rename: Geom -> Grid

PRIVATE

@@ -1 +1 @@
-Subproject commit fc27bbd6e028aa73545327aebdb206840063e135
+Subproject commit a0475c50bfaf6f86f75345754188918a6e9d7134

processing/pre/geom_fromDREAM3D.py

@@ -65,7 +65,7 @@ if filenames == []: parser.error('no input file specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
+    geom = damask.Grid.load_DREAM3D(name,options.basegroup,options.pointwise)
     damask.util.croak(geom)
 
     geom.save_ASCII(os.path.splitext(name)[0]+'.geom')

processing/pre/geom_fromOsteonGeometry.py

@@ -133,7 +133,7 @@ for i in range(3,np.max(microstructure)):
 
 header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
        + config_header
-geom = damask.Geom(microstructure.reshape(grid),
+geom = damask.Grid(microstructure.reshape(grid),
                    size,-size/2,
                    comments=header)
 damask.util.croak(geom)

processing/pre/geom_grainGrowth.py

@@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   grid_original = geom.cells
   damask.util.croak(geom)
@@ -169,7 +169,7 @@ for name in filenames:
     # undo any changes involving immutable materials
     material = np.where(immutable, material_original,material)
 
-  damask.Geom(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
+  damask.Grid(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
               size      = geom.size,
               origin    = geom.origin,
               comments  = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],

processing/pre/mentat_spectralBox.py

@@ -196,7 +196,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     material = geom.material.flatten(order='F')
 
     cmds = [\

processing/pre/seeds_fromDistribution.py

@@ -91,7 +91,7 @@ class myThread (threading.Thread):
       perturbedSeedsTable.set('pos',coords).save(perturbedSeedsVFile,legacy=True)
 
 #--- do tesselation with perturbed seed file ------------------------------------------------------
-      perturbedGeom = damask.Geom.from_Voronoi_tessellation(options.grid,np.ones(3),coords)
+      perturbedGeom = damask.Grid.from_Voronoi_tessellation(options.grid,np.ones(3),coords)
 
 
 #--- evaluate current seeds file ------------------------------------------------------------------
@@ -210,7 +210,7 @@ baseFile = os.path.splitext(os.path.basename(options.seedFile))[0]
 points = np.array(options.grid).prod().astype('float')
 
 # ----------- calculate target distribution and bin edges
-targetGeom = damask.Geom.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
+targetGeom = damask.Grid.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
 nMaterials = len(np.unique(targetGeom.material))
 targetVolFrac = np.bincount(targetGeom.material.flatten())/targetGeom.cells.prod().astype(np.float)
 target = []
@@ -229,7 +229,7 @@ bestSeedsUpdate = time.time()
 
 # ----------- tessellate initial seed file to get and evaluate geom file
 bestSeedsVFile.seek(0)
-initialGeom = damask.Geom.from_Voronoi_tessellation(options.grid,np.ones(3),initial_seeds)
+initialGeom = damask.Grid.from_Voronoi_tessellation(options.grid,np.ones(3),initial_seeds)
 
 if len(np.unique(targetGeom.material)) != nMaterials:
   damask.util.croak('error. Material count mismatch')

processing/pre/seeds_fromPokes.py

@@ -52,7 +52,7 @@ options.box = np.array(options.box).reshape(3,2)
 
 for name in filenames:
     damask.util.report(scriptName,name)
-    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Grid.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     offset =(np.amin(options.box, axis=1)*geom.cells/geom.size).astype(int)
     box    = np.amax(options.box, axis=1) \

python/damask/__init__.py

@@ -32,7 +32,7 @@ from ._vtk             import VTK              # noqa
 from ._colormap        import Colormap         # noqa
 from ._config          import Config           # noqa
 from ._configmaterial  import ConfigMaterial   # noqa
-from ._geom            import Geom             # noqa
+from ._grid            import Grid             # noqa
 from ._result          import Result           # noqa
 
 

python/damask/_grid.py

@@ -16,21 +16,21 @@ from . import grid_filters
 from . import Rotation
 
 
-class Geom:
+class Grid:
     """Geometry definition for grid solvers."""
 
     def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
         """
-        New geometry definition from array of materials, size, and origin.
+        New grid definition from array of materials, size, and origin.
 
         Parameters
         ----------
         material : numpy.ndarray
             Material index array (3D).
         size : list or numpy.ndarray
-            Physical size of the geometry in meter.
+            Physical size of the grid in meter.
         origin : list or numpy.ndarray, optional
-            Physical origin of the geometry in meter.
+            Physical origin of the grid in meter.
         comments : list of str, optional
             Comment lines.
 
@@ -42,7 +42,7 @@ class Geom:
 
 
     def __repr__(self):
-        """Basic information on geometry definition."""
+        """Basic information on grid definition."""
         return util.srepr([
                f'cells    a b c:  {util.srepr(self.cells, " x ")}',
                f'size     x y z:  {util.srepr(self.size,  " x ")}',
@@ -53,12 +53,12 @@ class Geom:
 
 
     def __copy__(self):
-        """Copy geometry."""
+        """Copy grid."""
         return copy.deepcopy(self)
 
 
     def copy(self):
-        """Copy geometry."""
+        """Copy grid."""
         return self.__copy__()
 
 
@@ -68,8 +68,8 @@ class Geom:
 
         Parameters
         ----------
-        other : Geom
+        other : damask.Grid
-            Geometry to compare self against.
+            Grid to compare self against.
 
         """
         message = []
@@ -117,7 +117,7 @@ class Geom:
 
     @property
     def size(self):
-        """Physical size of geometry in meter."""
+        """Physical size of grid in meter."""
         return self._size
 
     @size.setter
@@ -129,7 +129,7 @@ class Geom:
 
     @property
     def origin(self):
-        """Coordinates of geometry origin in meter."""
+        """Coordinates of grid origin in meter."""
         return self._origin
 
     @origin.setter
@@ -141,7 +141,7 @@ class Geom:
 
     @property
     def comments(self):
-        """Comments/history of geometry."""
+        """Comments, e.g. history of operations."""
         return self._comments
 
     @comments.setter
@@ -157,7 +157,7 @@ class Geom:
 
     @property
     def N_materials(self):
-        """Number of (unique) material indices within geometry."""
+        """Number of (unique) material indices within grid."""
         return np.unique(self.material).size
 
 
@@ -169,8 +169,8 @@ class Geom:
         Parameters
         ----------
         fname : str or or pathlib.Path
-            Geometry file to read.
+            Grid file to read. Valid extension is .vtr, which will be appended
-            Valid extension is .vtr, which will be appended if not given.
+            if not given.
 
         """
         v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
@@ -178,7 +178,7 @@ class Geom:
         cells = np.array(v.vtk_data.GetDimensions())-1
         bbox  = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
 
-        return Geom(material = v.get('material').reshape(cells,order='F'),
+        return Grid(material = v.get('material').reshape(cells,order='F'),
                     size = bbox[1] - bbox[0],
                     origin = bbox[0],
                     comments=comments)
@@ -248,7 +248,7 @@ class Geom:
         if not np.any(np.mod(material,1) != 0.0):                                                   # no float present
             material = material.astype('int') - (1 if material.min() > 0 else 0)
 
-        return Geom(material.reshape(cells,order='F'),size,origin,comments)
+        return Grid(material.reshape(cells,order='F'),size,origin,comments)
 
 
     @staticmethod
@@ -282,7 +282,7 @@ class Geom:
              if point_data is None else \
              np.reshape(f[path.join(root_dir,base_group,point_data,material)],cells.prod())
 
-        return Geom(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
+        return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
 
 
     @staticmethod
@@ -310,7 +310,7 @@ class Geom:
         ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
              np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
 
-        return Geom(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Geom','from_table'))
+        return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','from_table'))
 
 
     @staticmethod
@@ -327,7 +327,7 @@ class Geom:
         cells : int numpy.ndarray of shape (3)
             Number of cells in x,y,z direction.
         size : list or numpy.ndarray of shape (3)
-            Physical size of the geometry in meter.
+            Physical size of the grid in meter.
         seeds : numpy.ndarray of shape (:,3)
             Position of the seed points in meter. All points need to lay within the box.
         weights : numpy.ndarray of shape (seeds.shape[0])
@@ -336,7 +336,7 @@ class Geom:
             Material ID of the seeds.
             Defaults to None, in which case materials are consecutively numbered.
         periodic : Boolean, optional
-            Perform a periodic tessellation. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
 
         """
         if periodic:
@@ -351,7 +351,7 @@ class Geom:
             coords    = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
 
         pool = mp.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
-        result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
+        result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
         pool.close()
         pool.join()
         material_ = np.array(result.get())
@@ -362,9 +362,9 @@ class Geom:
         else:
             material_ = material_.reshape(cells)
 
-        return Geom(material = material_ if material is None else material[material_],
+        return Grid(material = material_ if material is None else material[material_],
                     size     = size,
-                    comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
+                    comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
                    )
 
 
@@ -378,23 +378,23 @@ class Geom:
         cells : int numpy.ndarray of shape (3)
             Number of cells in x,y,z direction.
         size : list or numpy.ndarray of shape (3)
-            Physical size of the geometry in meter.
+            Physical size of the grid in meter.
         seeds : numpy.ndarray of shape (:,3)
             Position of the seed points in meter. All points need to lay within the box.
         material : numpy.ndarray of shape (seeds.shape[0]), optional
             Material ID of the seeds.
             Defaults to None, in which case materials are consecutively numbered.
         periodic : Boolean, optional
-            Perform a periodic tessellation. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
 
         """
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
         KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
         devNull,material_ = KDTree.query(coords)
 
-        return Geom(material = (material_ if material is None else material[material_]).reshape(cells),
+        return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
                     size     = size,
-                    comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
+                    comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
                    )
 
 
@@ -450,7 +450,7 @@ class Geom:
         cells : int numpy.ndarray of shape (3)
             Number of cells in x,y,z direction.
         size : list or numpy.ndarray of shape (3)
-            Physical size of the geometry in meter.
+            Physical size of the grid in meter.
         surface : str
             Type of the minimal surface. See notes for details.
         threshold : float, optional.
@@ -497,9 +497,9 @@ class Geom:
                             periods*2.0*np.pi*(np.arange(cells[1])+0.5)/cells[1],
                             periods*2.0*np.pi*(np.arange(cells[2])+0.5)/cells[2],
                             indexing='ij',sparse=True)
-        return Geom(material = np.where(threshold < Geom._minimal_surface[surface](x,y,z),materials[1],materials[0]),
+        return Grid(material = np.where(threshold < Grid._minimal_surface[surface](x,y,z),materials[1],materials[0]),
                     size     = size,
-                    comments = util.execution_stamp('Geom','from_minimal_surface'),
+                    comments = util.execution_stamp('Grid','from_minimal_surface'),
                    )
 
 
@@ -583,7 +583,7 @@ class Geom:
             Retain original materials within primitive and fill outside.
             Defaults to False.
         periodic : Boolean, optional
-            Repeat primitive over boundaries. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
 
         """
         # radius and center
@@ -604,23 +604,23 @@ class Geom:
         if periodic:                                                                                # translate back to center
             mask = np.roll(mask,((c/self.size-0.5)*self.cells).round().astype(int),(0,1,2))
 
-        return Geom(material = np.where(np.logical_not(mask) if inverse else mask,
+        return Grid(material = np.where(np.logical_not(mask) if inverse else mask,
                                         self.material,
                                         np.nanmax(self.material)+1 if fill is None else fill),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','add_primitive')],
+                    comments = self.comments+[util.execution_stamp('Grid','add_primitive')],
                    )
 
 
     def mirror(self,directions,reflect=False):
         """
-        Mirror geometry along given directions.
+        Mirror grid along given directions.
 
         Parameters
         ----------
         directions : iterable containing str
-            Direction(s) along which the geometry is mirrored.
+            Direction(s) along which the grid is mirrored.
             Valid entries are 'x', 'y', 'z'.
         reflect : bool, optional
             Reflect (include) outermost layers. Defaults to False.
@@ -640,21 +640,21 @@ class Geom:
         if 'z' in directions:
             mat = np.concatenate([mat,mat[:,:,limits[0]:limits[1]:-1]],2)
 
-        return Geom(material = mat,
+        return Grid(material = mat,
                     size     = self.size/self.cells*np.asarray(mat.shape),
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','mirror')],
+                    comments = self.comments+[util.execution_stamp('Grid','mirror')],
                    )
 
 
     def flip(self,directions):
         """
-        Flip geometry along given directions.
+        Flip grid along given directions.
 
         Parameters
         ----------
         directions : iterable containing str
-            Direction(s) along which the geometry is flipped.
+            Direction(s) along which the grid is flipped.
             Valid entries are 'x', 'y', 'z'.
 
         """
@@ -664,26 +664,26 @@ class Geom:
 
         mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
 
-        return Geom(material = mat,
+        return Grid(material = mat,
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','flip')],
+                    comments = self.comments+[util.execution_stamp('Grid','flip')],
                    )
 
 
     def scale(self,cells,periodic=True):
         """
-        Scale geometry to new cells.
+        Scale grid to new cells.
 
         Parameters
         ----------
         cells : numpy.ndarray of shape (3)
             Number of cells in x,y,z direction.
         periodic : Boolean, optional
-            Assume geometry to be periodic. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
 
         """
-        return Geom(material = ndimage.interpolation.zoom(
+        return Grid(material = ndimage.interpolation.zoom(
                                                            self.material,
                                                            cells/self.cells,
                                                            output=self.material.dtype,
@@ -693,13 +693,13 @@ class Geom:
                                                           ),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','scale')],
+                    comments = self.comments+[util.execution_stamp('Grid','scale')],
                    )
 
 
     def clean(self,stencil=3,selection=None,periodic=True):
         """
-        Smooth geometry by selecting most frequent material index within given stencil at each location.
+        Smooth grid by selecting most frequent material index within given stencil at each location.
 
         Parameters
         ----------
@@ -708,7 +708,7 @@ class Geom:
         selection : list, optional
             Field values that can be altered. Defaults to all.
         periodic : Boolean, optional
-            Assume geometry to be periodic. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
 
         """
         def mostFrequent(arr,selection=None):
@@ -719,7 +719,7 @@ class Geom:
             else:
                 return me
 
-        return Geom(material = ndimage.filters.generic_filter(
+        return Grid(material = ndimage.filters.generic_filter(
                                                                self.material,
                                                                mostFrequent,
                                                                size=(stencil if selection is None else stencil//2*2+1,)*3,
@@ -728,7 +728,7 @@ class Geom:
                                                               ).astype(self.material.dtype),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','clean')],
+                    comments = self.comments+[util.execution_stamp('Grid','clean')],
                    )
 
 
@@ -736,21 +736,21 @@ class Geom:
         """Renumber sorted material indices as 0,...,N-1."""
         _,renumbered = np.unique(self.material,return_inverse=True)
 
-        return Geom(material = renumbered.reshape(self.cells),
+        return Grid(material = renumbered.reshape(self.cells),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','renumber')],
+                    comments = self.comments+[util.execution_stamp('Grid','renumber')],
                    )
 
 
     def rotate(self,R,fill=None):
         """
-        Rotate geometry (pad if required).
+        Rotate grid (pad if required).
 
         Parameters
         ----------
         R : damask.Rotation
-            Rotation to apply to the geometry.
+            Rotation to apply to the grid.
         fill : int or float, optional
             Material index to fill the corners. Defaults to material.max() + 1.
 
@@ -774,23 +774,23 @@ class Geom:
 
         origin = self.origin-(np.asarray(material_in.shape)-self.cells)*.5 * self.size/self.cells
 
-        return Geom(material = material_in,
+        return Grid(material = material_in,
                     size     = self.size/self.cells*np.asarray(material_in.shape),
                     origin   = origin,
-                    comments = self.comments+[util.execution_stamp('Geom','rotate')],
+                    comments = self.comments+[util.execution_stamp('Grid','rotate')],
                    )
 
 
     def canvas(self,cells=None,offset=None,fill=None):
         """
-        Crop or enlarge/pad geometry.
+        Crop or enlarge/pad grid.
 
         Parameters
         ----------
         cells : numpy.ndarray of shape (3)
             Number of cells  x,y,z direction.
         offset : numpy.ndarray of shape (3)
-            Offset (measured in cells) from old to new geometry [0,0,0].
+            Offset (measured in cells) from old to new grid [0,0,0].
         fill : int or float, optional
             Material index to fill the background. Defaults to material.max() + 1.
 
@@ -808,10 +808,10 @@ class Geom:
 
         canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
 
-        return Geom(material = canvas,
+        return Grid(material = canvas,
                     size     = self.size/self.cells*np.asarray(canvas.shape),
                     origin   = self.origin+offset*self.size/self.cells,
-                    comments = self.comments+[util.execution_stamp('Geom','canvas')],
+                    comments = self.comments+[util.execution_stamp('Grid','canvas')],
                    )
 
 
@@ -833,10 +833,10 @@ class Geom:
         mp = np.vectorize(mp)
         mapper = dict(zip(from_material,to_material))
 
-        return Geom(material = mp(self.material,mapper).reshape(self.cells),
+        return Grid(material = mp(self.material,mapper).reshape(self.cells),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','substitute')],
+                    comments = self.comments+[util.execution_stamp('Grid','substitute')],
                    )
 
 
@@ -847,10 +847,10 @@ class Geom:
         sort_idx = np.argsort(from_ma)
         ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]
 
-        return Geom(material = ma.reshape(self.cells,order='F'),
+        return Grid(material = ma.reshape(self.cells,order='F'),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','sort')],
+                    comments = self.comments+[util.execution_stamp('Grid','sort')],
                    )
 
 
@@ -860,7 +860,7 @@ class Geom:
 
         Different from themselves (or listed as triggers) within a given (cubic) vicinity,
         i.e. within the region close to a grain/phase boundary.
-        ToDo: use include/exclude as in seeds.from_geom
+        ToDo: use include/exclude as in seeds.from_grid
 
         Parameters
         ----------
@@ -874,7 +874,7 @@ class Geom:
             List of material indices that trigger a change.
             Defaults to [], meaning that any different neighbor triggers a change.
         periodic : Boolean, optional
-            Assume geometry to be periodic. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
 
         """
         def tainted_neighborhood(stencil,trigger):
@@ -891,10 +891,10 @@ class Geom:
                                               mode='wrap' if periodic else 'nearest',
                                               extra_keywords={'trigger':trigger})
 
-        return Geom(material = np.where(mask, self.material + offset_,self.material),
+        return Grid(material = np.where(mask, self.material + offset_,self.material),
                     size     = self.size,
                     origin   = self.origin,
-                    comments = self.comments+[util.execution_stamp('Geom','vicinity_offset')],
+                    comments = self.comments+[util.execution_stamp('Grid','vicinity_offset')],
                    )
 
 
@@ -904,10 +904,10 @@ class Geom:
 
         Parameters
         ----------
-        periodic : bool, optional
+        periodic : Boolean, optional
-            Show boundaries across periodicity. Defaults to True.
+            Assume grid to be periodic. Defaults to True.
         directions : iterable containing str, optional
-            Direction(s) along which the geometry is mirrored.
+            Direction(s) along which the boundaries are determined.
             Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.
 
         """

python/damask/grid_filters.py

@@ -4,7 +4,7 @@ Filters for operations on regular grids.
 Notes
 -----
 The grids are defined as (x,y,z,...) where x is fastest and z is slowest.
-This convention is consistent with the geom file format.
+This convention is consistent with the layout in grid vtr files.
 When converting to/from a plain list (e.g. storage in ASCII table),
 the following operations are required for tensorial data:
 

python/damask/seeds.py

@@ -77,14 +77,14 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
     return coords
 
 
-def from_geom(geom,selection=None,invert=False,average=False,periodic=True):
+def from_grid(grid,selection=None,invert=False,average=False,periodic=True):
     """
-    Create seed from existing geometry description.
+    Create seed from existing grid description.
 
     Parameters
     ----------
-    geom : damask.Geom
+    grid : damask.Grid
-        Geometry, from which the material IDs are used as seeds.
+        Grid, from which the material IDs are used as seeds.
     selection : iterable of integers, optional
         Material IDs to consider.
     invert : boolean, false
@@ -95,10 +95,10 @@ def from_geom(geom,selection=None,invert=False,average=False,periodic=True):
         Center of gravity with periodic boundaries.
 
     """
-    material = geom.material.reshape((-1,1),order='F')
+    material = grid.material.reshape((-1,1),order='F')
-    mask = _np.full(geom.cells.prod(),True,dtype=bool) if selection is None else \
+    mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
            _np.isin(material,selection,invert=invert).flatten()
-    coords = grid_filters.coordinates0_point(geom.cells,geom.size).reshape(-1,3,order='F')
+    coords = grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
 
     if not average:
         return (coords[mask],material[mask])
@@ -106,8 +106,8 @@ def from_geom(geom,selection=None,invert=False,average=False,periodic=True):
         materials = _np.unique(material[mask])
         coords_ = _np.zeros((materials.size,3),dtype=float)
         for i,mat in enumerate(materials):
-            pc = (2*_np.pi*coords[material[:,0]==mat,:]-geom.origin)/geom.size
+            pc = (2*_np.pi*coords[material[:,0]==mat,:]-grid.origin)/grid.size
-            coords_[i] = geom.origin + geom.size / 2 / _np.pi * (_np.pi +
+            coords_[i] = grid.origin + grid.size / 2 / _np.pi * (_np.pi +
                          _np.arctan2(-_np.average(_np.sin(pc),axis=0),
                                      -_np.average(_np.cos(pc),axis=0))) \
                          if periodic else \

python/tests/test_Grid.py

@@ -2,7 +2,7 @@ import pytest
 import numpy as np
 
 from damask import VTK
-from damask import Geom
+from damask import Grid
 from damask import Table
 from damask import Rotation
 from damask import util
@@ -10,7 +10,7 @@ from damask import seeds
 from damask import grid_filters
 
 
-def geom_equal(a,b):
+def grid_equal(a,b):
     return np.all(a.material == b.material) and \
            np.all(a.cells    == b.cells) and \
            np.allclose(a.size, b.size) and \
@@ -23,15 +23,15 @@ def default():
                       np.arange(2,42),
                       np.ones(40,dtype=int)*2,
                       np.arange(1,41))).reshape(8,5,4,order='F')
-    return Geom(x,[8e-6,5e-6,4e-6])
+    return Grid(x,[8e-6,5e-6,4e-6])
 
 @pytest.fixture
 def ref_path(ref_path_base):
     """Directory containing reference results."""
-    return ref_path_base/'Geom'
+    return ref_path_base/'Grid'
 
 
-class TestGeom:
+class TestGrid:
 
     @pytest.fixture(autouse=True)
     def _patch_execution_stamp(self, patch_execution_stamp):
@@ -46,7 +46,7 @@ class TestGeom:
 
 
     def test_diff_not_equal(self,default):
-        new = Geom(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
+        new = Grid(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
         assert str(default.diff(new)) != ''
 
     def test_repr(self,default):
@@ -54,36 +54,36 @@ class TestGeom:
 
     def test_read_write_vtr(self,default,tmp_path):
         default.save(tmp_path/'default')
-        new = Geom.load(tmp_path/'default.vtr')
+        new = Grid.load(tmp_path/'default.vtr')
-        assert geom_equal(new,default)
+        assert grid_equal(new,default)
 
     def test_invalid_vtr(self,tmp_path):
         v = VTK.from_rectilinear_grid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
         v.save(tmp_path/'no_materialpoint.vtr',parallel=False)
         with pytest.raises(ValueError):
-            Geom.load(tmp_path/'no_materialpoint.vtr')
+            Grid.load(tmp_path/'no_materialpoint.vtr')
 
     def test_invalid_material(self):
         with pytest.raises(TypeError):
-            Geom(np.zeros((3,3,3),dtype='complex'),np.ones(3))
+            Grid(np.zeros((3,3,3),dtype='complex'),np.ones(3))
 
     def test_cast_to_int(self):
-        g = Geom(np.zeros((3,3,3)),np.ones(3))
+        g = Grid(np.zeros((3,3,3)),np.ones(3))
         assert g.material.dtype in np.sctypes['int']
 
     def test_invalid_size(self,default):
         with pytest.raises(ValueError):
-            Geom(default.material[1:,1:,1:],
+            Grid(default.material[1:,1:,1:],
                  size=np.ones(2))
 
     def test_save_load_ASCII(self,default,tmp_path):
         default.save_ASCII(tmp_path/'ASCII')
         default.material -= 1
-        assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
+        assert grid_equal(Grid.load_ASCII(tmp_path/'ASCII'),default)
 
     def test_invalid_origin(self,default):
         with pytest.raises(ValueError):
-            Geom(default.material[1:,1:,1:],
+            Grid(default.material[1:,1:,1:],
                  size=np.ones(3),
                  origin=np.ones(4))
 
@@ -91,14 +91,14 @@ class TestGeom:
     def test_invalid_materials_shape(self,default):
         material = np.ones((3,3))
         with pytest.raises(ValueError):
-            Geom(material,
+            Grid(material,
                  size=np.ones(3))
 
 
     def test_invalid_materials_type(self,default):
         material = np.random.randint(1,300,(3,4,5))==1
         with pytest.raises(TypeError):
-            Geom(material)
+            Grid(material)
 
 
     @pytest.mark.parametrize('directions,reflect',[
@@ -113,7 +113,7 @@ class TestGeom:
         tag = f'directions_{"-".join(directions)}+reflect_{reflect}'
         reference = ref_path/f'mirror_{tag}.vtr'
         if update: modified.save(reference)
-        assert geom_equal(Geom.load(reference),
+        assert grid_equal(Grid.load(reference),
                           modified)
 
 
@@ -135,17 +135,17 @@ class TestGeom:
         tag = f'directions_{"-".join(directions)}'
         reference = ref_path/f'flip_{tag}.vtr'
         if update: modified.save(reference)
-        assert geom_equal(Geom.load(reference),
+        assert grid_equal(Grid.load(reference),
                           modified)
 
 
     def test_flip_invariant(self,default):
-        assert geom_equal(default,default.flip([]))
+        assert grid_equal(default,default.flip([]))
 
 
     @pytest.mark.parametrize('direction',[['x'],['x','y']])
     def test_flip_double(self,default,direction):
-        assert geom_equal(default,default.flip(direction).flip(direction))
+        assert grid_equal(default,default.flip(direction).flip(direction))
 
 
     @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
@@ -162,7 +162,7 @@ class TestGeom:
         reference = ref_path/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
         if update and stencil > 1:
             current.save(reference)
-        assert geom_equal(Geom.load(reference) if stencil > 1 else default,
+        assert grid_equal(Grid.load(reference) if stencil > 1 else default,
                           current
                          )
 
@@ -181,7 +181,7 @@ class TestGeom:
         tag = f'grid_{util.srepr(cells,"-")}'
         reference = ref_path/f'scale_{tag}.vtr'
         if update: modified.save(reference)
-        assert geom_equal(Geom.load(reference),
+        assert grid_equal(Grid.load(reference),
                           modified)
 
 
@@ -190,21 +190,21 @@ class TestGeom:
         for m in np.unique(material):
             material[material==m] = material.max() + np.random.randint(1,30)
         default.material -= 1
-        modified = Geom(material,
+        modified = Grid(material,
                         default.size,
                         default.origin)
-        assert not geom_equal(modified,default)
+        assert not grid_equal(modified,default)
-        assert geom_equal(default,
+        assert grid_equal(default,
                           modified.renumber())
 
 
     def test_substitute(self,default):
         offset = np.random.randint(1,500)
-        modified = Geom(default.material + offset,
+        modified = Grid(default.material + offset,
                         default.size,
                         default.origin)
-        assert not geom_equal(modified,default)
+        assert not grid_equal(modified,default)
-        assert geom_equal(default,
+        assert grid_equal(default,
                           modified.substitute(np.arange(default.material.max())+1+offset,
                                               np.arange(default.material.max())+1))
 
@@ -212,12 +212,12 @@ class TestGeom:
         f = np.unique(default.material.flatten())[:np.random.randint(1,default.material.max())]
         t = np.random.permutation(f)
         modified = default.substitute(f,t)
-        assert np.array_equiv(t,f) or (not geom_equal(modified,default))
+        assert np.array_equiv(t,f) or (not grid_equal(modified,default))
-        assert geom_equal(default, modified.substitute(t,f))
+        assert grid_equal(default, modified.substitute(t,f))
 
     def test_sort(self):
         cells = np.random.randint(5,20,3)
-        m = Geom(np.random.randint(1,20,cells)*3,np.ones(3)).sort().material.flatten(order='F')
+        m = Grid(np.random.randint(1,20,cells)*3,np.ones(3)).sort().material.flatten(order='F')
         for i,v in enumerate(m):
             assert i==0 or v > m[:i].max() or v in m[:i]
 
@@ -227,7 +227,7 @@ class TestGeom:
         modified = default.copy()
         for i in range(np.rint(360/axis_angle[3]).astype(int)):
             modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
-        assert geom_equal(default,modified)
+        assert grid_equal(default,modified)
 
 
     @pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
@@ -237,7 +237,7 @@ class TestGeom:
         tag = f'Eulers_{util.srepr(Eulers,"-")}'
         reference = ref_path/f'rotate_{tag}.vtr'
         if update: modified.save(reference)
-        assert geom_equal(Geom.load(reference),
+        assert grid_equal(Grid.load(reference),
                           modified)
 
 
@@ -263,8 +263,8 @@ class TestGeom:
         o = np.random.random(3)-.5
         g = np.random.randint(8,32,(3))
         s = np.random.random(3)+.5
-        G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
+        G_1 = Grid(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
-        G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
+        G_2 = Grid(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
         assert np.count_nonzero(G_1.material!=2) == np.count_nonzero(G_2.material!=2)
 
 
@@ -279,9 +279,9 @@ class TestGeom:
         g = np.random.randint(8,32,(3))
         s = np.random.random(3)+.5
         fill = np.random.randint(10)+2
-        G_1 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
+        G_1 = Grid(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
-        G_2 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,Rotation.from_random(),inverse,periodic=periodic)
+        G_2 = Grid(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,Rotation.from_random(),inverse,periodic=periodic)
-        assert geom_equal(G_1,G_2)
+        assert grid_equal(G_1,G_2)
 
 
     @pytest.mark.parametrize('trigger',[[1],[]])
@@ -300,9 +300,9 @@ class TestGeom:
         if len(trigger) > 0:
             m2[m==1] = 1
 
-        geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
+        grid = Grid(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
 
-        assert np.all(m2==geom.material)
+        assert np.all(m2==grid.material)
 
 
     @pytest.mark.parametrize('periodic',[True,False])
@@ -318,9 +318,9 @@ class TestGeom:
         size   = np.random.random(3) + 1.0
         N_seeds= np.random.randint(10,30)
         seeds  = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
-        Voronoi  = Geom.from_Voronoi_tessellation( cells,size,seeds,                 np.arange(N_seeds)+5,periodic)
+        Voronoi  = Grid.from_Voronoi_tessellation( cells,size,seeds,                 np.arange(N_seeds)+5,periodic)
-        Laguerre = Geom.from_Laguerre_tessellation(cells,size,seeds,np.ones(N_seeds),np.arange(N_seeds)+5,periodic)
+        Laguerre = Grid.from_Laguerre_tessellation(cells,size,seeds,np.ones(N_seeds),np.arange(N_seeds)+5,periodic)
-        assert geom_equal(Laguerre,Voronoi)
+        assert grid_equal(Laguerre,Voronoi)
 
 
     def test_Laguerre_weights(self):
@@ -331,7 +331,7 @@ class TestGeom:
         weights= np.full((N_seeds),-np.inf)
         ms     = np.random.randint(N_seeds)
         weights[ms] = np.random.random()
-        Laguerre = Geom.from_Laguerre_tessellation(cells,size,seeds,weights,periodic=np.random.random()>0.5)
+        Laguerre = Grid.from_Laguerre_tessellation(cells,size,seeds,weights,periodic=np.random.random()>0.5)
         assert np.all(Laguerre.material == ms)
 
 
@@ -343,10 +343,10 @@ class TestGeom:
         material = np.zeros(cells)
         material[:,cells[1]//2:,:] = 1
         if   approach == 'Laguerre':
-            geom = Geom.from_Laguerre_tessellation(cells,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
+            grid = Grid.from_Laguerre_tessellation(cells,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
         elif approach == 'Voronoi':
-            geom = Geom.from_Voronoi_tessellation(cells,size,seeds,            periodic=np.random.random()>0.5)
+            grid = Grid.from_Voronoi_tessellation(cells,size,seeds,            periodic=np.random.random()>0.5)
-        assert np.all(geom.material == material)
+        assert np.all(grid.material == material)
 
 
     @pytest.mark.parametrize('surface',['Schwarz P',
@@ -368,9 +368,9 @@ class TestGeom:
         threshold = 2*np.random.rand()-1.
         periods = np.random.randint(2)+1
         materials = np.random.randint(0,40,2)
-        geom = Geom.from_minimal_surface(cells,size,surface,threshold,periods,materials)
+        grid = Grid.from_minimal_surface(cells,size,surface,threshold,periods,materials)
-        assert set(geom.material.flatten()) | set(materials) == set(materials) \
+        assert set(grid.material.flatten()) | set(materials) == set(materials) \
-               and (geom.size == size).all() and (geom.cells == cells).all()
+               and (grid.size == size).all() and (grid.cells == cells).all()
 
     @pytest.mark.parametrize('surface,threshold',[('Schwarz P',0),
                                         ('Double Primitive',-1./6.),
@@ -387,8 +387,8 @@ class TestGeom:
                                         ])
     def test_minimal_surface_volume(self,surface,threshold):
         cells = np.ones(3,dtype=int)*64
-        geom = Geom.from_minimal_surface(cells,np.ones(3),surface,threshold)
+        grid = Grid.from_minimal_surface(cells,np.ones(3),surface,threshold)
-        assert np.isclose(np.count_nonzero(geom.material==1)/np.prod(geom.cells),.5,rtol=1e-3)
+        assert np.isclose(np.count_nonzero(grid.material==1)/np.prod(grid.cells),.5,rtol=1e-3)
 
 
     def test_from_table(self):
@@ -398,7 +398,7 @@ class TestGeom:
         z=np.ones(cells.prod())
         z[cells[:2].prod()*int(cells[2]/2):]=0
         t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
-        g = Geom.from_table(t,'coords',['1_coords','z'])
+        g = Grid.from_table(t,'coords',['1_coords','z'])
         assert g.N_materials == g.cells[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == cells[0]).all()
 
 
@@ -406,16 +406,16 @@ class TestGeom:
         cells = np.random.randint(60,100,3)
         size = np.ones(3)+np.random.rand(3)
         s = seeds.from_random(size,np.random.randint(60,100))
-        geom = Geom.from_Voronoi_tessellation(cells,size,s)
+        grid = Grid.from_Voronoi_tessellation(cells,size,s)
         coords = grid_filters.coordinates0_point(cells,size)
-        t = Table(np.column_stack((coords.reshape(-1,3,order='F'),geom.material.flatten(order='F'))),{'c':3,'m':1})
+        t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
-        assert geom_equal(geom.sort().renumber(),Geom.from_table(t,'c',['m']))
+        assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
 
     @pytest.mark.parametrize('periodic',[True,False])
     @pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
     def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
-        geom=Geom.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
+        grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
-        current=geom.get_grain_boundaries(periodic,direction)
+        current=grid.get_grain_boundaries(periodic,direction)
         if update:
             current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
         reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')

python/tests/test_seeds.py

@@ -4,7 +4,7 @@ from scipy.spatial import cKDTree
 
 from damask import seeds
 from damask import grid_filters
-from damask import Geom
+from damask import Grid
 
 class TestSeeds:
 
@@ -26,37 +26,37 @@ class TestSeeds:
                        cKDTree(coords).query(coords, 2)
         assert (0<= coords).all() and (coords<size).all() and np.min(min_dists[:,1])>=distance
 
-    def test_from_geom_reconstruct(self):
+    def test_from_grid_reconstruct(self):
         cells = np.random.randint(10,20,3)
         N_seeds = np.random.randint(30,300)
         size = np.ones(3) + np.random.random(3)
         coords = seeds.from_random(size,N_seeds,cells)
-        geom_1 = Geom.from_Voronoi_tessellation(cells,size,coords)
+        grid_1 = Grid.from_Voronoi_tessellation(cells,size,coords)
-        coords,material = seeds.from_geom(geom_1)
+        coords,material = seeds.from_grid(grid_1)
-        geom_2 = Geom.from_Voronoi_tessellation(cells,size,coords,material)
+        grid_2 = Grid.from_Voronoi_tessellation(cells,size,coords,material)
-        assert (geom_2.material==geom_1.material).all()
+        assert (grid_2.material==grid_1.material).all()
 
     @pytest.mark.parametrize('periodic',[True,False])
     @pytest.mark.parametrize('average',[True,False])
-    def test_from_geom_grid(self,periodic,average):
+    def test_from_grid_grid(self,periodic,average):
         cells = np.random.randint(10,20,3)
         size  = np.ones(3) + np.random.random(3)
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
         np.random.shuffle(coords)
-        geom_1 = Geom.from_Voronoi_tessellation(cells,size,coords)
+        grid_1 = Grid.from_Voronoi_tessellation(cells,size,coords)
-        coords,material = seeds.from_geom(geom_1,average=average,periodic=periodic)
+        coords,material = seeds.from_grid(grid_1,average=average,periodic=periodic)
-        geom_2 = Geom.from_Voronoi_tessellation(cells,size,coords,material)
+        grid_2 = Grid.from_Voronoi_tessellation(cells,size,coords,material)
-        assert (geom_2.material==geom_1.material).all()
+        assert (grid_2.material==grid_1.material).all()
 
     @pytest.mark.parametrize('periodic',[True,False])
     @pytest.mark.parametrize('average',[True,False])
     @pytest.mark.parametrize('invert',[True,False])
-    def test_from_geom_selection(self,periodic,average,invert):
+    def test_from_grid_selection(self,periodic,average,invert):
         cells = np.random.randint(10,20,3)
         N_seeds = np.random.randint(30,300)
         size = np.ones(3) + np.random.random(3)
         coords = seeds.from_random(size,N_seeds,cells)
-        geom = Geom.from_Voronoi_tessellation(cells,size,coords)
+        grid = Grid.from_Voronoi_tessellation(cells,size,coords)
         selection=np.random.randint(N_seeds)+1
-        coords,material = seeds.from_geom(geom,average=average,periodic=periodic,invert=invert,selection=[selection])
+        coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert=invert,selection=[selection])
         assert selection not in material if invert else (selection==material).all()