Merge branch 'development' into 284-more-friendly-output-name-of-add_strain-or-a-better-presentation-in-documentation-webpage

.gitattributes

@@ -12,12 +12,12 @@
 *.pbz2 binary
 
 # ignore files from MSC.Marc in language statistics
-install/MarcMentat/**     linguist-vendored
-src/Marc/include/*             linguist-vendored
+install/MarcMentat/** linguist-vendored
+src/Marc/include/* linguist-vendored
 install/MarcMentat/MSC_modifications.py linguist-vendored=false
 
 # ignore reference files for tests in language statistics
-python/tests/reference/**           linguist-vendored
+python/tests/resources/** linguist-vendored
 
 # ignore deprecated scripts
-processing/legacy/**                linguist-vendored
+processing/legacy/** linguist-vendored

.github/workflows/Fortran.yml

@@ -82,7 +82,7 @@ jobs:
 
       - name: DAMASK - Run
         run: |
-          ./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -w examples/grid
+          ./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -m material.yaml -w examples/grid
           ./bin/DAMASK_mesh -h
 
 
@@ -189,5 +189,5 @@ jobs:
 
       - name: DAMASK - Run
         run: |
-          ./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -w examples/grid
+          ./bin/DAMASK_grid -l tensionX.yaml -g 20grains16x16x16.vti -m material.yaml -w examples/grid
           ./bin/DAMASK_mesh -h

.github/workflows/Python.yml

@@ -75,7 +75,7 @@ jobs:
         run: >
           sudo apt-get update &&
           sudo apt-get remove mysql* &&
-          sudo apt-get install python3-pandas python3-scipy python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
+          sudo apt-get install python3-pandas python3-scipy python3-h5py python3-vtk9 python3-matplotlib python3-yaml -y
 
       - name: Run unit tests
         run: |

CMakeLists.txt

@@ -11,7 +11,7 @@ endif()
 project(Prerequisites LANGUAGES)
 set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
 pkg_check_modules(PETSC_MIN REQUIRED PETSc>=3.12.0 QUIET) #CMake does not support version range
-pkg_check_modules(PETSC REQUIRED PETSc<3.19.0)
+pkg_check_modules(PETSC REQUIRED PETSc<3.20.0)
 
 pkg_get_variable(CMAKE_Fortran_COMPILER PETSc fcompiler)
 pkg_get_variable(CMAKE_C_COMPILER PETSc ccompiler)

PRIVATE

@@ -1 +1 @@
-Subproject commit 8fbc1dd8a26bf359b72bc076dac8ea3edef3be6d
+Subproject commit 9f4ffce8b2df951191a14dc3229de1aee6e544e6

VERSION

@@ -1 +1 @@
-3.0.0-alpha7-488-gf6c761980
+3.0.0-alpha7-604-g65fa62b3f

examples/config/phase/mechanical/elastic/Hooke_Fe.yaml

@@ -3,7 +3,7 @@ type: Hooke
 references:
   - D.J. Dever,
     Journal of Applied Physics 43(8):3293-3301, 1972,
-    https://doi.org/10.1063/1.1661710
+    https://doi.org/10.1063/1.1661710,
     fit to Tab. II (T_min=25ºC, T_max=880ºC)
 
 C_11: 232.2e+9

examples/config/phase/mechanical/elastic/Hooke_SAE1050-martensite.yaml

@@ -3,8 +3,9 @@ type: Hooke
 references:
   - S.A. Kim and W.L. Johnson,
     Materials Science & Engineering A 452-453:633-639, 2007,
-    https://doi.org/10.1016/j.msea.2006.11.147
+    https://doi.org/10.1016/j.msea.2006.11.147,
+    Tab. 1 (averaged for bcc)
 
-C_11: 268.1e+9
-C_12: 111.2e+9
-C_44: 79.06e+9
+C_11: 267.9e+9
+C_12: 110.8e+9
+C_44: 78.9e+9

examples/config/phase/mechanical/plastic/dislotungsten_W.yaml

@@ -3,7 +3,7 @@ type: dislotungsten
 references:
   - D. Cereceda et al.,
     International Journal of Plasticity 78:242-265, 2016,
-    http://dx.doi.org/10.1016/j.ijplas.2015.09.002
+    https://doi.org/10.1016/j.ijplas.2015.09.002
   - R. Gröger et al.,
     Acta Materialia 56(19):5412-5425, 2008,
     https://doi.org/10.1016/j.actamat.2008.07.037

examples/config/phase/mechanical/plastic/dislotwin_IF-steel.yaml

@@ -12,6 +12,7 @@ output: [rho_dip, rho_mob]
 
 N_sl: [12, 12]
 
+f_edge: [1.0, 1.0]
 b_sl: [2.49e-10, 2.49e-10]
 rho_mob_0: [2.81e+12, 2.8e+12]
 rho_dip_0: [1.0, 1.0] # not given

examples/config/phase/mechanical/plastic/dislotwin_TWIP-TRIP.yaml

@@ -15,6 +15,8 @@ output: [rho_mob, rho_dip, gamma_sl, Lambda_sl, tau_pass, f_tw, Lambda_tw, f_tr]
 
 # Glide
 N_sl: [12]
+
+f_edge: [1.0]
 b_sl: [2.56e-10] # a/sqrt(2)
 Q_sl: [3.5e-19]
 p_sl: [0.325]

examples/config/phase/mechanical/plastic/kinehardening_317L.yaml

@@ -0,0 +1,23 @@
+type: kinehardening
+
+references:
+  - J.A. Wollmershauser et al.,
+    International Journal of Fatigue 36(1):181-193, 2012,
+    https://doi.org/10.1016/j.ijfatigue.2011.07.008
+
+output: [xi, chi, chi_flip, gamma_flip, gamma, sgn(gamma)]
+
+N_sl: [12]
+
+xi_0:     [0.070e+9] # τ_0,for
+xi_inf:   [0.015e+9] # τ_1,for
+h_0_xi:   [0.065e+9] # θ_0,for
+h_inf_xi: [0.045e+9] # θ_1,for
+
+chi_inf:  [0.027e+9] # τ_1,bs
+h_0_chi:     [55e+9] # θ_0,bs
+h_inf_chi:  [1.3e+9] # θ_1,bs
+
+n: 20                # not mentioned in the reference
+dot_gamma_0: 1e-4    # not mentioned in the reference
+h_sl-sl: [1, 1, 1, 1, 1, 1, 1]

python/damask/__init__.py

@@ -25,5 +25,6 @@ from ._colormap        import Colormap         # noqa
 from ._vtk             import VTK              # noqa
 from ._config          import Config           # noqa
 from ._configmaterial  import ConfigMaterial   # noqa
+from ._loadcasegrid    import LoadcaseGrid     # noqa
 from ._grid            import Grid             # noqa
 from ._result          import Result           # noqa

python/damask/_grid.py

@@ -317,6 +317,11 @@ class Grid:
         loaded : damask.Grid
             Grid-based geometry from file.
 
+        Notes
+        -----
+        Material indices in Neper usually start at 1 unless
+        a buffer material with index 0 is added.
+
         Examples
         --------
         Read a periodic polycrystal generated with Neper.
@@ -325,7 +330,7 @@ class Grid:
         >>> N_grains = 20
         >>> cells = (32,32,32)
         >>> damask.util.run(f'neper -T -n {N_grains} -tesrsize {cells[0]}:{cells[1]}:{cells[2]} -periodicity all -format vtk')
-        >>> damask.Grid.load_Neper(f'n{N_grains}-id1.vtk')
+        >>> damask.Grid.load_Neper(f'n{N_grains}-id1.vtk').renumber()
         cells:  32 × 32 × 32
         size:   1.0 × 1.0 × 1.0 m³
         origin: 0.0   0.0   0.0 m
@@ -336,7 +341,7 @@ class Grid:
         cells = np.array(v.vtk_data.GetDimensions())-1
         bbox  = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
 
-        return Grid(material = v.get('MaterialId').reshape(cells,order='F').astype('int32',casting='unsafe') - 1,
+        return Grid(material = v.get('MaterialId').reshape(cells,order='F').astype('int32',casting='unsafe'),
                     size     = bbox[1] - bbox[0],
                     origin   = bbox[0],
                     comments = util.execution_stamp('Grid','load_Neper'),
@@ -1044,7 +1049,7 @@ class Grid:
         Parameters
         ----------
         idx : numpy.ndarray of int, shape (:,:,:) or (:,:,:,3)
-          Grid of flat indices or coordinate indices.
+            Grid of flat indices or coordinate indices.
 
         Returns
         -------

python/damask/_loadcasegrid.py

@@ -0,0 +1,78 @@
+from typing import Optional, Union, Dict, Any, List
+
+from numpy import ma
+import yaml
+
+from ._typehints import FileHandle
+from ._config import NiceDumper
+from . import util
+from . import Config
+
+
+class MaskedMatrixDumper(NiceDumper):
+    """Format masked matrices."""
+
+    def represent_data(self, data: Any):
+        return super().represent_data(data.astype(object).filled('x') if isinstance(data, ma.core.MaskedArray) else data) # type: ignore[attr-defined]
+
+
+class LoadcaseGrid(Config):
+    """Load case for grid solver."""
+
+    def __init__(self,
+                 config: Optional[Union[str,Dict[str,Any]]] = None,
+                 *,
+                 solver: Optional[Dict[str,str]] = None,
+                 loadstep: Optional[List[Dict[str,Any]]] = None):
+        """
+        New grid solver load case.
+
+        Parameters
+        ----------
+        config : dict or str, optional
+            Grid solver load case. String needs to be valid YAML.
+        solver : dict, optional
+            Solver configuration.
+            Defaults to an empty dict if 'config' is not given.
+        loadstep : list of dict, optional
+            Load step configuration.
+            Defaults to an empty list if 'config' is not given.
+
+        """
+        kwargs: Dict[str,Union[Dict[str,str],List[Dict[str,Any]]]] = {}
+        default: Union[List,Dict]
+        for arg,value,default in [('solver',solver,{}),('loadstep',loadstep,[])]: # type: ignore[assignment]
+            if value is not None:
+                kwargs[arg] = value
+            elif config is None:
+                kwargs[arg] = default
+
+        super().__init__(config,**kwargs)
+
+
+    def save(self,
+             fname: FileHandle,
+             **kwargs):
+        """
+        Save to YAML file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file to write.
+        **kwargs : dict
+            Keyword arguments parsed to yaml.dump.
+
+        """
+        for key,default in dict(width=256,
+                                default_flow_style=None,
+                                sort_keys=False).items():
+            if key not in kwargs:
+                kwargs[key] = default
+
+        fhandle = util.open_text(fname,'w')
+        try:
+            fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))
+        except TypeError:                                                                           # compatibility with old pyyaml
+            del kwargs['sort_keys']
+            fhandle.write(yaml.dump(self,Dumper=MaskedMatrixDumper,**kwargs))

python/damask/_result.py

@@ -15,7 +15,7 @@ from typing import Optional, Union, Callable, Any, Sequence, Literal, Dict, List
 
 import h5py
 import numpy as np
-import numpy.ma as ma
+from numpy import ma
 
 import damask
 from . import VTK
@@ -106,10 +106,8 @@ class Result:
             self.version_major = f.attrs['DADF5_version_major']
             self.version_minor = f.attrs['DADF5_version_minor']
 
-            if (self.version_major != 0 or not 12 <= self.version_minor <= 14) and self.version_major != 1:
+            if (self.version_major != 0 or not 14 <= self.version_minor <= 14) and self.version_major != 1:
                 raise TypeError(f'unsupported DADF5 version "{self.version_major}.{self.version_minor}"')
-            if self.version_major == 0 and self.version_minor < 14:
-                self.export_simulation_setup = None                                                 # type: ignore
 
             self.structured = 'cells' in f['geometry'].attrs.keys()
 
@@ -1940,7 +1938,8 @@ class Result:
 
     def export_DADF5(self,
                      fname,
-                     output: Union[str, List[str]] = '*'):
+                     output: Union[str, List[str]] = '*',
+                     mapping = None):
         """
         Export visible components into a new DADF5 file.
 
@@ -1954,20 +1953,61 @@ class Result:
         output : (list of) str, optional
             Names of the datasets to export.
             Defaults to '*', in which case all visible datasets are exported.
+        mapping : numpy.ndarray of int, shape (:,:,:), optional
+            Indices for regridding.
 
         """
         if Path(fname).expanduser().absolute() == self.fname:
             raise PermissionError(f'cannot overwrite {self.fname}')
+
+        def cp(path_in,path_out,label,mapping):
+            if mapping is None:
+                path_in.copy(label,path_out)
+            else:
+                path_out.create_dataset(label,data=path_in[label][()][mapping])
+                path_out[label].attrs.update(path_in[label].attrs)
+
+
         with h5py.File(self.fname,'r') as f_in, h5py.File(fname,'w') as f_out:
-            for k,v in f_in.attrs.items():
-                f_out.attrs.create(k,v)
-            for g in ['setup','geometry','cell_to']:
+            f_out.attrs.update(f_in.attrs)
+            for g in ['setup','geometry'] + (['cell_to'] if mapping is None else []):
                 f_in.copy(g,f_out)
 
+            if mapping is not None:
+                cells = mapping.shape
+                mapping_flat = mapping.flatten(order='F')
+                f_out['geometry'].attrs['cells'] = cells
+                f_out.create_group('cell_to')                                                       # ToDo: attribute missing
+                mappings = {'phase':{},'homogenization':{}}                                         # type: ignore
+
+                mapping_phase = f_in['cell_to']['phase'][()][mapping_flat]
+                for p in np.unique(mapping_phase['label']):
+                    m = mapping_phase['label'] == p
+                    mappings['phase'][p] = mapping_phase[m]['entry']
+                    c = np.count_nonzero(m)
+                    mapping_phase[m] = list(zip((p,)*c,tuple(np.arange(c))))
+                f_out['cell_to'].create_dataset('phase',data=mapping_phase.reshape(np.prod(mapping_flat.shape),-1))
+
+                mapping_homog = f_in['cell_to']['homogenization'][()][mapping]
+                for h in np.unique(mapping_homog['label']):
+                    m = mapping_homog['label'] == h
+                    mappings['homogenization'][h] = mapping_homog[m]['entry']
+                    c = np.count_nonzero(m)
+                    mapping_homog[mapping_homog['label'] == h] = list(zip((h,)*c,tuple(np.arange(c))))
+                f_out['cell_to'].create_dataset('homogenization',data=mapping_homog.flatten())
+
+
             for inc in util.show_progress(self.visible['increments']):
                 f_in.copy(inc,f_out,shallow=True)
-                for out in _match(output,f_in['/'.join([inc,'geometry'])].keys()):
-                    f_in[inc]['geometry'].copy(out,f_out[inc]['geometry'])
+                if mapping is None:
+                    for label in ['u_p','u_n']:
+                        f_in[inc]['geometry'].copy(label,f_out[inc]['geometry'])
+                else:
+                    u_p = f_in[inc]['geometry']['u_p'][()][mapping_flat]
+                    f_out[inc]['geometry'].create_dataset('u_p',data=u_p)
+                    u_n = np.zeros((len(mapping_flat),3))                                           # ToDo: needs implementation
+                    f_out[inc]['geometry'].create_dataset('u_n',data=u_n)
+
 
                 for label in self.homogenizations:
                     f_in[inc]['homogenization'].copy(label,f_out[inc]['homogenization'],shallow=True)
@@ -1979,7 +2019,7 @@ class Result:
                         for field in _match(self.visible['fields'],f_in['/'.join([inc,ty,label])].keys()):
                             p = '/'.join([inc,ty,label,field])
                             for out in _match(output,f_in[p].keys()):
-                                f_in[p].copy(out,f_out[p])
+                                cp(f_in[p],f_out[p],out,None if mapping is None else mappings[ty][label.encode()])
 
 
     def export_simulation_setup(self,

python/damask/_table.py

@@ -603,4 +603,7 @@ class Table:
         f = util.open_text(fname,'w')
 
         f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+('\n' if labels else ''))
-        self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')
+        try:                                                                                        # backward compatibility
+            self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,lineterminator='\n')
+        except TypeError:
+            self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False,line_terminator='\n')

python/damask/grid_filters.py

@@ -186,8 +186,6 @@ def displacement_fluct_point(size: _FloatSequence,
         Fluctuating part of the cell center displacements.
 
     """
-    integrator = 0.5j*_np.array(size,float)/_np.pi
-
     k_s = _ks(size,F.shape[:3],False)
     k_s_squared = _np.einsum('...l,...l',k_s,k_s)
     k_s_squared[0,0,0] = 1.0
@@ -195,8 +193,8 @@ def displacement_fluct_point(size: _FloatSequence,
     displacement = -_np.einsum('ijkml,ijkl,l->ijkm',
                               _np.fft.rfftn(F,axes=(0,1,2)),
                               k_s,
-                              integrator,
-                             ) / k_s_squared[...,_np.newaxis]
+                              _np.array([0.5j/_np.pi]*3),
+                              ) / k_s_squared[...,_np.newaxis]
 
     return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
 

python/tests/conftest.py

@@ -60,9 +60,9 @@ def update(request):
 
 
 @pytest.fixture
-def ref_path_base():
-    """Directory containing reference results."""
-    return Path(__file__).parent/'reference'
+def res_path_base():
+    """Directory containing testing resources."""
+    return Path(__file__).parent/'resources'
 
 
 @pytest.fixture

python/tests/resources/Grid/.gitattributes

@@ -0,0 +1 @@
+n10-id1_scaled.vtk binary