Merge remote-tracking branch 'origin/development' into polishing

PRIVATE

@@ -1 +1 @@
-Subproject commit 5c10f4a5b00c67382d7b02ec1f1f1da8b203bb4a
+Subproject commit 8fc3c44f533f5addbea8a787239627cb850206ac

VERSION

@@ -1 +1 @@
-v3.0.0-alpha3-235-gdee255ae7
+v3.0.0-alpha3-252-g723737c99

python/damask/_grid.py

@@ -32,7 +32,8 @@ class Grid:
         Parameters
         ----------
         material : numpy.ndarray of shape (:,:,:)
-            Material indices.
+            Material indices. The shape of the material array defines
+            the number of cells.
         size : list or numpy.ndarray of shape (3)
             Physical size of grid in meter.
         origin : list or numpy.ndarray of shape (3), optional

python/damask/_result.py

@@ -1437,7 +1437,7 @@ class Result:
 
                 topology = ET.SubElement(grid, 'Topology')
                 topology.attrib = {'TopologyType': '3DCoRectMesh',
-                                   'Dimensions':   '{} {} {}'.format(*(self.cells+1))}
+                                   'Dimensions':   '{} {} {}'.format(*(self.cells[::-1]+1))}
 
                 geometry = ET.SubElement(grid, 'Geometry')
                 geometry.attrib = {'GeometryType':'Origin_DxDyDz'}
@@ -1446,13 +1446,13 @@ class Result:
                 origin.attrib = {'Format':     'XML',
                                  'NumberType': 'Float',
                                  'Dimensions': '3'}
-                origin.text = "{} {} {}".format(*self.origin)
+                origin.text = "{} {} {}".format(*self.origin[::-1])
 
                 delta = ET.SubElement(geometry, 'DataItem')
                 delta.attrib = {'Format':     'XML',
                                 'NumberType': 'Float',
                                 'Dimensions': '3'}
-                delta.text="{} {} {}".format(*(self.size/self.cells))
+                delta.text="{} {} {}".format(*(self.size/self.cells)[::-1])
 
                 attributes.append(ET.SubElement(grid, 'Attribute'))
                 attributes[-1].attrib = {'Name':          'u / m',
@@ -1461,7 +1461,7 @@ class Result:
                 data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
                 data_items[-1].attrib = {'Format':     'HDF',
                                          'Precision':  '8',
-                                         'Dimensions': '{} {} {} 3'.format(*(self.cells+1))}
+                                         'Dimensions': '{} {} {} 3'.format(*(self.cells[::-1]+1))}
                 data_items[-1].text = f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
 
                 for ty in ['phase','homogenization']:
@@ -1483,7 +1483,7 @@ class Result:
                                 data_items[-1].attrib = {'Format':     'HDF',
                                                          'NumberType': number_type_map(dtype),
                                                          'Precision':  f'{dtype.itemsize}',
-                                                         'Dimensions': '{} {} {} {}'.format(*self.cells,1 if shape == () else
+                                                         'Dimensions': '{} {} {} {}'.format(*self.cells[::-1],1 if shape == () else
                                                                                                         np.prod(shape))}
                                 data_items[-1].text = f'{os.path.split(self.fname)[1]}:{name}'
 
@@ -1516,10 +1516,9 @@ class Result:
         Export to VTK cell/point data.
 
         One VTK file per visible increment is created.
-        For cell data, the VTK format is a image data (.vti) for
+        For point data, the VTK format is poly data (.vtp).
-        grid-based simulations and an unstructured grid (.vtu) for
+        For cell data, either an image (.vti) or unstructured (.vtu) dataset
-        mesh-baed simulations. For point data, the VTK format is poly
+        is written for grid-based or mesh-based simulations, respectively.
-        data (.vtp).
 
         Parameters
         ----------
@@ -1539,7 +1538,7 @@ class Result:
             Fill value for non-existent entries of integer type.
             Defaults to 0.
         parallel : bool
-            Write out VTK files in parallel in a separate background process.
+            Write VTK files in parallel in a separate background process.
             Defaults to True.
 
         """

python/tests/test_Result.py

@@ -8,6 +8,7 @@ import hashlib
 from datetime import datetime
 
 import pytest
+import vtk
 import numpy as np
 
 from damask import Result
@@ -404,7 +405,7 @@ class TestResult:
         os.chdir(tmp_path)
         single_phase.export_VTK(mode=mode)
 
-    def test_XDMF(self,tmp_path,single_phase,update,ref_path):
+    def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
         for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
             for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
                  single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
@@ -413,8 +414,35 @@ class TestResult:
         single_phase.export_XDMF()
         if update:
             shutil.copy(tmp_path/fname,ref_path/fname)
+
         assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read())           # XML is not ordered
 
+    @pytest.mark.skipif(not hasattr(vtk,'vtkXdmfReader'),reason='https://discourse.vtk.org/t/2450')
+    def test_XDMF_shape(self,tmp_path,single_phase):
+        os.chdir(tmp_path)
+
+        single_phase.export_XDMF()
+        fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
+        reader_xdmf = vtk.vtkXdmfReader()
+        reader_xdmf.SetFileName(fname)
+        reader_xdmf.Update()
+        dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
+        bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
+
+        single_phase.view('increments',0).export_VTK()
+        fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
+        for i in range(10):                                                                         # waiting for parallel IO
+            reader_vti = vtk.vtkXMLImageDataReader()
+            reader_vti.SetFileName(fname)
+            reader_vti.Update()
+            dim_vti = reader_vti.GetOutput().GetDimensions()
+            bounds_vti = reader_vti.GetOutput().GetBounds()
+            if dim_vti == dim_xdmf and bounds_vti == bounds_xdmf:
+                return
+            time.sleep(.5)
+
+        assert False
+
     def test_XDMF_invalid(self,default):
         with pytest.raises(TypeError):
             default.export_XDMF()

src/discretization.f90

@@ -80,8 +80,8 @@ subroutine discretization_results
 
   call results_closeGroup(results_addGroup('current/geometry'))
 
-  u = discretization_NodeCoords (1:3,:discretization_sharedNodesBegin) &
+  u = discretization_NodeCoords (:,:discretization_sharedNodesBegin) &
-    - discretization_NodeCoords0(1:3,:discretization_sharedNodesBegin)
+    - discretization_NodeCoords0(:,:discretization_sharedNodesBegin)
   call results_writeDataset(u,'current/geometry','u_n','displacements of the nodes','m')
 
   u = discretization_IPcoords &

src/mesh/FEM_quadrature.f90

@@ -226,6 +226,7 @@ pure function permutationStar111(point) result(qPt)
 
   temp(:,1) = [point(1), point(2), 1.0_pReal - point(1) - point(2)]
   temp(:,2) = [point(1), 1.0_pReal - point(1) - point(2), point(2)]
+  temp(:,3) = [point(2), point(1), 1.0_pReal - point(1) - point(2)]
   temp(:,4) = [point(2), 1.0_pReal - point(1) - point(2), point(1)]
   temp(:,5) = [1.0_pReal - point(1) - point(2), point(2), point(1)]
   temp(:,6) = [1.0_pReal - point(1) - point(2), point(1), point(2)]

src/mesh/discretization_mesh.f90

@@ -146,10 +146,9 @@ subroutine discretization_mesh_init(restart)
 ! Get initial nodal coordinates
   call DMGetCoordinates(geomMesh,coords_node0,ierr)
   CHKERRQ(ierr)
-  allocate(mesh_node0_temp(dimPlex*mesh_Nnodes))
   call VecGetArrayF90(coords_node0, mesh_node0_temp,ierr)
   CHKERRQ(ierr)
-  
+
   mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
 
   call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
@@ -166,7 +165,8 @@ subroutine discretization_mesh_init(restart)
   if (debug_ip < 1 .or. debug_ip > mesh_maxNips)            call IO_error(602,ext_msg='IP')
 
   allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
-  mesh_node0 = reshape(mesh_node0_temp,[dimPlex,mesh_Nnodes])
+  mesh_node0(1:dimPlex,:) = reshape(mesh_node0_temp,[dimPlex,mesh_Nnodes])
+
 
   call discretization_init(materialAt,&
                            reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &