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DAMASK_EICMD
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Merge branch 'misc-improvements' into 'development' 

a number of small changes

See merge request damask/DAMASK!428
This commit is contained in:
Franz Roters 2021-08-27 16:22:53 +00:00
parent 3ba2ee6b41 566e0445fc
commit 3f9ee140fd
26 changed files with 88 additions and 61 deletions
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7
.gitlab-ci.yml
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@ -102,13 +102,6 @@ processing:
- master
- release
###################################################################################################
preprocessing_deprecated:
stage: python
script: PreProcessing/test.py
except:
- master
- release
###################################################################################################
compile_grid_Intel:

3
CMakeLists.txt
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@ -1,4 +1,4 @@
cmake_minimum_required (VERSION 3.10.0)
cmake_minimum_required (VERSION 3.12.0)
include (FindPkgConfig REQUIRED)
if (DEFINED ENV{PETSC_DIR})
@ -31,6 +31,7 @@ message ("\nBuilding ${CMAKE_PROJECT_NAME} ${DAMASK_VERSION}\n")
add_definitions (-DPETSC)
add_definitions (-DDAMASKVERSION="${DAMASK_VERSION}")
add_definitions (-DCMAKE_SYSTEM="${CMAKE_SYSTEM}")
if (CMAKE_BUILD_TYPE STREQUAL "")
set (CMAKE_BUILD_TYPE "RELEASE")

2
DAMASK_prerequisites.sh
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@ -74,7 +74,7 @@ echo PETSC_ARCH: $PETSC_ARCH
echo PETSC_DIR: $PETSC_DIR
echo
echo $PETSC_DIR/$PETSC_ARCH/lib:
/s $PETSC_DIR/$PETSC_ARCH/lib
ls $PETSC_DIR/$PETSC_ARCH/lib
echo
echo $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/petscvariables:
cat $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/petscvariables

2
PRIVATE

@ -1 +1 @@
Subproject commit 6037ed541710fc84699ee2ca1d36a69d7fa20f0f
Subproject commit 36ac61caef1eec1ac68cadbed1a8f6f07a035f54

6
python/damask/_config.py
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@ -146,12 +146,6 @@ class Config(dict):
if 'sort_keys' not in kwargs:
kwargs['sort_keys'] = False
def array_representer(dumper, data):
"""Convert numpy array to list of native types."""
return dumper.represent_list([d.item() for d in data])
NiceDumper.add_representer(np.ndarray, array_representer)
try:
fhandle.write(yaml.dump(self,Dumper=NiceDumper,**kwargs))
except TypeError: # compatibility with old pyyaml

8
python/damask/_result.py
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@ -567,9 +567,13 @@ class Result:
formula = kwargs['formula']
for d in re.findall(r'#(.*?)#',formula):
formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
data = eval(formula)
if not hasattr(data,'shape') or data.shape[0] != kwargs[d]['data'].shape[0]:
raise ValueError("'{}' results in invalid shape".format(kwargs['formula']))
return {
'data': eval(formula),
'data': data,
'label': kwargs['label'],
'meta': {
'unit': kwargs['unit'],
@ -1258,7 +1262,7 @@ class Result:
Arguments parsed to func.
"""
if len(datasets) != 1 or self.N_constituents !=1:
if len(datasets) != 1 or self.N_constituents != 1:
raise NotImplementedError
at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()

10
python/damask/mechanics.py
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@ -257,18 +257,18 @@ def _polar_decomposition(T,requested):
u, _, vh = _np.linalg.svd(T)
R = _np.einsum('...ij,...jk',u,vh)
output = []
output = ()
if 'R' in requested:
output.append(R)
output+=(R,)
if 'V' in requested:
output.append(_np.einsum('...ij,...kj',T,R))
output+=(_np.einsum('...ij,...kj',T,R),)
if 'U' in requested:
output.append(_np.einsum('...ji,...jk',R,T))
output+=(_np.einsum('...ji,...jk',R,T),)
if len(output) == 0:
raise ValueError('output needs to be out of V, R, U')
return tuple(output)
return output
def _equivalent_Mises(T_sym,s):

2
python/setup.py
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@ -23,7 +23,7 @@ setuptools.setup(
'h5py>=2.9', # requires numpy
'vtk>=8.1',
'matplotlib>=3.0', # requires numpy, pillow
'pyaml>=3.12'
'pyyaml>=3.12'
],
classifiers = [
'Intended Audience :: Science/Research',

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python/tests/reference/Result/12grains6x7x8_tensionY.hdf5 vendored
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python/tests/reference/Result/4grains2x4x3_compressionY.hdf5 vendored
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python/tests/reference/Result/6grains6x7x8_single_phase_tensionY.hdf5 vendored
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12
python/tests/reference/Result/compressionY.yaml vendored
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@ -5,12 +5,12 @@ solver:
loadstep:
- boundary_conditions:
mechanical:
dot_F: [x, 0, 0,
0, -1.0e-3, 0,
0, 0, x]
P: [0, x, x,
x, x, x,
x, x, 0]
dot_F: [[x, 0, 0],
[0, -1.0e-3, 0],
[0, 0, x]]
P: [[0, x, x],
[x, x, x],
[x, x, 0]]
discretization:
t: 5
N: 10

2
python/tests/reference/Result/export_VTK/test_vtk[0-0-0].md5 vendored
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@ -1 +1 @@
d5db0be324a959f00245e42704ea2d6f
a40baead936c79dd4f86f84ad858b9fa

2
python/tests/reference/Result/export_VTK/test_vtk[0-0-1].md5 vendored
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@ -1 +1 @@
fe9ddaf54ac1fb785094251d29fcdc9c
6fb37bd65934de859dd6b6e0191e7d64

2
python/tests/reference/Result/export_VTK/test_vtk[0-0-2].md5 vendored
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@ -1 +1 @@
9c8ac0bb1eb4a7b9ebc3e5fd5840b0a4
61953c35f61f3234b98d78a912e7dc83

1
python/tests/reference/Result/export_VTK/test_vtk[0-0-3].md5 vendored Normal file
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@ -0,0 +1 @@
bb783bb80ff04dd435e814f4b82a3234

2
python/tests/reference/Result/export_VTK/test_vtk[1-0-0].md5 vendored
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@ -1 +1 @@
1b9ebd17c5257e2edba48d006f25d4e6
4f85d2613aa70622a2d5f49dc8bf2eb2

2
python/tests/reference/Result/export_VTK/test_vtk[1-0-1].md5 vendored
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@ -1 +1 @@
8967bb1a6c329a072baaa83da534ae56
e1ca5306082fc3ab411f5ddab1a2e370

2
python/tests/reference/Result/export_VTK/test_vtk[1-0-2].md5 vendored
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@ -1 +1 @@
752e8b6186ad2b6b1b5c781940669cb1
1641c3b3641e942ffc325d471bdfaf00

1
python/tests/reference/Result/export_VTK/test_vtk[1-0-3].md5 vendored Normal file
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@ -0,0 +1 @@
ba97286c5d95bf817143f7bb9cf58421

12
python/tests/reference/Result/tensionY.yaml vendored
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@ -5,12 +5,12 @@ solver:
loadstep:
- boundary_conditions:
mechanical:
dot_F: [x, 0, 0,
0, 1.0e-3, 0,
0, 0, x]
P: [0, x, x,
x, x, x,
x, x, 0]
dot_F: [[x, 0, 0],
[0, 1.0e-3, 0],
[0, 0, x]]
P: [[0, x, x],
[x, x, x],
[x, x, 0]]
discretization:
t: 20
N: 40

11
python/tests/test_Crystal.py
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@ -1,10 +1,20 @@
import pytest
import numpy as np
import damask
from damask import Crystal
class TestCrystal:
@pytest.mark.parametrize('lattice,family',[('aP','cubic'),('xI','cubic')])
def test_invalid_init(self,lattice,family):
with pytest.raises(KeyError):
Crystal(family=family,lattice=lattice)
def test_eq(self):
family = np.random.choice(list(damask._crystal.lattice_symmetries.values()))
assert Crystal(family=family) == Crystal(family=family)
def test_double_to_lattice(self):
c = Crystal(lattice='cF')
with pytest.raises(KeyError):
@ -55,3 +65,4 @@ class TestCrystal:
alpha=alpha,beta=beta,gamma=gamma)
assert np.allclose(vector,
c.to_frame(**{keyFrame:c.to_lattice(**{keyLattice:vector})}))

47
python/tests/test_Result.py
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@ -13,6 +13,7 @@ import numpy as np
from damask import Result
from damask import Orientation
from damask import VTK
from damask import tensor
from damask import mechanics
from damask import grid_filters
@ -106,7 +107,8 @@ class TestResult:
in_file = default.place('|F_e|')
assert np.allclose(in_memory,in_file)
@pytest.mark.parametrize('mode',['direct','function'])
@pytest.mark.parametrize('mode',
['direct',pytest.param('function',marks=pytest.mark.xfail(sys.platform=="darwin",reason='n/a'))])
def test_add_calculation(self,default,tmp_path,mode):
if mode == 'direct':
@ -123,6 +125,10 @@ class TestResult:
in_file = default.place('x')
assert np.allclose(in_memory,in_file)
def test_add_calculation_invalid(self,default):
default.add_calculation('np.linalg.norm(#F#,axis=0)','wrong_dim')
assert default.get('wrong_dim') is None
def test_add_stress_Cauchy(self,default):
default.add_stress_Cauchy('P','F')
in_memory = mechanics.stress_Cauchy(default.place('P'), default.place('F'))
@ -264,10 +270,15 @@ class TestResult:
in_file = default.place('V(F)')
assert np.allclose(in_memory,in_file)
def test_add_invalid(self,default):
def test_add_invalid_dataset(self,default):
with pytest.raises(TypeError):
default.add_calculation('#invalid#*2')
def test_add_generic_grid_invalid(self,ref_path):
result = Result(ref_path/'4grains2x4x3_compressionY.hdf5')
with pytest.raises(NotImplementedError):
result.add_curl('F')
@pytest.mark.parametrize('shape',['vector','tensor'])
def test_add_curl(self,default,shape):
@ -360,25 +371,19 @@ class TestResult:
b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
assert np.allclose(a,b)
# need to wait for writing in parallel, output order might change if select more then one
@pytest.mark.parametrize('output',['F','*',['P']],ids=range(3))
@pytest.mark.parametrize('output',['F','*',['P'],['P','F']],ids=range(4))
@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
@pytest.mark.parametrize('inc',[4,0],ids=range(2))
def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
result = Result(ref_path/fname).view('increments',inc)
os.chdir(tmp_path)
result.export_VTK(output)
result.export_VTK(output,parallel=False)
fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
last = ''
for i in range(10):
if os.path.isfile(tmp_path/fname):
v = VTK.load(tmp_path/fname)
v.set_comments('n/a')
v.save(tmp_path/fname,parallel=False)
with open(fname) as f:
cur = hashlib.md5(f.read().encode()).hexdigest()
if cur == last:
break
else:
last = cur
time.sleep(.5)
if update:
with open((ref_path/'export_VTK'/request.node.name).with_suffix('.md5'),'w') as f:
f.write(cur)
@ -403,6 +408,11 @@ class TestResult:
os.chdir(tmp_path)
single_phase.export_VTK(mode=mode)
def test_vtk_invalid_mode(self,single_phase):
with pytest.raises(ValueError):
single_phase.export_VTK(mode='invalid')
def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
@ -494,3 +504,14 @@ class TestResult:
with bz2.BZ2File((ref_path/'place'/fname).with_suffix('.pbz2')) as f:
ref = pickle.load(f)
assert cur is None if ref is None else dict_equal(cur,ref)
@pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
'6grains6x7x8_single_phase_tensionY.hdf5'])
@pytest.mark.parametrize('output',['material.yaml','*'])
@pytest.mark.parametrize('overwrite',[True,False])
def test_export_setup(self,ref_path,tmp_path,fname,output,overwrite):
os.chdir(tmp_path)
r = Result(ref_path/fname)
r.export_setup(output,overwrite)
r.export_setup(output,overwrite)

6
src/CMakeLists.txt
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@ -4,7 +4,7 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
SET_SOURCE_FILES_PROPERTIES("lattice.f90" PROPERTIES COMPILE_FLAGS "-ffree-line-length-240")
endif()
file(GLOB damask-sources *.f90 *.c)
file(GLOB damask-sources CONFIGURE_DEPENDS *.f90 *.c)
# probably we should have a subfolder for MSC.Marc
list(FILTER damask-sources EXCLUDE REGEX ".*CPFEM.f90")
@ -14,7 +14,7 @@ list(FILTER damask-sources EXCLUDE REGEX ".*commercialFEM_fileList.*.f90")
if (PROJECT_NAME STREQUAL "damask-grid")
file(GLOB grid-sources grid/*.f90)
file(GLOB grid-sources CONFIGURE_DEPENDS grid/*.f90)
if (NOT CMAKE_BUILD_TYPE STREQUAL "SYNTAXONLY")
add_executable(DAMASK_grid ${damask-sources} ${grid-sources})
@ -28,7 +28,7 @@ if (PROJECT_NAME STREQUAL "damask-grid")
elseif (PROJECT_NAME STREQUAL "damask-mesh")
file(GLOB mesh-sources mesh/*.f90)
file(GLOB mesh-sources CONFIGURE_DEPENDS mesh/*.f90)
add_executable(DAMASK_mesh ${damask-sources} ${mesh-sources})
install (TARGETS DAMASK_mesh RUNTIME DESTINATION bin)

1
src/DAMASK_interface.f90
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@ -102,6 +102,7 @@ subroutine DAMASK_interface_init
print'(/,a)', ' Version: '//DAMASKVERSION
print'(/,a)', ' Compiled with: '//compiler_version()
print'(a)', ' Compiled on: '//CMAKE_SYSTEM
print'(a)', ' Compiler options: '//compiler_options()
! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md

2
src/prec.f90
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@ -13,7 +13,7 @@ module prec
implicit none
public
! https://software.intel.com/en-us/blogs/2017/03/27/doctor-fortran-in-it-takes-all-kinds
! https://stevelionel.com/drfortran/2017/03/27/doctor-fortran-in-it-takes-all-kinds
integer, parameter :: pReal = IEEE_selected_real_kind(15,307) !< number with 15 significant digits, up to 1e+-307 (typically 64 bit)
integer, parameter :: pI32 = selected_int_kind(9) !< number with at least up to +-1e9 (typically 32 bit)
integer, parameter :: pI64 = selected_int_kind(18) !< number with at least up to +-1e18 (typically 64 bit)