Merge branch 'development' into 'export_DAMASK_to_DREAM3D'

# Conflicts:
#   python/damask/_result.py

.gitlab-ci.yml

@@ -89,10 +89,10 @@ unittest_GNU_DEBUG:
   stage: compile
   script:
     - module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
-    - TMPDIR=$(mktemp -d)
+    - TEMPDIR=$(mktemp -d)
-    - cmake -B ${TMPDIR} -DDAMASK_SOLVER=test -DCMAKE_INSTALL_PREFIX=${TMPDIR} -DCMAKE_BUILD_TYPE=RELEASE -DBUILDCMD_POST=-coverage
+    - cmake -B ${TEMPDIR} -DDAMASK_SOLVER=test -DCMAKE_INSTALL_PREFIX=${TEMPDIR} -DCMAKE_BUILD_TYPE=RELEASE -DBUILDCMD_POST=-coverage
-    - cmake --build ${TMPDIR} --target install
+    - cmake --build ${TEMPDIR} --target install
-    - cd ${TMPDIR}
+    - cd ${TEMPDIR}
     - ./bin/DAMASK_test
     - find -name \*.gcda -not -path "**/test/*" | xargs gcov
 
@@ -100,10 +100,10 @@ unittest_GNU_RELEASE:
   stage: compile
   script:
     - module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
-    - TMPDIR=$(mktemp -d)
+    - TEMPDIR=$(mktemp -d)
-    - cmake -B ${TMPDIR} -DDAMASK_SOLVER=test -DCMAKE_INSTALL_PREFIX=${TMPDIR} -DCMAKE_BUILD_TYPE=RELEASE -DBUILDCMD_POST=-coverage
+    - cmake -B ${TEMPDIR} -DDAMASK_SOLVER=test -DCMAKE_INSTALL_PREFIX=${TEMPDIR} -DCMAKE_BUILD_TYPE=RELEASE -DBUILDCMD_POST=-coverage
-    - cmake --build ${TMPDIR} --target install
+    - cmake --build ${TEMPDIR} --target install
-    - cd ${TMPDIR}
+    - cd ${TEMPDIR}
     - ./bin/DAMASK_test
     - find -name \*.gcda -not -path "**/test/*" | xargs gcov
 
@@ -111,10 +111,10 @@ unittest_GNU_PERFORMANCE:
   stage: compile
   script:
     - module load ${COMPILER_GNU} ${MPI_GNU} ${PETSC_GNU}
-    - TMPDIR=$(mktemp -d)
+    - TEMPDIR=$(mktemp -d)
-    - cmake -B ${TMPDIR} -DDAMASK_SOLVER=test -DCMAKE_INSTALL_PREFIX=${TMPDIR} -DCMAKE_BUILD_TYPE=PERFORMANCE -DBUILDCMD_POST=-coverage
+    - cmake -B ${TEMPDIR} -DDAMASK_SOLVER=test -DCMAKE_INSTALL_PREFIX=${TEMPDIR} -DCMAKE_BUILD_TYPE=PERFORMANCE -DBUILDCMD_POST=-coverage
-    - cmake --build ${TMPDIR} --target install
+    - cmake --build ${TEMPDIR} --target install
-    - cd ${TMPDIR}
+    - cd ${TEMPDIR}
     - ./bin/DAMASK_test
     - find -name \*.gcda -not -path "**/test/*" | xargs gcov
 

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<3.20.0)
+pkg_check_modules(PETSC REQUIRED PETSc<3.21.0)
 
 pkg_get_variable(CMAKE_Fortran_COMPILER PETSc fcompiler)
 pkg_get_variable(CMAKE_C_COMPILER PETSc ccompiler)

VERSION

@@ -1 +1 @@
-3.0.0-alpha7-864-g9cf37c493
+3.0.0-alpha7-880-g3644fe586

python/damask/_orientation.py

@@ -434,30 +434,20 @@ class Orientation(Rotation,Crystal):
         https://doi.org/10.1107/S0108767391006864
 
         """
-        rho = self.as_Rodrigues_vector(compact=True)*(1.0-1.0e-9)
+        def larger_or_equal(v,c):
+            return ((np.isclose(c[0],v[...,0]) | (v[...,0] > c[0])) &
+                    (np.isclose(c[1],v[...,1]) | (v[...,1] > c[1])) &
+                    (np.isclose(c[2],v[...,2]) | (v[...,2] > c[2]))).astype(bool)
 
-        with np.errstate(invalid='ignore'):
+        rho  = self.as_Rodrigues_vector(compact=True)
-            if   self.family == 'cubic':
+        return larger_or_equal(rho,
-                return ((rho[...,0] >= rho[...,1]) &
+                                     [rho[...,1],           rho[...,2],0] if self.family == 'cubic'
-                        (rho[...,1] >= rho[...,2]) &
+                                else [rho[...,1]*np.sqrt(3),0,         0] if self.family == 'hexagonal'
-                        (rho[...,2] >= 0)).astype(bool)
+                                else [rho[...,1],           0,         0] if self.family == 'tetragonal'
-            if self.family == 'hexagonal':
+                                else [0,                    0,         0] if self.family == 'orthorhombic'
-                return ((rho[...,0] >= rho[...,1]*np.sqrt(3)) &
+                                else [-np.inf,              0,         0] if self.family == 'monoclinic'
-                        (rho[...,1] >= 0) &
+                                else [-np.inf,        -np.inf,   -np.inf]) & self.in_FZ
-                        (rho[...,2] >= 0)).astype(bool)
-            if self.family == 'tetragonal':
-                return ((rho[...,0] >= rho[...,1]) &
-                        (rho[...,1] >= 0) &
-                        (rho[...,2] >= 0)).astype(bool)
-            if self.family == 'orthorhombic':
-                return ((rho[...,0] >= 0) &
-                        (rho[...,1] >= 0) &
-                        (rho[...,2] >= 0)).astype(bool)
-            if self.family == 'monoclinic':
-                return ((rho[...,1] >= 0) &
-                        (rho[...,2] >= 0)).astype(bool)
 
-            return np.ones_like(rho[...,0],dtype=bool)
 
     def disorientation(self,
                        other: 'Orientation',
@@ -522,19 +512,20 @@ class Orientation(Rotation,Crystal):
             raise NotImplementedError('disorientation between different crystal families')
 
         blend = util.shapeblender( self.shape,other.shape)
-        s = self.equivalent
+        s_m   = util.shapeshifter( self.shape,blend,mode='right')
-        o = other.equivalent
+        s_o   = util.shapeshifter(other.shape,blend,mode='left')
 
-        s_ = s.reshape((s.shape[0],1)+ self.shape).broadcast_to((s.shape[0],o.shape[0])+blend,mode='right')
+        s =  self.broadcast_to(s_m).equivalent
-        o_ = o.reshape((1,o.shape[0])+other.shape).broadcast_to((s.shape[0],o.shape[0])+blend,mode='right')
+        o = other.broadcast_to(s_o).equivalent
-        r_ = s_.misorientation(o_)
+
+        r_ = s[:,np.newaxis,...].misorientation(o[np.newaxis,:,...]) # type: ignore[index]
         _r = ~r_
 
-        forward = r_.in_FZ & r_.in_disorientation_FZ
+        forward = r_.in_disorientation_FZ
-        reverse = _r.in_FZ & _r.in_disorientation_FZ
+        reverse = _r.in_disorientation_FZ
         ok  = forward | reverse
-        ok &= (np.cumsum(ok.reshape((-1,)+ok.shape[2:]),axis=0) == 1).reshape(ok.shape)
+        ok &= (np.cumsum(ok.reshape((-1,)+blend),axis=0) == 1).reshape(ok.shape)
-        r = np.where(np.any(forward[...,np.newaxis],axis=(0,1),keepdims=True),
+        r = np.where(np.any((ok&forward)[...,np.newaxis],axis=(0,1),keepdims=True),
                      r_.quaternion,
                      _r.quaternion)
         loc  = np.where(ok)
@@ -584,6 +575,7 @@ class Orientation(Rotation,Crystal):
                                                    np.argmin(m,axis=0)[np.newaxis,...,np.newaxis],
                                                    axis=0),
                                 axis=0))
+
         return ((self.copy(Rotation(r).average(weights)),self.copy(Rotation(r))) if return_cloud else
                 self.copy(Rotation(r).average(weights))
                )
@@ -620,17 +612,19 @@ class Orientation(Rotation,Crystal):
         vector_ = np.array(vector,float)
         if vector_.shape[-1] != 3:
             raise ValueError('input is not a field of three-dimensional vectors')
-        eq  = self.equivalent
+
-        blend = util.shapeblender(eq.shape,vector_.shape[:-1])
+        blend = util.shapeblender( self.shape,vector_.shape[:-1])
-        poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(vector_,blend+(3,))
+        eq    = self.broadcast_to(util.shapeshifter( self.shape,blend,mode='right')).equivalent
+        poles = np.atleast_2d(eq @ np.broadcast_to(vector_,(1,)+blend+(3,)))
         ok    = self.in_SST(poles,proper=proper)
         ok   &= np.cumsum(ok,axis=0) == 1
         loc   = np.where(ok)
         sort  = 0 if len(loc) == 1 else np.lexsort(loc[:0:-1])
+
         return (
-                (poles[ok][sort].reshape(blend[1:]+(3,)), (np.vstack(loc[:1]).T)[sort].reshape(blend[1:]))
+                (poles[ok][sort].reshape(blend+(3,)), (np.vstack(loc[:1]).T)[sort].reshape(blend))
                 if return_operators else
-                poles[ok][sort].reshape(blend[1:]+(3,))
+                poles[ok][sort].reshape(blend+(3,))
                )
 
 
@@ -795,15 +789,16 @@ class Orientation(Rotation,Crystal):
 
         """
         v = self.to_frame(uvw=uvw,hkl=hkl)
-        blend = util.shapeblender(self.shape,v.shape[:-1])
+        s_v = v.shape[:-1]
+        blend = util.shapeblender(self.shape,s_v)
         if normalize:
-            v /= np.linalg.norm(v,axis=-1,keepdims=len(v.shape)>1)
+            v /= np.linalg.norm(v,axis=-1,keepdims=len(s_v)>0)
         if with_symmetry:
             sym_ops = self.symmetry_operations
-            shape = v.shape[:-1]+sym_ops.shape
+            s_v   += sym_ops.shape
             blend += sym_ops.shape
-            v = sym_ops.broadcast_to(shape) \
+            v = sym_ops.broadcast_to(s_v) @ v[...,np.newaxis,:]
-              @ np.broadcast_to(v.reshape(util.shapeshifter(v.shape,shape+(3,))),shape+(3,))
+
         return ~(self.broadcast_to(blend)) @ np.broadcast_to(v,blend+(3,))
 
 
@@ -854,6 +849,7 @@ class Orientation(Rotation,Crystal):
                                   p/np.linalg.norm(p,axis=1,keepdims=True))
 
         shape = P.shape[0:1]+self.shape+(3,3)
+
         return ~self.broadcast_to(shape[:-2]) \
                @ np.broadcast_to(P.reshape(util.shapeshifter(P.shape,shape)),shape)
 
@@ -897,6 +893,7 @@ class Orientation(Rotation,Crystal):
         lattice,o = self.relation_operations(model)
         target = Crystal(lattice=lattice)
         o = o.broadcast_to(o.shape+self.shape,mode='right')
+
         return Orientation(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'),
                           lattice=lattice,
                           b = self.b if target.ratio['b'] is None else self.a*target.ratio['b'],

python/damask/_result.py

@@ -23,7 +23,7 @@ from . import grid_filters
 from . import mechanics
 from . import tensor
 from . import util
-from ._typehints import FloatSequence, IntSequence
+from ._typehints import FloatSequence, IntSequence, DADF5Dataset
 
 h5py3 = h5py.__version__[0] == '3'
 
@@ -37,7 +37,7 @@ def _read(dataset: h5py._hl.dataset.Dataset) -> np.ndarray:
     return np.array(dataset,dtype=dtype)
 
 def _match(requested,
-           existing: h5py._hl.base.KeysViewHDF5) -> List[Any]:
+           existing: h5py._hl.base.KeysViewHDF5) -> List[str]:
     """Find matches among two sets of labels."""
     def flatten_list(list_of_lists):
         return [e for e_ in list_of_lists for e in e_]
@@ -646,7 +646,7 @@ class Result:
             Name of scalar, vector, or tensor dataset to take absolute value of.
 
         """
-        def absolute(x: Dict[str, Any]) -> Dict[str, Any]:
+        def absolute(x: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  np.abs(x['data']),
                     'label': f'|{x["label"]}|',
@@ -708,7 +708,7 @@ class Result:
         ...                   'Mises equivalent of the Cauchy stress')
 
         """
-        def calculation(**kwargs) -> Dict[str, Any]:
+        def calculation(**kwargs) -> DADF5Dataset:
             formula = kwargs['formula']
             for d in re.findall(r'#(.*?)#',formula):
                 formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
@@ -749,7 +749,7 @@ class Result:
 
         """
 
-        def stress_Cauchy(P: Dict[str, Any], F: Dict[str, Any]) -> Dict[str, Any]:
+        def stress_Cauchy(P: DADF5Dataset, F: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  mechanics.stress_Cauchy(P['data'],F['data']),
                     'label': 'sigma',
@@ -784,7 +784,7 @@ class Result:
 
         """
 
-        def determinant(T: Dict[str, Any]) -> Dict[str, Any]:
+        def determinant(T: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  np.linalg.det(T['data']),
                     'label': f"det({T['label']})",
@@ -817,7 +817,7 @@ class Result:
 
         """
 
-        def deviator(T: Dict[str, Any]) -> Dict[str, Any]:
+        def deviator(T: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  tensor.deviatoric(T['data']),
                     'label': f"s_{T['label']}",
@@ -854,7 +854,7 @@ class Result:
 
         """
 
-        def eigenval(T_sym: Dict[str, Any], eigenvalue: Literal['max, mid, min']) -> Dict[str, Any]:
+        def eigenval(T_sym: DADF5Dataset, eigenvalue: Literal['max', 'mid', 'min']) -> DADF5Dataset:
             if   eigenvalue == 'max':
                 label,p = 'maximum',2
             elif eigenvalue == 'mid':
@@ -893,7 +893,7 @@ class Result:
 
         """
 
-        def eigenvector(T_sym: Dict[str, Any], eigenvalue: Literal['max', 'mid', 'min']) -> Dict[str, Any]:
+        def eigenvector(T_sym: DADF5Dataset, eigenvalue: Literal['max', 'mid', 'min']) -> DADF5Dataset:
             if   eigenvalue == 'max':
                 label,p = 'maximum',2
             elif eigenvalue == 'mid':
@@ -941,13 +941,13 @@ class Result:
 
         """
 
-        def IPF_color(l: FloatSequence, q: Dict[str, Any]) -> Dict[str, Any]:
+        def IPF_color(l: FloatSequence, q: DADF5Dataset) -> DADF5Dataset:
             m = util.scale_to_coprime(np.array(l))
             lattice =  q['meta']['lattice']
             o = Orientation(rotation = q['data'],lattice=lattice)
 
             return {
-                    'data': np.uint8(o.IPF_color(l)*255),
+                    'data': (o.IPF_color(l)*255).astype(np.uint8),
                     'label': 'IPFcolor_({} {} {})'.format(*m),
                     'meta' : {
                               'unit':        '8-bit RGB',
@@ -970,7 +970,7 @@ class Result:
             Name of symmetric tensor dataset.
 
         """
-        def maximum_shear(T_sym: Dict[str, Any]) -> Dict[str, Any]:
+        def maximum_shear(T_sym: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  mechanics.maximum_shear(T_sym['data']),
                     'label': f"max_shear({T_sym['label']})",
@@ -1013,7 +1013,7 @@ class Result:
         >>> r.add_equivalent_Mises('epsilon_V^0.0(F)')
 
         """
-        def equivalent_Mises(T_sym: Dict[str, Any], kind: str) -> Dict[str, Any]:
+        def equivalent_Mises(T_sym: DADF5Dataset, kind: str) -> DADF5Dataset:
             k = kind
             if k is None:
                 if T_sym['meta']['unit'] == '1':
@@ -1051,7 +1051,7 @@ class Result:
             Order of the norm. inf means NumPy's inf object. For details refer to numpy.linalg.norm.
 
         """
-        def norm(x: Dict[str, Any], ord: Union[int, float, Literal['fro', 'nuc']]) ->  Dict[str, Any]:
+        def norm(x: DADF5Dataset, ord: Union[int, float, Literal['fro', 'nuc']]) -> DADF5Dataset:
             o = ord
             if len(x['data'].shape) == 2:
                 axis: Union[int, Tuple[int, int]] = 1
@@ -1099,7 +1099,7 @@ class Result:
         is taken into account.
 
         """
-        def stress_second_Piola_Kirchhoff(P: Dict[str, Any], F: Dict[str, Any]) -> Dict[str, Any]:
+        def stress_second_Piola_Kirchhoff(P: DADF5Dataset, F: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  mechanics.stress_second_Piola_Kirchhoff(P['data'],F['data']),
                     'label': 'S',
@@ -1141,12 +1141,11 @@ class Result:
             Defaults to True.
 
         """
-        def pole(q: Dict[str, Any],
+        def pole(q: DADF5Dataset,
-                      uvw: FloatSequence,
+                 uvw: FloatSequence, hkl: FloatSequence,
-                      hkl: FloatSequence,
                  with_symmetry: bool,
-                      normalize: bool) -> Dict[str, Any]:
+                 normalize: bool) -> DADF5Dataset:
-            c = q['meta']['c/a'] if 'c/a' in q['meta'] else 1
+            c = q['meta']['c/a'] if 'c/a' in q['meta'] else 1.0
             brackets = ['[]','()','⟨⟩','{}'][(uvw is None)*1+with_symmetry*2]
             label = 'p^' + '{}{} {} {}{}'.format(brackets[0],
                                                   *(uvw if uvw else hkl),
@@ -1186,7 +1185,7 @@ class Result:
         >>> r.add_rotation('F')
 
         """
-        def rotation(F: Dict[str, Any]) -> Dict[str, Any]:
+        def rotation(F: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  mechanics.rotation(F['data']).as_matrix(),
                     'label': f"R({F['label']})",
@@ -1218,7 +1217,7 @@ class Result:
         >>> r.add_spherical('sigma')
 
         """
-        def spherical(T: Dict[str, Any]) -> Dict[str, Any]:
+        def spherical(T: DADF5Dataset) -> DADF5Dataset:
             return {
                     'data':  tensor.spherical(T['data'],False),
                     'label': f"p_{T['label']}",
@@ -1292,14 +1291,14 @@ class Result:
         | https://de.wikipedia.org/wiki/Verzerrungstensor
 
         """
-        def strain(F: Dict[str, Any], t: Literal['V', 'U'], m: float) -> Dict[str, Any]:
+        def strain(F: DADF5Dataset, t: Literal['V', 'U'], m: float) -> DADF5Dataset:
             side = 'left' if t == 'V' else 'right'
             return {
                     'data':  mechanics.strain(F['data'],t,m),
                     'label': f"epsilon_{t}^{m}({F['label']})",
                     'meta':  {
                               'unit':        F['meta']['unit'],
-                              'description': f'Seth-Hill strain tensor of order {m} based on {side} stretch tensor '+\
+                              'description': f'Seth-Hill strain tensor of order {m} based on {side} stretch tensor '
                                              f"of {F['label']} ({F['meta']['description']})",
                               'creator':     'add_strain'
                               }
@@ -1323,14 +1322,14 @@ class Result:
             Defaults to 'V'.
 
         """
-        def stretch_tensor(F: Dict[str, Any], t: str) -> Dict[str, Any]:
+        def stretch_tensor(F: DADF5Dataset, t: str) -> DADF5Dataset:
             return {
                     'data':  (mechanics.stretch_left if t.upper() == 'V' else mechanics.stretch_right)(F['data']),
                     'label': f"{t}({F['label']})",
                     'meta':  {
                               'unit':        F['meta']['unit'],
-                              'description': f"{'left' if t.upper() == 'V' else 'right'} stretch tensor "\
+                              'description': f"{'left' if t.upper() == 'V' else 'right'} stretch tensor "
-                                            +f"of {F['label']} ({F['meta']['description']})",           # noqa
+                                             f"of {F['label']} ({F['meta']['description']})",           # noqa
                               'creator':     'add_stretch_tensor'
                               }
                      }
@@ -1353,7 +1352,7 @@ class Result:
         i.e. fields resulting from the grid solver.
 
         """
-        def curl(f: Dict[str, Any], size: np.ndarray) -> Dict[str, Any]:
+        def curl(f: DADF5Dataset, size: np.ndarray) -> DADF5Dataset:
             return {
                     'data':  grid_filters.curl(size,f['data']),
                     'label': f"curl({f['label']})",
@@ -1382,7 +1381,7 @@ class Result:
         i.e. fields resulting from the grid solver.
 
         """
-        def divergence(f: Dict[str, Any], size: np.ndarray) -> Dict[str, Any]:
+        def divergence(f: DADF5Dataset, size: np.ndarray) -> DADF5Dataset:
             return {
                     'data':  grid_filters.divergence(size,f['data']),
                     'label': f"divergence({f['label']})",
@@ -1411,7 +1410,7 @@ class Result:
         i.e. fields resulting from the grid solver.
 
         """
-        def gradient(f: Dict[str, Any], size: np.ndarray) -> Dict[str, Any]:
+        def gradient(f: DADF5Dataset, size: np.ndarray) -> DADF5Dataset:
             return {
                     'data':  grid_filters.gradient(size,f['data'] if len(f['data'].shape) == 4 else \
                                                         f['data'].reshape(f['data'].shape+(1,))),
@@ -1427,7 +1426,7 @@ class Result:
 
 
     def _add_generic_grid(self,
-                          func: Callable,
+                          func: Callable[..., DADF5Dataset],
                           datasets: Dict[str, str],
                           args: Dict[str, str] = {},
                           constituents = None):
@@ -1478,7 +1477,7 @@ class Result:
                                                           now.strftime('%Y-%m-%d %H:%M:%S%z').encode()
 
                             for l,v in r['meta'].items():
-                                h5_dataset.attrs[l.lower()]=v if h5py3 else v.encode()
+                                h5_dataset.attrs[l.lower()]=v.encode() if not h5py3 and type(v) is str else v
                             creator = h5_dataset.attrs['creator'] if h5py3 else \
                                       h5_dataset.attrs['creator'].decode()
                             h5_dataset.attrs['creator'] = f'damask.Result.{creator} v{damask.version}' if h5py3 else \
@@ -1488,8 +1487,8 @@ class Result:
 
 
     def _add_generic_pointwise(self,
-                               func: Callable,
+                               func: Callable[..., DADF5Dataset],
-                               datasets: Dict[str, Any],
+                               datasets: Dict[str, str],
                                args: Dict[str, Any] = {}):
         """
         General function to add pointwise data.
@@ -1508,9 +1507,9 @@ class Result:
         """
 
         def job_pointwise(group: str,
-                          callback: Callable,
+                          callback: Callable[..., DADF5Dataset],
                           datasets: Dict[str, str],
-                          args: Dict[str, str]) -> Union[None, Any]:
+                          args: Dict[str, str]) -> Union[None, DADF5Dataset]:
             try:
                 datasets_in = {}
                 with h5py.File(self.fname,'r') as f:
@@ -1598,7 +1597,7 @@ class Result:
     def get(self,
             output: Union[str, List[str]] = '*',
             flatten: bool = True,
-            prune: bool = True) -> Optional[Dict[str,Any]]:
+            prune: bool = True) -> Union[None,Dict[str,Any]]:
         """
         Collect data per phase/homogenization reflecting the group/folder structure in the DADF5 file.
 

python/damask/_rotation.py

@@ -112,7 +112,7 @@ class Rotation:
 
 
     def __getitem__(self,
-                    item: Union[Tuple[int], int, bool, np.bool_, np.ndarray]):
+                    item: Union[Tuple[Union[None, int, slice]], int, bool, np.bool_, np.ndarray]):
         """
         Return self[item].
 
@@ -295,6 +295,7 @@ class Rotation:
         ----------
         other : Rotation, shape (self.shape)
             Rotation for composition.
+            Compatible innermost dimensions will blend.
 
         Returns
         -------
@@ -303,10 +304,15 @@ class Rotation:
 
         """
         if isinstance(other,Rotation):
-            q_m = self.quaternion[...,0:1]
+            blend = util.shapeblender( self.shape,other.shape)
-            p_m = self.quaternion[...,1:]
+            s_m   = util.shapeshifter( self.shape,blend,mode='right')
-            q_o = other.quaternion[...,0:1]
+            s_o   = util.shapeshifter(other.shape,blend,mode='left')
-            p_o = other.quaternion[...,1:]
+
+            q_m = self.broadcast_to(s_m).quaternion[...,0:1]
+            p_m = self.broadcast_to(s_m).quaternion[...,1:]
+            q_o = other.broadcast_to(s_o).quaternion[...,0:1]
+            p_o = other.broadcast_to(s_o).quaternion[...,1:]
+
             qmo = q_m*q_o
             q = (qmo - np.einsum('...i,...i',p_m,p_o).reshape(qmo.shape))
             p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
@@ -325,6 +331,7 @@ class Rotation:
         ----------
         other : Rotation, shape (self.shape)
             Rotation for composition.
+            Compatible innermost dimensions will blend.
 
         """
         return self*other
@@ -341,6 +348,7 @@ class Rotation:
         ----------
         other : damask.Rotation, shape (self.shape)
             Rotation to invert for composition.
+            Compatible innermost dimensions will blend.
 
         Returns
         -------
@@ -434,7 +442,7 @@ class Rotation:
 
         """
         if isinstance(other, np.ndarray):
-            obs = util.shapeblender(self.shape,other.shape,keep_ones=False)[len(self.shape):]
+            obs = util.shapeblender(self.shape,other.shape)[len(self.shape):]
             for l in [4,2,1]:
                 if obs[-l:] == l*(3,):
                     bs = util.shapeblender(self.shape,other.shape[:-l],False)

python/damask/_typehints.py

@@ -1,6 +1,6 @@
 """Functionality for typehints."""
 
-from typing import Sequence, Union, Literal, TextIO
+from typing import Sequence, Union, TypedDict, Literal, TextIO
 from pathlib import Path
 
 import numpy as np
@@ -16,3 +16,15 @@ CrystalKinematics = Literal['slip', 'twin']
 NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
 # BitGenerator does not exists in older numpy versions
 #NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.BitGenerator, np.random.Generator]
+
+# https://peps.python.org/pep-0655/
+# Metadata = TypedDict('Metadata', {'unit': str, 'description': str, 'creator': str, 'lattice': NotRequired[str]})
+_Metadata = TypedDict('_Metadata', {'lattice': str, 'c/a': float}, total=False)
+
+class Metadata(_Metadata):
+    unit: str
+    description: str
+    creator: str
+
+
+DADF5Dataset = TypedDict('DADF5Dataset', {'data': np.ndarray, 'label': str, 'meta': Metadata})

python/damask/util.py

@@ -513,7 +513,7 @@ def shapeshifter(fro: _Tuple[int, ...],
 
 def shapeblender(a: _Tuple[int, ...],
                  b: _Tuple[int, ...],
-                 keep_ones: bool = True) -> _Tuple[int, ...]:
+                 keep_ones: bool = False) -> _Tuple[int, ...]:
     """
     Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
 
@@ -525,20 +525,24 @@ def shapeblender(a: _Tuple[int, ...],
         Shape of second array.
     keep_ones : bool, optional
         Treat innermost '1's as literal value instead of dimensional placeholder.
-        Defaults to True.
+        Defaults to False.
 
     Examples
     --------
-    >>> shapeblender((4,4,3),(3,2,1))
-        (4,4,3,2,1)
-    >>> shapeblender((1,2),(1,2,3))
-        (1,2,3)
-    >>> shapeblender((1,),(2,2,1))
-        (1,2,2,1)
-    >>> shapeblender((1,),(2,2,1),False)
-        (2,2,1)
     >>> shapeblender((3,2),(3,2))
         (3,2)
+    >>> shapeblender((4,3),(3,2))
+        (4,3,2)
+    >>> shapeblender((4,4),(3,2))
+        (4,4,3,2)
+    >>> shapeblender((1,2),(1,2,3))
+        (1,2,3)
+    >>> shapeblender((),(2,2,1))
+        (2,2,1)
+    >>> shapeblender((1,),(2,2,1))
+        (2,2,1)
+    >>> shapeblender((1,),(2,2,1),True)
+        (1,2,2,1)
 
     """
     def is_broadcastable(a,b):

python/tests/test_Orientation.py

@@ -358,7 +358,9 @@ class TestOrientation:
                                     a=a,b=b,c=c,
                                     alpha=alpha,beta=beta,gamma=gamma)
         assert o.to_pole(**{kw:vector,'with_symmetry':with_symmetry}).shape \
-            == o.shape + vector.shape[:-1] + (o.symmetry_operations.shape if with_symmetry else ()) + vector.shape[-1:]
+            == util.shapeblender(o.shape,vector.shape[:-1]) \
+             + (o.symmetry_operations.shape if with_symmetry else ()) \
+             + vector.shape[-1:]
 
     @pytest.mark.parametrize('lattice',['hP','cI','cF']) #tI not included yet
     def test_Schmid(self,update,res_path,lattice):

python/tests/test_util.py

@@ -136,11 +136,13 @@ class TestUtil:
                               ((1,),(7,),False,(7,)),
                               ((1,),(7,),True,(1,7)),
                               ((2,),(2,2),False,(2,2)),
-                              ((1,2),(2,2),False,(2,2)),
+                              ((1,3),(2,3),False,(2,3)),
                               ((1,1,2),(2,2),False,(1,2,2)),
                               ((1,1,2),(2,2),True,(1,1,2,2)),
                               ((1,2,3),(2,3,4),False,(1,2,3,4)),
                               ((1,2,3),(1,2,3),False,(1,2,3)),
+                              ((2,3,1,1),(2,3),False,(2,3,2,3)),
+                              ((2,3,1,1),(2,3),True,(2,3,1,1,2,3)),
                              ])
     def test_shapeblender(self,a,b,ones,answer):
         assert util.shapeblender(a,b,ones) == answer

src/CLI.f90

@@ -6,7 +6,7 @@
 !> @brief Parse command line interface for PETSc-based solvers
 !--------------------------------------------------------------------------------------------------
 #define PETSC_MINOR_MIN 12
-#define PETSC_MINOR_MAX 19
+#define PETSC_MINOR_MAX 20
 
 module CLI
   use, intrinsic :: ISO_fortran_env

src/YAML_parse.f90

@@ -48,7 +48,7 @@ subroutine YAML_parse_init()
 #ifdef FYAML
   print'(/,1x,a)', 'libfyaml powered'
 #else
-  call selfTest()
+  call YAML_parse_selfTest()
 #endif
 
 end subroutine YAML_parse_init
@@ -870,7 +870,7 @@ end function to_flow
 !--------------------------------------------------------------------------------------------------
 !> @brief Check correctness of some YAML functions.
 !--------------------------------------------------------------------------------------------------
-subroutine selfTest()
+subroutine YAML_parse_selfTest()
 
   if (indentDepth(' a') /= 1)     error stop 'indentDepth'
   if (indentDepth('a')  /= 0)     error stop 'indentDepth'
@@ -1031,7 +1031,7 @@ subroutine selfTest()
 
   end block parse
 
-end subroutine selfTest
+end subroutine YAML_parse_selfTest
 #endif
 
 end module YAML_parse

src/YAML_types.f90

@@ -150,6 +150,7 @@ module YAML_types
 
   public :: &
     YAML_types_init, &
+    YAML_types_selfTest, &
 #ifdef __GFORTRAN__
     output_as1dStr, &                                       !ToDo: Hack for GNU. Remove later
 #endif
@@ -164,7 +165,7 @@ subroutine YAML_types_init
 
   print'(/,1x,a)', '<<<+-  YAML_types init  -+>>>'
 
-  call selfTest()
+  call YAML_types_selfTest()
 
 end subroutine YAML_types_init
 
@@ -172,7 +173,7 @@ end subroutine YAML_types_init
 !--------------------------------------------------------------------------------------------------
 !> @brief Check correctness of some type bound procedures.
 !--------------------------------------------------------------------------------------------------
-subroutine selfTest()
+subroutine YAML_types_selfTest()
 
   scalar: block
     type(tScalar), target :: s
@@ -266,7 +267,7 @@ subroutine selfTest()
 
   end block dict
 
-end subroutine selfTest
+end subroutine YAML_types_selfTest
 
 
 !---------------------------------------------------------------------------------------------------

src/crystal.f90

@@ -2223,7 +2223,7 @@ end function crystal_isotropic_mu
 !--------------------------------------------------------------------------------------------------
 !> @brief Check correctness of some crystal functions.
 !--------------------------------------------------------------------------------------------------
-subroutine crystal_selfTest
+subroutine crystal_selfTest()
 
   real(pREAL), dimension(:,:,:), allocatable :: CoSy
   real(pREAL), dimension(:,:),   allocatable :: system

src/mesh/mesh_mech_FEM.f90

@@ -74,6 +74,9 @@ module mesh_mechanical_FEM
   external :: &                                                                                     ! ToDo: write interfaces
 #if defined(PETSC_USE_64BIT_INDICES) || PETSC_VERSION_MINOR < 17
     ISDestroy, &
+#endif
+#if PETSC_VERSION_MINOR > 18
+    DMAddField, &
 #endif
     PetscSectionGetNumFields, &
     PetscFESetQuadrature, &

src/test/DAMASK_test.f90

@@ -12,6 +12,7 @@ program DAMASK_test
   use test_crystal
   use test_rotations
   use test_IO
+  use test_YAML_types
   use test_HDF5_utilities
 
   external :: quit
@@ -57,6 +58,10 @@ program DAMASK_test
   call test_IO_run()
   write(IO_STDOUT,fmt='(a)') ok
 
+  write(IO_STDOUT,fmt=fmt, advance='no') 'YAML_types','...'
+  call test_YAML_types_run()
+  write(IO_STDOUT,fmt='(a)') ok
+
   write(IO_STDOUT,fmt=fmt, advance='no') 'HDF5_utilities','...'
   call test_HDF5_utilities_run()
   write(IO_STDOUT,fmt='(a)') ok

src/test/test_YAML_types.f90

@@ -0,0 +1,17 @@
+module test_YAML_types
+  use YAML_types
+
+  implicit none(type,external)
+
+  private
+  public :: test_YAML_types_run
+
+  contains
+
+subroutine test_YAML_types_run()
+
+  call YAML_types_selfTest()
+
+end subroutine test_YAML_types_run
+
+end module test_YAML_types