PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
const char *filename = user->filename;
PetscInt dim = user->dim;
size_t len;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (!len) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);}
else {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);}
ierr = DMViewFromOptions(*dm, NULL, "-orig_dm_view");CHKERRQ(ierr);
{
DM distributedMesh = NULL;
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
ierr = DMViewFromOptions(*dm, NULL, "-dist_dm_view");CHKERRQ(ierr);
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
if (user->uninterpolate) {
DM udm = NULL;
ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = udm;
ierr = DMViewFromOptions(*dm, NULL, "-un_dm_view");CHKERRQ(ierr);
}
ierr = PetscObjectSetName((PetscObject) *dm, "Test Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *ctx, DM *dm)
{
PetscInt dim = ctx->dim;
PetscBool cellSimplex = ctx->cellSimplex;
const char *filename = ctx->filename;
const PetscInt cells[3] = {1, 1, 1};
size_t len;
PetscMPIInt rank, size;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);}
else {ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);}
{
DM distributedMesh = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
const char *partitioner = user->partitioner;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
{
DM refinedMesh = NULL;
DM distributedMesh = NULL;
/* Refine mesh using a volume constraint */
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool refinementUniform = user->refinementUniform;
PetscBool cellSimplex = user->cellSimplex;
const char *partitioner = "chaco";
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);
switch(dim) {
case 2:
if (cellSimplex) {
ierr = CreateSimplexHybrid_2D(comm, *dm);CHKERRQ(ierr);
} else {
SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make hybrid meshes for quadrilaterals");
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make hybrid meshes for dimension %d", dim);
}
{
DM refinedMesh = PETSC_NULL;
DM distributedMesh = PETSC_NULL;
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
PetscInt cMax = PETSC_DETERMINE, fMax = PETSC_DETERMINE;
/* Do not know how to preserve this after distribution */
if (rank) {
cMax = 1;
fMax = 11;
}
ierr = DMPlexSetHybridBounds(distributedMesh, cMax, PETSC_DETERMINE, fMax, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
if (refinementUniform) {
ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Hybrid Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
DM createMesh(MPI_Comm comm, const char name[])
{
DM dm = NULL;
DM dmDist = NULL;
DMPlexCreateExodusFromFile(comm, name, PETSC_TRUE, &dm);
DMPlexDistribute(dm, 0, NULL, &dmDist);
if (dmDist) {DMDestroy(&dm);}
return dmDist;
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Create box mesh */
ierr = DMPlexCreateBoxMesh(comm, user->dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
/* Distribute mesh over processes */
{
DM dmDist = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmDist;
}
}
/* TODO: This should be pulled into the library */
{
char convType[256];
PetscBool flg;
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_plex_convert_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM dmConv;
ierr = DMConvert(*dm,convType,&dmConv);CHKERRQ(ierr);
if (dmConv) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
}
}
/* TODO: This should be pulled into the library */
ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMSetApplicationContext(*dm, user);CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
/* TODO: Add a hierachical viewer */
if (user->spectral) {
PetscInt planeDir[2] = {0, 1};
PetscReal planeCoord[2] = {0., 1.};
ierr = CreateSpectralPlanes(*dm, 2, planeDir, planeCoord, user);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexCreateBoxMesh(comm, dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
{
Parameter *param;
Vec coordinates;
PetscScalar *coords;
PetscReal alpha;
PetscInt cdim, N, bs, i;
ierr = DMGetCoordinateDim(*dm, &cdim);CHKERRQ(ierr);
ierr = DMGetCoordinates(*dm, &coordinates);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr);
ierr = VecGetBlockSize(coordinates, &bs);CHKERRQ(ierr);
if (bs != cdim) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Invalid coordinate blocksize %D != embedding dimension %D", bs, cdim);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr);
alpha = param->alpha;
for (i = 0; i < N; i += cdim) {
PetscScalar x = coords[i+0];
PetscScalar y = coords[i+1];
coords[i+0] = PetscCosReal(alpha)*x - PetscSinReal(alpha)*y;
coords[i+1] = PetscSinReal(alpha)*x + PetscCosReal(alpha)*y;
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinates(*dm, coordinates);CHKERRQ(ierr);
}
{
DM pdm = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr);
if (pdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = pdm;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
DM distributedMesh = NULL;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexCreateBoxMesh(comm, 2, PETSC_TRUE, dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool cellSimplex = user->cellSimplex;
const char *filename = user->filename;
size_t len;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {
ierr = DMPlexCreateFromFile(comm, filename, PETSC_FALSE, dm);CHKERRQ(ierr);
ierr = DMGetDimension(*dm, &dim);CHKERRQ(ierr);
} else {
PetscReal L[3] = {1.0, 1.0, 1.0};
PetscReal maxCell[3];
PetscInt d;
for (d = 0; d < dim; ++d) {maxCell[d] = (1.0/user->faces[d])*1.1;}
ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, user->faces, NULL, NULL, user->periodicity, PETSC_TRUE, dm);CHKERRQ(ierr);
ierr = DMSetPeriodicity(*dm, user->isPeriodic, maxCell, L, user->periodicity);CHKERRQ(ierr);
}
{
DM pdm = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr);
if (pdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = pdm;
}
}
ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
const char *partitioner = "chaco";
PetscErrorCode ierr;
PetscFunctionBegin;
if (user->simplex) {
DM refinedMesh = NULL;
DM distributedMesh = NULL;
ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
/* Refine mesh using a volume constraint */
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr);
} else {
switch (user->dim) {
case 2:
ierr = DMDACreate2d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_BOX, -3, -3, PETSC_DETERMINE, PETSC_DETERMINE, 1, 1, NULL, NULL, dm);CHKERRQ(ierr);
ierr = DMDASetVertexCoordinates(*dm, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
break;
default:
SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot create structured mesh of dimension %d", dim);
}
ierr = PetscObjectSetName((PetscObject) *dm, "Hexahedral Mesh");CHKERRQ(ierr);
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool simplex = user->cellSimplex;
PetscInt cells[3] = {1, 1, 1};
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexCreateBoxMesh(comm, dim, simplex, cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
{
DM ddm = NULL;
ierr = DMPlexDistribute(*dm, 0, NULL, &ddm);CHKERRQ(ierr);
if (ddm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = ddm;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-orig_dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, DM *dm, AppCtx *ctx)
{
DM pdm = NULL;
const PetscInt dim = ctx->dim;
PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */
PetscBool hasLabel;
PetscErrorCode ierr;
PetscFunctionBeginUser;
if (ctx->simplex) {
ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_TRUE, dm);
CHKERRQ(ierr);
} else {
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);
CHKERRQ(ierr);
}
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");
CHKERRQ(ierr);
/* If no boundary marker exists, mark the whole boundary */
ierr = DMHasLabel(*dm, "marker", &hasLabel);
CHKERRQ(ierr);
if (!hasLabel) {
ierr = CreateBCLabel(*dm, "marker");
CHKERRQ(ierr);
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);
CHKERRQ(ierr);
if (pdm) {
ierr = DMDestroy(dm);
CHKERRQ(ierr);
*dm = pdm;
}
ierr = DMSetFromOptions(*dm);
CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscBool flg;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexCreateBoxMesh(comm, user->dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
{
DM pdm = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr);
if (pdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = pdm;
}
}
ierr = PetscStrcmp(user->dmType, DMPLEX, &flg);CHKERRQ(ierr);
if (flg) {
DM ndm;
ierr = DMConvert(*dm, user->dmType, &ndm);CHKERRQ(ierr);
if (ndm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = ndm;
}
}
ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
ierr = DMSetApplicationContext(*dm, user);CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMNetworkDistribute - Distributes the network and moves associated component data.
Collective
Input Parameter:
+ oldDM - the original DMNetwork object
- overlap - The overlap of partitions, 0 is the default
Output Parameter:
. distDM - the distributed DMNetwork object
Notes:
This routine should be called only when using multiple processors.
Distributes the network with <overlap>-overlapping partitioning of the edges.
Level: intermediate
.seealso: DMNetworkCreate
@*/
PetscErrorCode DMNetworkDistribute(DM oldDM, PetscInt overlap,DM *distDM)
{
PetscErrorCode ierr;
DM_Network *oldDMnetwork = (DM_Network*)oldDM->data;
PetscSF pointsf;
DM newDM;
DM_Network *newDMnetwork;
PetscFunctionBegin;
ierr = DMNetworkCreate(PetscObjectComm((PetscObject)oldDM),&newDM);CHKERRQ(ierr);
newDMnetwork = (DM_Network*)newDM->data;
newDMnetwork->dataheadersize = sizeof(struct _p_DMNetworkComponentHeader)/sizeof(DMNetworkComponentGenericDataType);
/* Distribute plex dm and dof section */
ierr = DMPlexDistribute(oldDMnetwork->plex,overlap,&pointsf,&newDMnetwork->plex);CHKERRQ(ierr);
/* Distribute dof section */
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)oldDM),&newDMnetwork->DofSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointsf,oldDMnetwork->DofSection,NULL,newDMnetwork->DofSection);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject)oldDM),&newDMnetwork->DataSection);CHKERRQ(ierr);
/* Distribute data and associated section */
ierr = DMPlexDistributeData(newDMnetwork->plex,pointsf,oldDMnetwork->DataSection,MPI_INT,(void*)oldDMnetwork->componentdataarray,newDMnetwork->DataSection,(void**)&newDMnetwork->componentdataarray);CHKERRQ(ierr);
/* Destroy point SF */
ierr = PetscSFDestroy(&pointsf);CHKERRQ(ierr);
ierr = PetscSectionGetChart(newDMnetwork->DataSection,&newDMnetwork->pStart,&newDMnetwork->pEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(newDMnetwork->plex,0, &newDMnetwork->eStart,&newDMnetwork->eEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(newDMnetwork->plex,1,&newDMnetwork->vStart,&newDMnetwork->vEnd);CHKERRQ(ierr);
newDMnetwork->nEdges = newDMnetwork->eEnd - newDMnetwork->eStart;
newDMnetwork->nNodes = newDMnetwork->vEnd - newDMnetwork->vStart;
newDMnetwork->NNodes = oldDMnetwork->NNodes;
newDMnetwork->NEdges = oldDMnetwork->NEdges;
/* Set Dof section as the default section for dm */
ierr = DMSetDefaultSection(newDMnetwork->plex,newDMnetwork->DofSection);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(newDMnetwork->plex,&newDMnetwork->GlobalDofSection);CHKERRQ(ierr);
*distDM = newDM;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool cellSimplex = user->cellSimplex;
PetscBool useGenerator = user->useGenerator;
const char *filename = user->filename;
size_t len;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {
ierr = DMPlexCreateFromFile(comm, filename, PETSC_FALSE, dm);CHKERRQ(ierr);
ierr = DMGetDimension(*dm, &dim);CHKERRQ(ierr);
} else if (useGenerator) {
if (cellSimplex) {
ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, PETSC_FALSE, dm);CHKERRQ(ierr);
} else {
const PetscInt cells[3] = {2, 2, 2};
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, dm);CHKERRQ(ierr);
}
} else {
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
switch (dim) {
case 2:
if (cellSimplex) {
ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr);
} else {
ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr);
}
break;
case 3:
if (cellSimplex) {
ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr);
} else {
ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr);
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
}
}
{
DM interpolatedMesh = NULL;
ierr = CheckMesh(*dm, user);CHKERRQ(ierr);
ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr);
ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = interpolatedMesh;
}
{
DM distributedMesh = NULL;
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMViewFromOptions(distributedMesh, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
int main(int argc,char **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;
}
int main(int argc, char **argv)
{
MPI_Comm comm;
DM dm;
Vec v, nv, rv, coord;
PetscBool test_read = PETSC_FALSE, verbose = PETSC_FALSE, flg;
PetscViewer hdf5Viewer;
PetscInt dim = 2;
PetscInt numFields = 1;
PetscInt numBC = 0;
PetscInt numComp[1] = {2};
PetscInt numDof[3] = {2, 0, 0};
PetscInt bcFields[1] = {0};
IS bcPoints[1] = {NULL};
PetscSection section;
PetscReal norm;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, (char *) 0, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Test Options","none");CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_read","Test reading from the HDF5 file","",PETSC_FALSE,&test_read,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-verbose","print the Vecs","",PETSC_FALSE,&verbose,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim","the dimension of the problem","",2,&dim,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, &dm);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
numDof[0] = dim;
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, NULL, NULL, §ion);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMSetUseNatural(dm, PETSC_TRUE);CHKERRQ(ierr);
{
DM dmDist;
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = dmDist;
}
}
ierr = DMCreateGlobalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) v, "V");CHKERRQ(ierr);
ierr = DMGetCoordinates(dm, &coord);CHKERRQ(ierr);
ierr = VecCopy(coord, v);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(v, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== original V in global ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(v, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = DMCreateGlobalVector(dm, &nv);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) nv, "NV");CHKERRQ(ierr);
ierr = DMPlexGlobalToNaturalBegin(dm, v, nv);CHKERRQ(ierr);
ierr = DMPlexGlobalToNaturalEnd(dm, v, nv);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(nv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(nv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== V in natural ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(nv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecViewFromOptions(v, NULL, "-global_vec_view");CHKERRQ(ierr);
if (test_read) {
ierr = DMCreateGlobalVector(dm, &rv);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) rv, "V");CHKERRQ(ierr);
/* Test native read */
ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(rv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecEqual(rv, v, &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are not equal\n\n");CHKERRQ(ierr);
ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr);
ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Test raw read */
ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr);
ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(rv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecEqual(rv, nv, &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are not equal\n\n");CHKERRQ(ierr);
ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr);
ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecDestroy(&rv);CHKERRQ(ierr);
}
ierr = VecDestroy(&nv);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
PetscBool cellSimplex = user->cellSimplex;
const char *filename = user->filename;
PetscInt triSizes_n2[2] = {4, 4};
PetscInt triPoints_n2[8] = {3, 5, 6, 7, 0, 1, 2, 4};
PetscInt triSizes_n8[8] = {1, 1, 1, 1, 1, 1, 1, 1};
PetscInt triPoints_n8[8] = {0, 1, 2, 3, 4, 5, 6, 7};
PetscInt quadSizes[2] = {2, 2};
PetscInt quadPoints[4] = {2, 3, 0, 1};
const PetscInt cells[3] = {2, 2, 2};
size_t len;
PetscMPIInt rank, numProcs;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr);}
else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, dim == 2 ? 2 : 1, interpolate, dm);CHKERRQ(ierr);}
else {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);}
{
DM refinedMesh = NULL;
DM distributedMesh = NULL;
if (user->testPartition) {
const PetscInt *sizes = NULL;
const PetscInt *points = NULL;
PetscPartitioner part;
if (!rank) {
if (dim == 2 && cellSimplex && numProcs == 2) {
sizes = triSizes_n2; points = triPoints_n2;
} else if (dim == 2 && cellSimplex && numProcs == 8) {
sizes = triSizes_n8; points = triPoints_n8;
} else if (dim == 2 && !cellSimplex && numProcs == 2) {
sizes = quadSizes; points = quadPoints;
}
}
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr);
ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr);
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
/* Refine mesh using a volume constraint */
ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
if (user->overlap) {
DM overlapMesh = NULL;
/* Add the level-1 overlap to refined mesh */
ierr = DMPlexDistributeOverlap(*dm, 1, NULL, &overlapMesh);CHKERRQ(ierr);
if (overlapMesh) {
ierr = DMView(overlapMesh, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = overlapMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Simplicial Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool cellHybrid = user->cellHybrid;
PetscBool cellSimplex = user->cellSimplex;
PetscMPIInt rank, size;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
switch (dim) {
case 1:
if (cellHybrid) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make hybrid meshes for dimension %d", dim);
ierr = CreateSimplex_1D(comm, dm);CHKERRQ(ierr);
break;
case 2:
if (cellSimplex) {
if (cellHybrid) {
ierr = CreateSimplexHybrid_2D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateSimplex_2D(comm, dm);CHKERRQ(ierr);
}
} else {
if (cellHybrid) {
ierr = CreateTensorProductHybrid_2D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateTensorProduct_2D(comm, user->testNum, dm);CHKERRQ(ierr);
}
}
break;
case 3:
if (cellSimplex) {
if (cellHybrid) {
ierr = CreateSimplexHybrid_3D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateSimplex_3D(comm, user->testNum, dm);CHKERRQ(ierr);
}
} else {
if (cellHybrid) {
ierr = CreateTensorProductHybrid_3D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateTensorProduct_3D(comm, user->testNum, dm);CHKERRQ(ierr);
}
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
}
if (user->testPartition && size > 1) {
PetscPartitioner part;
PetscInt *sizes = NULL;
PetscInt *points = NULL;
if (!rank) {
if (dim == 2 && cellSimplex && !cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt triSizes_p2[2] = {1, 1};
PetscInt triPoints_p2[2] = {0, 1};
ierr = PetscMalloc2(2, &sizes, 2, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, triSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, triPoints_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for triangular mesh on 2 procs", user->testNum);
}
} else if (dim == 2 && cellSimplex && cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt triSizes_p2[2] = {1, 2};
PetscInt triPoints_p2[3] = {0, 1, 2};
ierr = PetscMalloc2(2, &sizes, 3, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, triSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, triPoints_p2, 3 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for triangular hybrid mesh on 2 procs", user->testNum);
}
} else if (dim == 2 && !cellSimplex && !cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt quadSizes_p2[2] = {1, 1};
PetscInt quadPoints_p2[2] = {0, 1};
ierr = PetscMalloc2(2, &sizes, 2, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, quadSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, quadPoints_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for quadrilateral mesh on 2 procs", user->testNum);
}
} else if (dim == 2 && !cellSimplex && cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt quadSizes_p2[2] = {1, 2};
PetscInt quadPoints_p2[3] = {0, 1, 2};
ierr = PetscMalloc2(2, &sizes, 3, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, quadSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, quadPoints_p2, 3 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for quadrilateral hybrid mesh on 2 procs", user->testNum);
}
} else if (dim == 3 && cellSimplex && !cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt tetSizes_p2[2] = {1, 1};
PetscInt tetPoints_p2[2] = {0, 1};
ierr = PetscMalloc2(2, &sizes, 2, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, tetSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, tetPoints_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);break;}
case 1: {
PetscInt tetSizes_p2[2] = {1, 1};
PetscInt tetPoints_p2[2] = {0, 1};
ierr = PetscMalloc2(2, &sizes, 2, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, tetSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, tetPoints_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for tetrahedral mesh on 2 procs", user->testNum);
}
} else if (dim == 3 && cellSimplex && cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt tetSizes_p2[2] = {1, 2};
PetscInt tetPoints_p2[3] = {0, 1, 2};
ierr = PetscMalloc2(2, &sizes, 3, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, tetSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, tetPoints_p2, 3 * sizeof(PetscInt));CHKERRQ(ierr);break;}
case 1: {
PetscInt tetSizes_p2[2] = {3, 4};
PetscInt tetPoints_p2[7] = {0, 3, 5, 1, 2, 4, 6};
ierr = PetscMalloc2(2, &sizes, 7, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, tetSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, tetPoints_p2, 7 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for tetrahedral hybrid mesh on 2 procs", user->testNum);
}
} else if (dim == 3 && !cellSimplex && !cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt hexSizes_p2[2] = {1, 1};
PetscInt hexPoints_p2[2] = {0, 1};
ierr = PetscMalloc2(2, &sizes, 2, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, hexSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, hexPoints_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for hexahedral mesh on 2 procs", user->testNum);
}
} else if (dim == 3 && !cellSimplex && cellHybrid && size == 2) {
switch (user->testNum) {
case 0: {
PetscInt hexSizes_p2[2] = {1, 1};
PetscInt hexPoints_p2[2] = {0, 1};
ierr = PetscMalloc2(2, &sizes, 2, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, hexSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, hexPoints_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);break;}
case 1: {
PetscInt hexSizes_p2[2] = {5, 4};
PetscInt hexPoints_p2[9] = {3, 4, 5, 7, 8, 0, 1, 2, 6};
ierr = PetscMalloc2(2, &sizes, 9, &points);CHKERRQ(ierr);
ierr = PetscMemcpy(sizes, hexSizes_p2, 2 * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscMemcpy(points, hexPoints_p2, 9 * sizeof(PetscInt));CHKERRQ(ierr);break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for hexahedral hybrid mesh on 2 procs", user->testNum);
}
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test partition");
}
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr);
ierr = PetscPartitionerShellSetPartition(part, size, sizes, points);CHKERRQ(ierr);
ierr = PetscFree2(sizes, points);CHKERRQ(ierr);
} else {
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm,&part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
}
{
DM pdm = NULL;
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr);
if (pdm) {
ierr = DMViewFromOptions(pdm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = pdm;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
if (user->simplex2tensor) {
DM rdm = NULL;
ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexRefineSimplexToTensor(*dm, &rdm);CHKERRQ(ierr);
if (rdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = rdm;
}
user->cellSimplex = PETSC_FALSE;
}
if (user->uninterpolate || user->reinterpolate) {
DM udm = NULL;
ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = udm;
}
if (user->reinterpolate) {
DM idm = NULL;
ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = idm;
}
ierr = PetscObjectSetName((PetscObject) *dm, "Hybrid Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) *dm, "hyb_");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// Read in a mesh from a file
DM NewMesh(MPI_Comm comm, unsigned overlap) {
FILE * input = fopen("CubedSphere.mesh","r");
// Read in vertex co-ordinates
size_t dim = 3;
size_t vertex_count;
fscanf(input, " %zu ", &vertex_count);
assert(vertex_count == 1572866);
double * vertices = calloc(vertex_count*dim, sizeof(*vertices));
for (size_t vertex=0; vertex<vertex_count; ++vertex) {
for (int d=0; d<dim; ++d) {
int read = fscanf(input, " %lf ", &vertices[vertex*dim+d]);
assert(read == 1);
}
}
assert(vertices[0] == -1.00000000000000000);
assert(vertices[3] == -0.99999529380957619);
// Read in each face's vertex id
size_t corners = 4;
size_t face_count;
fscanf(input, " %zu ", &face_count);
assert(face_count == 1572864);
int * faces = calloc(face_count*corners, sizeof(*faces));
for (size_t face=0; face<face_count; ++face) {
for (int c=0; c<corners; ++c) {
int read = fscanf(input, " %d ", &faces[corners*face+c]);
assert(read == 1);
// Vertex ids are 0-based in petsc
--faces[corners*face+c];
}
}
assert(faces[0] == 1232838-1);
assert(faces[4] == 1233870-1);
fclose(input);
int rank;
MPI_Comm_rank(comm,&rank);
DM mesh = NULL;
if (rank == 0) {
DMPlexCreateFromCellList(comm, // MPI Communicator
2, // Spatial dimension of graph
face_count, // Number of faces
vertex_count, // Number of vertices
corners, // Number of vertices per face
PETSC_FALSE, // Create edges
faces, // Vertex IDs for each face
dim, // Vertex dimension
vertices, // Co-ordinates of each vertex
&mesh); // Output
} else {
DMPlexCreateFromCellList(comm, 2, 0, 0, corners, PETSC_FALSE,
NULL, dim, NULL, &mesh);
}
DM distmesh = NULL;
DMPlexDistribute(mesh, NULL, overlap, &distmesh);
if (distmesh) {
mesh = distmesh;
}
free(faces);
free(vertices);
return mesh;
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
PetscBool cellSimplex = user->cellSimplex;
PetscBool cellWedge = user->cellWedge;
PetscBool simplex2tensor = user->simplex2tensor;
const char *filename = user->filename;
const char *bdfilename = user->bdfilename;
const char *extfilename = user->extfilename;
PetscBool testp4est_seq = user->testp4est[0];
PetscBool testp4est_par = user->testp4est[1];
PetscInt triSizes_n2[2] = {4, 4};
PetscInt triPoints_n2[8] = {3, 5, 6, 7, 0, 1, 2, 4};
PetscInt triSizes_n8[8] = {1, 1, 1, 1, 1, 1, 1, 1};
PetscInt triPoints_n8[8] = {0, 1, 2, 3, 4, 5, 6, 7};
PetscInt quadSizes[2] = {2, 2};
PetscInt quadPoints[4] = {2, 3, 0, 1};
PetscInt gmshSizes_n3[3] = {14, 14, 14};
PetscInt gmshPoints_n3[42] = {1, 2, 4, 5, 9, 10, 11, 15, 16, 20, 21, 27, 28, 29,
3, 8, 12, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
0, 6, 7, 13, 14, 17, 18, 19, 22, 23, 24, 25, 26, 41};
PetscInt fluentSizes_n3[3] = {50, 50, 50};
PetscInt fluentPoints_n3[150] = { 5, 6, 7, 8, 12, 14, 16, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 50, 51, 80, 81, 89,
91, 93, 94, 95, 96, 97, 98, 99, 100, 101, 104, 121, 122, 124, 125, 126, 127, 128, 129, 131, 133, 143, 144, 145, 147,
1, 3, 4, 9, 10, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 47, 61, 71, 72, 73, 74,
75, 76, 77, 78, 79, 86, 87, 88, 90, 92, 113, 115, 116, 117, 118, 119, 120, 123, 138, 140, 141, 142, 146, 148, 149,
0, 2, 11, 13, 15, 20, 21, 22, 23, 49, 52, 53, 54, 55, 56, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67,
68, 69, 70, 82, 83, 84, 85, 102, 103, 105, 106, 107, 108, 109, 110, 111, 112, 114, 130, 132, 134, 135, 136, 137, 139};
size_t len, bdlen, extlen;
PetscMPIInt rank, size;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
ierr = PetscStrlen(bdfilename, &bdlen);CHKERRQ(ierr);
ierr = PetscStrlen(extfilename, &extlen);CHKERRQ(ierr);
ierr = PetscLogStagePush(user->stages[STAGE_LOAD]);CHKERRQ(ierr);
if (len) {
ierr = DMPlexCreateFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr);
} else if (bdlen) {
DM boundary;
ierr = DMPlexCreateFromFile(comm, bdfilename, interpolate, &boundary);CHKERRQ(ierr);
ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr);
ierr = DMDestroy(&boundary);CHKERRQ(ierr);
} else if (extlen) {
DM edm;
ierr = DMPlexCreateFromFile(comm, extfilename, interpolate, &edm);CHKERRQ(ierr);
ierr = DMPlexExtrude(edm, user->extrude_layers, user->extrude_thickness, PETSC_TRUE, interpolate, dm);CHKERRQ(ierr);
ierr = DMDestroy(&edm);CHKERRQ(ierr);
} else {
switch (user->domainShape) {
case BOX:
if (cellWedge) {
if (dim != 3) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Dimension must be 3 for a wedge mesh, not %D", dim);
ierr = DMPlexCreateWedgeBoxMesh(comm, user->domainBoxSizes, user->domainBoxL, user->domainBoxU, user->periodicity, PETSC_FALSE, interpolate, dm);CHKERRQ(ierr);
} else {
ierr = DMPlexCreateBoxMesh(comm, dim, cellSimplex, user->domainBoxSizes, user->domainBoxL, user->domainBoxU, user->periodicity, interpolate, dm);CHKERRQ(ierr);
}
break;
case CYLINDER:
if (cellSimplex) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Cannot mesh a cylinder with simplices");
if (dim != 3) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Dimension must be 3 for a cylinder mesh, not %D", dim);
if (cellWedge) {
ierr = DMPlexCreateWedgeCylinderMesh(comm, 6, interpolate, dm);CHKERRQ(ierr);
} else {
ierr = DMPlexCreateHexCylinderMesh(comm, 3, user->periodicity[2], dm);CHKERRQ(ierr);
}
break;
default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Unknown domain shape %D", user->domainShape);
}
}
ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); /* needed for periodic */
ierr = DMViewFromOptions(*dm,NULL,"-init_dm_view");CHKERRQ(ierr);
ierr = DMGetDimension(*dm,&dim);CHKERRQ(ierr);
if (testp4est_seq) {
#if defined(PETSC_HAVE_P4EST)
DM dmConv = NULL;
ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexRefineSimplexToTensor(*dm, &dmConv);CHKERRQ(ierr);
if (dmConv) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
user->cellSimplex = PETSC_FALSE;
ierr = DMConvert(*dm,dim == 2 ? DMP4EST : DMP8EST,&dmConv);CHKERRQ(ierr);
if (dmConv) {
ierr = DMSetFromOptions(dmConv);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-conv_seq_1_dm_view");CHKERRQ(ierr);
ierr = DMConvert(*dm,DMPLEX,&dmConv);CHKERRQ(ierr);
if (dmConv) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
ierr = DMViewFromOptions(*dm, NULL, "-conv_seq_2_dm_view");CHKERRQ(ierr);
#else
SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Recompile with --download-p4est");
#endif
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
if (!testp4est_seq) {
DM refinedMesh = NULL;
DM distributedMesh = NULL;
if (user->testPartition) {
const PetscInt *sizes = NULL;
const PetscInt *points = NULL;
PetscPartitioner part;
if (!rank) {
if (dim == 2 && cellSimplex && size == 2) {
sizes = triSizes_n2; points = triPoints_n2;
} else if (dim == 2 && cellSimplex && size == 8) {
sizes = triSizes_n8; points = triPoints_n8;
} else if (dim == 2 && !cellSimplex && size == 2) {
sizes = quadSizes; points = quadPoints;
} else if (dim == 2 && size == 3) {
PetscInt Nc;
ierr = DMPlexGetHeightStratum(*dm, 0, NULL, &Nc);CHKERRQ(ierr);
if (Nc == 42) { /* Gmsh 3 & 4 */
sizes = gmshSizes_n3; points = gmshPoints_n3;
} else if (Nc == 150) { /* Fluent 1 */
sizes = fluentSizes_n3; points = fluentPoints_n3;
} else if (Nc == 42) { /* Med 1 */
} else if (Nc == 161) { /* Med 3 */
}
}
}
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr);
ierr = PetscPartitionerShellSetPartition(part, size, sizes, points);CHKERRQ(ierr);
} else {
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm,&part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
}
/* Distribute mesh over processes */
ierr = PetscLogStagePush(user->stages[STAGE_DISTRIBUTE]);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-distributed_dm_view");CHKERRQ(ierr);
/* Refine mesh using a volume constraint */
ierr = PetscLogStagePush(user->stages[STAGE_REFINE]);CHKERRQ(ierr);
ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
}
ierr = PetscLogStagePush(user->stages[STAGE_REFINE]);CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
if (testp4est_par) {
#if defined(PETSC_HAVE_P4EST)
DM dmConv = NULL;
ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexRefineSimplexToTensor(*dm, &dmConv);CHKERRQ(ierr);
if (dmConv) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
user->cellSimplex = PETSC_FALSE;
ierr = DMConvert(*dm,dim == 2 ? DMP4EST : DMP8EST,&dmConv);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dmConv, "conv_par_1_");CHKERRQ(ierr);
if (dmConv) {
ierr = DMSetFromOptions(dmConv);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
ierr = DMSetUp(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMConvert(*dm,DMPLEX,&dmConv);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dmConv, "conv_par_2_");CHKERRQ(ierr);
if (dmConv) {
ierr = DMSetFromOptions(dmConv);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmConv;
}
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
#else
SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Recompile with --download-p4est");
#endif
}
if (user->overlap) {
DM overlapMesh = NULL;
/* Add the level-1 overlap to refined mesh */
ierr = PetscLogStagePush(user->stages[STAGE_OVERLAP]);CHKERRQ(ierr);
ierr = DMPlexDistributeOverlap(*dm, 1, NULL, &overlapMesh);CHKERRQ(ierr);
if (overlapMesh) {
ierr = DMView(overlapMesh, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = overlapMesh;
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
}
if (simplex2tensor) {
DM rdm = NULL;
ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexRefineSimplexToTensor(*dm, &rdm);CHKERRQ(ierr);
if (rdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = rdm;
}
user->cellSimplex = PETSC_FALSE;
}
ierr = PetscObjectSetName((PetscObject) *dm, "Simplicial Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm, dmDist = NULL;
Vec u;
PetscSection section;
PetscViewer viewer;
PetscInt dim = 2, numFields, numBC, i;
PetscInt numComp[3];
PetscInt numDof[12];
PetscInt bcField[1];
IS bcPointIS[1];
PetscBool interpolate = PETSC_TRUE;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL);CHKERRQ(ierr);
/* Create a mesh */
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, PETSC_TRUE, NULL, NULL, NULL, NULL, interpolate, &dm);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist;}
/* Create a scalar field u, a vector field v, and a surface vector field w */
numFields = 3;
numComp[0] = 1;
numComp[1] = dim;
numComp[2] = dim-1;
for (i = 0; i < numFields*(dim+1); ++i) numDof[i] = 0;
/* Let u be defined on vertices */
numDof[0*(dim+1)+0] = 1;
/* Let v be defined on cells */
numDof[1*(dim+1)+dim] = dim;
/* Let v be defined on faces */
numDof[2*(dim+1)+dim-1] = dim-1;
/* Setup boundary conditions */
numBC = 1;
/* Prescribe a Dirichlet condition on u on the boundary
Label "marker" is made by the mesh creation routine */
bcField[0] = 0;
ierr = DMGetStratumIS(dm, "marker", 1, &bcPointIS[0]);CHKERRQ(ierr);
/* Create a PetscSection with this data layout */
ierr = DMSetNumFields(dm, numFields);CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, NULL, numComp, numDof, numBC, bcField, NULL, bcPointIS, NULL, §ion);CHKERRQ(ierr);
ierr = ISDestroy(&bcPointIS[0]);CHKERRQ(ierr);
/* Name the Field variables */
ierr = PetscSectionSetFieldName(section, 0, "u");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 1, "v");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 2, "w");CHKERRQ(ierr);
ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Tell the DM to use this data layout */
ierr = DMSetSection(dm, section);CHKERRQ(ierr);
/* Create a Vec with this layout and view it */
ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "sol.vtk");CHKERRQ(ierr);
ierr = VecView(u, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr);
/* Cleanup */
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscInt numRefinements = user->numRefinements;
PetscBool cellHybrid = user->cellHybrid;
PetscBool cellSimplex = user->cellSimplex;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
switch (dim) {
case 1:
if (cellHybrid) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make hybrid meshes for dimension %d", dim);
ierr = CreateSimplex_1D(comm, dm);CHKERRQ(ierr);
break;
case 2:
if (cellSimplex) {
if (cellHybrid) {
ierr = CreateSimplexHybrid_2D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateSimplex_2D(comm, dm);CHKERRQ(ierr);
}
} else {
if (cellHybrid) {
ierr = CreateTensorProductHybrid_2D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateTensorProduct_2D(comm, user->testNum, dm);CHKERRQ(ierr);
}
}
break;
case 3:
if (cellSimplex) {
if (cellHybrid) {
ierr = CreateSimplexHybrid_3D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateSimplex_3D(comm, user->testNum, dm);CHKERRQ(ierr);
}
} else {
if (cellHybrid) {
ierr = CreateTensorProductHybrid_3D(comm, user->testNum, dm);CHKERRQ(ierr);
} else {
ierr = CreateTensorProduct_3D(comm, user->testNum, dm);CHKERRQ(ierr);
}
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
}
{
DM refinedMesh = NULL;
DM distributedMesh = NULL;
PetscInt r;
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMViewFromOptions(distributedMesh, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
for (r = 0; r < numRefinements; ++r) {
ierr = DMViewFromOptions(*dm, NULL, "-orig_dm_view");CHKERRQ(ierr);
ierr = DMPlexCheckSymmetry(*dm);CHKERRQ(ierr);
ierr = DMPlexCheckSkeleton(*dm, user->cellSimplex, 0);CHKERRQ(ierr);
ierr = DMPlexCheckFaces(*dm, user->cellSimplex, 0);CHKERRQ(ierr);
ierr = DMPlexSetRefinementUniform(*dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
}
}
if (user->uninterpolate) {
DM udm = NULL;
ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = udm;
}
ierr = PetscObjectSetName((PetscObject) *dm, "Hybrid Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
DM dmDist = NULL;
PetscInt dim = user->dim;
PetscBool cellSimplex = user->cellSimplex;
const char *filename = user->filename;
const PetscInt cells[3] = {2, 2, 2};
size_t len;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, dm);CHKERRQ(ierr);}
else if (cellSimplex) {ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, dm);CHKERRQ(ierr);}
else {ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, dm);CHKERRQ(ierr);}
if (user->testPartition) {
PetscPartitioner part;
const PetscInt *sizes = NULL;
const PetscInt *points = NULL;
PetscMPIInt rank, numProcs;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
if (!rank) {
if (dim == 2 && cellSimplex && numProcs == 2) {
switch (user->testNum) {
case 0: {
PetscInt triSizes_p2[2] = {4, 4};
PetscInt triPoints_p2[8] = {3, 5, 6, 7, 0, 1, 2, 4};
sizes = triSizes_p2; points = triPoints_p2;break;}
case 1: {
PetscInt triSizes_p2[2] = {6, 2};
PetscInt triPoints_p2[8] = {1, 2, 3, 4, 6, 7, 0, 5};
sizes = triSizes_p2; points = triPoints_p2;break;}
default:
SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test number %d for triangular mesh on 2 procs", user->testNum);
}
} else if (dim == 2 && cellSimplex && numProcs == 3) {
PetscInt triSizes_p3[3] = {3, 3, 2};
PetscInt triPoints_p3[8] = {1, 2, 4, 3, 6, 7, 0, 5};
sizes = triSizes_p3; points = triPoints_p3;
} else if (dim == 2 && !cellSimplex && numProcs == 2) {
PetscInt quadSizes_p2[2] = {2, 2};
PetscInt quadPoints_p2[4] = {2, 3, 0, 1};
sizes = quadSizes_p2; points = quadPoints_p2;
} else SETERRQ3(PETSC_COMM_WORLD, PETSC_ERR_ARG_WRONG, "Could not find matching test partition dim: %D simplex: %D numProcs: %D", dim, (PetscInt) cellSimplex, (PetscInt) numProcs);
}
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);CHKERRQ(ierr);
ierr = PetscPartitionerShellSetPartition(part, numProcs, sizes, points);CHKERRQ(ierr);
}
ierr = DMPlexDistribute(*dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = dmDist;
}
ierr = PetscObjectSetName((PetscObject) *dm, cellSimplex ? "Simplicial Mesh" : "Tensor Product Mesh");CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
#include <petsc-private/fortranimpl.h>
#include <petscdmplex.h>
#if defined(PETSC_HAVE_FORTRAN_CAPS)
#define dmplexdistribute_ DMPLEXDISTRIBUTE
#define dmplexcreatefromcelllist_ DMPLEXCREATEFROMCELLLIST
#elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) && !defined(FORTRANDOUBLEUNDERSCORE)
#define dmplexdistribute_ dmplexdistribute
#define dmplexcreatefromcelllist_ dmplexcreatefromcelllist
#endif
/* Definitions of Fortran Wrapper routines */
PETSC_EXTERN void PETSC_STDCALL dmplexdistribute_(DM *dm, CHAR name PETSC_MIXED_LEN(lenN), PetscInt *overlap, PetscSF *sf, DM *dmParallel, int *ierr PETSC_END_LEN(lenN))
{
char *partitioner;
FIXCHAR(name, lenN, partitioner);
*ierr = DMPlexDistribute(*dm, partitioner, *overlap, sf, dmParallel);
FREECHAR(name, partitioner);
}
PETSC_EXTERN void PETSC_STDCALL dmplexcreatefromcelllist_(MPI_Comm *comm, PetscInt *dim, PetscInt *numCells, PetscInt *numVertices, PetscInt *numCorners, PetscBool *interpolate, const int cells[], PetscInt *spaceDim, const double vertexCoords[], DM *dm, int *ierr)
{
*ierr = DMPlexCreateFromCellList(*comm, *dim, *numCells, *numVertices, *numCorners, *interpolate, cells, *spaceDim, vertexCoords, dm);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
const char *filename = user->filename;
PetscBool interpolate = user->interpolate;
PetscReal refinementLimit = user->refinementLimit;
PetscBool refinementUniform = user->refinementUniform;
PetscInt refinementRounds = user->refinementRounds;
const char *partitioner = user->partitioner;
size_t len;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (!len) {
ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dm, "Mesh");CHKERRQ(ierr);
} else if (user->checkpoint) {
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMLoad(*dm, user->checkpoint);CHKERRQ(ierr);
ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
} else {
PetscMPIInt rank;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr);
ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
/* Must have boundary marker for Dirichlet conditions */
}
{
DM refinedMesh = NULL;
DM distributedMesh = NULL;
/* Refine mesh using a volume constraint */
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
const char *name;
ierr = PetscObjectGetName((PetscObject) *dm, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) refinedMesh, name);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, NULL, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
/* Use regular refinement in parallel */
if (refinementUniform) {
PetscInt r;
ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr);
for (r = 0; r < refinementRounds; ++r) {
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
}
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool interpolate = user->interpolate;
PetscBool refinementUniform = user->refinementUniform;
PetscReal refinementLimit = user->refinementLimit;
PetscBool cellSimplex = user->cellSimplex;
const char *filename = user->filename;
const char *partitioner = "chaco";
size_t len;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogEventBegin(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {
#if defined(PETSC_HAVE_CGNS)
int cgid = -1;
if (!rank) {
ierr = cg_open(filename, CG_MODE_READ, &cgid);CHKERRQ(ierr);
if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename);
}
ierr = DMPlexCreateCGNS(comm, cgid, interpolate, dm);CHKERRQ(ierr);
if (!rank) {ierr = cg_close(cgid);CHKERRQ(ierr);}
#else
SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir");
#endif
} else if (cellSimplex) {
ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);
} else {
const PetscInt cells[3] = {2, 2, 2};
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, dm);CHKERRQ(ierr);
}
{
DM refinedMesh = NULL;
DM distributedMesh = NULL;
/* Refine mesh using a volume constraint */
ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
ierr = DMPlexSetRefinementLimit(*dm, refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
if (refinementUniform) {
ierr = DMPlexSetRefinementUniform(*dm, refinementUniform);CHKERRQ(ierr);
ierr = DMRefine(*dm, comm, &refinedMesh);CHKERRQ(ierr);
if (refinedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = refinedMesh;
}
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Simplical Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(user->createMeshEvent,0,0,0,0);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}
PetscErrorCode CreateMesh(MPI_Comm comm, PetscInt testNum, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscBool cellSimplex = user->cellSimplex;
PetscBool useGenerator = user->useGenerator;
const char *filename = user->filename;
const char *partitioner = "chaco";
size_t len;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscStrlen(filename, &len);CHKERRQ(ierr);
if (len) {
#if defined(PETSC_HAVE_EXODUSII)
int CPU_word_size = 0, IO_word_size = 0, exoid = -1;
float version;
if (!rank) {
exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);
if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename);
}
ierr = DMPlexCreateExodus(comm, exoid, PETSC_FALSE, dm);CHKERRQ(ierr);
if (!rank) {ierr = ex_close(exoid);CHKERRQ(ierr);}
ierr = DMPlexGetDimension(*dm, &dim);CHKERRQ(ierr);
#else
SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires ExodusII support. Reconfigure using --download-exodusii");
#endif
} else if (useGenerator) {
if (cellSimplex) {
ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr);
} else {
ierr = DMPlexCreateHexBoxMesh(comm, dim, PETSC_FALSE, dm);CHKERRQ(ierr);
}
} else {
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);
switch (dim) {
case 2:
if (cellSimplex) {
ierr = CreateSimplex_2D(comm, *dm);CHKERRQ(ierr);
} else {
ierr = CreateQuad_2D(comm, testNum, *dm);CHKERRQ(ierr);
}
break;
case 3:
if (cellSimplex) {
ierr = CreateSimplex_3D(comm, *dm);CHKERRQ(ierr);
} else {
ierr = CreateHex_3D(comm, *dm);CHKERRQ(ierr);
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
}
}
{
DM interpolatedMesh = NULL;
ierr = CheckMesh(*dm);CHKERRQ(ierr);
ierr = DMPlexInterpolate(*dm, &interpolatedMesh);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(*dm, interpolatedMesh);CHKERRQ(ierr);
ierr = CompareCones(*dm, interpolatedMesh);CHKERRQ(ierr);
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = interpolatedMesh;
}
{
DM distributedMesh = NULL;
/* Distribute mesh over processes */
ierr = DMPlexDistribute(*dm, partitioner, 0, &distributedMesh);CHKERRQ(ierr);
if (distributedMesh) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = distributedMesh;
}
}
ierr = PetscObjectSetName((PetscObject) *dm, "Interpolated Mesh");CHKERRQ(ierr);
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
user->dm = *dm;
PetscFunctionReturn(0);
}