Merge branch 'housekeeping_2025-02-22' into 'development'

several small improvements

See merge request damask/DAMASK!1034

Author: eisenlohr

.gitlab-ci.yml

@@ -122,7 +122,7 @@ doctest:
     - export DAMASK_ROOT=$(pwd)
     - PYTHONPATH=${DAMASK_ROOT}/python:$PYTHONPATH
     - cd python
-    - python3 -m pytest -v --doctest-modules -k 'not result and not configmaterial and not orientation and not rotation and not geomgrid' damask
+    - python3 -m pytest -v --doctest-modules -k 'not result and not configmaterial and not orientation and not geomgrid' damask
 
 mypy:
   extends: .python_default

examples/grid/20grains.seeds

@@ -1,21 +1,21 @@
-1_pos      2_pos      3_pos    1_euler 2_euler 3_euler
-0.375488   0.161813   0.891040 197.572861  16.816409 129.422844
-0.187988   0.849313   0.953540 257.468172  53.250534 157.331503
-0.750488   0.349313   0.953540 216.994815  94.418518 251.147231
-0.312988   0.099313   0.891040 196.157946  55.870978  21.681170
-0.562988   0.536813   0.703540 152.515728 139.769395 240.036018
-0.750488   0.036813   0.641040 232.521881  73.749222 241.429633
-0.812988   0.724313   0.016040 157.531396 135.503513  75.737722
-0.187988   0.161813   0.266040 321.038280  27.209843  46.413467
-0.562988   0.286813   0.203540 346.918594  87.495569 113.554206
-0.937988   0.599313   0.953540 138.038947  99.827132 130.935878
-0.937988   0.349313   0.578540 285.021014 118.092004 205.270837
-0.812988   0.661813   0.453540 190.402171  56.738068 157.896545
-0.125488   0.411813   0.203540 204.496042  95.031265 355.814582
-0.625488   0.224313   0.578540 333.214790  82.133355  36.736132
-0.687988   0.161813   0.891040  25.572981 164.242648  75.195632
-0.625488   0.161813   0.766040  31.366548  76.392403  58.071426
-0.437988   0.724313   0.266040   7.278623  77.044663 235.118997
-0.437988   0.099313   0.641040 299.743144  76.475096  91.184977
-0.937988   0.911813   0.828540 280.136430  27.439718 167.871878
-0.437988   0.411813   0.516040 313.204373  68.676053  87.993213
+1_pos      2_pos      3_pos
+0.375488   0.161813   0.891040
+0.187988   0.849313   0.953540
+0.750488   0.349313   0.953540
+0.312988   0.099313   0.891040
+0.562988   0.536813   0.703540
+0.750488   0.036813   0.641040
+0.812988   0.724313   0.016040
+0.187988   0.161813   0.266040
+0.562988   0.286813   0.203540
+0.937988   0.599313   0.953540
+0.937988   0.349313   0.578540
+0.812988   0.661813   0.453540
+0.125488   0.411813   0.203540
+0.625488   0.224313   0.578540
+0.687988   0.161813   0.891040
+0.625488   0.161813   0.766040
+0.437988   0.724313   0.266040
+0.437988   0.099313   0.641040
+0.937988   0.911813   0.828540
+0.437988   0.411813   0.516040

python/damask/_configmaterial.py

@@ -242,7 +242,7 @@ def from_table(table: Table,*,
         kwargs = {}
         for arg,val in zip(['homogenization','phase','v','O','V_e'],[homogenization,phase,v,O,V_e]):
             if val is not None:
-                kwargs[arg] = table.get(val) if val in table.labels else np.atleast_2d([val]*len(table)).T # type: ignore
+                kwargs[arg] = table.get(val) if val in table.labels else np.atleast_2d([val]*len(table)).T # type: ignore[arg-type]
 
         _,idx = np.unique(np.hstack(list(kwargs.values())),return_index=True,axis=0)
         idx = np.sort(idx)
@@ -584,7 +584,7 @@ def material_add(self,*,
         for arg,val in zip(['homogenization','phase','v','O','V_e'],[homogenization,phase,v,O,V_e]):
             if val is None: continue
             shape[arg] = np.array(val)
-            s = shape[arg].shape[:ex.get(arg,None)]                                                 # type: ignore
+            s = shape[arg].shape[:ex.get(arg,None)]
             N_materials = max(N_materials,s[0]) if len(s)>0 else N_materials
             N_constituents = max(N_constituents,s[1]) if len(s)>1 else N_constituents
 
@@ -617,7 +617,7 @@ def material_add(self,*,
         dup['material'] = dup['material'] + mat if 'material' in dup else mat
 
         for what in [item for item in ['phase','homogenization'] if item in shape]:
-            for k in np.unique(shape[what]):                                                        # type: ignore
+            for k in np.unique(shape[what]):
                 if k not in dup[what]: dup[what][str(k)] = None
 
         return dup

python/damask/_crystal.py

@@ -801,7 +801,7 @@ def __eq__(self,
         return (NotImplemented if not isinstance(other, Crystal) else
                 self.lattice == other.lattice and
                 self.parameters == other.parameters and
-                self.family == other.family)                                                        # type: ignore
+                self.family == other.family)
 
     @property
     def parameters(self) -> Optional[Dict]:
@@ -1230,7 +1230,7 @@ def characteristic_shear_twin(self,
             return np.array([[0.5*np.sqrt(2.0)]*N_twin_[0]])
         elif self.lattice == 'hP':
             N_twin_ = [len(a) for a in _kinematics[self.lattice]['twin']] if N_twin == '*' else N_twin
-            c_a = self.c/self.a                                                                     #type: ignore
+            c_a = self.c/self.a                                                                     # type: ignore[operator]
             return np.array([[(3.0-c_a**2)/np.sqrt(3.0)/c_a]*N_twin_[0],
                              [1.0/c_a]*N_twin_[1],
                              [(9.0-4.0*c_a**2)/np.sqrt(48.0)/c_a]*N_twin_[2],
@@ -1285,15 +1285,15 @@ def relation_operations(self,
             raise KeyError(f'unknown orientation relationship "{model}"')
 
         sep = '-->'
-        search = self.lattice+sep+('' if target is None else target.lattice)                        # type: ignore
-        transform = [t for t in orientation_relationships[model].keys() if t.startswith(search)]    # type: ignore
+        search = self.lattice+sep+('' if target is None else target.lattice)                        # type: ignore[operator]
+        transform = [t for t in orientation_relationships[model].keys() if t.startswith(search)]
 
         if len(transform) != 1:
             raise ValueError(f'invalid target lattice "{search.split(sep)[1]}"')
 
-        m_l,o_l = transform[0].split(sep)                                                           # type: ignore
+        m_l,o_l = transform[0].split(sep)                                                           # type: ignore[assignment]
         m_p,o_p = orientation_relationships[model][m_l+sep+o_l]
-        m = Crystal(lattice=m_l) if self.parameters is None else Crystal(lattice=m_l,**self.parameters) # type: ignore
+        m = Crystal(lattice=m_l) if self.parameters is None else Crystal(lattice=m_l,**self.parameters)
         o = Crystal(lattice=o_l) if target is None else target
         m_p = np.stack((m.to_frame(uvw=m_p[:,0] if m_l != 'hP' else util.Bravais_to_Miller(uvtw=m_p[:,0])),
                         m.to_frame(hkl=m_p[:,1] if m_l != 'hP' else util.Bravais_to_Miller(hkil=m_p[:,1]))),

python/damask/_geomgrid.py

@@ -18,7 +18,7 @@
 from . import Colormap
 from ._typehints import FloatSequence, IntSequence, NumpyRngSeed
 try:
-    import numba as nb                                                                              # type: ignore
+    import numba as nb                                                                              # type: ignore[import-not-found]
 except ImportError:
     nb = False
 
@@ -61,8 +61,8 @@ def __init__(self,
 
         """
         self.material = material
-        self.size = size                                                                            # type: ignore
-        self.origin = origin                                                                        # type: ignore
+        self.size = size                                                                            # type: ignore[assignment]
+        self.origin = origin                                                                        # type: ignore[assignment]
         self.initial_conditions = {} if initial_conditions is None else initial_conditions
         self.comments = [] if comments is None else \
                         [comments] if isinstance(comments,str) else \
@@ -169,9 +169,9 @@ def origin(self,
     @property
     def initial_conditions(self) -> Dict[str,np.ndarray]:
         """Fields of initial conditions."""
-        self._ic = dict(zip(self._ic.keys(),                                                        # type: ignore
+        self._ic = dict(zip(self._ic.keys(),                                                        # type: ignore[has-type]
                         [v if isinstance(v,np.ndarray) else
-                         np.broadcast_to(v,self.cells) for v in self._ic.values()]))                # type: ignore
+                         np.broadcast_to(v,self.cells) for v in self._ic.values()]))                # type: ignore[has-type]
         return self._ic
 
     @initial_conditions.setter
@@ -214,7 +214,7 @@ def _load(fname: Union[str, Path], label: str) -> 'GeomGrid':
 
         """
         v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
-        cells = np.array(v.vtk_data.GetDimensions())-1                                              # type: ignore
+        cells = np.array(v.vtk_data.GetDimensions())-1                                              # type: ignore[attr-defined]
         bbox  = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
         ic = {l:v.get(l).reshape(cells,order='F') for l in set(v.labels['Cell Data']) - {label}}
 
@@ -307,7 +307,7 @@ def load_Neper(fname: Union[str, Path]) -> 'GeomGrid':
 
         """
         v = VTK.load(fname,'ImageData')
-        cells = np.array(v.vtk_data.GetDimensions())-1                                              # type: ignore
+        cells = np.array(v.vtk_data.GetDimensions())-1                                              # type: ignore[attr-defined]
         bbox  = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
 
         return GeomGrid(material = v.get('MaterialId').reshape(cells,order='F').astype('int32',casting='unsafe'),

python/damask/_loadcasegrid.py

@@ -11,7 +11,9 @@ 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]
+        return super().represent_data(data.astype(object).filled('x')                               # type: ignore[attr-defined]
+                                      if isinstance(data, ma.core.MaskedArray) else
+                                      data)
 
 
 class LoadcaseGrid(YAML):

python/damask/_orientation.py

@@ -983,11 +983,27 @@ def from_fiber_component(crystal: IntSequence,
 
         Ranges 0≤θ≤π and 0≤φ≤2π give a unique set of coordinates.
 
+        Notes
+        -----
+        The value for sigma should be small enough to avoid values
+        larger than the maximum disorientation of the crystal family
+        when sampling from a normal distribution.
+        The maximum disorientation angle d_max is 62.80°, 93.84°,
+        98.43°, and 120° for cubic, hexagonal, tetragonal, and
+        orthorhombic crystal families, respectively.
+        A typically safe value is σ = d_max/5.
+
+        References
+        ----------
+        A. Heinz and P. Neumann, Acta Crystallographica Section A 47:780-789, 1991
+        https://doi.org/10.1107/S0108767391006864
+
         """
         return Orientation(Rotation.from_fiber_component(crystal,sample,sigma,shape,degrees,rng_seed),
                            family=family,lattice=lattice,
                            a=a,b=b,c=c, alpha=alpha,beta=beta,gamma=gamma,
                            degrees=degrees)
+
     @staticmethod
     def from_directions(uvw: IntSequence,
                         hkl: IntSequence,
@@ -1142,6 +1158,14 @@ def larger_or_equal(v,c):
                                 else [-np.inf,        -np.inf,   -np.inf]) & self.in_FZ
 
 
+    @overload
+    def disorientation(self: MyType, other: MyType,
+                       return_operators: Literal[False] = False) -> MyType:
+        ...
+    @overload
+    def disorientation(self: MyType, other: MyType,
+                       return_operators: Literal[True] = True) -> DisorientationTuple:
+        ...
     def disorientation(self: MyType,
                        other: MyType,
                        return_operators: bool = False) -> Union[MyType, DisorientationTuple]:
@@ -1206,7 +1230,7 @@ def disorientation(self: MyType,
         s =  self.broadcast_to(s_m).equivalent
         o = other.broadcast_to(s_o).equivalent
 
-        r_ = s[:,np.newaxis,...].misorientation(o[np.newaxis,:,...])                                # type: ignore[index]
+        r_ = s[:,np.newaxis,...].misorientation(o[np.newaxis,:,...])
         _r = ~r_
         shp = r_.shape[2:]
 
@@ -1309,14 +1333,14 @@ def disorientation_angle(self: MyType,
             trace_max = np.maximum.reduce([trace_max,m1,(m1+m2)*np.sqrt(2.)/2.])
 
         else:
-            return self.disorientation(other).as_axis_angle(pair=True)[1]                           # type: ignore
+            return self.disorientation(other).as_axis_angle(pair=True)[1]
 
         return 2.*np.arccos(np.clip(trace_max[...,0].round(15),None,1.))
 
 
     def average(self: MyType,                                                                       # type: ignore[override]
                 weights: Optional[FloatSequence] = None,
-                return_cloud: bool = False) -> Union[MyType, AverageTuple]:
+                return_cloud: Optional[bool] = False) -> Union[MyType, AverageTuple]:
         """
         Return orientation average over last dimension.
 
@@ -1512,7 +1536,7 @@ def IPF_color(self,
             raise ValueError('input is not a field of three-dimensional vectors')
 
         vector_:np.ndarray = self.to_SST(vector,proper) if in_SST else \
-                             self @ np.broadcast_to(vector,self.shape+(3,))                         #type: ignore
+                             self @ np.broadcast_to(vector,self.shape+(3,))
 
         if self.standard_triangle is None:                                                          # direct exit for no symmetry
             return np.zeros_like(vector_)
@@ -1533,7 +1557,7 @@ def IPF_color(self,
                                              np.broadcast_to(self.standard_triangle['improper'], vector_.shape+(3,)),
                                              np.block([vector_[...,:2],np.abs(vector_[...,2:3])])), 12)
 
-            in_SST_ = np.all(components >= 0.0,axis=-1)                                             #type: ignore
+            in_SST_ = np.all(components >= 0.0,axis=-1)
 
         with np.errstate(invalid='ignore',divide='ignore'):
             rgb = (components/np.linalg.norm(components,axis=-1,keepdims=True))**(1./3.)            # smoothen color ramps
@@ -1719,7 +1743,7 @@ def related(self: MyType,
         """
         lattice,o = self.relation_operations(model,target)
         target = Crystal(lattice=lattice) if target is None else target
-        return Orientation(rotation=o*Rotation(self.quaternion)[np.newaxis,...],                    # type: ignore
+        return Orientation(rotation=o*Rotation(self.quaternion)[np.newaxis,...],                    # type: ignore[return-value]
                            lattice=target.lattice,
                            a=target.a,
                            b=target.b,