Actual source code: plexcgns.c
petsc-3.9.4 2018-09-11
1: #define PETSCDM_DLL
2: #include <petsc/private/dmpleximpl.h>
4: #undef I /* Very old CGNS stupidly uses I as a variable, which fails when using complex. Curse you idiot package managers */
5: #if defined(PETSC_HAVE_CGNS)
6: #include <cgnslib.h>
7: #include <cgns_io.h>
8: #endif
9: #if !defined(CGNS_ENUMT)
10: #define CGNS_ENUMT(a) a
11: #endif
12: #if !defined(CGNS_ENUMV)
13: #define CGNS_ENUMV(a) a
14: #endif
16: /*@C
17: DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file.
19: Collective on comm
21: Input Parameters:
22: + comm - The MPI communicator
23: . filename - The name of the CGNS file
24: - interpolate - Create faces and edges in the mesh
26: Output Parameter:
27: . dm - The DM object representing the mesh
29: Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html
31: Level: beginner
33: .keywords: mesh,CGNS
34: .seealso: DMPlexCreate(), DMPlexCreateCGNS(), DMPlexCreateExodus()
35: @*/
36: PetscErrorCode DMPlexCreateCGNSFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
37: {
38: PetscMPIInt rank;
40: #if defined(PETSC_HAVE_CGNS)
41: int cgid = -1;
42: #endif
46: MPI_Comm_rank(comm, &rank);
47: #if defined(PETSC_HAVE_CGNS)
48: if (!rank) {
49: cg_open(filename, CG_MODE_READ, &cgid);
50: if (cgid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "cg_open(\"%s\",...) did not return a valid file ID", filename);
51: }
52: DMPlexCreateCGNS(comm, cgid, interpolate, dm);
53: if (!rank) {cg_close(cgid);}
54: #else
55: SETERRQ(comm, PETSC_ERR_SUP, "Loading meshes requires CGNS support. Reconfigure using --with-cgns-dir");
56: #endif
57: return(0);
58: }
60: /*@
61: DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID.
63: Collective on comm
65: Input Parameters:
66: + comm - The MPI communicator
67: . cgid - The CG id associated with a file and obtained using cg_open
68: - interpolate - Create faces and edges in the mesh
70: Output Parameter:
71: . dm - The DM object representing the mesh
73: Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html
75: Level: beginner
77: .keywords: mesh,CGNS
78: .seealso: DMPlexCreate(), DMPlexCreateExodus()
79: @*/
80: PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm)
81: {
82: #if defined(PETSC_HAVE_CGNS)
83: PetscMPIInt num_proc, rank;
84: PetscSection coordSection;
85: Vec coordinates;
86: PetscScalar *coords;
87: PetscInt *cellStart, *vertStart;
88: PetscInt coordSize, v;
90: /* Read from file */
91: char basename[CGIO_MAX_NAME_LENGTH+1];
92: char buffer[CGIO_MAX_NAME_LENGTH+1];
93: int dim = 0, physDim = 0, numVertices = 0, numCells = 0;
94: int nzones = 0;
95: #endif
98: #if defined(PETSC_HAVE_CGNS)
99: MPI_Comm_rank(comm, &rank);
100: MPI_Comm_size(comm, &num_proc);
101: DMCreate(comm, dm);
102: DMSetType(*dm, DMPLEX);
103: /* Open CGNS II file and read basic informations on rank 0, then broadcast to all processors */
104: if (!rank) {
105: int nbases, z;
107: cg_nbases(cgid, &nbases);
108: if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases);
109: cg_base_read(cgid, 1, basename, &dim, &physDim);
110: cg_nzones(cgid, 1, &nzones);
111: PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);
112: for (z = 1; z <= nzones; ++z) {
113: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
115: cg_zone_read(cgid, 1, z, buffer, sizes);
116: numVertices += sizes[0];
117: numCells += sizes[1];
118: cellStart[z] += sizes[1] + cellStart[z-1];
119: vertStart[z] += sizes[0] + vertStart[z-1];
120: }
121: for (z = 1; z <= nzones; ++z) {
122: vertStart[z] += numCells;
123: }
124: }
125: MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);
126: MPI_Bcast(&dim, 1, MPI_INT, 0, comm);
127: MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);
128: PetscObjectSetName((PetscObject) *dm, basename);
129: DMSetDimension(*dm, dim);
130: DMPlexSetChart(*dm, 0, numCells+numVertices);
132: /* Read zone information */
133: if (!rank) {
134: int z, c, c_loc, v, v_loc;
136: /* Read the cell set connectivity table and build mesh topology
137: CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */
138: /* First set sizes */
139: for (z = 1, c = 0; z <= nzones; ++z) {
140: CGNS_ENUMT( ZoneType_t ) zonetype;
141: int nsections;
142: CGNS_ENUMT( ElementType_t ) cellType;
143: cgsize_t start, end;
144: int nbndry, parentFlag;
145: PetscInt numCorners;
147: cg_zone_type(cgid, 1, z, &zonetype);
148: if (zonetype == CGNS_ENUMV( Structured )) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS");
149: cg_nsections(cgid, 1, z, &nsections);
150: if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections);
151: cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);
152: /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
153: if (cellType == CGNS_ENUMV( MIXED )) {
154: cgsize_t elementDataSize, *elements;
155: PetscInt off;
157: cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);
158: PetscMalloc1(elementDataSize, &elements);
159: cg_elements_read(cgid, 1, z, 1, elements, NULL);
160: for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
161: switch (elements[off]) {
162: case CGNS_ENUMV( TRI_3 ): numCorners = 3;break;
163: case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break;
164: case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break;
165: case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break;
166: default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]);
167: }
168: DMPlexSetConeSize(*dm, c, numCorners);
169: off += numCorners+1;
170: }
171: PetscFree(elements);
172: } else {
173: switch (cellType) {
174: case CGNS_ENUMV( TRI_3 ): numCorners = 3;break;
175: case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break;
176: case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break;
177: case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break;
178: default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
179: }
180: for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
181: DMPlexSetConeSize(*dm, c, numCorners);
182: }
183: }
184: }
185: DMSetUp(*dm);
186: for (z = 1, c = 0; z <= nzones; ++z) {
187: CGNS_ENUMT( ElementType_t ) cellType;
188: cgsize_t *elements, elementDataSize, start, end;
189: int nbndry, parentFlag;
190: PetscInt *cone, numc, numCorners, maxCorners = 27;
192: cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);
193: numc = end - start;
194: /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
195: cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);
196: PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);
197: cg_elements_read(cgid, 1, z, 1, elements, NULL);
198: if (cellType == CGNS_ENUMV( MIXED )) {
199: /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
200: for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
201: switch (elements[v]) {
202: case CGNS_ENUMV( TRI_3 ): numCorners = 3;break;
203: case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break;
204: case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break;
205: case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break;
206: default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]);
207: }
208: ++v;
209: for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
210: cone[v_loc] = elements[v]+numCells-1;
211: }
212: /* Tetrahedra are inverted */
213: if (elements[v] == CGNS_ENUMV( TETRA_4 )) {
214: PetscInt tmp = cone[0];
215: cone[0] = cone[1];
216: cone[1] = tmp;
217: }
218: /* Hexahedra are inverted */
219: if (elements[v] == CGNS_ENUMV( HEXA_8 )) {
220: PetscInt tmp = cone[5];
221: cone[5] = cone[7];
222: cone[7] = tmp;
223: }
224: DMPlexSetCone(*dm, c, cone);
225: DMSetLabelValue(*dm, "zone", c, z);
226: }
227: } else {
228: switch (cellType) {
229: case CGNS_ENUMV( TRI_3 ): numCorners = 3;break;
230: case CGNS_ENUMV( QUAD_4 ): numCorners = 4;break;
231: case CGNS_ENUMV( TETRA_4 ): numCorners = 4;break;
232: case CGNS_ENUMV( HEXA_8 ): numCorners = 8;break;
233: default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
234: }
236: /* CGNS uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
237: for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
238: for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
239: cone[v_loc] = elements[v]+numCells-1;
240: }
241: /* Tetrahedra are inverted */
242: if (cellType == CGNS_ENUMV( TETRA_4 )) {
243: PetscInt tmp = cone[0];
244: cone[0] = cone[1];
245: cone[1] = tmp;
246: }
247: /* Hexahedra are inverted, and they give the top first */
248: if (cellType == CGNS_ENUMV( HEXA_8 )) {
249: PetscInt tmp = cone[5];
250: cone[5] = cone[7];
251: cone[7] = tmp;
252: }
253: DMPlexSetCone(*dm, c, cone);
254: DMSetLabelValue(*dm, "zone", c, z);
255: }
256: }
257: PetscFree2(elements,cone);
258: }
259: }
260: DMPlexSymmetrize(*dm);
261: DMPlexStratify(*dm);
262: if (interpolate) {
263: DM idm;
265: DMPlexInterpolate(*dm, &idm);
266: DMDestroy(dm);
267: *dm = idm;
268: }
270: /* Read coordinates */
271: DMGetCoordinateSection(*dm, &coordSection);
272: PetscSectionSetNumFields(coordSection, 1);
273: PetscSectionSetFieldComponents(coordSection, 0, dim);
274: PetscSectionSetChart(coordSection, numCells, numCells + numVertices);
275: for (v = numCells; v < numCells+numVertices; ++v) {
276: PetscSectionSetDof(coordSection, v, dim);
277: PetscSectionSetFieldDof(coordSection, v, 0, dim);
278: }
279: PetscSectionSetUp(coordSection);
280: PetscSectionGetStorageSize(coordSection, &coordSize);
281: VecCreate(PETSC_COMM_SELF, &coordinates);
282: PetscObjectSetName((PetscObject) coordinates, "coordinates");
283: VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);
284: VecSetType(coordinates,VECSTANDARD);
285: VecGetArray(coordinates, &coords);
286: if (!rank) {
287: PetscInt off = 0;
288: float *x[3];
289: int z, d;
291: PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);
292: for (z = 1; z <= nzones; ++z) {
293: CGNS_ENUMT( DataType_t ) datatype;
294: cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
295: cgsize_t range_min[3] = {1, 1, 1};
296: cgsize_t range_max[3] = {1, 1, 1};
297: int ngrids, ncoords;
300: cg_zone_read(cgid, 1, z, buffer, sizes);
301: range_max[0] = sizes[0];
302: cg_ngrids(cgid, 1, z, &ngrids);
303: if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids);
304: cg_ncoords(cgid, 1, z, &ncoords);
305: if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords);
306: for (d = 0; d < dim; ++d) {
307: cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);
308: cg_coord_read(cgid, 1, z, buffer, CGNS_ENUMV( RealSingle ), range_min, range_max, x[d]);
309: }
310: if (dim > 0) {
311: for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v];
312: }
313: if (dim > 1) {
314: for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v];
315: }
316: if (dim > 2) {
317: for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v];
318: }
319: off += sizes[0];
320: }
321: PetscFree3(x[0],x[1],x[2]);
322: }
323: VecRestoreArray(coordinates, &coords);
324: DMSetCoordinatesLocal(*dm, coordinates);
325: VecDestroy(&coordinates);
326: /* Read boundary conditions */
327: if (!rank) {
328: DMLabel label;
329: CGNS_ENUMT( BCType_t ) bctype;
330: CGNS_ENUMT( DataType_t ) datatype;
331: CGNS_ENUMT( PointSetType_t ) pointtype;
332: cgsize_t *points;
333: PetscReal *normals;
334: int normal[3];
335: char *bcname = buffer;
336: cgsize_t npoints, nnormals;
337: int z, nbc, bc, c, ndatasets;
339: for (z = 1; z <= nzones; ++z) {
340: cg_nbocos(cgid, 1, z, &nbc);
341: for (bc = 1; bc <= nbc; ++bc) {
342: cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);
343: DMCreateLabel(*dm, bcname);
344: DMGetLabel(*dm, bcname, &label);
345: PetscMalloc2(npoints, &points, nnormals, &normals);
346: cg_boco_read(cgid, 1, z, bc, points, (void *) normals);
347: if (pointtype == CGNS_ENUMV( ElementRange )) {
348: /* Range of cells: assuming half-open interval since the documentation sucks */
349: for (c = points[0]; c < points[1]; ++c) {
350: DMLabelSetValue(label, c - cellStart[z-1], 1);
351: }
352: } else if (pointtype == CGNS_ENUMV( ElementList )) {
353: /* List of cells */
354: for (c = 0; c < npoints; ++c) {
355: DMLabelSetValue(label, points[c] - cellStart[z-1], 1);
356: }
357: } else if (pointtype == CGNS_ENUMV( PointRange )) {
358: CGNS_ENUMT( GridLocation_t ) gridloc;
360: /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
361: cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");
362: cg_gridlocation_read(&gridloc);
363: /* Range of points: assuming half-open interval since the documentation sucks */
364: for (c = points[0]; c < points[1]; ++c) {
365: if (gridloc == CGNS_ENUMV( Vertex )) {DMLabelSetValue(label, c - vertStart[z-1], 1);}
366: else {DMLabelSetValue(label, c - cellStart[z-1], 1);}
367: }
368: } else if (pointtype == CGNS_ENUMV( PointList )) {
369: CGNS_ENUMT( GridLocation_t ) gridloc;
371: /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
372: cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");
373: cg_gridlocation_read(&gridloc);
374: for (c = 0; c < npoints; ++c) {
375: if (gridloc == CGNS_ENUMV( Vertex )) {DMLabelSetValue(label, points[c] - vertStart[z-1], 1);}
376: else {DMLabelSetValue(label, points[c] - cellStart[z-1], 1);}
377: }
378: } else SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype);
379: PetscFree2(points, normals);
380: }
381: }
382: PetscFree2(cellStart, vertStart);
383: }
384: #else
385: SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir");
386: #endif
387: return(0);
388: }