Merge branch 'development' into compressed-hdf5

.gitlab-ci.yml

@@ -353,7 +353,6 @@ backupData:
     - mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
     - mv $LOCAL_HOME/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
     - mv $LOCAL_HOME/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
-    - mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
   only:
     - development
 

PRIVATE

@@ -1 +1 @@
-Subproject commit a0475c50bfaf6f86f75345754188918a6e9d7134
+Subproject commit fd99d76d1eaa42fd36971ff2f79a59d98534fc27

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-920-gccf1a849f
+v3.0.0-alpha2

processing/post/addCompatibilityMismatch.py

@@ -71,7 +71,7 @@ for name in filenames:
   damask.util.report(scriptName,name)
 
   table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-  grid,size,origin = damask.grid_filters.cellSizeOrigin_coordinates0_point(table.get(options.pos))
+  grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
 
   F = table.get(options.defgrad).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
   nodes = damask.grid_filters.coordinates_node(size,F)

processing/post/addCurl.py

@@ -44,7 +44,7 @@ for name in filenames:
     damask.util.report(scriptName,name)
 
     table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    grid,size,origin = damask.grid_filters.cellSizeOrigin_coordinates0_point(table.get(options.pos))
+    grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
 
     for label in options.labels:
         field = table.get(label)

processing/post/addDisplacement.py

@@ -48,7 +48,7 @@ for name in filenames:
     damask.util.report(scriptName,name)
 
     table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    grid,size,origin = damask.grid_filters.cellSizeOrigin_coordinates0_point(table.get(options.pos))
+    grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
 
     F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
     if options.nodal:

processing/post/addDivergence.py

@@ -44,7 +44,7 @@ for name in filenames:
     damask.util.report(scriptName,name)
 
     table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    grid,size,origin = damask.grid_filters.cellSizeOrigin_coordinates0_point(table.get(options.pos))
+    grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
 
     for label in options.labels:
         field = table.get(label)

processing/post/addEuclideanDistance.py

@@ -143,7 +143,7 @@ for name in filenames:
     damask.util.report(scriptName,name)
 
     table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    grid,size,origin = damask.grid_filters.cellSizeOrigin_coordinates0_point(table.get(options.pos))
+    grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
 
     neighborhood = neighborhoods[options.neighborhood]
     diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')

processing/post/addGradient.py

@@ -44,7 +44,7 @@ for name in filenames:
     damask.util.report(scriptName,name)
 
     table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    grid,size,origin = damask.grid_filters.cellSizeOrigin_coordinates0_point(table.get(options.pos))
+    grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
 
     for label in options.labels:
         field = table.get(label)

python/damask/_grid.py

@@ -302,7 +302,7 @@ class Grid:
             Each unique combintation of values results in one material ID.
 
         """
-        cells,size,origin = grid_filters.cellSizeOrigin_coordinates0_point(table.get(coordinates))
+        cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
 
         labels_ = [labels] if isinstance(labels,str) else labels
         unique,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)

python/damask/_rotation.py

@@ -763,7 +763,7 @@ class Rotation:
         def _dg(eu,deg):
             """Return infinitesimal Euler space volume of bin(s)."""
             phi_sorted = eu[np.lexsort((eu[:,0],eu[:,1],eu[:,2]))]
-            steps,size,_ = grid_filters.cellSizeOrigin_coordinates0_point(phi_sorted)
+            steps,size,_ = grid_filters.cellsSizeOrigin_coordinates0_point(phi_sorted)
             delta = np.radians(size/steps) if deg else size/steps
             return delta[0]*2.0*np.sin(delta[1]/2.0)*delta[2] / 8.0 / np.pi**2 * np.sin(np.radians(eu[:,1]) if deg else eu[:,1])
 

python/damask/grid_filters.py

@@ -208,7 +208,7 @@ def coordinates_point(size,F,origin=_np.zeros(3)):
     return coordinates0_point(F.shape[:3],size,origin) + displacement_point(size,F)
 
 
-def cellSizeOrigin_coordinates0_point(coordinates0,ordered=True):
+def cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True):
     """
     Return grid 'DNA', i.e. cells, size, and origin from 1D array of point positions.
 
@@ -218,6 +218,7 @@ def cellSizeOrigin_coordinates0_point(coordinates0,ordered=True):
         Undeformed cell coordinates.
     ordered : bool, optional
         Expect coordinates0 data to be ordered (x fast, z slow).
+        Defaults to True.
 
     """
     coords    = [_np.unique(coordinates0[:,i]) for i in range(3)]
@@ -242,7 +243,7 @@ def cellSizeOrigin_coordinates0_point(coordinates0,ordered=True):
     if not (_np.allclose(coords[0],_np.linspace(start[0],end[0],cells[0]),atol=atol) and \
             _np.allclose(coords[1],_np.linspace(start[1],end[1],cells[1]),atol=atol) and \
             _np.allclose(coords[2],_np.linspace(start[2],end[2],cells[2]),atol=atol)):
-        raise ValueError('Regular cells spacing violated.')
+        raise ValueError('Regular cell spacing violated.')
 
     if ordered and not _np.allclose(coordinates0.reshape(tuple(cells)+(3,),order='F'),
                                     coordinates0_point(cells,size,origin),atol=atol):
@@ -261,7 +262,7 @@ def coordinates0_check(coordinates0):
         Array of undeformed cell coordinates.
 
     """
-    cellSizeOrigin_coordinates0_point(coordinates0,ordered=True)
+    cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True)
 
 
 def coordinates0_node(cells,size,origin=_np.zeros(3)):
@@ -296,7 +297,7 @@ def displacement_fluct_node(size,F):
         Deformation gradient field.
 
     """
-    return point_2_node(displacement_fluct_point(size,F))
+    return point_to_node(displacement_fluct_point(size,F))
 
 
 def displacement_avg_node(size,F):
@@ -347,7 +348,7 @@ def coordinates_node(size,F,origin=_np.zeros(3)):
     return coordinates0_node(F.shape[:3],size,origin) + displacement_node(size,F)
 
 
-def point_2_node(cell_data):
+def point_to_node(cell_data):
     """Interpolate periodic point data to nodal data."""
     n = (  cell_data + _np.roll(cell_data,1,(0,1,2))
          + _np.roll(cell_data,1,(0,))  + _np.roll(cell_data,1,(1,))  + _np.roll(cell_data,1,(2,))
@@ -365,7 +366,7 @@ def node_2_point(node_data):
     return c[1:,1:,1:]
 
 
-def cellSizeOrigin_coordinates0_node(coordinates0,ordered=True):
+def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
     """
     Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
 
@@ -375,6 +376,7 @@ def cellSizeOrigin_coordinates0_node(coordinates0,ordered=True):
         Undeformed nodal coordinates.
     ordered : bool, optional
         Expect coordinates0 data to be ordered (x fast, z slow).
+        Defaults to True.
 
     """
     coords    = [_np.unique(coordinates0[:,i]) for i in range(3)]
@@ -391,7 +393,7 @@ def cellSizeOrigin_coordinates0_node(coordinates0,ordered=True):
     if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],cells[0]+1),atol=atol) and \
             _np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],cells[1]+1),atol=atol) and \
             _np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],cells[2]+1),atol=atol)):
-        raise ValueError('Regular cells spacing violated.')
+        raise ValueError('Regular cell spacing violated.')
 
     if ordered and not _np.allclose(coordinates0.reshape(tuple(cells+1)+(3,),order='F'),
                                     coordinates0_node(cells,size,origin),atol=atol):
@@ -400,9 +402,9 @@ def cellSizeOrigin_coordinates0_node(coordinates0,ordered=True):
     return (cells,size,origin)
 
 
-def regrid(size,F,cells_new):
+def regrid(size,F,cells):
     """
-    Return mapping from coordinates in deformed configuration to a regular cells.
+    Return mapping from coordinates in deformed configuration to a regular grid.
 
     Parameters
     ----------
@@ -410,13 +412,11 @@ def regrid(size,F,cells_new):
         Physical size.
     F : numpy.ndarray of shape (:,:,:,3,3)
         Deformation gradient field.
-    cells_new : numpy.ndarray of shape (3)
+    cells : numpy.ndarray of shape (3)
-        New cells for undeformed coordinates.
+        Cell count along x,y,z of remapping grid.
 
     """
-    c = coordinates0_point(F.shape[:3],size) \
+    c = coordinates_point(size,F)
-      + displacement_avg_point(size,F) \
-      + displacement_fluct_point(size,F)
 
     outer = _np.dot(_np.average(F,axis=(0,1,2)),size)
     for d in range(3):
@@ -424,4 +424,4 @@ def regrid(size,F,cells_new):
         c[_np.where(c[:,:,:,d]>outer[d])] -= outer[d]
 
     tree = _spatial.cKDTree(c.reshape(-1,3),boxsize=outer)
-    return tree.query(coordinates0_point(cells_new,outer))[1].flatten()
+    return tree.query(coordinates0_point(cells,outer))[1].flatten()

python/damask/seeds.py

@@ -18,8 +18,8 @@ def from_random(size,N_seeds,cells=None,rng_seed=None):
     N_seeds : int
         Number of seeds.
     cells : numpy.ndarray of shape (3), optional.
-        If given, ensures that all seeds initiate one grain if using a
+        If given, ensures that each seed results in a grain when a standard Voronoi
-        standard Voronoi tessellation.
+        tessellation is performed using the given grid resolution (i.e. size/cells).
     rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
         A seed to initialize the BitGenerator. Defaults to None.
         If None, then fresh, unpredictable entropy will be pulled from the OS.
@@ -51,7 +51,7 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
     distance : float
         Minimum acceptable distance to other seeds.
     periodic : boolean, optional
-        Calculate minimum distance for periodically repeated cells.
+        Calculate minimum distance for periodically repeated grid.
     rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
         A seed to initialize the BitGenerator. Defaults to None.
         If None, then fresh, unpredictable entropy will be pulled from the OS.

python/tests/test_grid_filters.py

@@ -26,12 +26,12 @@ class TestGridFilters:
 
     @pytest.mark.parametrize('mode',['point','node'])
     def test_grid_DNA(self,mode):
-         """Ensure that cellSizeOrigin_coordinates0_xx is the inverse of coordinates0_xx."""
+         """Ensure that cellsSizeOrigin_coordinates0_xx is the inverse of coordinates0_xx."""
          cells   = np.random.randint(8,32,(3))
          size   = np.random.random(3)
          origin = np.random.random(3)
          coord0 = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)')                     # noqa
-         _cells,_size,_origin = eval(f'grid_filters.cellSizeOrigin_coordinates0_{mode}(coord0.reshape(-1,3,order="F"))')
+         _cells,_size,_origin = eval(f'grid_filters.cellsSizeOrigin_coordinates0_{mode}(coord0.reshape(-1,3,order="F"))')
          assert np.allclose(cells,_cells) and np.allclose(size,_size) and np.allclose(origin,_origin)
 
     def test_displacement_fluct_equivalence(self):
@@ -40,14 +40,14 @@ class TestGridFilters:
          cells = np.random.randint(8,32,(3))
          F    = np.random.random(tuple(cells)+(3,3))
          assert np.allclose(grid_filters.displacement_fluct_node(size,F),
-                            grid_filters.point_2_node(grid_filters.displacement_fluct_point(size,F)))
+                            grid_filters.point_to_node(grid_filters.displacement_fluct_point(size,F)))
 
     def test_interpolation_to_node(self):
          size = np.random.random(3)
          cells = np.random.randint(8,32,(3))
          F    = np.random.random(tuple(cells)+(3,3))
          assert np.allclose(grid_filters.coordinates_node(size,F) [1:-1,1:-1,1:-1],
-                            grid_filters.point_2_node(grid_filters.coordinates_point(size,F))[1:-1,1:-1,1:-1])
+                            grid_filters.point_to_node(grid_filters.coordinates_point(size,F))[1:-1,1:-1,1:-1])
 
     def test_interpolation_to_cell(self):
          cells = np.random.randint(1,30,(3))
@@ -94,15 +94,15 @@ class TestGridFilters:
          assert np.allclose(function(size,F),0.0)
 
     @pytest.mark.parametrize('function',[grid_filters.coordinates0_check,
-                                         grid_filters.cellSizeOrigin_coordinates0_node,
+                                         grid_filters.cellsSizeOrigin_coordinates0_node,
-                                         grid_filters.cellSizeOrigin_coordinates0_point])
+                                         grid_filters.cellsSizeOrigin_coordinates0_point])
     def test_invalid_coordinates(self,function):
         invalid_coordinates = np.random.random((np.random.randint(12,52),3))
         with pytest.raises(ValueError):
             function(invalid_coordinates)
 
-    @pytest.mark.parametrize('function',[grid_filters.cellSizeOrigin_coordinates0_node,
+    @pytest.mark.parametrize('function',[grid_filters.cellsSizeOrigin_coordinates0_node,
-                                         grid_filters.cellSizeOrigin_coordinates0_point])
+                                         grid_filters.cellsSizeOrigin_coordinates0_point])
     def test_uneven_spaced_coordinates(self,function):
         start = np.random.random(3)
         end   = np.random.random(3)*10. + start
@@ -116,8 +116,8 @@ class TestGridFilters:
 
 
     @pytest.mark.parametrize('mode',[True,False])
-    @pytest.mark.parametrize('function',[grid_filters.cellSizeOrigin_coordinates0_node,
+    @pytest.mark.parametrize('function',[grid_filters.cellsSizeOrigin_coordinates0_node,
-                                         grid_filters.cellSizeOrigin_coordinates0_point])
+                                         grid_filters.cellsSizeOrigin_coordinates0_point])
     def test_unordered_coordinates(self,function,mode):
         origin = np.random.random(3)
         size   = np.random.random(3)*10.+origin