PetscErrorCode MyPetscReadExodusII(MPI_Comm comm,const char filename[],DM dmBody,DM dmFS)
{
ALE::Obj<PETSC_MESH_TYPE> meshBody,meshFS;
typedef ALE::Mesh<PetscInt,PetscScalar> FlexMesh;
//typedef std::set<FlexMesh::point_type> PointSet;
//ALE::Obj<FlexMesh> boundarymesh;
PetscMPIInt rank;
int CPU_word_size = 0;
int IO_word_size = 0;
PetscBool interpolate = PETSC_FALSE;
int **connect = PETSC_NULL;
int exoid;
char title[MAX_LINE_LENGTH+1];
float version;
int num_dim,num_nodes = 0,num_elem = 0;
int num_eb = 0,num_ns = 0,num_ss = 0;
PetscErrorCode ierr;
//const char known_elements[] = "tri,tri3,triangle,triangle3,quad,quad4,tet,tet4,tetra,tetra4,hex,hex8";
float *x = PETSC_NULL,*y = PETSC_NULL,*z = PETSC_NULL;
PetscBool debug = PETSC_FALSE;
PetscFunctionBegin;
ierr = PetscOptionsGetBool(PETSC_NULL,"-interpolate",&interpolate,PETSC_NULL);CHKERRQ(ierr);
/*
Get the sieve meshes from the dms
*/
ierr = DMMeshGetMesh(dmBody,meshBody);CHKERRQ(ierr);
ierr = DMMeshGetMesh(dmFS,meshFS);CHKERRQ(ierr);
rank = meshBody->commRank();
/*
Open EXODUS II file and read basic informations on rank 0,
then broadcast to all nodes
*/
if (rank == 0) {
exoid = ex_open(filename,EX_READ,&CPU_word_size,&IO_word_size,&version);CHKERRQ(!exoid);
ierr = ex_get_init(exoid,title,&num_dim,&num_nodes,&num_elem,&num_eb,&num_ns,&num_ss);CHKERRQ(ierr);
if (num_eb == 0) {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any element block\n");
}
ierr = PetscMalloc3(num_nodes,float,&x,num_nodes,float,&y,num_nodes,float,&z);CHKERRQ(ierr);
ierr = ex_get_coord(exoid,x,y,z);CHKERRQ(ierr);
}
int main (int argc,char ** argv) {
DM dmBody,dmFS;
DM dmBodyDist,dmFSDist;
ALE::Obj<PETSC_MESH_TYPE> meshBody,meshBodyDist,meshFS,meshFSDist;
PetscBool inflag,outflag;
char infilename[PETSC_MAX_PATH_LEN+1],outfilename[PETSC_MAX_PATH_LEN+1];
PetscViewer viewer;
int rank,numproc;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,(char *)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-i",infilename,PETSC_MAX_PATH_LEN,&inflag);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&numproc);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
if (inflag) {
ierr = MyDMMeshCreateExodus(PETSC_COMM_WORLD,infilename,&dmBody,&dmFS);CHKERRQ(ierr);
ierr = DMMeshGetMesh(dmBody,meshBody);CHKERRQ(ierr);
meshBody->view("meshBody");
ierr = DMMeshGetMesh(dmFS,meshFS);CHKERRQ(ierr);
meshFS->view("meshFS");
if (numproc > 1) {
ierr = DMMeshDistribute(dmBody,PETSC_NULL,&dmBodyDist);CHKERRQ(ierr);
//ierr = DMMeshDistribute(dmFS,PETSC_NULL,&dmFSDist);CHKERRQ(ierr);
ierr = DMMeshGetMesh(dmBodyDist,meshBodyDist);CHKERRQ(ierr);
meshBodyDist->view("meshBodyDist");
//ierr = DMMeshGetMesh(dmFSDist,meshFSDist);CHKERRQ(ierr);
//meshFSDist->view("meshFS");
//ierr = DMDestroy(&dmBodyDist);CHKERRQ(ierr);
//ierr = DMDestroy(&dmFSDist);CHKERRQ(ierr);
}
//ierr = DMDestroy(&dmBody);CHKERRQ(ierr);
//ierr = DMDestroy(&dmFS);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"No file name given\n");CHKERRQ(ierr);
}
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DMMeshConvertOverlapToSF(DM dm, PetscSF *sf)
{
ALE::Obj<PETSC_MESH_TYPE> mesh;
PetscInt *local;
PetscSFNode *remote;
PetscInt numPoints;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscSFCreate(((PetscObject) dm)->comm, sf);
CHKERRQ(ierr);
ierr = DMMeshGetMesh(dm, mesh);
CHKERRQ(ierr);
{
/* The local points have degree 1
We use the recv overlap
*/
ALE::Obj<PETSC_MESH_TYPE::recv_overlap_type> overlap = mesh->getRecvOverlap();
numPoints = overlap->getNumPoints();
ierr = PetscMalloc(numPoints * sizeof(PetscInt), &local);
CHKERRQ(ierr);
ierr = PetscMalloc(numPoints * sizeof(PetscSFNode), &remote);
CHKERRQ(ierr);
for (PetscInt r = 0, i = 0; r < overlap->getNumRanks(); ++r) {
const PetscInt rank = overlap->getRank(r);
const PETSC_MESH_TYPE::recv_overlap_type::supportSequence::iterator cBegin = overlap->supportBegin(rank);
const PETSC_MESH_TYPE::recv_overlap_type::supportSequence::iterator cEnd = overlap->supportEnd(rank);
for (PETSC_MESH_TYPE::recv_overlap_type::supportSequence::iterator c_iter = cBegin; c_iter != cEnd; ++c_iter, ++i) {
local[i] = *c_iter;
remote[i].rank = rank;
remote[i].index = c_iter.color();
}
}
ierr = PetscSFSetGraph(*sf, numPoints, numPoints, local, PETSC_OWN_POINTER, remote, PETSC_OWN_POINTER);
CHKERRQ(ierr);
ierr = PetscSFView(*sf, NULL);
CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main (int argc,char ** argv) {
DM dmBody,dmFS;
PetscBool inflag;
char infilename[PETSC_MAX_PATH_LEN+1];
PetscErrorCode ierr;
SectionReal sec1;
Mat mat1;
PetscInt dof=1;
int rank;
PetscInt cell,face,conesize,my_num_cells,my_num_faces,my_num_vertices;
PetscInt i,j,c,d,k;
PetscReal *m_array;
ierr = PetscInitialize(&argc,&argv,(char *)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
ierr = PetscOptionsGetString(PETSC_NULL,"-i",infilename,PETSC_MAX_PATH_LEN,&inflag);CHKERRQ(ierr);
if (!inflag) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"No file name given\n");CHKERRQ(ierr);
PetscFinalize();
return 0;
}
/*
Reads a mesh
*/
ierr = DMMeshCreateExodusNG(PETSC_COMM_WORLD,infilename,&dmBody,&dmFS);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr);
ierr = DMMeshSetMaxDof(dmBody,dof);CHKERRQ(ierr);
ierr = DMMeshSetMaxDof(dmFS,dof);CHKERRQ(ierr);
/*
Testing matrices
*/
{
ALE::Obj<PETSC_MESH_TYPE> meshBody,meshFS;
ierr = DMMeshGetMesh(dmBody,meshBody);CHKERRQ(ierr);
ierr = DMMeshGetMesh(dmFS,meshFS);CHKERRQ(ierr);
my_num_cells = meshBody->heightStratum(0)->size();
my_num_vertices = meshBody->depthStratum(0)->size();
my_num_faces = meshFS->heightStratum(0)->size();
}
ierr = DMMeshGetVertexSectionReal(dmBody,"sec1",dof,&sec1);CHKERRQ(ierr);
ierr = DMMeshCreateMatrix(dmBody,sec1,MATMPIAIJ,&mat1);CHKERRQ(ierr);
for (cell = 0; cell < my_num_cells; cell++) {
ierr = DMMeshGetConeSize(dmBody,cell,&conesize);CHKERRQ(ierr);
ierr = PetscMalloc(conesize*dof*conesize*dof*sizeof(PetscReal),&m_array);CHKERRQ(ierr);
for (k = 0,i = 0; i < conesize; i++) {
for (c = 0; c < dof; c++) {
for (j = 0; j < conesize; j++) {
for (d = 0; d < dof; d++,k++) {
m_array[k] = 1.;
}
}
}
}
ierr = DMMeshAssembleMatrix(mat1,dmBody,sec1,cell,m_array,ADD_VALUES);CHKERRQ(ierr);
ierr = PetscFree(m_array);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(mat1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n==================== Matrix on body mesh\n");
ierr = MatView(mat1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatZeroEntries(mat1);CHKERRQ(ierr);
for (face = 0; face < my_num_faces; face++) {
ierr = DMMeshGetConeSize(dmFS,face,&conesize);CHKERRQ(ierr);
ierr = PetscMalloc(conesize*dof*conesize*dof*sizeof(PetscReal),&m_array);CHKERRQ(ierr);
for (k = 0,i = 0; i < conesize; i++) {
for (c = 0; c < dof; c++) {
for (j = 0; j < conesize; j++) {
for (d = 0; d < dof; d++,k++) {
m_array[k] = 1.;
}
}
}
}
ierr = DMMeshAssembleMatrix(mat1,dmFS,sec1,face,m_array,ADD_VALUES);CHKERRQ(ierr);
ierr = PetscFree(m_array);CHKERRQ(ierr);
ierr = MatAssemblyBegin(mat1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat1,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n==================== Matrix on FS mesh\n");
ierr = MatView(mat1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SectionRealDestroy(&sec1);CHKERRQ(ierr);
ierr = MatDestroy(&mat1);CHKERRQ(ierr);
ierr = DMDestroy(&dmBody);CHKERRQ(ierr);
ierr = DMDestroy(&dmFS);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}