PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscReal refinementLimit = user->refinementLimit; const char *partitioner = user->partitioner; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr); { DM refinedMesh = NULL; DM distributedMesh = NULL; /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm, dmAdapt; DMLabel adaptLabel; PetscInt dim, nfaces, cStart, cEnd; PetscBool interpolate; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr; dim = 2; nfaces = 3; interpolate = PETSC_TRUE; ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"ex20",NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dim","domain dimension",NULL,dim,&dim,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-nfaces","number of faces per dimension",NULL,nfaces,&nfaces,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD,dim,nfaces,interpolate,&dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)dm,"Pre Adaptation Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(dm,NULL,"-pre_adapt_dm_view");CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); ierr = DMLabelCreate("adapt",&adaptLabel);CHKERRQ(ierr); ierr = DMLabelSetDefaultValue(adaptLabel,DM_ADAPT_COARSEN);CHKERRQ(ierr); if (cEnd > cStart) {ierr = DMLabelSetValue(adaptLabel,cStart,DM_ADAPT_REFINE);CHKERRQ(ierr);} ierr = DMAdaptLabel(dm,adaptLabel,&dmAdapt);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)dmAdapt,"Post Adaptation Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(dmAdapt,NULL,"-post_adapt_dm_view");CHKERRQ(ierr); ierr = DMDestroy(&dmAdapt);CHKERRQ(ierr); ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { const char *filename = user->filename; PetscInt dim = user->dim; size_t len; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (!len) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);} else {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);} ierr = DMViewFromOptions(*dm, NULL, "-orig_dm_view");CHKERRQ(ierr); { DM distributedMesh = NULL; ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; ierr = DMViewFromOptions(*dm, NULL, "-dist_dm_view");CHKERRQ(ierr); } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); if (user->uninterpolate) { DM udm = NULL; ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = udm; ierr = DMViewFromOptions(*dm, NULL, "-un_dm_view");CHKERRQ(ierr); } ierr = PetscObjectSetName((PetscObject) *dm, "Test Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *ctx, DM *dm) { PetscInt dim = ctx->dim; PetscBool cellSimplex = ctx->cellSimplex; const char *filename = ctx->filename; const PetscInt cells[3] = {1, 1, 1}; size_t len; PetscMPIInt rank, size; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);} else {ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);} { DM distributedMesh = NULL; PetscPartitioner part; ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscErrorCode ierr; PetscFunctionBeginUser; /* Create box mesh */ ierr = DMPlexCreateBoxMesh(comm, user->dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); /* Distribute mesh over processes */ { DM dmDist = NULL; PetscPartitioner part; ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmDist; } } /* TODO: This should be pulled into the library */ { char convType[256]; PetscBool flg; ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); ierr = PetscOptionsFList("-dm_plex_convert_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); ierr = PetscOptionsEnd(); if (flg) { DM dmConv; ierr = DMConvert(*dm,convType,&dmConv);CHKERRQ(ierr); if (dmConv) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } } } /* TODO: This should be pulled into the library */ ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); ierr = DMSetApplicationContext(*dm, user);CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); /* TODO: Add a hierachical viewer */ if (user->spectral) { PetscInt planeDir[2] = {0, 1}; PetscReal planeCoord[2] = {0., 1.}; ierr = CreateSpectralPlanes(*dm, 2, planeDir, planeCoord, user);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *options, DM *dm) { PetscInt dim = options->dim; PetscInt *faces = options->faces; PetscBool simplex = options->simplex; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexCreateBoxMesh(comm, dim, simplex, faces, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, "Serial Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMPlexCreateBoxMesh(comm, dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); { Parameter *param; Vec coordinates; PetscScalar *coords; PetscReal alpha; PetscInt cdim, N, bs, i; ierr = DMGetCoordinateDim(*dm, &cdim);CHKERRQ(ierr); ierr = DMGetCoordinates(*dm, &coordinates);CHKERRQ(ierr); ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); ierr = VecGetBlockSize(coordinates, &bs);CHKERRQ(ierr); if (bs != cdim) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Invalid coordinate blocksize %D != embedding dimension %D", bs, cdim); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr); alpha = param->alpha; for (i = 0; i < N; i += cdim) { PetscScalar x = coords[i+0]; PetscScalar y = coords[i+1]; coords[i+0] = PetscCosReal(alpha)*x - PetscSinReal(alpha)*y; coords[i+1] = PetscSinReal(alpha)*x + PetscCosReal(alpha)*y; } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinates(*dm, coordinates);CHKERRQ(ierr); } { DM pdm = NULL; PetscPartitioner part; ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr); if (pdm) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = pdm; } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { DM distributedMesh = NULL; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMPlexCreateBoxMesh(comm, 2, PETSC_TRUE, dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { ierr = DMPlexCreateFromFile(comm, filename, PETSC_FALSE, dm);CHKERRQ(ierr); ierr = DMGetDimension(*dm, &dim);CHKERRQ(ierr); } else { PetscReal L[3] = {1.0, 1.0, 1.0}; PetscReal maxCell[3]; PetscInt d; for (d = 0; d < dim; ++d) {maxCell[d] = (1.0/user->faces[d])*1.1;} ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, user->faces, NULL, NULL, user->periodicity, PETSC_TRUE, dm);CHKERRQ(ierr); ierr = DMSetPeriodicity(*dm, user->isPeriodic, maxCell, L, user->periodicity);CHKERRQ(ierr); } { DM pdm = NULL; PetscPartitioner part; ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr); if (pdm) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = pdm; } } ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscReal refinementLimit = user->refinementLimit; const char *partitioner = "chaco"; PetscErrorCode ierr; PetscFunctionBegin; if (user->simplex) { DM refinedMesh = NULL; DM distributedMesh = NULL; ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr); /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr); } else { switch (user->dim) { case 2: ierr = DMDACreate2d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_BOX, -3, -3, PETSC_DETERMINE, PETSC_DETERMINE, 1, 1, NULL, NULL, dm);CHKERRQ(ierr); ierr = DMDASetVertexCoordinates(*dm, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr); break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot create structured mesh of dimension %d", dim); } ierr = PetscObjectSetName((PetscObject) *dm, "Hexahedral Mesh");CHKERRQ(ierr); } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *options, DM *dm) { PetscInt dim = options->dim; PetscInt *faces = options->faces; PetscBool simplex = options->simplex; PetscBool interpolate = options->interpolate; const char *filename = options->filename; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); ierr = DMGetDimension(*dm, &options->dim);CHKERRQ(ierr); } else { ierr = DMPlexCreateBoxMesh(comm, dim, simplex, faces, NULL, NULL, NULL, interpolate, dm);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool simplex = user->cellSimplex; PetscInt cells[3] = {1, 1, 1}; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexCreateBoxMesh(comm, dim, simplex, cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); { DM ddm = NULL; ierr = DMPlexDistribute(*dm, 0, NULL, &ddm);CHKERRQ(ierr); if (ddm) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = ddm; } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-orig_dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, DM *dm, AppCtx *ctx) { DM pdm = NULL; const PetscInt dim = ctx->dim; PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */ PetscBool hasLabel; PetscErrorCode ierr; PetscFunctionBeginUser; if (ctx->simplex) { ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_TRUE, dm); CHKERRQ(ierr); } else { ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm); CHKERRQ(ierr); } ierr = PetscObjectSetName((PetscObject) *dm, "Mesh"); CHKERRQ(ierr); /* If no boundary marker exists, mark the whole boundary */ ierr = DMHasLabel(*dm, "marker", &hasLabel); CHKERRQ(ierr); if (!hasLabel) { ierr = CreateBCLabel(*dm, "marker"); CHKERRQ(ierr); } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &pdm); CHKERRQ(ierr); if (pdm) { ierr = DMDestroy(dm); CHKERRQ(ierr); *dm = pdm; } ierr = DMSetFromOptions(*dm); CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view"); CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscBool flg; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMPlexCreateBoxMesh(comm, user->dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); { DM pdm = NULL; PetscPartitioner part; ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr); if (pdm) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = pdm; } } ierr = PetscStrcmp(user->dmType, DMPLEX, &flg);CHKERRQ(ierr); if (flg) { DM ndm; ierr = DMConvert(*dm, user->dmType, &ndm);CHKERRQ(ierr); if (ndm) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = ndm; } } ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); ierr = DMSetApplicationContext(*dm, user);CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm; PetscSection section; PetscFE fe; PetscInt cells[3] = {2, 2, 2},dim = 2,c,cStart,cEnd,tmp; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr; ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Spectral/tensor element restrictions",NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dim","Topological dimension",NULL,dim,&dim,NULL);CHKERRQ(ierr); tmp = dim; ierr = PetscOptionsIntArray("-cells","Number of cells per dimension",NULL,cells,&tmp,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD,dim,PETSC_FALSE,cells,NULL,NULL,NULL,PETSC_TRUE,&dm);CHKERRQ(ierr); ierr = PetscFECreateDefault(PETSC_COMM_SELF,dim,1,PETSC_FALSE,NULL,PETSC_DETERMINE,&fe);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); ierr = DMAddField(dm,NULL,(PetscObject)fe);CHKERRQ(ierr); ierr = DMCreateDS(dm);CHKERRQ(ierr); ierr = DMPlexSetClosurePermutationTensor(dm,PETSC_DETERMINE,NULL);CHKERRQ(ierr); ierr = DMGetDefaultSection(dm,§ion);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr); for (c=cStart; c<cEnd; c++) { PetscInt numindices,*indices; ierr = DMPlexGetClosureIndices(dm,section,section,c,&numindices,&indices,NULL);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"Element #%D\n",c-cStart);CHKERRQ(ierr); ierr = PetscIntView(numindices,indices,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = DMPlexRestoreClosureIndices(dm,section,section,c,&numindices,&indices,NULL);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; PetscBool useGenerator = user->useGenerator; const char *filename = user->filename; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { ierr = DMPlexCreateFromFile(comm, filename, PETSC_FALSE, dm);CHKERRQ(ierr); ierr = DMGetDimension(*dm, &dim);CHKERRQ(ierr); } else if (useGenerator) { if (cellSimplex) { ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_FALSE, dm);CHKERRQ(ierr); } else { const PetscInt cells[3] = {2, 2, 2}; ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, dm);CHKERRQ(ierr); } } else { ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); switch (dim) { case 2: if (cellSimplex) { ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr); } break; case 3: if (cellSimplex) { ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); } } { DM interpolatedMesh = NULL; ierr = CheckMesh(*dm, user);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = interpolatedMesh; } { DM distributedMesh = NULL; /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMViewFromOptions(distributedMesh, NULL, "-dm_view");CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
int main(int argc, char **argv) { MPI_Comm comm; DM dm; Vec v, nv, rv, coord; PetscBool test_read = PETSC_FALSE, verbose = PETSC_FALSE, flg; PetscViewer hdf5Viewer; PetscInt dim = 2; PetscInt numFields = 1; PetscInt numBC = 0; PetscInt numComp[1] = {2}; PetscInt numDof[3] = {2, 0, 0}; PetscInt bcFields[1] = {0}; IS bcPoints[1] = {NULL}; PetscSection section; PetscReal norm; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, (char *) 0, help);CHKERRQ(ierr); comm = PETSC_COMM_WORLD; ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Test Options","none");CHKERRQ(ierr); ierr = PetscOptionsBool("-test_read","Test reading from the HDF5 file","",PETSC_FALSE,&test_read,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-verbose","print the Vecs","",PETSC_FALSE,&verbose,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dim","the dimension of the problem","",2,&dim,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd(); ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, &dm);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); numDof[0] = dim; ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, NULL, NULL, §ion);CHKERRQ(ierr); ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr); ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); ierr = DMSetUseNatural(dm, PETSC_TRUE);CHKERRQ(ierr); { DM dmDist; ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) { ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist; } } ierr = DMCreateGlobalVector(dm, &v);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) v, "V");CHKERRQ(ierr); ierr = DMGetCoordinates(dm, &coord);CHKERRQ(ierr); ierr = VecCopy(coord, v);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(v, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== original V in global ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(v, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = DMCreateGlobalVector(dm, &nv);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) nv, "NV");CHKERRQ(ierr); ierr = DMPlexGlobalToNaturalBegin(dm, v, nv);CHKERRQ(ierr); ierr = DMPlexGlobalToNaturalEnd(dm, v, nv);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(nv, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(nv, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== V in natural ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(nv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecViewFromOptions(v, NULL, "-global_vec_view");CHKERRQ(ierr); if (test_read) { ierr = DMCreateGlobalVector(dm, &rv);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) rv, "V");CHKERRQ(ierr); /* Test native read */ ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr); ierr = PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_NATIVE);CHKERRQ(ierr); ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(rv, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecEqual(rv, v, &flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are equal\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are not equal\n\n");CHKERRQ(ierr); ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr); ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Test raw read */ ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr); ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(rv, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecEqual(rv, nv, &flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are equal\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are not equal\n\n");CHKERRQ(ierr); ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr); ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecDestroy(&rv);CHKERRQ(ierr); } ierr = VecDestroy(&nv);CHKERRQ(ierr); ierr = VecDestroy(&v);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscReal refinementLimit = user->refinementLimit; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; PetscInt triSizes_n2[2] = {4, 4}; PetscInt triPoints_n2[8] = {3, 5, 6, 7, 0, 1, 2, 4}; PetscInt triSizes_n8[8] = {1, 1, 1, 1, 1, 1, 1, 1}; PetscInt triPoints_n8[8] = {0, 1, 2, 3, 4, 5, 6, 7}; PetscInt quadSizes[2] = {2, 2}; PetscInt quadPoints[4] = {2, 3, 0, 1}; const PetscInt cells[3] = {2, 2, 2}; size_t len; PetscMPIInt rank, numProcs; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) {ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr);} else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, interpolate, dm);CHKERRQ(ierr);} else {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);} { DM refinedMesh = NULL; DM distributedMesh = NULL; if (user->testPartition) { const PetscInt *sizes = NULL; const PetscInt *points = NULL; PetscPartitioner part; if (!rank) { if (dim == 2 && cellSimplex && numProcs == 2) { sizes = triSizes_n2; points = triPoints_n2; } else if (dim == 2 && cellSimplex && numProcs == 8) { sizes = triSizes_n8; points = triPoints_n8; } else if (dim == 2 && !cellSimplex && numProcs == 2) { sizes = quadSizes; points = quadPoints; } } ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr); ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr); } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); if (user->overlap) { DM overlapMesh = NULL; /* Add the level-1 overlap to refined mesh */ ierr = DMPlexDistributeOverlap(*dm, 1, NULL, &overlapMesh);CHKERRQ(ierr); if (overlapMesh) { ierr = DMView(overlapMesh, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = overlapMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Simplicial Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
PETSC_EXTERN void PETSC_STDCALL dmplexcreateboxmesh_(MPI_Fint * comm,PetscInt *dim,PetscBool *interpolate,DM *dm, int *__ierr ){ *__ierr = DMPlexCreateBoxMesh( MPI_Comm_f2c( *(comm) ),*dim,*interpolate,dm); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; const char *filename = user->filename; PetscBool interpolate = user->interpolate; PetscReal refinementLimit = user->refinementLimit; PetscBool refinementUniform = user->refinementUniform; PetscInt refinementRounds = user->refinementRounds; const char *partitioner = user->partitioner; size_t len; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (!len) { ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr); } else if (user->checkpoint) { ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMLoad(*dm, user->checkpoint);CHKERRQ(ierr); ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); } else { PetscMPIInt rank; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); /* Must have boundary marker for Dirichlet conditions */ } { DM refinedMesh = NULL; DM distributedMesh = NULL; /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { const char *name; ierr = PetscObjectGetName((PetscObject) *dm, &name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) refinedMesh, name);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } /* Use regular refinement in parallel */ if (refinementUniform) { PetscInt r; ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr); for (r = 0; r < refinementRounds; ++r) { ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } } } } ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscReal refinementLimit = user->refinementLimit; PetscBool cellSimplex = user->cellSimplex; PetscBool cellWedge = user->cellWedge; PetscBool simplex2tensor = user->simplex2tensor; const char *filename = user->filename; const char *bdfilename = user->bdfilename; const char *extfilename = user->extfilename; PetscBool testp4est_seq = user->testp4est[0]; PetscBool testp4est_par = user->testp4est[1]; PetscInt triSizes_n2[2] = {4, 4}; PetscInt triPoints_n2[8] = {3, 5, 6, 7, 0, 1, 2, 4}; PetscInt triSizes_n8[8] = {1, 1, 1, 1, 1, 1, 1, 1}; PetscInt triPoints_n8[8] = {0, 1, 2, 3, 4, 5, 6, 7}; PetscInt quadSizes[2] = {2, 2}; PetscInt quadPoints[4] = {2, 3, 0, 1}; PetscInt gmshSizes_n3[3] = {14, 14, 14}; PetscInt gmshPoints_n3[42] = {1, 2, 4, 5, 9, 10, 11, 15, 16, 20, 21, 27, 28, 29, 3, 8, 12, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 6, 7, 13, 14, 17, 18, 19, 22, 23, 24, 25, 26, 41}; PetscInt fluentSizes_n3[3] = {50, 50, 50}; PetscInt fluentPoints_n3[150] = { 5, 6, 7, 8, 12, 14, 16, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 50, 51, 80, 81, 89, 91, 93, 94, 95, 96, 97, 98, 99, 100, 101, 104, 121, 122, 124, 125, 126, 127, 128, 129, 131, 133, 143, 144, 145, 147, 1, 3, 4, 9, 10, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 47, 61, 71, 72, 73, 74, 75, 76, 77, 78, 79, 86, 87, 88, 90, 92, 113, 115, 116, 117, 118, 119, 120, 123, 138, 140, 141, 142, 146, 148, 149, 0, 2, 11, 13, 15, 20, 21, 22, 23, 49, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 82, 83, 84, 85, 102, 103, 105, 106, 107, 108, 109, 110, 111, 112, 114, 130, 132, 134, 135, 136, 137, 139}; size_t len, bdlen, extlen; PetscMPIInt rank, size; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); ierr = PetscStrlen(bdfilename, &bdlen);CHKERRQ(ierr); ierr = PetscStrlen(extfilename, &extlen);CHKERRQ(ierr); ierr = PetscLogStagePush(user->stages[STAGE_LOAD]);CHKERRQ(ierr); if (len) { ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); } else if (bdlen) { DM boundary; ierr = DMPlexCreateFromFile(comm, bdfilename, interpolate, &boundary);CHKERRQ(ierr); ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); ierr = DMDestroy(&boundary);CHKERRQ(ierr); } else if (extlen) { DM edm; ierr = DMPlexCreateFromFile(comm, extfilename, interpolate, &edm);CHKERRQ(ierr); ierr = DMPlexExtrude(edm, user->extrude_layers, user->extrude_thickness, PETSC_TRUE, interpolate, dm);CHKERRQ(ierr); ierr = DMDestroy(&edm);CHKERRQ(ierr); } else { switch (user->domainShape) { case BOX: if (cellWedge) { if (dim != 3) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Dimension must be 3 for a wedge mesh, not %D", dim); ierr = DMPlexCreateWedgeBoxMesh(comm, user->domainBoxSizes, user->domainBoxL, user->domainBoxU, user->periodicity, PETSC_FALSE, interpolate, dm);CHKERRQ(ierr); } else { ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, user->domainBoxSizes, user->domainBoxL, user->domainBoxU, user->periodicity, interpolate, dm);CHKERRQ(ierr); } break; case CYLINDER: if (cellSimplex) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Cannot mesh a cylinder with simplices"); if (dim != 3) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Dimension must be 3 for a cylinder mesh, not %D", dim); if (cellWedge) { ierr = DMPlexCreateWedgeCylinderMesh(comm, 6, interpolate, dm);CHKERRQ(ierr); } else { ierr = DMPlexCreateHexCylinderMesh(comm, 3, user->periodicity[2], dm);CHKERRQ(ierr); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Unknown domain shape %D", user->domainShape); } } ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); /* needed for periodic */ ierr = DMViewFromOptions(*dm,NULL,"-init_dm_view");CHKERRQ(ierr); ierr = DMGetDimension(*dm,&dim);CHKERRQ(ierr); if (testp4est_seq) { #if defined(PETSC_HAVE_P4EST) DM dmConv = NULL; ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr); ierr = DMPlexRefineSimplexToTensor(*dm, &dmConv);CHKERRQ(ierr); if (dmConv) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } user->cellSimplex = PETSC_FALSE; ierr = DMConvert(*dm,dim == 2 ? DMP4EST : DMP8EST,&dmConv);CHKERRQ(ierr); if (dmConv) { ierr = DMSetFromOptions(dmConv);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } ierr = DMSetUp(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-conv_seq_1_dm_view");CHKERRQ(ierr); ierr = DMConvert(*dm,DMPLEX,&dmConv);CHKERRQ(ierr); if (dmConv) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } ierr = DMViewFromOptions(*dm, NULL, "-conv_seq_2_dm_view");CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Recompile with --download-p4est"); #endif } ierr = PetscLogStagePop();CHKERRQ(ierr); if (!testp4est_seq) { DM refinedMesh = NULL; DM distributedMesh = NULL; if (user->testPartition) { const PetscInt *sizes = NULL; const PetscInt *points = NULL; PetscPartitioner part; if (!rank) { if (dim == 2 && cellSimplex && size == 2) { sizes = triSizes_n2; points = triPoints_n2; } else if (dim == 2 && cellSimplex && size == 8) { sizes = triSizes_n8; points = triPoints_n8; } else if (dim == 2 && !cellSimplex && size == 2) { sizes = quadSizes; points = quadPoints; } else if (dim == 2 && size == 3) { PetscInt Nc; ierr = DMPlexGetHeightStratum(*dm, 0, NULL, &Nc);CHKERRQ(ierr); if (Nc == 42) { /* Gmsh 3 & 4 */ sizes = gmshSizes_n3; points = gmshPoints_n3; } else if (Nc == 150) { /* Fluent 1 */ sizes = fluentSizes_n3; points = fluentPoints_n3; } else if (Nc == 42) { /* Med 1 */ } else if (Nc == 161) { /* Med 3 */ } } } ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr); ierr = PetscPartitionerShellSetPartition(part, size, sizes, points);CHKERRQ(ierr); } else { PetscPartitioner part; ierr = DMPlexGetPartitioner(*dm,&part);CHKERRQ(ierr); ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); } /* Distribute mesh over processes */ ierr = PetscLogStagePush(user->stages[STAGE_DISTRIBUTE]);CHKERRQ(ierr); ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } ierr = PetscLogStagePop();CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-distributed_dm_view");CHKERRQ(ierr); /* Refine mesh using a volume constraint */ ierr = PetscLogStagePush(user->stages[STAGE_REFINE]);CHKERRQ(ierr); ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } ierr = PetscLogStagePop();CHKERRQ(ierr); } ierr = PetscLogStagePush(user->stages[STAGE_REFINE]);CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); if (testp4est_par) { #if defined(PETSC_HAVE_P4EST) DM dmConv = NULL; ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr); ierr = DMPlexRefineSimplexToTensor(*dm, &dmConv);CHKERRQ(ierr); if (dmConv) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } user->cellSimplex = PETSC_FALSE; ierr = DMConvert(*dm,dim == 2 ? DMP4EST : DMP8EST,&dmConv);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) dmConv, "conv_par_1_");CHKERRQ(ierr); if (dmConv) { ierr = DMSetFromOptions(dmConv);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } ierr = DMSetUp(*dm);CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); ierr = DMConvert(*dm,DMPLEX,&dmConv);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) dmConv, "conv_par_2_");CHKERRQ(ierr); if (dmConv) { ierr = DMSetFromOptions(dmConv);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmConv; } ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); #else SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Recompile with --download-p4est"); #endif } if (user->overlap) { DM overlapMesh = NULL; /* Add the level-1 overlap to refined mesh */ ierr = PetscLogStagePush(user->stages[STAGE_OVERLAP]);CHKERRQ(ierr); ierr = DMPlexDistributeOverlap(*dm, 1, NULL, &overlapMesh);CHKERRQ(ierr); if (overlapMesh) { ierr = DMView(overlapMesh, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = overlapMesh; } ierr = PetscLogStagePop();CHKERRQ(ierr); } if (simplex2tensor) { DM rdm = NULL; ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr); ierr = DMPlexRefineSimplexToTensor(*dm, &rdm);CHKERRQ(ierr); if (rdm) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = rdm; } user->cellSimplex = PETSC_FALSE; } ierr = PetscObjectSetName((PetscObject) *dm, "Simplicial Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm, dmDist = NULL; Vec u; PetscSection section; PetscViewer viewer; PetscInt dim = 2, numFields, numBC, i; PetscInt numComp[3]; PetscInt numDof[12]; PetscInt bcField[1]; IS bcPointIS[1]; PetscBool interpolate = PETSC_TRUE; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL);CHKERRQ(ierr); /* Create a mesh */ ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, PETSC_TRUE, NULL, NULL, NULL, NULL, interpolate, &dm);CHKERRQ(ierr); /* Distribute mesh over processes */ ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) {ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist;} /* Create a scalar field u, a vector field v, and a surface vector field w */ numFields = 3; numComp[0] = 1; numComp[1] = dim; numComp[2] = dim-1; for (i = 0; i < numFields*(dim+1); ++i) numDof[i] = 0; /* Let u be defined on vertices */ numDof[0*(dim+1)+0] = 1; /* Let v be defined on cells */ numDof[1*(dim+1)+dim] = dim; /* Let v be defined on faces */ numDof[2*(dim+1)+dim-1] = dim-1; /* Setup boundary conditions */ numBC = 1; /* Prescribe a Dirichlet condition on u on the boundary Label "marker" is made by the mesh creation routine */ bcField[0] = 0; ierr = DMGetStratumIS(dm, "marker", 1, &bcPointIS[0]);CHKERRQ(ierr); /* Create a PetscSection with this data layout */ ierr = DMSetNumFields(dm, numFields);CHKERRQ(ierr); ierr = DMPlexCreateSection(dm, NULL, numComp, numDof, numBC, bcField, NULL, bcPointIS, NULL, §ion);CHKERRQ(ierr); ierr = ISDestroy(&bcPointIS[0]);CHKERRQ(ierr); /* Name the Field variables */ ierr = PetscSectionSetFieldName(section, 0, "u");CHKERRQ(ierr); ierr = PetscSectionSetFieldName(section, 1, "v");CHKERRQ(ierr); ierr = PetscSectionSetFieldName(section, 2, "w");CHKERRQ(ierr); ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* Tell the DM to use this data layout */ ierr = DMSetSection(dm, section);CHKERRQ(ierr); /* Create a Vec with this layout and view it */ ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr); ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr); ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr); ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr); ierr = PetscViewerFileSetName(viewer, "sol.vtk");CHKERRQ(ierr); ierr = VecView(u, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr); /* Cleanup */ ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; PetscBool useGenerator = user->useGenerator; const char *filename = user->filename; const char *partitioner = "chaco"; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { #if defined(PETSC_HAVE_EXODUSII) int CPU_word_size = 0, IO_word_size = 0, exoid = -1; float version; if (!rank) { exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version); if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename); } ierr = DMPlexCreateExodus(comm, exoid, PETSC_FALSE, dm);CHKERRQ(ierr); if (!rank) {ierr = ex_close(exoid);CHKERRQ(ierr);} ierr = DMPlexGetDimension(*dm, &dim);CHKERRQ(ierr); #else SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires ExodusII support. Reconfigure using --download-exodusii"); #endif } else if (useGenerator) { if (cellSimplex) { ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr); } else { ierr = DMPlexCreateHexBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr); } } else { ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); switch (dim) { case 2: if (cellSimplex) { ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr); } break; case 3: if (cellSimplex) { ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr); } else { ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr); } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); } } { DM interpolatedMesh = NULL; ierr = CheckMesh(*dm);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = interpolatedMesh; } { DM distributedMesh = NULL; /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } } ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { DM dmDist = NULL; PetscInt dim = user->dim; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; const PetscInt cells[3] = {2, 2, 2}; size_t len; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);} else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);} else {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);} if (user->testPartition) { PetscPartitioner part; const PetscInt *sizes = NULL; const PetscInt *points = NULL; PetscMPIInt rank, numProcs; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); if (!rank) { if (dim == 2 && cellSimplex && numProcs == 2) { switch (user->testNum) { case 0: { PetscInt triSizes_p2[2] = {4, 4}; PetscInt triPoints_p2[8] = {3, 5, 6, 7, 0, 1, 2, 4}; sizes = triSizes_p2; points = triPoints_p2;break;} case 1: { PetscInt triSizes_p2[2] = {6, 2}; PetscInt triPoints_p2[8] = {1, 2, 3, 4, 6, 7, 0, 5}; sizes = triSizes_p2; points = triPoints_p2;break;} default: SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for triangular mesh on 2 procs", user->testNum); } } else if (dim == 2 && cellSimplex && numProcs == 3) { PetscInt triSizes_p3[3] = {3, 3, 2}; PetscInt triPoints_p3[8] = {1, 2, 4, 3, 6, 7, 0, 5}; sizes = triSizes_p3; points = triPoints_p3; } else if (dim == 2 && !cellSimplex && numProcs == 2) { PetscInt quadSizes_p2[2] = {2, 2}; PetscInt quadPoints_p2[4] = {2, 3, 0, 1}; sizes = quadSizes_p2; points = quadPoints_p2; } else SETERRQ3(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test partition dim: %D simplex: %D numProcs: %D", dim, (PetscInt) cellSimplex, (PetscInt) numProcs); } ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr); ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr); ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr); } ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = dmDist; } ierr = PetscObjectSetName((PetscObject) *dm, cellSimplex ? "Simplicial Mesh" : "Tensor Product Mesh");CHKERRQ(ierr); ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) { PetscInt dim = user->dim; PetscBool interpolate = user->interpolate; PetscBool refinementUniform = user->refinementUniform; PetscReal refinementLimit = user->refinementLimit; PetscBool cellSimplex = user->cellSimplex; const char *filename = user->filename; const char *partitioner = "chaco"; size_t len; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); if (len) { #if defined(PETSC_HAVE_CGNS) int cgid = -1; if (!rank) { ierr = cg_open(filename, CG_MODE_READ, &cgid);CHKERRQ(ierr); if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename); } ierr = DMPlexCreateCGNS(comm, cgid, interpolate, dm);CHKERRQ(ierr); if (!rank) {ierr = cg_close(cgid);CHKERRQ(ierr);} #else SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir"); #endif } else if (cellSimplex) { ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr); } else { const PetscInt cells[3] = {2, 2, 2}; ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, dm);CHKERRQ(ierr); } { DM refinedMesh = NULL; DM distributedMesh = NULL; /* Refine mesh using a volume constraint */ ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } /* Distribute mesh over processes */ ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr); if (distributedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = distributedMesh; } if (refinementUniform) { ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr); ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr); if (refinedMesh) { ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = refinedMesh; } } } ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr); user->dm = *dm; PetscFunctionReturn(0); }