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Merge branch 'new-ASCII' of magit1.mpie.de:/damask/DAMASK into new-ASCII

This commit is contained in:
Martin Diehl 2019-12-04 05:08:52 +01:00
parent ca92400c2f 3effea8e1d
commit 1110affec2
44 changed files with 1759 additions and 310 deletions
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2
.gitattributes vendored
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@ -3,8 +3,8 @@
# always use LF, even if the files are edited on windows, they need to be compiled/used on unix
* text eol=lf
installation/mods_Abaqus/abaqus_v6_windows.env eol=crlf
# Denote all files that are truly binary and should not be modified.
*.png binary
*.jpg binary
*.cae binary
*.hdf5 binary

18
.gitlab-ci.yml
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@ -1,6 +1,7 @@
---
stages:
- prepareAll
- python
- preprocessing
- postprocessing
- compilePETSc
@ -103,6 +104,16 @@ checkout:
- master
- release
###################################################################################################
Pytest:
stage: python
script:
- cd $DAMASKROOT/python
- pytest
except:
- master
- release
###################################################################################################
OrientationRelationship:
stage: preprocessing
@ -308,13 +319,6 @@ nonlocal_densityConservation:
- master
- release
Spectral_ipNeighborhood:
stage: grid
script: Spectral_ipNeighborhood/test.py
except:
- master
- release
RGC_DetectChanges:
stage: grid
script: RGC_DetectChanges/test.py

2
PRIVATE

@ -1 +1 @@
Subproject commit a3a88933cbb92b81d481305ce93374917baf3980
Subproject commit 66d562c755cd9aa4bbb8280c509383014acd52db

2
VERSION
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@ -1 +1 @@
v2.0.3-1097-ga7fca4df
v2.0.3-1133-gfede8225

9
examples/ConfigFiles/Crystallite_All.config
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@ -1,9 +0,0 @@
[all]
(output) orientation # quaternion
(output) grainrotation # deviation from initial orientation as axis (1-3) and angle in degree (4) in crystal reference coordinates
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) S # second Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor

12
examples/SpectralMethod/Polycrystal/material.config
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@ -5,18 +5,6 @@
[SX]
mech none
#-------------------#
<crystallite>
#-------------------#
[almostAll]
(output) orientation # quaternion
(output) grainrotation # deviation from initial orientation as axis (1-3) and angle in degree (4)
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor
#-------------------#
<phase>
#-------------------#

50
processing/post/DADF5_postResults.py
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@ -59,35 +59,35 @@ for filename in options.filenames:
data = np.concatenate((data,coords),1)
header+=' 1_pos 2_pos 3_pos'
results.set_visible('materialpoints',False)
results.set_visible('constituents', True)
for label in options.con:
for p in results.iter_visible('con_physics'):
for c in results.iter_visible('constituents'):
x = results.get_dataset_location(label)
if len(x) == 0:
continue
array = results.read_dataset(x,0,plain=True)
d = int(np.product(np.shape(array)[1:]))
data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
if d>1:
header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
else:
header+=' '+label
x = results.get_dataset_location(label)
if len(x) == 0:
continue
array = results.read_dataset(x,0,plain=True)
d = np.product(np.shape(array)[1:])
data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
if d>1:
header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
else:
header+=' '+label
results.set_visible('constituents', False)
results.set_visible('materialpoints',True)
for label in options.mat:
for p in results.iter_visible('mat_physics'):
for m in results.iter_visible('materialpoints'):
x = results.get_dataset_location(label)
if len(x) == 0:
continue
array = results.read_dataset(x,0,plain=True)
d = int(np.product(np.shape(array)[1:]))
data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
x = results.get_dataset_location(label)
if len(x) == 0:
continue
array = results.read_dataset(x,0,plain=True)
d = np.product(np.shape(array)[1:])
data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
if d>1:
header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
else:
header+=' '+label
if d>1:
header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
else:
header+=' '+label
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
if not os.path.isdir(dirname):

1
processing/post/DADF5_vtk_cells.py
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@ -74,7 +74,6 @@ for filename in options.filenames:
results.set_visible('materialpoints',False)
results.set_visible('constituents', True)
for label in options.con:
for p in results.iter_visible('con_physics'):
if p != 'generic':
for c in results.iter_visible('constituents'):

75
python/damask/table.py
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@ -6,7 +6,7 @@ import numpy as np
class Table():
"""Store spreadsheet-like data."""
def __init__(self,array,columns,comments=None):
def __init__(self,array,headings,comments=None):
"""
New spreadsheet data.
@ -14,8 +14,8 @@ class Table():
----------
array : numpy.ndarray
Data.
columns : dict
Column labels and shape. Example 'F':(3,3) for a deformation gradient.
headings : dict
Column headings. Labels as keys and shape as tuple. Example 'F':(3,3) for a deformation gradient.
comments : iterable of str, optional
Additional, human-readable information
@ -24,11 +24,14 @@ class Table():
d = {}
i = 0
for label in columns:
for components in range(np.prod(columns[label])):
for label in headings:
for components in range(np.prod(headings[label])):
d[i] = label
i+=1
if i != self.data.shape[1]:
raise IndexError('Mismatch between array shape and headings')
self.data.rename(columns=d,inplace=True)
if comments is None:
@ -36,7 +39,7 @@ class Table():
else:
self.comments = [c for c in comments]
self.columns = columns
self.headings = headings
@staticmethod
def from_ASCII(fname):
@ -44,8 +47,8 @@ class Table():
Create table from ASCII file.
The first line needs to indicate the number of subsequent header lines as 'n header'.
Vector data labels are indicated by '1_x, 2_x, ..., n_x'.
Tensor data labels are indicated by '3x3:1_x, 3x3:2_x, ..., 3x3:9_x'.
Vector data labels are indicated by '1_v, 2_v, ..., n_v'.
Tensor data labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
Parameters
----------
@ -66,28 +69,36 @@ class Table():
comments = [f.readline()[:-1] for i in range(header-1)]
labels = f.readline().split()
columns = {}
headings = {}
for label in labels:
tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
if tensor_column:
my_shape = tensor_column.group().split(':',1)[0].split('x')
columns[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
headings[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
else:
vector_column = re.match(r'[0-9]*?_',label)
if vector_column:
columns[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
headings[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
else:
columns[label]=(1,)
headings[label]=(1,)
return Table(np.loadtxt(f),columns,comments)
return Table(np.loadtxt(f),headings,comments)
def get_array(self,label):
"""Return data as array."""
"""
Return data as array.
Parameters
----------
label : str
Label of the array.
"""
if re.match(r'[0-9]*?_',label):
idx,key = label.split('_',1)
return self.data[key].to_numpy()[:,int(idx)-1]
else:
return self.data[label].to_numpy().reshape((-1,)+self.columns[label])
return self.data[label].to_numpy().reshape((-1,)+self.headings[label])
def set_array(self,label,array,info):
"""
@ -96,11 +107,11 @@ class Table():
Parameters
----------
label : str
Label for the new data
Label for the new data.
array : np.ndarray
New data
New data.
info : str
Human-readable information about the new data
Human-readable information about the new data.
"""
if np.prod(array.shape[1:],dtype=int) == 1:
@ -115,22 +126,23 @@ class Table():
else:
self.data[label] = array.reshape(self.data[label].shape)
def get_labels(self):
"""Return the labels of all columns."""
return [label for label in self.columns]
return [label for label in self.headings]
def add_array(self,label,array,info):
"""
Add data to the spreadsheet.
Parameters
----------
label : str
Label for the new data
Label for the new data.
array : np.ndarray
New data
New data.
info : str
Human-readable information about the new data
Human-readable information about the new data.
"""
if np.prod(array.shape[1:],dtype=int) == 1:
@ -138,7 +150,7 @@ class Table():
else:
self.comments.append('{} {}: {}'.format(label,array.shape[1:],info))
self.columns[label] = array.shape[1:] if len(array.shape) > 1 else (1,)
self.headings[label] = array.shape[1:] if len(array.shape) > 1 else (1,)
size = np.prod(array.shape[1:],dtype=int)
new_data = pd.DataFrame(data=array.reshape(-1,size),
columns=[label for l in range(size)])
@ -147,24 +159,23 @@ class Table():
def to_ASCII(self,fname):
"""
Store as plain text file.
Parameters
----------
fname : file, str, or pathlib.Path
Filename or file for reading.
"""
labels = []
for l in self.columns:
if(self.columns[l] == (1,)):
for l in self.headings:
if(self.headings[l] == (1,)):
labels.append('{}'.format(l))
elif(len(self.columns[l]) == 1):
elif(len(self.headings[l]) == 1):
labels+=['{}_{}'.format(i+1,l)\
for i in range(self.columns[l][0])]
for i in range(self.headings[l][0])]
else:
labels+=['{}:{}_{}'.format(i+1,'x'.join([str(d) for d in self.columns[l]]),l)\
for i in range(np.prod(self.columns[l],dtype=int))]
labels+=['{}:{}_{}'.format('x'.join([str(d) for d in self.headings[l]]),i+1,l)\
for i in range(np.prod(self.headings[l],dtype=int))]
header = ['{} header'.format(len(self.comments)+1)]\
+ self.comments\

21
python/tests/conftest.py Normal file
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@ -0,0 +1,21 @@
import os
import pytest
import damask
def pytest_addoption(parser):
parser.addoption("--update",
action="store_true",
default=False)
@pytest.fixture
def update(request):
"""Store current results as new reference results."""
return request.config.getoption("--update")
@pytest.fixture
def reference_dir_base():
"""Directory containing reference results."""
env = damask.Environment()
return os.path.join(env.rootDir(),'python','tests','reference')

125
python/tests/reference/DADF5/12grains6x7x8.geom Normal file
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@ -0,0 +1,125 @@
68 header
geom_fromVoronoiTessellation 2.0.3-1073-g6f3cb071
<texture>
[Grain1]
(gauss) phi1 358.98 Phi 65.62 phi2 24.48
[Grain2]
(gauss) phi1 121.05 Phi 176.11 phi2 295.73
[Grain3]
(gauss) phi1 43.79 Phi 113.76 phi2 345.90
[Grain4]
(gauss) phi1 265.15 Phi 62.52 phi2 299.71
[Grain5]
(gauss) phi1 221.23 Phi 26.54 phi2 207.05
[Grain6]
(gauss) phi1 249.81 Phi 61.47 phi2 152.14
[Grain7]
(gauss) phi1 332.45 Phi 99.16 phi2 345.34
[Grain8]
(gauss) phi1 312.27 Phi 118.27 phi2 181.59
[Grain9]
(gauss) phi1 303.10 Phi 48.21 phi2 358.03
[Grain10]
(gauss) phi1 338.26 Phi 48.11 phi2 176.78
[Grain11]
(gauss) phi1 115.17 Phi 56.54 phi2 223.84
[Grain12]
(gauss) phi1 281.04 Phi 97.48 phi2 27.94
<microstructure>
[Grain1]
crystallite 1
(constituent) phase 1 texture 1 fraction 1.0
[Grain2]
crystallite 1
(constituent) phase 1 texture 2 fraction 1.0
[Grain3]
crystallite 1
(constituent) phase 1 texture 3 fraction 1.0
[Grain4]
crystallite 1
(constituent) phase 1 texture 4 fraction 1.0
[Grain5]
crystallite 1
(constituent) phase 1 texture 5 fraction 1.0
[Grain6]
crystallite 1
(constituent) phase 1 texture 6 fraction 1.0
[Grain7]
crystallite 1
(constituent) phase 1 texture 7 fraction 1.0
[Grain8]
crystallite 1
(constituent) phase 1 texture 8 fraction 1.0
[Grain9]
crystallite 1
(constituent) phase 1 texture 9 fraction 1.0
[Grain10]
crystallite 1
(constituent) phase 1 texture 10 fraction 1.0
[Grain11]
crystallite 1
(constituent) phase 1 texture 11 fraction 1.0
[Grain12]
crystallite 1
(constituent) phase 1 texture 12 fraction 1.0
<!skip>
grid a 6 b 7 c 8
size x 0.75 y 0.875 z 1.0
origin x 0.0 y 0.0 z 0.0
homogenization 1
9 3 3 10 9 9
9 1 1 1 9 9
9 11 1 1 7 9
7 11 11 7 7 7
7 11 11 7 7 7
12 3 3 10 7 12
12 3 3 10 10 12
12 3 3 1 9 9
9 1 1 1 9 9
9 1 1 1 7 7
7 1 1 7 7 7
12 12 3 7 7 7
12 3 3 3 12 12
12 3 3 3 12 12
12 3 3 1 1 12
9 1 1 1 1 9
6 1 1 1 8 8
7 6 8 8 8 8
12 12 8 8 8 12
12 3 3 3 12 12
12 3 3 3 12 12
5 6 6 6 1 12
6 6 6 6 8 8
6 6 6 8 8 8
8 6 8 8 8 8
12 5 8 8 8 8
12 5 5 8 8 12
5 5 5 3 12 12
5 5 6 6 6 5
6 6 6 6 6 6
6 6 6 6 8 8
4 4 6 8 8 8
4 4 2 2 2 8
5 5 5 2 2 2
5 5 5 5 2 5
5 5 5 10 10 5
6 6 6 6 10 4
4 4 11 11 2 4
4 4 11 2 2 4
4 4 2 2 2 2
5 5 5 2 2 2
5 5 5 10 10 5
5 5 10 10 10 9
4 11 11 11 10 9
4 4 11 11 11 4
4 4 11 11 2 4
4 4 2 2 2 2
5 5 2 2 2 2
5 5 10 10 10 10
9 10 10 10 10 9
9 11 11 10 9 9
4 11 11 11 9 9
4 11 11 11 7 7
4 4 11 2 7 7
12 10 10 10 10 7
9 10 10 10 10 9

BIN
python/tests/reference/DADF5/12grains6x7x8_tensionY.hdf5 Normal file
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Binary file not shown.

129
python/tests/reference/DADF5/material.config Normal file
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@ -0,0 +1,129 @@
<homogenization>
[none]
mech none
ngrains 1
<texture>
[Grain1]
(gauss) phi1 358.98 Phi 65.62 phi2 24.48
[Grain2]
(gauss) phi1 121.05 Phi 176.11 phi2 295.73
[Grain3]
(gauss) phi1 43.79 Phi 113.76 phi2 345.90
[Grain4]
(gauss) phi1 265.15 Phi 62.52 phi2 299.71
[Grain5]
(gauss) phi1 221.23 Phi 26.54 phi2 207.05
[Grain6]
(gauss) phi1 249.81 Phi 61.47 phi2 152.14
[Grain7]
(gauss) phi1 332.45 Phi 99.16 phi2 345.34
[Grain8]
(gauss) phi1 312.27 Phi 118.27 phi2 181.59
[Grain9]
(gauss) phi1 303.10 Phi 48.21 phi2 358.03
[Grain10]
(gauss) phi1 338.26 Phi 48.11 phi2 176.78
[Grain11]
(gauss) phi1 115.17 Phi 56.54 phi2 223.84
[Grain12]
(gauss) phi1 281.04 Phi 97.48 phi2 27.94
<microstructure>
[Grain1]
crystallite 1
(constituent) phase 1 texture 1 fraction 1.0
[Grain2]
crystallite 1
(constituent) phase 1 texture 2 fraction 1.0
[Grain3]
crystallite 1
(constituent) phase 1 texture 3 fraction 1.0
[Grain4]
crystallite 1
(constituent) phase 1 texture 4 fraction 1.0
[Grain5]
crystallite 1
(constituent) phase 1 texture 5 fraction 1.0
[Grain6]
crystallite 1
(constituent) phase 1 texture 6 fraction 1.0
[Grain7]
crystallite 1
(constituent) phase 2 texture 7 fraction 1.0
[Grain8]
crystallite 1
(constituent) phase 2 texture 8 fraction 1.0
[Grain9]
crystallite 1
(constituent) phase 2 texture 9 fraction 1.0
[Grain10]
crystallite 1
(constituent) phase 2 texture 10 fraction 1.0
[Grain11]
crystallite 1
(constituent) phase 2 texture 11 fraction 1.0
[Grain12]
crystallite 1
(constituent) phase 2 texture 12 fraction 1.0
<phase>
[pheno_fcc]
elasticity hooke
plasticity phenopowerlaw
(output) orientation # quaternion
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor
lattice_structure fcc
Nslip 12 # per family
Ntwin 0 # per family
c11 106.75e9
c12 60.41e9
c44 28.34e9
gdot0_slip 0.001
n_slip 20
tau0_slip 31e6 # per family
tausat_slip 63e6 # per family
a_slip 2.25
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
atol_resistance 1
[pheno_bcc]
elasticity hooke
plasticity phenopowerlaw
(output) orientation # quaternion
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor
lattice_structure bcc
Nslip 12 # per family
c11 106.75e9
c12 60.41e9
c44 28.34e9
gdot0_slip 0.001
n_slip 20
tau0_slip 31e6 # per family
tausat_slip 63e6 # per family
a_slip 2.25
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
atol_resistance 1
<crystallite>
[dummy]

1
python/tests/reference/DADF5/tensionY.load Normal file
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@ -0,0 +1 @@
fdot * 0 0 0 1.0e-3 0 0 0 * stress 0 * * * * * * * 0 time 20 incs 40 freq 4

25
python/tests/reference/Geom/clean_stencil=1.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 22 2 2 1 21
1 1 6 26 2 2 5 25
1 1 10 30 2 2 9 29
1 1 14 34 2 2 13 33
1 1 18 38 2 2 17 37
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 5 25 2 2 4 24
1 1 9 29 2 2 8 28
1 1 13 33 2 2 12 32
1 1 17 37 2 2 16 36
1 1 21 41 2 2 20 40

25
python/tests/reference/Geom/clean_stencil=2.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 2 2 2 1 1
1 1 1 2 2 2 2 1
1 1 1 6 2 2 2 5
1 1 1 10 2 2 2 9
1 1 1 14 2 2 2 13
1 1 1 2 2 2 2 1
1 1 1 2 2 2 2 1
1 1 1 6 2 2 2 5
1 1 1 10 2 2 2 9
1 1 1 14 2 2 2 13
1 1 1 3 2 2 2 2
1 1 1 3 2 2 2 2
1 1 1 7 2 2 2 6
1 1 1 11 2 2 2 10
1 1 1 15 2 2 2 14
1 1 1 4 2 2 2 3
1 1 1 4 2 2 2 3
1 1 1 8 2 2 2 7
1 1 1 12 2 2 2 11
1 1 1 16 2 2 2 15

25
python/tests/reference/Geom/clean_stencil=3.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 25
1 1 1 2 2 2 2 29
1 1 1 2 2 2 2 37
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 25
1 1 1 2 2 2 2 29
1 1 1 2 2 2 2 37
1 1 1 2 2 2 2 22
1 1 1 2 2 2 2 22
1 1 1 2 2 2 2 26
1 1 1 2 2 2 2 30
1 1 1 2 2 2 2 38
1 1 1 2 2 2 2 24
1 1 1 2 2 2 2 24
1 1 1 2 2 2 2 28
1 1 1 2 2 2 2 32
1 1 1 2 2 2 2 40

25
python/tests/reference/Geom/clean_stencil=4.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2

85
python/tests/reference/Geom/mirror_directions=x-y-z_reflect=True.geom Normal file
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@ -0,0 +1,85 @@
4 header
grid a 16 b 10 c 8
size x 1.6e-05 y 1e-05 z 8e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 22 2 2 1 21 21 1 2 2 22 2 1 1
1 1 6 26 2 2 5 25 25 5 2 2 26 6 1 1
1 1 10 30 2 2 9 29 29 9 2 2 30 10 1 1
1 1 14 34 2 2 13 33 33 13 2 2 34 14 1 1
1 1 18 38 2 2 17 37 37 17 2 2 38 18 1 1
1 1 18 38 2 2 17 37 37 17 2 2 38 18 1 1
1 1 14 34 2 2 13 33 33 13 2 2 34 14 1 1
1 1 10 30 2 2 9 29 29 9 2 2 30 10 1 1
1 1 6 26 2 2 5 25 25 5 2 2 26 6 1 1
1 1 2 22 2 2 1 21 21 1 2 2 22 2 1 1
1 1 3 23 2 2 2 22 22 2 2 2 23 3 1 1
1 1 7 27 2 2 6 26 26 6 2 2 27 7 1 1
1 1 11 31 2 2 10 30 30 10 2 2 31 11 1 1
1 1 15 35 2 2 14 34 34 14 2 2 35 15 1 1
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25
python/tests/reference/Geom/mirror_directions=x_reflect=False.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 14 b 5 c 4
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origin x 0.0 y 0.0 z 0.0
homogenization 1
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1 1 6 26 2 2 5 25 5 2 2 26 6 1
1 1 10 30 2 2 9 29 9 2 2 30 10 1
1 1 14 34 2 2 13 33 13 2 2 34 14 1
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1 1 3 23 2 2 2 22 2 2 2 23 3 1
1 1 7 27 2 2 6 26 6 2 2 27 7 1
1 1 11 31 2 2 10 30 10 2 2 31 11 1
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1 1 4 24 2 2 3 23 3 2 2 24 4 1
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1 1 12 32 2 2 11 31 11 2 2 32 12 1
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1 1 5 25 2 2 4 24 4 2 2 25 5 1
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1 1 13 33 2 2 12 32 12 2 2 33 13 1
1 1 17 37 2 2 16 36 16 2 2 37 17 1
1 1 21 41 2 2 20 40 20 2 2 41 21 1

53
python/tests/reference/Geom/mirror_directions=y-z_reflect=False.geom Normal file
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@ -0,0 +1,53 @@
4 header
grid a 8 b 8 c 6
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origin x 0.0 y 0.0 z 0.0
homogenization 1
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1 1 10 30 2 2 9 29
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1 1 18 38 2 2 17 37
1 1 14 34 2 2 13 33
1 1 10 30 2 2 9 29
1 1 6 26 2 2 5 25
1 1 3 23 2 2 2 22
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1 1 11 31 2 2 10 30
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1 1 4 24 2 2 3 23
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1 1 17 37 2 2 16 36
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1 1 13 33 2 2 12 32
1 1 9 29 2 2 8 28
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
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1 1 20 40 2 2 19 39
1 1 16 36 2 2 15 35
1 1 12 32 2 2 11 31
1 1 8 28 2 2 7 27
1 1 3 23 2 2 2 22
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1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 15 35 2 2 14 34
1 1 11 31 2 2 10 30
1 1 7 27 2 2 6 26

53
python/tests/reference/Geom/mirror_directions=z-x-y_reflect=False.geom Normal file
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@ -0,0 +1,53 @@
4 header
grid a 14 b 8 c 6
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homogenization 1
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1 1 6 26 2 2 5 25 5 2 2 26 6 1
1 1 10 30 2 2 9 29 9 2 2 30 10 1
1 1 14 34 2 2 13 33 13 2 2 34 14 1
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1 1 15 35 2 2 14 34 14 2 2 35 15 1
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1 1 7 27 2 2 6 26 6 2 2 27 7 1
1 1 4 24 2 2 3 23 3 2 2 24 4 1
1 1 8 28 2 2 7 27 7 2 2 28 8 1
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1 1 16 36 2 2 15 35 15 2 2 36 16 1
1 1 20 40 2 2 19 39 19 2 2 40 20 1
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1 1 5 25 2 2 4 24 4 2 2 25 5 1
1 1 9 29 2 2 8 28 8 2 2 29 9 1
1 1 13 33 2 2 12 32 12 2 2 33 13 1
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1 1 21 41 2 2 20 40 20 2 2 41 21 1
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1 1 13 33 2 2 12 32 12 2 2 33 13 1
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1 1 12 32 2 2 11 31 11 2 2 32 12 1
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105
python/tests/reference/Geom/scale_grid=10-10-10.geom Normal file
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@ -0,0 +1,105 @@
4 header
grid a 10 b 10 c 10
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homogenization 1
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1 1 6 6 26 2 2 2 5 25
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1 1 7 7 27 2 2 2 6 26
1 1 11 11 31 2 2 2 10 30
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1 1 15 15 35 2 2 2 14 34
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1 1 19 19 39 2 2 2 18 38
1 1 3 3 23 2 2 2 2 22
1 1 3 3 23 2 2 2 2 22
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1 1 7 7 27 2 2 2 6 26
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1 1 15 15 35 2 2 2 14 34
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1 1 19 19 39 2 2 2 18 38
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1 1 21 21 41 2 2 2 20 40

115
python/tests/reference/Geom/scale_grid=10-11-10.geom Normal file
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@ -0,0 +1,115 @@
4 header
grid a 10 b 11 c 10
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homogenization 1
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1 1 18 18 38 2 2 2 17 37
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1 1 7 7 27 2 2 2 6 26
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1 1 7 7 27 2 2 2 6 26
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1 1 7 7 27 2 2 2 6 26
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1 1 21 21 41 2 2 2 20 40

135
python/tests/reference/Geom/scale_grid=10-13-10.geom Normal file
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@ -0,0 +1,135 @@
4 header
grid a 10 b 13 c 10
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origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 2 22 2 2 2 1 21
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1 1 6 6 26 2 2 2 5 25
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1 1 10 10 30 2 2 2 9 29
1 1 14 14 34 2 2 2 13 33
1 1 14 14 34 2 2 2 13 33
1 1 14 14 34 2 2 2 13 33
1 1 18 18 38 2 2 2 17 37
1 1 18 18 38 2 2 2 17 37
1 1 3 3 23 2 2 2 2 22
1 1 3 3 23 2 2 2 2 22
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1 1 7 7 27 2 2 2 6 26
1 1 11 11 31 2 2 2 10 30
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1 1 5 5 25 2 2 2 4 24
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45
python/tests/reference/Geom/scale_grid=10-20-2.geom Normal file
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@ -0,0 +1,45 @@
4 header
grid a 10 b 20 c 2
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 2 22 2 2 2 1 21
1 1 2 2 22 2 2 2 1 21
1 1 2 2 22 2 2 2 1 21
1 1 6 6 26 2 2 2 5 25
1 1 6 6 26 2 2 2 5 25
1 1 6 6 26 2 2 2 5 25
1 1 6 6 26 2 2 2 5 25
1 1 6 6 26 2 2 2 5 25
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1 1 10 10 30 2 2 2 9 29
1 1 10 10 30 2 2 2 9 29
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1 1 5 5 25 2 2 2 4 24
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1 1 9 9 29 2 2 2 8 28
1 1 9 9 29 2 2 2 8 28
1 1 9 9 29 2 2 2 8 28
1 1 9 9 29 2 2 2 8 28
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1 1 21 21 41 2 2 2 20 40
1 1 21 21 41 2 2 2 20 40

85
python/tests/reference/Geom/scale_grid=5-4-20.geom Normal file
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@ -0,0 +1,85 @@
4 header
grid a 5 b 4 c 20
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 2 2 2 21
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1 14 2 2 33
1 18 2 2 37
1 2 2 2 21
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1 21 2 2 40
1 5 2 2 24
1 9 2 2 28
1 17 2 2 36
1 21 2 2 40
1 5 2 2 24
1 9 2 2 28
1 17 2 2 36
1 21 2 2 40

125
python/tests/reference/Geom/scale_grid=8-10-12.geom Normal file
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@ -0,0 +1,125 @@
4 header
grid a 8 b 10 c 12
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 22 2 2 1 21
1 1 2 22 2 2 1 21
1 1 6 26 2 2 5 25
1 1 6 26 2 2 5 25
1 1 10 30 2 2 9 29
1 1 10 30 2 2 9 29
1 1 14 34 2 2 13 33
1 1 14 34 2 2 13 33
1 1 18 38 2 2 17 37
1 1 18 38 2 2 17 37
1 1 2 22 2 2 1 21
1 1 2 22 2 2 1 21
1 1 6 26 2 2 5 25
1 1 6 26 2 2 5 25
1 1 10 30 2 2 9 29
1 1 10 30 2 2 9 29
1 1 14 34 2 2 13 33
1 1 14 34 2 2 13 33
1 1 18 38 2 2 17 37
1 1 18 38 2 2 17 37
1 1 3 23 2 2 2 22
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 19 39 2 2 18 38
1 1 3 23 2 2 2 22
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 19 39 2 2 18 38
1 1 3 23 2 2 2 22
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 19 39 2 2 18 38
1 1 3 23 2 2 2 22
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 19 39 2 2 18 38
1 1 4 24 2 2 3 23
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 20 40 2 2 19 39
1 1 4 24 2 2 3 23
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 20 40 2 2 19 39
1 1 4 24 2 2 3 23
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 20 40 2 2 19 39
1 1 4 24 2 2 3 23
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 20 40 2 2 19 39
1 1 5 25 2 2 4 24
1 1 5 25 2 2 4 24
1 1 9 29 2 2 8 28
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1 1 13 33 2 2 12 32
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1 1 17 37 2 2 16 36
1 1 17 37 2 2 16 36
1 1 21 41 2 2 20 40
1 1 21 41 2 2 20 40
1 1 5 25 2 2 4 24
1 1 5 25 2 2 4 24
1 1 9 29 2 2 8 28
1 1 9 29 2 2 8 28
1 1 13 33 2 2 12 32
1 1 13 33 2 2 12 32
1 1 17 37 2 2 16 36
1 1 17 37 2 2 16 36
1 1 21 41 2 2 20 40
1 1 21 41 2 2 20 40

67
python/tests/test_DADF5.py Normal file
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@ -0,0 +1,67 @@
import shutil
import os
import pytest
import numpy as np
from damask import DADF5
from damask import mechanics
@pytest.fixture
def default(tmp_path,reference_dir):
"""Small DADF5 file in temp location for modification."""
fname = '12grains6x7x8_tensionY.hdf5'
shutil.copy(os.path.join(reference_dir,fname),tmp_path)
f = DADF5(os.path.join(tmp_path,fname))
f.set_by_time(20.0,20.0)
return f
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'DADF5')
class TestDADF5:
def test_add_deviator(self,default):
default.add_deviator('P')
loc = {'P' :default.get_dataset_location('P'),
's_P':default.get_dataset_location('s_P')}
in_memory = mechanics.deviatoric_part(default.read_dataset(loc['P'],0))
in_file = default.read_dataset(loc['s_P'],0)
assert np.allclose(in_memory,in_file)
def test_add_Cauchy(self,default):
default.add_Cauchy('P','F')
loc = {'F': default.get_dataset_location('F'),
'P': default.get_dataset_location('P'),
'sigma':default.get_dataset_location('sigma')}
in_memory = mechanics.Cauchy(default.read_dataset(loc['F'],0),
default.read_dataset(loc['P'],0))
in_file = default.read_dataset(loc['sigma'],0)
assert np.allclose(in_memory,in_file)
def test_add_absolute(self,default):
default.add_absolute('Fe')
loc = {'Fe': default.get_dataset_location('Fe'),
'|Fe|': default.get_dataset_location('|Fe|')}
in_memory = np.abs(default.read_dataset(loc['Fe'],0))
in_file = default.read_dataset(loc['|Fe|'],0)
assert np.allclose(in_memory,in_file)
def test_add_determinant(self,default):
default.add_determinant('P')
loc = {'P': default.get_dataset_location('P'),
'det(P)': default.get_dataset_location('det(P)')}
in_memory = np.linalg.det(default.read_dataset(loc['P'],0)).reshape(-1,1)
in_file = default.read_dataset(loc['det(P)'],0)
assert np.allclose(in_memory,in_file)
def test_add_spherical(self,default):
default.add_spherical('P')
loc = {'P': default.get_dataset_location('P'),
'p_P': default.get_dataset_location('p_P')}
in_memory = mechanics.spherical_part(default.read_dataset(loc['P'],0)).reshape(-1,1)
in_file = default.read_dataset(loc['p_P'],0)
assert np.allclose(in_memory,in_file)

99
python/tests/test_Geom.py Normal file
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@ -0,0 +1,99 @@
import copy
import os
import pytest
import numpy as np
from damask import Geom
def geom_equal(a,b):
return np.all(a.get_microstructure() == b.get_microstructure()) and \
np.all(a.get_size() == b.get_size()) and \
np.all(a.get_grid() == b.get_grid())
@pytest.fixture
def default():
"""Simple geometry."""
x=np.concatenate((np.ones(40,dtype=int),
np.arange(2,42),
np.ones(40,dtype=int)*2,
np.arange(1,41))).reshape((8,5,4))
return Geom(x,[8e-6,5e-6,4e-6])
@pytest.fixture
def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return os.path.join(reference_dir_base,'Geom')
class TestGeom:
def test_update(self,default):
modified = copy.deepcopy(default)
modified.update(
default.get_microstructure(),
default.get_size(),
default.get_origin()
)
assert geom_equal(modified,default)
def test_write_read_str(self,default,tmpdir):
default.to_file(str(tmpdir.join('default.geom')))
new = Geom.from_file(str(tmpdir.join('default.geom')))
assert geom_equal(new,default)
def test_write_read_file(self,default,tmpdir):
with open(tmpdir.join('default.geom'),'w') as f:
default.to_file(f)
with open(tmpdir.join('default.geom')) as f:
new = Geom.from_file(f)
assert geom_equal(new,default)
@pytest.mark.parametrize('pack',[True,False])
def test_pack(self,default,tmpdir,pack):
default.to_file(tmpdir.join('default.geom'),pack=pack)
new = Geom.from_file(tmpdir.join('default.geom'))
assert geom_equal(new,default)
@pytest.mark.parametrize('directions,reflect',[
(['x'], False),
(['x','y','z'],True),
(['z','x','y'],False),
(['y','z'], False)
]
)
def test_mirror(self,default,update,reference_dir,directions,reflect):
modified = copy.deepcopy(default)
modified.mirror(directions,reflect)
tag = 'directions={}_reflect={}'.format('-'.join(directions),reflect)
reference = os.path.join(reference_dir,'mirror_{}.geom'.format(tag))
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@pytest.mark.parametrize('stencil',[(1),(2),(3),(4)])
def test_clean(self,default,update,reference_dir,stencil):
modified = copy.deepcopy(default)
modified.clean(stencil)
tag = 'stencil={}'.format(stencil)
reference = os.path.join(reference_dir,'clean_{}.geom'.format(tag))
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
@pytest.mark.parametrize('grid',[
((10,11,10)),
([10,13,10]),
(np.array((10,10,10))),
(np.array((8, 10,12))),
(np.array((5, 4, 20))),
(np.array((10,20,2)) )
]
)
def test_scale(self,default,update,reference_dir,grid):
modified = copy.deepcopy(default)
modified.scale(grid)
tag = 'grid={}'.format('-'.join([str(x) for x in grid]))
reference = os.path.join(reference_dir,'scale_{}.geom'.format(tag))
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))

55
python/tests/test_Rotation.py Normal file
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@ -0,0 +1,55 @@
import pytest
import numpy as np
from damask import Rotation
n = 1000
@pytest.fixture
def default():
"""A set of n random rotations."""
return [Rotation.fromRandom() for r in range(n)]
class TestRotation:
def test_Eulers(self,default):
for rot in default:
assert np.allclose(rot.asQuaternion(),
Rotation.fromEulers(rot.asEulers()).asQuaternion())
def test_AxisAngle(self,default):
for rot in default:
assert np.allclose(rot.asEulers(),
Rotation.fromAxisAngle(rot.asAxisAngle()).asEulers())
def test_Matrix(self,default):
for rot in default:
assert np.allclose(rot.asAxisAngle(),
Rotation.fromMatrix(rot.asMatrix()).asAxisAngle())
def test_Rodriques(self,default):
for rot in default:
assert np.allclose(rot.asMatrix(),
Rotation.fromRodrigues(rot.asRodrigues()).asMatrix())
def test_Homochoric(self,default):
for rot in default:
assert np.allclose(rot.asRodrigues(),
Rotation.fromHomochoric(rot.asHomochoric()).asRodrigues())
def test_Cubochoric(self,default):
for rot in default:
assert np.allclose(rot.asHomochoric(),
Rotation.fromCubochoric(rot.asCubochoric()).asHomochoric())
def test_Quaternion(self,default):
for rot in default:
assert np.allclose(rot.asCubochoric(),
Rotation.fromQuaternion(rot.asQuaternion()).asCubochoric())

57
python/tests/test_Table.py Normal file
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@ -0,0 +1,57 @@
import pytest
import numpy as np
from damask import Table
@pytest.fixture
def default():
"""Simple Table."""
x = np.ones((5,13))
return Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['test data','contains only ones'])
class TestTable:
def test_get_tensor(self,default):
d = default.get_array('F')
assert np.allclose(d,1.0) and d.shape[1:] == (3,3)
def test_get_vector(self,default):
d = default.get_array('v')
assert np.allclose(d,1.0) and d.shape[1:] == (3,)
def test_write_read_str(self,default,tmpdir):
default.to_ASCII(str(tmpdir.join('default.txt')))
new = Table.from_ASCII(str(tmpdir.join('default.txt')))
assert all(default.data==new.data)
def test_write_read_file(self,default,tmpdir):
with open(tmpdir.join('default.txt'),'w') as f:
default.to_ASCII(f)
with open(tmpdir.join('default.txt')) as f:
new = Table.from_ASCII(f)
assert all(default.data==new.data)
def test_set_array(self,default):
default.set_array('F',np.zeros((5,3,3)),'set to zero')
d=default.get_array('F')
assert np.allclose(d,0.0) and d.shape[1:] == (3,3)
def test_get_labels(self,default):
assert default.get_labels() == ['F','v','s']
def test_add_array(self,default):
d = np.random.random((5,9))
default.add_array('nine',d,'random data')
assert np.allclose(d,default.get_array('nine'))
def test_invalid_initialization(self,default):
x = default.get_array('v')
with pytest.raises(IndexError):
Table(x,{'F':(3,3)})
def test_invalid_set(self,default):
x = default.get_array('v')
with pytest.raises(ValueError):
default.set_array('F',x,'does not work')

142
python/tests/test_mechanics.py Normal file
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@ -0,0 +1,142 @@
import numpy as np
from damask import mechanics
class TestMechanics:
n = 1000
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(F,P)[self.c],
mechanics.Cauchy(F[self.c],P[self.c]))
def test_vectorize_strain_tensor(self):
F = np.random.random((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_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_spherical_part(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.spherical_part(x)[self.c],
mechanics.spherical_part(x[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_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_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_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_principal_components(self):
x = np.random.random((self.n,3,3))
assert np.allclose(mechanics.principal_components(x)[self.c],
mechanics.principal_components(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_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_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_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_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(np.broadcast_to(np.eye(3),(self.n,3,3)),P),
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))
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(self):
"""Ensure that pure rotation results in no strain."""
F = mechanics.rotational_part(np.random.random((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),
0.0)
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))
sph = np.broadcast_to(np.eye(3),(self.n,3,3))\
* np.repeat(mechanics.spherical_part(x),9).reshape(self.n,3,3)
assert np.allclose(sph + mechanics.deviatoric_part(x),
x)
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))
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)))
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))
assert np.allclose(mechanics.Mises_stress(x)/mechanics.Mises_strain(x),
1.5)

2
src/CPFEM2.f90
View File

@ -57,10 +57,10 @@ subroutine CPFEM_initAll
call config_init
call math_init
call rotations_init
call mesh_init
call lattice_init
call HDF5_utilities_init
call results_init
call mesh_init
call material_init
call constitutive_init
call crystallite_init

30
src/config.f90
View File

@ -85,6 +85,7 @@ subroutine config_init
case (trim('crystallite'))
call parse_materialConfig(config_name_crystallite,config_crystallite,line,fileContent(i+1:))
if (verbose) write(6,'(a)') ' Crystallite parsed'; flush(6)
deallocate(config_crystallite)
case (trim('homogenization'))
call parse_materialConfig(config_name_homogenization,config_homogenization,line,fileContent(i+1:))
@ -102,27 +103,25 @@ subroutine config_init
call IO_error(160,ext_msg='<homogenization>')
if (.not. allocated(config_microstructure) .or. size(config_microstructure) < 1) &
call IO_error(160,ext_msg='<microstructure>')
if (.not. allocated(config_crystallite) .or. size(config_crystallite) < 1) &
call IO_error(160,ext_msg='<crystallite>')
if (.not. allocated(config_phase) .or. size(config_phase) < 1) &
call IO_error(160,ext_msg='<phase>')
if (.not. allocated(config_texture) .or. size(config_texture) < 1) &
call IO_error(160,ext_msg='<texture>')
inquire(file='numerics.config', exist=fileExists)
if (fileExists) then
write(6,'(/,a)') ' reading numerics.config'; flush(6)
fileContent = IO_read_ASCII('numerics.config')
call parse_debugAndNumericsConfig(config_numerics,fileContent)
endif
inquire(file='numerics.config', exist=fileExists)
if (fileExists) then
write(6,'(/,a)') ' reading numerics.config'; flush(6)
fileContent = IO_read_ASCII('numerics.config')
call parse_debugAndNumericsConfig(config_numerics,fileContent)
endif
inquire(file='debug.config', exist=fileExists)
if (fileExists) then
write(6,'(/,a)') ' reading debug.config'; flush(6)
fileContent = IO_read_ASCII('debug.config')
call parse_debugAndNumericsConfig(config_debug,fileContent)
endif
inquire(file='debug.config', exist=fileExists)
if (fileExists) then
write(6,'(/,a)') ' reading debug.config'; flush(6)
fileContent = IO_read_ASCII('debug.config')
call parse_debugAndNumericsConfig(config_debug,fileContent)
endif
contains
@ -295,9 +294,6 @@ subroutine config_deallocate(what)
case('material.config/microstructure')
deallocate(config_microstructure)
case('material.config/crystallite')
deallocate(config_crystallite)
case('material.config/homogenization')
deallocate(config_homogenization)

159
src/crystallite.f90
View File

@ -22,22 +22,10 @@ module crystallite
use discretization
use lattice
use plastic_nonlocal
use geometry_plastic_nonlocal, only: &
nIPneighbors => geometry_plastic_nonlocal_nIPneighbors, &
IPneighborhood => geometry_plastic_nonlocal_IPneighborhood
use HDF5_utilities
use results
implicit none
private
character(len=64), dimension(:,:), allocatable :: &
crystallite_output !< name of each post result output
integer, public, protected :: &
crystallite_maxSizePostResults !< description not available
integer, dimension(:), allocatable, public, protected :: &
crystallite_sizePostResults !< description not available
integer, dimension(:,:), allocatable :: &
crystallite_sizePostResult !< description not available
real(pReal), dimension(:,:,:), allocatable, public :: &
crystallite_dt !< requested time increment of each grain
@ -90,21 +78,11 @@ module crystallite
enum, bind(c)
enumerator :: undefined_ID, &
phase_ID, &
texture_ID, &
orientation_ID, &
grainrotation_ID, &
defgrad_ID, &
fe_ID, &
fp_ID, &
fi_ID, &
lp_ID, &
li_ID, &
p_ID, &
s_ID, &
elasmatrix_ID, &
neighboringip_ID, &
neighboringelement_ID
elasmatrix_ID
end enum
integer(kind(undefined_ID)),dimension(:,:), allocatable :: &
crystallite_outputID !< ID of each post result output
@ -213,13 +191,6 @@ subroutine crystallite_init
allocate(crystallite_requested(cMax,iMax,eMax), source=.false.)
allocate(crystallite_todo(cMax,iMax,eMax), source=.false.)
allocate(crystallite_converged(cMax,iMax,eMax), source=.true.)
allocate(crystallite_output(maxval(crystallite_Noutput), &
size(config_crystallite))) ; crystallite_output = ''
allocate(crystallite_outputID(maxval(crystallite_Noutput), &
size(config_crystallite)), source=undefined_ID)
allocate(crystallite_sizePostResults(size(config_crystallite)),source=0)
allocate(crystallite_sizePostResult(maxval(crystallite_Noutput), &
size(config_crystallite)), source=0)
num%subStepMinCryst = config_numerics%getFloat('substepmincryst', defaultVal=1.0e-3_pReal)
num%subStepSizeCryst = config_numerics%getFloat('substepsizecryst', defaultVal=0.25_pReal)
@ -266,55 +237,6 @@ subroutine crystallite_init
integrateState => integrateStateRKCK45
end select
do c = 1, size(config_crystallite)
#if defined(__GFORTRAN__)
str = ['GfortranBug86277']
str = config_crystallite(c)%getStrings('(output)',defaultVal=str)
if (str(1) == 'GfortranBug86277') str = [character(len=65536)::]
#else
str = config_crystallite(c)%getStrings('(output)',defaultVal=[character(len=65536)::])
#endif
do o = 1, size(str)
crystallite_output(o,c) = str(o)
outputName: select case(str(o))
case ('phase') outputName
crystallite_outputID(o,c) = phase_ID
case ('texture') outputName
crystallite_outputID(o,c) = texture_ID
case ('orientation') outputName
crystallite_outputID(o,c) = orientation_ID
case ('grainrotation') outputName
crystallite_outputID(o,c) = grainrotation_ID
case ('defgrad','f') outputName ! ToDo: no alias (f only)
crystallite_outputID(o,c) = defgrad_ID
case ('fe') outputName
crystallite_outputID(o,c) = fe_ID
case ('fp') outputName
crystallite_outputID(o,c) = fp_ID
case ('fi') outputName
crystallite_outputID(o,c) = fi_ID
case ('lp') outputName
crystallite_outputID(o,c) = lp_ID
case ('li') outputName
crystallite_outputID(o,c) = li_ID
case ('p','firstpiola','1stpiola') outputName ! ToDo: no alias (p only)
crystallite_outputID(o,c) = p_ID
case ('s','tstar','secondpiola','2ndpiola') outputName ! ToDo: no alias (s only)
crystallite_outputID(o,c) = s_ID
case ('elasmatrix') outputName
crystallite_outputID(o,c) = elasmatrix_ID
case ('neighboringip') outputName ! ToDo: this is not a result, it is static. Should be written out by mesh
crystallite_outputID(o,c) = neighboringip_ID
case ('neighboringelement') outputName ! ToDo: this is not a result, it is static. Should be written out by mesh
crystallite_outputID(o,c) = neighboringelement_ID
case default outputName
call IO_error(105,ext_msg=trim(str(o))//' (Crystallite)')
end select outputName
enddo
enddo
allocate(output_constituent(size(config_phase)))
do c = 1, size(config_phase)
#if defined(__GFORTRAN__)
@ -327,47 +249,14 @@ subroutine crystallite_init
#endif
enddo
do r = 1,size(config_crystallite)
do o = 1,crystallite_Noutput(r)
select case(crystallite_outputID(o,r))
case(orientation_ID)
mySize = 4
case(defgrad_ID,fp_ID,p_ID)
mySize = 9
case(neighboringip_ID,neighboringelement_ID)
mySize = nIPneighbors
case default
mySize = 0
end select
crystallite_sizePostResult(o,r) = mySize
crystallite_sizePostResults(r) = crystallite_sizePostResults(r) + mySize
enddo
enddo
crystallite_maxSizePostResults = &
maxval(crystallite_sizePostResults(microstructure_crystallite),microstructure_active)
!--------------------------------------------------------------------------------------------------
! write description file for crystallite output
if (worldrank == 0) then
call IO_write_jobFile(FILEUNIT,'outputCrystallite')
do r = 1,size(config_crystallite)
if (any(microstructure_crystallite(discretization_microstructureAt) == r)) then
write(FILEUNIT,'(/,a,/)') '['//trim(config_name_crystallite(r))//']'
do o = 1,crystallite_Noutput(r)
write(FILEUNIT,'(a,i4)') trim(crystallite_output(o,r))//char(9),crystallite_sizePostResult(o,r)
enddo
endif
enddo
write(FILEUNIT,'(/,a,/)') '[not supported anymore]'
close(FILEUNIT)
endif
call config_deallocate('material.config/phase')
call config_deallocate('material.config/crystallite')
!--------------------------------------------------------------------------------------------------
! initialize
@ -869,59 +758,21 @@ function crystallite_postResults(ipc, ip, el)
ip, & !< integration point index
ipc !< grain index
real(pReal), dimension(1+crystallite_sizePostResults(microstructure_crystallite(discretization_microstructureAt(el))) + &
real(pReal), dimension(1+ &
1+plasticState(material_phaseAt(ipc,el))%sizePostResults + &
sum(sourceState(material_phaseAt(ipc,el))%p(:)%sizePostResults)) :: &
crystallite_postResults
integer :: &
o, &
c, &
crystID, &
mySize, &
n
crystID = microstructure_crystallite(discretization_microstructureAt(el))
crystallite_postResults = 0.0_pReal
crystallite_postResults(1) = real(crystallite_sizePostResults(crystID),pReal) ! header-like information (length)
crystallite_postResults(1) = 0.0_pReal ! header-like information (length)
c = 1
do o = 1,crystallite_Noutput(crystID)
mySize = 0
select case(crystallite_outputID(o,crystID))
case (orientation_ID)
mySize = 4
crystallite_postResults(c+1:c+mySize) = crystallite_orientation(ipc,ip,el)%asQuaternion()
! remark: tensor output is of the form 11,12,13, 21,22,23, 31,32,33
! thus row index i is slow, while column index j is fast. reminder: "row is slow"
case (defgrad_ID)
mySize = 9
crystallite_postResults(c+1:c+mySize) = &
reshape(transpose(crystallite_partionedF(1:3,1:3,ipc,ip,el)),[mySize])
case (fp_ID)
mySize = 9
crystallite_postResults(c+1:c+mySize) = &
reshape(transpose(crystallite_Fp(1:3,1:3,ipc,ip,el)),[mySize])
case (p_ID)
mySize = 9
crystallite_postResults(c+1:c+mySize) = &
reshape(transpose(crystallite_P(1:3,1:3,ipc,ip,el)),[mySize])
case(neighboringelement_ID)
mySize = nIPneighbors
crystallite_postResults(c+1:c+mySize) = 0.0_pReal
forall (n = 1:mySize) &
crystallite_postResults(c+n) = real(IPneighborhood(1,n,ip,el),pReal)
case(neighboringip_ID)
mySize = nIPneighbors
crystallite_postResults(c+1:c+mySize) = 0.0_pReal
forall (n = 1:mySize) &
crystallite_postResults(c+n) = real(IPneighborhood(2,n,ip,el),pReal)
end select
c = c + mySize
enddo
crystallite_postResults(c+1) = real(plasticState(material_phaseAt(ipc,el))%sizePostResults,pReal) ! size of constitutive results
c = c + 1
if (size(crystallite_postResults)-c > 0) &
@ -945,7 +796,7 @@ subroutine crystallite_results
do p=1,size(config_name_phase)
group = trim('current/constituent')//'/'//trim(config_name_phase(p))//'/generic'
call HDF5_closeGroup(results_addGroup(group))
call results_closeGroup(results_addGroup(group))
do o = 1, size(output_constituent(p)%label)
select case (output_constituent(p)%label(o))

5
src/discretization.f90
View File

@ -6,9 +6,6 @@ module discretization
use prec
use results
#if defined(PETSc) || defined(DAMASK_HDF5)
use HDF5_utilities
#endif
implicit none
private
@ -84,7 +81,7 @@ subroutine discretization_results
#if defined(PETSc) || defined(DAMASK_HDF5)
real(pReal), dimension(:,:), allocatable :: u
call HDF5_closeGroup(results_addGroup(trim('current/geometry')))
call results_closeGroup(results_addGroup(trim('current/geometry')))
u = discretization_NodeCoords (1:3,:discretization_sharedNodesBeginn) &
- discretization_NodeCoords0(1:3,:discretization_sharedNodesBeginn)

2
src/geometry_plastic_nonlocal.f90
View File

@ -122,7 +122,7 @@ subroutine geometry_plastic_nonlocal_results
integer, dimension(:), allocatable :: shp
#if defined(DAMASK_HDF5)
#if defined(PETSc) || defined(DAMASK_HDF5)
call results_openJobFile
writeVolume: block

9
src/grid/DAMASK_grid.f90
View File

@ -27,7 +27,6 @@ program DAMASK_spectral
use grid_mech_FEM
use grid_damage_spectral
use grid_thermal_spectral
use HDF5_utilities
use results
use rotations
@ -319,15 +318,9 @@ program DAMASK_spectral
enddo
close(fileUnit)
call results_openJobFile
call HDF5_closeGroup(results_addGroup('geometry'))
call results_addAttribute('grid',grid,'geometry')
call results_addAttribute('size',geomSize,'geometry')
call results_closeJobFile
!--------------------------------------------------------------------------------------------------
! doing initialization depending on active solvers
call Utilities_init()
call Utilities_init
do field = 1, nActiveFields
select case (loadCases(1)%ID(field))
case(FIELD_MECH_ID)

8
src/homogenization.f90
View File

@ -262,7 +262,7 @@ subroutine homogenization_init
materialpoint_sizeResults = 1 & ! grain count
+ 1 + thermal_maxSizePostResults &
+ damage_maxSizePostResults &
+ homogenization_maxNgrains * (1 + crystallite_maxSizePostResults & ! crystallite size & crystallite results
+ homogenization_maxNgrains * (1 & ! crystallite size
+ 1 + constitutive_plasticity_maxSizePostResults & ! constitutive size & constitutive results
+ constitutive_source_maxSizePostResults)
allocate(materialpoint_results(materialpoint_sizeResults,discretization_nIP,discretization_nElem))
@ -592,15 +592,13 @@ subroutine materialpoint_postResults
thePos, &
theSize, &
myNgrains, &
myCrystallite, &
g, & !< grain number
i, & !< integration point number
e !< element number
!$OMP PARALLEL DO PRIVATE(myNgrains,myCrystallite,thePos,theSize)
!$OMP PARALLEL DO PRIVATE(myNgrains,thePos,theSize)
elementLooping: do e = FEsolving_execElem(1),FEsolving_execElem(2)
myNgrains = homogenization_Ngrains(material_homogenizationAt(e))
myCrystallite = microstructure_crystallite(discretization_microstructureAt(e))
IpLooping: do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e)
thePos = 0
@ -618,7 +616,7 @@ subroutine materialpoint_postResults
thePos = thePos + 1
grainLooping :do g = 1,myNgrains
theSize = 1 + crystallite_sizePostResults(myCrystallite) + &
theSize = 1 + &
1 + plasticState (material_phaseAt(g,e))%sizePostResults + &
sum(sourceState(material_phaseAt(g,e))%p(:)%sizePostResults)
materialpoint_results(thePos+1:thePos+theSize,i,e) = crystallite_postResults(g,i,e) ! tell crystallite results

32
src/material.f90
View File

@ -116,13 +116,11 @@ module material
phase_Noutput, & !< number of '(output)' items per phase
phase_elasticityInstance, & !< instance of particular elasticity of each phase
phase_plasticityInstance, & !< instance of particular plasticity of each phase
crystallite_Noutput, & !< number of '(output)' items per crystallite setting
homogenization_Ngrains, & !< number of grains in each homogenization
homogenization_Noutput, & !< number of '(output)' items per homogenization
homogenization_typeInstance, & !< instance of particular type of each homogenization
thermal_typeInstance, & !< instance of particular type of each thermal transport
damage_typeInstance, & !< instance of particular type of each nonlocal damage
microstructure_crystallite !< crystallite setting ID of each microstructure ! DEPRECATED !!!!
damage_typeInstance !< instance of particular type of each nonlocal damage
real(pReal), dimension(:), allocatable, public, protected :: &
thermal_initialT, & !< initial temperature per each homogenization
@ -245,9 +243,6 @@ subroutine material_init
call material_parseMicrostructure()
if (iand(myDebug,debug_levelBasic) /= 0) write(6,'(a)') ' Microstructure parsed'; flush(6)
call material_parseCrystallite()
if (iand(myDebug,debug_levelBasic) /= 0) write(6,'(a)') ' Crystallite parsed'; flush(6)
call material_parseHomogenization()
if (iand(myDebug,debug_levelBasic) /= 0) write(6,'(a)') ' Homogenization parsed'; flush(6)
@ -277,9 +272,6 @@ subroutine material_init
allocate(temperatureRate (material_Nhomogenization))
do m = 1,size(config_microstructure)
if(microstructure_crystallite(m) < 1 .or. &
microstructure_crystallite(m) > size(config_crystallite)) &
call IO_error(150,m,ext_msg='crystallite')
if(minval(microstructure_phase(1:microstructure_Nconstituents(m),m)) < 1 .or. &
maxval(microstructure_phase(1:microstructure_Nconstituents(m),m)) > size(config_phase)) &
call IO_error(150,m,ext_msg='phase')
@ -298,9 +290,8 @@ subroutine material_init
enddo
write(6,'(/,a14,18x,1x,a11,1x,a12,1x,a13)') 'microstructure','crystallite','constituents'
do m = 1,size(config_microstructure)
write(6,'(1x,a32,1x,i11,1x,i12)') config_name_microstructure(m), &
microstructure_crystallite(m), &
microstructure_Nconstituents(m)
write(6,'(1x,a32,1x,i12)') config_name_microstructure(m), &
microstructure_Nconstituents(m)
if (microstructure_Nconstituents(m) > 0) then
do c = 1,microstructure_Nconstituents(m)
write(6,'(a1,1x,a32,1x,a32,1x,f7.4)') '>',config_name_phase(microstructure_phase(c,m)),&
@ -500,7 +491,6 @@ subroutine material_parseMicrostructure
character(len=65536) :: &
tag
allocate(microstructure_crystallite(size(config_microstructure)), source=0)
allocate(microstructure_Nconstituents(size(config_microstructure)), source=0)
allocate(microstructure_active(size(config_microstructure)), source=.false.)
@ -512,7 +502,6 @@ subroutine material_parseMicrostructure
do m=1, size(config_microstructure)
microstructure_Nconstituents(m) = config_microstructure(m)%countKeys('(constituent)')
microstructure_crystallite(m) = config_microstructure(m)%getInt('crystallite')
enddo
microstructure_maxNconstituents = maxval(microstructure_Nconstituents)
@ -547,21 +536,6 @@ subroutine material_parseMicrostructure
end subroutine material_parseMicrostructure
!--------------------------------------------------------------------------------------------------
!> @brief parses the crystallite part in the material configuration file
!--------------------------------------------------------------------------------------------------
subroutine material_parseCrystallite
integer :: c
allocate(crystallite_Noutput(size(config_crystallite)),source=0)
do c=1, size(config_crystallite)
crystallite_Noutput(c) = config_crystallite(c)%countKeys('(output)')
enddo
end subroutine material_parseCrystallite
!--------------------------------------------------------------------------------------------------
!> @brief parses the phase part in the material configuration file
!--------------------------------------------------------------------------------------------------

9
src/mesh_grid.f90
View File

@ -14,6 +14,7 @@ module mesh_grid
use IO
use debug
use numerics
use results
use discretization
use geometry_plastic_nonlocal
use FEsolving
@ -99,6 +100,14 @@ subroutine mesh_init(ip,el)
FEsolving_execElem = [1,product(myGrid)] ! parallel loop bounds set to comprise all elements
allocate(FEsolving_execIP(2,product(myGrid)),source=1) ! parallel loop bounds set to comprise the only IP
!--------------------------------------------------------------------------------------------------
! store geometry information for post processing
call results_openJobFile
call results_closeGroup(results_addGroup('geometry'))
call results_addAttribute('grid',grid,'geometry')
call results_addAttribute('size',geomSize,'geometry')
call results_closeJobFile
!--------------------------------------------------------------------------------------------------
! geometry information required by the nonlocal CP model
call geometry_plastic_nonlocal_setIPvolume(reshape([(product(mySize/real(myGrid,pReal)),j=1,product(myGrid))], &

6
src/mesh_marc.f90
View File

@ -69,7 +69,7 @@ subroutine mesh_init(ip,el)
microstructureAt, &
homogenizationAt
integer:: &
Nnodes !< total number of nodes in mesh
Nnodes !< total number of nodes in mesh
real(pReal), dimension(:,:), allocatable :: &
ip_reshaped
@ -119,15 +119,17 @@ subroutine mesh_init(ip,el)
reshape(connectivity_cell,[elem%NcellNodesPerCell,elem%nIPs*nElems]),&
node0_cell,ip_reshaped)
!--------------------------------------------------------------------------------------------------
! geometry information required by the nonlocal CP model
call geometry_plastic_nonlocal_setIPvolume(IPvolume(elem,node0_cell,connectivity_cell))
unscaledNormals = IPareaNormal(elem,nElems,connectivity_cell,node0_cell)
call geometry_plastic_nonlocal_setIParea(norm2(unscaledNormals,1))
call geometry_plastic_nonlocal_setIPareaNormal(unscaledNormals/spread(norm2(unscaledNormals,1),1,3))
call geometry_plastic_nonlocal_results
end subroutine mesh_init
!--------------------------------------------------------------------------------------------------
!> @brief Writes all information needed for the DADF5 geometry
!--------------------------------------------------------------------------------------------------

14
src/results.f90
View File

@ -50,6 +50,7 @@ module results
results_addIncrement, &
results_addGroup, &
results_openGroup, &
results_closeGroup, &
results_writeDataset, &
results_setLink, &
results_addAttribute, &
@ -120,6 +121,7 @@ subroutine results_addIncrement(inc,time)
end subroutine results_addIncrement
!--------------------------------------------------------------------------------------------------
!> @brief open a group from the results file
!--------------------------------------------------------------------------------------------------
@ -144,6 +146,18 @@ integer(HID_T) function results_addGroup(groupName)
end function results_addGroup
!--------------------------------------------------------------------------------------------------
!> @brief close a group
!--------------------------------------------------------------------------------------------------
subroutine results_closeGroup(group_id)
integer(HID_T), intent(in) :: group_id
call HDF5_closeGroup(group_id)
end subroutine results_closeGroup
!--------------------------------------------------------------------------------------------------
!> @brief set link to object in results file
!--------------------------------------------------------------------------------------------------