Actual source code: plexfluent.c
petsc-3.7.1 2016-05-15
Report Typos and Errors

      1: #define PETSCDM_DLL
      2: #include <petsc/private/dmpleximpl.h>    /*I   "petscdmplex.h"   I*/

      6: /*@C
      7:   DMPlexCreateFluentFromFile - Create a DMPlex mesh from a Fluent mesh file

      9: + comm        - The MPI communicator
     10: . filename    - Name of the Fluent mesh file
     11: - interpolate - Create faces and edges in the mesh

     13:   Output Parameter:
     14: . dm  - The DM object representing the mesh

     16:   Level: beginner

     18: .seealso: DMPlexCreateFromFile(), DMPlexCreateFluent(), DMPlexCreate()
     19: @*/
     20: PetscErrorCode DMPlexCreateFluentFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
     21: {
     22:   PetscViewer     viewer;
     23:   PetscErrorCode  ierr;

     26:   /* Create file viewer and build plex */
     27:   PetscViewerCreate(comm, &viewer);
     28:   PetscViewerSetType(viewer, PETSCVIEWERASCII);
     29:   PetscViewerFileSetMode(viewer, FILE_MODE_READ);
     30:   PetscViewerFileSetName(viewer, filename);
     31:   DMPlexCreateFluent(comm, viewer, interpolate, dm);
     32:   PetscViewerDestroy(&viewer);
     33:   return(0);
     34: }

     38: PetscErrorCode DMPlexCreateFluent_ReadString(PetscViewer viewer, char *buffer, char delim)
     39: {
     40:   PetscInt ret, i = 0;

     44:   do {PetscViewerRead(viewer, &(buffer[i++]), 1, &ret, PETSC_CHAR);}
     45:   while (ret > 0 && buffer[i-1] != '\0' && buffer[i-1] != delim);
     46:   buffer[i] = '\0';
     47:   return(0);
     48: }

     52: PetscErrorCode DMPlexCreateFluent_ReadValues(PetscViewer viewer, void *data, PetscInt count, PetscDataType dtype, PetscBool binary)
     53: {
     54:   int            fdes=0;
     55:   FILE          *file;
     56:   PetscInt       i;

     60:   if (binary) {
     61:     /* Extract raw file descriptor to read binary block */
     62:     PetscViewerASCIIGetPointer(viewer, &file);
     63:     fflush(file); fdes = fileno(file);
     64:   }

     66:   if (!binary && dtype == PETSC_INT) {
     67:     char     cbuf[256];
     68:     int      ibuf, snum;
     69:     /* Parse hexadecimal ascii integers */
     70:     for (i = 0; i < count; i++) {
     71:       PetscViewerRead(viewer, cbuf, 1, NULL, PETSC_STRING);
     72:       snum = sscanf(cbuf, "%x", &ibuf);
     73:       if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
     74:       ((PetscInt*)data)[i] = (PetscInt)ibuf;
     75:     }
     76:   } else if (binary && dtype == PETSC_INT) {
     77:     /* Always read 32-bit ints and cast to PetscInt */
     78:     int *ibuf;
     79:     PetscMalloc1(count, &ibuf);
     80:     PetscBinaryRead(fdes, ibuf, count, PETSC_ENUM);
     81:     PetscByteSwap(ibuf, PETSC_ENUM, count);
     82:     for (i = 0; i < count; i++) ((PetscInt*)data)[i] = (PetscInt)(ibuf[i]);
     83:     PetscFree(ibuf);

     85:  } else if (binary && dtype == PETSC_SCALAR) {
     86:     float *fbuf;
     87:     /* Always read 32-bit floats and cast to PetscScalar */
     88:     PetscMalloc1(count, &fbuf);
     89:     PetscBinaryRead(fdes, fbuf, count, PETSC_FLOAT);
     90:     PetscByteSwap(fbuf, PETSC_FLOAT, count);
     91:     for (i = 0; i < count; i++) ((PetscScalar*)data)[i] = (PetscScalar)(fbuf[i]);
     92:     PetscFree(fbuf);
     93:   } else {
     94:     PetscViewerASCIIRead(viewer, data, count, NULL, dtype);
     95:   }
     96:   return(0);
     97: }

    101: PetscErrorCode DMPlexCreateFluent_ReadSection(PetscViewer viewer, FluentSection *s)
    102: {
    103:   char           buffer[PETSC_MAX_PATH_LEN];
    104:   int            snum;

    108:   /* Fast-forward to next section and derive its index */
    109:   DMPlexCreateFluent_ReadString(viewer, buffer, '(');
    110:   DMPlexCreateFluent_ReadString(viewer, buffer, ' ');
    111:   snum = sscanf(buffer, "%d", &(s->index));
    112:   /* If we can't match an index return -1 to signal end-of-file */
    113:   if (snum < 1) {s->index = -1;   return(0);}

    115:   if (s->index == 0) {           /* Comment */
    116:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');

    118:   } else if (s->index == 2) {    /* Dimension */
    119:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    120:     snum = sscanf(buffer, "%d", &(s->nd));
    121:     if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");

    123:   } else if (s->index == 10 || s->index == 2010) {   /* Vertices */
    124:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    125:     snum = sscanf(buffer, "(%x %x %x %d %d)", &(s->zoneID), &(s->first), &(s->last), &(s->type), &(s->nd));
    126:     if (snum != 5) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    127:     if (s->zoneID > 0) {
    128:       PetscInt numCoords = s->last - s->first + 1;
    129:       DMPlexCreateFluent_ReadString(viewer, buffer, '(');
    130:       PetscMalloc1(s->nd*numCoords, (PetscScalar**)&s->data);
    131:       DMPlexCreateFluent_ReadValues(viewer, s->data, s->nd*numCoords, PETSC_SCALAR, s->index==2010 ? PETSC_TRUE : PETSC_FALSE);
    132:       DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    133:     }
    134:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');

    136:   } else if (s->index == 12 || s->index == 2012) {   /* Cells */
    137:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    138:     snum = sscanf(buffer, "(%x", &(s->zoneID));
    139:     if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    140:     if (s->zoneID == 0) {  /* Header section */
    141:       snum = sscanf(buffer, "(%x %x %x %d)", &(s->zoneID), &(s->first), &(s->last), &(s->nd));
    142:       if (snum != 4) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    143:     } else {               /* Data section */
    144:       snum = sscanf(buffer, "(%x %x %x %d %d)", &(s->zoneID), &(s->first), &(s->last), &(s->type), &(s->nd));
    145:       if (snum != 5) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    146:       if (s->nd == 0) {
    147:         /* Read cell type definitions for mixed cells */
    148:         PetscInt numCells = s->last - s->first + 1;
    149:         DMPlexCreateFluent_ReadString(viewer, buffer, '(');
    150:         PetscMalloc1(numCells, (PetscInt**)&s->data);
    151:         DMPlexCreateFluent_ReadValues(viewer, s->data, numCells, PETSC_INT, s->index==2012 ? PETSC_TRUE : PETSC_FALSE);
    152:         PetscFree(s->data);
    153:         DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    154:       }
    155:     }
    156:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');

    158:   } else if (s->index == 13 || s->index == 2013) {   /* Faces */
    159:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    160:     snum = sscanf(buffer, "(%x", &(s->zoneID));
    161:     if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    162:     if (s->zoneID == 0) {  /* Header section */
    163:       snum = sscanf(buffer, "(%x %x %x %d)", &(s->zoneID), &(s->first), &(s->last), &(s->nd));
    164:       if (snum != 4) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    165:     } else {               /* Data section */
    166:       PetscInt f, numEntries, numFaces, numFaceVert;
    167:       snum = sscanf(buffer, "(%x %x %x %d %d)", &(s->zoneID), &(s->first), &(s->last), &(s->type), &(s->nd));
    168:       if (snum != 5) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Fluent file");
    169:       DMPlexCreateFluent_ReadString(viewer, buffer, '(');
    170:       switch (s->nd) {
    171:       case 0: numEntries = PETSC_DETERMINE; break;
    172:       case 2: numEntries = 2 + 2; break;  /* linear */
    173:       case 3: numEntries = 2 + 3; break;  /* triangular */
    174:       case 4: numEntries = 2 + 4; break;  /* quadrilateral */
    175:       default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown face type in Fluent file");
    176:       }
    177:       numFaces = s->last-s->first + 1;
    178:       if (numEntries != PETSC_DETERMINE) {
    179:         /* Allocate space only if we already know the size of the block */
    180:         PetscMalloc1(numEntries*numFaces, (PetscInt**)&s->data);
    181:       }
    182:       for (f = 0; f < numFaces; f++) {
    183:         if (s->nd == 0) {
    184:           /* Determine the size of the block for "mixed" facets */
    185:           DMPlexCreateFluent_ReadValues(viewer, &numFaceVert, 1, PETSC_INT, s->index==2013 ? PETSC_TRUE : PETSC_FALSE);
    186:           if (numEntries == PETSC_DETERMINE) {
    187:             numEntries = numFaceVert + 2;
    188:             PetscMalloc1(numEntries*numFaces, (PetscInt**)&s->data);
    189:           } else {
    190:             if (numEntries != numFaceVert + 2) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No support for mixed faces in Fluent files");
    191:           }
    192:         }
    193:         DMPlexCreateFluent_ReadValues(viewer, &(((PetscInt*)s->data)[f*numEntries]), numEntries, PETSC_INT, s->index==2013 ? PETSC_TRUE : PETSC_FALSE);
    194:       }
    195:       s->nd = numEntries - 2;
    196:       DMPlexCreateFluent_ReadString(viewer, buffer, ')');
    197:     }
    198:     DMPlexCreateFluent_ReadString(viewer, buffer, ')');

    200:   } else {                       /* Unknown section type */
    201:     PetscInt depth = 1;
    202:     do {
    203:       /* Match parentheses when parsing unknown sections */
    204:       do {PetscViewerRead(viewer, &(buffer[0]), 1, NULL, PETSC_CHAR);}
    205:       while (buffer[0] != '(' && buffer[0] != ')');
    206:       if (buffer[0] == '(') depth++;
    207:       if (buffer[0] == ')') depth--;
    208:     } while (depth > 0);
    209:     DMPlexCreateFluent_ReadString(viewer, buffer, '\n');
    210:   }
    211:   return(0);
    212: }

    216: /*@C
    217:   DMPlexCreateFluent - Create a DMPlex mesh from a Fluent mesh file.

    219:   Collective on comm

    221:   Input Parameters:
    222: + comm  - The MPI communicator
    223: . viewer - The Viewer associated with a Fluent mesh file
    224: - interpolate - Create faces and edges in the mesh

    226:   Output Parameter:
    227: . dm  - The DM object representing the mesh

    229:   Note: http://aerojet.engr.ucdavis.edu/fluenthelp/html/ug/node1490.htm

    231:   Level: beginner

    233: .keywords: mesh, fluent, case
    234: .seealso: DMPLEX, DMCreate()
    235: @*/
    236: PetscErrorCode DMPlexCreateFluent(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
    237: {
    238:   PetscMPIInt    rank;
    239:   PetscInt       c, f, v, dim = PETSC_DETERMINE, numCells = 0, numVertices = 0, numCellVertices = PETSC_DETERMINE;
    240:   PetscInt       numFaces = PETSC_DETERMINE, numFaceEntries = PETSC_DETERMINE, numFaceVertices = PETSC_DETERMINE;
    241:   PetscInt      *faces = NULL, *cellVertices = NULL, *faceZoneIDs = NULL;
    242:   PetscInt       d, coordSize;
    243:   PetscScalar   *coords, *coordsIn = NULL;
    244:   PetscSection   coordSection;
    245:   Vec            coordinates;

    249:   MPI_Comm_rank(comm, &rank);

    251:   if (!rank) {
    252:     FluentSection s;
    253:     do {
    254:       DMPlexCreateFluent_ReadSection(viewer, &s);
    255:       if (s.index == 2) {                 /* Dimension */
    256:         dim = s.nd;

    258:       } else if (s.index == 10 || s.index == 2010) { /* Vertices */
    259:         if (s.zoneID == 0) numVertices = s.last;
    260:         else {
    261:           if (coordsIn) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Currently no support for multiple coordinate sets in Fluent files");
    262:           coordsIn = (PetscScalar *) s.data;
    263:         }

    265:       } else if (s.index == 12 || s.index == 2012) { /* Cells */
    266:         if (s.zoneID == 0) numCells = s.last;
    267:         else {
    268:           switch (s.nd) {
    269:           case 0: numCellVertices = PETSC_DETERMINE; break;
    270:           case 1: numCellVertices = 3; break;  /* triangular */
    271:           case 2: numCellVertices = 4; break;  /* tetrahedral */
    272:           case 3: numCellVertices = 4; break;  /* quadrilateral */
    273:           case 4: numCellVertices = 8; break;  /* hexahedral */
    274:           case 5: numCellVertices = 5; break;  /* pyramid */
    275:           case 6: numCellVertices = 6; break;  /* wedge */
    276:           default: numCellVertices = PETSC_DETERMINE;
    277:           }
    278:         }

    280:       } else if (s.index == 13 || s.index == 2013) { /* Facets */
    281:         if (s.zoneID == 0) {  /* Header section */
    282:           numFaces = s.last - s.first + 1;
    283:           if (s.nd == 0 || s.nd == 5) numFaceVertices = PETSC_DETERMINE;
    284:           else numFaceVertices = s.nd;
    285:         } else {              /* Data section */
    286:           if (numFaceVertices != PETSC_DETERMINE && s.nd != numFaceVertices) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mixed facets in Fluent files are not supported");
    287:           if (numFaces < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No header section for facets in Fluent file");
    288:           if (numFaceVertices == PETSC_DETERMINE) numFaceVertices = s.nd;
    289:           numFaceEntries = numFaceVertices + 2;
    290:           if (!faces) {PetscMalloc1(numFaces*numFaceEntries, &faces);}
    291:           if (!faceZoneIDs) {PetscMalloc1(numFaces, &faceZoneIDs);}
    292:           PetscMemcpy(&(faces[(s.first-1)*numFaceEntries]), s.data, (s.last-s.first+1)*numFaceEntries*sizeof(PetscInt));
    293:           /* Record the zoneID for each face set */
    294:           for (f = s.first -1; f < s.last; f++) faceZoneIDs[f] = s.zoneID;
    295:           PetscFree(s.data);
    296:         }
    297:       }
    298:     } while (s.index >= 0);
    299:   }
    300:   MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);
    301:   if (dim < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Fluent file does not include dimension");

    303:   /* Allocate cell-vertex mesh */
    304:   DMCreate(comm, dm);
    305:   DMSetType(*dm, DMPLEX);
    306:   DMSetDimension(*dm, dim);
    307:   DMPlexSetChart(*dm, 0, numCells + numVertices);
    308:   if (!rank) {
    309:     if (numCells < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown number of cells in Fluent file");
    310:     /* If no cell type was given we assume simplices */
    311:     if (numCellVertices == PETSC_DETERMINE) numCellVertices = numFaceVertices + 1;
    312:     for (c = 0; c < numCells; ++c) {DMPlexSetConeSize(*dm, c, numCellVertices);}
    313:   }
    314:   DMSetUp(*dm);

    316:   if (!rank && faces) {
    317:     /* Derive cell-vertex list from face-vertex and face-cell maps */
    318:     PetscMalloc1(numCells*numCellVertices, &cellVertices);
    319:     for (c = 0; c < numCells*numCellVertices; c++) cellVertices[c] = -1;
    320:     for (f = 0; f < numFaces; f++) {
    321:       PetscInt *cell;
    322:       const PetscInt cl = faces[f*numFaceEntries + numFaceVertices];
    323:       const PetscInt cr = faces[f*numFaceEntries + numFaceVertices + 1];
    324:       const PetscInt *face = &(faces[f*numFaceEntries]);

    326:       if (cl > 0) {
    327:         cell = &(cellVertices[(cl-1) * numCellVertices]);
    328:         for (v = 0; v < numFaceVertices; v++) {
    329:           PetscBool found = PETSC_FALSE;
    330:           for (c = 0; c < numCellVertices; c++) {
    331:             if (cell[c] < 0) break;
    332:             if (cell[c] == face[v]-1 + numCells) {found = PETSC_TRUE; break;}
    333:           }
    334:           if (!found) cell[c] = face[v]-1 + numCells;
    335:         }
    336:       }
    337:       if (cr > 0) {
    338:         cell = &(cellVertices[(cr-1) * numCellVertices]);
    339:         for (v = 0; v < numFaceVertices; v++) {
    340:           PetscBool found = PETSC_FALSE;
    341:           for (c = 0; c < numCellVertices; c++) {
    342:             if (cell[c] < 0) break;
    343:             if (cell[c] == face[v]-1 + numCells) {found = PETSC_TRUE; break;}
    344:           }
    345:           if (!found) cell[c] = face[v]-1 + numCells;
    346:         }
    347:       }
    348:     }
    349:     for (c = 0; c < numCells; c++) {
    350:       DMPlexSetCone(*dm, c, &(cellVertices[c*numCellVertices]));
    351:     }
    352:   }
    353:   DMPlexSymmetrize(*dm);
    354:   DMPlexStratify(*dm);
    355:   if (interpolate) {
    356:     DM idm = NULL;

    358:     DMPlexInterpolate(*dm, &idm);
    359:     DMDestroy(dm);
    360:     *dm  = idm;
    361:   }

    363:   if (!rank && faces) {
    364:     PetscInt fi, joinSize, meetSize, *fverts, cells[2];
    365:     const PetscInt *join, *meet;
    366:     PetscMalloc1(numFaceVertices, &fverts);
    367:     /* Mark facets by finding the full join of all adjacent vertices */
    368:     for (f = 0; f < numFaces; f++) {
    369:       const PetscInt cl = faces[f*numFaceEntries + numFaceVertices] - 1;
    370:       const PetscInt cr = faces[f*numFaceEntries + numFaceVertices + 1] - 1;
    371:       if (cl > 0 && cr > 0) {
    372:         /* If we know both adjoining cells we can use a single-level meet */
    373:         cells[0] = cl; cells[1] = cr;
    374:         DMPlexGetMeet(*dm, 2, cells, &meetSize, &meet);
    375:         if (meetSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %d", f);
    376:         DMSetLabelValue(*dm, "Face Sets", meet[0], faceZoneIDs[f]);
    377:         DMPlexRestoreMeet(*dm, numFaceVertices, fverts, &meetSize, &meet);
    378:       } else {
    379:         for (fi = 0; fi < numFaceVertices; fi++) fverts[fi] = faces[f*numFaceEntries + fi] + numCells - 1;
    380:         DMPlexGetFullJoin(*dm, numFaceVertices, fverts, &joinSize, &join);
    381:         if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %d", f);
    382:         DMSetLabelValue(*dm, "Face Sets", join[0], faceZoneIDs[f]);
    383:         DMPlexRestoreJoin(*dm, numFaceVertices, fverts, &joinSize, &join);
    384:       }
    385:     }
    386:     PetscFree(fverts);
    387:   }

    389:   /* Read coordinates */
    390:   DMGetCoordinateSection(*dm, &coordSection);
    391:   PetscSectionSetNumFields(coordSection, 1);
    392:   PetscSectionSetFieldComponents(coordSection, 0, dim);
    393:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
    394:   for (v = numCells; v < numCells+numVertices; ++v) {
    395:     PetscSectionSetDof(coordSection, v, dim);
    396:     PetscSectionSetFieldDof(coordSection, v, 0, dim);
    397:   }
    398:   PetscSectionSetUp(coordSection);
    399:   PetscSectionGetStorageSize(coordSection, &coordSize);
    400:   VecCreate(comm, &coordinates);
    401:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
    402:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
    403:   VecSetType(coordinates, VECSTANDARD);
    404:   VecGetArray(coordinates, &coords);
    405:   if (!rank && coordsIn) {
    406:     for (v = 0; v < numVertices; ++v) {
    407:       for (d = 0; d < dim; ++d) {
    408:         coords[v*dim+d] = coordsIn[v*dim+d];
    409:       }
    410:     }
    411:   }
    412:   VecRestoreArray(coordinates, &coords);
    413:   DMSetCoordinatesLocal(*dm, coordinates);
    414:   VecDestroy(&coordinates);
    415:   if (!rank) {
    416:     if (cellVertices) {PetscFree(cellVertices);}
    417:     PetscFree(faces);
    418:     PetscFree(faceZoneIDs);
    419:     PetscFree(coordsIn);
    420:   }
    421:   return(0);
    422: }