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; }
int main(int argc, char **argv) { DM dm, subdm, auxdm; Vec la; AppCtx user; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(&user);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SetupDiscretization(dm, user.dim, user.cellSimplex, &user);CHKERRQ(ierr); /* Volumetric Mesh Projection */ ierr = TestFunctionProjection(dm, NULL, NULL, NULL, "Volumetric Primary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(dm, NULL, NULL, NULL, "Volumetric Primary", &user);CHKERRQ(ierr); if (user.auxfield) { /* Volumetric Mesh Projection with Volumetric Data */ ierr = CreateAuxiliaryData(dm, &auxdm, &la, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(dm, auxdm, NULL, la, "Volumetric Primary and Volumetric Auxiliary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(dm, auxdm, NULL, la, "Volumetric Primary and Volumetric Auxiliary", &user);CHKERRQ(ierr); ierr = VecDestroy(&la);CHKERRQ(ierr); /* Update of Volumetric Auxiliary Data with primary Volumetric Data */ ierr = DMGetLocalVector(dm, &la);CHKERRQ(ierr); ierr = VecSet(la, 1.0);CHKERRQ(ierr); ierr = TestFieldProjection(auxdm, dm, NULL, la, "Volumetric Auxiliary Update with Volumetric Primary", &user);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &la);CHKERRQ(ierr); ierr = DMDestroy(&auxdm);CHKERRQ(ierr); } if (user.submesh) { DMLabel bdLabel; /* Boundary Mesh Projection */ ierr = CreateBoundaryMesh(dm, &bdLabel, &subdm, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(subdm, NULL, NULL, NULL, "Boundary Primary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(subdm, NULL, NULL, NULL, "Boundary Primary", &user);CHKERRQ(ierr); if (user.auxfield) { /* Boundary Mesh Projection with Boundary Data */ ierr = CreateAuxiliaryData(subdm, &auxdm, &la, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(subdm, auxdm, NULL, la, "Boundary Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(subdm, auxdm, NULL, la, "Boundary Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = VecDestroy(&la);CHKERRQ(ierr); ierr = DMDestroy(&auxdm);CHKERRQ(ierr); /* Volumetric Mesh Projection with Boundary Data */ ierr = CreateAuxiliaryData(subdm, &auxdm, &la, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(dm, auxdm, bdLabel, la, "Volumetric Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(dm, auxdm, bdLabel, la, "Volumetric Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = VecDestroy(&la);CHKERRQ(ierr); ierr = DMDestroy(&auxdm);CHKERRQ(ierr); } ierr = DMLabelDestroy(&bdLabel);CHKERRQ(ierr); ierr = DMDestroy(&subdm);CHKERRQ(ierr); } ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char **argv) { DMLabel label; AppCtx user; /* user-defined work context */ PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = DMLabelCreate(PETSC_COMM_SELF, "Test Label", &label);CHKERRQ(ierr); ierr = TestSetup(label, &user);CHKERRQ(ierr); ierr = TestLookup(label, &user);CHKERRQ(ierr); ierr = TestClear(label,&user);CHKERRQ(ierr); ierr = DMLabelDestroy(&label);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
static PetscErrorCode CreateBoundaryMesh(DM dm, DMLabel *bdLabel, DM *subdm, AppCtx *user) { DMLabel label; PetscInt dim; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMLabelCreate(PETSC_COMM_SELF, "sub", &label);CHKERRQ(ierr); ierr = DMPlexMarkBoundaryFaces(dm, 1, label);CHKERRQ(ierr); ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr); ierr = DMPlexCreateSubmesh(dm, label, 1, PETSC_TRUE, subdm);CHKERRQ(ierr); ierr = DMGetDimension(*subdm, &dim);CHKERRQ(ierr); ierr = SetupDiscretization(*subdm, dim, user->cellSimplex, user);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *subdm, "boundary");CHKERRQ(ierr); ierr = DMViewFromOptions(*subdm, NULL, "-sub_dm_view");CHKERRQ(ierr); if (bdLabel) *bdLabel = label; else ierr = DMLabelDestroy(&label);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode CreateTensorProductHybrid_2D(MPI_Comm comm, PetscInt testNum, DM *dm) { DM idm, hdm = NULL; DMLabel faultLabel, hybridLabel; PetscInt p; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); if (!rank) { PetscInt numPoints[2] = {6, 2}; PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4,}; PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5}; PetscInt faultPoints[2] = {3, 4}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for(p = 0; p < 2; ++p) {ierr = DMSetLabelValue(*dm, "fault", faultPoints[p], 1);CHKERRQ(ierr);} ierr = PetscObjectSetOptionsPrefix((PetscObject) *dm, "orig_");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) idm, "in_");CHKERRQ(ierr); ierr = DMSetFromOptions(idm);CHKERRQ(ierr); ierr = DMViewFromOptions(idm, NULL, "-dm_view");CHKERRQ(ierr); ierr = DMGetLabel(*dm, "fault", &faultLabel);CHKERRQ(ierr); ierr = DMPlexCreateHybridMesh(idm, faultLabel, NULL, &hybridLabel, NULL, NULL, &hdm);CHKERRQ(ierr); ierr = DMLabelDestroy(&hybridLabel);CHKERRQ(ierr); } else { PetscInt numPoints[3] = {0, 0, 0}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMViewFromOptions(idm, NULL, "-in_dm_view");CHKERRQ(ierr); ierr = DMPlexCreateHybridMesh(idm, NULL, NULL, NULL, NULL, NULL, &hdm);CHKERRQ(ierr); } ierr = DMDestroy(&idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = hdm; PetscFunctionReturn(0); }
/* Two tetrahedrons separated by a zero-volume cell with 6 vertices cell 6 ___33___10______ cell 0 / | \ |\ \ 1 21 | 23 | 29 27 /12 24 14\ 30 \ \ 3-20-|----5--32-|---9--26--7 \ 13| 11/ |18 / / 19 | 22 | 28 25 \ | / |/ / 4----31----8------ cell 2 */ PetscErrorCode CreateSimplexHybrid_3D(MPI_Comm comm, PetscInt testNum, DM *dm) { DM idm, hdm = NULL; DMLabel faultLabel, hybridLabel; PetscInt p; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); if (!rank) { switch (testNum) { case 0: { PetscInt numPoints[2] = {5, 2}; PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0}; PetscInt faultPoints[3] = {3, 4, 5}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for(p = 0; p < 3; ++p) {ierr = DMSetLabelValue(*dm, "fault", faultPoints[p], 1);CHKERRQ(ierr);} } break; case 1: { /* Tets 0,3,5 and 1,2,4 */ PetscInt numPoints[2] = {9, 6}; PetscInt coneSize[15] = {4, 4, 4, 4, 4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0}; PetscInt cones[24] = { 7, 9, 8, 6, 11, 9, 13, 14, 10, 13, 11, 9, 10, 9, 11, 7, 9, 13, 14, 12, 7, 11, 8, 9}; PetscInt coneOrientations[24] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[27] = {-2.0, -1.0, 0.0, -2.0, 0.0, 0.0, -2.0, 0.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 2.0, -1.0, 0.0, 2.0, 0.0, 0.0, 2.0, 0.0, 1.0}; PetscInt faultPoints[3] = {9, 10, 11}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for(p = 0; p < 3; ++p) {ierr = DMSetLabelValue(*dm, "fault", faultPoints[p], 1);CHKERRQ(ierr);} } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No test mesh %d", testNum); } ierr = PetscObjectSetOptionsPrefix((PetscObject) *dm, "orig_");CHKERRQ(ierr); ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) idm, "in_");CHKERRQ(ierr); ierr = DMSetFromOptions(idm);CHKERRQ(ierr); ierr = DMViewFromOptions(idm, NULL, "-dm_view");CHKERRQ(ierr); ierr = DMGetLabel(*dm, "fault", &faultLabel);CHKERRQ(ierr); ierr = DMPlexCreateHybridMesh(idm, faultLabel, NULL, &hybridLabel, NULL, NULL, &hdm);CHKERRQ(ierr); ierr = DMLabelDestroy(&hybridLabel);CHKERRQ(ierr); ierr = DMDestroy(&idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = hdm; } else { PetscInt numPoints[4] = {0, 0, 0, 0}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMViewFromOptions(idm, NULL, "-in_dm_view");CHKERRQ(ierr); ierr = DMPlexCreateHybridMesh(idm, NULL, NULL, NULL, NULL, NULL, &hdm);CHKERRQ(ierr); ierr = DMDestroy(&idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = hdm; } PetscFunctionReturn(0); }
int main(int argc, char **argv) { MPI_Comm comm; DM base, preForest, postForest; PetscInt dim = 2; PetscInt preCount, postCount; Vec preVec, postVecTransfer, postVecExact; PetscErrorCode (*funcs[1]) (PetscInt,PetscReal,const PetscReal [],PetscInt,PetscScalar [], void *) = {MultiaffineFunction}; void *ctxs[1] = {NULL}; const PetscInt cells[] = {3, 3, 3}; PetscReal diff, tol = PETSC_SMALL; PetscBool linear = PETSC_FALSE; PetscBool useFV = PETSC_FALSE; PetscDS ds; bc_func_ctx bcCtx; DMLabel adaptLabel; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; comm = PETSC_COMM_WORLD; ierr = PetscOptionsBegin(comm, "", "DMForestTransferVec() Test Options", "DMFOREST");CHKERRQ(ierr); ierr = PetscOptionsInt("-dim", "The dimension (2 or 3)", "ex2.c", dim, &dim, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-linear","Transfer a simple linear function", "ex2.c", linear, &linear, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-use_fv","Use a finite volume approximation", "ex2.c", useFV, &useFV, NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); if (linear) { funcs[0] = LinearFunction; } bcCtx.func = funcs[0]; bcCtx.dim = dim; bcCtx.Nf = 1; bcCtx.ctx = NULL; /* the base mesh */ ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &base);CHKERRQ(ierr); if (useFV) { PetscFV fv; PetscLimiter limiter; DM baseFV; ierr = DMPlexConstructGhostCells(base,NULL,NULL,&baseFV);CHKERRQ(ierr); ierr = DMDestroy(&base);CHKERRQ(ierr); base = baseFV; ierr = PetscFVCreate(comm, &fv);CHKERRQ(ierr); ierr = PetscFVSetSpatialDimension(fv,dim);CHKERRQ(ierr); ierr = PetscFVSetType(fv,PETSCFVLEASTSQUARES);CHKERRQ(ierr); ierr = PetscFVSetNumComponents(fv,1);CHKERRQ(ierr); ierr = PetscLimiterCreate(comm,&limiter);CHKERRQ(ierr); ierr = PetscLimiterSetType(limiter,PETSCLIMITERNONE);CHKERRQ(ierr); ierr = PetscFVSetLimiter(fv,limiter);CHKERRQ(ierr); ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr); ierr = PetscFVSetFromOptions(fv);CHKERRQ(ierr); ierr = DMSetField(base,0,(PetscObject)fv);CHKERRQ(ierr); ierr = PetscFVDestroy(&fv);CHKERRQ(ierr); } else { PetscFE fe; ierr = PetscFECreateDefault(base,dim,1,PETSC_FALSE,NULL,PETSC_DEFAULT,&fe);CHKERRQ(ierr); ierr = DMSetField(base,0,(PetscObject)fe);CHKERRQ(ierr); ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); } { PetscDS prob; PetscInt comps[] = {0}; PetscInt ids[] = {1, 2, 3, 4, 5, 6}; ierr = DMGetDS(base,&prob);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob,PETSC_TRUE, "bc", "marker", 0, 1, comps, useFV ? (void(*)()) bc_func_fv : (void(*)()) funcs[0], 2 * dim, ids, useFV ? (void *) &bcCtx : NULL);CHKERRQ(ierr); } ierr = AddIdentityLabel(base);CHKERRQ(ierr); ierr = DMViewFromOptions(base,NULL,"-dm_base_view");CHKERRQ(ierr); /* the pre adaptivity forest */ ierr = DMCreate(comm,&preForest);CHKERRQ(ierr); ierr = DMSetType(preForest,(dim == 2) ? DMP4EST : DMP8EST);CHKERRQ(ierr); ierr = DMGetDS(base,&ds);CHKERRQ(ierr); ierr = DMSetDS(preForest,ds);CHKERRQ(ierr); ierr = DMForestSetBaseDM(preForest,base);CHKERRQ(ierr); ierr = DMForestSetMinimumRefinement(preForest,1);CHKERRQ(ierr); ierr = DMForestSetInitialRefinement(preForest,1);CHKERRQ(ierr); ierr = DMSetFromOptions(preForest);CHKERRQ(ierr); ierr = DMSetUp(preForest);CHKERRQ(ierr); ierr = DMViewFromOptions(preForest,NULL,"-dm_pre_view");CHKERRQ(ierr); /* the pre adaptivity field */ ierr = DMCreateGlobalVector(preForest,&preVec);CHKERRQ(ierr); ierr = DMProjectFunction(preForest,0.,funcs,ctxs,INSERT_VALUES,preVec);CHKERRQ(ierr); ierr = VecViewFromOptions(preVec,NULL,"-vec_pre_view");CHKERRQ(ierr); ierr = PetscObjectGetReference((PetscObject)preForest,&preCount);CHKERRQ(ierr); /* adapt */ ierr = CreateAdaptivityLabel(preForest,&adaptLabel);CHKERRQ(ierr); ierr = DMForestTemplate(preForest,comm,&postForest);CHKERRQ(ierr); ierr = DMForestSetMinimumRefinement(postForest,0);CHKERRQ(ierr); ierr = DMForestSetInitialRefinement(postForest,0);CHKERRQ(ierr); ierr = DMForestSetAdaptivityLabel(postForest,adaptLabel);CHKERRQ(ierr); ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); ierr = DMSetUp(postForest);CHKERRQ(ierr); ierr = DMViewFromOptions(postForest,NULL,"-dm_post_view");CHKERRQ(ierr); /* transfer */ ierr = DMCreateGlobalVector(postForest,&postVecTransfer);CHKERRQ(ierr); ierr = DMForestTransferVec(preForest,preVec,postForest,postVecTransfer,PETSC_TRUE,0.0);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_post_transfer_view");CHKERRQ(ierr); /* the exact post adaptivity field */ ierr = DMCreateGlobalVector(postForest,&postVecExact);CHKERRQ(ierr); ierr = DMProjectFunction(postForest,0.,funcs,ctxs,INSERT_VALUES,postVecExact);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecExact,NULL,"-vec_post_exact_view");CHKERRQ(ierr); /* compare */ ierr = VecAXPY(postVecTransfer,-1.,postVecExact);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_diff_view");CHKERRQ(ierr); ierr = VecNorm(postVecTransfer,NORM_2,&diff);CHKERRQ(ierr); /* output */ if (diff < tol) { ierr = PetscPrintf(comm,"DMForestTransferVec() passes.\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(comm,"DMForestTransferVec() fails with error %g and tolerance %g\n",diff,tol);CHKERRQ(ierr); } /* disconnect preForest from postForest */ ierr = DMForestSetAdaptivityForest(postForest,NULL);CHKERRQ(ierr); ierr = PetscObjectGetReference((PetscObject)preForest,&postCount);CHKERRQ(ierr); if (postCount != preCount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Adaptation not memory neutral: reference count increase from %d to %d\n",preCount,postCount); /* cleanup */ ierr = VecDestroy(&postVecExact);CHKERRQ(ierr); ierr = VecDestroy(&postVecTransfer);CHKERRQ(ierr); ierr = DMDestroy(&postForest);CHKERRQ(ierr); ierr = VecDestroy(&preVec);CHKERRQ(ierr); ierr = DMDestroy(&preForest);CHKERRQ(ierr); ierr = DMDestroy(&base);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened) { DM_Plex *mesh = (DM_Plex*) dm->data; #ifdef PETSC_HAVE_PRAGMATIC DM udm, coordDM; DMLabel bd; Mat A; Vec coordinates, mb, mx; PetscSection coordSection; const PetscScalar *coords; double *coarseCoords; IS bdIS; PetscReal *x, *y, *z, *eqns, *metric; PetscReal coarseRatio = PetscSqr(0.5); const PetscInt *faces; PetscInt *cells, *bdFaces, *bdFaceIds; PetscInt dim, numCorners, cStart, cEnd, numCells, numCoarseCells, c, vStart, vEnd, numVertices, numCoarseVertices, v, numBdFaces, f, maxConeSize, size, bdSize, coff; #endif PetscErrorCode ierr; PetscFunctionBegin; #ifdef PETSC_HAVE_PRAGMATIC if (!mesh->coarseMesh) { ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dm, &coordDM);CHKERRQ(ierr); ierr = DMGetDefaultSection(coordDM, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr); ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr); numCells = cEnd - cStart; numVertices = vEnd - vStart; ierr = PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices*PetscSqr(dim), &metric, numCells*maxConeSize, &cells);CHKERRQ(ierr); ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { PetscInt off; ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); x[v-vStart] = coords[off+0]; y[v-vStart] = coords[off+1]; if (dim > 2) z[v-vStart] = coords[off+2]; } ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); for (c = 0, coff = 0; c < numCells; ++c) { const PetscInt *cone; PetscInt coneSize, cl; ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr); ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr); for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart; } switch (dim) { case 2: pragmatic_2d_init(&numVertices, &numCells, cells, x, y); break; case 3: pragmatic_3d_init(&numVertices, &numCells, cells, x, y, z); break; default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim); } /* Create boundary mesh */ ierr = DMLabelCreate("boundary", &bd);CHKERRQ(ierr); ierr = DMPlexMarkBoundaryFaces(dm, bd);CHKERRQ(ierr); ierr = DMLabelGetStratumIS(bd, 1, &bdIS);CHKERRQ(ierr); ierr = DMLabelGetStratumSize(bd, 1, &numBdFaces);CHKERRQ(ierr); ierr = ISGetIndices(bdIS, &faces);CHKERRQ(ierr); for (f = 0, bdSize = 0; f < numBdFaces; ++f) { PetscInt *closure = NULL; PetscInt closureSize, cl; ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for (cl = 0; cl < closureSize*2; cl += 2) { if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize; } ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr); for (f = 0, bdSize = 0; f < numBdFaces; ++f) { PetscInt *closure = NULL; PetscInt closureSize, cl; ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); for (cl = 0; cl < closureSize*2; cl += 2) { if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart; } /* TODO Fix */ bdFaceIds[f] = 1; ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); } ierr = ISDestroy(&bdIS);CHKERRQ(ierr); ierr = DMLabelDestroy(&bd);CHKERRQ(ierr); pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds); /* Create metric */ size = (dim*(dim+1))/2; ierr = PetscMalloc1(PetscSqr(size), &eqns);CHKERRQ(ierr); ierr = MatCreateSeqDense(PETSC_COMM_SELF, size, size, eqns, &A);CHKERRQ(ierr); ierr = MatCreateVecs(A, &mx, &mb);CHKERRQ(ierr); ierr = VecSet(mb, 1.0);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { const PetscScalar *sol; PetscScalar *cellCoords = NULL; PetscReal e[3], vol; const PetscInt *cone; PetscInt coneSize, cl, i, j, d, r; ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr); /* Only works for simplices */ for (i = 0, r = 0; i < dim+1; ++i) { for (j = 0; j < i; ++j, ++r) { for (d = 0; d < dim; ++d) e[d] = cellCoords[i*dim+d] - cellCoords[j*dim+d]; /* FORTRAN ORDERING */ if (dim == 2) { eqns[0*size+r] = PetscSqr(e[0]); eqns[1*size+r] = 2.0*e[0]*e[1]; eqns[2*size+r] = PetscSqr(e[1]); } else { eqns[0*size+r] = PetscSqr(e[0]); eqns[1*size+r] = 2.0*e[0]*e[1]; eqns[2*size+r] = 2.0*e[0]*e[2]; eqns[3*size+r] = PetscSqr(e[1]); eqns[4*size+r] = 2.0*e[1]*e[2]; eqns[5*size+r] = PetscSqr(e[2]); } } } ierr = MatSetUnfactored(A);CHKERRQ(ierr); ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr); ierr = MatLUFactor(A, NULL, NULL, NULL);CHKERRQ(ierr); ierr = MatSolve(A, mb, mx);CHKERRQ(ierr); ierr = VecGetArrayRead(mx, &sol);CHKERRQ(ierr); ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr); ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr); for (cl = 0; cl < coneSize; ++cl) { const PetscInt v = cone[cl] - vStart; if (dim == 2) { metric[v*4+0] += vol*coarseRatio*sol[0]; metric[v*4+1] += vol*coarseRatio*sol[1]; metric[v*4+2] += vol*coarseRatio*sol[1]; metric[v*4+3] += vol*coarseRatio*sol[2]; } else { metric[v*9+0] += vol*coarseRatio*sol[0]; metric[v*9+1] += vol*coarseRatio*sol[1]; metric[v*9+3] += vol*coarseRatio*sol[1]; metric[v*9+2] += vol*coarseRatio*sol[2]; metric[v*9+6] += vol*coarseRatio*sol[2]; metric[v*9+4] += vol*coarseRatio*sol[3]; metric[v*9+5] += vol*coarseRatio*sol[4]; metric[v*9+7] += vol*coarseRatio*sol[4]; metric[v*9+8] += vol*coarseRatio*sol[5]; } } ierr = VecRestoreArrayRead(mx, &sol);CHKERRQ(ierr); } for (v = 0; v < numVertices; ++v) { const PetscInt *support; PetscInt supportSize, s; PetscReal vol, totVol = 0.0; ierr = DMPlexGetSupport(udm, v+vStart, &support);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(udm, v+vStart, &supportSize);CHKERRQ(ierr); for (s = 0; s < supportSize; ++s) {ierr = DMPlexComputeCellGeometryFVM(dm, support[s], &vol, NULL, NULL);CHKERRQ(ierr); totVol += vol;} for (s = 0; s < PetscSqr(dim); ++s) metric[v*PetscSqr(dim)+s] /= totVol; } ierr = VecDestroy(&mx);CHKERRQ(ierr); ierr = VecDestroy(&mb);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&udm);CHKERRQ(ierr); ierr = PetscFree(eqns);CHKERRQ(ierr); pragmatic_set_metric(metric); pragmatic_adapt(); /* Read out mesh */ pragmatic_get_info(&numCoarseVertices, &numCoarseCells); ierr = PetscMalloc1(numCoarseVertices*dim, &coarseCoords);CHKERRQ(ierr); switch (dim) { case 2: pragmatic_get_coords_2d(x, y); numCorners = 3; for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*2+0] = x[v]; coarseCoords[v*2+1] = y[v];} break; case 3: pragmatic_get_coords_3d(x, y, z); numCorners = 4; for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*3+0] = x[v]; coarseCoords[v*3+1] = y[v]; coarseCoords[v*3+2] = z[v];} break; default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim); } pragmatic_get_elements(cells); /* TODO Read out markers for boundary */ ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject) dm), dim, numCoarseCells, numCoarseVertices, numCorners, PETSC_TRUE, cells, dim, coarseCoords, &mesh->coarseMesh);CHKERRQ(ierr); pragmatic_finalize(); ierr = PetscFree5(x, y, z, metric, cells);CHKERRQ(ierr); ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr); ierr = PetscFree(coarseCoords);CHKERRQ(ierr); } #endif ierr = PetscObjectReference((PetscObject) mesh->coarseMesh);CHKERRQ(ierr); *dmCoarsened = mesh->coarseMesh; PetscFunctionReturn(0); }
/* Two triangles separated by a zero-volume cell with 4 vertices/2 edges 5--16--8 / | | \ 11 | | 12 / | | \ 3 0 10 2 14 1 6 \ | | / 9 | | 13 \ | | / 4--15--7 */ PetscErrorCode CreateSimplexHybrid_2D(MPI_Comm comm, PetscInt testNum, DM *dm) { DM idm = NULL, hdm = NULL; DMLabel faultLabel, hybridLabel; PetscInt p; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBegin; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); if (!rank) { switch (testNum) { case 0: { PetscInt numPoints[2] = {4, 2}; PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[8] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, 1.0, 0.5}; PetscInt faultPoints[2] = {3, 4}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for(p = 0; p < 2; ++p) {ierr = DMSetLabelValue(*dm, "fault", faultPoints[p], 1);CHKERRQ(ierr);} } break; case 1: { PetscInt numPoints[2] = {5, 4}; PetscInt coneSize[9] = {3, 3, 3, 3, 0, 0, 0, 0, 0}; PetscInt cones[12] = {4, 5, 6, 6, 7, 4, 6, 5, 8, 6, 8, 7}; PetscInt coneOrientations[12] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; PetscScalar vertexCoords[10] = {-1.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0}; PetscInt faultPoints[3] = {5, 6, 7}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); for(p = 0; p < 3; ++p) {ierr = DMSetLabelValue(*dm, "fault", faultPoints[p], 1);CHKERRQ(ierr);} } break; default: SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No test mesh %d", testNum); } ierr = DMPlexCheckSymmetry(*dm);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); ierr = DMViewFromOptions(idm, NULL, "-in_dm_view");CHKERRQ(ierr); ierr = DMPlexCheckSymmetry(idm);CHKERRQ(ierr); ierr = DMGetLabel(*dm, "fault", &faultLabel);CHKERRQ(ierr); ierr = DMPlexCreateHybridMesh(idm, faultLabel, &hybridLabel, &hdm);CHKERRQ(ierr); ierr = DMLabelDestroy(&hybridLabel);CHKERRQ(ierr); ierr = DMDestroy(&idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = hdm; } else { PetscInt numPoints[2] = {0, 0}; ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); ierr = DMViewFromOptions(idm, NULL, "-in_dm_view");CHKERRQ(ierr); ierr = DMPlexCreateHybridMesh(idm, NULL, NULL, &hdm);CHKERRQ(ierr); ierr = DMDestroy(&idm);CHKERRQ(ierr); ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = hdm; } PetscFunctionReturn(0); }