/*@C
MyDMMeshCreateExodus - Create a Mesh from an ExodusII file.
Not Collective
Input Parameters:
+ comm - The MPI communicator
- filename - The ExodusII filename
Output Parameter:
. dmBody - The DM object representing the body
. dmFS - The DM object representing the face sets
Level: beginner
.keywords: mesh,ExodusII
.seealso: MeshCreate()
@*/
PetscErrorCode MyDMMeshCreateExodus(MPI_Comm comm,const char filename[],DM *dmBody,DM *dmFS)
{
PetscInt debug = 0;
PetscBool flag;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsGetInt(PETSC_NULL,"-debug",&debug,&flag);CHKERRQ(ierr);
ierr = DMMeshCreate(comm,dmBody);CHKERRQ(ierr);
ALE::Obj<PETSC_MESH_TYPE> meshBody = new PETSC_MESH_TYPE(comm,-1,debug);
ierr = DMMeshSetMesh(*dmBody,meshBody);CHKERRQ(ierr);
ierr = DMMeshCreate(comm,dmFS);CHKERRQ(ierr);
ALE::Obj<PETSC_MESH_TYPE> meshFS = new PETSC_MESH_TYPE(comm,-1,debug);
ierr = DMMeshSetMesh(*dmFS,meshFS);CHKERRQ(ierr);
#ifdef PETSC_HAVE_EXODUSII
try {
ierr = MyPetscReadExodusII(comm,filename,*dmBody,*dmFS);CHKERRQ(ierr);
} catch(ALE::Exception e) {
std::cerr << "Error: " << e << std::endl;
}
#else
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This method requires ExodusII support. Reconfigure using --with-exodusii-dir=/path/to/exodus");
#endif
//if (debug) {mesh->view("Mesh");}
//ierr = DMMeshSetMesh(*dm,mesh);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMMeshCreateMeshFromAdjacency - Create an unstrctured mesh from a list of the vertices for each cell, and the coordinates for each vertex.
Collective on comm
Input Parameters:
+ comm - An MPI communicator
. dim - The dimension of the cells, e.g. triangles have dimension 2
. numCells - The number of cells in the mesh
. numCorners - The number of vertices in each cell
. cellVertices - An array of the vertices for each cell, numbered 0 to numVertices-1
. spatialDim - The dimension for coordinates, e.g. for a triangle in 3D this would be 3
. numVertices - The number of mesh vertices
. coordinates - An array of the coordinates for each vertex
- interpolate - Flag to create faces and edges
Output Parameter:
. dm - The DMMesh object
Level: beginner
.seealso DMMESH, DMMeshCreateMeshFromAdjacencyHybrid(), DMMeshCreateBoxMesh()
@*/
PetscErrorCode DMMeshCreateMeshFromAdjacency(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numCorners, PetscInt cellVertices[], PetscInt spatialDim, PetscInt numVertices, const PetscReal coordinates[], PetscBool interpolate, DM *dm) {
PetscInt *cone;
PetscInt *coneO;
PetscInt debug = 0;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidPointer(cellVertices, 5);
/* PetscValidLogicalCollectiveBool(comm,interpolate,6); */
PetscValidPointer(dm, 7);
if (interpolate) {SETERRQ(comm, PETSC_ERR_SUP, "Interpolation (creation of faces and edges) is not yet supported.");}
ierr = PetscOptionsGetInt(PETSC_NULL, "-dm_mesh_debug", &debug, PETSC_NULL);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> mesh = new PETSC_MESH_TYPE(comm, dim, debug);
Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(comm, 0, numCells+numVertices, debug);
mesh->setSieve(sieve);
for(PetscInt c = 0; c < numCells; ++c) {
sieve->setConeSize(c, numCorners);
}
sieve->symmetrizeSizes(numCells, numCorners, cellVertices, numCells);
sieve->allocate();
ierr = PetscMalloc2(numCorners,PetscInt,&cone,numCorners,PetscInt,&coneO);CHKERRQ(ierr);
for(PetscInt v = 0; v < numCorners; ++v) {
coneO[v] = 1;
}
for(PetscInt c = 0; c < numCells; ++c) {
for(PetscInt v = 0; v < numCorners; ++v) {
cone[v] = cellVertices[c*numCorners+v]+numCells;
}
sieve->setCone(cone, c);
sieve->setConeOrientation(coneO, c);
}
ierr = PetscFree2(cone,coneO);CHKERRQ(ierr);
sieve->symmetrize();
mesh->stratify();
ALE::SieveBuilder<PETSC_MESH_TYPE>::buildCoordinates(mesh, spatialDim, coordinates, numCells);
ierr = DMCreate(comm, dm);CHKERRQ(ierr);
ierr = DMSetType(*dm, DMMESH);CHKERRQ(ierr);
ierr = DMMeshSetMesh(*dm, mesh);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "DMConvert_DA_Mesh"
PetscErrorCode DMConvert_DA_Mesh(DM dm, const DMType newtype, DM *dmNew)
{
PetscSection section;
DM cda;
DMDALocalInfo info;
Vec coordinates;
PetscInt *cone, *coneO;
PetscInt dim, M, N, P, numCells, numGlobalCells, numCorners, numVertices, c = 0, v = 0;
PetscInt ye, ze;
PetscInt debug = 0;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsGetInt(PETSC_NULL, "-dm_mesh_debug", &debug, PETSC_NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm, &dim, &M, &N, &P, 0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
if (info.sw > 1) SETERRQ(((PetscObject) dm)->comm, PETSC_ERR_SUP, "Currently, only DMDAs with unti stencil width can be converted to DMMeshes.");
/* In order to get a partition of cells, rather than vertices, we give each process the cells between vertices it owns
and also higher numbered ghost vertices (vertices to the right and up) */
numCorners = 1 << dim;
numCells = ((info.gxm+info.gxs - info.xs) - 1);
if (dim > 1) {numCells *= ((info.gym+info.gys - info.ys) - 1);}
if (dim > 2) {numCells *= ((info.gzm+info.gzs - info.zs) - 1);}
numVertices = (info.gxm+info.gxs - info.xs);
if (dim > 1) {numVertices *= (info.gym+info.gys - info.ys);}
if (dim > 2) {numVertices *= (info.gzm+info.gzs - info.zs);}
numGlobalCells = M-1;
if (dim > 1) {numGlobalCells *= N-1;}
if (dim > 2) {numGlobalCells *= P-1;}
ALE::Obj<PETSC_MESH_TYPE> mesh = new PETSC_MESH_TYPE(((PetscObject) dm)->comm, info.dim, debug);
ALE::Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(((PetscObject) dm)->comm, 0, numCells+numVertices, debug);
PETSC_MESH_TYPE::renumbering_type renumbering;
mesh->setSieve(sieve);
/* Number each cell for the vertex in the lower left corner */
if (dim < 3) {ze = 1; P = 1;} else {ze = info.gzs+info.gzm-1;}
if (dim < 2) {ye = 1; N = 1;} else {ye = info.gys+info.gym-1;}
for(PetscInt k = info.zs; k < ze; ++k) {
for(PetscInt j = info.ys; j < ye; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm-1; ++i, ++c) {
PetscInt globalC = (k*(N-1) + j)*(M-1) + i;
renumbering[globalC] = c;
sieve->setConeSize(c, numCorners);
}
}
}
if (c != numCells) {SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Error in generated cell numbering, %d should be %d", c, numCells);}
/* Get vertex renumbering */
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i, ++v) {
PetscInt globalV = (k*N + j)*M + i + numGlobalCells;
renumbering[globalV] = v+numCells;
}
}
}
if (v != numVertices) {SETERRQ2(((PetscObject) dm)->comm, PETSC_ERR_PLIB, "Error in generated vertex numbering, %d should be %d", v, numVertices);}
/* Calculate support sizes */
for(PetscInt k = info.zs; k < ze; ++k, ++c) {
for(PetscInt j = info.ys; j < ye; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm-1; ++i) {
for(PetscInt kp = k; kp <= k+(dim>2); ++kp) {
for(PetscInt jp = j; jp <= j+(dim>1); ++jp) {
for(PetscInt ip = i; ip <= i+1; ++ip) {
PetscInt globalV = (kp*N + jp)*M + ip + numGlobalCells;
sieve->addSupportSize(renumbering[globalV], 1);
}
}
}
}
}
}
sieve->allocate();
ierr = PetscMalloc2(numCorners,PetscInt,&cone,numCorners,PetscInt,&coneO);CHKERRQ(ierr);
for(PetscInt v = 0; v < numCorners; ++v) {
coneO[v] = 1;
}
for(PetscInt k = info.zs; k < ze; ++k) {
for(PetscInt j = info.ys; j < ye; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm-1; ++i) {
PetscInt globalC = (k*(N-1) + j)*(M-1) + i;
PetscInt v = 0;
cone[v++] = renumbering[(k*N + j)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[(k*N + j)*M + i+1 + numGlobalCells];
if (dim > 1) {
cone[v++] = renumbering[(k*N + j+1)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[(k*N + j+1)*M + i+1 + numGlobalCells];
}
if (dim > 2) {
cone[v++] = renumbering[((k+1)*N + j+0)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[((k+1)*N + j+0)*M + i+1 + numGlobalCells];
cone[v++] = renumbering[((k+1)*N + j+1)*M + i+0 + numGlobalCells];
cone[v++] = renumbering[((k+1)*N + j+1)*M + i+1 + numGlobalCells];
}
sieve->setCone(cone, renumbering[globalC]);
sieve->setConeOrientation(coneO, renumbering[globalC]);
}
}
}
ierr = PetscFree2(cone,coneO);CHKERRQ(ierr);
sieve->symmetrize();
mesh->stratify();
/* Create boundary marker */
{
const Obj<PETSC_MESH_TYPE::label_type>& boundary = mesh->createLabel("marker");
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
if (info.xs == 0) {
PetscInt globalV = (k*N + j)*M + info.xs + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
if (info.gxs+info.gxm-1 == M-1) {
PetscInt globalV = (k*N + j)*M + info.gxs+info.gxm-1 + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
}
}
if (dim > 1) {
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
if (info.ys == 0) {
PetscInt globalV = (k*N + info.ys)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
if (info.gys+info.gym-1 == N-1) {
PetscInt globalV = (k*N + info.gys+info.gym-1)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
}
}
}
if (dim > 2) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
if (info.zs == 0) {
PetscInt globalV = (info.zs*N + j)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
if (info.gzs+info.gzm-1 == P-1) {
PetscInt globalV = ((info.gzs+info.gzm-1)*N + j)*M + i + numGlobalCells;
mesh->setValue(boundary, renumbering[globalV], 1);
}
}
}
}
}
/* Create new DM */
ierr = DMMeshCreate(((PetscObject) dm)->comm, dmNew);CHKERRQ(ierr);
ierr = DMMeshSetMesh(*dmNew, mesh);CHKERRQ(ierr);
/* Set coordinates */
ierr = PetscSectionCreate(((PetscObject) dm)->comm, §ion);CHKERRQ(ierr);
ierr = PetscSectionSetChart(section, numCells, numCells+numVertices);CHKERRQ(ierr);
for(PetscInt v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(section, v, dim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(section);CHKERRQ(ierr);
ierr = DMMeshSetCoordinateSection(*dmNew, section);CHKERRQ(ierr);
ierr = DMDAGetCoordinateDA(dm, &cda);CHKERRQ(ierr);
ierr = DMDAGetGhostedCoordinates(dm, &coordinates);CHKERRQ(ierr);
{
Obj<PETSC_MESH_TYPE::real_section_type> coordSection = mesh->getRealSection("coordinates");
switch(dim) {
case 1:
{
PetscScalar **coords;
ierr = DMDAVecGetArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
PetscInt globalV = i + numGlobalCells;
coordSection->updatePoint(renumbering[globalV], coords[i]);
}
ierr = DMDAVecRestoreArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
break;
}
case 2:
{
PetscScalar ***coords;
ierr = DMDAVecGetArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
PetscInt globalV = j*M + i + numGlobalCells;
coordSection->updatePoint(renumbering[globalV], coords[j][i]);
}
}
ierr = DMDAVecRestoreArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
break;
}
case 3:
{
PetscScalar ****coords;
ierr = DMDAVecGetArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
for(PetscInt k = info.zs; k < info.gzs+info.gzm; ++k, ++v) {
for(PetscInt j = info.ys; j < info.gys+info.gym; ++j) {
for(PetscInt i = info.xs; i < info.gxs+info.gxm; ++i) {
PetscInt globalV = (k*N + j)*M + i + numGlobalCells;
coordSection->updatePoint(renumbering[globalV], coords[k][j][i]);
}
}
}
ierr = DMDAVecRestoreArrayDOF(cda, coordinates, &coords);CHKERRQ(ierr);
break;
}
default:
SETERRQ1(((PetscObject) dm)->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid DMDA dimension %d", dim);
}
}
/* Get overlap for interdomain communication */
{
typedef PETSC_MESH_TYPE::point_type point_type;
PETSc::Log::Event("CreateOverlap").begin();
ALE::Obj<PETSC_MESH_TYPE::send_overlap_type> sendParallelMeshOverlap = mesh->getSendOverlap();
ALE::Obj<PETSC_MESH_TYPE::recv_overlap_type> recvParallelMeshOverlap = mesh->getRecvOverlap();
// Can I figure this out in a nicer way?
ALE::SetFromMap<std::map<point_type,point_type> > globalPoints(renumbering);
ALE::OverlapBuilder<>::constructOverlap(globalPoints, renumbering, sendParallelMeshOverlap, recvParallelMeshOverlap);
if (debug) {
sendParallelMeshOverlap->view("Send Overlap");
recvParallelMeshOverlap->view("Recieve Overlap");
}
mesh->setCalculatedOverlap(true);
PETSc::Log::Event("CreateOverlap").end();
}
PetscFunctionReturn(0);
}
