Actual source code: dmmbutil.cxx
1: #include <petsc/private/dmmbimpl.h>
2: #include <petsc/private/vecimpl.h>
4: #include <petscdmmoab.h>
5: #include <MBTagConventions.hpp>
6: #include <moab/ReadUtilIface.hpp>
7: #include <moab/MergeMesh.hpp>
8: #include <moab/CN.hpp>
10: typedef struct {
11: // options
12: PetscInt A, B, C, M, N, K, dim;
13: PetscInt blockSizeVertexXYZ[3]; // Number of element blocks per partition
14: PetscInt blockSizeElementXYZ[3];
15: PetscReal xyzbounds[6]; // the physical size of the domain
16: bool newMergeMethod, keep_skins, simplex, adjEnts;
18: // compute params
19: PetscReal dx, dy, dz;
20: PetscInt NX, NY, NZ, nex, ney, nez;
21: PetscInt q, xstride, ystride, zstride;
22: PetscBool usrxyzgrid, usrprocgrid, usrrefgrid;
23: PetscInt fraction, remainder, cumfraction;
24: PetscLogEvent generateMesh, generateElements, generateVertices, parResolve;
25: } DMMoabMeshGeneratorCtx;
27: static PetscInt DMMoab_SetTensorElementConnectivity_Private(DMMoabMeshGeneratorCtx &genCtx, PetscInt offset, PetscInt corner, std::vector<PetscInt> &subent_conn, moab::EntityHandle *connectivity)
28: {
29: switch (genCtx.dim) {
30: case 1:
31: subent_conn.resize(2);
32: moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
33: connectivity[offset + subent_conn[0]] = corner;
34: connectivity[offset + subent_conn[1]] = corner + 1;
35: break;
36: case 2:
37: subent_conn.resize(4);
38: moab::CN::SubEntityVertexIndices(moab::MBQUAD, 2, 0, subent_conn.data());
39: connectivity[offset + subent_conn[0]] = corner;
40: connectivity[offset + subent_conn[1]] = corner + 1;
41: connectivity[offset + subent_conn[2]] = corner + 1 + genCtx.ystride;
42: connectivity[offset + subent_conn[3]] = corner + genCtx.ystride;
43: break;
44: case 3:
45: default:
46: subent_conn.resize(8);
47: moab::CN::SubEntityVertexIndices(moab::MBHEX, 3, 0, subent_conn.data());
48: connectivity[offset + subent_conn[0]] = corner;
49: connectivity[offset + subent_conn[1]] = corner + 1;
50: connectivity[offset + subent_conn[2]] = corner + 1 + genCtx.ystride;
51: connectivity[offset + subent_conn[3]] = corner + genCtx.ystride;
52: connectivity[offset + subent_conn[4]] = corner + genCtx.zstride;
53: connectivity[offset + subent_conn[5]] = corner + 1 + genCtx.zstride;
54: connectivity[offset + subent_conn[6]] = corner + 1 + genCtx.ystride + genCtx.zstride;
55: connectivity[offset + subent_conn[7]] = corner + genCtx.ystride + genCtx.zstride;
56: break;
57: }
58: return subent_conn.size();
59: }
61: static PetscInt DMMoab_SetSimplexElementConnectivity_Private(DMMoabMeshGeneratorCtx &genCtx, PetscInt subelem, PetscInt offset, PetscInt corner, std::vector<PetscInt> &subent_conn, moab::EntityHandle *connectivity)
62: {
63: PetscInt A, B, C, D, E, F, G, H, M;
64: const PetscInt trigen_opts = 1; /* 1 - Aligned diagonally to right, 2 - Aligned diagonally to left, 3 - 4 elements per quad */
65: A = corner;
66: B = corner + 1;
67: switch (genCtx.dim) {
68: case 1:
69: subent_conn.resize(2); /* only linear EDGE supported now */
70: moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
71: connectivity[offset + subent_conn[0]] = A;
72: connectivity[offset + subent_conn[1]] = B;
73: break;
74: case 2:
75: C = corner + 1 + genCtx.ystride;
76: D = corner + genCtx.ystride;
77: M = corner + 0.5; /* technically -- need to modify vertex generation */
78: subent_conn.resize(3); /* only linear TRI supported */
79: moab::CN::SubEntityVertexIndices(moab::MBTRI, 2, 0, subent_conn.data());
80: if (trigen_opts == 1) {
81: if (subelem) { /* 0 1 2 of a QUAD */
82: connectivity[offset + subent_conn[0]] = B;
83: connectivity[offset + subent_conn[1]] = C;
84: connectivity[offset + subent_conn[2]] = A;
85: } else { /* 2 3 0 of a QUAD */
86: connectivity[offset + subent_conn[0]] = D;
87: connectivity[offset + subent_conn[1]] = A;
88: connectivity[offset + subent_conn[2]] = C;
89: }
90: } else if (trigen_opts == 2) {
91: if (subelem) { /* 0 1 2 of a QUAD */
92: connectivity[offset + subent_conn[0]] = A;
93: connectivity[offset + subent_conn[1]] = B;
94: connectivity[offset + subent_conn[2]] = D;
95: } else { /* 2 3 0 of a QUAD */
96: connectivity[offset + subent_conn[0]] = C;
97: connectivity[offset + subent_conn[1]] = D;
98: connectivity[offset + subent_conn[2]] = B;
99: }
100: } else {
101: switch (subelem) { /* 0 1 2 of a QUAD */
102: case 0:
103: connectivity[offset + subent_conn[0]] = A;
104: connectivity[offset + subent_conn[1]] = B;
105: connectivity[offset + subent_conn[2]] = M;
106: break;
107: case 1:
108: connectivity[offset + subent_conn[0]] = B;
109: connectivity[offset + subent_conn[1]] = C;
110: connectivity[offset + subent_conn[2]] = M;
111: break;
112: case 2:
113: connectivity[offset + subent_conn[0]] = C;
114: connectivity[offset + subent_conn[1]] = D;
115: connectivity[offset + subent_conn[2]] = M;
116: break;
117: case 3:
118: connectivity[offset + subent_conn[0]] = D;
119: connectivity[offset + subent_conn[1]] = A;
120: connectivity[offset + subent_conn[2]] = M;
121: break;
122: }
123: }
124: break;
125: case 3:
126: default:
127: C = corner + 1 + genCtx.ystride;
128: D = corner + genCtx.ystride;
129: E = corner + genCtx.zstride;
130: F = corner + 1 + genCtx.zstride;
131: G = corner + 1 + genCtx.ystride + genCtx.zstride;
132: H = corner + genCtx.ystride + genCtx.zstride;
133: subent_conn.resize(4); /* only linear TET supported */
134: moab::CN::SubEntityVertexIndices(moab::MBTET, 3, 0, subent_conn.data());
135: switch (subelem) {
136: case 0: /* 4 3 7 6 of a HEX */
137: connectivity[offset + subent_conn[0]] = E;
138: connectivity[offset + subent_conn[1]] = D;
139: connectivity[offset + subent_conn[2]] = H;
140: connectivity[offset + subent_conn[3]] = G;
141: break;
142: case 1: /* 0 1 2 5 of a HEX */
143: connectivity[offset + subent_conn[0]] = A;
144: connectivity[offset + subent_conn[1]] = B;
145: connectivity[offset + subent_conn[2]] = C;
146: connectivity[offset + subent_conn[3]] = F;
147: break;
148: case 2: /* 0 3 4 5 of a HEX */
149: connectivity[offset + subent_conn[0]] = A;
150: connectivity[offset + subent_conn[1]] = D;
151: connectivity[offset + subent_conn[2]] = E;
152: connectivity[offset + subent_conn[3]] = F;
153: break;
154: case 3: /* 2 6 3 5 of a HEX */
155: connectivity[offset + subent_conn[0]] = C;
156: connectivity[offset + subent_conn[1]] = G;
157: connectivity[offset + subent_conn[2]] = D;
158: connectivity[offset + subent_conn[3]] = F;
159: break;
160: case 4: /* 0 2 3 5 of a HEX */
161: connectivity[offset + subent_conn[0]] = A;
162: connectivity[offset + subent_conn[1]] = C;
163: connectivity[offset + subent_conn[2]] = D;
164: connectivity[offset + subent_conn[3]] = F;
165: break;
166: case 5: /* 3 6 4 5 of a HEX */
167: connectivity[offset + subent_conn[0]] = D;
168: connectivity[offset + subent_conn[1]] = G;
169: connectivity[offset + subent_conn[2]] = E;
170: connectivity[offset + subent_conn[3]] = F;
171: break;
172: }
173: break;
174: }
175: return subent_conn.size();
176: }
178: static std::pair<PetscInt, PetscInt> DMMoab_SetElementConnectivity_Private(DMMoabMeshGeneratorCtx &genCtx, PetscInt offset, PetscInt corner, moab::EntityHandle *connectivity)
179: {
180: PetscInt vcount = 0;
181: PetscInt simplices_per_tensor[4] = {0, 1, 2, 6};
182: std::vector<PetscInt> subent_conn; /* only linear edge, tri, tet supported now */
183: subent_conn.reserve(27);
184: PetscInt m, subelem;
185: if (genCtx.simplex) {
186: subelem = simplices_per_tensor[genCtx.dim];
187: for (m = 0; m < subelem; m++) {
188: vcount = DMMoab_SetSimplexElementConnectivity_Private(genCtx, m, offset, corner, subent_conn, connectivity);
189: offset += vcount;
190: }
191: } else {
192: subelem = 1;
193: vcount = DMMoab_SetTensorElementConnectivity_Private(genCtx, offset, corner, subent_conn, connectivity);
194: }
195: return std::pair<PetscInt, PetscInt>(vcount * subelem, subelem);
196: }
198: static PetscErrorCode DMMoab_GenerateVertices_Private(moab::Interface *mbImpl, moab::ReadUtilIface *iface, DMMoabMeshGeneratorCtx &genCtx, PetscInt m, PetscInt n, PetscInt k, PetscInt a, PetscInt b, PetscInt c, moab::Tag &global_id_tag, moab::EntityHandle &startv, moab::Range &uverts)
199: {
200: PetscInt x, y, z, ix, nnodes;
201: PetscInt ii, jj, kk;
202: std::vector<PetscReal *> arrays;
203: PetscInt *gids;
204: moab::ErrorCode merr;
206: PetscFunctionBegin;
207: /* we will generate (q*block+1)^3 vertices, and block^3 hexas; q is 1 for linear, 2 for quadratic
208: * the global id of the vertices will come from m, n, k, a, b, c
209: * x will vary from m*A*q*block + a*q*block to m*A*q*block+(a+1)*q*block etc.
210: */
211: nnodes = genCtx.blockSizeVertexXYZ[0] * (genCtx.dim > 1 ? genCtx.blockSizeVertexXYZ[1] * (genCtx.dim > 2 ? genCtx.blockSizeVertexXYZ[2] : 1) : 1);
212: PetscCall(PetscMalloc1(nnodes, &gids));
214: merr = iface->get_node_coords(3, nnodes, 0, startv, arrays);
215: MBERR("Can't get node coords.", merr);
217: /* will start with the lower corner: */
218: /* x = ( m * genCtx.A + a) * genCtx.q * genCtx.blockSizeElementXYZ[0]; */
219: /* y = ( n * genCtx.B + b) * genCtx.q * genCtx.blockSizeElementXYZ[1]; */
220: /* z = ( k * genCtx.C + c) * genCtx.q * genCtx.blockSizeElementXYZ[2]; */
222: x = (m * genCtx.A + a) * genCtx.q;
223: y = (n * genCtx.B + b) * genCtx.q;
224: z = (k * genCtx.C + c) * genCtx.q;
225: PetscCall(PetscInfo(NULL, "Starting offset for coordinates := %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", x, y, z));
226: ix = 0;
227: moab::Range verts(startv, startv + nnodes - 1);
228: for (kk = 0; kk < (genCtx.dim > 2 ? genCtx.blockSizeVertexXYZ[2] : 1); kk++) {
229: for (jj = 0; jj < (genCtx.dim > 1 ? genCtx.blockSizeVertexXYZ[1] : 1); jj++) {
230: for (ii = 0; ii < genCtx.blockSizeVertexXYZ[0]; ii++, ix++) {
231: /* set coordinates for the vertices */
232: arrays[0][ix] = (x + ii) * genCtx.dx + genCtx.xyzbounds[0];
233: arrays[1][ix] = (y + jj) * genCtx.dy + genCtx.xyzbounds[2];
234: arrays[2][ix] = (z + kk) * genCtx.dz + genCtx.xyzbounds[4];
235: PetscCall(PetscInfo(NULL, "Creating vertex with coordinates := %f, %f, %f\n", arrays[0][ix], arrays[1][ix], arrays[2][ix]));
237: /* If we want to set some tags on the vertices -> use the following entity handle definition:
238: moab::EntityHandle v = startv + ix;
239: */
240: /* compute the global ID for vertex */
241: gids[ix] = 1 + (x + ii) + (y + jj) * genCtx.NX + (z + kk) * (genCtx.NX * genCtx.NY);
242: }
243: }
244: }
245: /* set global ID data on vertices */
246: mbImpl->tag_set_data(global_id_tag, verts, &gids[0]);
247: verts.swap(uverts);
248: PetscCall(PetscFree(gids));
249: PetscFunctionReturn(PETSC_SUCCESS);
250: }
252: static PetscErrorCode DMMoab_GenerateElements_Private(moab::Interface *mbImpl, moab::ReadUtilIface *iface, DMMoabMeshGeneratorCtx &genCtx, PetscInt m, PetscInt n, PetscInt k, PetscInt a, PetscInt b, PetscInt c, moab::Tag &global_id_tag, moab::EntityHandle startv, moab::Range &cells)
253: {
254: moab::ErrorCode merr;
255: PetscInt ix, ie, xe, ye, ze;
256: PetscInt ii, jj, kk, nvperelem;
257: PetscInt simplices_per_tensor[4] = {0, 1, 2, 6};
258: PetscInt ntensorelems = genCtx.blockSizeElementXYZ[0] * (genCtx.dim > 1 ? genCtx.blockSizeElementXYZ[1] * (genCtx.dim > 2 ? genCtx.blockSizeElementXYZ[2] : 1) : 1); /*pow(genCtx.blockSizeElement,genCtx.dim);*/
259: PetscInt nelems = ntensorelems;
260: moab::EntityHandle starte; /* connectivity */
261: moab::EntityHandle *conn;
263: PetscFunctionBegin;
264: switch (genCtx.dim) {
265: case 1:
266: nvperelem = 2;
267: merr = iface->get_element_connect(nelems, 2, moab::MBEDGE, 0, starte, conn);
268: MBERR("Can't get EDGE2 element connectivity.", merr);
269: break;
270: case 2:
271: if (genCtx.simplex) {
272: nvperelem = 3;
273: nelems = ntensorelems * simplices_per_tensor[genCtx.dim];
274: merr = iface->get_element_connect(nelems, 3, moab::MBTRI, 0, starte, conn);
275: MBERR("Can't get TRI3 element connectivity.", merr);
276: } else {
277: nvperelem = 4;
278: merr = iface->get_element_connect(nelems, 4, moab::MBQUAD, 0, starte, conn);
279: MBERR("Can't get QUAD4 element connectivity.", merr);
280: }
281: break;
282: case 3:
283: default:
284: if (genCtx.simplex) {
285: nvperelem = 4;
286: nelems = ntensorelems * simplices_per_tensor[genCtx.dim];
287: merr = iface->get_element_connect(nelems, 4, moab::MBTET, 0, starte, conn);
288: MBERR("Can't get TET4 element connectivity.", merr);
289: } else {
290: nvperelem = 8;
291: merr = iface->get_element_connect(nelems, 8, moab::MBHEX, 0, starte, conn);
292: MBERR("Can't get HEX8 element connectivity.", merr);
293: }
294: break;
295: }
297: ix = ie = 0; /* index now in the elements, for global ids */
299: /* create a temporary range to store local element handles */
300: moab::Range tmp(starte, starte + nelems - 1);
301: std::vector<PetscInt> gids(nelems);
303: /* identify the elements at the lower corner, for their global ids */
304: xe = m * genCtx.A * genCtx.blockSizeElementXYZ[0] + a * genCtx.blockSizeElementXYZ[0];
305: ye = (genCtx.dim > 1 ? n * genCtx.B * genCtx.blockSizeElementXYZ[1] + b * genCtx.blockSizeElementXYZ[1] : 0);
306: ze = (genCtx.dim > 2 ? k * genCtx.C * genCtx.blockSizeElementXYZ[2] + c * genCtx.blockSizeElementXYZ[2] : 0);
308: /* create owned elements requested by genCtx */
309: for (kk = 0; kk < (genCtx.dim > 2 ? genCtx.blockSizeElementXYZ[2] : 1); kk++) {
310: for (jj = 0; jj < (genCtx.dim > 1 ? genCtx.blockSizeElementXYZ[1] : 1); jj++) {
311: for (ii = 0; ii < genCtx.blockSizeElementXYZ[0]; ii++) {
312: moab::EntityHandle corner = startv + genCtx.q * ii + genCtx.q * jj * genCtx.ystride + genCtx.q * kk * genCtx.zstride;
314: std::pair<PetscInt, PetscInt> entoffset = DMMoab_SetElementConnectivity_Private(genCtx, ix, corner, conn);
316: for (PetscInt j = 0; j < entoffset.second; j++) {
317: /* The entity handle for the particular element -> if we want to set some tags is
318: moab::EntityHandle eh = starte + ie + j;
319: */
320: gids[ie + j] = 1 + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney));
321: /* gids[ie+j] = ie + j + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney)); */
322: /* gids[ie+j] = 1 + ie; */
323: /* ie++; */
324: }
326: ix += entoffset.first;
327: ie += entoffset.second;
328: }
329: }
330: }
331: if (genCtx.adjEnts) { /* we need to update adjacencies now, because some elements are new */
332: merr = iface->update_adjacencies(starte, nelems, nvperelem, conn);
333: MBERR("Can't update adjacencies", merr);
334: }
335: tmp.swap(cells);
336: merr = mbImpl->tag_set_data(global_id_tag, cells, &gids[0]);
337: MBERR("Can't set global ids to elements.", merr);
338: PetscFunctionReturn(PETSC_SUCCESS);
339: }
341: static PetscErrorCode DMMBUtil_InitializeOptions(DMMoabMeshGeneratorCtx &genCtx, PetscInt dim, PetscBool simplex, PetscInt rank, PetscInt nprocs, const PetscReal *bounds, PetscInt nelems)
342: {
343: PetscFunctionBegin;
344: /* Initialize all genCtx data */
345: genCtx.dim = dim;
346: genCtx.simplex = simplex;
347: genCtx.newMergeMethod = genCtx.keep_skins = genCtx.adjEnts = true;
348: /* determine other global quantities for the mesh used for nodes increments */
349: genCtx.q = 1;
350: genCtx.fraction = genCtx.remainder = genCtx.cumfraction = 0;
352: if (!genCtx.usrxyzgrid) { /* not overridden by genCtx - assume nele equally and that genCtx wants a uniform cube mesh */
354: genCtx.fraction = nelems / nprocs; /* partition only by the largest dimension */
355: genCtx.remainder = nelems % nprocs; /* remainder after partition which gets evenly distributed by round-robin */
356: genCtx.cumfraction = (rank > 0 ? (genCtx.fraction) * (rank) + (rank - 1 < genCtx.remainder ? rank : genCtx.remainder) : 0);
357: if (rank < genCtx.remainder) /* This process gets "fraction+1" elements */
358: genCtx.fraction++;
360: PetscCall(PetscInfo(NULL, "Fraction = %" PetscInt_FMT ", Remainder = %" PetscInt_FMT ", Cumulative fraction = %" PetscInt_FMT "\n", genCtx.fraction, genCtx.remainder, genCtx.cumfraction));
361: switch (genCtx.dim) {
362: case 1:
363: genCtx.blockSizeElementXYZ[0] = genCtx.fraction;
364: genCtx.blockSizeElementXYZ[1] = 1;
365: genCtx.blockSizeElementXYZ[2] = 1;
366: break;
367: case 2:
368: genCtx.blockSizeElementXYZ[0] = nelems;
369: genCtx.blockSizeElementXYZ[1] = genCtx.fraction;
370: genCtx.blockSizeElementXYZ[2] = 1;
371: break;
372: case 3:
373: default:
374: genCtx.blockSizeElementXYZ[0] = nelems;
375: genCtx.blockSizeElementXYZ[1] = nelems;
376: genCtx.blockSizeElementXYZ[2] = genCtx.fraction;
377: break;
378: }
379: }
381: /* partition only by the largest dimension */
382: /* Total number of local elements := genCtx.blockSizeElementXYZ[0]*(genCtx.dim>1? genCtx.blockSizeElementXYZ[1]*(genCtx.dim>2 ? genCtx.blockSizeElementXYZ[2]:1) :1); */
383: if (bounds) {
384: for (PetscInt i = 0; i < 6; i++) genCtx.xyzbounds[i] = bounds[i];
385: } else {
386: genCtx.xyzbounds[0] = genCtx.xyzbounds[2] = genCtx.xyzbounds[4] = 0.0;
387: genCtx.xyzbounds[1] = genCtx.xyzbounds[3] = genCtx.xyzbounds[5] = 1.0;
388: }
390: if (!genCtx.usrprocgrid) {
391: switch (genCtx.dim) {
392: case 1:
393: genCtx.M = nprocs;
394: genCtx.N = genCtx.K = 1;
395: break;
396: case 2:
397: genCtx.N = nprocs;
398: genCtx.M = genCtx.K = 1;
399: break;
400: default:
401: genCtx.K = nprocs;
402: genCtx.M = genCtx.N = 1;
403: break;
404: }
405: }
407: if (!genCtx.usrrefgrid) genCtx.A = genCtx.B = genCtx.C = 1;
409: /* more default values */
410: genCtx.nex = genCtx.ney = genCtx.nez = 0;
411: genCtx.xstride = genCtx.ystride = genCtx.zstride = 0;
412: genCtx.NX = genCtx.NY = genCtx.NZ = 0;
413: genCtx.nex = genCtx.ney = genCtx.nez = 0;
414: genCtx.blockSizeVertexXYZ[0] = genCtx.blockSizeVertexXYZ[1] = genCtx.blockSizeVertexXYZ[2] = 1;
416: switch (genCtx.dim) {
417: case 3:
418: genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
419: genCtx.blockSizeVertexXYZ[1] = genCtx.q * genCtx.blockSizeElementXYZ[1] + 1;
420: genCtx.blockSizeVertexXYZ[2] = genCtx.q * genCtx.blockSizeElementXYZ[2] + 1;
422: genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0]; /* number of elements in x direction, used for global id on element */
423: genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (nelems * genCtx.q); /* distance between 2 nodes in x direction */
424: genCtx.NX = (genCtx.q * genCtx.nex + 1);
425: genCtx.xstride = 1;
426: genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1]; /* number of elements in y direction .... */
427: genCtx.dy = (genCtx.xyzbounds[3] - genCtx.xyzbounds[2]) / (nelems * genCtx.q); /* distance between 2 nodes in y direction */
428: genCtx.NY = (genCtx.q * genCtx.ney + 1);
429: genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
430: genCtx.nez = genCtx.K * genCtx.C * genCtx.blockSizeElementXYZ[2]; /* number of elements in z direction .... */
431: genCtx.dz = (genCtx.xyzbounds[5] - genCtx.xyzbounds[4]) / (nelems * genCtx.q); /* distance between 2 nodes in z direction */
432: genCtx.NZ = (genCtx.q * genCtx.nez + 1);
433: genCtx.zstride = genCtx.blockSizeVertexXYZ[0] * genCtx.blockSizeVertexXYZ[1];
434: break;
435: case 2:
436: genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
437: genCtx.blockSizeVertexXYZ[1] = genCtx.q * genCtx.blockSizeElementXYZ[1] + 1;
438: genCtx.blockSizeVertexXYZ[2] = 0;
440: genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0]; /* number of elements in x direction, used for global id on element */
441: genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (genCtx.nex * genCtx.q); /* distance between 2 nodes in x direction */
442: genCtx.NX = (genCtx.q * genCtx.nex + 1);
443: genCtx.xstride = 1;
444: genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1]; /* number of elements in y direction .... */
445: genCtx.dy = (genCtx.xyzbounds[3] - genCtx.xyzbounds[2]) / (nelems * genCtx.q); /* distance between 2 nodes in y direction */
446: genCtx.NY = (genCtx.q * genCtx.ney + 1);
447: genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
448: break;
449: case 1:
450: genCtx.blockSizeVertexXYZ[1] = genCtx.blockSizeVertexXYZ[2] = 0;
451: genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
453: genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0]; /* number of elements in x direction, used for global id on element */
454: genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (nelems * genCtx.q); /* distance between 2 nodes in x direction */
455: genCtx.NX = (genCtx.q * genCtx.nex + 1);
456: genCtx.xstride = 1;
457: break;
458: }
460: /* Lets check for some valid input */
461: PetscCheck(genCtx.dim >= 1 && genCtx.dim <= 3, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid topological dimension specified: %" PetscInt_FMT ".", genCtx.dim);
462: PetscCheck(genCtx.M * genCtx.N * genCtx.K == nprocs, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid [m, n, k] data: %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT ". Product must be equal to global size = %" PetscInt_FMT ".", genCtx.M,
463: genCtx.N, genCtx.K, nprocs);
464: /* validate the bounds data */
465: PetscCheck(genCtx.xyzbounds[0] < genCtx.xyzbounds[1], PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "X-dim: Left boundary cannot be greater than right. [%G >= %G]", genCtx.xyzbounds[0], genCtx.xyzbounds[1]);
466: PetscCheck(genCtx.dim <= 1 || genCtx.xyzbounds[2] < genCtx.xyzbounds[3], PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Y-dim: Left boundary cannot be greater than right. [%G >= %G]", genCtx.xyzbounds[2], genCtx.xyzbounds[3]);
467: PetscCheck(genCtx.dim <= 2 || genCtx.xyzbounds[4] < genCtx.xyzbounds[5], PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Z-dim: Left boundary cannot be greater than right. [%G >= %G]", genCtx.xyzbounds[4], genCtx.xyzbounds[5]);
469: PetscCall(PetscInfo(NULL, "Local elements:= %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", genCtx.blockSizeElementXYZ[0], genCtx.blockSizeElementXYZ[1], genCtx.blockSizeElementXYZ[2]));
470: PetscCall(PetscInfo(NULL, "Local vertices:= %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", genCtx.blockSizeVertexXYZ[0], genCtx.blockSizeVertexXYZ[1], genCtx.blockSizeVertexXYZ[2]));
471: PetscCall(PetscInfo(NULL, "Local blocks/processors := %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", genCtx.A, genCtx.B, genCtx.C));
472: PetscCall(PetscInfo(NULL, "Local processors := %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", genCtx.M, genCtx.N, genCtx.K));
473: PetscCall(PetscInfo(NULL, "Local nexyz:= %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", genCtx.nex, genCtx.ney, genCtx.nez));
474: PetscCall(PetscInfo(NULL, "Local delxyz:= %g, %g, %g\n", genCtx.dx, genCtx.dy, genCtx.dz));
475: PetscCall(PetscInfo(NULL, "Local strides:= %" PetscInt_FMT ", %" PetscInt_FMT ", %" PetscInt_FMT "\n", genCtx.xstride, genCtx.ystride, genCtx.zstride));
476: PetscFunctionReturn(PETSC_SUCCESS);
477: }
479: /*@C
480: DMMoabCreateBoxMesh - Creates a mesh on the tensor product (box) of intervals with genCtx specified bounds.
482: Collective
484: Input Parameters:
485: + comm - The communicator for the DM object
486: . dim - The spatial dimension
487: . useSimplex - use a simplex mesh
488: . bounds - The bounds of the box specified with [x-left, x-right, y-bottom, y-top, z-bottom, z-top] depending on the spatial dimension
489: . nele - The number of discrete elements in each direction
490: - nghost - The number of ghosted layers needed in the partitioned mesh
492: Output Parameter:
493: . dm - The `DM` object
495: Level: beginner
497: .seealso: `DMSetType()`, `DMCreate()`, `DMMoabLoadFromFile()`
498: @*/
499: PetscErrorCode DMMoabCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool useSimplex, const PetscReal *bounds, PetscInt nele, PetscInt nghost, DM *dm)
500: {
501: moab::ErrorCode merr;
502: PetscInt a, b, c, n, global_size, global_rank;
503: DM_Moab *dmmoab;
504: moab::Interface *mbImpl;
505: #ifdef MOAB_HAVE_MPI
506: moab::ParallelComm *pcomm;
507: #endif
508: moab::ReadUtilIface *readMeshIface;
509: moab::Range verts, cells, edges, faces, adj, dim3, dim2;
510: DMMoabMeshGeneratorCtx genCtx;
511: const PetscInt npts = nele + 1; /* Number of points in every dimension */
513: moab::Tag global_id_tag, part_tag, geom_tag, mat_tag, dir_tag, neu_tag;
514: moab::Range ownedvtx, ownedelms, localvtxs, localelms;
515: moab::EntityHandle regionset;
516: PetscInt ml = 0, nl = 0, kl = 0;
518: PetscFunctionBegin;
519: PetscCheck(dim >= 1 && dim <= 3, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension argument for mesh: dim=[1,3].");
521: PetscCall(PetscLogEventRegister("GenerateMesh", DM_CLASSID, &genCtx.generateMesh));
522: PetscCall(PetscLogEventRegister("AddVertices", DM_CLASSID, &genCtx.generateVertices));
523: PetscCall(PetscLogEventRegister("AddElements", DM_CLASSID, &genCtx.generateElements));
524: PetscCall(PetscLogEventRegister("ParResolve", DM_CLASSID, &genCtx.parResolve));
525: PetscCall(PetscLogEventBegin(genCtx.generateMesh, 0, 0, 0, 0));
526: PetscCallMPI(MPI_Comm_size(comm, &global_size));
527: /* total number of vertices in all dimensions */
528: n = pow(npts, dim);
530: /* do some error checking */
531: PetscCheck(n >= 2, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of points must be >= 2.");
532: PetscCheck(global_size <= n, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of processors must be less than or equal to number of elements.");
533: PetscCheck(nghost >= 0, PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of ghost layers cannot be negative.");
535: /* Create the basic DMMoab object and keep the default parameters created by DM impls */
536: PetscCall(DMMoabCreateMoab(comm, NULL, NULL, NULL, dm));
538: /* get all the necessary handles from the private DM object */
539: dmmoab = (DM_Moab *)(*dm)->data;
540: mbImpl = dmmoab->mbiface;
541: #ifdef MOAB_HAVE_MPI
542: pcomm = dmmoab->pcomm;
543: global_rank = pcomm->rank();
544: #else
545: global_rank = 0;
546: global_size = 1;
547: #endif
548: global_id_tag = dmmoab->ltog_tag;
549: dmmoab->dim = dim;
550: dmmoab->nghostrings = nghost;
551: dmmoab->refct = 1;
553: /* create a file set to associate all entities in current mesh */
554: merr = mbImpl->create_meshset(moab::MESHSET_SET, dmmoab->fileset);
555: MBERR("Creating file set failed", merr);
557: /* No errors yet; proceed with building the mesh */
558: merr = mbImpl->query_interface(readMeshIface);
559: MBERRNM(merr);
561: genCtx.M = genCtx.N = genCtx.K = 1;
562: genCtx.A = genCtx.B = genCtx.C = 1;
563: genCtx.blockSizeElementXYZ[0] = 0;
564: genCtx.blockSizeElementXYZ[1] = 0;
565: genCtx.blockSizeElementXYZ[2] = 0;
567: PetscOptionsBegin(comm, "", "DMMoab Creation Options", "DMMOAB");
568: /* Handle DMMoab spatial resolution */
569: PetscCall(PetscOptionsInt("-dmb_grid_x", "Number of grid points in x direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[0], &genCtx.blockSizeElementXYZ[0], &genCtx.usrxyzgrid));
570: if (dim > 1) PetscCall(PetscOptionsInt("-dmb_grid_y", "Number of grid points in y direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[1], &genCtx.blockSizeElementXYZ[1], &genCtx.usrxyzgrid));
571: if (dim > 2) PetscCall(PetscOptionsInt("-dmb_grid_z", "Number of grid points in z direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[2], &genCtx.blockSizeElementXYZ[2], &genCtx.usrxyzgrid));
573: /* Handle DMMoab parallel distribution */
574: PetscCall(PetscOptionsInt("-dmb_processors_x", "Number of processors in x direction", "DMMoabSetNumProcs", genCtx.M, &genCtx.M, &genCtx.usrprocgrid));
575: if (dim > 1) PetscCall(PetscOptionsInt("-dmb_processors_y", "Number of processors in y direction", "DMMoabSetNumProcs", genCtx.N, &genCtx.N, &genCtx.usrprocgrid));
576: if (dim > 2) PetscCall(PetscOptionsInt("-dmb_processors_z", "Number of processors in z direction", "DMMoabSetNumProcs", genCtx.K, &genCtx.K, &genCtx.usrprocgrid));
578: /* Handle DMMoab block refinement */
579: PetscCall(PetscOptionsInt("-dmb_refine_x", "Number of refinement blocks in x direction", "DMMoabSetRefinement", genCtx.A, &genCtx.A, &genCtx.usrrefgrid));
580: if (dim > 1) PetscCall(PetscOptionsInt("-dmb_refine_y", "Number of refinement blocks in y direction", "DMMoabSetRefinement", genCtx.B, &genCtx.B, &genCtx.usrrefgrid));
581: if (dim > 2) PetscCall(PetscOptionsInt("-dmb_refine_z", "Number of refinement blocks in z direction", "DMMoabSetRefinement", genCtx.C, &genCtx.C, &genCtx.usrrefgrid));
582: PetscOptionsEnd();
584: PetscCall(DMMBUtil_InitializeOptions(genCtx, dim, useSimplex, global_rank, global_size, bounds, nele));
586: //PetscCheck(nele>=nprocs,PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The dimensional discretization size should be greater or equal to number of processors: %" PetscInt_FMT " < %" PetscInt_FMT,nele,nprocs);
588: if (genCtx.adjEnts) genCtx.keep_skins = true; /* do not delete anything - consumes more memory */
590: /* determine m, n, k for processor rank */
591: ml = nl = kl = 0;
592: switch (genCtx.dim) {
593: case 1:
594: ml = (genCtx.cumfraction);
595: break;
596: case 2:
597: nl = (genCtx.cumfraction);
598: break;
599: default:
600: kl = (genCtx.cumfraction) / genCtx.q / genCtx.blockSizeElementXYZ[2] / genCtx.C; //genCtx.K
601: break;
602: }
604: /*
605: * so there are a total of M * A * blockSizeElement elements in x direction (so M * A * blockSizeElement + 1 verts in x direction)
606: * so there are a total of N * B * blockSizeElement elements in y direction (so N * B * blockSizeElement + 1 verts in y direction)
607: * so there are a total of K * C * blockSizeElement elements in z direction (so K * C * blockSizeElement + 1 verts in z direction)
609: * there are ( M * A blockSizeElement) * ( N * B * blockSizeElement) * (K * C * blockSizeElement) hexas
610: * there are ( M * A * blockSizeElement + 1) * ( N * B * blockSizeElement + 1) * (K * C * blockSizeElement + 1) vertices
611: * x is the first dimension that varies
612: */
614: /* generate the block at (a, b, c); it will represent a partition , it will get a partition tag */
615: PetscInt dum_id = -1;
616: merr = mbImpl->tag_get_handle("GLOBAL_ID", 1, moab::MB_TYPE_INTEGER, global_id_tag);
617: MBERR("Getting Global_ID Tag handle failed", merr);
619: merr = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, mat_tag);
620: MBERR("Getting Material set Tag handle failed", merr);
621: merr = mbImpl->tag_get_handle(DIRICHLET_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, dir_tag);
622: MBERR("Getting Dirichlet set Tag handle failed", merr);
623: merr = mbImpl->tag_get_handle(NEUMANN_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, neu_tag);
624: MBERR("Getting Neumann set Tag handle failed", merr);
626: merr = mbImpl->tag_get_handle("PARALLEL_PARTITION", 1, moab::MB_TYPE_INTEGER, part_tag, moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE, &dum_id);
627: MBERR("Getting Partition Tag handle failed", merr);
629: /* lets create some sets */
630: merr = mbImpl->tag_get_handle(GEOM_DIMENSION_TAG_NAME, 1, moab::MB_TYPE_INTEGER, geom_tag, moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE, &dum_id);
631: MBERRNM(merr);
632: merr = mbImpl->create_meshset(moab::MESHSET_SET, regionset);
633: MBERRNM(merr);
634: PetscCall(PetscLogEventEnd(genCtx.generateMesh, 0, 0, 0, 0));
636: for (a = 0; a < (genCtx.dim > 0 ? genCtx.A : genCtx.A); a++) {
637: for (b = 0; b < (genCtx.dim > 1 ? genCtx.B : 1); b++) {
638: for (c = 0; c < (genCtx.dim > 2 ? genCtx.C : 1); c++) {
639: moab::EntityHandle startv;
641: PetscCall(PetscLogEventBegin(genCtx.generateVertices, 0, 0, 0, 0));
642: PetscCall(DMMoab_GenerateVertices_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, verts));
643: PetscCall(PetscLogEventEnd(genCtx.generateVertices, 0, 0, 0, 0));
645: PetscCall(PetscLogEventBegin(genCtx.generateElements, 0, 0, 0, 0));
646: PetscCall(DMMoab_GenerateElements_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, cells));
647: PetscCall(PetscLogEventEnd(genCtx.generateElements, 0, 0, 0, 0));
649: PetscInt part_num = 0;
650: switch (genCtx.dim) {
651: case 3:
652: part_num += (c + kl * genCtx.C) * (genCtx.M * genCtx.A * genCtx.N * genCtx.B);
653: case 2:
654: part_num += (b + nl * genCtx.B) * (genCtx.M * genCtx.A);
655: case 1:
656: part_num += (a + ml * genCtx.A);
657: break;
658: }
660: moab::EntityHandle part_set;
661: merr = mbImpl->create_meshset(moab::MESHSET_SET, part_set);
662: MBERR("Can't create mesh set.", merr);
664: merr = mbImpl->add_entities(part_set, verts);
665: MBERR("Can't add vertices to set.", merr);
666: merr = mbImpl->add_entities(part_set, cells);
667: MBERR("Can't add entities to set.", merr);
668: merr = mbImpl->add_entities(regionset, cells);
669: MBERR("Can't add entities to set.", merr);
671: /* if needed, add all edges and faces */
672: if (genCtx.adjEnts) {
673: if (genCtx.dim > 1) {
674: merr = mbImpl->get_adjacencies(cells, 1, true, edges, moab::Interface::UNION);
675: MBERR("Can't get edges", merr);
676: merr = mbImpl->add_entities(part_set, edges);
677: MBERR("Can't add edges to partition set.", merr);
678: }
679: if (genCtx.dim > 2) {
680: merr = mbImpl->get_adjacencies(cells, 2, true, faces, moab::Interface::UNION);
681: MBERR("Can't get faces", merr);
682: merr = mbImpl->add_entities(part_set, faces);
683: MBERR("Can't add faces to partition set.", merr);
684: }
685: edges.clear();
686: faces.clear();
687: }
688: verts.clear();
689: cells.clear();
691: merr = mbImpl->tag_set_data(part_tag, &part_set, 1, &part_num);
692: MBERR("Can't set part tag on set", merr);
693: if (dmmoab->fileset) {
694: merr = mbImpl->add_parent_child(dmmoab->fileset, part_set);
695: MBERR("Can't add part set to file set.", merr);
696: merr = mbImpl->unite_meshset(dmmoab->fileset, part_set);
697: MBERRNM(merr);
698: }
699: merr = mbImpl->add_entities(dmmoab->fileset, &part_set, 1);
700: MBERRNM(merr);
701: }
702: }
703: }
705: merr = mbImpl->add_parent_child(dmmoab->fileset, regionset);
706: MBERRNM(merr);
708: /* Only in parallel: resolve shared entities between processors and exchange ghost layers */
709: if (global_size > 1) {
710: PetscCall(PetscLogEventBegin(genCtx.parResolve, 0, 0, 0, 0));
712: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, genCtx.dim, cells);
713: MBERR("Can't get all d-dimensional elements.", merr);
714: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 0, verts);
715: MBERR("Can't get all vertices.", merr);
717: if (genCtx.A * genCtx.B * genCtx.C != 1) { // merge needed
718: moab::MergeMesh mm(mbImpl);
719: if (genCtx.newMergeMethod) {
720: merr = mm.merge_using_integer_tag(verts, global_id_tag);
721: MBERR("Can't merge with GLOBAL_ID tag", merr);
722: } else {
723: merr = mm.merge_entities(cells, 0.0001);
724: MBERR("Can't merge with coordinates", merr);
725: }
726: }
728: #ifdef MOAB_HAVE_MPI
729: /* check the handles */
730: merr = pcomm->check_all_shared_handles();
731: MBERRV(mbImpl, merr);
733: /* resolve the shared entities by exchanging information to adjacent processors */
734: merr = pcomm->resolve_shared_ents(dmmoab->fileset, cells, dim, dim - 1, NULL, &global_id_tag);
735: MBERRV(mbImpl, merr);
736: if (dmmoab->fileset) {
737: merr = pcomm->exchange_ghost_cells(dim, 0, nghost, dim, true, false, &dmmoab->fileset);
738: MBERRV(mbImpl, merr);
739: } else {
740: merr = pcomm->exchange_ghost_cells(dim, 0, nghost, dim, true, false);
741: MBERRV(mbImpl, merr);
742: }
744: /* Reassign global IDs on all entities. */
745: merr = pcomm->assign_global_ids(dmmoab->fileset, dim, 1, false, true, false);
746: MBERRNM(merr);
747: #endif
749: PetscCall(PetscLogEventEnd(genCtx.parResolve, 0, 0, 0, 0));
750: }
752: if (!genCtx.keep_skins) { // default is to delete the 1- and 2-dimensional entities
753: // delete all quads and edges
754: moab::Range toDelete;
755: if (genCtx.dim > 1) {
756: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 1, toDelete);
757: MBERR("Can't get edges", merr);
758: }
760: if (genCtx.dim > 2) {
761: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 2, toDelete);
762: MBERR("Can't get faces", merr);
763: }
765: #ifdef MOAB_HAVE_MPI
766: merr = dmmoab->pcomm->delete_entities(toDelete);
767: MBERR("Can't delete entities", merr);
768: #endif
769: }
771: /* set geometric dimension tag for regions */
772: merr = mbImpl->tag_set_data(geom_tag, ®ionset, 1, &dmmoab->dim);
773: MBERRNM(merr);
774: /* set default material ID for regions */
775: int default_material = 1;
776: merr = mbImpl->tag_set_data(mat_tag, ®ionset, 1, &default_material);
777: MBERRNM(merr);
778: /*
779: int default_dbc = 0;
780: merr = mbImpl->tag_set_data(dir_tag, &vertexset, 1, &default_dbc);MBERRNM(merr);
781: */
782: PetscFunctionReturn(PETSC_SUCCESS);
783: }
785: static PetscErrorCode DMMoab_GetReadOptions_Private(PetscBool by_rank, PetscInt numproc, PetscInt dim, PetscInt nghost, MoabReadMode mode, PetscInt dbglevel, const char *dm_opts, const char *extra_opts, const char **read_opts)
786: {
787: char *ropts;
788: char ropts_par[PETSC_MAX_PATH_LEN], ropts_pargh[PETSC_MAX_PATH_LEN];
789: char ropts_dbg[PETSC_MAX_PATH_LEN];
791: PetscFunctionBegin;
792: PetscCall(PetscMalloc1(PETSC_MAX_PATH_LEN, &ropts));
793: PetscCall(PetscMemzero(&ropts_par, PETSC_MAX_PATH_LEN));
794: PetscCall(PetscMemzero(&ropts_pargh, PETSC_MAX_PATH_LEN));
795: PetscCall(PetscMemzero(&ropts_dbg, PETSC_MAX_PATH_LEN));
797: /* do parallel read unless using only one processor */
798: if (numproc > 1) {
799: // PetscCall(PetscSNPrintf(ropts_par, PETSC_MAX_PATH_LEN, "PARALLEL=%s;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=%d.0.1%s;",MoabReadModes[mode],dim,(by_rank ? ";PARTITION_BY_RANK":"")));
800: PetscCall(PetscSNPrintf(ropts_par, PETSC_MAX_PATH_LEN, "PARALLEL=%s;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;%s", MoabReadModes[mode], (by_rank ? "PARTITION_BY_RANK;" : "")));
801: if (nghost) PetscCall(PetscSNPrintf(ropts_pargh, PETSC_MAX_PATH_LEN, "PARALLEL_GHOSTS=%" PetscInt_FMT ".0.%" PetscInt_FMT ";", dim, nghost));
802: }
804: if (dbglevel) {
805: if (numproc > 1) {
806: PetscCall(PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "CPUTIME;DEBUG_IO=%" PetscInt_FMT ";DEBUG_PIO=%" PetscInt_FMT ";", dbglevel, dbglevel));
807: } else PetscCall(PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "CPUTIME;DEBUG_IO=%" PetscInt_FMT ";", dbglevel));
808: }
810: PetscCall(PetscSNPrintf(ropts, PETSC_MAX_PATH_LEN, "%s%s%s%s%s", ropts_par, (nghost ? ropts_pargh : ""), ropts_dbg, (extra_opts ? extra_opts : ""), (dm_opts ? dm_opts : "")));
811: *read_opts = ropts;
812: PetscFunctionReturn(PETSC_SUCCESS);
813: }
815: /*@C
816: DMMoabLoadFromFile - Creates a `DMMOAB` object by loading the mesh from a user specified file
817: <https://www.mcs.anl.gov/~fathom/moab-docs/html/contents.html#fivetwo>
819: Collective
821: Input Parameters:
822: + comm - The communicator for the `DMOAB` object
823: . dim - The spatial dimension
824: . nghost - The number of ghosted layers needed in the partitioned mesh
825: . filename - The name of the mesh file to be loaded
826: - usrreadopts - The options string to read a MOAB mesh.
828: Output Parameter:
829: . dm - The `DM` object
831: Level: beginner
833: .seealso: `DMSetType()`, `DMCreate()`, `DMMoabCreateBoxMesh()`
834: @*/
835: PetscErrorCode DMMoabLoadFromFile(MPI_Comm comm, PetscInt dim, PetscInt nghost, const char *filename, const char *usrreadopts, DM *dm)
836: {
837: moab::ErrorCode merr;
838: PetscInt nprocs;
839: DM_Moab *dmmoab;
840: moab::Interface *mbiface;
841: #ifdef MOAB_HAVE_MPI
842: moab::ParallelComm *pcomm;
843: #endif
844: moab::Range verts, elems;
845: const char *readopts;
847: PetscFunctionBegin;
848: PetscAssertPointer(dm, 6);
850: /* Create the basic DMMoab object and keep the default parameters created by DM impls */
851: PetscCall(DMMoabCreateMoab(comm, NULL, NULL, NULL, dm));
853: /* get all the necessary handles from the private DM object */
854: dmmoab = (DM_Moab *)(*dm)->data;
855: mbiface = dmmoab->mbiface;
856: #ifdef MOAB_HAVE_MPI
857: pcomm = dmmoab->pcomm;
858: nprocs = pcomm->size();
859: #else
860: nprocs = 1;
861: #endif
862: /* TODO: Decipher dimension based on the loaded mesh instead of getting from user */
863: dmmoab->dim = dim;
864: dmmoab->nghostrings = nghost;
865: dmmoab->refct = 1;
867: /* create a file set to associate all entities in current mesh */
868: merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, dmmoab->fileset);
869: MBERR("Creating file set failed", merr);
871: /* add mesh loading options specific to the DM */
872: PetscCall(DMMoab_GetReadOptions_Private(dmmoab->partition_by_rank, nprocs, dim, nghost, dmmoab->read_mode, dmmoab->rw_dbglevel, dmmoab->extra_read_options, usrreadopts, &readopts));
874: PetscCall(PetscInfo(*dm, "Reading file %s with options: %s\n", filename, readopts));
876: /* Load the mesh from a file. */
877: if (dmmoab->fileset) {
878: merr = mbiface->load_file(filename, &dmmoab->fileset, readopts);
879: MBERRVM(mbiface, "Reading MOAB file failed.", merr);
880: } else {
881: merr = mbiface->load_file(filename, 0, readopts);
882: MBERRVM(mbiface, "Reading MOAB file failed.", merr);
883: }
885: #ifdef MOAB_HAVE_MPI
886: /* Reassign global IDs on all entities. */
887: /* merr = pcomm->assign_global_ids(dmmoab->fileset, dim, 1, true, true, true);MBERRNM(merr); */
888: #endif
890: /* load the local vertices */
891: merr = mbiface->get_entities_by_type(dmmoab->fileset, moab::MBVERTEX, verts, true);
892: MBERRNM(merr);
893: /* load the local elements */
894: merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, elems, true);
895: MBERRNM(merr);
897: #ifdef MOAB_HAVE_MPI
898: /* Everything is set up, now just do a tag exchange to update tags
899: on all of the ghost vertexes */
900: merr = pcomm->exchange_tags(dmmoab->ltog_tag, verts);
901: MBERRV(mbiface, merr);
902: merr = pcomm->exchange_tags(dmmoab->ltog_tag, elems);
903: MBERRV(mbiface, merr);
904: merr = pcomm->collective_sync_partition();
905: MBERR("Collective sync failed", merr);
906: #endif
908: PetscCall(PetscInfo(*dm, "MOAB file '%s' was successfully loaded. Found %zu vertices and %zu elements.\n", filename, verts.size(), elems.size()));
909: PetscCall(PetscFree(readopts));
910: PetscFunctionReturn(PETSC_SUCCESS);
911: }
913: /*@C
914: DMMoabRenumberMeshEntities - Order and number all entities (vertices->elements) to be contiguously ordered
915: in parallel
917: Collective
919: Input Parameters:
920: . dm - The DM object
922: Level: advanced
924: .seealso: `DMSetUp()`, `DMCreate()`
925: @*/
926: PetscErrorCode DMMoabRenumberMeshEntities(DM dm)
927: {
928: moab::Range verts;
930: PetscFunctionBegin;
933: #ifdef MOAB_HAVE_MPI
934: /* Insert new points */
935: moab::ErrorCode merr;
936: merr = ((DM_Moab *)dm->data)->pcomm->assign_global_ids(((DM_Moab *)dm->data)->fileset, 3, 0, false, true, false);
937: MBERRNM(merr);
938: #endif
939: PetscFunctionReturn(PETSC_SUCCESS);
940: }