def CreateXdmfSpatialGrid(h5_model_part):
"""Return an XDMF Grid object corresponding to a mesh in an HDF5 file.
Keyword arguments:
h5_model_part -- the HDF5 group containing the model part
Expects:
- element connectivities in h5_model_part["Xdmf/Elements/<element-name>"].
Each connectivities has attributes "Dimension" and "NumberOfNodes". For
example, "Element2D3N" has "Dimension" 2 and "NumberOfNodes" 3. The
connectivities differ from the normal mdpa connectivities in that they
directly index the array of nodal coordinates. Currently there is
no other way to post-process the mesh with Xdmf.
See:
- core.operations.ModelPartOutput,
- core.operations.PartitionedModelPartOutput,
- RenumberConnectivitiesForXdmf.
"""
sgrid = SpatialGrid()
geom = Geometry(HDF5UniformDataItem(
h5_model_part["Nodes/Local/Coordinates"]))
for name, value in h5_model_part["Xdmf/Elements"].items():
cell_type = TopologyCellType(
value.attrs["Dimension"], value.attrs["NumberOfNodes"])
connectivities = HDF5UniformDataItem(value["Connectivities"])
topology = UniformMeshTopology(cell_type, connectivities)
sgrid.add_grid(UniformGrid(name, geom, topology))
return sgrid
def CreateXdmfSpatialGrid(h5_model_part):
"""Return an XDMF Grid object corresponding to a mesh in an HDF5 file.
Keyword arguments:
h5_model_part -- the HDF5 group containing the model part
Expects:
- element connectivities in h5_model_part["Xdmf/Elements/<element-name>"].
Each connectivities has attributes "Dimension" and "NumberOfNodes". For
example, "Element2D3N" has "Dimension" 2 and "NumberOfNodes" 3. The
connectivities differ from the normal mdpa connectivities in that they
directly index the array of nodal coordinates. Currently there is
no other way to post-process the mesh with Xdmf.
See:
- core.operations.ModelPartOutput,
- core.operations.PartitionedModelPartOutput,
- RenumberConnectivitiesForXdmf.
"""
sgrid = SpatialGrid()
geom = Geometry(
HDF5UniformDataItem(h5_model_part["Nodes/Local/Coordinates"]))
spatial_grids_list = []
GetListOfSpatialGrids(spatial_grids_list, h5_model_part["Xdmf"],
"RootModelPart")
for spatial_grid in spatial_grids_list:
spatial_grid_location = spatial_grid[0]
spatial_grid_name = spatial_grid[1]
current_h5_item = h5_model_part[spatial_grid_location]
if (isinstance(current_h5_item, h5py.Dataset)):
cell_type = TopologyCellType(3, 1)
points = HDF5UniformDataItem(current_h5_item)
topology = UniformMeshTopology(cell_type, points)
sgrid.add_grid(
UniformGrid(spatial_grid_name + "." + name, geom, topology))
KratosMultiphysics.Logger.PrintInfo(
"XDMF", "Added " + spatial_grid_name + " spatial grid.")
else:
for name, value in current_h5_item.items():
cell_type = TopologyCellType(value.attrs["Dimension"],
value.attrs["NumberOfNodes"])
connectivities = HDF5UniformDataItem(value["Connectivities"])
topology = UniformMeshTopology(cell_type, connectivities)
sgrid.add_grid(
UniformGrid(spatial_grid_name + "." + name, geom,
topology))
KratosMultiphysics.Logger.PrintInfo(
"XDMF", "Added " + spatial_grid_name + "." + name +
" spatial grid.")
return sgrid
def CreateXdmfTemporalGridFromMultifile(list_of_h5_files, h5path_to_mesh,
h5path_to_results):
"""Return an XDMF Grid object for a list of temporal results in HDF5 files.
Keyword arguments:
list_of_h5_files -- the list of HDF5 files to be parsed
h5path_to_mesh -- the internal HDF5 file path to the mesh
h5path_to_results -- the internal HDF5 file path to the results
Expects:
- each file corresponds to a separate time step
- the first file includes a mesh. Subsequent files may include their own
meshes. If a file does not contain a mesh, it is assumed to have the
same mesh as the most recent file containing a mesh.
- meshes include XDMF mesh connectivities under the internal HDF5 file path
"<h5path_to_mesh>/Xdmf". If XDMF connectivities are not found, the file is
skipped. See RenumberConnectivitiesForXdmf.
- file names contain their time step as a substring. Optionally the first
file may omit the time step in which case it is assumed to be zero.
If a file cannot be opened, it is skipped.
"""
tgrid = TemporalGrid()
for path in list_of_h5_files:
with TryOpenH5File(path, "r") as file_:
if not file_:
continue
if h5path_to_mesh in file_:
if not "Xdmf" in file_[h5path_to_mesh]:
continue
sgrid = CreateXdmfSpatialGrid(file_[h5path_to_mesh])
current_sgrid = SpatialGrid()
for g in sgrid.grids:
current_sgrid.add_grid(
UniformGrid(g.name, g.geometry, g.topology))
if h5path_to_results in file_:
for result in XdmfResults(file_[h5path_to_results]):
current_sgrid.add_attribute(result)
time_label = TimeLabel(path)
if time_label == "":
time_label = "0.0"
tgrid.add_grid(Time(time_label), current_sgrid)
return tgrid
def CreateXdmfTemporalGridFromSinglefile(h5_file_name, h5path_pattern_to_mesh,
h5path_pattern_to_results):
"""Return an XDMF Grid object for a list of temporal results in a single HDF5 file.
Keyword arguments:
h5_file_name -- the HDF5 file to be parsed
h5path_pattern_to_mesh -- the internal HDF5 file path pattern to the mesh [ only <step> flag is supported ]
h5path_pattern_to_results -- the internal HDF5 file path pattern to the results [ only <step> flag is supported ]
Expects:
- In prefixes, <step> flag is used maximum of one time only
- If single mesh description is found, it is considered as single mesh temporal output
"""
tgrid = TemporalGrid()
h5path_pattern_to_mesh_wild_cards = h5path_pattern_to_mesh.replace(
"<step>", "\d*")
h5path_patterns_to_mesh = h5path_pattern_to_mesh.split("<step>")
if (len(h5path_patterns_to_mesh) > 2):
raise RuntimeError("'<step>' flag can only be used once in a prefix")
h5path_pattern_to_results_wild_cards = h5path_pattern_to_results.replace(
"<step>", "\d*")
h5path_patterns_to_results = h5path_pattern_to_results.split("<step>")
if (len(h5path_patterns_to_results) > 2):
raise RuntimeError("'<step>' flag can only be used once in a prefix")
renumbering_mesh_paths = []
with TryOpenH5File(h5_file_name, "r") as file_:
if not file_:
raise RuntimeError(
"Unsupported h5 file provided [ file_name = {:s} ].".format(
h5_file_name))
output_meshes_dict = {}
file_.visit(lambda x: GetMatchingGroupNames(
output_meshes_dict, x, h5path_patterns_to_mesh,
h5path_pattern_to_mesh_wild_cards))
for _, v in output_meshes_dict.items():
if "Xdmf" not in file_[v]:
renumbering_mesh_paths.append(v)
if len(output_meshes_dict.keys()) == 0:
raise RuntimeError(
"No grid information is found in the given hdf5 file matching the given pattern [ file_name = {:s}, pattern = {:s} ]."
.format(h5_file_name, h5path_pattern_to_mesh))
# renumber xdmf connectivities
for v in renumbering_mesh_paths:
KratosHDF5.HDF5XdmfConnectivitiesWriterProcess(h5_file_name,
v).Execute()
with TryOpenH5File(h5_file_name, "r") as file_:
output_results_dict = {}
file_.visit(lambda x: GetMatchingGroupNames(
output_results_dict, x, h5path_patterns_to_results,
h5path_pattern_to_results_wild_cards))
if len(output_results_dict.keys()) == 0:
raise RuntimeError(
"No results data is found in the given hdf5 file matching the given pattern [ file_name = {:s}, pattern = {:s} ]."
.format(h5_file_name, h5path_pattern_to_results))
for k, v in output_results_dict.items():
if k in output_meshes_dict:
sgrid = CreateXdmfSpatialGrid(file_[output_meshes_dict[k]])
current_sgrid = SpatialGrid()
for g in sgrid.grids:
current_sgrid.add_grid(
UniformGrid(g.name, g.geometry, g.topology))
for result in XdmfResults(file_[v]):
current_sgrid.add_attribute(result)
tgrid.add_grid(Time(k), current_sgrid)
return tgrid