/*! Returns the number of Zone_t under the Base_t * \return Number of Zone_t structures */ int Base_t::getNbZone() const { int nzones; int ier = cg_nzones( getFileID(), getID(), &nzones ); check_error( "Base_t::getNbZone", "cg_nzones", ier ); return nzones; }
int main() { int itranfrm[3]; int index_file,index_base,nzone,index_zone,n1to1,index_conn; char donorname[33],connectname[33]; cgsize_t ipnts[2][3],ipntsdonor[2][3]; /* READ 1-TO-1 CONNECTIVITY INFORMATION FROM EXISTING CGNS FILE */ /* open CGNS file for read-only */ if (cg_open("grid_c.cgns",CG_MODE_READ,&index_file)) cg_error_exit(); /* we know there is only one base (real working code would check!) */ index_base=1; /* get number of zones (should be 2 for our case) */ cg_nzones(index_file,index_base,&nzone); if (nzone != 2) { printf("\nError. This program expects 2 zones. %d read.\n",nzone); return 1; } /* loop over zones */ for (index_zone=1; index_zone <= nzone; ++index_zone) { /* find out how many 1-to-1 interfaces there are in this zone */ /* (for this program, there should only be one) */ cg_n1to1(index_file,index_base,index_zone,&n1to1); if (n1to1 != 1) { printf("\nError. Expecting one 1-to-1 interface. %i read\n",n1to1); return 1; } index_conn=n1to1; /* read 1-to-1 info */ cg_1to1_read(index_file,index_base,index_zone,index_conn,connectname,donorname, ipnts[0],ipntsdonor[0],itranfrm); printf("\nIn zone %i:\n",index_zone); printf(" donor name=%s\n",donorname); printf(" range (this zone)=%i,%i,%i,%i,%i,%i\n",(int)ipnts[0][0], (int)ipnts[0][1],(int)ipnts[0][2],(int)ipnts[1][0], (int)ipnts[1][1],(int)ipnts[1][2]); printf(" range (donor zone)=%i,%i,%i,%i,%i,%i\n",(int)ipntsdonor[0][0], (int)ipntsdonor[0][1],(int)ipntsdonor[0][2],(int)ipntsdonor[1][0], (int)ipntsdonor[1][1],(int)ipntsdonor[1][2]); printf(" transform=%i,%i,%i\n",itranfrm[0],itranfrm[1],itranfrm[2]); } /* close CGNS file */ cg_close(index_file); printf("\nSuccessfully read 1-to-1 connectivity info from file grid_c.cgns\n"); return 0; }
unsigned short GetnDim(string val_mesh_filename, unsigned short val_format) { string text_line, Marker_Tag; ifstream mesh_file; short nDim = 3; unsigned short iLine, nLine = 10; char cstr[200]; string::size_type position; /*--- Open grid file ---*/ strcpy (cstr, val_mesh_filename.c_str()); mesh_file.open(cstr, ios::in); switch (val_format) { case SU2: /*--- Read SU2 mesh file ---*/ for (iLine = 0; iLine < nLine ; iLine++) { getline (mesh_file, text_line); /*--- Search for the "NDIM" keyword to see if there are multiple Zones ---*/ position = text_line.find ("NDIME=",0); if (position != string::npos) { text_line.erase (0,6); nDim = atoi(text_line.c_str()); } } break; case CGNS: #ifdef HAVE_CGNS /*--- Local variables which are needed when calling the CGNS mid-level API. ---*/ int fn, nbases = 0, nzones = 0, file_type; int cell_dim = 0, phys_dim = 0; char basename[CGNS_STRING_SIZE]; /*--- Check whether the supplied file is truly a CGNS file. ---*/ if ( cg_is_cgns(val_mesh_filename.c_str(), &file_type) != CG_OK ) { printf( "\n\n !!! Error !!!\n" ); printf( " %s is not a CGNS file.\n", val_mesh_filename.c_str()); printf( " Now exiting...\n\n"); exit(EXIT_FAILURE); } /*--- Open the CGNS file for reading. The value of fn returned is the specific index number for this file and will be repeatedly used in the function calls. ---*/ if (cg_open(val_mesh_filename.c_str(), CG_MODE_READ, &fn)) cg_error_exit(); /*--- Get the number of databases. This is the highest node in the CGNS heirarchy. ---*/ if (cg_nbases(fn, &nbases)) cg_error_exit(); /*--- Check if there is more than one database. Throw an error if there is because this reader can currently only handle one database. ---*/ if ( nbases > 1 ) { printf("\n\n !!! Error !!!\n" ); printf("CGNS reader currently incapable of handling more than 1 database."); printf("Now exiting...\n\n"); exit(EXIT_FAILURE); } /*--- Read the databases. Note that the indexing starts at 1. ---*/ for ( int i = 1; i <= nbases; i++ ) { if (cg_base_read(fn, i, basename, &cell_dim, &phys_dim)) cg_error_exit(); /*--- Get the number of zones for this base. ---*/ if (cg_nzones(fn, i, &nzones)) cg_error_exit(); } /*--- Set the problem dimension as read from the CGNS file ---*/ nDim = cell_dim; #endif break; } mesh_file.close(); return (unsigned short) nDim; }
int main() { int ilo[2],ihi[2],jlo[2],jhi[2],klo[2],khi[2]; int icount,j,k; int index_file,index_base,nzone,index_zone,nconns,n1to1,index_conn,iz; char donorname[33],zonename0[33],zonename1[33],zn[33]; cgsize_t isize[3][3],ipnts[maxcount][3],ipntsdonor[maxcount][3]; /* WRITE GENERAL CONNECTIVITY INFORMATION TO EXISTING CGNS FILE */ /* open CGNS file for modify */ if (cg_open("grid_c.cgns",CG_MODE_MODIFY,&index_file)) cg_error_exit(); /* we know there is only one base (real working code would check!) */ index_base=1; /* get number of zones (should be 2 for our case) */ cg_nzones(index_file,index_base,&nzone); if (nzone != 2) { printf("\nError. This program expects 2 zones. %d read.\n",nzone); return 1; } /* loop over zones to get zone sizes and names */ for (index_zone=0; index_zone < nzone; ++index_zone) { iz=index_zone+1; cg_zone_read(index_file,index_base,iz,zn,isize[0]); if (index_zone == 0) { strcpy(zonename0,zn); } else { strcpy(zonename1,zn); } ilo[index_zone]=1; ihi[index_zone]=isize[0][0]; jlo[index_zone]=1; jhi[index_zone]=isize[0][1]; klo[index_zone]=1; khi[index_zone]=isize[0][2]; } /* loop over zones again */ for (index_zone=0; index_zone < nzone; ++index_zone) { iz=index_zone+1; /* for this program, there should be no existing connectivity info: */ cg_nconns(index_file,index_base,iz,&nconns); if (nconns != 0) { printf("\nError. This program expects no interfaces yet. %d read.\n",nconns); return 1; } cg_n1to1(index_file,index_base,iz,&n1to1); if (n1to1 != 0) { printf("\nError. This program expects no interfaces yet. %d read.\n",n1to1); return 1; } /* set up point lists */ if (index_zone == 0) { strcpy(donorname,zonename1); icount=0; for (j=jlo[index_zone]; j <= jhi[index_zone]; j++) { for (k=klo[index_zone]; k <= khi[index_zone]; k++) { ipnts[icount][0]=ihi[0]; ipnts[icount][1]=j; ipnts[icount][2]=k; ipntsdonor[icount][0]=ilo[1]; ipntsdonor[icount][1]=j; ipntsdonor[icount][2]=k; icount=icount+1; } } if (icount > maxcount) { printf("\nError. Need to increase maxcount to at least %i\n",icount); return 1; } } else { strcpy(donorname,zonename0); icount=0; for (j=jlo[index_zone]; j <= jhi[index_zone]; j++) { for (k=klo[index_zone]; k <= khi[index_zone]; k++) { ipnts[icount][0]=ilo[1]; ipnts[icount][1]=j; ipnts[icount][2]=k; ipntsdonor[icount][0]=ihi[0]; ipntsdonor[icount][1]=j; ipntsdonor[icount][2]=k; icount=icount+1; } } if (icount > maxcount) { printf("\nError. Need to increase maxcount to at least %i\n",icount); return 1; } } /* write integer connectivity info (user can give any name) */ cg_conn_write(index_file,index_base,iz,"GenInterface",Vertex,Abutting1to1, PointList,icount,ipnts[0],donorname,Structured, PointListDonor,Integer,icount,ipntsdonor[0],&index_conn); } /* close CGNS file */ cg_close(index_file); printf("\nSuccessfully added 1-to-1 connectivity info to file grid_c.cgns (using GENERAL method)\n"); return 0; }
/*---------- PostProcesssing -------------------------------------- * Post-Analysis of CFD Data * Developed only for CFD-Tutor with single base - single zone 2D * -------------------------------------------------------------*/ int PostProcessing(const char *file) { int visual; int nbases, ncoords, celldim, phydim; char basename[33]; ZONE *z; int i, j, nz; SOLUTION *s; /* Checks for existance of file */ if (!file_exists(file)) FATAL(NULL, "File does not exist"); /* Read CGNS file */ printf("Reading CGNS file from %s\n", file); fflush(stdout); /* Open CGNS File */ nbases = open_cgns(file, 0); if (!nbases) FATAL(NULL, "No bases in CGNS file"); cg_version(cgnsfn, &Version); printf("File version = %lf\n", Version); printf("No of Bases = %d\n", nbases); if (nbases == 1) cgnsbase = 1; else { printf("Give base No to Post-Processed : "); scanf("%d", &cgnsbase); if (cgnsbase < 1 || cgnsbase > nbases) FATAL(NULL, "Invailed base index"); } if (cg_base_read(cgnsfn, cgnsbase, basename, &celldim, &phydim) || cg_nzones(cgnsfn, cgnsbase, &nZones)) FATAL(NULL, NULL); if (celldim != 2 || phydim != 2) FATAL(NULL, "Not A 2D Grid"); if (nZones > 1) FATAL(NULL, "Not A Single Zone"); printf("Base Number = %d\n", cgnsbase); printf("Base Name = %s\n", basename); printf("Cell Dimension = %d\n", celldim); printf("Physical Dimension = %d\n", phydim); read_cgns(); printf("No of Zones = %d\n", nZones); /* Print Zone Information */ for (z = Zones, nz = 1; nz <= nZones; nz++, z++) { printf("Zone No = %d\n", z->id); printf("Zone Name = %s\n", z->name); if (cg_ncoords(cgnsfn, cgnsbase, nz, &ncoords)) FATAL("Post-Processing ncoords", NULL); if (ncoords != 2) FATAL(NULL, "No 3D Support Now"); print_ZoneType(z->type); switch (z->type) { case 2: /* For Structured Grid */ printf("Dimensions = %d x %d x %d\n", z->dim[0], z->dim[1], z->dim[2]); break; case 3: /* For Unstructured Grid */ printf("No of Nodes = %d\n", z->dim[0]); printf("No of Cells = %d\n", z->dim[1]); break; default: /* Unknown Type Grids */ FATAL(NULL, "Unknown Grid Type"); } } /* Print Available Solution Fields */ for (z = Zones, nz = 1; nz <= nZones; nz++, z++) { if (z->nsols) { printf("No of Solutions Nodes = %d\n", z->nsols); for (s = z->sols, i = 1; i <= z->nsols; i++, s++) { printf("Solution Node = %d\n", i); if (s->nflds == 0) FATAL(NULL, "No Solution Fields: Exiting"); printf("\tNo of Fields = %d\n", s->nflds); for (j = 0; j < s->nflds; j++) { printf("\tField = %s\n", s->flds[j].name); } } } else FATAL(NULL, "No Solution Node Available: Exiting"); } /* Initialize Data Structure Only Once */ for (z = Zones, nz = 1; nz <= nZones; nz++, z++) InitializeGrid_2D(z); /* Do Post-Processing Operation Below */ /*****************/ /* Post Analysis Function Calls */ for (z = Zones, nz = 1; nz <= nZones; nz++, z++) { InitializeSolutionCGNS_2D(z); InitializeSolution_2D(); GetSolutionList_2D(); /* Visual Mode Option */ printf("Goto Visual Mode (0/1):"); scanf("%d", &visual); if (visual == 1) Graphics_2D(); else { GetFluidProperties(); GetReferenceQuantities(); PostAnalysis_2D(); } } /*****************/ /* Do Post-Processing Operation Above */ /* Close cgns Interface */ if (cg_close(cgnsfn)) FATAL(NULL, NULL); return 0; }
int main() { int i,index_file,index_base,nzone,index_zone,nconns,index_conn; char donorname[33],connectname[33]; GridLocation_t location; GridConnectivityType_t iconnect_type; PointSetType_t iptset_type,idonor_ptset_type; ZoneType_t idonor_zonetype; DataType_t idonor_datatype; cgsize_t npts,ndata_donor; cgsize_t ipnts[maxpnts][3],ipntsdonor[maxpnts][3]; /* READ GENERAL CONNECTIVITY INFORMATION FROM EXISTING CGNS FILE */ /* open CGNS file for read-only */ if (cg_open("grid_c.cgns",CG_MODE_READ,&index_file)) cg_error_exit(); /* we know there is only one base (real working code would check!) */ index_base=1; /* get number of zones (should be 2 for our case) */ cg_nzones(index_file,index_base,&nzone); if (nzone != 2) { printf("\nError. This program expects 2 zones. %d read.\n",nzone); return 1; } /* loop over zones */ for (index_zone=1; index_zone <= nzone; ++index_zone) { /* find out how many general interfaces there are in this zone */ /* (for this program, there should only be one) */ cg_nconns(index_file,index_base,index_zone,&nconns); if (nconns != 1) { printf("\nError. Expecting one general interface. %i read\n",nconns); return 1; } index_conn=nconns; /* read general connectivity info */ cg_conn_info(index_file,index_base,index_zone,index_conn,connectname,&location, &iconnect_type,&iptset_type,&npts,donorname,&idonor_zonetype, &idonor_ptset_type,&idonor_datatype,&ndata_donor); if (npts > maxpnts) { printf("\nError. Must increase maxpnts to at least %i\n",(int)npts); return 1; } cg_conn_read(index_file,index_base,index_zone,index_conn,ipnts[0], idonor_datatype,ipntsdonor[0]); printf("\nIn zone %i:\n",index_zone); printf(" donor name=%s\n",donorname); printf(" number of connectivity pts=%i\n",(int)npts); printf(" grid location=%s\n",GridLocationName[location]); printf(" connectivity type=%s\n",GridConnectivityTypeName[iconnect_type]); printf(" pointset type=%s\n",PointSetTypeName[iptset_type]); printf(" donor zonetype=%s\n",ZoneTypeName[idonor_zonetype]); printf(" donor pointset type=%s\n",PointSetTypeName[idonor_ptset_type]); printf(" data type=%s\n",DataTypeName[idonor_datatype]); printf(" ipnts and ipntsdonor arrays read, only some written out here:\n"); for (i=0; i < 10; i++) { printf(" ipnts[%i][0], [%i][1], [%i][2]=%i,%i,%i", i,i,i,(int)ipnts[i][0],(int)ipnts[i][1],(int)ipnts[i][2]); printf(" ipntsdonor[%i][0], [%i][1], [%i][2]=%i,%i,%i\n", i,i,i,(int)ipntsdonor[i][0],(int)ipntsdonor[i][1],(int)ipntsdonor[i][2]); } } /* close CGNS file */ cg_close(index_file); printf("\nSuccessfully read general 1-to-1 connectivity info from file grid_c.cgns\n"); return 0; }
/*@ DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID. Collective on comm Input Parameters: + comm - The MPI communicator . cgid - The CG id associated with a file and obtained using cg_open - interpolate - Create faces and edges in the mesh Output Parameter: . dm - The DM object representing the mesh Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html Level: beginner .keywords: mesh,CGNS .seealso: DMPlexCreate(), DMPlexCreateExodus() @*/ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm) { #if defined(PETSC_HAVE_CGNS) PetscMPIInt num_proc, rank; PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt *cellStart, *vertStart; PetscInt coordSize, v; PetscErrorCode ierr; /* Read from file */ char basename[CGIO_MAX_NAME_LENGTH+1]; char buffer[CGIO_MAX_NAME_LENGTH+1]; int dim = 0, physDim = 0, numVertices = 0, numCells = 0; int nzones = 0; #endif PetscFunctionBegin; #if defined(PETSC_HAVE_CGNS) ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr); ierr = DMCreate(comm, dm);CHKERRQ(ierr); ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); /* Open CGNS II file and read basic informations on rank 0, then broadcast to all processors */ if (!rank) { int nbases, z; ierr = cg_nbases(cgid, &nbases);CHKERRQ(ierr); if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases); ierr = cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRQ(ierr); ierr = cg_nzones(cgid, 1, &nzones);CHKERRQ(ierr); ierr = PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);CHKERRQ(ierr); for (z = 1; z <= nzones; ++z) { cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); numVertices += sizes[0]; numCells += sizes[1]; cellStart[z] += sizes[1] + cellStart[z-1]; vertStart[z] += sizes[0] + vertStart[z-1]; } for (z = 1; z <= nzones; ++z) { vertStart[z] += numCells; } } ierr = MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);CHKERRQ(ierr); ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr); ierr = MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *dm, basename);CHKERRQ(ierr); ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); /* Read zone information */ if (!rank) { int z, c, c_loc, v, v_loc; /* Read the cell set connectivity table and build mesh topology CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */ /* First set sizes */ for (z = 1, c = 0; z <= nzones; ++z) { ZoneType_t zonetype; int nsections; ElementType_t cellType; cgsize_t start, end; int nbndry, parentFlag; PetscInt numCorners; ierr = cg_zone_type(cgid, 1, z, &zonetype);CHKERRQ(ierr); if (zonetype == Structured) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS"); ierr = cg_nsections(cgid, 1, z, &nsections);CHKERRQ(ierr); if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections); ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ if (cellType == MIXED) { cgsize_t elementDataSize, *elements; PetscInt off; ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); ierr = PetscMalloc1(elementDataSize, &elements);CHKERRQ(ierr); ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) { switch (elements[off]) { case TRI_3: numCorners = 3;break; case QUAD_4: numCorners = 4;break; case TETRA_4: numCorners = 4;break; case HEXA_8: numCorners = 8;break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]); } ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); off += numCorners+1; } ierr = PetscFree(elements);CHKERRQ(ierr); } else { switch (cellType) { case TRI_3: numCorners = 3;break; case QUAD_4: numCorners = 4;break; case TETRA_4: numCorners = 4;break; case HEXA_8: numCorners = 8;break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); } for (c_loc = start; c_loc <= end; ++c_loc, ++c) { ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr); } } } ierr = DMSetUp(*dm);CHKERRQ(ierr); for (z = 1, c = 0; z <= nzones; ++z) { ElementType_t cellType; cgsize_t *elements, elementDataSize, start, end; int nbndry, parentFlag; PetscInt *cone, numc, numCorners, maxCorners = 27; ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr); numc = end - start; /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */ ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr); ierr = PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);CHKERRQ(ierr); ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr); if (cellType == MIXED) { /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */ for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { switch (elements[v]) { case TRI_3: numCorners = 3;break; case QUAD_4: numCorners = 4;break; case TETRA_4: numCorners = 4;break; case HEXA_8: numCorners = 8;break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]); } ++v; for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { cone[v_loc] = elements[v]+numCells-1; } /* Tetrahedra are inverted */ if (elements[v] == TETRA_4) { PetscInt tmp = cone[0]; cone[0] = cone[1]; cone[1] = tmp; } /* Hexahedra are inverted */ if (elements[v] == HEXA_8) { PetscInt tmp = cone[5]; cone[5] = cone[7]; cone[7] = tmp; } ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); } } else { switch (cellType) { case TRI_3: numCorners = 3;break; case QUAD_4: numCorners = 4;break; case TETRA_4: numCorners = 4;break; case HEXA_8: numCorners = 8;break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType); } /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */ for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) { for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) { cone[v_loc] = elements[v]+numCells-1; } /* Tetrahedra are inverted */ if (cellType == TETRA_4) { PetscInt tmp = cone[0]; cone[0] = cone[1]; cone[1] = tmp; } /* Hexahedra are inverted, and they give the top first */ if (cellType == HEXA_8) { PetscInt tmp = cone[5]; cone[5] = cone[7]; cone[7] = tmp; } ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr); } } ierr = PetscFree2(elements,cone);CHKERRQ(ierr); } } ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); ierr = DMPlexStratify(*dm);CHKERRQ(ierr); if (interpolate) { DM idm = NULL; ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); /* Maintain zone label */ { DMLabel label; ierr = DMPlexRemoveLabel(*dm, "zone", &label);CHKERRQ(ierr); if (label) {ierr = DMPlexAddLabel(idm, label);CHKERRQ(ierr);} } ierr = DMDestroy(dm);CHKERRQ(ierr); *dm = idm; } /* Read coordinates */ ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); for (v = numCells; v < numCells+numVertices; ++v) { ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); ierr = VecCreate(comm, &coordinates);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); if (!rank) { PetscInt off = 0; float *x[3]; int z, d; ierr = PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);CHKERRQ(ierr); for (z = 1; z <= nzones; ++z) { DataType_t datatype; cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */ cgsize_t range_min[3] = {1, 1, 1}; cgsize_t range_max[3] = {1, 1, 1}; int ngrids, ncoords; ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr); range_max[0] = sizes[0]; ierr = cg_ngrids(cgid, 1, z, &ngrids);CHKERRQ(ierr); if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids); ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr); if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords); for (d = 0; d < dim; ++d) { ierr = cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRQ(ierr); ierr = cg_coord_read(cgid, 1, z, buffer, RealSingle, range_min, range_max, x[d]);CHKERRQ(ierr); } if (dim > 0) { for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v]; } if (dim > 1) { for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v]; } if (dim > 2) { for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v]; } off += sizes[0]; } ierr = PetscFree3(x[0],x[1],x[2]);CHKERRQ(ierr); } ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); ierr = VecDestroy(&coordinates);CHKERRQ(ierr); /* Read boundary conditions */ if (!rank) { DMLabel label; BCType_t bctype; DataType_t datatype; PointSetType_t pointtype; cgsize_t *points; PetscReal *normals; int normal[3]; char *bcname = buffer; cgsize_t npoints, nnormals; int z, nbc, bc, c, ndatasets; for (z = 1; z <= nzones; ++z) { ierr = cg_nbocos(cgid, 1, z, &nbc);CHKERRQ(ierr); for (bc = 1; bc <= nbc; ++bc) { ierr = cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);CHKERRQ(ierr); ierr = DMPlexCreateLabel(*dm, bcname);CHKERRQ(ierr); ierr = DMPlexGetLabel(*dm, bcname, &label);CHKERRQ(ierr); ierr = PetscMalloc2(npoints, &points, nnormals, &normals);CHKERRQ(ierr); ierr = cg_boco_read(cgid, 1, z, bc, points, (void *) normals);CHKERRQ(ierr); if (pointtype == ElementRange) { /* Range of cells: assuming half-open interval since the documentation sucks */ for (c = points[0]; c < points[1]; ++c) { ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr); } } else if (pointtype == ElementList) { /* List of cells */ for (c = 0; c < npoints; ++c) { ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr); } } else if (pointtype == PointRange) { GridLocation_t gridloc; /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */ ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");CHKERRQ(ierr); ierr = cg_gridlocation_read(&gridloc);CHKERRQ(ierr); /* Range of points: assuming half-open interval since the documentation sucks */ for (c = points[0]; c < points[1]; ++c) { if (gridloc == Vertex) {ierr = DMLabelSetValue(label, c - vertStart[z-1], 1);CHKERRQ(ierr);} else {ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr);} } } else if (pointtype == PointList) { GridLocation_t gridloc; /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */ ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end"); ierr = cg_gridlocation_read(&gridloc); for (c = 0; c < npoints; ++c) { if (gridloc == Vertex) {ierr = DMLabelSetValue(label, points[c] - vertStart[z-1], 1);CHKERRQ(ierr);} else {ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr);} } } else SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype); ierr = PetscFree2(points, normals);CHKERRQ(ierr); } } ierr = PetscFree2(cellStart, vertStart);CHKERRQ(ierr); } #else SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir"); #endif PetscFunctionReturn(0); }
int main() { int ilo[2],ihi[2],jlo[2],jhi[2],klo[2],khi[2]; int itranfrm[3]; int index_file,index_base,nzone,index_zone,nconns,n1to1,index_conn,iz; char donorname[33],zonename0[33],zonename1[33],zn[33]; cgsize_t isize[3][3],ipnts[2][3],ipntsdonor[2][3]; printf("\nProgram write_con2zn_str\n"); /* WRITE 1-TO-1 CONNECTIVITY INFORMATION TO EXISTING CGNS FILE */ /* open CGNS file for modify */ if (cg_open("grid_c.cgns",CG_MODE_MODIFY,&index_file)) cg_error_exit(); /* we know there is only one base (real working code would check!) */ index_base=1; /* get number of zones (should be 2 for our case) */ cg_nzones(index_file,index_base,&nzone); if (nzone != 2) { printf("\nError. This program expects 2 zones. %d read.\n",nzone); return 1; } /* loop over zones to get zone sizes and names */ for (index_zone=0; index_zone < nzone; ++index_zone) { iz=index_zone+1; cg_zone_read(index_file,index_base,iz,zn,isize[0]); if (index_zone == 0) { strcpy(zonename0,zn); } else { strcpy(zonename1,zn); } ilo[index_zone]=1; ihi[index_zone]=isize[0][0]; jlo[index_zone]=1; jhi[index_zone]=isize[0][1]; klo[index_zone]=1; khi[index_zone]=isize[0][2]; } /* loop over zones again */ for (index_zone=0; index_zone < nzone; ++index_zone) { iz=index_zone+1; /* for this program, there should be no existing connectivity info: */ cg_nconns(index_file,index_base,iz,&nconns); if (nconns != 0) { printf("\nError. This program expects no interfaces yet. %d read.\n",nconns); return 1; } cg_n1to1(index_file,index_base,iz,&n1to1); if (n1to1 != 0) { printf("\nError. This program expects no interfaces yet. %d read.\n",n1to1); return 1; } /* set up index ranges */ if (index_zone == 0) { strcpy(donorname,zonename1); /* lower point of receiver range */ ipnts[0][0]=ihi[0]; ipnts[0][1]=jlo[0]; ipnts[0][2]=klo[0]; /* upper point of receiver range */ ipnts[1][0]=ihi[0]; ipnts[1][1]=jhi[0]; ipnts[1][2]=khi[0]; /* lower point of donor range */ ipntsdonor[0][0]=ilo[1]; ipntsdonor[0][1]=jlo[1]; ipntsdonor[0][2]=klo[1]; /* upper point of donor range */ ipntsdonor[1][0]=ilo[1]; ipntsdonor[1][1]=jhi[1]; ipntsdonor[1][2]=khi[1]; } else { strcpy(donorname,zonename0); /* lower point of receiver range */ ipnts[0][0]=ilo[1]; ipnts[0][1]=jlo[1]; ipnts[0][2]=klo[1]; /* upper point of receiver range */ ipnts[1][0]=ilo[1]; ipnts[1][1]=jhi[1]; ipnts[1][2]=khi[1]; /* lower point of donor range */ ipntsdonor[0][0]=ihi[0]; ipntsdonor[0][1]=jlo[0]; ipntsdonor[0][2]=klo[0]; /* upper point of donor range */ ipntsdonor[1][0]=ihi[0]; ipntsdonor[1][1]=jhi[0]; ipntsdonor[1][2]=khi[0]; } /* set up Transform */ itranfrm[0]=1; itranfrm[1]=2; itranfrm[2]=3; /* write 1-to-1 info (user can give any name) */ cg_1to1_write(index_file,index_base,iz,"Interface",donorname, ipnts[0],ipntsdonor[0],itranfrm,&index_conn); } /* close CGNS file */ cg_close(index_file); printf("\nSuccessfully added 1-to-1 connectivity info to file grid_c.cgns\n"); return 0; }
ErrorCode ReadCGNS::load_file(const char* filename, const EntityHandle * /*file_set*/, const FileOptions& opts, const ReaderIface::SubsetList* subset_list, const Tag* file_id_tag) { int num_material_sets = 0; const int* material_set_list = 0; if (subset_list) { if (subset_list->tag_list_length > 1 && !strcmp(subset_list->tag_list[0].tag_name, MATERIAL_SET_TAG_NAME)) { MB_SET_ERR(MB_UNSUPPORTED_OPERATION, "CGNS supports subset read only by material ID"); } material_set_list = subset_list->tag_list[0].tag_values; num_material_sets = subset_list->tag_list[0].num_tag_values; } ErrorCode result; geomSets.clear(); result = mbImpl->tag_get_handle(GLOBAL_ID_TAG_NAME, 1, MB_TYPE_INTEGER, globalId, MB_TAG_DENSE | MB_TAG_CREAT, 0); if (MB_SUCCESS != result) return result; // Create set for more convienient check for material set ids std::set<int> blocks; for (const int* mat_set_end = material_set_list + num_material_sets; material_set_list != mat_set_end; ++material_set_list) blocks.insert(*material_set_list); // Map of ID->handle for nodes std::map<long, EntityHandle> node_id_map; // Save filename to member variable so we don't need to pass as an argument // to called functions fileName = filename; // Process options; see src/FileOptions.hpp for API for FileOptions class, and doc/metadata_info.doc for // a description of various options used by some of the readers in MOAB result = process_options(opts);MB_CHK_SET_ERR(result, fileName << ": problem reading options"); // Open file int filePtr = 0; cg_open(filename, CG_MODE_READ, &filePtr); if (filePtr <= 0) { MB_SET_ERR(MB_FILE_DOES_NOT_EXIST, fileName << ": fopen returned error"); } // Read number of verts, elements, sets long num_verts = 0, num_elems = 0, num_sets = 0; int num_bases = 0, num_zones = 0, num_sections = 0; char zoneName[128]; cgsize_t size[3]; mesh_dim = 3; // Default to 3D // Read number of bases; cg_nbases(filePtr, &num_bases); if (num_bases > 1) { MB_SET_ERR(MB_NOT_IMPLEMENTED, fileName << ": support for number of bases > 1 not implemented"); } for (int indexBase = 1; indexBase <= num_bases; ++indexBase) { // Get the number of zones/blocks in current base. cg_nzones(filePtr, indexBase, &num_zones); if (num_zones > 1) { MB_SET_ERR(MB_NOT_IMPLEMENTED, fileName << ": support for number of zones > 1 not implemented"); } for (int indexZone = 1; indexZone <= num_zones; ++indexZone) { // Get zone name and size. cg_zone_read(filePtr, indexBase, indexZone, zoneName, size); // Read number of sections/Parts in current zone. cg_nsections(filePtr, indexBase, indexZone, &num_sections); num_verts = size[0]; num_elems = size[1]; num_sets = num_sections; std::cout << "\nnumber of nodes = " << num_verts; std::cout << "\nnumber of elems = " << num_elems; std::cout << "\nnumber of parts = " << num_sets << std::endl; // ////////////////////////////////// // Read Nodes // Allocate nodes; these are allocated in one shot, get contiguous handles starting with start_handle, // and the reader is passed back double*'s pointing to MOAB's native storage for vertex coordinates // for those verts std::vector<double*> coord_arrays; EntityHandle handle = 0; result = readMeshIface->get_node_coords(3, num_verts, MB_START_ID, handle, coord_arrays);MB_CHK_SET_ERR(result, fileName << ": Trouble reading vertices"); // Fill in vertex coordinate arrays cgsize_t beginPos = 1, endPos = num_verts; // Read nodes coordinates. cg_coord_read(filePtr, indexBase, indexZone, "CoordinateX", RealDouble, &beginPos, &endPos, coord_arrays[0]); cg_coord_read(filePtr, indexBase, indexZone, "CoordinateY", RealDouble, &beginPos, &endPos, coord_arrays[1]); cg_coord_read(filePtr, indexBase, indexZone, "CoordinateZ", RealDouble, &beginPos, &endPos, coord_arrays[2]); // CGNS seems to always include the Z component, even if the mesh is 2D. // Check if Z is zero and determine mesh dimension. // Also create the node_id_map data. double sumZcoord = 0.0; double eps = 1.0e-12; for (long i = 0; i < num_verts; ++i, ++handle) { int index = i + 1; node_id_map.insert(std::pair<long, EntityHandle>(index, handle)).second; sumZcoord += *(coord_arrays[2] + i); } if (std::abs(sumZcoord) <= eps) mesh_dim = 2; // Create reverse map from handle to id std::vector<int> ids(num_verts); std::vector<int>::iterator id_iter = ids.begin(); std::vector<EntityHandle> handles(num_verts); std::vector<EntityHandle>::iterator h_iter = handles.begin(); for (std::map<long, EntityHandle>::iterator i = node_id_map.begin(); i != node_id_map.end(); ++i, ++id_iter, ++h_iter) { *id_iter = i->first; * h_iter = i->second; } // Store IDs in tags result = mbImpl->tag_set_data(globalId, &handles[0], num_verts, &ids[0]); if (MB_SUCCESS != result) return result; if (file_id_tag) { result = mbImpl->tag_set_data(*file_id_tag, &handles[0], num_verts, &ids[0]); if (MB_SUCCESS != result) return result; } ids.clear(); handles.clear(); // ////////////////////////////////// // Read elements data EntityType ent_type; long section_offset = 0; // Define which mesh parts are volume families. // Mesh parts with volumeID[X] = 0 are boundary parts. std::vector<int> volumeID(num_sections, 0); for (int section = 0; section < num_sections; ++section) { ElementType_t elemsType; int iparent_flag, nbndry; char sectionName[128]; int verts_per_elem; int cgSection = section + 1; cg_section_read(filePtr, indexBase, indexZone, cgSection, sectionName, &elemsType, &beginPos, &endPos, &nbndry, &iparent_flag); size_t section_size = endPos - beginPos + 1; // Read element description in current section switch (elemsType) { case BAR_2: ent_type = MBEDGE; verts_per_elem = 2; break; case TRI_3: ent_type = MBTRI; verts_per_elem = 3; if (mesh_dim == 2) volumeID[section] = 1; break; case QUAD_4: ent_type = MBQUAD; verts_per_elem = 4; if (mesh_dim == 2) volumeID[section] = 1; break; case TETRA_4: ent_type = MBTET; verts_per_elem = 4; if (mesh_dim == 3) volumeID[section] = 1; break; case PYRA_5: ent_type = MBPYRAMID; verts_per_elem = 5; if (mesh_dim == 3) volumeID[section] = 1; break; case PENTA_6: ent_type = MBPRISM; verts_per_elem = 6; if (mesh_dim == 3) volumeID[section] = 1; break; case HEXA_8: ent_type = MBHEX; verts_per_elem = 8; if (mesh_dim == 3) volumeID[section] = 1; break; case MIXED: ent_type = MBMAXTYPE; verts_per_elem = 0; break; default: MB_SET_ERR(MB_INDEX_OUT_OF_RANGE, fileName << ": Trouble determining element type"); } if (elemsType == TETRA_4 || elemsType == PYRA_5 || elemsType == PENTA_6 || elemsType == HEXA_8 || elemsType == TRI_3 || elemsType == QUAD_4 || ((elemsType == BAR_2) && mesh_dim == 2)) { // Read connectivity into conn_array directly cgsize_t iparentdata; cgsize_t connDataSize; // Get number of entries on the connectivity list for this section cg_ElementDataSize(filePtr, indexBase, indexZone, cgSection, &connDataSize); // Need a temporary vector to later cast to conn_array. std::vector<cgsize_t> elemNodes(connDataSize); cg_elements_read(filePtr, indexBase, indexZone, cgSection, &elemNodes[0], &iparentdata); // ////////////////////////////////// // Create elements, sets and tags create_elements(sectionName, file_id_tag, ent_type, verts_per_elem, section_offset, section_size , elemNodes); } // Homogeneous mesh type else if (elemsType == MIXED) { // We must first sort all elements connectivities into continuous vectors cgsize_t connDataSize; cgsize_t iparentdata; cg_ElementDataSize(filePtr, indexBase, indexZone, cgSection, &connDataSize); std::vector< cgsize_t > elemNodes(connDataSize); cg_elements_read(filePtr, indexBase, indexZone, cgSection, &elemNodes[0], &iparentdata); std::vector<cgsize_t> elemsConn_EDGE; std::vector<cgsize_t> elemsConn_TRI, elemsConn_QUAD; std::vector<cgsize_t> elemsConn_TET, elemsConn_PYRA, elemsConn_PRISM, elemsConn_HEX; cgsize_t count_EDGE, count_TRI, count_QUAD; cgsize_t count_TET, count_PYRA, count_PRISM, count_HEX; // First, get elements count for current section count_EDGE = count_TRI = count_QUAD = 0; count_TET = count_PYRA = count_PRISM = count_HEX = 0; int connIndex = 0; for (int i = beginPos; i <= endPos; i++) { elemsType = ElementType_t(elemNodes[connIndex]); // Get current cell node count. cg_npe(elemsType, &verts_per_elem); switch (elemsType) { case BAR_2: count_EDGE += 1; break; case TRI_3: count_TRI += 1; break; case QUAD_4: count_QUAD += 1; break; case TETRA_4: count_TET += 1; break; case PYRA_5: count_PYRA += 1; break; case PENTA_6: count_PRISM += 1; break; case HEXA_8: count_HEX += 1; break; default: MB_SET_ERR(MB_INDEX_OUT_OF_RANGE, fileName << ": Trouble determining element type"); } connIndex += (verts_per_elem + 1); // Add one to skip next element descriptor } if (count_EDGE > 0) elemsConn_EDGE.resize(count_EDGE * 2); if (count_TRI > 0) elemsConn_TRI.resize(count_TRI * 3); if (count_QUAD > 0) elemsConn_QUAD.resize(count_QUAD * 4); if (count_TET > 0) elemsConn_TET.resize(count_TET * 4); if (count_PYRA > 0) elemsConn_PYRA.resize(count_PYRA * 5); if (count_PRISM > 0) elemsConn_PRISM.resize(count_PRISM * 6); if (count_HEX > 0) elemsConn_HEX.resize(count_HEX * 8); // Grab mixed section elements connectivity int idx_edge, idx_tri, idx_quad; int idx_tet, idx_pyra, idx_prism, idx_hex; idx_edge = idx_tri = idx_quad = 0; idx_tet = idx_pyra = idx_prism = idx_hex = 0; connIndex = 0; for (int i = beginPos; i <= endPos; i++) { elemsType = ElementType_t(elemNodes[connIndex]); // Get current cell node count. cg_npe(elemsType, &verts_per_elem); switch (elemsType) { case BAR_2: for (int j = 0; j < 2; ++j) elemsConn_EDGE[idx_edge + j] = elemNodes[connIndex + j + 1]; idx_edge += 2; break; case TRI_3: for (int j = 0; j < 3; ++j) elemsConn_TRI[idx_tri + j] = elemNodes[connIndex + j + 1]; idx_tri += 3; break; case QUAD_4: for (int j = 0; j < 4; ++j) elemsConn_QUAD[idx_quad + j] = elemNodes[connIndex + j + 1]; idx_quad += 4; break; case TETRA_4: for (int j = 0; j < 4; ++j) elemsConn_TET[idx_tet + j] = elemNodes[connIndex + j + 1]; idx_tet += 4; break; case PYRA_5: for (int j = 0; j < 5; ++j) elemsConn_PYRA[idx_pyra + j] = elemNodes[connIndex + j + 1]; idx_pyra += 5; break; case PENTA_6: for (int j = 0; j < 6; ++j) elemsConn_PRISM[idx_prism + j] = elemNodes[connIndex + j + 1]; idx_prism += 6; break; case HEXA_8: for (int j = 0; j < 8; ++j) elemsConn_HEX[idx_hex + j] = elemNodes[connIndex + j + 1]; idx_hex += 8; break; default: MB_SET_ERR(MB_INDEX_OUT_OF_RANGE, fileName << ": Trouble determining element type"); } connIndex += (verts_per_elem + 1); // Add one to skip next element descriptor } // ////////////////////////////////// // Create elements, sets and tags if (count_EDGE > 0) create_elements(sectionName, file_id_tag, MBEDGE, 2, section_offset, count_EDGE, elemsConn_EDGE); if (count_TRI > 0) create_elements(sectionName, file_id_tag, MBTRI, 3, section_offset, count_TRI, elemsConn_TRI); if (count_QUAD > 0) create_elements(sectionName, file_id_tag, MBQUAD, 4, section_offset, count_QUAD, elemsConn_QUAD); if (count_TET > 0) create_elements(sectionName, file_id_tag, MBTET, 4, section_offset, count_TET, elemsConn_TET); if (count_PYRA > 0) create_elements(sectionName, file_id_tag, MBPYRAMID, 5, section_offset, count_PYRA, elemsConn_PYRA); if (count_PRISM > 0) create_elements(sectionName, file_id_tag, MBPRISM, 6, section_offset, count_PRISM, elemsConn_PRISM); if (count_HEX > 0) create_elements(sectionName, file_id_tag, MBHEX, 8, section_offset, count_HEX, elemsConn_HEX); } // Mixed mesh type } // num_sections cg_close(filePtr); return result; } // indexZone for } // indexBase for return MB_SUCCESS; }