PETSc updates #3997
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| Original file line number | Diff line number | Diff line change |
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@@ -2120,6 +2120,8 @@ def mark_entity_classes_using_cell_dm(PETSc.DM swarm): | |
| PetscInt nswarmCells, swarmCell, blocksize | ||
| PetscInt *swarmParentCells = NULL | ||
| PetscDataType ctype = PETSC_DATATYPE_UNKNOWN | ||
| const char *cellid = NULL | ||
| PETSc.PetscDMSwarmCellDM celldm | ||
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| plex = swarm.getCellDM() | ||
| get_height_stratum(plex.dm, 0, &cStart, &cEnd) | ||
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@@ -2145,14 +2147,16 @@ def mark_entity_classes_using_cell_dm(PETSc.DM swarm): | |
| for ilabel, op2class in enumerate([b"pyop2_core", b"pyop2_owned", b"pyop2_ghost"]): | ||
| CHKERR(DMCreateLabel(swarm.dm, op2class)) | ||
| CHKERR(DMGetLabel(swarm.dm, op2class, &swarm_labels[ilabel])) | ||
| CHKERR(DMSwarmGetCellDMActive(swarm.dm, &celldm)) | ||
| CHKERR(DMSwarmCellDMGetCellID(celldm, &cellid)) | ||
| CHKERR(DMSwarmGetField(swarm.dm, cellid, &blocksize, &ctype, <void**> &swarmParentCells)) | ||
| assert ctype == PETSC_INT | ||
| assert blocksize == 1 | ||
| CHKERR(DMSwarmGetLocalSize(swarm.dm, &nswarmCells)) | ||
| for swarmCell in range(nswarmCells): | ||
| plex_cell_class = plex_cell_classes[swarmParentCells[swarmCell] - cStart] | ||
| CHKERR(DMLabelSetValue(swarm_labels[plex_cell_class], swarmCell, label_value)) | ||
| CHKERR(DMSwarmRestoreField(swarm.dm, cellid, &blocksize, &ctype, <void**> &swarmParentCells)) | ||
| CHKERR(PetscFree(plex_cell_classes)) | ||
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@@ -79,6 +79,8 @@ cdef extern from "petscdm.h" nogil: | |
| cdef extern from "petscdmswarm.h" nogil: | ||
| int DMSwarmGetLocalSize(PETSc.PetscDM,PetscInt*) | ||
| int DMSwarmGetCellDM(PETSc.PetscDM, PETSc.PetscDM*) | ||
| int DMSwarmGetCellDMActive(PETSc.PetscDM, PETSc.PetscDMSwarmCellDM*) | ||
| int DMSwarmCellDMGetCellID(PETSc.PetscDMSwarmCellDM, const char *[]) | ||
| int DMSwarmGetField(PETSc.PetscDM,const char[],PetscInt*,PetscDataType*,void**) | ||
| int DMSwarmRestoreField(PETSc.PetscDM,const char[],PetscInt*,PetscDataType*,void**) | ||
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@@ -1966,14 +1966,15 @@ def _renumber_entities(self, reorder): | |
| if reorder: | ||
| swarm = self.topology_dm | ||
| parent = self._parent_mesh.topology_dm | ||
| cell_id_name = swarm.getCellDMActive().getCellID() | ||
| swarm_parent_cell_nums = swarm.getField(cell_id_name).ravel() | ||
| parent_renum = self._parent_mesh._dm_renumbering.getIndices() | ||
| pStart, _ = parent.getChart() | ||
| parent_renum_inv = np.empty_like(parent_renum) | ||
| parent_renum_inv[parent_renum - pStart] = np.arange(len(parent_renum)) | ||
| # Use kind = 'stable' to make the ordering deterministic. | ||
| perm = np.argsort(parent_renum_inv[swarm_parent_cell_nums - pStart], kind='stable').astype(IntType) | ||
| swarm.restoreField(cell_id_name) | ||
| perm_is = PETSc.IS().create(comm=swarm.comm) | ||
| perm_is.setType("general") | ||
| perm_is.setIndices(perm) | ||
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@@ -3557,11 +3558,9 @@ def _pic_swarm_in_mesh( | |
| #. ``parentcellextrusionheight`` which contains the extrusion height of | ||
| the immersed vertex in the parent mesh cell. | ||
| Another two are required for proper functioning of the DMSwarm: | ||
| #. ``DMSwarmPIC_coor`` which contains the coordinates of the point. | ||
| #. ``DMSwarm_rank``: the MPI rank which owns the DMSwarm point. | ||
| .. note:: | ||
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@@ -3794,7 +3793,6 @@ def _dmswarm_create( | |
| # These are created by default for a PIC DMSwarm | ||
| default_fields = [ | ||
| ("DMSwarmPIC_coor", gdim, RealType), | ||
| ("DMSwarm_rank", 1, IntType), | ||
| ] | ||
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@@ -3853,12 +3851,6 @@ def _dmswarm_create( | |
| # Set to Particle In Cell (PIC) type | ||
| if not isinstance(plex, PETSc.DMSwarm): | ||
| swarm.setType(PETSc.DMSwarm.Type.PIC) | ||
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| # Register any fields | ||
| for name, size, dtype in swarm.default_extra_fields + swarm.other_fields: | ||
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@@ -3872,14 +3864,15 @@ def _dmswarm_create( | |
| # Add point coordinates. This amounts to our own implementation of | ||
| # DMSwarmSetPointCoordinates because Firedrake's mesh coordinate model | ||
| # doesn't always exactly coincide with that of DMPlex: in most cases the | ||
| # plex_parent_cell_nums and parent_cell_nums (parentcellnum field), the | ||
| # latter being the numbering used by firedrake, refer fundamentally to the | ||
| # same cells. For extruded meshes the DMPlex dimension is based on the | ||
| # topological dimension of the base mesh. | ||
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| # NOTE ensure that swarm.restoreField is called for each field too! | ||
| swarm_coords = swarm.getField("DMSwarmPIC_coor").reshape((num_vertices, gdim)) | ||
| cell_id_name = swarm.getCellDMActive().getCellID() | ||
| swarm_parent_cell_nums = swarm.getField(cell_id_name).ravel() | ||
| field_parent_cell_nums = swarm.getField("parentcellnum").ravel() | ||
| field_reference_coords = swarm.getField("refcoord").reshape((num_vertices, tdim)) | ||
| field_global_index = swarm.getField("globalindex").ravel() | ||
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@@ -3903,7 +3896,7 @@ def _dmswarm_create( | |
| swarm.restoreField("refcoord") | ||
| swarm.restoreField("parentcellnum") | ||
| swarm.restoreField("DMSwarmPIC_coor") | ||
| swarm.restoreField(cell_id_name) | ||
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| if extruded: | ||
| field_base_parent_cell_nums = swarm.getField("parentcellbasenum").ravel() | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -218,8 +218,9 @@ def test_pic_swarm_in_mesh(parentmesh, redundant, exclude_halos): | |
| nptslocal = len(localpointcoords) | ||
| nptsglobal = MPI.COMM_WORLD.allreduce(nptslocal, op=MPI.SUM) | ||
| # Get parent PETSc cell indices on current MPI rank | ||
| cell_id = swarm.getCellDMActive().getCellID() | ||
| localparentcellindices = np.copy(swarm.getField(cell_id).ravel()) | ||
| swarm.restoreField(cell_id) | ||
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| # also get the global coordinate numbering | ||
| globalindices = np.copy(swarm.getField("globalindex").ravel()) | ||
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@@ -242,7 +243,6 @@ def test_pic_swarm_in_mesh(parentmesh, redundant, exclude_halos): | |
| # Check swarm fields are correct | ||
| default_fields = [ | ||
| ("DMSwarmPIC_coor", parentmesh.geometric_dimension(), RealType), | ||
| ("DMSwarm_rank", 1, IntType), | ||
| ] | ||
| default_extra_fields = [ | ||
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@@ -378,8 +378,9 @@ def test_pic_swarm_in_mesh(parentmesh, redundant, exclude_halos): | |
| ): | ||
| swarm.setPointCoordinates(localpointcoords, redundant=False, | ||
| mode=PETSc.InsertMode.INSERT_VALUES) | ||
| cell_id = swarm.getCellDMActive().getCellID() | ||
| petsclocalparentcellindices = np.copy(swarm.getField(cell_id).ravel()) | ||
| swarm.restoreField(cell_id) | ||
| if exclude_halos: | ||
| assert np.all(petsclocalparentcellindices == localparentcellindices) | ||
| elif parentmesh.comm.size > 1: | ||
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