PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId)
{
hid_t file_id, group;
const char *groupName = NULL;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerHDF5GetFileId(viewer, &file_id);CHKERRQ(ierr);
ierr = PetscViewerHDF5GetGroup(viewer, &groupName);CHKERRQ(ierr);
/* Open group */
if (groupName) {
PetscBool root;
ierr = PetscStrcmp(groupName, "/", &root);CHKERRQ(ierr);
if (!root && !H5Lexists(file_id, groupName, H5P_DEFAULT)) {
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
group = H5Gcreate2(file_id, groupName, 0, H5P_DEFAULT, H5P_DEFAULT);
#else /* deprecated HDF5 1.6 API */
group = H5Gcreate(file_id, groupName, 0);
#endif
if (group < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Could not create group %s", groupName);
ierr = H5Gclose(group);CHKERRQ(ierr);
}
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
group = H5Gopen2(file_id, groupName, H5P_DEFAULT);
#else
group = H5Gopen(file_id, groupName);
#endif
if (group < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Could not open group %s", groupName);
} else group = file_id;
*fileId = file_id;
*groupId = group;
PetscFunctionReturn(0);
}
int main(int argc, char *args[])
{
PFLOTRANMesh data;
Mat Adj; /* The adjacency matrix of the mesh */
PetscInt bs = 3;
PetscScalar values[9],*cc;
PetscMPIInt size;
PetscInt i;
PetscErrorCode ierr;
PetscViewer binaryviewer;
Vec cellCenters;
PetscViewer hdf5viewer;
hid_t file_id, dataset_id, dataspace_id;
herr_t status;
PetscFunctionBegin;
ierr = PetscInitialize(&argc, &args, (char *) 0, help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_ERR_SUP,"This preprocessor runs only on one process");
/* Open Glenn's file */
ierr = PetscViewerCreate(PETSC_COMM_SELF, &hdf5viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(hdf5viewer, PETSC_VIEWER_HDF5);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(hdf5viewer, FILE_MODE_READ);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(hdf5viewer, "mesh.h5");CHKERRQ(ierr);
ierr = PetscViewerHDF5GetFileId(hdf5viewer, &file_id);CHKERRQ(ierr);
/* get number of cells and then number of edges */
dataset_id = H5Dopen(file_id, "/Cells/Natural IDs");
dataspace_id = H5Dget_space(dataset_id);
status = H5Sget_simple_extent_dims(dataspace_id, &data.numCells, NULL);if (status < 0) SETERRQ(PETSC_ERR_LIB,"Bad dimension");
status = H5Sclose(dataspace_id);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Areas");
dataspace_id = H5Dget_space(dataset_id);
status = H5Sget_simple_extent_dims(dataspace_id, &data.numFaces, NULL);if (status < 0) SETERRQ(PETSC_ERR_LIB,"Bad dimension");
status = H5Sclose(dataspace_id);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
ierr = PetscPrintf(PETSC_COMM_SELF, "Number of cells %D Number of faces %D \n",(PetscInt)data.numCells,(PetscInt)data.numFaces);CHKERRQ(ierr);
/* read face data */
ierr = PetscMalloc5(data.numFaces,double,&data.faceAreas,data.numFaces,int,&data.downCells,data.numFaces,double,&data.downX,data.numFaces,double,&data.downY,data.numFaces,double,&data.downZ);CHKERRQ(ierr);
dataset_id = H5Dopen(file_id, "/Connections/Areas");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.faceAreas);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Cell IDs");
status = H5Dread(dataset_id, H5T_STD_I32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downCells);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Distance X");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downX);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Distance Y");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downY);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Distance Z");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downZ);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
ierr = PetscMalloc4(data.numFaces,int,&data.upCells,data.numFaces,double,&data.upX,data.numFaces,double,&data.upY,data.numFaces,double,&data.upZ);CHKERRQ(ierr);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Cell IDs");
status = H5Dread(dataset_id, H5T_STD_I32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upCells);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Distance X");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upX);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Distance Y");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upY);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Distance Z");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upZ);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
// Put face data into matrix
ierr = MatCreate(PETSC_COMM_WORLD, &Adj);CHKERRQ(ierr);
ierr = MatSetSizes(Adj, data.numCells*bs, data.numCells*bs, PETSC_DECIDE, PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetFromOptions(Adj);CHKERRQ(ierr);
ierr = MatSetType(Adj,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(Adj, bs, 6,PETSC_NULL);CHKERRQ(ierr);
//ierr = MatSetType(Adj,MATSEQAIJ);CHKERRQ(ierr);
//ierr = MatSeqAIJSetPreallocation(Adj, 6,PETSC_NULL);CHKERRQ(ierr);
for(i = 0; i < data.numFaces; ++i) {
values[0] = data.faceAreas[i];
values[1] = data.downCells[i];
values[2] = data.downX[i];
values[3] = data.downY[i];
values[4] = data.downZ[i];
values[5] = data.upCells[i];
values[6] = data.upX[i];
values[7] = data.upY[i];
values[8] = data.upZ[i];
ierr = MatSetValuesBlocked(Adj, 1, &data.downCells[i], 1, &data.upCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesBlocked(Adj, 1, &data.upCells[i], 1, &data.downCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
//ierr = MatSetValues(Adj, 1, &data.downCells[i], 1, &data.upCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
//ierr = MatSetValues(Adj, 1, &data.upCells[i], 1, &data.downCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Adj, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Adj, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscFree5(data.faceAreas, data.downCells, data.downX, data.downY, data.downZ);CHKERRQ(ierr);
ierr = PetscFree4(data.upCells, data.upX, data.upY, data.upZ);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"mesh.petsc", FILE_MODE_WRITE,&binaryviewer);CHKERRQ(ierr);
ierr = MatView(Adj, binaryviewer);CHKERRQ(ierr);
ierr = MatDestroy(Adj);CHKERRQ(ierr);
/* read cell information */
ierr = PetscMalloc5(data.numCells,int,&data.cellIds,data.numCells,double,&data.cellVols,data.numCells,double,&data.cellX,data.numCells,double,&data.cellY,data.numCells,double,&data.cellZ);CHKERRQ(ierr);
dataset_id = H5Dopen(file_id, "/Cells/Natural IDs");
status = H5Dread(dataset_id, H5T_STD_I32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellIds);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/Volumes");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellVols);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/X-Coordinates");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellX);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/Y-Coordinates");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellY);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/Z-Coordinates");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellZ);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
ierr = PetscViewerDestroy(hdf5viewer);CHKERRQ(ierr);
/* put cell information into vectors */
ierr = VecCreateSeq(PETSC_COMM_SELF,3*data.numCells,&cellCenters);CHKERRQ(ierr);
ierr = VecSetBlockSize(cellCenters,3);CHKERRQ(ierr);
ierr = VecGetArray(cellCenters,&cc);CHKERRQ(ierr);
for (i=0; i<data.numCells; i++) {
cc[3*i] = data.cellX[i];
cc[3*i+1] = data.cellY[i];
cc[3*i+2] = data.cellZ[i];
}
ierr = VecRestoreArray(cellCenters,&cc);CHKERRQ(ierr);
ierr = VecView(cellCenters,binaryviewer);CHKERRQ(ierr);
ierr = VecGetArray(cellCenters,&cc);CHKERRQ(ierr);
for (i=0; i<data.numCells; i++) {
cc[3*i] = data.cellIds[i];
cc[3*i+1] = data.cellVols[i];
cc[3*i+2] = 0.0;
}
ierr = VecRestoreArray(cellCenters,&cc);CHKERRQ(ierr);
ierr = VecView(cellCenters,binaryviewer);CHKERRQ(ierr);
ierr = PetscFree5(data.cellIds, data.cellVols, data.cellX, data.cellY, data.cellZ);CHKERRQ(ierr);
ierr = VecDestroy(cellCenters);
ierr = PetscViewerDestroy(binaryviewer);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
