int main(int argc, char* argv[]) {
int err;
int comm_size;
int comm_rank;
MPI_Info info;
int fn;
int B;
char basename[100];
int cell_dim = 3;
int phys_dim = 3;
err = MPI_Init(&argc,&argv);
if(err!=MPI_SUCCESS) cgp_doError;
err = MPI_Comm_size(MPI_COMM_WORLD, &comm_size);
if(err!=MPI_SUCCESS) cgp_doError;
err = MPI_Comm_rank(MPI_COMM_WORLD, &comm_rank);
if(err!=MPI_SUCCESS) cgp_doError;
err = MPI_Info_create(&(info));
if(err!=MPI_SUCCESS) cgp_doError;
if (cgp_open("test_base.cgns", CG_MODE_WRITE, &fn) ||
cg_base_write(fn, "Base 1", cell_dim, phys_dim, &B) ||
cgp_close(fn))
cgp_error_exit();
if (cgp_open("test_base.cgns", CG_MODE_READ, &fn) ||
cg_base_read(fn, B, basename, &cell_dim, &phys_dim) ||
cgp_close(fn))
cgp_error_exit();
err = MPI_Finalize();
if(err!=MPI_SUCCESS) cgp_doError;
return err;
}
Base_t file::readBase( int ibase, string& name, int& celldim, int& physdim ) const
{
cgnsstring cname;
int ier = cg_base_read( _fileindex, ++ibase, cname, &celldim, &physdim );
check_error( "file::readBase", "cg_base_read", ier );
name = cname;
return Base_t( *this, ibase, physdim );
}
int main (int argc, char *argv[])
{
int i, n, ib, nb, nz, nv, celldim, phydim;
int nn, type, *elems = 0, idata[5];
cgsize_t ne;
char *p, basename[33], title[65];
float value, *var;
SOLUTION *sol;
FILE *fp;
if (argc < 2)
print_usage (usgmsg, NULL);
ib = 0;
basename[0] = 0;
while ((n = getargs (argc, argv, options)) > 0) {
switch (n) {
case 'a':
ascii = 1;
break;
case 'b':
ib = atoi (argarg);
break;
case 'B':
strncpy (basename, argarg, 32);
basename[32] = 0;
break;
case 'w':
weighting = 1;
break;
case 'S':
usesol = atoi (argarg);
break;
}
}
if (argind > argc - 2)
print_usage (usgmsg, "CGNSfile and/or Tecplotfile not given");
if (!file_exists (argv[argind]))
FATAL (NULL, "CGNSfile does not exist or is not a file");
/* open CGNS file */
printf ("reading CGNS file from %s\n", argv[argind]);
nb = open_cgns (argv[argind], 1);
if (!nb)
FATAL (NULL, "no bases found in CGNS file");
if (*basename && 0 == (ib = find_base (basename)))
FATAL (NULL, "specified base not found");
if (ib > nb) FATAL (NULL, "base index out of range");
cgnsbase = ib ? ib : 1;
if (cg_base_read (cgnsfn, cgnsbase, basename, &celldim, &phydim))
FATAL (NULL, NULL);
if (celldim != 3 || phydim != 3)
FATAL (NULL, "cell and physical dimension must be 3");
printf (" using base %d - %s\n", cgnsbase, basename);
if (NULL == (p = strrchr (argv[argind], '/')) &&
NULL == (p = strrchr (argv[argind], '\\')))
strncpy (title, argv[argind], sizeof(title));
else
strncpy (title, ++p, sizeof(title));
title[sizeof(title)-1] = 0;
if ((p = strrchr (title, '.')) != NULL)
*p = 0;
read_zones ();
if (!nZones)
FATAL (NULL, "no zones in the CGNS file");
/* verify dimensions fit in an integer */
for (nz = 0; nz < nZones; nz++) {
if (Zones[nz].nverts > CG_MAX_INT32)
FATAL(NULL, "zone size too large to write with integers");
if (Zones[nz].type == CGNS_ENUMV(Unstructured)) {
count_elements (nz, &ne, &type);
if (ne > CG_MAX_INT32)
FATAL(NULL, "too many elements to write with integers");
}
}
nv = 3 + check_solution ();
/* open Tecplot file */
printf ("writing %s Tecplot data to <%s>\n",
ascii ? "ASCII" : "binary", argv[++argind]);
if (NULL == (fp = fopen (argv[argind], ascii ? "w+" : "w+b")))
FATAL (NULL, "couldn't open Tecplot output file");
/* write file header */
if (ascii)
fprintf (fp, "TITLE = \"%s\"\n", title);
else {
fwrite ("#!TDV75 ", 1, 8, fp);
i = 1;
write_ints (fp, 1, &i);
write_string (fp, title);
}
/* write variables */
if (ascii) {
fprintf (fp, "VARIABLES = \"X\", \"Y\", \"Z\"");
if (usesol) {
sol = Zones->sols;
for (n = 0; n < sol->nflds; n++)
fprintf (fp, ",\n\"%s\"", sol->flds[n].name);
}
}
else {
write_ints (fp, 1, &nv);
write_string (fp, "X");
write_string (fp, "Y");
write_string (fp, "Z");
if (usesol) {
sol = Zones->sols;
for (n = 0; n < sol->nflds; n++)
write_string (fp, sol->flds[n].name);
}
}
/* write zones */
if (!ascii) {
for (nz = 0; nz < nZones; nz++) {
if (Zones[nz].type == CGNS_ENUMV(Structured)) {
idata[0] = 0; /* BLOCK */
idata[1] = -1; /* color not specified */
idata[2] = (int)Zones[nz].dim[0];
idata[3] = (int)Zones[nz].dim[1];
idata[4] = (int)Zones[nz].dim[2];
}
else {
count_elements (nz, &ne, &type);
idata[0] = 2; /* FEBLOCK */
idata[1] = -1; /* color not specified */
idata[2] = (int)Zones[nz].dim[0];
idata[3] = (int)ne;
idata[4] = type;
}
value = 299.0;
write_floats (fp, 1, &value);
write_string (fp, Zones[nz].name);
write_ints (fp, 5, idata);
}
value = 357.0;
write_floats (fp, 1, &value);
}
for (nz = 0; nz < nZones; nz++) {
printf (" zone %d...", nz+1);
fflush (stdout);
read_zone_grid (nz+1);
ne = 0;
type = 2;
nn = (int)Zones[nz].nverts;
var = (float *) malloc (nn * sizeof(float));
if (NULL == var)
FATAL (NULL, "malloc failed for temp float array");
if (Zones[nz].type == CGNS_ENUMV(Unstructured))
elems = volume_elements (nz, &ne, &type);
if (ascii) {
if (Zones[nz].type == CGNS_ENUMV(Structured))
fprintf (fp, "\nZONE T=\"%s\", I=%d, J=%d, K=%d, F=BLOCK\n",
Zones[nz].name, (int)Zones[nz].dim[0],
(int)Zones[nz].dim[1], (int)Zones[nz].dim[2]);
else
fprintf (fp, "\nZONE T=\"%s\", N=%d, E=%d, F=FEBLOCK, ET=%s\n",
Zones[nz].name, nn, (int)ne, type == 2 ? "TETRAHEDRON" : "BRICK");
}
else {
value = 299.0;
write_floats (fp, 1, &value);
i = 0;
write_ints (fp, 1, &i);
i = 1;
for (n = 0; n < nv; n++)
write_ints (fp, 1, &i);
}
for (n = 0; n < nn; n++)
var[n] = (float)Zones[nz].verts[n].x;
write_floats (fp, nn, var);
for (n = 0; n < nn; n++)
var[n] = (float)Zones[nz].verts[n].y;
write_floats (fp, nn, var);
for (n = 0; n < nn; n++)
var[n] = (float)Zones[nz].verts[n].z;
write_floats (fp, nn, var);
if (usesol) {
read_solution_field (nz+1, usesol, 0);
sol = &Zones[nz].sols[usesol-1];
if (sol->location != CGNS_ENUMV(Vertex))
cell_vertex_solution (nz+1, usesol, weighting);
for (nv = 0; nv < sol->nflds; nv++) {
for (n = 0; n < nn; n++)
var[n] = (float)sol->flds[nv].data[n];
write_floats (fp, nn, var);
}
}
free (var);
if (Zones[nz].type == CGNS_ENUMV(Unstructured)) {
if (!ascii) {
i = 0;
write_ints (fp, 1, &i);
}
nn = 1 << type;
for (i = 0, n = 0; n < ne; n++, i += nn)
write_ints (fp, nn, &elems[i]);
free (elems);
}
puts ("done");
}
fclose (fp);
cg_close (cgnsfn);
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;
}
/*---------- 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;
}
/*@
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 argc, char *argv[])
{
int n, ib, nb, is, nz, celldim, phydim;
cgsize_t imax;
char basename[33];
if (argc < 2)
print_usage (usgmsg, NULL);
ib = 0;
basename[0] = 0;
while ((n = getargs (argc, argv, options)) > 0) {
switch (n) {
case 's':
mblock = 0;
break;
case 'p':
whole = 0;
break;
case 'n':
use_iblank = 0;
break;
case 'f':
case 'u':
format = n;
break;
case 'd':
use_double = 1;
break;
case 'b':
ib = atoi (argarg);
break;
case 'B':
strncpy (basename, argarg, 32);
basename[32] = 0;
break;
case 'g':
gamma = atof (argarg);
if (gamma <= 1.0)
FATAL (NULL, "invalid value for gamma");
break;
case 'w':
weighting = 1;
break;
case 'S':
usesol = atoi (argarg);
break;
}
}
if (argind > argc - 2)
print_usage (usgmsg, "CGNSfile and/or XYZfile not given");
if (!file_exists (argv[argind]))
FATAL (NULL, "CGNSfile does not exist or is not a file");
/* open CGNS file */
printf ("reading CGNS file from %s\n", argv[argind]);
nb = open_cgns (argv[argind], 1);
if (!nb)
FATAL (NULL, "no bases found in CGNS file");
if (*basename && 0 == (ib = find_base (basename)))
FATAL (NULL, "specified base not found");
if (ib > nb) FATAL (NULL, "base index out of range");
cgnsbase = ib ? ib : 1;
if (cg_base_read (cgnsfn, cgnsbase, basename, &celldim, &phydim))
FATAL (NULL, NULL);
if (celldim != 3 || phydim != 3)
FATAL (NULL, "cell and/or physical dimension must be 3");
printf (" using base %d - %s\n", cgnsbase, basename);
read_zones ();
for (nz = 0; nz < nZones; nz++) {
if (Zones[nz].type == CGNS_ENUMV(Structured)) {
/* verify we can write out using ints */
for (n = 0; n < 3; n++) {
if (Zones[nz].dim[n] > CG_MAX_INT32)
FATAL(NULL, "zone dimensions too large for integer");
}
if (whole) {
if (Zones[nz].nverts > CG_MAX_INT32)
FATAL(NULL, "zone too large to write as whole using an integer");
}
else {
if (Zones[nz].dim[0]*Zones[nz].dim[1] > CG_MAX_INT32)
FATAL(NULL, "zone too large to write using an integer");
}
nblocks++;
}
}
if (!nblocks) FATAL (NULL, "no structured zones found");
/* read the nodes */
printf ("reading %d zones\n", nblocks);
ib = is = 0;
imax = 0;
for (nz = 0; nz < nZones; nz++) {
if (Zones[nz].type == CGNS_ENUMV(Structured)) {
printf (" zone %d - %s ... ", nz+1, Zones[nz].name);
fflush (stdout);
read_zone_grid (nz+1);
ib += read_zone_interface (nz+1);
is += check_solution (nz);
if (imax < Zones[nz].nverts) imax = Zones[nz].nverts;
puts ("done");
}
}
if (!ib) use_iblank = 0;
if (use_iblank) {
iblank = (int *) malloc ((size_t)imax * sizeof(int));
if (NULL == iblank)
FATAL (NULL, "malloc failed for iblank array");
}
/* write Plot3d XYZ file */
if (format == 'f')
write_xyz_formatted (argv[++argind]);
else if (format == 'u')
write_xyz_unformatted (argv[++argind]);
else
write_xyz_binary (argv[++argind]);
if (use_iblank) free (iblank);
/* write solution file */
if (++argind < argc) {
if (is != nblocks) {
fprintf (stderr, "solution file is not being written since not\n");
fprintf (stderr, "all the blocks contain a complete solution\n");
cg_close (cgnsfn);
exit (1);
}
for (n = 0; n < 5; n++) {
q[n] = (double *) malloc ((size_t)imax * sizeof(double));
if (NULL == q[n])
FATAL (NULL, "malloc failed for solution working array");
}
get_reference ();
if (format == 'f')
write_q_formatted (argv[argind]);
else if (format == 'u')
write_q_unformatted (argv[argind]);
else
write_q_binary (argv[argind]);
}
cg_close (cgnsfn);
return 0;
}
int main (int argc, char *argv[])
{
int n, ib = 0, nb, flags = 0, has_q = 0;
BINARYIO *bf;
static char basename[33] = "Base";
if (argc < 3)
print_usage (usgmsg, NULL);
/* get options */
while ((n = getargs (argc, argv, options)) > 0) {
switch (n) {
case 'f':
flags &= ~OPEN_FORTRAN;
flags |= OPEN_ASCII;
break;
case 'u':
flags &= ~OPEN_ASCII;
flags |= OPEN_FORTRAN;
break;
case 's':
mblock = 0;
break;
case 'p':
whole = 0;
break;
case 'i':
use_iblank = 1;
/* fall through */
case 'n':
has_iblank = 1;
break;
case 'd':
is_double = 1;
break;
case 'M':
flags &= ~MACH_UNKNOWN;
flags |= get_machine (argarg);
break;
case 'b':
ib = atoi (argarg);
break;
case 'B':
strncpy (basename, argarg, 32);
basename[32] = 0;
break;
case 'g':
gamma = atof (argarg);
if (gamma <= 1.0)
FATAL (NULL, "invalid value for gamma");
break;
case 'c':
convert = 1;
break;
}
}
if (argind > argc - 2)
print_usage (usgmsg, "XYZfile and/or CGNSfile not given");
/* read Plot3d file */
printf ("reading PLOT3D grid file %s\n", argv[argind]);
printf (" as %s-block %s", mblock ? "multi" : "single",
flags == OPEN_ASCII ? "ASCII" :
(flags == OPEN_FORTRAN ? "FORTRAN unformatted" : "binary"));
if (has_iblank) printf (" with iblank array");
putchar ('\n');
if (!file_exists (argv[argind]))
FATAL (NULL, "XYZ file does not exist or is not a file");
if (NULL == (bf = bf_open (argv[argind], flags | OPEN_READ))) {
fprintf (stderr, "can't open <%s> for reading", argv[argind]);
exit (1);
}
read_xyz (bf);
bf_close (bf);
if (use_iblank) build_interfaces ();
/* read solution file if given */
if (++argind < argc-1) {
printf ("\nreading PLOT3D solution file %s\n", argv[argind]);
if (!file_exists (argv[argind]))
FATAL (NULL, "Solution file does not exist or is not a file");
if (NULL == (bf = bf_open (argv[argind], flags | OPEN_READ))) {
fprintf (stderr, "can't open <%s> for reading", argv[argind]);
exit (1);
}
read_q (bf);
bf_close (bf);
argind++;
has_q = 1;
}
/* open CGNS file */
printf ("\nwriting CGNS file to %s\n", argv[argind]);
nb = open_cgns (argv[argind], 0);
if (ib) {
if (ib > nb)
FATAL (NULL, "specified base index out of range");
if (cg_base_read (cgnsfn, ib, basename, &n, &n))
FATAL (NULL, NULL);
}
if (cg_base_write (cgnsfn, basename, 3, 3, &cgnsbase) ||
cg_goto (cgnsfn, cgnsbase, "end") ||
cg_dataclass_write (CGNS_ENUMV(NormalizedByUnknownDimensional)))
FATAL (NULL, NULL);
printf (" output to base %d - %s\n", cgnsbase, basename);
write_zones ();
for (n = 1; n <= nZones; n++) {
printf ("writing zone %d ... grid", n);
fflush (stdout);
write_zone_grid (n);
write_zone_interface (n);
if (has_q) {
printf (", solution");
fflush (stdout);
write_zone_solution (n, 1);
write_solution_field (n, 1, 0);
}
puts (" done");
}
if (has_q) write_reference ();
cg_close (cgnsfn);
return 0;
}
