int main()
{
int index_file,index_base,index_zone,nbocos,ib;
int normalindex[3],ndataset;
int i,normallist;
char boconame[33];
BCType_t ibocotype;
PointSetType_t iptset;
DataType_t normaldatatype;
GridLocation_t igr;
cgsize_t npts,normallistflag;
cgsize_t ipnts[maxpnts];
/* READ BOUNDARY CONDITIONS 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;
/* we know there is only one zone (real working code would check!) */
index_zone=1;
/* find out number of BCs that exist under this zone */
cg_nbocos(index_file,index_base,index_zone,&nbocos);
/* do loop over the total number of BCs */
for (ib=1; ib <= nbocos; ib++)
{
/* find out what BC grid location is (expecting FaceCenter) */
cg_goto(index_file,index_base,"Zone_t",1,"ZoneBC_t",1,"BC_t",ib,"end");
cg_gridlocation_read(&igr);
if (igr == FaceCenter)
{
printf("\nGridLocation=FaceCenter means BC data refers to elements, not nodes\n");
}
/* get BC info */
cg_boco_info(index_file,index_base,index_zone,ib,boconame,&ibocotype,
&iptset,&npts,normalindex,&normallistflag,&normaldatatype,&ndataset);
if (iptset != PointList)
{
printf("\nError. For this program, BCs must be set up as PointList type %s\n",
PointSetTypeName[iptset]);
return 1;
}
printf("\nBC number: %i\n",ib);
printf(" name= %s\n",boconame);
printf(" type= %s\n",BCTypeName[ibocotype]);
printf(" no of elements= %i\n",(int)npts);
if (npts > maxpnts)
{
printf("\nError. Must increase maxpnts to at least %i\n",(int)npts);
return 1;
}
/* read point list in here (nothing done with them in this program) */
cg_boco_read(index_file,index_base,index_zone,ib,ipnts,&normallist);
printf(" (these elements read here, but only some printed out:)\n");
for (i=0; i < 10; i++)
{
printf(" ipnts[%i]=%i\n",i,(int)ipnts[i]);
}
}
/* close CGNS file */
cg_close(index_file);
printf("\nSuccessfully read BCs (PointList format) from file grid_c.cgns\n");
return 0;
}
int main (int argc, char **argv)
{
int n, i, j, k, nuser, dim = 1;
int cgfile, cgbase, cgzone, cgcoord, cgdset;
int size[9];
int ptlist[3] = {1, 2, 3};
int ptrange[6] = {1, 1, 1, 2, 2, 2};
int bcpoints[6], bcfaces[6];
static char *fname = "gotest.cgns";
char name[33];
float data1 = 1;
float data2 = 2;
float exponents[8], rate[3], center[3];
GridLocation_t gridloc;
int ordinal, ndata, cgfam, cgbc, nunits, nexps;
int elecflag, magnflag, condflag, dirichlet, neumann;
PointSetType_t pttype;
DataClass_t dclass;
DataType_t dtype;
BCType_t bctype;
MassUnits_t mass;
LengthUnits_t length;
TimeUnits_t time;
TemperatureUnits_t temp;
AngleUnits_t angle;
ElectricCurrentUnits_t current;
SubstanceAmountUnits_t amount;
LuminousIntensityUnits_t intensity;
ModelType_t elecmodel;
ModelType_t magnmodel;
ModelType_t emconduct;
/* errors and warnings go to error_exit */
cg_configure(CG_CONFIG_ERROR, (void *)error_exit);
for (n = 0; n < 8; n++)
exponents[n] = (float)n;
for (n = 0; n < 3; n++) {
rate[n] = (float)n;
center[n] = (float)n;
}
for (n = 0; n < NUM_SIDE*NUM_SIDE*NUM_SIDE; n++)
coord[n] = (float)n;
unlink (fname);
printf ("creating CGNS file %s\n", fname);
cg_open (fname, CG_MODE_WRITE, &cgfile);
cg_base_write (cgfile, "Base", 3, 3, &cgbase);
/* write electomagnetics model under base */
puts ("writing electromagnetics");
cg_goto(cgfile, cgbase, NULL);
cg_equationset_write (3);
cg_goto(cgfile, cgbase, "FlowEquationSet_t", 1, NULL);
cg_model_write("EMElectricFieldModel_t", Voltage);
cg_model_write("EMMagneticFieldModel_t", Interpolated);
cg_model_write("EMConductivityModel_t", Equilibrium_LinRessler);
/* write rotating coordinates under family_t */
puts ("writing family/rotating");
cg_family_write(cgfile, cgbase, "Family", &cgfam);
/* go to a named node */
cg_goto(cgfile, cgbase, "Family", 0, NULL);
cg_rotating_write (rate, center);
/* write BCDataSet under FamilyBC_t */
puts("writing FamilyBCDataSet");
cg_fambc_write(cgfile, cgbase, cgfam, "FamilyBC", BCWall, &cgbc);
/* relative go to */
cg_gorel(cgfile, "FamilyBC_t", cgbc, NULL);
cg_bcdataset_write ("FamilyBCDataSet", BCWallInviscid, Dirichlet);
/* write user data under base */
puts("writing user defined data under base");
/* relative path */
cg_gopath (cgfile, "../..");
cg_user_data_write ("User");
/* absolute path */
cg_gopath (cgfile, "/Base/User");
cg_gridlocation_write (CellCenter);
cg_famname_write ("Family");
cg_ordinal_write (0);
cg_array_write ("Data1", RealSingle, 1, &dim, &data1);
cg_array_write ("Data2", RealSingle, 1, &dim, &data2);
for (n = 1; n <= 2; n++) {
cg_goto (cgfile, cgbase, "User", 0, "DataArray_t", n, "end");
cg_dataclass_write (Dimensional);
cg_units_write (Kilogram, Meter, Second, Kelvin, Radian);
cg_exponents_write (RealSingle, exponents);
}
/* this should fail since ptset not allowed as child of
user data, except below a zone_t node */
cg_configure(CG_CONFIG_ERROR, NULL);
if (cg_ptset_write (PointList, 1, ptlist) == CG_OK)
printf ("WHAT!! - ptset should not work under base/userdata\n");
cg_configure(CG_CONFIG_ERROR, (void *)error_exit);
/* write zone */
puts("writing zone");
for (n = 0; n < 3; n++) {
size[n] = NUM_SIDE;
size[n+3] = NUM_SIDE - 1;
size[n+6] = 0;
}
cg_zone_write (cgfile, cgbase, "Zone", size, Structured, &cgzone);
cg_coord_write(cgfile, cgbase, cgzone, RealSingle,
"CoordinateX", coord, &cgcoord);
cg_coord_write(cgfile, cgbase, cgzone, RealSingle,
"CoordinateY", coord, &cgcoord);
cg_coord_write(cgfile, cgbase, cgzone, RealSingle,
"CoordinateZ", coord, &cgcoord);
/* create a BC node with point range and Dirichlet node*/
puts("writing Dirichlet BC with vertex range");
for (n = 0; n < 3; n++) {
bcpoints[n] = 1;
bcpoints[n+3] = NUM_SIDE;
bcfaces[n] = 1;
bcfaces[n+3] = NUM_SIDE - 1;
}
bcpoints[5] = bcfaces[5] = 1;
cg_boco_write (cgfile, cgbase, cgzone, "BC", BCWall,
PointList, 1, bcpoints, &cgbc);
cg_dataset_write (cgfile, cgbase, cgzone, cgbc,
"DataSet", BCWallViscous, &cgdset);
cg_bcdata_write (cgbase, cgfile, cgzone, cgbc, cgdset, Dirichlet);
/* create Dirichlet data at faces */
puts("writing Dirichlet data at faces");
cg_gopath (cgfile, "/Base/Zone/ZoneBC/BC/DataSet");
cg_gridlocation_write (KFaceCenter);
cg_ptset_write (PointRange, 2, bcfaces);
size[0] = (NUM_SIDE - 1) * (NUM_SIDE - 1);
cg_gorel (cgfile, "BCData_t", Dirichlet, NULL);
cg_array_write ("Data", RealSingle, 1, size, coord);
/* write recursive user data */
puts("writing recursive user defined data under zone");
cg_goto(cgfile, cgbase, "Zone", 0, NULL);
for (i = 1; i <= 4; i++) {
sprintf (name, "User%d", i);
cg_user_data_write (name);
cg_gorel(cgfile, name, 0, NULL);
cg_gridlocation_write (CellCenter);
cg_famname_write ("Family");
cg_ordinal_write (i);
cg_ptset_write (PointList, 1, ptlist);
cg_array_write ("Data1", RealSingle, 1, &dim, &data1);
cg_array_write ("Data2", RealSingle, 1, &dim, &data2);
for (n = 1; n <= 2; n++) {
cg_gorel (cgfile, "DataArray_t", n, "end");
cg_dataclass_write (Dimensional);
cg_unitsfull_write (Kilogram, Meter, Second, Kelvin, Radian,
Ampere, Mole, Candela);
cg_expfull_write (RealSingle, exponents);
cg_gopath (cgfile, "..");
}
for (j = 1; j <= 3; j++) {
sprintf (name, "User%d.%d", i, j);
cg_user_data_write (name);
cg_gopath (cgfile, name);
cg_gridlocation_write (Vertex);
cg_famname_write ("Family");
cg_ordinal_write (i + j);
cg_ptset_write (PointRange, 2, ptrange);
cg_array_write ("Data1", RealSingle, 1, &dim, &data1);
cg_array_write ("Data2", RealSingle, 1, &dim, &data2);
for (n = 1; n <= 2; n++) {
cg_gorel (cgfile, "DataArray_t", n, "end");
cg_dataclass_write (Dimensional);
cg_unitsfull_write (Kilogram, Meter, Second, Kelvin,
Radian, Ampere, Mole, Candela);
cg_expfull_write (RealSingle, exponents);
cg_gorel (cgfile, "..", 0, NULL);
}
for (k = 1; k <= 2; k++) {
sprintf (name, "User%d.%d.%d", i, j, k);
cg_user_data_write (name);
cg_gorel (cgfile, name, 0, NULL);
cg_array_write ("Data1", RealSingle, 1, &dim, &data1);
cg_array_write ("Data2", RealSingle, 1, &dim, &data2);
for (n = 1; n <= 2; n++) {
cg_gorel (cgfile, "DataArray_t", n, "end");
cg_dataclass_write (Dimensional);
cg_unitsfull_write (Kilogram, Meter, Second, Kelvin,
Radian, Ampere, Mole, Candela);
cg_expfull_write (RealSingle, exponents);
cg_gopath (cgfile, "..");
}
for (n = 1; n <= 2; n++) {
sprintf (name, "User%d.%d.%d.%d", i, j, k, n);
cg_user_data_write (name);
cg_gopath (cgfile, name);
cg_array_write ("Data1", RealSingle, 1, &dim, &data1);
cg_array_write ("Data2", RealSingle, 1, &dim, &data2);
cg_gopath (cgfile, "..");
}
cg_gopath (cgfile, "..");
}
cg_gopath (cgfile, "..");
}
cg_gopath (cgfile, "..");
}
puts ("closing and reopening in read mode");
cg_close (cgfile);
/* read file and check values */
cg_configure(CG_CONFIG_ERROR, NULL);
if (cg_open (fname, CG_MODE_READ, &cgfile))
cg_error_exit ();
cgbase = cgzone = 1;
/* check electomagnetics model under base */
puts ("checking electromagnetics");
if (cg_goto(cgfile, cgbase, NULL) ||
cg_equationset_elecmagn_read(&elecflag, &magnflag, &condflag) ||
cg_goto(cgfile, cgbase, "FlowEquationSet_t", 1, NULL) ||
cg_model_read ("EMElectricFieldModel_t", &elecmodel) ||
cg_model_read ("EMMagneticFieldModel_t", &magnmodel) ||
cg_model_read ("EMConductivityModel_t", &emconduct))
cg_error_exit();
CHECK ("ElectricFieldFlag", elecflag == 1);
CHECK ("ElectricFieldModel", elecmodel == Voltage);
CHECK ("MagneticFieldFlag", magnflag == 1);
CHECK ("MagneticFieldModel", magnmodel == Interpolated);
CHECK ("EMConductivityFlag", condflag == 1);
CHECK ("EMConductivityModel", emconduct == Equilibrium_LinRessler);
/* check rotating coordinates under family_t */
puts ("checking family/rotating");
if (cg_goto(cgfile, cgbase, "Family_t", 1, NULL) ||
cg_rotating_read (rate, center))
cg_error_exit();
for (n = 0; n < 3; n++) {
CHECK ("rotation rate", rate[n] == (float)n);
CHECK ("rotation center", center[n] == (float)n);
}
/* check BCDataSet under FamilyBC_t */
puts("checking FamilyBCDataSet");
*name = 0;
if (cg_goto(cgfile, cgbase, "Family_t", 1, "FamilyBC_t", 1, NULL) ||
cg_bcdataset_info(&ndata) ||
cg_bcdataset_read (1, name, &bctype, &dirichlet, &neumann))
cg_error_exit();
CHECK("bcdataset_info", ndata == 1);
CHECK("bcdatset name", strcmp(name, "FamilyBCDataSet") == 0);
CHECK("bcdatset type", bctype == BCWallInviscid);
CHECK("bcdatset dirichlet", dirichlet == 1);
CHECK("bcdatset neumann", neumann == 0);
/* check BC data */
puts("checking BC data");
if (cg_boco_info (cgfile, cgbase, cgzone, 1, name, &bctype, &pttype,
&n, size, &i, &dtype, &ndata))
cg_error_exit();
CHECK("BC_t name", strcmp(name, "BC") == 0);
CHECK("BC_t type", bctype == BCWall);
CHECK("BC_t pntset type", pttype == PointList);
CHECK("BC_t npnts", n == 1);
if (cg_dataset_read (cgfile, cgbase, cgzone, 1, 1, name,
&bctype, &dirichlet, &neumann) ||
cg_goto (cgfile, cgbase, "Zone_t", 1, "ZoneBC_t", 1, "BC_t", 1,
"BCDataSet_t", 1, NULL) ||
cg_gridlocation_read (&gridloc) ||
cg_ptset_info (&pttype, &n))
cg_error_exit();
CHECK("BCDataSet_t name", strcmp(name, "DataSet") == 0);
CHECK("BCDataSet_t type", bctype == BCWallViscous);
CHECK("BCDataSet_t location", gridloc == KFaceCenter);
CHECK("BCDataSet_t pntset type", pttype == PointRange);
CHECK("BC_t npnts", n == 2);
CHECK("BCDataSet_t dirichlet", dirichlet == 1);
CHECK("BCDataSet_t neumann", neumann == 0);
/* check user defined data */
puts("checking user defined data");
*name = 0;
if (cg_goto (cgfile, cgbase, "UserDefinedData_t", 1, "end") ||
cg_gridlocation_read (&gridloc) ||
cg_famname_read (name) ||
cg_ordinal_read (&ordinal) ||
cg_narrays (&ndata))
cg_error_exit ();
CHECK ("gridlocation", gridloc == CellCenter);
CHECK ("famname", strcmp (name, "Family") == 0);
CHECK ("ordinal", ordinal == 0);
CHECK ("narrays", ndata == 2);
if (cg_goto (cgfile, cgbase, "Zone_t", cgzone, "end") ||
cg_nuser_data (&nuser))
cg_error_exit ();
CHECK ("nuserdata", nuser == 4);
for (i = 1; i <= 4; i++) {
*name = 0;
if (cg_goto (cgfile, cgbase, "Zone_t", cgzone,
"UserDefinedData_t", i, "end") ||
cg_gridlocation_read (&gridloc) ||
cg_famname_read (name) ||
cg_ordinal_read (&ordinal) ||
cg_ptset_info (&pttype, &n) ||
cg_ptset_read (ptlist) ||
cg_narrays (&ndata) ||
cg_nuser_data (&nuser))
cg_error_exit ();
CHECK ("gridlocation", gridloc == CellCenter);
CHECK ("famname", strcmp (name, "Family") == 0);
CHECK ("ordinal", ordinal == i);
CHECK ("pointtype", pttype == PointList);
CHECK ("npoints", n == 1);
CHECK ("narrays", ndata == 2);
CHECK ("nuserdata", nuser == 3);
for (j = 1; j <= 3; j++) {
*name = 0;
if (cg_goto (cgfile, cgbase, "Zone_t", cgzone,
"UserDefinedData_t", i,
"UserDefinedData_t", j, "end") ||
cg_gridlocation_read (&gridloc) ||
cg_famname_read (name) ||
cg_ordinal_read (&ordinal) ||
cg_ptset_info (&pttype, &n) ||
cg_ptset_read (ptlist) ||
cg_narrays (&ndata) ||
cg_nuser_data (&nuser))
cg_error_exit ();
CHECK ("gridlocation", gridloc == Vertex);
CHECK ("famname", strcmp (name, "Family") == 0);
CHECK ("ordinal", ordinal == (i + j));
CHECK ("pointtype", pttype == PointRange);
CHECK ("npoints", n == 2);
CHECK ("narrays", ndata == 2);
CHECK ("nuserdata", nuser == 2);
for (n = 1; n <= 2; n++) {
if (cg_goto (cgfile, cgbase, "Zone_t", cgzone,
"UserDefinedData_t", i,
"UserDefinedData_t", j,
"DataArray_t", n, "end") ||
cg_dataclass_read (&dclass) ||
cg_nunits (&nunits) ||
cg_unitsfull_read (&mass, &length, &time, &temp, &angle,
¤t, &amount, &intensity) ||
cg_nexponents (&nexps) ||
cg_expfull_read (exponents))
cg_error_exit ();
CHECK ("dataclass", dclass == Dimensional);
CHECK ("nunits", nunits == 8);
CHECK ("massunits", mass == Kilogram);
CHECK ("lengthunits", length == Meter);
CHECK ("timeunits", time == Second);
CHECK ("tempunits", temp == Kelvin);
CHECK ("angleunits", angle == Radian);
CHECK ("currentunits", current == Ampere);
CHECK ("amountunits", amount == Mole);
CHECK ("intensityunits", intensity == Candela);
CHECK ("nexponents", nexps == 8);
for (n = 0; n < 8; n++)
CHECK ("exponents", exponents[n] == (float)n);
}
}
}
if (cg_goto (cgfile, cgbase, "Zone_t", cgzone,
"UserDefinedData_t", 2, "UserDefinedData_t", 2,
"UserDefinedData_t", 2, "UserDefinedData_t", 1, "end") ||
cg_narrays (&ndata) ||
cg_nuser_data (&nuser) ||
cg_array_info (2, name, &dtype, &n, &dim) ||
cg_array_read (1, &data1) ||
cg_array_read (2, &data2))
cg_error_exit ();
CHECK ("narrays", ndata == 2);
CHECK ("nuserdata", nuser == 0);
CHECK ("arrayname", strcmp (name, "Data2") == 0);
CHECK ("datatype", dtype == RealSingle);
CHECK ("ndims", n == 1);
CHECK ("dims", dim == 1);
CHECK ("data1", data1 == 1.0);
CHECK ("data2", data2 == 2.0);
/* read partial units/exponents as full */
puts("checking units and exponents");
if (cg_goto(cgfile, cgbase, "UserDefinedData_t", 1,
"DataArray_t", 1, NULL) ||
cg_nunits (&nunits) ||
cg_unitsfull_read (&mass, &length, &time, &temp, &angle,
¤t, &amount, &intensity) ||
cg_nexponents (&nexps) ||
cg_expfull_read (exponents))
cg_error_exit ();
CHECK ("nunits", nunits == 5);
CHECK ("massunits", mass == Kilogram);
CHECK ("lengthunits", length == Meter);
CHECK ("timeunits", time == Second);
CHECK ("tempunits", temp == Kelvin);
CHECK ("angleunits", angle == Radian);
CHECK ("currentunits", current == 0);
CHECK ("amountunits", amount == 0);
CHECK ("intensityunits", intensity == 0);
CHECK ("nexponents", nexps == 5);
for (n = 0; n < 5; n++)
CHECK ("exponents", exponents[n] == (float)n);
for (n = 6; n < 8; n++)
CHECK ("exponents", exponents[n] == (float)0.0);
/* read full units/exponents as partial */
if (cg_goto(cgfile, cgbase, "Zone_t", 1, "UserDefinedData_t", 1,
"DataArray_t", 1, NULL) ||
cg_nunits (&nunits) ||
cg_units_read (&mass, &length, &time, &temp, &angle) ||
cg_nexponents (&nexps) ||
cg_exponents_read (exponents))
cg_error_exit ();
CHECK ("nunits", nunits == 8);
CHECK ("massunits", mass == Kilogram);
CHECK ("lengthunits", length == Meter);
CHECK ("timeunits", time == Second);
CHECK ("tempunits", temp == Kelvin);
CHECK ("angleunits", angle == Radian);
CHECK ("nexponents", nexps == 8);
for (n = 0; n < 5; n++)
CHECK ("exponents", exponents[n] == (float)n);
puts ("closing file and reopening in modify mode");
cg_close (cgfile);
/* delete userdata node */
if (cg_open (fname, CG_MODE_MODIFY, &cgfile))
cg_error_exit ();
puts ("deleting user defined data and checking");
if (cg_goto (cgfile, 1, "Zone_t", 1,
"UserDefinedData_t", 3,
"UserDefinedData_t", 2,
"UserDefinedData_t", 1, "end") ||
cg_nuser_data (&nuser))
cg_error_exit ();
CHECK ("nuserdata", nuser == 2);
if (cg_delete_node ("User3.2.1.1") ||
cg_nuser_data (&nuser))
cg_error_exit ();
CHECK ("nuserdata", nuser == 1);
/* don't compress file on close */
cg_configure(CG_CONFIG_COMPRESS, (void *)0);
puts ("closing file");
cg_close (cgfile);
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);
}
