Merge remote-tracking branch 'origin/development' into polishing
This commit is contained in:
Martin Diehl
commit
abd660e62d
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit 5c10f4a5b00c67382d7b02ec1f1f1da8b203bb4a
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Subproject commit 8fc3c44f533f5addbea8a787239627cb850206ac
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@ -32,7 +32,8 @@ class Grid:
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Parameters
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----------
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material : numpy.ndarray of shape (:,:,:)
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Material indices.
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Material indices. The shape of the material array defines
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the number of cells.
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size : list or numpy.ndarray of shape (3)
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Physical size of grid in meter.
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origin : list or numpy.ndarray of shape (3), optional
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@ -1437,7 +1437,7 @@ class Result:
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topology = ET.SubElement(grid, 'Topology')
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topology.attrib = {'TopologyType': '3DCoRectMesh',
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'Dimensions': '{} {} {}'.format(*(self.cells+1))}
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'Dimensions': '{} {} {}'.format(*(self.cells[::-1]+1))}
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geometry = ET.SubElement(grid, 'Geometry')
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geometry.attrib = {'GeometryType':'Origin_DxDyDz'}
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@ -1446,13 +1446,13 @@ class Result:
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origin.attrib = {'Format': 'XML',
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'NumberType': 'Float',
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'Dimensions': '3'}
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origin.text = "{} {} {}".format(*self.origin)
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origin.text = "{} {} {}".format(*self.origin[::-1])
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delta = ET.SubElement(geometry, 'DataItem')
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delta.attrib = {'Format': 'XML',
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'NumberType': 'Float',
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'Dimensions': '3'}
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delta.text="{} {} {}".format(*(self.size/self.cells))
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delta.text="{} {} {}".format(*(self.size/self.cells)[::-1])
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attributes.append(ET.SubElement(grid, 'Attribute'))
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attributes[-1].attrib = {'Name': 'u / m',
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@ -1461,7 +1461,7 @@ class Result:
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data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
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data_items[-1].attrib = {'Format': 'HDF',
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'Precision': '8',
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'Dimensions': '{} {} {} 3'.format(*(self.cells+1))}
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'Dimensions': '{} {} {} 3'.format(*(self.cells[::-1]+1))}
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data_items[-1].text = f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
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for ty in ['phase','homogenization']:
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@ -1483,7 +1483,7 @@ class Result:
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data_items[-1].attrib = {'Format': 'HDF',
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'NumberType': number_type_map(dtype),
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'Precision': f'{dtype.itemsize}',
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'Dimensions': '{} {} {} {}'.format(*self.cells,1 if shape == () else
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'Dimensions': '{} {} {} {}'.format(*self.cells[::-1],1 if shape == () else
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np.prod(shape))}
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data_items[-1].text = f'{os.path.split(self.fname)[1]}:{name}'
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@ -1516,10 +1516,9 @@ class Result:
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Export to VTK cell/point data.
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One VTK file per visible increment is created.
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For cell data, the VTK format is a image data (.vti) for
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grid-based simulations and an unstructured grid (.vtu) for
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mesh-baed simulations. For point data, the VTK format is poly
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data (.vtp).
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For point data, the VTK format is poly data (.vtp).
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For cell data, either an image (.vti) or unstructured (.vtu) dataset
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is written for grid-based or mesh-based simulations, respectively.
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Parameters
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----------
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@ -1539,7 +1538,7 @@ class Result:
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Fill value for non-existent entries of integer type.
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Defaults to 0.
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parallel : bool
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Write out VTK files in parallel in a separate background process.
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Write VTK files in parallel in a separate background process.
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Defaults to True.
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"""
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@ -8,6 +8,7 @@ import hashlib
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from datetime import datetime
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import pytest
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import vtk
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import numpy as np
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from damask import Result
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@ -404,7 +405,7 @@ class TestResult:
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os.chdir(tmp_path)
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single_phase.export_VTK(mode=mode)
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def test_XDMF(self,tmp_path,single_phase,update,ref_path):
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def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
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for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
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for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
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@ -413,8 +414,35 @@ class TestResult:
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single_phase.export_XDMF()
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if update:
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shutil.copy(tmp_path/fname,ref_path/fname)
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assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read()) # XML is not ordered
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@pytest.mark.skipif(not hasattr(vtk,'vtkXdmfReader'),reason='https://discourse.vtk.org/t/2450')
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def test_XDMF_shape(self,tmp_path,single_phase):
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os.chdir(tmp_path)
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single_phase.export_XDMF()
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
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reader_xdmf = vtk.vtkXdmfReader()
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reader_xdmf.SetFileName(fname)
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reader_xdmf.Update()
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dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
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bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
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single_phase.view('increments',0).export_VTK()
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
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for i in range(10): # waiting for parallel IO
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reader_vti = vtk.vtkXMLImageDataReader()
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reader_vti.SetFileName(fname)
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reader_vti.Update()
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dim_vti = reader_vti.GetOutput().GetDimensions()
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bounds_vti = reader_vti.GetOutput().GetBounds()
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if dim_vti == dim_xdmf and bounds_vti == bounds_xdmf:
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return
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time.sleep(.5)
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assert False
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def test_XDMF_invalid(self,default):
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with pytest.raises(TypeError):
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default.export_XDMF()
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@ -80,8 +80,8 @@ subroutine discretization_results
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call results_closeGroup(results_addGroup('current/geometry'))
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u = discretization_NodeCoords (1:3,:discretization_sharedNodesBegin) &
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- discretization_NodeCoords0(1:3,:discretization_sharedNodesBegin)
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u = discretization_NodeCoords (:,:discretization_sharedNodesBegin) &
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- discretization_NodeCoords0(:,:discretization_sharedNodesBegin)
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call results_writeDataset(u,'current/geometry','u_n','displacements of the nodes','m')
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u = discretization_IPcoords &
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@ -226,6 +226,7 @@ pure function permutationStar111(point) result(qPt)
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temp(:,1) = [point(1), point(2), 1.0_pReal - point(1) - point(2)]
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temp(:,2) = [point(1), 1.0_pReal - point(1) - point(2), point(2)]
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temp(:,3) = [point(2), point(1), 1.0_pReal - point(1) - point(2)]
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temp(:,4) = [point(2), 1.0_pReal - point(1) - point(2), point(1)]
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temp(:,5) = [1.0_pReal - point(1) - point(2), point(2), point(1)]
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temp(:,6) = [1.0_pReal - point(1) - point(2), point(1), point(2)]
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@ -146,10 +146,9 @@ subroutine discretization_mesh_init(restart)
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! Get initial nodal coordinates
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call DMGetCoordinates(geomMesh,coords_node0,ierr)
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CHKERRQ(ierr)
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allocate(mesh_node0_temp(dimPlex*mesh_Nnodes))
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call VecGetArrayF90(coords_node0, mesh_node0_temp,ierr)
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CHKERRQ(ierr)
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mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
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call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
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@ -166,7 +165,8 @@ subroutine discretization_mesh_init(restart)
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if (debug_ip < 1 .or. debug_ip > mesh_maxNips) call IO_error(602,ext_msg='IP')
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allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
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mesh_node0 = reshape(mesh_node0_temp,[dimPlex,mesh_Nnodes])
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mesh_node0(1:dimPlex,:) = reshape(mesh_node0_temp,[dimPlex,mesh_Nnodes])
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call discretization_init(materialAt,&
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reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
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