Actual source code: plexexodusii.c

petsc-3.5.1 2014-08-06
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  1: #define PETSCDM_DLL
  2: #include <petsc-private/dmpleximpl.h>    /*I   "petscdmplex.h"   I*/

  4: #if defined(PETSC_HAVE_EXODUSII)
  5: #include <netcdf.h>
  6: #include <exodusII.h>
  7: #endif

 11: /*@C
 12:   DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file.

 14:   Collective on comm

 16:   Input Parameters:
 17: + comm  - The MPI communicator
 18: . filename - The name of the ExodusII file
 19: - interpolate - Create faces and edges in the mesh

 21:   Output Parameter:
 22: . dm  - The DM object representing the mesh

 24:   Level: beginner

 26: .keywords: mesh,ExodusII
 27: .seealso: DMPLEX, DMCreate(), DMPlexCreateExodus()
 28: @*/
 29: PetscErrorCode DMPlexCreateExodusFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
 30: {
 31:   PetscMPIInt    rank;
 33: #if defined(PETSC_HAVE_EXODUSII)
 34:   int   CPU_word_size = 0, IO_word_size = 0, exoid = -1;
 35:   float version;
 36: #endif

 40:   MPI_Comm_rank(comm, &rank);
 41: #if defined(PETSC_HAVE_EXODUSII)
 42:   if (!rank) {
 43:     exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);
 44:     if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename);
 45:   }
 46:   DMPlexCreateExodus(comm, exoid, interpolate, dm);
 47:   if (!rank) {ex_close(exoid);}
 48: #else
 49:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
 50: #endif
 51:   return(0);
 52: }

 56: /*@
 57:   DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file ID.

 59:   Collective on comm

 61:   Input Parameters:
 62: + comm  - The MPI communicator
 63: . exoid - The ExodusII id associated with a exodus file and obtained using ex_open
 64: - interpolate - Create faces and edges in the mesh

 66:   Output Parameter:
 67: . dm  - The DM object representing the mesh

 69:   Level: beginner

 71: .keywords: mesh,ExodusII
 72: .seealso: DMPLEX, DMCreate()
 73: @*/
 74: PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
 75: {
 76: #if defined(PETSC_HAVE_EXODUSII)
 77:   PetscMPIInt    num_proc, rank;
 78:   PetscSection   coordSection;
 79:   Vec            coordinates;
 80:   PetscScalar    *coords;
 81:   PetscInt       coordSize, v;
 83:   /* Read from ex_get_init() */
 84:   char title[PETSC_MAX_PATH_LEN+1];
 85:   int  dim    = 0, numVertices = 0, numCells = 0;
 86:   int  num_cs = 0, num_vs = 0, num_fs = 0;
 87: #endif

 90: #if defined(PETSC_HAVE_EXODUSII)
 91:   MPI_Comm_rank(comm, &rank);
 92:   MPI_Comm_size(comm, &num_proc);
 93:   DMCreate(comm, dm);
 94:   DMSetType(*dm, DMPLEX);
 95:   /* Open EXODUS II file and read basic informations on rank 0, then broadcast to all processors */
 96:   if (!rank) {
 97:     PetscMemzero(title,(PETSC_MAX_PATH_LEN+1)*sizeof(char));
 98:     ex_get_init(exoid, title, &dim, &numVertices, &numCells, &num_cs, &num_vs, &num_fs);
 99:     if (ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"ExodusII ex_get_init() failed with error code %D\n",ierr);
100:     if (!num_cs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any cell set\n");
101:   }
102:   MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);
103:   MPI_Bcast(&dim, 1, MPI_INT, 0, comm);
104:   PetscObjectSetName((PetscObject) *dm, title);
105:   DMPlexSetDimension(*dm, dim);
106:   DMPlexSetChart(*dm, 0, numCells+numVertices);

108:   /* Read cell sets information */
109:   if (!rank) {
110:     PetscInt *cone;
111:     int      c, cs, c_loc, v, v_loc;
112:     /* Read from ex_get_elem_blk_ids() */
113:     int *cs_id;
114:     /* Read from ex_get_elem_block() */
115:     char buffer[PETSC_MAX_PATH_LEN+1];
116:     int  num_cell_in_set, num_vertex_per_cell, num_attr;
117:     /* Read from ex_get_elem_conn() */
118:     int *cs_connect;

120:     /* Get cell sets IDs */
121:     PetscMalloc1(num_cs, &cs_id);
122:     ex_get_elem_blk_ids(exoid, cs_id);
123:     /* Read the cell set connectivity table and build mesh topology
124:        EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
125:     /* First set sizes */
126:     for (cs = 0, c = 0; cs < num_cs; cs++) {
127:       ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);
128:       for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
129:         DMPlexSetConeSize(*dm, c, num_vertex_per_cell);
130:       }
131:     }
132:     DMSetUp(*dm);
133:     for (cs = 0, c = 0; cs < num_cs; cs++) {
134:       ex_get_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &num_attr);
135:       PetscMalloc2(num_vertex_per_cell*num_cell_in_set,&cs_connect,num_vertex_per_cell,&cone);
136:       ex_get_elem_conn(exoid, cs_id[cs], cs_connect);
137:       /* EXO uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
138:       for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
139:         for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
140:           cone[v_loc] = cs_connect[v]+numCells-1;
141:         }
142:         if (dim == 3) {
143:           /* Tetrahedra are inverted */
144:           if (num_vertex_per_cell == 4) {
145:             PetscInt tmp = cone[0];
146:             cone[0] = cone[1];
147:             cone[1] = tmp;
148:           }
149:           /* Hexahedra are inverted */
150:           if (num_vertex_per_cell == 8) {
151:             PetscInt tmp = cone[1];
152:             cone[1] = cone[3];
153:             cone[3] = tmp;
154:           }
155:         }
156:         DMPlexSetCone(*dm, c, cone);
157:         DMPlexSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);
158:       }
159:       PetscFree2(cs_connect,cone);
160:     }
161:     PetscFree(cs_id);
162:   }
163:   DMPlexSymmetrize(*dm);
164:   DMPlexStratify(*dm);
165:   if (interpolate) {
166:     DM idm = NULL;

168:     DMPlexInterpolate(*dm, &idm);
169:     /* Maintain Cell Sets label */
170:     {
171:       DMLabel label;

173:       DMPlexRemoveLabel(*dm, "Cell Sets", &label);
174:       if (label) {DMPlexAddLabel(idm, label);}
175:     }
176:     DMDestroy(dm);
177:     *dm  = idm;
178:   }

180:   /* Create vertex set label */
181:   if (!rank && (num_vs > 0)) {
182:     int vs, v;
183:     /* Read from ex_get_node_set_ids() */
184:     int *vs_id;
185:     /* Read from ex_get_node_set_param() */
186:     int num_vertex_in_set, num_attr;
187:     /* Read from ex_get_node_set() */
188:     int *vs_vertex_list;

190:     /* Get vertex set ids */
191:     PetscMalloc1(num_vs, &vs_id);
192:     ex_get_node_set_ids(exoid, vs_id);
193:     for (vs = 0; vs < num_vs; ++vs) {
194:       ex_get_node_set_param(exoid, vs_id[vs], &num_vertex_in_set, &num_attr);
195:       PetscMalloc1(num_vertex_in_set, &vs_vertex_list);
196:       ex_get_node_set(exoid, vs_id[vs], vs_vertex_list);
197:       for (v = 0; v < num_vertex_in_set; ++v) {
198:         DMPlexSetLabelValue(*dm, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);
199:       }
200:       PetscFree(vs_vertex_list);
201:     }
202:     PetscFree(vs_id);
203:   }
204:   /* Read coordinates */
205:   DMGetCoordinateSection(*dm, &coordSection);
206:   PetscSectionSetNumFields(coordSection, 1);
207:   PetscSectionSetFieldComponents(coordSection, 0, dim);
208:   PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
209:   for (v = numCells; v < numCells+numVertices; ++v) {
210:     PetscSectionSetDof(coordSection, v, dim);
211:     PetscSectionSetFieldDof(coordSection, v, 0, dim);
212:   }
213:   PetscSectionSetUp(coordSection);
214:   PetscSectionGetStorageSize(coordSection, &coordSize);
215:   VecCreate(comm, &coordinates);
216:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
217:   VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
218:   VecSetType(coordinates,VECSTANDARD);
219:   VecGetArray(coordinates, &coords);
220:   if (!rank) {
221:     float *x, *y, *z;

223:     PetscMalloc3(numVertices,&x,numVertices,&y,numVertices,&z);
224:     ex_get_coord(exoid, x, y, z);
225:     if (dim > 0) {
226:       for (v = 0; v < numVertices; ++v) coords[v*dim+0] = x[v];
227:     }
228:     if (dim > 1) {
229:       for (v = 0; v < numVertices; ++v) coords[v*dim+1] = y[v];
230:     }
231:     if (dim > 2) {
232:       for (v = 0; v < numVertices; ++v) coords[v*dim+2] = z[v];
233:     }
234:     PetscFree3(x,y,z);
235:   }
236:   VecRestoreArray(coordinates, &coords);
237:   DMSetCoordinatesLocal(*dm, coordinates);
238:   VecDestroy(&coordinates);

240:   /* Create side set label */
241:   if (!rank && interpolate && (num_fs > 0)) {
242:     int fs, f, voff;
243:     /* Read from ex_get_side_set_ids() */
244:     int *fs_id;
245:     /* Read from ex_get_side_set_param() */
246:     int num_side_in_set, num_dist_fact_in_set;
247:     /* Read from ex_get_side_set_node_list() */
248:     int *fs_vertex_count_list, *fs_vertex_list;

250:     /* Get side set ids */
251:     PetscMalloc1(num_fs, &fs_id);
252:     ex_get_side_set_ids(exoid, fs_id);
253:     for (fs = 0; fs < num_fs; ++fs) {
254:       ex_get_side_set_param(exoid, fs_id[fs], &num_side_in_set, &num_dist_fact_in_set);
255:       PetscMalloc2(num_side_in_set,&fs_vertex_count_list,num_side_in_set*4,&fs_vertex_list);
256:       ex_get_side_set_node_list(exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list);
257:       for (f = 0, voff = 0; f < num_side_in_set; ++f) {
258:         const PetscInt *faces   = NULL;
259:         PetscInt       faceSize = fs_vertex_count_list[f], numFaces;
260:         PetscInt       faceVertices[4], v;

262:         if (faceSize > 4) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %d > 4 vertices", faceSize);
263:         for (v = 0; v < faceSize; ++v, ++voff) {
264:           faceVertices[v] = fs_vertex_list[voff]+numCells-1;
265:         }
266:         DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
267:         if (numFaces != 1) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %d faces", f, fs, numFaces);
268:         DMPlexSetLabelValue(*dm, "Face Sets", faces[0], fs_id[fs]);
269:         DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);
270:       }
271:       PetscFree2(fs_vertex_count_list,fs_vertex_list);
272:     }
273:     PetscFree(fs_id);
274:   }
275: #else
276:   SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
277: #endif
278:   return(0);
279: }