Merge branch 'drop-old-DADF5-support' into 'development'
Improvements to damask.Result See merge request damask/DAMASK!373
This commit is contained in:
Philip Eisenlohr
commit
e9cfb2f968
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@ -34,7 +34,7 @@ def _read(dataset):
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return np.array(dataset,dtype=dtype)
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def _match(requested,existing):
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"""Find matches among two sets of names."""
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"""Find matches among two sets of labels."""
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def flatten_list(list_of_lists):
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return [e for e_ in list_of_lists for e in e_]
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@ -98,35 +98,26 @@ class Result:
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self.version_major = f.attrs['DADF5_version_major']
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self.version_minor = f.attrs['DADF5_version_minor']
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if self.version_major != 0 or not 7 <= self.version_minor <= 12:
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if self.version_major != 0 or not 12 <= self.version_minor <= 13:
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raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
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self.structured = 'grid' in f['geometry'].attrs.keys() or \
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'cells' in f['geometry'].attrs.keys()
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self.structured = 'cells' in f['geometry'].attrs.keys()
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if self.structured:
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try:
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self.cells = f['geometry'].attrs['cells']
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except KeyError:
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self.cells = f['geometry'].attrs['grid']
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self.cells = f['geometry'].attrs['cells']
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self.size = f['geometry'].attrs['size']
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self.origin = f['geometry'].attrs['origin']
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r=re.compile('inc[0-9]+' if self.version_minor < 12 else 'increment_[0-9]+')
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r=re.compile('increment_[0-9]+')
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self.increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort)
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self.times = [round(f[i].attrs['time/s' if self.version_minor < 12 else
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't/s'],12) for i in self.increments]
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self.times = [round(f[i].attrs['t/s'],12) for i in self.increments]
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grp = 'mapping' if self.version_minor < 12 else 'cell_to'
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self.N_materialpoints, self.N_constituents = np.shape(f['cell_to/phase'])
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self.N_materialpoints, self.N_constituents = np.shape(f[f'{grp}/phase'])
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self.homogenizations = [m.decode() for m in np.unique(f[f'{grp}/homogenization']
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['Name' if self.version_minor < 12 else 'label'])]
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self.homogenizations = sorted(self.homogenizations,key=util.natural_sort)
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self.phases = [c.decode() for c in np.unique(f[f'{grp}/phase']
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['Name' if self.version_minor < 12 else 'label'])]
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self.phases = sorted(self.phases,key=util.natural_sort)
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self.homogenization = f['cell_to/homogenization']['label'].astype('str')
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self.homogenizations = sorted(np.unique(self.homogenization),key=util.natural_sort)
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self.phase = f['cell_to/phase']['label'].astype('str')
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self.phases = sorted(np.unique(self.phase),key=util.natural_sort)
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self.fields = []
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for c in self.phases:
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@ -196,11 +187,10 @@ class Result:
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choice = list(datasets).copy() if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
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[datasets]
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inc = 'inc' if self.version_minor < 12 else 'increment_' # compatibility hack
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if what == 'increments':
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choice = [c if isinstance(c,str) and c.startswith(inc) else
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f'{inc}{c}' for c in choice]
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if datasets == -1: choice = [self.increments[-1]]
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choice = [c if isinstance(c,str) and c.startswith('increment_') else
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self.increments[c] if isinstance(c,int) and c<0 else
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f'increment_{c}' for c in choice]
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elif what == 'times':
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what = 'increments'
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if choice == ['*']:
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@ -279,13 +269,11 @@ class Result:
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Increment number of all increments within the given bounds.
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"""
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# compatibility hack
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ln = 3 if self.version_minor < 12 else 10
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selected = []
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for i,inc in enumerate([int(i[ln:]) for i in self.increments]):
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s,e = map(lambda x: int(x[ln:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
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for i,inc in enumerate([int(i[10:]) for i in self.increments]):
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s,e = map(lambda x: int(x[10:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
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if s <= inc <= e:
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selected.append(int(self.increments[i].split('_')[1]))
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selected.append(self.increments[i])
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return selected
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@ -412,8 +400,7 @@ class Result:
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Rename/move datasets (within the same group/folder).
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This operation is discouraged because the history of the
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data becomes untracable and scientific integrity cannot be
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ensured.
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data becomes untraceable and data integrity is not ensured.
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Parameters
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----------
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@ -454,8 +441,7 @@ class Result:
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Remove/delete datasets.
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This operation is discouraged because the history of the
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data becomes untracable and scientific integrity cannot be
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ensured.
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data becomes untraceable and data integrity is not ensured.
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Parameters
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----------
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@ -486,9 +472,6 @@ class Result:
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def list_data(self):
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"""Return information on all active datasets in the file."""
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# compatibility hack
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de = 'Description' if self.version_minor < 12 else 'description'
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un = 'Unit' if self.version_minor < 12 else 'unit'
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msg = ''
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with h5py.File(self.fname,'r') as f:
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for inc in self.visible['increments']:
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@ -501,10 +484,10 @@ class Result:
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msg = ' '.join([msg,f'{field}\n'])
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for d in f['/'.join([inc,ty,label,field])].keys():
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dataset = f['/'.join([inc,ty,label,field,d])]
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unit = f' / {dataset.attrs[un]}' if h5py3 else \
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f' / {dataset.attrs[un].decode()}'
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description = dataset.attrs[de] if h5py3 else \
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dataset.attrs[de].decode()
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unit = f' / {dataset.attrs["unit"]}' if h5py3 else \
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f' / {dataset.attrs["unit"].decode()}'
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description = dataset.attrs['description'] if h5py3 else \
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dataset.attrs['description'].decode()
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msg = ' '.join([msg,f'{d}{unit}: {description}\n'])
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return msg
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@ -522,7 +505,7 @@ class Result:
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return grid_filters.coordinates0_point(self.cells,self.size,self.origin).reshape(-1,3,order='F')
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else:
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with h5py.File(self.fname,'r') as f:
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return f['geometry/x_c'][()]
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return f['geometry/x_p'][()]
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@property
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def coordinates0_node(self):
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@ -611,7 +594,7 @@ class Result:
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>>> r = damask.Result('my_file.hdf5')
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>>> r.add_calculation('np.sum(#rho_mob#,axis=1)','rho_mob_total',
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... '1/m²','total mobile dislocation density')
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>>> r.add_calculation(''np.sum(#rho_dip#,axis=1)',rho_dip_total',
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>>> r.add_calculation('np.sum(#rho_dip#,axis=1)','rho_dip_total',
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... '1/m²','total dislocation dipole density')
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>>> r.add_calculation('#rho_dip_total#+#rho_mob_total','rho_total',
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... '1/m²','total dislocation density')
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@ -968,6 +951,13 @@ class Result:
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F : str, optional
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Name of deformation gradient dataset. Defaults to 'F'.
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Notes
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-----
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The definition of the second Piola-Kirchhoff stress (S = [F^-1 P]_sym)
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follows the standard definition in nonlinear continuum mechanics.
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As such, no intermediate configuration, for instance that reached by F_p,
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is taken into account.
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"""
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self._add_generic_pointwise(self._add_stress_second_Piola_Kirchhoff,{'P':P,'F':F})
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@ -1262,7 +1252,6 @@ class Result:
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Defaults to '*', in which case all datasets are considered.
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"""
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u = 'Unit' if self.version_minor < 12 else 'unit' # compatibility hack
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if self.N_constituents != 1 or len(self.phases) != 1 or not self.structured:
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raise TypeError('XDMF output requires structured grid with single phase and single constituent.')
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@ -1343,7 +1332,8 @@ class Result:
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shape = f[name].shape[1:]
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dtype = f[name].dtype
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unit = f[name].attrs[u] if h5py3 else f[name].attrs[u].decode()
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unit = f[name].attrs['unit'] if h5py3 else \
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f[name].attrs['unit'].decode()
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attributes.append(ET.SubElement(grid, 'Attribute'))
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attributes[-1].attrib = {'Name': '/'.join([ty,field,out])+f' / {unit}',
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@ -1362,23 +1352,20 @@ class Result:
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def _mappings(self):
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grp = 'mapping' if self.version_minor < 12 else 'cell_to' # compatibility hack
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name = 'Name' if self.version_minor < 12 else 'label' # compatibility hack
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member = 'member' if self.version_minor < 12 else 'entry' # compatibility hack
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"""Mappings to place data spatially."""
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with h5py.File(self.fname,'r') as f:
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at_cell_ph = []
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in_data_ph = []
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for c in range(self.N_constituents):
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at_cell_ph.append({label: np.where(f['/'.join([grp,'phase'])][:,c][name] == label.encode())[0] \
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at_cell_ph.append({label: np.where(self.phase[:,c] == label)[0] \
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for label in self.visible['phases']})
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in_data_ph.append({label: f['/'.join([grp,'phase'])][member][at_cell_ph[c][label]][:,c] \
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in_data_ph.append({label: f['/'.join(['cell_to','phase'])]['entry'][at_cell_ph[c][label]][:,c] \
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for label in self.visible['phases']})
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at_cell_ho = {label: np.where(f['/'.join([grp,'homogenization'])][:][name] == label.encode())[0] \
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at_cell_ho = {label: np.where(self.homogenization[:] == label)[0] \
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for label in self.visible['homogenizations']}
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in_data_ho = {label: f['/'.join([grp,'homogenization'])][member][at_cell_ho[label]] \
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in_data_ho = {label: f['/'.join(['cell_to','homogenization'])]['entry'][at_cell_ho[label]] \
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for label in self.visible['homogenizations']}
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return at_cell_ph,in_data_ph,at_cell_ho,in_data_ho
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@ -1420,9 +1407,9 @@ class Result:
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v = self.geometry0
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elif mode.lower()=='point':
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v = VTK.from_poly_data(self.coordinates0_point)
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v.set_comments(util.execution_stamp('Result','save_VTK'))
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ln = 3 if self.version_minor < 12 else 10 # compatibility hack
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N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][ln:])))))+1
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N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][10:])))))+1
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constituents_ = constituents if isinstance(constituents,Iterable) else \
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(range(self.N_constituents) if constituents is None else [constituents])
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@ -1433,6 +1420,10 @@ class Result:
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at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
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with h5py.File(self.fname,'r') as f:
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if self.version_minor >= 13:
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creator = f.attrs['creator'] if h5py3 else f.attrs['creator'].decode()
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created = f.attrs['created'] if h5py3 else f.attrs['created'].decode()
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v.add_comments(f'{creator} ({created})')
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for inc in util.show_progress(self.visible['increments']):
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@ -1466,7 +1457,7 @@ class Result:
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for label,dataset in outs.items():
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v.add(dataset,' / '.join(['/'.join([ty,field,label]),dataset.dtype.metadata['unit']]))
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v.save(f'{self.fname.stem}_inc{inc[ln:].zfill(N_digits)}',parallel=parallel)
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v.save(f'{self.fname.stem}_inc{inc[10:].zfill(N_digits)}',parallel=parallel)
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def get(self,output='*',flatten=True,prune=True):
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|
|
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@ -265,10 +265,18 @@ class VTK:
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raise ValueError('No label defined for numpy.ndarray')
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N_data = data.shape[0]
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data_ = np.where(data.mask,data.fill_value,data) if isinstance(data,np.ma.MaskedArray) else\
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data
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d = np_to_vtk((data_.astype(np.single) if data_.dtype in [np.double, np.longdouble] else
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data_).reshape(N_data,-1),deep=True) # avoid large files
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data_ = (data if not isinstance(data,np.ma.MaskedArray) else
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np.where(data.mask,data.fill_value,data)).reshape(N_data,-1)
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if data_.dtype in [np.double,np.longdouble]:
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d = np_to_vtk(data_.astype(np.single),deep=True) # avoid large files
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elif data_.dtype.type is np.str_:
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d = vtk.vtkStringArray()
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for s in np.squeeze(data_):
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d.InsertNextValue(s)
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else:
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d = np_to_vtk(data_,deep=True)
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d.SetName(label)
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if N_data == N_points:
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|
|
@ -305,14 +313,24 @@ class VTK:
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cell_data = self.vtk_data.GetCellData()
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for a in range(cell_data.GetNumberOfArrays()):
|
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if cell_data.GetArrayName(a) == label:
|
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return vtk_to_np(cell_data.GetArray(a))
|
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try:
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return vtk_to_np(cell_data.GetArray(a))
|
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except AttributeError:
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vtk_array = cell_data.GetAbstractArray(a) # string array
|
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|
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point_data = self.vtk_data.GetPointData()
|
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for a in range(point_data.GetNumberOfArrays()):
|
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if point_data.GetArrayName(a) == label:
|
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return vtk_to_np(point_data.GetArray(a))
|
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try:
|
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return vtk_to_np(point_data.GetArray(a))
|
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except AttributeError:
|
||||
vtk_array = point_data.GetAbstractArray(a) # string array
|
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|
||||
raise ValueError(f'Array "{label}" not found.')
|
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try:
|
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# string array
|
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return np.array([vtk_array.GetValue(i) for i in range(vtk_array.GetNumberOfValues())]).astype(str)
|
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except UnboundLocalError:
|
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raise ValueError(f'Array "{label}" not found.')
|
||||
|
||||
|
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def get_comments(self):
|
||||
|
|
|
|||
Binary file not shown.
Binary file not shown.
|
|
@ -1 +1 @@
|
|||
3b83384def67552ab7dd211efc0d54fd
|
||||
0f68c932b85aac1d30e03e05a16c4605
|
||||
|
|
@ -1 +1 @@
|
|||
c32c86ed50dbb39a93ca2a2ebe47d9cb
|
||||
b206ef9e7a096586c7d71d58fc7278bd
|
||||
|
|
@ -1 +1 @@
|
|||
ead4f6fcaff174fddc041d701e54ac60
|
||||
11bd422f0a6c78ee1d3c939b1fccf1ee
|
||||
|
|
@ -1 +1 @@
|
|||
bde8b728110c2c05a6a4740f7c5f9c06
|
||||
541f423cfde8e2a98582491f7af3add5
|
||||
|
|
@ -1 +1 @@
|
|||
e09bfa9248283fc390003ad28d15d36e
|
||||
82e309984cab644fd94f433d5ec24133
|
||||
|
|
@ -1 +1 @@
|
|||
3f21254164f96de8ee4a28249ae72cc6
|
||||
f1f85bcdba23e3e4001512c1c6c4707a
|
||||
|
|
@ -333,7 +333,7 @@ class TestResult:
|
|||
@pytest.mark.parametrize('output',['F','*',['P']],ids=range(3))
|
||||
@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,output,fname,inc):
|
||||
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.save_VTK(output)
|
||||
|
|
@ -354,6 +354,19 @@ class TestResult:
|
|||
with open((ref_path/'save_VTK'/request.node.name).with_suffix('.md5')) as f:
|
||||
assert cur == f.read()
|
||||
|
||||
@pytest.mark.parametrize('mode',['point','cell'])
|
||||
@pytest.mark.parametrize('output',[False,True])
|
||||
def test_vtk_marc(self,tmp_path,ref_path,mode,output):
|
||||
os.chdir(tmp_path)
|
||||
result = Result(ref_path/'check_compile_job1.hdf5')
|
||||
result.save_VTK(output,mode)
|
||||
|
||||
def test_marc_coordinates(self,ref_path):
|
||||
result = Result(ref_path/'check_compile_job1.hdf5').view('increments',-1)
|
||||
c_n = result.coordinates0_node + result.get('u_n')
|
||||
c_p = result.coordinates0_point + result.get('u_p')
|
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assert len(c_n) > len(c_p)
|
||||
|
||||
@pytest.mark.parametrize('mode',['point','cell'])
|
||||
def test_vtk_mode(self,tmp_path,single_phase,mode):
|
||||
os.chdir(tmp_path)
|
||||
|
|
|
|||
|
|
@ -135,6 +135,18 @@ class TestVTK:
|
|||
with pytest.raises(TypeError):
|
||||
default.add('invalid_type','valid')
|
||||
|
||||
@pytest.mark.parametrize('data_type,shape',[(float,(3,)),
|
||||
(float,(3,3)),
|
||||
(float,(1,)),
|
||||
(int,(4,)),
|
||||
(str,(1,))])
|
||||
@pytest.mark.parametrize('N_values',[5*6*7,6*7*8])
|
||||
def test_add_get(self,default,data_type,shape,N_values):
|
||||
data = np.squeeze(np.random.randint(0,100,(N_values,)+shape)).astype(data_type)
|
||||
default.add(data,'data')
|
||||
assert (np.squeeze(data.reshape(N_values,-1)) == default.get('data')).all()
|
||||
|
||||
|
||||
def test_add_masked(self,default):
|
||||
data = np.random.rand(5*6*7,3)
|
||||
masked = ma.MaskedArray(data,mask=data<.4,fill_value=42.)
|
||||
|
|
|
|||
|
|
@ -57,7 +57,7 @@ subroutine results_init(restart)
|
|||
|
||||
logical, intent(in) :: restart
|
||||
|
||||
character(len=pStringLen) :: commandLine
|
||||
character(len=pPathLen) :: commandLine
|
||||
|
||||
print'(/,a)', ' <<<+- results init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
|
|
@ -67,8 +67,10 @@ subroutine results_init(restart)
|
|||
if(.not. restart) then
|
||||
resultsFile = HDF5_openFile(getSolverJobName()//'.hdf5','w')
|
||||
call results_addAttribute('DADF5_version_major',0)
|
||||
call results_addAttribute('DADF5_version_minor',12)
|
||||
call results_addAttribute('DAMASK_version',DAMASKVERSION)
|
||||
call results_addAttribute('DADF5_version_minor',13)
|
||||
call get_command_argument(0,commandLine)
|
||||
call results_addAttribute('creator',trim(commandLine)//' '//DAMASKVERSION)
|
||||
call results_addAttribute('created',now())
|
||||
call get_command(commandLine)
|
||||
call results_addAttribute('call',trim(commandLine))
|
||||
call results_closeGroup(results_addGroup('cell_to'))
|
||||
|
|
|
|||
Loading…
Reference in New Issue