Actual source code: plexfluent.c

petsc-3.7.3 2016-08-01
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  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: }