""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
assert np.allclose(np.abs(np.linalg.det(mechanics.rotational_part(x))),
1.0)
def test_spherical_deviatoric_part(self):
"""Ensure that full tensor is sum of spherical and deviatoric part."""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
sph = mechanics.spherical_part(x,True)
assert np.allclose(sph + mechanics.deviatoric_part(x),
x)
def test_deviatoric_Mises(self):
"""Ensure that Mises equivalent stress depends only on deviatoric part."""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
full = mechanics.Mises_stress(x)
dev = mechanics.Mises_stress(mechanics.deviatoric_part(x))
assert np.allclose(full,
@ -161,7 +112,7 @@ class TestMechanics:
def test_spherical_mapping(self):
"""Ensure that mapping to tensor is correct."""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
tensor = mechanics.spherical_part(x,True)
scalar = mechanics.spherical_part(x)
assert np.allclose(np.linalg.det(tensor),
@ -169,35 +120,32 @@ class TestMechanics:
def test_spherical_Mises(self):
"""Ensure that Mises equivalent strrain of spherical strain is 0."""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
sph = mechanics.spherical_part(x,True)
assert np.allclose(mechanics.Mises_strain(sph),
0.0)
def test_symmetric(self):
"""Ensure that a symmetric tensor is half of the sum of a tensor and its transpose."""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
assert np.allclose(mechanics.symmetric(x)*2.0,
mechanics.transpose(x)+x)
def test_transpose(self):
"""Ensure that a symmetric tensor equals its transpose."""
x = mechanics.symmetric(np.random.random((self.n,3,3)))
x = mechanics.symmetric(np.random.rand(self.n,3,3))
assert np.allclose(mechanics.transpose(x),
x)
def test_Mises(self):
"""Ensure that equivalent stress is 3/2 of equivalent strain."""
x = np.random.random((self.n,3,3))
x = np.random.rand(self.n,3,3)
assert np.allclose(mechanics.Mises_stress(x)/mechanics.Mises_strain(x),
1.5)
def test_eigenvalues(self):
"""Ensure that the characteristic polynomial can be solved."""
A = mechanics.symmetric(np.random.random((self.n,3,3)))
A = mechanics.symmetric(np.random.rand(self.n,3,3))
lambd = mechanics.eigenvalues(A)
s = np.random.randint(self.n)
for i in range(3):
@ -205,7 +153,7 @@ class TestMechanics:
def test_eigenvalues_and_vectors(self):
"""Ensure that eigenvalues and -vectors are the solution to the characteristic polynomial."""
A = mechanics.symmetric(np.random.random((self.n,3,3)))
A = mechanics.symmetric(np.random.rand(self.n,3,3))
lambd = mechanics.eigenvalues(A)
x = mechanics.eigenvectors(A)
s = np.random.randint(self.n)
@ -214,12 +162,12 @@ class TestMechanics:
def test_eigenvectors_RHS(self):
"""Ensure that RHS coordinate system does only change sign of determinant."""
A = mechanics.symmetric(np.random.random((self.n,3,3)))
A = mechanics.symmetric(np.random.rand(self.n,3,3))
LRHS = np.linalg.det(mechanics.eigenvectors(A,RHS=False))
RHS = np.linalg.det(mechanics.eigenvectors(A,RHS=True))
assert np.allclose(np.abs(LRHS),RHS)
def test_spherical_no_shear(self):
"""Ensure that sherical stress has max shear of 0.0."""
A = mechanics.spherical_part(mechanics.symmetric(np.random.random((self.n,3,3))),True)
A = mechanics.spherical_part(mechanics.symmetric(np.random.rand(self.n,3,3)),True)
assert np.allclose(mechanics.maximum_shear(A),0.0)

42
src/CPFEM.f90
View File

@ -74,29 +74,25 @@ subroutine CPFEM_initAll(el,ip)
integer(pInt), intent(in) :: el, & !< FE el number
ip !< FE integration point number
!$OMP CRITICAL(init)
if (.not. CPFEM_init_done) then
call DAMASK_interface_init
call prec_init
call IO_init
call numerics_init
call debug_init
call config_init
call math_init
call rotations_init
call YAML_types_init
call HDF5_utilities_init
call results_init
call discretization_marc_init(ip, el)
call lattice_init
call material_init
call constitutive_init
call crystallite_init
call homogenization_init
call CPFEM_init
CPFEM_init_done = .true.
endif
!$OMP END CRITICAL(init)
CPFEM_init_done = .true.
call DAMASK_interface_init
call prec_init
call IO_init
call numerics_init
call debug_init
call config_init
call math_init
call rotations_init
call YAML_types_init
call HDF5_utilities_init
call results_init
call discretization_marc_init(ip, el)
call lattice_init
call material_init
call constitutive_init
call crystallite_init
call homogenization_init
call CPFEM_init
end subroutine CPFEM_initAll

3
src/DAMASK_marc.f90
View File

@ -261,11 +261,10 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
endif
!$ defaultNumThreadsInt = omp_get_num_threads() ! remember number of threads set by Marc
!$ call omp_set_num_threads(DAMASK_NumThreadsInt) ! set number of threads for parallel execution set by DAMASK_NUM_THREADS
if (.not. CPFEM_init_done) call CPFEM_initAll(m(1),nn)
!$ call omp_set_num_threads(DAMASK_NumThreadsInt) ! set number of threads for parallel execution set by DAMASK_NUM_THREADS
computationMode = 0 ! save initialization value, since it does not result in any calculation
if (lovl == 4 ) then ! jacobian requested by marc
if (timinc < theDelta .and. theInc == inc .and. lastLovl /= lovl) & ! first after cutback

74
src/constitutive.f90
View File

@ -327,7 +327,7 @@ module constitutive
constitutive_initialFi, &
constitutive_SandItsTangents, &
constitutive_collectDotState, &
constitutive_collectDeltaState, &
constitutive_deltaState, &
constitutive_results
contains
@ -709,12 +709,14 @@ end subroutine constitutive_hooke_SandItsTangents
!--------------------------------------------------------------------------------------------------
!> @brief contains the constitutive equation for calculating the rate of change of microstructure
!--------------------------------------------------------------------------------------------------
subroutine constitutive_collectDotState(S, FArray, Fi, FpArray, subdt, ipc, ip, el)
function constitutive_collectDotState(S, FArray, Fi, FpArray, subdt, ipc, ip, el,phase,of) result(broken)
integer, intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
el, & !< element
phase, &
of
real(pReal), intent(in) :: &
subdt !< timestep
real(pReal), intent(in), dimension(3,3,homogenization_maxNgrains,discretization_nIP,discretization_nElem) :: &
@ -730,16 +732,16 @@ subroutine constitutive_collectDotState(S, FArray, Fi, FpArray, subdt, ipc, ip,
ho, & !< homogenization
tme, & !< thermal member position
i, & !< counter in source loop
instance, of
instance
logical :: broken
ho = material_homogenizationAt(el)
tme = thermalMapping(ho)%p(ip,el)
of = material_phasememberAt(ipc,ip,el)
instance = phase_plasticityInstance(material_phaseAt(ipc,el))
instance = phase_plasticityInstance(phase)
Mp = matmul(matmul(transpose(Fi),Fi),S)
plasticityType: select case (phase_plasticity(material_phaseAt(ipc,el)))
plasticityType: select case (phase_plasticity(phase))
case (PLASTICITY_ISOTROPIC_ID) plasticityType
call plastic_isotropic_dotState (Mp,instance,of)
@ -760,10 +762,11 @@ subroutine constitutive_collectDotState(S, FArray, Fi, FpArray, subdt, ipc, ip,
call plastic_nonlocal_dotState (Mp,FArray,FpArray,temperature(ho)%p(tme),subdt, &
instance,of,ip,el)
end select plasticityType
broken = any(IEEE_is_NaN(plasticState(phase)%dotState(:,of)))
SourceLoop: do i = 1, phase_Nsources(material_phaseAt(ipc,el))
SourceLoop: do i = 1, phase_Nsources(phase)
sourceType: select case (phase_source(i,material_phaseAt(ipc,el)))
sourceType: select case (phase_source(i,phase))
case (SOURCE_damage_anisoBrittle_ID) sourceType
call source_damage_anisoBrittle_dotState (S, ipc, ip, el) !< correct stress?
@ -775,25 +778,29 @@ subroutine constitutive_collectDotState(S, FArray, Fi, FpArray, subdt, ipc, ip,
call source_damage_anisoDuctile_dotState ( ipc, ip, el)
case (SOURCE_thermal_externalheat_ID) sourceType
call source_thermal_externalheat_dotState(material_phaseAt(ipc,el),of)
call source_thermal_externalheat_dotState(phase,of)
end select sourceType
broken = broken .or. any(IEEE_is_NaN(sourceState(phase)%p(i)%dotState(:,of)))
enddo SourceLoop
end subroutine constitutive_collectDotState
end function constitutive_collectDotState
!--------------------------------------------------------------------------------------------------
!> @brief for constitutive models having an instantaneous change of state
!> will return false if delta state is not needed/supported by the constitutive model
!--------------------------------------------------------------------------------------------------
subroutine constitutive_collectDeltaState(S, Fe, Fi, ipc, ip, el)
function constitutive_deltaState(S, Fe, Fi, ipc, ip, el, phase, of) result(broken)
integer, intent(in) :: &
ipc, & !< component-ID of integration point
ip, & !< integration point
el !< element
el, & !< element
phase, &
of
real(pReal), intent(in), dimension(3,3) :: &
S, & !< 2nd Piola Kirchhoff stress
Fe, & !< elastic deformation gradient
@ -802,35 +809,62 @@ subroutine constitutive_collectDeltaState(S, Fe, Fi, ipc, ip, el)
Mp
integer :: &
i, &
instance, of
instance, &
myOffset, &
mySize
logical :: &
broken
Mp = matmul(matmul(transpose(Fi),Fi),S)
of = material_phasememberAt(ipc,ip,el)
instance = phase_plasticityInstance(material_phaseAt(ipc,el))
instance = phase_plasticityInstance(phase)
plasticityType: select case (phase_plasticity(material_phaseAt(ipc,el)))
plasticityType: select case (phase_plasticity(phase))
case (PLASTICITY_KINEHARDENING_ID) plasticityType
call plastic_kinehardening_deltaState(Mp,instance,of)
broken = any(IEEE_is_NaN(plasticState(phase)%deltaState(:,of)))
case (PLASTICITY_NONLOCAL_ID) plasticityType
call plastic_nonlocal_deltaState(Mp,instance,of,ip,el)
broken = any(IEEE_is_NaN(plasticState(phase)%deltaState(:,of)))
case default
broken = .false.
end select plasticityType
sourceLoop: do i = 1, phase_Nsources(material_phaseAt(ipc,el))
if(.not. broken) then
select case(phase_plasticity(phase))
case (PLASTICITY_NONLOCAL_ID,PLASTICITY_KINEHARDENING_ID)
sourceType: select case (phase_source(i,material_phaseAt(ipc,el)))
myOffset = plasticState(phase)%offsetDeltaState
mySize = plasticState(phase)%sizeDeltaState
plasticState(phase)%state(myOffset + 1:myOffset + mySize,of) = &
plasticState(phase)%state(myOffset + 1:myOffset + mySize,of) + plasticState(phase)%deltaState(1:mySize,of)
end select
endif
sourceLoop: do i = 1, phase_Nsources(phase)
sourceType: select case (phase_source(i,phase))
case (SOURCE_damage_isoBrittle_ID) sourceType
call source_damage_isoBrittle_deltaState (constitutive_homogenizedC(ipc,ip,el), Fe, &
ipc, ip, el)
broken = broken .or. any(IEEE_is_NaN(sourceState(phase)%p(i)%deltaState(:,of)))
if(.not. broken) then
myOffset = sourceState(phase)%p(i)%offsetDeltaState
mySize = sourceState(phase)%p(i)%sizeDeltaState
sourceState(phase)%p(i)%state(myOffset + 1: myOffset + mySize,of) = &
sourceState(phase)%p(i)%state(myOffset + 1: myOffset + mySize,of) + sourceState(phase)%p(i)%deltaState(1:mySize,of)
endif
end select sourceType
enddo SourceLoop
end subroutine constitutive_collectDeltaState
end function constitutive_deltaState
!--------------------------------------------------------------------------------------------------

2
src/constitutive_plastic_disloUCLA.f90
View File

@ -209,7 +209,7 @@ module subroutine plastic_disloUCLA_init
sizeDotState = size(['rho_mob ','rho_dip ','gamma_sl']) * prm%sum_N_sl
sizeState = sizeDotState
call material_allocatePlasticState(p,NipcMyPhase,sizeState,sizeDotState,0)
call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,0)
!--------------------------------------------------------------------------------------------------
! state aliases and initialization

2
src/constitutive_plastic_dislotwin.f90
View File

@ -399,7 +399,7 @@ module subroutine plastic_dislotwin_init
+ size(['f_tr']) * prm%sum_N_tr
sizeState = sizeDotState
call material_allocatePlasticState(p,NipcMyPhase,sizeState,sizeDotState,0)
call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,0)
!--------------------------------------------------------------------------------------------------
! locally defined state aliases and initialization of state0 and atol

2
src/constitutive_plastic_isotropic.f90
View File

@ -117,7 +117,7 @@ module subroutine plastic_isotropic_init
sizeDotState = size(['xi ','accumulated_shear'])
sizeState = sizeDotState
call material_allocatePlasticState(p,NipcMyPhase,sizeState,sizeDotState,0)
call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,0)
!--------------------------------------------------------------------------------------------------
! state aliases and initialization

2
src/constitutive_plastic_kinehardening.f90
View File

@ -164,7 +164,7 @@ module subroutine plastic_kinehardening_init
sizeDeltaState = size(['sense ', 'chi0 ', 'gamma0' ]) * prm%sum_N_sl
sizeState = sizeDotState + sizeDeltaState
call material_allocatePlasticState(p,NipcMyPhase,sizeState,sizeDotState,sizeDeltaState)
call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,sizeDeltaState)
!--------------------------------------------------------------------------------------------------
! state aliases and initialization

2
src/constitutive_plastic_none.f90
View File

@ -29,7 +29,7 @@ module subroutine plastic_none_init
if (phase_plasticity(p) /= PLASTICITY_NONE_ID) cycle
NipcMyPhase = count(material_phaseAt == p) * discretization_nIP
call material_allocatePlasticState(p,NipcMyPhase,0,0,0)
call material_allocateState(plasticState(p),NipcMyPhase,0,0,0)
enddo

305
src/constitutive_plastic_nonlocal.f90
View File

@ -320,6 +320,7 @@ module subroutine plastic_nonlocal_init
prm%fEdgeMultiplication = config%getFloat('edgemultiplication')
prm%shortRangeStressCorrection = config%keyExists('/shortrangestresscorrection/')
!--------------------------------------------------------------------------------------------------
! sanity checks
if (any(prm%burgers < 0.0_pReal)) extmsg = trim(extmsg)//' burgers'
@ -384,9 +385,9 @@ module subroutine plastic_nonlocal_init
'maxDipoleHeightEdge ','maxDipoleHeightScrew' ]) * prm%sum_N_sl !< other dependent state variables that are not updated by microstructure
sizeDeltaState = sizeDotState
call material_allocatePlasticState(p,NipcMyPhase,sizeState,sizeDotState,sizeDeltaState)
call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,sizeDeltaState)
plasticState(p)%nonlocal = .true.
plasticState(p)%nonlocal = config%KeyExists('/nonlocal/')
plasticState(p)%offsetDeltaState = 0 ! ToDo: state structure does not follow convention
st0%rho => plasticState(p)%state0 (0*prm%sum_N_sl+1:10*prm%sum_N_sl,:)
@ -961,39 +962,24 @@ module subroutine plastic_nonlocal_dotState(Mp, F, Fp, Temperature,timestep, &
integer :: &
ph, &
neighbor_instance, & !< instance of my neighbor's plasticity
ns, & !< short notation for the total number of active slip systems
c, & !< character of dislocation
n, & !< index of my current neighbor
neighbor_el, & !< element number of my neighbor
neighbor_ip, & !< integration point of my neighbor
neighbor_n, & !< neighbor index pointing to me when looking from my neighbor
opposite_neighbor, & !< index of my opposite neighbor
opposite_ip, & !< ip of my opposite neighbor
opposite_el, & !< element index of my opposite neighbor
opposite_n, & !< neighbor index pointing to me when looking from my opposite neighbor
t, & !< type of dislocation
no,& !< neighbor offset shortcut
np,& !< neighbor phase shortcut
topp, & !< type of dislocation with opposite sign to t
s !< index of my current slip system
real(pReal), dimension(param(instance)%sum_N_sl,10) :: &
rho, &
rho0, & !< dislocation density at beginning of time step
rhoDot, & !< density evolution
rhoDotMultiplication, & !< density evolution by multiplication
rhoDotFlux, & !< density evolution by flux
rhoDotSingle2DipoleGlide, & !< density evolution by dipole formation (by glide)
rhoDotAthermalAnnihilation, & !< density evolution by athermal annihilation
rhoDotThermalAnnihilation !< density evolution by thermal annihilation
real(pReal), dimension(param(instance)%sum_N_sl,8) :: &
rhoSgl, & !< current single dislocation densities (positive/negative screw and edge without dipoles)
neighbor_rhoSgl0, & !< current single dislocation densities of neighboring ip (positive/negative screw and edge without dipoles)
my_rhoSgl0 !< single dislocation densities of central ip (positive/negative screw and edge without dipoles)
real(pReal), dimension(param(instance)%sum_N_sl,4) :: &
v, & !< current dislocation glide velocity
v0, &
neighbor_v0, & !< dislocation glide velocity of enighboring ip
gdot !< shear rates
real(pReal), dimension(param(instance)%sum_N_sl) :: &
tau, & !< current resolved shear stress
@ -1002,23 +988,7 @@ module subroutine plastic_nonlocal_dotState(Mp, F, Fp, Temperature,timestep, &
rhoDip, & !< current dipole dislocation densities (screw and edge dipoles)
dLower, & !< minimum stable dipole distance for edges and screws
dUpper !< current maximum stable dipole distance for edges and screws
real(pReal), dimension(3,param(instance)%sum_N_sl,4) :: &
m !< direction of dislocation motion
real(pReal), dimension(3,3) :: &
my_F, & !< my total deformation gradient
neighbor_F, & !< total deformation gradient of my neighbor
my_Fe, & !< my elastic deformation gradient
neighbor_Fe, & !< elastic deformation gradient of my neighbor
Favg !< average total deformation gradient of me and my neighbor
real(pReal), dimension(3) :: &
normal_neighbor2me, & !< interface normal pointing from my neighbor to me in neighbor's lattice configuration
normal_neighbor2me_defConf, & !< interface normal pointing from my neighbor to me in shared deformed configuration
normal_me2neighbor, & !< interface normal pointing from me to my neighbor in my lattice configuration
normal_me2neighbor_defConf !< interface normal pointing from me to my neighbor in shared deformed configuration
real(pReal) :: &
area, & !< area of the current interface
transmissivity, & !< overall transmissivity of dislocation flux to neighboring material point
lineLength, & !< dislocation line length leaving the current interface
selfDiffusion !< self diffusion
ph = material_phaseAt(1,el)
@ -1091,6 +1061,172 @@ module subroutine plastic_nonlocal_dotState(Mp, F, Fp, Temperature,timestep, &
* sqrt(stt%rho_forest(:,of)) / prm%lambda0 / prm%burgers, 2, 4)
endif isBCC
forall (s = 1:ns, t = 1:4) v0(s,t) = plasticState(ph)%state0(iV(s,t,instance),of)
!****************************************************************************
!*** calculate dipole formation and annihilation
!*** formation by glide
do c = 1,2
rhoDotSingle2DipoleGlide(:,2*c-1) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* ( rhoSgl(:,2*c-1) * abs(gdot(:,2*c)) & ! negative mobile --> positive mobile
+ rhoSgl(:,2*c) * abs(gdot(:,2*c-1)) & ! positive mobile --> negative mobile
+ abs(rhoSgl(:,2*c+4)) * abs(gdot(:,2*c-1))) ! positive mobile --> negative immobile
rhoDotSingle2DipoleGlide(:,2*c) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* ( rhoSgl(:,2*c-1) * abs(gdot(:,2*c)) & ! negative mobile --> positive mobile
+ rhoSgl(:,2*c) * abs(gdot(:,2*c-1)) & ! positive mobile --> negative mobile
+ abs(rhoSgl(:,2*c+3)) * abs(gdot(:,2*c))) ! negative mobile --> positive immobile
rhoDotSingle2DipoleGlide(:,2*c+3) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* rhoSgl(:,2*c+3) * abs(gdot(:,2*c)) ! negative mobile --> positive immobile
rhoDotSingle2DipoleGlide(:,2*c+4) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* rhoSgl(:,2*c+4) * abs(gdot(:,2*c-1)) ! positive mobile --> negative immobile
rhoDotSingle2DipoleGlide(:,c+8) = abs(rhoDotSingle2DipoleGlide(:,2*c+3)) &
+ abs(rhoDotSingle2DipoleGlide(:,2*c+4)) &
- rhoDotSingle2DipoleGlide(:,2*c-1) &
- rhoDotSingle2DipoleGlide(:,2*c)
enddo
!*** athermal annihilation
rhoDotAthermalAnnihilation = 0.0_pReal
forall (c=1:2) &
rhoDotAthermalAnnihilation(:,c+8) = -2.0_pReal * dLower(:,c) / prm%burgers &
* ( 2.0_pReal * (rhoSgl(:,2*c-1) * abs(gdot(:,2*c)) + rhoSgl(:,2*c) * abs(gdot(:,2*c-1))) & ! was single hitting single
+ 2.0_pReal * (abs(rhoSgl(:,2*c+3)) * abs(gdot(:,2*c)) + abs(rhoSgl(:,2*c+4)) * abs(gdot(:,2*c-1))) & ! was single hitting immobile single or was immobile single hit by single
+ rhoDip(:,c) * (abs(gdot(:,2*c-1)) + abs(gdot(:,2*c)))) ! single knocks dipole constituent
! annihilated screw dipoles leave edge jogs behind on the colinear system
if (lattice_structure(ph) == LATTICE_fcc_ID) &
forall (s = 1:ns, prm%colinearSystem(s) > 0) &
rhoDotAthermalAnnihilation(prm%colinearSystem(s),1:2) = - rhoDotAthermalAnnihilation(s,10) &
* 0.25_pReal * sqrt(stt%rho_forest(s,of)) * (dUpper(s,2) + dLower(s,2)) * prm%edgeJogFactor
!*** thermally activated annihilation of edge dipoles by climb
rhoDotThermalAnnihilation = 0.0_pReal
selfDiffusion = prm%Dsd0 * exp(-prm%selfDiffusionEnergy / (kB * Temperature))
vClimb = prm%atomicVolume * selfDiffusion * prm%mu &
/ ( kB * Temperature * PI * (1.0_pReal-prm%nu) * (dUpper(:,1) + dLower(:,1)))
forall (s = 1:ns, dUpper(s,1) > dLower(s,1)) &
rhoDotThermalAnnihilation(s,9) = max(- 4.0_pReal * rhoDip(s,1) * vClimb(s) / (dUpper(s,1) - dLower(s,1)), &
- rhoDip(s,1) / timestep - rhoDotAthermalAnnihilation(s,9) &
- rhoDotSingle2DipoleGlide(s,9)) ! make sure that we do not annihilate more dipoles than we have
rhoDot = rhoDotFlux(F,Fp,timestep, instance,of,ip,el) &
+ rhoDotMultiplication &
+ rhoDotSingle2DipoleGlide &
+ rhoDotAthermalAnnihilation &
+ rhoDotThermalAnnihilation
if ( any(rho(:,mob) + rhoDot(:,1:4) * timestep < -prm%atol_rho) &
.or. any(rho(:,dip) + rhoDot(:,9:10) * timestep < -prm%atol_rho)) then
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0) then
write(6,'(a,i5,a,i2)') '<< CONST >> evolution rate leads to negative density at el ',el,' ip ',ip
write(6,'(a)') '<< CONST >> enforcing cutback !!!'
endif
#endif
plasticState(ph)%dotState = IEEE_value(1.0_pReal,IEEE_quiet_NaN)
else
dot%rho(:,of) = pack(rhoDot,.true.)
dot%gamma(:,of) = sum(gdot,2)
endif
end associate
end subroutine plastic_nonlocal_dotState
!---------------------------------------------------------------------------------------------------
!> @brief calculates the rate of change of microstructure
!---------------------------------------------------------------------------------------------------
function rhoDotFlux(F,Fp,timestep, instance,of,ip,el)
real(pReal), dimension(3,3,homogenization_maxNgrains,discretization_nIP,discretization_nElem), intent(in) :: &
F, & !< elastic deformation gradient
Fp !< plastic deformation gradient
real(pReal), intent(in) :: &
timestep !< substepped crystallite time increment
integer, intent(in) :: &
instance, &
of, &
ip, & !< current integration point
el !< current element number
integer :: &
ph, &
neighbor_instance, & !< instance of my neighbor's plasticity
ns, & !< short notation for the total number of active slip systems
c, & !< character of dislocation
n, & !< index of my current neighbor
neighbor_el, & !< element number of my neighbor
neighbor_ip, & !< integration point of my neighbor
neighbor_n, & !< neighbor index pointing to me when looking from my neighbor
opposite_neighbor, & !< index of my opposite neighbor
opposite_ip, & !< ip of my opposite neighbor
opposite_el, & !< element index of my opposite neighbor
opposite_n, & !< neighbor index pointing to me when looking from my opposite neighbor
t, & !< type of dislocation
no,& !< neighbor offset shortcut
np,& !< neighbor phase shortcut
topp, & !< type of dislocation with opposite sign to t
s !< index of my current slip system
real(pReal), dimension(param(instance)%sum_N_sl,10) :: &
rho, &
rho0, & !< dislocation density at beginning of time step
rhoDotFlux !< density evolution by flux
real(pReal), dimension(param(instance)%sum_N_sl,8) :: &
rhoSgl, & !< current single dislocation densities (positive/negative screw and edge without dipoles)
neighbor_rhoSgl0, & !< current single dislocation densities of neighboring ip (positive/negative screw and edge without dipoles)
my_rhoSgl0 !< single dislocation densities of central ip (positive/negative screw and edge without dipoles)
real(pReal), dimension(param(instance)%sum_N_sl,4) :: &
v, & !< current dislocation glide velocity
v0, &
neighbor_v0, & !< dislocation glide velocity of enighboring ip
gdot !< shear rates
real(pReal), dimension(3,param(instance)%sum_N_sl,4) :: &
m !< direction of dislocation motion
real(pReal), dimension(3,3) :: &
my_F, & !< my total deformation gradient
neighbor_F, & !< total deformation gradient of my neighbor
my_Fe, & !< my elastic deformation gradient
neighbor_Fe, & !< elastic deformation gradient of my neighbor
Favg !< average total deformation gradient of me and my neighbor
real(pReal), dimension(3) :: &
normal_neighbor2me, & !< interface normal pointing from my neighbor to me in neighbor's lattice configuration
normal_neighbor2me_defConf, & !< interface normal pointing from my neighbor to me in shared deformed configuration
normal_me2neighbor, & !< interface normal pointing from me to my neighbor in my lattice configuration
normal_me2neighbor_defConf !< interface normal pointing from me to my neighbor in shared deformed configuration
real(pReal) :: &
area, & !< area of the current interface
transmissivity, & !< overall transmissivity of dislocation flux to neighboring material point
lineLength !< dislocation line length leaving the current interface
ph = material_phaseAt(1,el)
associate(prm => param(instance), &
dst => microstructure(instance), &
dot => dotState(instance), &
stt => state(instance))
ns = prm%sum_N_sl
gdot = 0.0_pReal
rho = getRho(instance,of,ip,el)
rhoSgl = rho(:,sgl)
rho0 = getRho0(instance,of,ip,el)
my_rhoSgl0 = rho0(:,sgl)
forall (s = 1:ns, t = 1:4) v(s,t) = plasticState(ph)%state(iV(s,t,instance),of) !ToDo: MD: I think we should use state0 here
gdot = rhoSgl(:,1:4) * v * spread(prm%burgers,2,4)
forall (s = 1:ns, t = 1:4) v0(s,t) = plasticState(ph)%state0(iV(s,t,instance),of)
!****************************************************************************
@ -1113,7 +1249,7 @@ module subroutine plastic_nonlocal_dotState(Mp, F, Fp, Temperature,timestep, &
write(6,'(a)') '<< CONST >> enforcing cutback !!!'
endif
#endif
plasticState(ph)%dotState = IEEE_value(1.0_pReal,IEEE_quiet_NaN) ! -> return NaN and, hence, enforce cutback
rhoDotFlux = IEEE_value(1.0_pReal,IEEE_quiet_NaN) ! enforce cutback
return
endif
@ -1239,108 +1375,9 @@ module subroutine plastic_nonlocal_dotState(Mp, F, Fp, Temperature,timestep, &
enddo neighbors
endif
!****************************************************************************
!*** calculate dipole formation and annihilation
!*** formation by glide
do c = 1,2
rhoDotSingle2DipoleGlide(:,2*c-1) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* ( rhoSgl(:,2*c-1) * abs(gdot(:,2*c)) & ! negative mobile --> positive mobile
+ rhoSgl(:,2*c) * abs(gdot(:,2*c-1)) & ! positive mobile --> negative mobile
+ abs(rhoSgl(:,2*c+4)) * abs(gdot(:,2*c-1))) ! positive mobile --> negative immobile
rhoDotSingle2DipoleGlide(:,2*c) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* ( rhoSgl(:,2*c-1) * abs(gdot(:,2*c)) & ! negative mobile --> positive mobile
+ rhoSgl(:,2*c) * abs(gdot(:,2*c-1)) & ! positive mobile --> negative mobile
+ abs(rhoSgl(:,2*c+3)) * abs(gdot(:,2*c))) ! negative mobile --> positive immobile
rhoDotSingle2DipoleGlide(:,2*c+3) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* rhoSgl(:,2*c+3) * abs(gdot(:,2*c)) ! negative mobile --> positive immobile
rhoDotSingle2DipoleGlide(:,2*c+4) = -2.0_pReal * dUpper(:,c) / prm%burgers &
* rhoSgl(:,2*c+4) * abs(gdot(:,2*c-1)) ! positive mobile --> negative immobile
rhoDotSingle2DipoleGlide(:,c+8) = abs(rhoDotSingle2DipoleGlide(:,2*c+3)) &
+ abs(rhoDotSingle2DipoleGlide(:,2*c+4)) &
- rhoDotSingle2DipoleGlide(:,2*c-1) &
- rhoDotSingle2DipoleGlide(:,2*c)
enddo
!*** athermal annihilation
rhoDotAthermalAnnihilation = 0.0_pReal
forall (c=1:2) &
rhoDotAthermalAnnihilation(:,c+8) = -2.0_pReal * dLower(:,c) / prm%burgers &
* ( 2.0_pReal * (rhoSgl(:,2*c-1) * abs(gdot(:,2*c)) + rhoSgl(:,2*c) * abs(gdot(:,2*c-1))) & ! was single hitting single
+ 2.0_pReal * (abs(rhoSgl(:,2*c+3)) * abs(gdot(:,2*c)) + abs(rhoSgl(:,2*c+4)) * abs(gdot(:,2*c-1))) & ! was single hitting immobile single or was immobile single hit by single
+ rhoDip(:,c) * (abs(gdot(:,2*c-1)) + abs(gdot(:,2*c)))) ! single knocks dipole constituent
! annihilated screw dipoles leave edge jogs behind on the colinear system
if (lattice_structure(ph) == LATTICE_fcc_ID) &
forall (s = 1:ns, prm%colinearSystem(s) > 0) &
rhoDotAthermalAnnihilation(prm%colinearSystem(s),1:2) = - rhoDotAthermalAnnihilation(s,10) &
* 0.25_pReal * sqrt(stt%rho_forest(s,of)) * (dUpper(s,2) + dLower(s,2)) * prm%edgeJogFactor
!*** thermally activated annihilation of edge dipoles by climb
rhoDotThermalAnnihilation = 0.0_pReal
selfDiffusion = prm%Dsd0 * exp(-prm%selfDiffusionEnergy / (kB * Temperature))
vClimb = prm%atomicVolume * selfDiffusion * prm%mu &
/ ( kB * Temperature * PI * (1.0_pReal-prm%nu) * (dUpper(:,1) + dLower(:,1)))
forall (s = 1:ns, dUpper(s,1) > dLower(s,1)) &
rhoDotThermalAnnihilation(s,9) = max(- 4.0_pReal * rhoDip(s,1) * vClimb(s) / (dUpper(s,1) - dLower(s,1)), &
- rhoDip(s,1) / timestep - rhoDotAthermalAnnihilation(s,9) &
- rhoDotSingle2DipoleGlide(s,9)) ! make sure that we do not annihilate more dipoles than we have
rhoDot = rhoDotFlux &
+ rhoDotMultiplication &
+ rhoDotSingle2DipoleGlide &
+ rhoDotAthermalAnnihilation &
+ rhoDotThermalAnnihilation
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0 &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0 )) then
write(6,'(a,/,4(12x,12(e12.5,1x),/))') '<< CONST >> dislocation multiplication', &
rhoDotMultiplication(:,1:4) * timestep
write(6,'(a,/,8(12x,12(e12.5,1x),/))') '<< CONST >> dislocation flux', &
rhoDotFlux(:,1:8) * timestep
write(6,'(a,/,10(12x,12(e12.5,1x),/))') '<< CONST >> dipole formation by glide', &
rhoDotSingle2DipoleGlide * timestep
write(6,'(a,/,10(12x,12(e12.5,1x),/))') '<< CONST >> athermal dipole annihilation', &
rhoDotAthermalAnnihilation * timestep
write(6,'(a,/,2(12x,12(e12.5,1x),/))') '<< CONST >> thermally activated dipole annihilation', &
rhoDotThermalAnnihilation(:,9:10) * timestep
write(6,'(a,/,10(12x,12(e12.5,1x),/))') '<< CONST >> total density change', &
rhoDot * timestep
write(6,'(a,/,10(12x,12(f12.5,1x),/))') '<< CONST >> relative density change', &
rhoDot(:,1:8) * timestep / (abs(stt%rho(:,sgl))+1.0e-10), &
rhoDot(:,9:10) * timestep / (stt%rho(:,dip)+1.0e-10)
write(6,*)
endif
#endif
if ( any(rho(:,mob) + rhoDot(:,1:4) * timestep < -prm%atol_rho) &
.or. any(rho(:,dip) + rhoDot(:,9:10) * timestep < -prm%atol_rho)) then
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0) then
write(6,'(a,i5,a,i2)') '<< CONST >> evolution rate leads to negative density at el ',el,' ip ',ip
write(6,'(a)') '<< CONST >> enforcing cutback !!!'
endif
#endif
plasticState(ph)%dotState = IEEE_value(1.0_pReal,IEEE_quiet_NaN)
else
dot%rho(:,of) = pack(rhoDot,.true.)
dot%gamma(:,of) = sum(gdot,2)
endif
end associate
end subroutine plastic_nonlocal_dotState
end function rhoDotFlux
!--------------------------------------------------------------------------------------------------

2
src/constitutive_plastic_phenopowerlaw.f90
View File

@ -213,7 +213,7 @@ module subroutine plastic_phenopowerlaw_init
+ size(['xi_tw ','gamma_tw']) * prm%sum_N_tw
sizeState = sizeDotState
call material_allocatePlasticState(p,NipcMyPhase,sizeState,sizeDotState,0)
call material_allocateState(plasticState(p),NipcMyPhase,sizeState,sizeDotState,0)
!--------------------------------------------------------------------------------------------------
! state aliases and initialization

718
src/crystallite.f90
View File

File diff suppressed because it is too large Load Diff

66
src/material.f90
View File

@ -11,7 +11,6 @@ module material
use results
use IO
use debug
use numerics
use rotations
use discretization
@ -174,8 +173,7 @@ module material
public :: &
material_init, &
material_allocatePlasticState, &
material_allocateSourceState, &
material_allocateState, &
ELASTICITY_HOOKE_ID ,&
PLASTICITY_NONE_ID, &
PLASTICITY_ISOTROPIC_ID, &
@ -700,63 +698,35 @@ end subroutine material_parseTexture
!--------------------------------------------------------------------------------------------------
!> @brief allocates the plastic state of a phase
!> @brief Allocate the components of the state structure for a given phase
!--------------------------------------------------------------------------------------------------
subroutine material_allocatePlasticState(phase,NipcMyPhase,&
sizeState,sizeDotState,sizeDeltaState)
subroutine material_allocateState(state, &
NipcMyPhase,sizeState,sizeDotState,sizeDeltaState)
class(tState), intent(out) :: &
state
integer, intent(in) :: &
phase, &
NipcMyPhase, &
sizeState, &
sizeDotState, &
sizeDeltaState
plasticState(phase)%sizeState = sizeState
plasticState(phase)%sizeDotState = sizeDotState
plasticState(phase)%sizeDeltaState = sizeDeltaState
plasticState(phase)%offsetDeltaState = sizeState-sizeDeltaState ! deltaState occupies latter part of state by definition
state%sizeState = sizeState
state%sizeDotState = sizeDotState
state%sizeDeltaState = sizeDeltaState
state%offsetDeltaState = sizeState-sizeDeltaState ! deltaState occupies latter part of state by definition
allocate(plasticState(phase)%atol (sizeState), source=0.0_pReal)
allocate(plasticState(phase)%state0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(plasticState(phase)%partionedState0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(plasticState(phase)%subState0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(plasticState(phase)%state (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(state%atol (sizeState), source=0.0_pReal)
allocate(state%state0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(state%partionedState0(sizeState,NipcMyPhase), source=0.0_pReal)
allocate(state%subState0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(state%state (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(plasticState(phase)%dotState (sizeDotState,NipcMyPhase),source=0.0_pReal)
allocate(state%dotState (sizeDotState,NipcMyPhase), source=0.0_pReal)
allocate(plasticState(phase)%deltaState (sizeDeltaState,NipcMyPhase),source=0.0_pReal)
allocate(state%deltaState(sizeDeltaState,NipcMyPhase), source=0.0_pReal)
end subroutine material_allocatePlasticState
end subroutine material_allocateState
!--------------------------------------------------------------------------------------------------
!> @brief allocates the source state of a phase
!--------------------------------------------------------------------------------------------------
subroutine material_allocateSourceState(phase,of,NipcMyPhase,&
sizeState,sizeDotState,sizeDeltaState)
integer, intent(in) :: &
phase, &
of, &
NipcMyPhase, &
sizeState, sizeDotState,sizeDeltaState
sourceState(phase)%p(of)%sizeState = sizeState
sourceState(phase)%p(of)%sizeDotState = sizeDotState
sourceState(phase)%p(of)%sizeDeltaState = sizeDeltaState
sourceState(phase)%p(of)%offsetDeltaState = sizeState-sizeDeltaState ! deltaState occupies latter part of state by definition
allocate(sourceState(phase)%p(of)%atol (sizeState), source=0.0_pReal)
allocate(sourceState(phase)%p(of)%state0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(sourceState(phase)%p(of)%partionedState0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(sourceState(phase)%p(of)%subState0 (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(sourceState(phase)%p(of)%state (sizeState,NipcMyPhase), source=0.0_pReal)
allocate(sourceState(phase)%p(of)%dotState (sizeDotState,NipcMyPhase),source=0.0_pReal)
allocate(sourceState(phase)%p(of)%deltaState (sizeDeltaState,NipcMyPhase),source=0.0_pReal)
end subroutine material_allocateSourceState
end module material

23
src/numerics.f90
View File

@ -20,8 +20,7 @@ module numerics
iJacoStiffness = 1, & !< frequency of stiffness update
randomSeed = 0, & !< fixed seeding for pseudo-random number generator, Default 0: use random seed
worldrank = 0, & !< MPI worldrank (/=0 for MPI simulations only)
worldsize = 1, & !< MPI worldsize (/=1 for MPI simulations only)
numerics_integrator = 1 !< method used for state integration Default 1: fix-point iteration
worldsize = 1 !< MPI worldsize (/=1 for MPI simulations only)
integer(4), protected, public :: &
DAMASK_NumThreadsInt = 0 !< value stored in environment variable DAMASK_NUM_THREADS, set to zero if no OpenMP directive
real(pReal), protected, public :: &
@ -134,8 +133,6 @@ subroutine numerics_init
defgradTolerance = IO_floatValue(line,chunkPos,2)
case ('ijacostiffness')
iJacoStiffness = IO_intValue(line,chunkPos,2)
case ('integrator')
numerics_integrator = IO_intValue(line,chunkPos,2)
case ('usepingpong')
usepingpong = IO_intValue(line,chunkPos,2) > 0
case ('unitlength')
@ -176,6 +173,11 @@ subroutine numerics_init
case ('maxstaggerediter')
stagItMax = IO_intValue(line,chunkPos,2)
#ifdef PETSC
case ('petsc_options')
petsc_options = trim(line(chunkPos(4):))
#endif
!--------------------------------------------------------------------------------------------------
! spectral parameters
#ifdef Grid
@ -187,8 +189,6 @@ subroutine numerics_init
err_stress_tolrel = IO_floatValue(line,chunkPos,2)
case ('err_stress_tolabs')
err_stress_tolabs = IO_floatValue(line,chunkPos,2)
case ('petsc_options')
petsc_options = trim(line(chunkPos(4):))
case ('err_curl_tolabs')
err_curl_tolAbs = IO_floatValue(line,chunkPos,2)
case ('err_curl_tolrel')
@ -206,8 +206,6 @@ subroutine numerics_init
integrationorder = IO_intValue(line,chunkPos,2)
case ('structorder')
structorder = IO_intValue(line,chunkPos,2)
case ('petsc_options')
petsc_options = trim(line(chunkPos(4):))
case ('bbarstabilisation')
BBarStabilisation = IO_intValue(line,chunkPos,2) > 0
#endif
@ -223,7 +221,6 @@ subroutine numerics_init
! writing parameters to output
write(6,'(a24,1x,es8.1)') ' defgradTolerance: ',defgradTolerance
write(6,'(a24,1x,i8)') ' iJacoStiffness: ',iJacoStiffness
write(6,'(a24,1x,i8)') ' integrator: ',numerics_integrator
write(6,'(a24,1x,L8)') ' use ping pong scheme: ',usepingpong
write(6,'(a24,1x,es8.1,/)')' unitlength: ',numerics_unitlength
@ -266,7 +263,6 @@ subroutine numerics_init
write(6,'(a24,1x,es8.1)') ' err_curl_tolRel: ',err_curl_tolRel
write(6,'(a24,1x,es8.1)') ' polarAlpha: ',polarAlpha
write(6,'(a24,1x,es8.1)') ' polarBeta: ',polarBeta
write(6,'(a24,1x,a)') ' PETSc_options: ',trim(petsc_options)
#endif
!--------------------------------------------------------------------------------------------------
@ -274,16 +270,17 @@ subroutine numerics_init
#ifdef FEM
write(6,'(a24,1x,i8)') ' integrationOrder: ',integrationOrder
write(6,'(a24,1x,i8)') ' structOrder: ',structOrder
write(6,'(a24,1x,a)') ' PETSc_options: ',trim(petsc_options)
write(6,'(a24,1x,L8)') ' B-Bar stabilisation: ',BBarStabilisation
#endif
#ifdef PETSC
write(6,'(a24,1x,a)') ' PETSc_options: ',trim(petsc_options)
#endif
!--------------------------------------------------------------------------------------------------
! sanity checks
if (defgradTolerance <= 0.0_pReal) call IO_error(301,ext_msg='defgradTolerance')
if (iJacoStiffness < 1) call IO_error(301,ext_msg='iJacoStiffness')
if (numerics_integrator <= 0 .or. numerics_integrator >= 6) &
call IO_error(301,ext_msg='integrator')
if (numerics_unitlength <= 0.0_pReal) call IO_error(301,ext_msg='unitlength')
if (residualStiffness < 0.0_pReal) call IO_error(301,ext_msg='residualStiffness')
if (itmax <= 1) call IO_error(301,ext_msg='itmax')

3
src/prec.f90
View File

@ -53,8 +53,7 @@ module prec
logical :: &
nonlocal = .false.
real(pReal), pointer, dimension(:,:) :: &
slipRate, & !< slip rate
accumulatedSlip !< accumulated plastic slip
slipRate !< slip rate
end type
type :: tSourceState

2
src/source_damage_anisoBrittle.f90
View File

@ -107,7 +107,7 @@ subroutine source_damage_anisoBrittle_init
if (any(prm%critDisp < 0.0_pReal)) extmsg = trim(extmsg)//' anisobrittle_critDisp'
NipcMyPhase = count(material_phaseAt==p) * discretization_nIP
call material_allocateSourceState(p,sourceOffset,NipcMyPhase,1,1,0)
call material_allocateState(sourceState(p)%p(sourceOffset),NipcMyPhase,1,1,0)
sourceState(p)%p(sourceOffset)%atol = config%getFloat('anisobrittle_atol',defaultVal=1.0e-3_pReal)
if(any(sourceState(p)%p(sourceOffset)%atol < 0.0_pReal)) extmsg = trim(extmsg)//' anisobrittle_atol'

2
src/source_damage_anisoDuctile.f90
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@ -89,7 +89,7 @@ subroutine source_damage_anisoDuctile_init
if (any(prm%critPlasticStrain < 0.0_pReal)) extmsg = trim(extmsg)//' anisoductile_criticalplasticstrain'
NipcMyPhase=count(material_phaseAt==p) * discretization_nIP
call material_allocateSourceState(p,sourceOffset,NipcMyPhase,1,1,0)
call material_allocateState(sourceState(p)%p(sourceOffset),NipcMyPhase,1,1,0)
sourceState(p)%p(sourceOffset)%atol = config%getFloat('anisoductile_atol',defaultVal=1.0e-3_pReal)
if(any(sourceState(p)%p(sourceOffset)%atol < 0.0_pReal)) extmsg = trim(extmsg)//' anisoductile_atol'

2
src/source_damage_isoBrittle.f90
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@ -83,7 +83,7 @@ subroutine source_damage_isoBrittle_init
if (prm%critStrainEnergy <= 0.0_pReal) extmsg = trim(extmsg)//' isobrittle_criticalstrainenergy'
NipcMyPhase = count(material_phaseAt==p) * discretization_nIP
call material_allocateSourceState(p,sourceOffset,NipcMyPhase,1,1,1)
call material_allocateState(sourceState(p)%p(sourceOffset),NipcMyPhase,1,1,1)
sourceState(p)%p(sourceOffset)%atol = config%getFloat('isobrittle_atol',defaultVal=1.0e-3_pReal)
if(any(sourceState(p)%p(sourceOffset)%atol < 0.0_pReal)) extmsg = trim(extmsg)//' isobrittle_atol'

2
src/source_damage_isoDuctile.f90
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@ -82,7 +82,7 @@ subroutine source_damage_isoDuctile_init
if (prm%critPlasticStrain <= 0.0_pReal) extmsg = trim(extmsg)//' isoductile_criticalplasticstrain'
NipcMyPhase=count(material_phaseAt==p) * discretization_nIP
call material_allocateSourceState(p,sourceOffset,NipcMyPhase,1,1,0)
call material_allocateState(sourceState(p)%p(sourceOffset),NipcMyPhase,1,1,0)
sourceState(p)%p(sourceOffset)%atol = config%getFloat('isoductile_atol',defaultVal=1.0e-3_pReal)
if(any(sourceState(p)%p(sourceOffset)%atol < 0.0_pReal)) extmsg = trim(extmsg)//' isoductile_atol'

2
src/source_thermal_dissipation.f90
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@ -67,7 +67,7 @@ subroutine source_thermal_dissipation_init
prm%kappa = config%getFloat('dissipation_coldworkcoeff')
NipcMyPhase = count(material_phaseAt==p) * discretization_nIP
call material_allocateSourceState(p,sourceOffset,NipcMyPhase,0,0,0)
call material_allocateState(sourceState(p)%p(sourceOffset),NipcMyPhase,0,0,0)
end associate
enddo

2
src/source_thermal_externalheat.f90
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@ -74,7 +74,7 @@ subroutine source_thermal_externalheat_init
prm%heat_rate = config%getFloats('externalheat_rate',requiredSize = size(prm%time))
NipcMyPhase = count(material_phaseAt==p) * discretization_nIP
call material_allocateSourceState(p,sourceOffset,NipcMyPhase,1,1,0)
call material_allocateState(sourceState(p)%p(sourceOffset),NipcMyPhase,1,1,0)
end associate
enddo