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DAMASK_EICMD
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Merge branch 'development' into config2yaml

This commit is contained in:
Martin Diehl 2021-02-23 06:50:43 +01:00
parent 9fca65083c 8a1c73ebce
commit 86c6a354e2
20 changed files with 117 additions and 133 deletions
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6
DAMASK_prerequisites.sh
View File

@ -84,7 +84,7 @@ for executable in python python3; do
done
secondLevel "Details on $DEFAULT_PYTHON:"
echo $(ls -la $(which $DEFAULT_PYTHON))
for module in numpy scipy pandas;do
for module in numpy scipy pandas matplotlib yaml h5py;do
thirdLevel $module
$DEFAULT_PYTHON -c "import $module; \
print('Version: {}'.format($module.__version__)); \
@ -94,10 +94,6 @@ thirdLevel vtk
$DEFAULT_PYTHON -c "import vtk; \
print('Version: {}'.format(vtk.vtkVersion.GetVTKVersion())); \
print('Location: {}'.format(vtk.__file__))"
thirdLevel h5py
$DEFAULT_PYTHON -c "import h5py; \
print('Version: {}'.format(h5py.version.version)); \
print('Location: {}'.format(h5py.__file__))"
firstLevel "GNU Compiler Collection"
for executable in gcc g++ gfortran ;do

2
PRIVATE

@ -1 +1 @@
Subproject commit 866ed072549a3794f78339dedfb518a305c62d16
Subproject commit f654a4143b1fbbecd137dc5d2193f5cf48ab1448

2
VERSION
View File

@ -1 +1 @@
v3.0.0-alpha2-478-gc9e4dc21f
v3.0.0-alpha2-500-gfdb182b40

7
python/damask/_configmaterial.py
View File

@ -103,7 +103,6 @@ class ConfigMaterial(Config):
"""Check for completeness."""
ok = True
for top_level in ['homogenization','phase','material']:
# ToDo: With python 3.8 as prerequisite we can shorten with :=
ok &= top_level in self
if top_level not in self: print(f'{top_level} entry missing')
@ -203,7 +202,7 @@ class ConfigMaterial(Config):
"""
dup = self.copy()
for i,m in enumerate(dup['material']):
if ID and i not in ID: continue
if ID is not None and i not in ID: continue
for c in m['constituents']:
if constituent is not None and c not in constituent: continue
try:
@ -227,7 +226,7 @@ class ConfigMaterial(Config):
"""
dup = self.copy()
for i,m in enumerate(dup['material']):
if ID and i not in ID: continue
if ID is not None and i not in ID: continue
try:
m['homogenization'] = mapping[m['homogenization']]
except KeyError:
@ -249,7 +248,7 @@ class ConfigMaterial(Config):
Examples
--------
>>> import damask
>>> O = damask.Rotation.from_random(3).as_quaternion()
>>> O = damask.Rotation.from_random(3)
>>> phase = ['Aluminum','Steel','Aluminum']
>>> m = damask.ConfigMaterial().material_add(constituents={'phase':phase,'O':O},
... homogenization='SX')

6
python/damask/_grid.py
View File

@ -202,7 +202,7 @@ class Grid:
Geometry file to read.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
try:
f = open(fname)
except TypeError:
@ -541,7 +541,7 @@ class Grid:
Compress geometry with 'x of y' and 'a to b'.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
header = [f'{len(self.comments)+4} header'] + self.comments \
+ ['grid a {} b {} c {}'.format(*self.cells),
'size x {} y {} z {}'.format(*self.size),
@ -760,7 +760,7 @@ class Grid:
"""
if fill is None: fill = np.nanmax(self.material) + 1
dtype = float if np.isnan(fill) or int(fill) != fill or self.material.dtype==np.float else int
dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
material = self.material
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')

11
python/damask/_rotation.py
View File

@ -125,9 +125,18 @@ class Rotation:
return np.logical_not(self==other)
def __array__(self):
"""Initializer for numpy."""
return self.quaternion
@property
def size(self):
return self.quaternion[...,0].size
@property
def shape(self):
return self.quaternion.shape[:-1]
return self.quaternion[...,0].shape
def __len__(self):

4
python/damask/_vtk.py
View File

@ -246,8 +246,8 @@ class VTK:
raise ValueError('No label defined for numpy.ndarray')
N_data = data.shape[0]
d = np_to_vtk((data.astype(np.float32) if data.dtype in [np.float64, np.float128]
else data).reshape(N_data,-1),deep=True) # avoid large files
d = np_to_vtk((data.astype(np.single) if data.dtype in [np.double, np.longdouble] else
data).reshape(N_data,-1),deep=True) # avoid large files
d.SetName(label)
if N_data == N_points:

2
python/damask/util.py
View File

@ -183,7 +183,7 @@ def scale_to_coprime(v):
# Python 3.9 provides math.lcm, see https://stackoverflow.com/questions/51716916.
return a * b // np.gcd(a, b)
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
m = m//reduce(np.gcd,m)
with np.errstate(invalid='ignore'):

35
python/setup.py
View File

@ -6,28 +6,29 @@ with open(Path(__file__).parent/'damask/VERSION') as f:
version = re.sub(r'(-([^-]*)).*$',r'.\2',re.sub(r'^v(\d+\.\d+(\.\d+)?)',r'\1',f.readline().strip()))
setuptools.setup(
name="damask",
name='damask',
version=version,
author="The DAMASK team",
author_email="damask@mpie.de",
description="DAMASK library",
long_description="Python library for pre and post processing of DAMASK simulations",
url="https://damask.mpie.de",
author='The DAMASK team',
author_email='damask@mpie.de',
description='DAMASK library',
long_description='Python library for pre and post processing of DAMASK simulations',
url='https://damask.mpie.de',
packages=setuptools.find_packages(),
include_package_data=True,
python_requires = '>=3.6',
install_requires = [
"pandas", # requires numpy
"scipy",
"h5py", # requires numpy
"vtk",
"matplotlib", # requires numpy, pillow
"pyaml"
'pandas>=0.24', # requires numpy
'scipy>=1.2',
'h5py>=2.9', # requires numpy
'vtk>=8.1',
'matplotlib>=3.0', # requires numpy, pillow
'pyaml>=3.12'
],
classifiers = [
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering",
"Programming Language :: Python :: 3",
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
"Operating System :: OS Independent",
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'Programming Language :: Python :: 3',
'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
'Operating System :: OS Independent',
],
)

2
python/tests/test_Grid.py
View File

@ -347,7 +347,7 @@ class TestGrid:
@pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
def test_tessellate_bicrystal(self,approach):
cells = np.random.randint(5,10,3)*2
size = cells.astype(np.float)
size = cells.astype(float)
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
material = np.zeros(cells)
material[:,cells[1]//2:,:] = 1

10
python/tests/test_Rotation.py
View File

@ -689,6 +689,10 @@ class TestRotation:
with pytest.raises(TypeError):
Rotation(np.ones(3))
def test_to_numpy(self):
r = Rotation.from_random(np.random.randint(0,10,4))
assert np.all(r.as_quaternion() == np.array(r))
@pytest.mark.parametrize('degrees',[True,False])
def test_Eulers(self,set_of_rotations,degrees):
for rot in set_of_rotations:
@ -804,7 +808,11 @@ class TestRotation:
r = Rotation.from_random()
assert r == ~~r
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(1,1,1)])
@pytest.mark.parametrize('shape',[1,(1,),(4,2),(1,1,1),tuple(np.random.randint(0,10,4))])
def test_size(self,shape):
assert Rotation.from_random(shape).size == np.prod(shape)
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(1,1,1),tuple(np.random.randint(0,10,4))])
def test_shape(self,shape):
r = Rotation.from_random(shape=shape)
assert r.shape == (shape if isinstance(shape,tuple) else (shape,) if shape else ())

9
src/CPFEM2.f90
View File

@ -75,7 +75,6 @@ end subroutine CPFEM_initAll
subroutine CPFEM_init
integer(HID_T) :: fileHandle
character(len=pStringLen) :: fileName
print'(/,a)', ' <<<+- CPFEM init -+>>>'; flush(IO_STDOUT)
@ -83,8 +82,8 @@ subroutine CPFEM_init
if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart information of increment from file'; flush(IO_STDOUT)
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
call homogenization_restartRead(fileHandle)
call phase_restartRead(fileHandle)
@ -101,13 +100,11 @@ end subroutine CPFEM_init
subroutine CPFEM_restartWrite
integer(HID_T) :: fileHandle
character(len=pStringLen) :: fileName
print*, ' writing field and constitutive data required for restart to file';flush(IO_STDOUT)
write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'a')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a')
call homogenization_restartWrite(fileHandle)
call phase_restartWrite(fileHandle)

68
src/HDF5_utilities.f90
View File

@ -71,6 +71,12 @@ module HDF5_utilities
module procedure HDF5_addAttribute_real_array
end interface HDF5_addAttribute
#ifdef PETSc
logical, parameter, private :: parallel_default = .true.
#else
logical, parameter, private :: parallel_default = .false.
#endif
contains
@ -105,16 +111,16 @@ end subroutine HDF5_utilities_init
!--------------------------------------------------------------------------------------------------
!> @brief open and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
integer(HID_T) function HDF5_openFile(fileName,mode)
character(len=*), intent(in) :: fileName
character, intent(in), optional :: mode
logical, intent(in), optional :: parallel
character :: m
integer(HID_T) :: plist_id
integer :: hdferr
if (present(mode)) then
m = mode
else
@ -125,10 +131,8 @@ integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
if(hdferr < 0) error stop 'HDF5 error'
#ifdef PETSc
if (present(parallel)) then; if (parallel) then
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
endif; endif
#endif
if (m == 'w') then
@ -547,7 +551,7 @@ subroutine HDF5_read_real1(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -587,7 +591,7 @@ subroutine HDF5_read_real2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -627,7 +631,7 @@ subroutine HDF5_read_real3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -667,7 +671,7 @@ subroutine HDF5_read_real4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -707,7 +711,7 @@ subroutine HDF5_read_real5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -747,7 +751,7 @@ subroutine HDF5_read_real6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -787,7 +791,7 @@ subroutine HDF5_read_real7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
@ -829,7 +833,7 @@ subroutine HDF5_read_int1(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -869,7 +873,7 @@ subroutine HDF5_read_int2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -909,7 +913,7 @@ subroutine HDF5_read_int3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -949,7 +953,7 @@ subroutine HDF5_read_int4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -989,7 +993,7 @@ subroutine HDF5_read_int5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -1029,7 +1033,7 @@ subroutine HDF5_read_int6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -1069,7 +1073,7 @@ subroutine HDF5_read_int7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,parallel)
else
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
myStart, totalShape, loc_id,myShape,datasetName,parallel_default)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
@ -1109,7 +1113,7 @@ subroutine HDF5_write_real1(loc_id,dataset,datasetName,parallel)
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape,loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1150,7 +1154,7 @@ subroutine HDF5_write_real2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1191,7 +1195,7 @@ subroutine HDF5_write_real3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1232,7 +1236,7 @@ subroutine HDF5_write_real4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1274,7 +1278,7 @@ subroutine HDF5_write_real5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1315,7 +1319,7 @@ subroutine HDF5_write_real6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1356,7 +1360,7 @@ subroutine HDF5_write_real7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1398,7 +1402,7 @@ subroutine HDF5_write_int1(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1439,7 +1443,7 @@ subroutine HDF5_write_int2(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1480,7 +1484,7 @@ subroutine HDF5_write_int3(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1521,7 +1525,7 @@ subroutine HDF5_write_int4(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1562,7 +1566,7 @@ subroutine HDF5_write_int5(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1603,7 +1607,7 @@ subroutine HDF5_write_int6(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then
@ -1644,7 +1648,7 @@ subroutine HDF5_write_int7(loc_id,dataset,datasetName,parallel)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel)
else
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,.false.)
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_INTEGER,parallel_default)
endif
if (product(totalShape) /= 0) then

2
src/grid/DAMASK_grid.f90
View File

@ -225,8 +225,8 @@ program DAMASK_grid
loadCases(l)%t = step_discretization%get_asFloat('t')
loadCases(l)%N = step_discretization%get_asInt ('N')
loadCases(l)%r = step_discretization%get_asFloat('r', defaultVal= 1.0_pReal)
loadCases(l)%f_restart = step_discretization%get_asInt ('f_restart', defaultVal=huge(0))
loadCases(l)%f_restart = load_step%get_asInt('f_restart', defaultVal=huge(0))
loadCases(l)%f_out = load_step%get_asInt('f_out', defaultVal=1)
loadCases(l)%estimate_rate = (load_step%get_asBool('estimate_rate',defaultVal=.true.) .and. &
merge(.true.,.false.,l > 1))

7
src/grid/discretization_grid.f90
View File

@ -68,8 +68,11 @@ subroutine discretization_grid_init(restart)
print'(/,a)', ' <<<+- discretization_grid init -+>>>'; flush(IO_STDOUT)
if(worldrank == 0) call readVTR(grid,geomSize,origin,materialAt_global)
if(worldrank == 0) then
call readVTR(grid,geomSize,origin,materialAt_global)
else
allocate(materialAt_global(0)) ! needed for IntelMPI
endif
call MPI_Bcast(grid,3,MPI_INTEGER,0,PETSC_COMM_WORLD, ierr)
if (ierr /= 0) error stop 'MPI error'

10
src/grid/grid_mech_FEM.f90
View File

@ -108,8 +108,6 @@ subroutine grid_mechanical_FEM_init
u_current,u_lastInc
PetscInt, dimension(0:worldsize-1) :: localK
integer(HID_T) :: fileHandle, groupHandle
character(len=pStringLen) :: &
fileName
class(tNode), pointer :: &
num_grid, &
debug_grid
@ -234,8 +232,7 @@ subroutine grid_mechanical_FEM_init
restartRead: if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart data of increment ', interface_restartInc, ' from file'
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(groupHandle,P_aim, 'P_aim')
@ -422,7 +419,7 @@ subroutine grid_mechanical_FEM_restartWrite
PetscErrorCode :: ierr
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: u_current,u_lastInc
character(len=pStringLen) :: fileName
call DMDAVecGetArrayF90(mechanical_grid,solution_current,u_current,ierr)
CHKERRQ(ierr)
@ -431,8 +428,7 @@ subroutine grid_mechanical_FEM_restartWrite
print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'w')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(groupHandle,P_aim, 'P_aim')

9
src/grid/grid_mech_spectral_basic.f90
View File

@ -99,8 +99,6 @@ subroutine grid_mechanical_spectral_basic_init
PetscInt, dimension(0:worldsize-1) :: localK
integer(HID_T) :: fileHandle, groupHandle
integer :: fileUnit
character(len=pStringLen) :: &
fileName
class (tNode), pointer :: &
num_grid, &
debug_grid
@ -182,8 +180,7 @@ subroutine grid_mechanical_spectral_basic_init
restartRead: if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart data of increment ', interface_restartInc, ' from file'
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(groupHandle,P_aim, 'P_aim')
@ -365,14 +362,12 @@ subroutine grid_mechanical_spectral_basic_restartWrite
PetscErrorCode :: ierr
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: F
character(len=pStringLen) :: fileName
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'w')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(groupHandle,P_aim, 'P_aim')

9
src/grid/grid_mech_spectral_polarisation.f90
View File

@ -112,8 +112,6 @@ subroutine grid_mechanical_spectral_polarisation_init
PetscInt, dimension(0:worldsize-1) :: localK
integer(HID_T) :: fileHandle, groupHandle
integer :: fileUnit
character(len=pStringLen) :: &
fileName
class (tNode), pointer :: &
num_grid, &
debug_grid
@ -204,8 +202,7 @@ subroutine grid_mechanical_spectral_polarisation_init
restartRead: if (interface_restartInc > 0) then
print'(/,a,i0,a)', ' reading restart data of increment ', interface_restartInc, ' from file'
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName)
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','r')
groupHandle = HDF5_openGroup(fileHandle,'solver')
call HDF5_read(groupHandle,P_aim, 'P_aim')
@ -419,7 +416,6 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
PetscErrorCode :: ierr
integer(HID_T) :: fileHandle, groupHandle
PetscScalar, dimension(:,:,:,:), pointer :: FandF_tau, F, F_tau
character(len=pStringLen) :: fileName
call DMDAVecGetArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)
F => FandF_tau(0: 8,:,:,:)
@ -427,8 +423,7 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
fileHandle = HDF5_openFile(fileName,'w')
fileHandle = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
groupHandle = HDF5_addGroup(fileHandle,'solver')
call HDF5_write(groupHandle,F_aim, 'P_aim')

4
src/homogenization.f90
View File

@ -451,7 +451,7 @@ subroutine homogenization_restartWrite(fileHandle)
groupHandle(2) = HDF5_addGroup(groupHandle(1),material_name_homogenization(ho))
call HDF5_read(groupHandle(2),homogState(ho)%state,'omega') ! ToDo: should be done by mech
call HDF5_write(groupHandle(2),homogState(ho)%state,'omega') ! ToDo: should be done by mech
call HDF5_closeGroup(groupHandle(2))
@ -478,7 +478,7 @@ subroutine homogenization_restartRead(fileHandle)
groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_homogenization(ho))
call HDF5_write(groupHandle(2),homogState(ho)%state,'omega') ! ToDo: should be done by mech
call HDF5_read(groupHandle(2),homogState(ho)%state,'omega') ! ToDo: should be done by mech
call HDF5_closeGroup(groupHandle(2))

41
src/results.f90
View File

@ -65,7 +65,7 @@ subroutine results_init(restart)
print*, 'https://doi.org/10.1007/s40192-017-0084-5'//IO_EOL
if(.not. restart) then
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.)
resultsFile = HDF5_openFile(getSolverJobName()//'.hdf5','w')
call results_addAttribute('DADF5_version_major',0)
call results_addAttribute('DADF5_version_minor',11)
call results_addAttribute('DAMASK_version',DAMASKVERSION)
@ -83,7 +83,7 @@ end subroutine results_init
!--------------------------------------------------------------------------------------------------
subroutine results_openJobFile
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','a',.true.)
resultsFile = HDF5_openFile(getSolverJobName()//'.hdf5','a')
end subroutine results_openJobFile
@ -289,11 +289,7 @@ subroutine results_writeScalarDataset_real(group,dataset,label,description,SIuni
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -320,11 +316,7 @@ subroutine results_writeVectorDataset_real(group,dataset,label,description,SIuni
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -362,7 +354,7 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
endif
if(transposed_) then
if(size(dataset,1) /= size(dataset,2)) call IO_error(0,ext_msg='transpose non-symmetric tensor')
if(size(dataset,1) /= size(dataset,2)) error stop 'transpose non-symmetric tensor'
allocate(dataset_transposed,mold=dataset)
do i=1,size(dataset_transposed,3)
dataset_transposed(:,:,i) = transpose(dataset(:,:,i))
@ -373,11 +365,7 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset_transposed,label,.true.)
#else
call HDF5_write(groupHandle,dataset_transposed,label,.false.)
#endif
call HDF5_write(groupHandle,dataset_transposed,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -405,11 +393,7 @@ subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -437,11 +421,7 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit
groupHandle = results_openGroup(group)
#ifdef PETSc
call HDF5_write(groupHandle,dataset,label,.true.)
#else
call HDF5_write(groupHandle,dataset,label,.false.)
#endif
call HDF5_write(groupHandle,dataset,label)
if (HDF5_objectExists(groupHandle,label)) &
call HDF5_addAttribute(groupHandle,'Description',description,label)
@ -577,7 +557,7 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
!--------------------------------------------------------------------------------------------------
! write the components of the compound type individually
call h5pset_preserve_f(plist_id, .TRUE., hdferr)
call h5pset_preserve_f(plist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping')
@ -733,7 +713,8 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
!--------------------------------------------------------------------------------------------------
! write the components of the compound type individually
call h5pset_preserve_f(plist_id, .TRUE., hdferr)
call h5pset_preserve_f(plist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping')
call h5dcreate_f(loc_id, 'homogenization', dtype_id, filespace_id, dset_id, hdferr)