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Merge branch 'vtr-only' into development

This commit is contained in:
Sharan Roongta 2020-10-14 12:01:33 +02:00
parent d8f97c8d0b 2c608c1bcf
commit 02e4154e5e
68 changed files with 635 additions and 193308 deletions
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14
.gitlab-ci.yml
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@ -285,20 +285,6 @@ grid_all_restart:
- master
- release
grid_parsingLoadCase:
stage: grid
script: grid_parsingLoadCase/test.py
except:
- master
- release
grid_all_loadCaseRotation:
stage: grid
script: grid_all_loadCaseRotation/test.py
except:
- master
- release
grid_all_restartMPI:
stage: grid
script:

2
PRIVATE

@ -1 +1 @@
Subproject commit c92f6d3e23a4c310898b502f00e395dbe670a63c
Subproject commit dde6a5836089b14bd39d4393a47b82b351d2bd85

2
examples/ConfigFiles/Kinematics_Hydrogen_Strain.config
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@ -1,2 +0,0 @@
(kinematics) vacancy_strain
vacancy_strain_coeff 0.006

186629
examples/ConfigFiles/rollingTexture.linearODF
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File diff suppressed because it is too large Load Diff

262
examples/SpectralMethod/Polycrystal/20grains16x16x16.geom
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@ -1,262 +0,0 @@
5 header
grid a 16 b 16 c 16
size x 1.000000 y 1.000000 z 1.000000
origin x 0.000000 y 0.000000 z 0.000000
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homogenization 1
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examples/SpectralMethod/Polycrystal/20grains16x16x16.vtr Normal file
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@ -0,0 +1,30 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 16 0 16 0 16">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="2" format="binary">
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</Array>
</FieldData>
<Piece Extent="0 16 0 16 0 16">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="material" format="binary" RangeMin="0" RangeMax="19">
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</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
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</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
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</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

1030
examples/SpectralMethod/Polycrystal/20grains32x32x32.geom
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30
examples/SpectralMethod/Polycrystal/20grains32x32x32.vtr Normal file
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4102
examples/SpectralMethod/Polycrystal/20grains64x64x64.geom
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30
examples/SpectralMethod/Polycrystal/20grains64x64x64.vtr Normal file
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2
processing/pre/geom_fromDREAM3D.py
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@ -68,4 +68,4 @@ for name in filenames:
geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
damask.util.croak(geom)
geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)
geom.save_ASCII(os.path.splitext(name)[0]+'.geom')

2
processing/pre/geom_fromMinimalSurface.py
View File

@ -66,4 +66,4 @@ geom=damask.Geom.from_minimal_surface(options.grid,options.size,options.type,opt
options.periods,options.microstructure)
damask.util.croak(geom)
geom.save_ASCII(sys.stdout if name is None else name,compress=False)
geom.save_ASCII(sys.stdout if name is None else name)

2
processing/pre/geom_fromOsteonGeometry.py
View File

@ -138,4 +138,4 @@ geom = damask.Geom(microstructure.reshape(grid),
comments=header)
damask.util.croak(geom)
geom.save_ASCII(sys.stdout if name is None else name,compress=False)
geom.save_ASCII(sys.stdout if name is None else name)

2
processing/pre/geom_fromTable.py
View File

@ -54,4 +54,4 @@ for name in filenames:
geom = damask.Geom.from_table(t,options.pos,labels)
damask.util.croak(geom)
geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom')

2
processing/pre/geom_grainGrowth.py
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@ -174,4 +174,4 @@ for name in filenames:
origin = geom.origin,
comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
)\
.save_ASCII(sys.stdout if name is None else name,compress=False)
.save_ASCII(sys.stdout if name is None else name)

75
python/damask/_geom.py
View File

@ -320,7 +320,7 @@ class Geom:
else:
material_ = material_.reshape(grid)
return Geom(material = material_+1 if material is None else material[material_],
return Geom(material = material_ if material is None else material[material_],
size = size,
comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
)
@ -350,7 +350,7 @@ class Geom:
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,material_ = KDTree.query(coords)
return Geom(material = (material_+1 if material is None else material[material_]).reshape(grid),
return Geom(material = (material_ if material is None else material[material_]).reshape(grid),
size = size,
comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
)
@ -399,7 +399,7 @@ class Geom:
@staticmethod
def from_minimal_surface(grid,size,surface,threshold=0.0,periods=1,materials=(1,2)):
def from_minimal_surface(grid,size,surface,threshold=0.0,periods=1,materials=(0,1)):
"""
Generate geometry from definition of triply periodic minimal surface.
@ -417,7 +417,7 @@ class Geom:
Number of periods per unit cell. Defaults to 1.
materials : (int, int), optional
Material IDs. Defaults to (1,2).
Notes
-----
The following triply-periodic minimal surfaces are implemented:
@ -467,9 +467,8 @@ class Geom:
Parameters
----------
fname : str, optional
Filename to write. If no file is given, a string is returned.
Valid extension is .vtr, it will be appended if not given.
fname : str or or pathlib.Path
Filename to write. Valid extension is .vtr, it will be appended if not given.
compress : bool, optional
Compress with zlib algorithm. Defaults to True.
@ -481,9 +480,9 @@ class Geom:
v.save(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr',parallel=False,compress=compress)
def save_ASCII(self,fname,compress=None):
def save_ASCII(self,fname):
"""
Writes a geom file.
Write a geom file.
Parameters
----------
@ -500,57 +499,11 @@ class Geom:
'homogenization 1',
]
grid = self.grid
if compress is None:
plain = grid.prod()/self.N_materials < 250
else:
plain = not compress
if plain:
format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
np.savetxt(fname,
self.material.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
else:
try:
f = open(fname,'w')
except TypeError:
f = fname
compressType = None
former = start = -1
reps = 0
for current in self.material.flatten('F'):
if abs(current - former) == 1 and (start - current) == reps*(former - current):
compressType = 'to'
reps += 1
elif current == former and start == former:
compressType = 'of'
reps += 1
else:
if compressType is None:
f.write('\n'.join(header)+'\n')
elif compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write(f'{reps} of {former}\n')
compressType = '.'
start = current
reps = 1
former = current
if compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write(f'{reps} of {former}\n')
format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
np.savetxt(fname,
self.material.reshape([self.grid[0],np.prod(self.grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
def show(self):
@ -562,7 +515,7 @@ class Geom:
def add_primitive(self,dimension,center,exponent,
fill=None,R=Rotation(),inverse=False,periodic=True):
"""
Inserts a primitive geometric object at a given position.
Insert a primitive geometric object at a given position.
Parameters
----------

2
python/tests/reference/Geom/clean_2_1+2+3_False.vtr
View File

@ -3,7 +3,7 @@
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
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</FieldData>
<Piece Extent="0 8 0 5 0 4">

2
python/tests/reference/Geom/clean_2_1+2+3_True.vtr
View File

@ -3,7 +3,7 @@
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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<Piece Extent="0 8 0 5 0 4">

2
python/tests/reference/Geom/clean_2_1_False.vtr
View File

@ -3,7 +3,7 @@
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
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<Piece Extent="0 8 0 5 0 4">

2
python/tests/reference/Geom/clean_2_1_True.vtr
View File

@ -3,7 +3,7 @@
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_2_None_False.vtr
View File

@ -3,7 +3,7 @@
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFT8EKY=
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<Piece Extent="0 8 0 5 0 4">

2
python/tests/reference/Geom/clean_2_None_True.vtr
View File

@ -3,7 +3,7 @@
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_3_1+2+3_False.vtr
View File

@ -3,7 +3,7 @@
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<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_3_1+2+3_True.vtr
View File

@ -3,7 +3,7 @@
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<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_3_1_False.vtr
View File

@ -3,7 +3,7 @@
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<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_3_1_True.vtr
View File

@ -3,7 +3,7 @@
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<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_3_None_False.vtr
View File

@ -3,7 +3,7 @@
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<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_3_None_True.vtr
View File

@ -3,7 +3,7 @@
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<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
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2
python/tests/reference/Geom/clean_4_1+2+3_False.vtr
View File

@ -3,7 +3,7 @@
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2
python/tests/reference/Geom/clean_4_1+2+3_True.vtr
View File

@ -3,7 +3,7 @@
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2
python/tests/reference/Geom/clean_4_1_False.vtr
View File

@ -3,7 +3,7 @@
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2
python/tests/reference/Geom/clean_4_1_True.vtr
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2
python/tests/reference/Geom/clean_4_None_False.vtr
View File

@ -3,7 +3,7 @@
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2
python/tests/reference/Geom/clean_4_None_True.vtr
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25
python/tests/reference/Geom/flip_directions=x-y-z.geom
View File

@ -1,25 +0,0 @@
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
40 39 38 37 36 35 34 33
32 31 30 29 28 27 26 25
24 23 22 21 20 19 18 17
16 15 14 13 12 11 10 9
8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
41 40 39 38 37 36 35 34
33 32 31 30 29 28 27 26
25 24 23 22 21 20 19 18
17 16 15 14 13 12 11 10
9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

25
python/tests/reference/Geom/flip_directions=x.geom
View File

@ -1,25 +0,0 @@
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 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
9 8 7 6 5 4 3 2
17 16 15 14 13 12 11 10
25 24 23 22 21 20 19 18
33 32 31 30 29 28 27 26
41 40 39 38 37 36 35 34
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
8 7 6 5 4 3 2 1
16 15 14 13 12 11 10 9
24 23 22 21 20 19 18 17
32 31 30 29 28 27 26 25
40 39 38 37 36 35 34 33

25
python/tests/reference/Geom/flip_directions=y-z.geom
View File

@ -1,25 +0,0 @@
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
33 34 35 36 37 38 39 40
25 26 27 28 29 30 31 32
17 18 19 20 21 22 23 24
9 10 11 12 13 14 15 16
1 2 3 4 5 6 7 8
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
34 35 36 37 38 39 40 41
26 27 28 29 30 31 32 33
18 19 20 21 22 23 24 25
10 11 12 13 14 15 16 17
2 3 4 5 6 7 8 9
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

25
python/tests/reference/Geom/flip_directions=z-x-y.geom
View File

@ -1,25 +0,0 @@
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
40 39 38 37 36 35 34 33
32 31 30 29 28 27 26 25
24 23 22 21 20 19 18 17
16 15 14 13 12 11 10 9
8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
41 40 39 38 37 36 35 34
33 32 31 30 29 28 27 26
25 24 23 22 21 20 19 18
17 16 15 14 13 12 11 10
9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

30
python/tests/reference/Geom/flip_directions_x-y-z.vtr Normal file
View File

@ -0,0 +1,30 @@
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AQAAAACAAABYAAAARQAAAA==eF5jYIAAj/V7Zn26vsoOQu+yK2vm/fJV8QiUf8qu9+3WBd+PXYCKX7GLl0x1/1JzHSp/y87QVeTdB6N7UHUP7ACC9C8w
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAACoAAAAgQAAAA==eF5jYICAvrdbF3w/NsEOQi+wC30iUFistRLK32D3KeNxx9YfW6DiO+12xNtFGsbshcofsHNYfWbKtfuHoOqO2C1W+1UzRfA4VP1JO/ZF6qlBzqeh+s7aZcmG+gqUnofqv2CX7nNQKv3yRag5l+wkuW7wub25bPcRbN4VOwAdV1bT
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAYAAAAGAAAAA==eF5jYICA3rdbF3w/dsAOQl+wAwBg4gsl
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

30
python/tests/reference/Geom/scale_grid_5-4-20.vtr Normal file
View File

@ -0,0 +1,30 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 5 0 4 0 20">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9UrTk7MSVUos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFYKEKs=
</Array>
</FieldData>
<Piece Extent="0 5 0 4 0 20">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAACADAAAeAAAAA==eF7t1TkWggAUQ1EREZS5BFQmB9j/Bin++40b8OBJmtumSoKDJZDyBx7xhGeM8YJXzLDAEmts8YYP7HHECZ/4xg+uqH4W9bOon+W7n5Ryf/oPhxih70yCvjMp5ug7U2GDHd7Rd2ZA35kZX+g7s6D6Wf613wZ8oBHR
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICAjxmPO7b+2GIHoY/YZcmG+gqUnofyr9gBAEcwExU=
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

30
python/tests/reference/Geom/scale_grid_8-10-12.vtr Normal file
View File

@ -0,0 +1,30 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 10 0 12">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
AQAAAACAAAA+AAAAQQAAAA==eF5LScxNLM7Wc0/Nz9UrTk7MSVUos7TUAyNdSyDQLagsSS0uUdAwMjC01DU01DUwUjA0tDK1sDIw0GQAAFYKEKs=
</Array>
</FieldData>
<Piece Extent="0 8 0 10 0 12">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAAHgAAyAAAAA==eF7t2LcBAkEUxFDu8N5776H/BglQBwpvNnmRskn+FrX/K2KMsWKWWMcGNrGFbexgF23fwz4OcIgjHOMEp2j7Gc5xgUtc4Ro3uEXb73CPBzziCc94wSva/oZ3fOATX/jGD37R9nY/trf7sb3dj+3tfmxv92N7ux/b2/3Y3u7H9nY/trf7sb3dj+3tfmxv92N7ux/b2/3YvowxxhhjjJXS/gPa3t4htrd3iO3tHWJ7e4fY3u7H9nY/trf7sb3dj+3tfmz/A1V7KtE=
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

87
python/tests/test_Geom.py
View File

@ -1,6 +1,3 @@
import os
import time
import pytest
import numpy as np
@ -33,6 +30,10 @@ def reference_dir(reference_dir_base):
class TestGeom:
@pytest.fixture(autouse=True)
def _execution_stamp(self, execution_stamp):
print('patched damask.util.execution_stamp')
def test_diff_equal(self,default):
assert str(default.diff(default)) == ''
@ -42,44 +43,14 @@ class TestGeom:
assert str(default.diff(new)) != ''
def test_write_read_str(self,default,tmp_path):
default.save_ASCII(str(tmp_path/'default.geom'))
new = Geom.load_ASCII(str(tmp_path/'default.geom'))
assert geom_equal(default,new)
def test_write_read_file(self,default,tmp_path):
with open(tmp_path/'default.geom','w') as f:
default.save_ASCII(f,compress=True)
with open(tmp_path/'default.geom') as f:
new = Geom.load_ASCII(f)
assert geom_equal(default,new)
def test_read_write_vtr(self,default,tmp_path):
default.save(tmp_path/'default')
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmp_path/'default.vtr'): break
new = Geom.load(tmp_path/'default.vtr')
assert geom_equal(new,default)
def test_invalid_geom(self,tmp_path):
with open(tmp_path/'invalid_file','w') as f:
f.write('this is not a valid header')
with open(tmp_path/'invalid_file','r') as f:
with pytest.raises(TypeError):
Geom.load_ASCII(f)
def test_invalid_vtr(self,tmp_path):
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.save(tmp_path/'no_materialpoint.vtr')
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmp_path/'no_materialpoint.vtr'): break
with pytest.raises(ValueError):
Geom.load(tmp_path/'no_materialpoint.vtr')
@ -91,13 +62,6 @@ class TestGeom:
g = Geom(np.zeros((3,3,3)),np.ones(3))
assert g.material.dtype in np.sctypes['int']
@pytest.mark.parametrize('compress',[True,False])
def test_compress(self,default,tmp_path,compress):
default.save_ASCII(tmp_path/'default.geom',compress=compress)
new = Geom.load_ASCII(tmp_path/'default.geom')
assert geom_equal(new,default)
def test_invalid_size(self,default):
with pytest.raises(ValueError):
Geom(default.material[1:,1:,1:],
@ -133,10 +97,10 @@ class TestGeom:
)
def test_mirror(self,default,update,reference_dir,directions,reflect):
modified = default.mirror(directions,reflect)
tag = f'directions={"-".join(directions)}_reflect={reflect}'
reference = reference_dir/f'mirror_{tag}.geom'
if update: modified.save_ASCII(reference)
assert geom_equal(Geom.load_ASCII(reference),
tag = f'directions_{"-".join(directions)}+reflect_{reflect}'
reference = reference_dir/f'mirror_{tag}.vtr'
if update: modified.save(reference)
assert geom_equal(Geom.load(reference),
modified)
@ -155,10 +119,10 @@ class TestGeom:
)
def test_flip(self,default,update,reference_dir,directions):
modified = default.flip(directions)
tag = f'directions={"-".join(directions)}'
reference = reference_dir/f'flip_{tag}.geom'
if update: modified.save_ASCII(reference)
assert geom_equal(Geom.load_ASCII(reference),
tag = f'directions_{"-".join(directions)}'
reference = reference_dir/f'flip_{tag}.vtr'
if update: modified.save(reference)
assert geom_equal(Geom.load(reference),
modified)
@ -185,9 +149,6 @@ class TestGeom:
reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
if update and stencil > 1:
current.save(reference)
for _ in range(10):
time.sleep(.2)
if os.path.exists(reference.with_suffix('.vtr')): break
assert geom_equal(Geom.load(reference) if stencil > 1 else default,
current
)
@ -204,10 +165,10 @@ class TestGeom:
)
def test_scale(self,default,update,reference_dir,grid):
modified = default.scale(grid)
tag = f'grid={util.srepr(grid,"-")}'
reference = reference_dir/f'scale_{tag}.geom'
if update: modified.save_ASCII(reference)
assert geom_equal(Geom.load_ASCII(reference),
tag = f'grid_{util.srepr(grid,"-")}'
reference = reference_dir/f'scale_{tag}.vtr'
if update: modified.save(reference)
assert geom_equal(Geom.load(reference),
modified)
@ -247,10 +208,10 @@ class TestGeom:
[0.0,32.0,240.0]])
def test_rotate(self,default,update,reference_dir,Eulers):
modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
tag = f'Eulers={util.srepr(Eulers,"-")}'
reference = reference_dir/f'rotate_{tag}.geom'
if update: modified.save_ASCII(reference)
assert geom_equal(Geom.load_ASCII(reference),
tag = f'Eulers_{util.srepr(Eulers,"-")}'
reference = reference_dir/f'rotate_{tag}.vtr'
if update: modified.save(reference)
assert geom_equal(Geom.load(reference),
modified)
@ -342,8 +303,8 @@ class TestGeom:
N_seeds= np.random.randint(10,30)
seeds = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
weights= np.full((N_seeds),-np.inf)
ms = np.random.randint(1, N_seeds+1)
weights[ms-1] = np.random.random()
ms = np.random.randint(N_seeds)
weights[ms] = np.random.random()
Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,weights,periodic=np.random.random()>0.5)
assert np.all(Laguerre.material == ms)
@ -353,8 +314,8 @@ class TestGeom:
grid = np.random.randint(5,10,3)*2
size = grid.astype(np.float)
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
material = np.ones(grid)
material[:,grid[1]//2:,:] = 2
material = np.zeros(grid)
material[:,grid[1]//2:,:] = 1
if approach == 'Laguerre':
geom = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
elif approach == 'Voronoi':

9
src/grid/discretization_grid.f90
View File

@ -67,11 +67,7 @@ subroutine discretization_grid_init(restart)
print'(/,a)', ' <<<+- discretization_grid init -+>>>'; flush(IO_STDOUT)
if(index(interface_geomFile,'.vtr') /= 0) then
call readVTR(grid,geomSize,origin,materialAt)
else
call readGeom(grid,geomSize,origin,materialAt)
endif
call readVTR(grid,geomSize,origin,materialAt)
print'(/,a,3(i12 ))', ' grid a b c: ', grid
print'(a,3(es12.5))', ' size x y z: ', geomSize
@ -412,11 +408,12 @@ subroutine readVTR(grid,geomSize,origin,material)
startPos = endPos + 2_pI64
end do
material = material + 1
if(.not. allocated(material)) call IO_error(error_ID = 844, ext_msg='material data not found')
if(size(material) /= product(grid)) call IO_error(error_ID = 844, ext_msg='size(material)')
if(any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
if(any(grid<1)) call IO_error(error_ID = 844, ext_msg='grid')
if(any(material<0)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
contains