PetscErrorCode CreateQuad_2D(MPI_Comm comm, PetscInt testNum, DM dm)
{
PetscInt depth = 1, p;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (!rank) {
switch (testNum) {
case 0:
{
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] = {-0.5, 0.0, 0.0, 0.0, 0.0, 1.0, -0.5, 1.0, 0.5, 0.0, 0.5, 1.0};
PetscInt markerPoints[12] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1, 7, 1};
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for (p = 0; p < 6; ++p) {
ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);
}
}
break;
case 1:
{
PetscInt numPoints[2] = {5, 2};
PetscInt coneSize[7] = {4, 3, 0, 0, 0, 0, 0};
PetscInt cones[7] = {2, 3, 4, 5, 3, 6, 4};
PetscInt coneOrientations[7] = {0, 0, 0, 0, 0, 0, 0};
PetscScalar vertexCoords[10] = {-0.5, 0.0, 0.0, 0.0, 0.0, 1.0, -0.5, 1.0, 0.5, 0.0};
PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1};
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for (p = 0; p < 5; ++p) {
ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);
}
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No test mesh %d", testNum);
}
} else {
PetscInt numPoints[2] = {0, 0};
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode CreateHex_3D(MPI_Comm comm, DM *newdm)
{
DM dm;
PetscInt numPoints[2] = {12, 2};
PetscInt coneSize[14] = {8, 8, 0,0,0,0,0,0,0,0,0,0,0,0};
PetscInt cones[16] = {2,5,4,3,6,7,8,9, 3,4,11,10,7,12,13,8};
PetscInt coneOrientations[16] = {0,0,0,0,0,0,0,0, 0,0, 0, 0,0, 0, 0,0};
PetscScalar vertexCoords[36] = {-0.5,0.0,0.0, 0.0,0.0,0.0, 0.0,1.0,0.0, -0.5,1.0,0.0,
-0.5,0.0,1.0, 0.0,0.0,1.0, 0.0,1.0,1.0, -0.5,1.0,1.0,
0.5,0.0,0.0, 0.5,1.0,0.0, 0.5,0.0,1.0, 0.5,1.0,1.0};
PetscInt markerPoints[24] = {2,1,3,1,4,1,5,1,6,1,7,1,8,1,9,1,10,1,11,1,12,1,13,1};
PetscInt dim = 3, depth = 1, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(dm, dim);CHKERRQ(ierr);
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for(p = 0; p < 12; ++p) {
ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);
}
*newdm = dm;
PetscFunctionReturn(0);
}
static PetscErrorCode AddIdentityLabel(DM dm)
{
PetscInt pStart,pEnd,p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreateLabel(dm, "identity");CHKERRQ(ierr);
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; p++) {ierr = DMSetLabelValue(dm, "identity", p, p);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);
}
PetscErrorCode CreateHex_3D(MPI_Comm comm, DM dm)
{
PetscInt depth = 1, testNum = 0, p;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (!rank) {
switch (testNum) {
case 0:
{
PetscInt numPoints[2] = {12, 2};
PetscInt coneSize[14] = {8, 8, 0,0,0,0,0,0,0,0,0,0,0,0};
PetscInt cones[16] = {2,5,4,3,6,7,8,9, 3,4,11,10,7,12,13,8};
PetscInt coneOrientations[16] = {0,0,0,0,0,0,0,0, 0,0, 0, 0,0, 0, 0,0};
PetscScalar vertexCoords[36] = {-0.5,0.0,0.0, 0.0,0.0,0.0, 0.0,1.0,0.0, -0.5,1.0,0.0,
-0.5,0.0,1.0, 0.0,0.0,1.0, 0.0,1.0,1.0, -0.5,1.0,1.0,
0.5,0.0,0.0, 0.5,1.0,0.0, 0.5,0.0,1.0, 0.5,1.0,1.0};
PetscInt markerPoints[16] = {2,1,3,1,4,1,5,1,6,1,7,1,8,1,9,1};
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for(p = 0; p < 8; ++p) {
ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);
}
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "No test mesh %d", testNum);
}
} else {
PetscInt numPoints[2] = {0, 0};
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode CreateSimplex_2D(MPI_Comm comm, DM *newdm)
{
DM dm;
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] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5};
PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1};
PetscInt dim = 2, depth = 1, p;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(dm, dim);CHKERRQ(ierr);
ierr = DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for (p = 0; p < 4; ++p) {
ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);
}
*newdm = dm;
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat Amat;
PetscErrorCode ierr;
SNES snes;
KSP ksp;
MPI_Comm comm;
PetscMPIInt npe,rank;
PetscLogStage stage[7];
PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE;
Vec xx,bb;
PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1;
DM dm,distdm,basedm;
PetscBool flg;
char convType[256];
PetscReal Lx,mdisp[10],err[10];
const char * const options[10] = {"-ex56_dm_refine 0",
"-ex56_dm_refine 1",
"-ex56_dm_refine 2",
"-ex56_dm_refine 3",
"-ex56_dm_refine 4",
"-ex56_dm_refine 5",
"-ex56_dm_refine 6",
"-ex56_dm_refine 7",
"-ex56_dm_refine 8",
"-ex56_dm_refine 9"};
PetscFunctionBeginUser;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr);
/* options */
ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr);
{
i = 3;
ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr);
Lx = 1.; /* or ne for rod */
max_conv_its = 3;
ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr);
if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its);
ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr);
i = 3;
ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr);
if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr);
/* create DM, Plex calls DMSetup */
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
{
DMLabel label;
IS is;
ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr);
ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr);
if (run_type==0) {
ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr);
ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr);
if (is) {
PetscInt d, f, Nf;
const PetscInt *faces;
PetscInt csize;
PetscSection cs;
Vec coordinates ;
DM cdm;
ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr);
ierr = ISGetIndices(is, &faces);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr);
/* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
for (f = 0; f < Nf; ++f) {
PetscReal faceCoord;
PetscInt b,v;
PetscScalar *coords = NULL;
PetscInt Nv;
ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
Nv = csize/dim; /* Calculate mean coordinate vector */
for (d = 0; d < dim; ++d) {
faceCoord = 0.0;
for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
faceCoord /= Nv;
for (b = 0; b < 2; ++b) {
if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */
ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr);
}
}
}
ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr);
}
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr);
ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr);
}
}
{
PetscInt dimEmbed, i;
PetscInt nCoords;
PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */
Vec coordinates;
if (run_type==1) {
for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0;
}
ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr);
ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
for (i = 0; i < nCoords; i += dimEmbed) {
PetscInt j;
PetscScalar *coord = &coords[i];
for (j = 0; j < dimEmbed; j++) {
coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]);
}
}
ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
}
/* convert to p4est, and distribute */
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM newdm;
ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr);
if (newdm) {
const char *prefix;
PetscBool isForest;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr);
ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr);
if (isForest) {
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?");
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = newdm;
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?");
} else {
/* Plex Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr);
if (distdm) {
const char *prefix;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = distdm;
}
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
basedm = dm; dm = NULL;
for (iter=0 ; iter<max_conv_its ; iter++) {
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
/* make new DM */
ierr = DMClone(basedm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr);
ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr);
ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */
/* snes */
ierr = SNESCreate(comm, &snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
/* fem */
{
const PetscInt Ncomp = dim;
const PetscInt components[] = {0,1,2};
const PetscInt Nfid = 1, Npid = 1;
const PetscInt fid[] = {1}; /* The fixed faces (x=0) */
const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */
PetscFE fe;
PetscDS prob;
DM cdm = dm;
ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */
ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr);
/* FEM prob */
ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
/* setup problem */
if (run_type==1) {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr);
} else {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr);
}
/* bcs */
if (run_type==1) {
PetscInt id = 1;
ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr);
} else {
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr);
ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr);
}
while (cdm) {
ierr = DMSetDS(cdm,prob);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
}
/* vecs & mat */
ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr);
ierr = VecGetSize(bb,&N);CHKERRQ(ierr);
local_sizes[iter] = N;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr);
if (use_nearnullspace && N/dim > 1) {
/* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
DM subdm;
MatNullSpace nearNullSpace;
PetscInt fields = 0;
PetscObject deformation;
ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr);
ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr);
ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr);
ierr = DMDestroy(&subdm);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */
}
ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr);
/* ksp */
ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
/* test BCs */
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
if (test_nonzero_cols) {
if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(xx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(xx);CHKERRQ(ierr);
}
ierr = VecZeroEntries(bb);CHKERRQ(ierr);
ierr = VecGetSize(bb,&i);CHKERRQ(ierr);
local_sizes[iter] = i;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr);
/* setup solver, dummy solve to really setup */
if (0) {
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr);
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
/* solve */
ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
{
PetscViewer viewer = NULL;
PetscViewerFormat fmt;
ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
ierr = VecView(xx,viewer);CHKERRQ(ierr);
ierr = VecView(bb,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Free work space */
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&bb);CHKERRQ(ierr);
ierr = MatDestroy(&Amat);CHKERRQ(ierr);
}
ierr = DMDestroy(&basedm);CHKERRQ(ierr);
if (run_type==1) {
err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */
} else {
err[0] = 171.038 - mdisp[0];
}
for (iter=1 ; iter<max_conv_its ; iter++) {
if (run_type==1) {
err[iter] = 59.975208 - mdisp[iter];
} else {
err[iter] = 171.038 - mdisp[iter];
}
PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n",
rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter],
mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.));
}
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode CreateTensorProductHybrid_3D(MPI_Comm comm, PetscInt testNum, DM *dm)
{
DM idm, hdm = NULL;
DMLabel faultLabel;
PetscInt p;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
if (!rank) {
switch (testNum) {
case 0:
{
PetscInt numPoints[2] = {12, 2};
PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8};
PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5,
-1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5,
1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5};
PetscInt faultPoints[4] = {2, 3, 5, 6};
ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for(p = 0; p < 4; ++p) {ierr = DMSetLabelValue(*dm, "fault", faultPoints[p], 1);CHKERRQ(ierr);}
}
break;
case 1:
{
PetscInt numPoints[2] = {30, 7};
PetscInt coneSize[37] = {8,8,8,8,8,8,8, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
PetscInt cones[56] = { 8, 21, 20, 7, 13, 12, 23, 24,
14, 15, 10, 9, 13, 8, 21, 24,
15, 16, 11, 10, 24, 21, 22, 25,
30, 29, 28, 21, 35, 24, 33, 34,
24, 21, 30, 35, 25, 36, 31, 22,
27, 20, 21, 28, 32, 33, 24, 23,
15, 24, 13, 14, 19, 18, 17, 26};
PetscInt coneOrientations[56] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
PetscScalar vertexCoords[90] = {-2.0, -2.0, -2.0, -2.0, -1.0, -2.0, -3.0, 0.0, -2.0, -2.0, 1.0, -2.0, -2.0, 2.0, -2.0, -2.0, -2.0, 0.0,
-2.0, -1.0, 0.0, -3.0, 0.0, 0.0, -2.0, 1.0, 0.0, -2.0, 2.0, 0.0, -2.0, -1.0, 2.0, -3.0, 0.0, 2.0,
-2.0, 1.0, 2.0, 0.0, -2.0, -2.0, 0.0, 0.0, -2.0, 0.0, 2.0, -2.0, 0.0, -2.0, 0.0, 0.0, 0.0, 0.0,
0.0, 2.0, 0.0, 0.0, 0.0, 2.0, 2.0, -2.0, -2.0, 2.0, -1.0, -2.0, 3.0, 0.0, -2.0, 2.0, 1.0, -2.0,
2.0, 2.0, -2.0, 2.0, -2.0, 0.0, 2.0, -1.0, 0.0, 3.0, 0.0, 0.0, 2.0, 1.0, 0.0, 2.0, 2.0, 0.0};
PetscInt faultPoints[6] = {20, 21, 22, 23, 24, 25};
ierr = DMPlexCreateFromDAG(*dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr);
for(p = 0; p < 6; ++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, NULL, NULL, NULL, &hdm);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);
}
/* 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);
}
/*@
DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file ID.
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. exoid - The ExodusII id associated with a exodus file and obtained using ex_open
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Level: beginner
.keywords: mesh,ExodusII
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
{
#if defined(PETSC_HAVE_EXODUSII)
PetscMPIInt num_proc, rank;
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt coordSize, v;
PetscErrorCode ierr;
/* Read from ex_get_init() */
char title[PETSC_MAX_PATH_LEN+1];
int dim = 0, numVertices = 0, numCells = 0;
int num_cs = 0, num_vs = 0, num_fs = 0;
#endif
PetscFunctionBegin;
#if defined(PETSC_HAVE_EXODUSII)
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
/* Open EXODUS II file and read basic informations on rank 0, then broadcast to all processors */
if (!rank) {
ierr = PetscMemzero(title,(PETSC_MAX_PATH_LEN+1)*sizeof(char));CHKERRQ(ierr);
ierr = ex_get_init(exoid, title, &dim, &numVertices, &numCells, &num_cs, &num_vs, &num_fs);
if (ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"ExodusII ex_get_init() failed with error code %D\n",ierr);
if (!num_cs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any cell set\n");
}
ierr = MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, title);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);
/* Read cell sets information */
if (!rank) {
PetscInt *cone;
int c, cs, c_loc, v, v_loc;
/* Read from ex_get_elem_blk_ids() */
int *cs_id;
/* Read from ex_get_elem_block() */
char buffer[PETSC_MAX_PATH_LEN+1];
int num_cell_in_set, num_vertex_per_cell, num_attr;
/* Read from ex_get_elem_conn() */
int *cs_connect;
/* Get cell sets IDs */
ierr = PetscMalloc1(num_cs, &cs_id);CHKERRQ(ierr);
ierr = ex_get_elem_blk_ids(exoid, cs_id);CHKERRQ(ierr);
/* Read the cell set connectivity table and build mesh topology
EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
/* First set sizes */
for (cs = 0, c = 0; cs < num_cs; cs++) {
ierr = ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);CHKERRQ(ierr);
for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
ierr = DMPlexSetConeSize(*dm, c, num_vertex_per_cell);CHKERRQ(ierr);
}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
for (cs = 0, c = 0; cs < num_cs; cs++) {
ierr = ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);CHKERRQ(ierr);
ierr = PetscMalloc2(num_vertex_per_cell*num_cell_in_set,&cs_connect,num_vertex_per_cell,&cone);CHKERRQ(ierr);
ierr = ex_get_elem_conn(exoid, cs_id[cs], cs_connect);CHKERRQ(ierr);
/* EXO uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
cone[v_loc] = cs_connect[v]+numCells-1;
}
if (dim == 3) {
/* Tetrahedra are inverted */
if (num_vertex_per_cell == 4) {
PetscInt tmp = cone[0];
cone[0] = cone[1];
cone[1] = tmp;
}
/* Hexahedra are inverted */
if (num_vertex_per_cell == 8) {
PetscInt tmp = cone[1];
cone[1] = cone[3];
cone[3] = tmp;
}
}
ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
ierr = DMSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);CHKERRQ(ierr);
}
ierr = PetscFree2(cs_connect,cone);CHKERRQ(ierr);
}
ierr = PetscFree(cs_id);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
/* Maintain Cell Sets label */
{
DMLabel label;
ierr = DMRemoveLabel(*dm, "Cell Sets", &label);CHKERRQ(ierr);
if (label) {ierr = DMAddLabel(idm, label);CHKERRQ(ierr);}
}
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
/* Create vertex set label */
if (!rank && (num_vs > 0)) {
int vs, v;
/* Read from ex_get_node_set_ids() */
int *vs_id;
/* Read from ex_get_node_set_param() */
int num_vertex_in_set, num_attr;
/* Read from ex_get_node_set() */
int *vs_vertex_list;
/* Get vertex set ids */
ierr = PetscMalloc1(num_vs, &vs_id);CHKERRQ(ierr);
ierr = ex_get_node_set_ids(exoid, vs_id);CHKERRQ(ierr);
for (vs = 0; vs < num_vs; ++vs) {
ierr = ex_get_node_set_param(exoid, vs_id[vs], &num_vertex_in_set, &num_attr);CHKERRQ(ierr);
ierr = PetscMalloc1(num_vertex_in_set, &vs_vertex_list);CHKERRQ(ierr);
ierr = ex_get_node_set(exoid, vs_id[vs], vs_vertex_list);CHKERRQ(ierr);
for (v = 0; v < num_vertex_in_set; ++v) {
ierr = DMSetLabelValue(*dm, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);CHKERRQ(ierr);
}
ierr = PetscFree(vs_vertex_list);CHKERRQ(ierr);
}
ierr = PetscFree(vs_id);CHKERRQ(ierr);
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr);
ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
float *x, *y, *z;
ierr = PetscMalloc3(numVertices,&x,numVertices,&y,numVertices,&z);CHKERRQ(ierr);
ierr = ex_get_coord(exoid, x, y, z);CHKERRQ(ierr);
if (dim > 0) {
for (v = 0; v < numVertices; ++v) coords[v*dim+0] = x[v];
}
if (dim > 1) {
for (v = 0; v < numVertices; ++v) coords[v*dim+1] = y[v];
}
if (dim > 2) {
for (v = 0; v < numVertices; ++v) coords[v*dim+2] = z[v];
}
ierr = PetscFree3(x,y,z);CHKERRQ(ierr);
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
/* Create side set label */
if (!rank && interpolate && (num_fs > 0)) {
int fs, f, voff;
/* Read from ex_get_side_set_ids() */
int *fs_id;
/* Read from ex_get_side_set_param() */
int num_side_in_set, num_dist_fact_in_set;
/* Read from ex_get_side_set_node_list() */
int *fs_vertex_count_list, *fs_vertex_list;
/* Get side set ids */
ierr = PetscMalloc1(num_fs, &fs_id);CHKERRQ(ierr);
ierr = ex_get_side_set_ids(exoid, fs_id);CHKERRQ(ierr);
for (fs = 0; fs < num_fs; ++fs) {
ierr = ex_get_side_set_param(exoid, fs_id[fs], &num_side_in_set, &num_dist_fact_in_set);CHKERRQ(ierr);
ierr = PetscMalloc2(num_side_in_set,&fs_vertex_count_list,num_side_in_set*4,&fs_vertex_list);CHKERRQ(ierr);
ierr = ex_get_side_set_node_list(exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list);CHKERRQ(ierr);
for (f = 0, voff = 0; f < num_side_in_set; ++f) {
const PetscInt *faces = NULL;
PetscInt faceSize = fs_vertex_count_list[f], numFaces;
PetscInt faceVertices[4], v;
if (faceSize > 4) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %d > 4 vertices", faceSize);
for (v = 0; v < faceSize; ++v, ++voff) {
faceVertices[v] = fs_vertex_list[voff]+numCells-1;
}
ierr = DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);CHKERRQ(ierr);
if (numFaces != 1) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %d faces", f, fs, numFaces);
ierr = DMSetLabelValue(*dm, "Face Sets", faces[0], fs_id[fs]);CHKERRQ(ierr);
ierr = DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);CHKERRQ(ierr);
}
ierr = PetscFree2(fs_vertex_count_list,fs_vertex_list);CHKERRQ(ierr);
}
ierr = PetscFree(fs_id);CHKERRQ(ierr);
}
#else
SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
PetscFunctionReturn(0);
}
/*@
DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file viewer
Collective on comm
Input Parameters:
+ comm - The MPI communicator
. viewer - The Viewer associated with a Gmsh file
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format
and http://www.geuz.org/gmsh/doc/texinfo/#MSH-binary-file-format
Level: beginner
.keywords: mesh,Gmsh
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
PetscViewerType vtype;
GmshElement *gmsh_elem;
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords, *coordsIn = NULL;
PetscInt dim = 0, coordSize, c, v, d, r, cell;
int i, numVertices = 0, numCells = 0, trueNumCells = 0, numRegions = 0, snum;
PetscMPIInt num_proc, rank;
char line[PETSC_MAX_PATH_LEN];
PetscBool match, binary, bswap = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = PetscLogEventBegin(DMPLEX_CreateGmsh,*dm,0,0,0);CHKERRQ(ierr);
ierr = PetscViewerGetType(viewer, &vtype);CHKERRQ(ierr);
ierr = PetscStrcmp(vtype, PETSCVIEWERBINARY, &binary);CHKERRQ(ierr);
if (!rank || binary) {
PetscBool match;
int fileType, dataSize;
float version;
/* Read header */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$MeshFormat", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(viewer, line, 3, NULL, PETSC_STRING);CHKERRQ(ierr);
snum = sscanf(line, "%f %d %d", &version, &fileType, &dataSize);
if (snum != 3) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Gmsh file header: %s", line);
if (version < 2.0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Gmsh file must be at least version 2.0");
if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize);
if (binary) {
int checkInt;
ierr = PetscViewerRead(viewer, &checkInt, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
if (checkInt != 1) {
ierr = PetscByteSwap(&checkInt, PETSC_ENUM, 1);CHKERRQ(ierr);
if (checkInt == 1) bswap = PETSC_TRUE;
else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh binary file", fileType);
}
} else if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType);
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$EndMeshFormat", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* OPTIONAL Read physical names */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$PhysicalNames", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (match) {
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
snum = sscanf(line, "%d", &numRegions);
if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
for (r = 0; r < numRegions; ++r) {
PetscInt rdim, tag;
ierr = PetscViewerRead(viewer, &rdim, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, &tag, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
}
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$EndPhysicalNames", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* Initial read for vertex section */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
}
/* Read vertices */
ierr = PetscStrncmp(line, "$Nodes", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
snum = sscanf(line, "%d", &numVertices);
if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscMalloc1(numVertices*3, &coordsIn);CHKERRQ(ierr);
if (binary) {
size_t doubleSize, intSize;
PetscInt elementSize;
char *buffer;
PetscScalar *baseptr;
ierr = PetscDataTypeGetSize(PETSC_ENUM, &intSize);CHKERRQ(ierr);
ierr = PetscDataTypeGetSize(PETSC_DOUBLE, &doubleSize);CHKERRQ(ierr);
elementSize = (intSize + 3*doubleSize);
ierr = PetscMalloc1(elementSize*numVertices, &buffer);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, buffer, elementSize*numVertices, NULL, PETSC_CHAR);CHKERRQ(ierr);
if (bswap) ierr = PetscByteSwap(buffer, PETSC_CHAR, elementSize*numVertices);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
baseptr = ((PetscScalar*)(buffer+v*elementSize+intSize));
coordsIn[v*3+0] = baseptr[0];
coordsIn[v*3+1] = baseptr[1];
coordsIn[v*3+2] = baseptr[2];
}
ierr = PetscFree(buffer);CHKERRQ(ierr);
} else {
for (v = 0; v < numVertices; ++v) {
ierr = PetscViewerRead(viewer, &i, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerRead(viewer, &(coordsIn[v*3]), 3, NULL, PETSC_DOUBLE);CHKERRQ(ierr);
if (i != (int)v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1);
}
}
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
ierr = PetscStrncmp(line, "$EndNodes", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
/* Read cells */
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
ierr = PetscStrncmp(line, "$Elements", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
snum = sscanf(line, "%d", &numCells);
if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
}
if (!rank || binary) {
/* Gmsh elements can be of any dimension/co-dimension, so we need to traverse the
file contents multiple times to figure out the true number of cells and facets
in the given mesh. To make this more efficient we read the file contents only
once and store them in memory, while determining the true number of cells. */
ierr = DMPlexCreateGmsh_ReadElement(viewer, numCells, binary, bswap, &gmsh_elem);CHKERRQ(ierr);
for (trueNumCells=0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim > dim) {dim = gmsh_elem[c].dim; trueNumCells = 0;}
if (gmsh_elem[c].dim == dim) trueNumCells++;
}
ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
ierr = PetscStrncmp(line, "$EndElements", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
}
/* For binary we read on all ranks, but only build the plex on rank 0 */
if (binary && rank) {trueNumCells = 0; numVertices = 0;};
/* Allocate the cell-vertex mesh */
ierr = DMPlexSetChart(*dm, 0, trueNumCells+numVertices);CHKERRQ(ierr);
if (!rank) {
for (cell = 0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim) {
ierr = DMPlexSetConeSize(*dm, cell, gmsh_elem[c].numNodes);CHKERRQ(ierr);
cell++;
}
}
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
/* Add cell-vertex connections */
if (!rank) {
PetscInt pcone[8], corner;
for (cell = 0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim) {
for (corner = 0; corner < gmsh_elem[c].numNodes; ++corner) {
pcone[corner] = gmsh_elem[c].nodes[corner] + trueNumCells-1;
}
if (dim == 3) {
/* Tetrahedra are inverted */
if (gmsh_elem[c].numNodes == 4) {
PetscInt tmp = pcone[0];
pcone[0] = pcone[1];
pcone[1] = tmp;
}
/* Hexahedra are inverted */
if (gmsh_elem[c].numNodes == 8) {
PetscInt tmp = pcone[1];
pcone[1] = pcone[3];
pcone[3] = tmp;
}
}
ierr = DMPlexSetCone(*dm, cell, pcone);CHKERRQ(ierr);
cell++;
}
}
}
ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
if (interpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
if (!rank) {
/* Apply boundary IDs by finding the relevant facets with vertex joins */
PetscInt pcone[8], corner, vStart, vEnd;
ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim-1) {
PetscInt joinSize;
const PetscInt *join;
for (corner = 0; corner < gmsh_elem[c].numNodes; ++corner) {
pcone[corner] = gmsh_elem[c].nodes[corner] + vStart - 1;
}
ierr = DMPlexGetFullJoin(*dm, gmsh_elem[c].numNodes, (const PetscInt *) pcone, &joinSize, &join);CHKERRQ(ierr);
if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for element %d", gmsh_elem[c].id);
ierr = DMSetLabelValue(*dm, "Face Sets", join[0], gmsh_elem[c].tags[0]);CHKERRQ(ierr);
ierr = DMPlexRestoreJoin(*dm, gmsh_elem[c].numNodes, (const PetscInt *) pcone, &joinSize, &join);CHKERRQ(ierr);
}
}
/* Create cell sets */
for (cell = 0, c = 0; c < numCells; ++c) {
if (gmsh_elem[c].dim == dim) {
if (gmsh_elem[c].numTags > 0) {
ierr = DMSetLabelValue(*dm, "Cell Sets", cell, gmsh_elem[c].tags[0]);CHKERRQ(ierr);
cell++;
}
}
}
}
/* Read coordinates */
ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, trueNumCells, trueNumCells + numVertices);CHKERRQ(ierr);
for (v = trueNumCells; v < trueNumCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr);
ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
if (!rank) {
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < dim; ++d) {
coords[v*dim+d] = coordsIn[v*3+d];
}
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = PetscFree(coordsIn);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
/* Clean up intermediate storage */
if (!rank || binary) ierr = PetscFree(gmsh_elem);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_CreateGmsh,*dm,0,0,0);CHKERRQ(ierr);
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);
}
