static PetscErrorCode CreateBCLabel(DM dm, const char name[])
{
DMLabel label;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMCreateLabel(dm, name);
CHKERRQ(ierr);
ierr = DMGetLabel(dm, name, &label);
CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, label);
CHKERRQ(ierr);
ierr = DMPlexLabelComplete(dm, label);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
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);
}
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 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);
}
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);
if (user->bcType == NEUMANN) {
DMLabel label;
ierr = DMPlexCreateLabel(*dm, "boundary");CHKERRQ(ierr);
ierr = DMPlexGetLabel(*dm, "boundary", &label);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(*dm, label);CHKERRQ(ierr);
}
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN void PETSC_STDCALL dmplexmarkboundaryfaces_(DM dm,DMLabel label, int *__ierr ){
*__ierr = DMPlexMarkBoundaryFaces(
(DM)PetscToPointer((dm) ),
(DMLabel)PetscToPointer((label) ));
}
