Actual source code: dmmbutil.cxx
petsc-3.12.5 2020-03-29
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;
26: } DMMoabMeshGeneratorCtx;
29: PetscInt DMMoab_SetTensorElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, PetscInt offset, PetscInt corner, std::vector<PetscInt>& subent_conn, moab::EntityHandle *connectivity)
30: {
31: switch (genCtx.dim) {
32: case 1:
33: subent_conn.resize(2);
34: moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
35: connectivity[offset + subent_conn[0]] = corner;
36: connectivity[offset + subent_conn[1]] = corner + 1;
37: break;
38: case 2:
39: subent_conn.resize(4);
40: moab::CN::SubEntityVertexIndices(moab::MBQUAD, 2, 0, subent_conn.data());
41: connectivity[offset + subent_conn[0]] = corner;
42: connectivity[offset + subent_conn[1]] = corner + 1;
43: connectivity[offset + subent_conn[2]] = corner + 1 + genCtx.ystride;
44: connectivity[offset + subent_conn[3]] = corner + genCtx.ystride;
45: break;
46: case 3:
47: default:
48: subent_conn.resize(8);
49: moab::CN::SubEntityVertexIndices(moab::MBHEX, 3, 0, subent_conn.data());
50: connectivity[offset + subent_conn[0]] = corner;
51: connectivity[offset + subent_conn[1]] = corner + 1;
52: connectivity[offset + subent_conn[2]] = corner + 1 + genCtx.ystride;
53: connectivity[offset + subent_conn[3]] = corner + genCtx.ystride;
54: connectivity[offset + subent_conn[4]] = corner + genCtx.zstride;
55: connectivity[offset + subent_conn[5]] = corner + 1 + genCtx.zstride;
56: connectivity[offset + subent_conn[6]] = corner + 1 + genCtx.ystride + genCtx.zstride;
57: connectivity[offset + subent_conn[7]] = corner + genCtx.ystride + genCtx.zstride;
58: break;
59: }
60: return subent_conn.size();
61: }
64: PetscInt DMMoab_SetSimplexElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, PetscInt subelem, PetscInt offset, PetscInt corner, std::vector<PetscInt>& subent_conn, moab::EntityHandle *connectivity)
65: {
66: PetscInt A, B, C, D, E, F, G, H, M;
67: const PetscInt trigen_opts = 1; /* 1 - Aligned diagonally to right, 2 - Aligned diagonally to left, 3 - 4 elements per quad */
68: A = corner;
69: B = corner + 1;
70: switch (genCtx.dim) {
71: case 1:
72: subent_conn.resize(2); /* only linear EDGE supported now */
73: moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
74: connectivity[offset + subent_conn[0]] = A;
75: connectivity[offset + subent_conn[1]] = B;
76: break;
77: case 2:
78: C = corner + 1 + genCtx.ystride;
79: D = corner + genCtx.ystride;
80: M = corner + 0.5; /* technically -- need to modify vertex generation */
81: subent_conn.resize(3); /* only linear TRI supported */
82: moab::CN::SubEntityVertexIndices(moab::MBTRI, 2, 0, subent_conn.data());
83: if (trigen_opts == 1) {
84: if (subelem) { /* 0 1 2 of a QUAD */
85: connectivity[offset + subent_conn[0]] = B;
86: connectivity[offset + subent_conn[1]] = C;
87: connectivity[offset + subent_conn[2]] = A;
88: }
89: else { /* 2 3 0 of a QUAD */
90: connectivity[offset + subent_conn[0]] = D;
91: connectivity[offset + subent_conn[1]] = A;
92: connectivity[offset + subent_conn[2]] = C;
93: }
94: }
95: else if (trigen_opts == 2) {
96: if (subelem) { /* 0 1 2 of a QUAD */
97: connectivity[offset + subent_conn[0]] = A;
98: connectivity[offset + subent_conn[1]] = B;
99: connectivity[offset + subent_conn[2]] = D;
100: }
101: else { /* 2 3 0 of a QUAD */
102: connectivity[offset + subent_conn[0]] = C;
103: connectivity[offset + subent_conn[1]] = D;
104: connectivity[offset + subent_conn[2]] = B;
105: }
106: }
107: else {
108: switch (subelem) { /* 0 1 2 of a QUAD */
109: case 0:
110: connectivity[offset + subent_conn[0]] = A;
111: connectivity[offset + subent_conn[1]] = B;
112: connectivity[offset + subent_conn[2]] = M;
113: break;
114: case 1:
115: connectivity[offset + subent_conn[0]] = B;
116: connectivity[offset + subent_conn[1]] = C;
117: connectivity[offset + subent_conn[2]] = M;
118: break;
119: case 2:
120: connectivity[offset + subent_conn[0]] = C;
121: connectivity[offset + subent_conn[1]] = D;
122: connectivity[offset + subent_conn[2]] = M;
123: break;
124: case 3:
125: connectivity[offset + subent_conn[0]] = D;
126: connectivity[offset + subent_conn[1]] = A;
127: connectivity[offset + subent_conn[2]] = M;
128: break;
129: }
130: }
131: break;
132: case 3:
133: default:
134: C = corner + 1 + genCtx.ystride;
135: D = corner + genCtx.ystride;
136: E = corner + genCtx.zstride;
137: F = corner + 1 + genCtx.zstride;
138: G = corner + 1 + genCtx.ystride + genCtx.zstride;
139: H = corner + genCtx.ystride + genCtx.zstride;
140: subent_conn.resize(4); /* only linear TET supported */
141: moab::CN::SubEntityVertexIndices(moab::MBTET, 3, 0, subent_conn.data());
142: switch (subelem) {
143: case 0: /* 4 3 7 6 of a HEX */
144: connectivity[offset + subent_conn[0]] = E;
145: connectivity[offset + subent_conn[1]] = D;
146: connectivity[offset + subent_conn[2]] = H;
147: connectivity[offset + subent_conn[3]] = G;
148: break;
149: case 1: /* 0 1 2 5 of a HEX */
150: connectivity[offset + subent_conn[0]] = A;
151: connectivity[offset + subent_conn[1]] = B;
152: connectivity[offset + subent_conn[2]] = C;
153: connectivity[offset + subent_conn[3]] = F;
154: break;
155: case 2: /* 0 3 4 5 of a HEX */
156: connectivity[offset + subent_conn[0]] = A;
157: connectivity[offset + subent_conn[1]] = D;
158: connectivity[offset + subent_conn[2]] = E;
159: connectivity[offset + subent_conn[3]] = F;
160: break;
161: case 3: /* 2 6 3 5 of a HEX */
162: connectivity[offset + subent_conn[0]] = C;
163: connectivity[offset + subent_conn[1]] = G;
164: connectivity[offset + subent_conn[2]] = D;
165: connectivity[offset + subent_conn[3]] = F;
166: break;
167: case 4: /* 0 2 3 5 of a HEX */
168: connectivity[offset + subent_conn[0]] = A;
169: connectivity[offset + subent_conn[1]] = C;
170: connectivity[offset + subent_conn[2]] = D;
171: connectivity[offset + subent_conn[3]] = F;
172: break;
173: case 5: /* 3 6 4 5 of a HEX */
174: connectivity[offset + subent_conn[0]] = D;
175: connectivity[offset + subent_conn[1]] = G;
176: connectivity[offset + subent_conn[2]] = E;
177: connectivity[offset + subent_conn[3]] = F;
178: break;
179: }
180: break;
181: }
182: return subent_conn.size();
183: }
186: std::pair<PetscInt, PetscInt> DMMoab_SetElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, PetscInt offset, PetscInt corner, moab::EntityHandle *connectivity)
187: {
188: PetscInt vcount = 0;
189: PetscInt simplices_per_tensor[4] = {0, 1, 2, 6};
190: std::vector<PetscInt> subent_conn; /* only linear edge, tri, tet supported now */
191: subent_conn.reserve(27);
192: PetscInt m, subelem;
193: if (genCtx.simplex) {
194: subelem = simplices_per_tensor[genCtx.dim];
195: for (m = 0; m < subelem; m++) {
196: vcount = DMMoab_SetSimplexElementConnectivity_Private(genCtx, m, offset, corner, subent_conn, connectivity);
197: offset += vcount;
198: }
199: }
200: else {
201: subelem = 1;
202: vcount = DMMoab_SetTensorElementConnectivity_Private(genCtx, offset, corner, subent_conn, connectivity);
203: }
204: return std::pair<PetscInt, PetscInt>(vcount * subelem, subelem);
205: }
208: PetscErrorCode DMMoab_GenerateVertices_Private(moab::Interface *mbImpl, moab::ReadUtilIface *iface, DMMoabMeshGeneratorCtx& genCtx, PetscInt m, PetscInt n, PetscInt k,
209: PetscInt a, PetscInt b, PetscInt c, moab::Tag& global_id_tag, moab::EntityHandle& startv, moab::Range& uverts)
210: {
211: PetscInt x, y, z, ix, nnodes;
213: PetscInt ii, jj, kk;
214: std::vector<PetscReal*> arrays;
215: PetscInt* gids;
216: moab::ErrorCode merr;
219: /* we will generate (q*block+1)^3 vertices, and block^3 hexas; q is 1 for linear, 2 for quadratic
220: * the global id of the vertices will come from m, n, k, a, b, c
221: * x will vary from m*A*q*block + a*q*block to m*A*q*block+(a+1)*q*block etc.
222: */
223: nnodes = genCtx.blockSizeVertexXYZ[0] * (genCtx.dim > 1 ? genCtx.blockSizeVertexXYZ[1] * (genCtx.dim > 2 ? genCtx.blockSizeVertexXYZ[2] : 1) : 1);
224: PetscMalloc1(nnodes, &gids);
226: merr = iface->get_node_coords(3, nnodes, 0, startv, arrays);MBERR("Can't get node coords.", merr);
228: /* will start with the lower corner: */
229: /* x = ( m * genCtx.A + a ) * genCtx.q * genCtx.blockSizeElementXYZ[0]; */
230: /* y = ( n * genCtx.B + b ) * genCtx.q * genCtx.blockSizeElementXYZ[1]; */
231: /* z = ( k * genCtx.C + c ) * genCtx.q * genCtx.blockSizeElementXYZ[2]; */
233: x = ( m * genCtx.A + a ) * genCtx.q;
234: y = ( n * genCtx.B + b ) * genCtx.q;
235: z = ( k * genCtx.C + c ) * genCtx.q;
236: PetscInfo3(NULL, "Starting offset for coordinates := %d, %d, %d\n", x, y, z);
237: ix = 0;
238: moab::Range verts(startv, startv + nnodes - 1);
239: for (kk = 0; kk < (genCtx.dim > 2 ? genCtx.blockSizeVertexXYZ[2] : 1); kk++) {
240: for (jj = 0; jj < (genCtx.dim > 1 ? genCtx.blockSizeVertexXYZ[1] : 1); jj++) {
241: for (ii = 0; ii < genCtx.blockSizeVertexXYZ[0]; ii++, ix++) {
242: /* set coordinates for the vertices */
243: arrays[0][ix] = (x + ii) * genCtx.dx + genCtx.xyzbounds[0];
244: arrays[1][ix] = (y + jj) * genCtx.dy + genCtx.xyzbounds[2];
245: arrays[2][ix] = (z + kk) * genCtx.dz + genCtx.xyzbounds[4];
246: PetscInfo3(NULL, "Creating vertex with coordinates := %f, %f, %f\n", arrays[0][ix], arrays[1][ix], arrays[2][ix]);
248: /* If we want to set some tags on the vertices -> use the following entity handle definition:
249: moab::EntityHandle v = startv + ix;
250: */
251: /* compute the global ID for vertex */
252: gids[ix] = 1 + (x + ii) + (y + jj) * genCtx.NX + (z + kk) * (genCtx.NX * genCtx.NY);
253: }
254: }
255: }
256: /* set global ID data on vertices */
257: mbImpl->tag_set_data(global_id_tag, verts, &gids[0]);
258: verts.swap(uverts);
259: PetscFree(gids);
260: return(0);
261: }
263: PetscErrorCode DMMoab_GenerateElements_Private(moab::Interface* mbImpl, moab::ReadUtilIface* iface, DMMoabMeshGeneratorCtx& genCtx, PetscInt m, PetscInt n, PetscInt k,
264: PetscInt a, PetscInt b, PetscInt c, moab::Tag& global_id_tag, moab::EntityHandle startv, moab::Range& cells)
265: {
266: moab::ErrorCode merr;
267: PetscInt ix, ie, xe, ye, ze;
268: PetscInt ii, jj, kk, nvperelem;
269: PetscInt simplices_per_tensor[4] = {0, 1, 2, 6};
270: PetscInt ntensorelems = genCtx.blockSizeElementXYZ[0] * (genCtx.dim > 1 ? genCtx.blockSizeElementXYZ[1] * (genCtx.dim > 2 ? genCtx.blockSizeElementXYZ[2] : 1) : 1); /*pow(genCtx.blockSizeElement,genCtx.dim);*/
271: PetscInt nelems = ntensorelems;
272: moab::EntityHandle starte; /* connectivity */
273: moab::EntityHandle* conn;
276: switch (genCtx.dim) {
277: case 1:
278: nvperelem = 2;
279: merr = iface->get_element_connect(nelems, 2, moab::MBEDGE, 0, starte, conn);MBERR("Can't get EDGE2 element connectivity.", merr);
280: break;
281: case 2:
282: if (genCtx.simplex) {
283: nvperelem = 3;
284: nelems = ntensorelems * simplices_per_tensor[genCtx.dim];
285: merr = iface->get_element_connect(nelems, 3, moab::MBTRI, 0, starte, conn);MBERR("Can't get TRI3 element connectivity.", merr);
286: }
287: else {
288: nvperelem = 4;
289: merr = iface->get_element_connect(nelems, 4, moab::MBQUAD, 0, starte, conn);MBERR("Can't get QUAD4 element connectivity.", merr);
290: }
291: break;
292: case 3:
293: default:
294: if (genCtx.simplex) {
295: nvperelem = 4;
296: nelems = ntensorelems * simplices_per_tensor[genCtx.dim];
297: merr = iface->get_element_connect(nelems, 4, moab::MBTET, 0, starte, conn);MBERR("Can't get TET4 element connectivity.", merr);
298: }
299: else {
300: nvperelem = 8;
301: merr = iface->get_element_connect(nelems, 8, moab::MBHEX, 0, starte, conn);MBERR("Can't get HEX8 element connectivity.", merr);
302: }
303: break;
304: }
306: ix = ie = 0; /* index now in the elements, for global ids */
308: /* create a temporary range to store local element handles */
309: moab::Range tmp(starte, starte + nelems - 1);
310: std::vector<PetscInt> gids(nelems);
312: /* identify the elements at the lower corner, for their global ids */
313: xe = m * genCtx.A * genCtx.blockSizeElementXYZ[0] + a * genCtx.blockSizeElementXYZ[0];
314: ye = (genCtx.dim > 1 ? n * genCtx.B * genCtx.blockSizeElementXYZ[1] + b * genCtx.blockSizeElementXYZ[1] : 0);
315: ze = (genCtx.dim > 2 ? k * genCtx.C * genCtx.blockSizeElementXYZ[2] + c * genCtx.blockSizeElementXYZ[2] : 0);
317: /* create owned elements requested by genCtx */
318: for (kk = 0; kk < (genCtx.dim > 2 ? genCtx.blockSizeElementXYZ[2] : 1); kk++) {
319: for (jj = 0; jj < (genCtx.dim > 1 ? genCtx.blockSizeElementXYZ[1] : 1); jj++) {
320: for (ii = 0; ii < genCtx.blockSizeElementXYZ[0]; ii++) {
322: moab::EntityHandle corner = startv + genCtx.q * ii + genCtx.q * jj * genCtx.ystride + genCtx.q * kk * genCtx.zstride;
324: std::pair<PetscInt, PetscInt> entoffset = DMMoab_SetElementConnectivity_Private(genCtx, ix, corner, conn);
326: for (PetscInt j = 0; j < entoffset.second; j++) {
327: /* The entity handle for the particular element -> if we want to set some tags is
328: moab::EntityHandle eh = starte + ie + j;
329: */
330: gids[ie + j] = 1 + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney));
331: /* gids[ie+j] = ie + j + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney)); */
332: /* gids[ie+j] = 1 + ie; */
333: /* ie++; */
334: }
336: ix += entoffset.first;
337: ie += entoffset.second;
338: }
339: }
340: }
341: if (genCtx.adjEnts) { /* we need to update adjacencies now, because some elements are new */
342: merr = iface->update_adjacencies(starte, nelems, nvperelem, conn);MBERR("Can't update adjacencies", merr);
343: }
344: tmp.swap(cells);
345: merr = mbImpl->tag_set_data(global_id_tag, cells, &gids[0]);MBERR("Can't set global ids to elements.", merr);
346: return(0);
347: }
349: PetscErrorCode DMMBUtil_InitializeOptions(DMMoabMeshGeneratorCtx& genCtx, PetscInt dim, PetscBool simplex, PetscInt rank, PetscInt nprocs, const PetscReal* bounds, PetscInt nelems)
350: {
352: /* Initialize all genCtx data */
353: genCtx.dim = dim;
354: genCtx.simplex = simplex;
355: genCtx.newMergeMethod = genCtx.keep_skins = genCtx.adjEnts = true;
356: /* determine other global quantities for the mesh used for nodes increments */
357: genCtx.q = 1;
358: genCtx.fraction = genCtx.remainder = genCtx.cumfraction = 0;
360: if (!genCtx.usrxyzgrid) { /* not overridden by genCtx - assume nele equally and that genCtx wants a uniform cube mesh */
362: genCtx.fraction = nelems / nprocs; /* partition only by the largest dimension */
363: genCtx.remainder = nelems % nprocs; /* remainder after partition which gets evenly distributed by round-robin */
364: genCtx.cumfraction = (rank > 0 ? (genCtx.fraction) * (rank) + (rank - 1 < genCtx.remainder ? rank : genCtx.remainder ) : 0);
365: if (rank < genCtx.remainder) /* This process gets "fraction+1" elements */
366: genCtx.fraction++;
368: PetscInfo3(NULL, "Fraction = %D, Remainder = %D, Cumulative fraction = %D\n", genCtx.fraction, genCtx.remainder, genCtx.cumfraction);
369: switch (genCtx.dim) {
370: case 1:
371: genCtx.blockSizeElementXYZ[0] = genCtx.fraction;
372: genCtx.blockSizeElementXYZ[1] = 1;
373: genCtx.blockSizeElementXYZ[2] = 1;
374: break;
375: case 2:
376: genCtx.blockSizeElementXYZ[0] = nelems;
377: genCtx.blockSizeElementXYZ[1] = genCtx.fraction;
378: genCtx.blockSizeElementXYZ[2] = 1;
379: break;
380: case 3:
381: default:
382: genCtx.blockSizeElementXYZ[0] = nelems;
383: genCtx.blockSizeElementXYZ[1] = nelems;
384: genCtx.blockSizeElementXYZ[2] = genCtx.fraction;
385: break;
386: }
387: }
389: /* partition only by the largest dimension */
390: /* Total number of local elements := genCtx.blockSizeElementXYZ[0]*(genCtx.dim>1? genCtx.blockSizeElementXYZ[1]*(genCtx.dim>2 ? genCtx.blockSizeElementXYZ[2]:1) :1); */
391: if (bounds) {
392: for (PetscInt i = 0; i < 6; i++)
393: genCtx.xyzbounds[i] = bounds[i];
394: }
395: else {
396: genCtx.xyzbounds[0] = genCtx.xyzbounds[2] = genCtx.xyzbounds[4] = 0.0;
397: genCtx.xyzbounds[1] = genCtx.xyzbounds[3] = genCtx.xyzbounds[5] = 1.0;
398: }
400: if (!genCtx.usrprocgrid) {
401: switch (genCtx.dim) {
402: case 1:
403: genCtx.M = nprocs;
404: genCtx.N = genCtx.K = 1;
405: break;
406: case 2:
407: genCtx.N = nprocs;
408: genCtx.M = genCtx.K = 1;
409: break;
410: default:
411: genCtx.K = nprocs;
412: genCtx.M = genCtx.N = 1;
413: break;
414: }
415: }
417: if (!genCtx.usrrefgrid) {
418: genCtx.A = genCtx.B = genCtx.C = 1;
419: }
421: /* more default values */
422: genCtx.nex = genCtx.ney = genCtx.nez = 0;
423: genCtx.xstride = genCtx.ystride = genCtx.zstride = 0;
424: genCtx.NX = genCtx.NY = genCtx.NZ = 0;
425: genCtx.nex = genCtx.ney = genCtx.nez = 0;
426: genCtx.blockSizeVertexXYZ[0] = genCtx.blockSizeVertexXYZ[1] = genCtx.blockSizeVertexXYZ[2] = 1;
428: switch (genCtx.dim) {
429: case 3:
430: genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
431: genCtx.blockSizeVertexXYZ[1] = genCtx.q * genCtx.blockSizeElementXYZ[1] + 1;
432: genCtx.blockSizeVertexXYZ[2] = genCtx.q * genCtx.blockSizeElementXYZ[2] + 1;
434: genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0]; /* number of elements in x direction, used for global id on element */
435: genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (nelems * genCtx.q); /* distance between 2 nodes in x direction */
436: genCtx.NX = (genCtx.q * genCtx.nex + 1);
437: genCtx.xstride = 1;
438: genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1]; /* number of elements in y direction .... */
439: genCtx.dy = (genCtx.xyzbounds[3] - genCtx.xyzbounds[2]) / (nelems * genCtx.q); /* distance between 2 nodes in y direction */
440: genCtx.NY = (genCtx.q * genCtx.ney + 1);
441: genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
442: genCtx.nez = genCtx.K * genCtx.C * genCtx.blockSizeElementXYZ[2]; /* number of elements in z direction .... */
443: genCtx.dz = (genCtx.xyzbounds[5] - genCtx.xyzbounds[4]) / (nelems * genCtx.q); /* distance between 2 nodes in z direction */
444: genCtx.NZ = (genCtx.q * genCtx.nez + 1);
445: genCtx.zstride = genCtx.blockSizeVertexXYZ[0] * genCtx.blockSizeVertexXYZ[1];
446: break;
447: case 2:
448: genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
449: genCtx.blockSizeVertexXYZ[1] = genCtx.q * genCtx.blockSizeElementXYZ[1] + 1;
450: genCtx.blockSizeVertexXYZ[2] = 0;
452: genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0]; /* number of elements in x direction, used for global id on element */
453: genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (genCtx.nex * genCtx.q); /* distance between 2 nodes in x direction */
454: genCtx.NX = (genCtx.q * genCtx.nex + 1);
455: genCtx.xstride = 1;
456: genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1]; /* number of elements in y direction .... */
457: genCtx.dy = (genCtx.xyzbounds[3] - genCtx.xyzbounds[2]) / (nelems * genCtx.q); /* distance between 2 nodes in y direction */
458: genCtx.NY = (genCtx.q * genCtx.ney + 1);
459: genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
460: break;
461: case 1:
462: genCtx.blockSizeVertexXYZ[1] = genCtx.blockSizeVertexXYZ[2] = 0;
463: genCtx.blockSizeVertexXYZ[0] = genCtx.q * genCtx.blockSizeElementXYZ[0] + 1;
465: genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0]; /* number of elements in x direction, used for global id on element */
466: genCtx.dx = (genCtx.xyzbounds[1] - genCtx.xyzbounds[0]) / (nelems * genCtx.q); /* distance between 2 nodes in x direction */
467: genCtx.NX = (genCtx.q * genCtx.nex + 1);
468: genCtx.xstride = 1;
469: break;
470: }
472: /* Lets check for some valid input */
473: if (genCtx.dim < 1 || genCtx.dim > 3) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid topological dimension specified: %d.\n", genCtx.dim);
474: if (genCtx.M * genCtx.N * genCtx.K != nprocs) SETERRQ4(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid [m, n, k] data: %d, %d, %d. Product must be equal to global size = %d.\n", genCtx.M, genCtx.N, genCtx.K, nprocs);
475: /* validate the bounds data */
476: if (genCtx.xyzbounds[0] >= genCtx.xyzbounds[1]) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "X-dim: Left boundary cannot be greater than right. [%G >= %G]\n", genCtx.xyzbounds[0], genCtx.xyzbounds[1]);
477: if (genCtx.dim > 1 && (genCtx.xyzbounds[2] >= genCtx.xyzbounds[3])) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Y-dim: Left boundary cannot be greater than right. [%G >= %G]\n", genCtx.xyzbounds[2], genCtx.xyzbounds[3]);
478: if (genCtx.dim > 2 && (genCtx.xyzbounds[4] >= genCtx.xyzbounds[5])) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Z-dim: Left boundary cannot be greater than right. [%G >= %G]\n", genCtx.xyzbounds[4], genCtx.xyzbounds[5]);
480: PetscInfo3(NULL, "Local elements:= %d, %d, %d\n", genCtx.blockSizeElementXYZ[0], genCtx.blockSizeElementXYZ[1], genCtx.blockSizeElementXYZ[2]);
481: PetscInfo3(NULL, "Local vertices:= %d, %d, %d\n", genCtx.blockSizeVertexXYZ[0], genCtx.blockSizeVertexXYZ[1], genCtx.blockSizeVertexXYZ[2]);
482: PetscInfo3(NULL, "Local blocks/processors := %d, %d, %d\n", genCtx.A, genCtx.B, genCtx.C);
483: PetscInfo3(NULL, "Local processors := %d, %d, %d\n", genCtx.M, genCtx.N, genCtx.K);
484: PetscInfo3(NULL, "Local nexyz:= %d, %d, %d\n", genCtx.nex, genCtx.ney, genCtx.nez);
485: PetscInfo3(NULL, "Local delxyz:= %g, %g, %g\n", genCtx.dx, genCtx.dy, genCtx.dz);
486: PetscInfo3(NULL, "Local strides:= %d, %d, %d\n", genCtx.xstride, genCtx.ystride, genCtx.zstride);
487: return(0);
488: }
490: /*@
491: DMMoabCreateBoxMesh - Creates a mesh on the tensor product (box) of intervals with genCtx specified bounds.
493: Collective
495: Input Parameters:
496: + comm - The communicator for the DM object
497: . dim - The spatial dimension
498: . 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
499: . nele - The number of discrete elements in each direction
500: - user_nghost - The number of ghosted layers needed in the partitioned mesh
502: Output Parameter:
503: . dm - The DM object
505: Level: beginner
507: .seealso: DMSetType(), DMCreate(), DMMoabLoadFromFile()
508: @*/
509: PetscErrorCode DMMoabCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool useSimplex, const PetscReal* bounds, PetscInt nele, PetscInt nghost, DM *dm)
510: {
511: PetscErrorCode ierr;
512: moab::ErrorCode merr;
513: PetscInt a, b, c, n, global_size, global_rank;
514: DM_Moab *dmmoab;
515: moab::Interface *mbImpl;
516: #ifdef MOAB_HAVE_MPI
517: moab::ParallelComm *pcomm;
518: #endif
519: moab::ReadUtilIface *readMeshIface;
520: moab::Range verts, cells, edges, faces, adj, dim3, dim2;
521: DMMoabMeshGeneratorCtx genCtx;
522: const PetscInt npts = nele + 1; /* Number of points in every dimension */
524: moab::Tag global_id_tag, part_tag, geom_tag, mat_tag, dir_tag, neu_tag;
525: moab::Range ownedvtx, ownedelms, localvtxs, localelms;
526: moab::EntityHandle regionset;
527: PetscInt ml = 0, nl = 0, kl = 0;
530: if (dim < 1 || dim > 3) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension argument for mesh: dim=[1,3].\n");
532: PetscLogEventRegister("GenerateMesh", DM_CLASSID, &genCtx.generateMesh);
533: PetscLogEventRegister("AddVertices", DM_CLASSID, &genCtx.generateVertices);
534: PetscLogEventRegister("AddElements", DM_CLASSID, &genCtx.generateElements);
535: PetscLogEventRegister("ParResolve", DM_CLASSID, &genCtx.parResolve);
536: PetscLogEventBegin(genCtx.generateMesh, 0, 0, 0, 0);
537: MPI_Comm_size(comm, &global_size);
538: /* total number of vertices in all dimensions */
539: n = pow(npts, dim);
541: /* do some error checking */
542: if (n < 2) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of points must be >= 2.\n");
543: if (global_size > n) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of processors must be less than or equal to number of elements.\n");
544: if (nghost < 0) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Number of ghost layers cannot be negative.\n");
546: /* Create the basic DMMoab object and keep the default parameters created by DM impls */
547: DMMoabCreateMoab(comm, NULL, NULL, NULL, dm);
549: /* get all the necessary handles from the private DM object */
550: dmmoab = (DM_Moab*)(*dm)->data;
551: mbImpl = dmmoab->mbiface;
552: #ifdef MOAB_HAVE_MPI
553: pcomm = dmmoab->pcomm;
554: global_rank = pcomm->rank();
555: #else
556: global_rank = 0;
557: global_size = 1;
558: #endif
559: global_id_tag = dmmoab->ltog_tag;
560: dmmoab->dim = dim;
561: dmmoab->nghostrings = nghost;
562: dmmoab->refct = 1;
564: /* create a file set to associate all entities in current mesh */
565: merr = mbImpl->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);
567: /* No errors yet; proceed with building the mesh */
568: merr = mbImpl->query_interface(readMeshIface);MBERRNM(merr);
570: genCtx.M = genCtx.N = genCtx.K = 1;
571: genCtx.A = genCtx.B = genCtx.C = 1;
572: genCtx.blockSizeElementXYZ[0] = 0;
573: genCtx.blockSizeElementXYZ[1] = 0;
574: genCtx.blockSizeElementXYZ[2] = 0;
576: PetscOptionsBegin(comm, "", "DMMoab Creation Options", "DMMOAB");
577: /* Handle DMMoab spatial resolution */
578: PetscOptionsInt("-dmb_grid_x", "Number of grid points in x direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[0], &genCtx.blockSizeElementXYZ[0], &genCtx.usrxyzgrid);
579: if (dim > 1) {PetscOptionsInt("-dmb_grid_y", "Number of grid points in y direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[1], &genCtx.blockSizeElementXYZ[1], &genCtx.usrxyzgrid);}
580: if (dim > 2) {PetscOptionsInt("-dmb_grid_z", "Number of grid points in z direction", "DMMoabSetSizes", genCtx.blockSizeElementXYZ[2], &genCtx.blockSizeElementXYZ[2], &genCtx.usrxyzgrid);}
582: /* Handle DMMoab parallel distibution */
583: PetscOptionsInt("-dmb_processors_x", "Number of processors in x direction", "DMMoabSetNumProcs", genCtx.M, &genCtx.M, &genCtx.usrprocgrid);
584: if (dim > 1) {PetscOptionsInt("-dmb_processors_y", "Number of processors in y direction", "DMMoabSetNumProcs", genCtx.N, &genCtx.N, &genCtx.usrprocgrid);}
585: if (dim > 2) {PetscOptionsInt("-dmb_processors_z", "Number of processors in z direction", "DMMoabSetNumProcs", genCtx.K, &genCtx.K, &genCtx.usrprocgrid);}
587: /* Handle DMMoab block refinement */
588: PetscOptionsInt("-dmb_refine_x", "Number of refinement blocks in x direction", "DMMoabSetRefinement", genCtx.A, &genCtx.A, &genCtx.usrrefgrid);
589: if (dim > 1) {PetscOptionsInt("-dmb_refine_y", "Number of refinement blocks in y direction", "DMMoabSetRefinement", genCtx.B, &genCtx.B, &genCtx.usrrefgrid);}
590: if (dim > 2) {PetscOptionsInt("-dmb_refine_z", "Number of refinement blocks in z direction", "DMMoabSetRefinement", genCtx.C, &genCtx.C, &genCtx.usrrefgrid);}
591: PetscOptionsEnd();
593: DMMBUtil_InitializeOptions(genCtx, dim, useSimplex, global_rank, global_size, bounds, nele);
595: //if(nele<nprocs) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The dimensional discretization size should be greater or equal to number of processors: %D < %D",nele,nprocs);
597: if (genCtx.adjEnts) genCtx.keep_skins = true; /* do not delete anything - consumes more memory */
599: /* determine m, n, k for processor rank */
600: ml = nl = kl = 0;
601: switch (genCtx.dim) {
602: case 1:
603: ml = (genCtx.cumfraction);
604: break;
605: case 2:
606: nl = (genCtx.cumfraction);
607: break;
608: default:
609: kl = (genCtx.cumfraction) / genCtx.q / genCtx.blockSizeElementXYZ[2] / genCtx.C; //genCtx.K
610: break;
611: }
613: /*
614: * so there are a total of M * A * blockSizeElement elements in x direction (so M * A * blockSizeElement + 1 verts in x direction)
615: * so there are a total of N * B * blockSizeElement elements in y direction (so N * B * blockSizeElement + 1 verts in y direction)
616: * so there are a total of K * C * blockSizeElement elements in z direction (so K * C * blockSizeElement + 1 verts in z direction)
618: * there are ( M * A blockSizeElement ) * ( N * B * blockSizeElement) * (K * C * blockSizeElement ) hexas
619: * there are ( M * A * blockSizeElement + 1) * ( N * B * blockSizeElement + 1 ) * (K * C * blockSizeElement + 1) vertices
620: * x is the first dimension that varies
621: */
623: /* generate the block at (a, b, c); it will represent a partition , it will get a partition tag */
624: PetscInt dum_id = -1;
625: merr = mbImpl->tag_get_handle("GLOBAL_ID", 1, moab::MB_TYPE_INTEGER, global_id_tag);MBERR("Getting Global_ID Tag handle failed", merr);
627: merr = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, mat_tag);MBERR("Getting Material set Tag handle failed", merr);
628: merr = mbImpl->tag_get_handle(DIRICHLET_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, dir_tag);MBERR("Getting Dirichlet set Tag handle failed", merr);
629: merr = mbImpl->tag_get_handle(NEUMANN_SET_TAG_NAME, 1, moab::MB_TYPE_INTEGER, neu_tag);MBERR("Getting Neumann set Tag handle failed", merr);
631: merr = mbImpl->tag_get_handle("PARALLEL_PARTITION", 1, moab::MB_TYPE_INTEGER, part_tag, moab::MB_TAG_CREAT | moab::MB_TAG_SPARSE, &dum_id);MBERR("Getting Partition Tag handle failed", merr);
633: /* lets create some sets */
634: 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);MBERRNM(merr);
635: merr = mbImpl->create_meshset(moab::MESHSET_SET, regionset);MBERRNM(merr);
636: PetscLogEventEnd(genCtx.generateMesh, 0, 0, 0, 0);
638: for (a = 0; a < (genCtx.dim > 0 ? genCtx.A : genCtx.A); a++) {
639: for (b = 0; b < (genCtx.dim > 1 ? genCtx.B : 1); b++) {
640: for (c = 0; c < (genCtx.dim > 2 ? genCtx.C : 1); c++) {
642: moab::EntityHandle startv;
644: PetscLogEventBegin(genCtx.generateVertices, 0, 0, 0, 0);
645: DMMoab_GenerateVertices_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, verts);
646: PetscLogEventEnd(genCtx.generateVertices, 0, 0, 0, 0);
648: PetscLogEventBegin(genCtx.generateElements, 0, 0, 0, 0);
649: DMMoab_GenerateElements_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, cells);
650: PetscLogEventEnd(genCtx.generateElements, 0, 0, 0, 0);
652: PetscInt part_num = 0;
653: switch (genCtx.dim) {
654: case 3:
655: part_num += (c + kl * genCtx.C) * (genCtx.M * genCtx.A * genCtx.N * genCtx.B);
656: case 2:
657: part_num += (b + nl * genCtx.B) * (genCtx.M * genCtx.A);
658: case 1:
659: part_num += (a + ml * genCtx.A);
660: break;
661: }
663: moab::EntityHandle part_set;
664: merr = mbImpl->create_meshset(moab::MESHSET_SET, part_set);MBERR("Can't create mesh set.", merr);
666: merr = mbImpl->add_entities(part_set, verts);MBERR("Can't add vertices to set.", merr);
667: merr = mbImpl->add_entities(part_set, cells);MBERR("Can't add entities to set.", merr);
668: merr = mbImpl->add_entities(regionset, cells);MBERR("Can't add entities to set.", merr);
670: /* if needed, add all edges and faces */
671: if (genCtx.adjEnts)
672: {
673: if (genCtx.dim > 1) {
674: merr = mbImpl->get_adjacencies(cells, 1, true, edges, moab::Interface::UNION);MBERR("Can't get edges", merr);
675: merr = mbImpl->add_entities(part_set, edges);MBERR("Can't add edges to partition set.", merr);
676: }
677: if (genCtx.dim > 2) {
678: merr = mbImpl->get_adjacencies(cells, 2, true, faces, moab::Interface::UNION);MBERR("Can't get faces", merr);
679: merr = mbImpl->add_entities(part_set, faces);MBERR("Can't add faces to partition set.", merr);
680: }
681: edges.clear();
682: faces.clear();
683: }
684: verts.clear(); cells.clear();
686: merr = mbImpl->tag_set_data(part_tag, &part_set, 1, &part_num);MBERR("Can't set part tag on set", merr);
687: if (dmmoab->fileset) {
688: merr = mbImpl->add_parent_child(dmmoab->fileset, part_set);MBERR("Can't add part set to file set.", merr);
689: merr = mbImpl->unite_meshset(dmmoab->fileset, part_set);MBERRNM(merr);
690: }
691: merr = mbImpl->add_entities(dmmoab->fileset, &part_set, 1);MBERRNM(merr);
692: }
693: }
694: }
696: merr = mbImpl->add_parent_child(dmmoab->fileset, regionset);MBERRNM(merr);
698: /* Only in parallel: resolve shared entities between processors and exchange ghost layers */
699: if (global_size > 1) {
701: PetscLogEventBegin(genCtx.parResolve, 0, 0, 0, 0);
703: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, genCtx.dim, cells);MBERR("Can't get all d-dimensional elements.", merr);
704: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 0, verts);MBERR("Can't get all vertices.", merr);
706: if (genCtx.A * genCtx.B * genCtx.C != 1) { // merge needed
707: moab::MergeMesh mm(mbImpl);
708: if (genCtx.newMergeMethod) {
709: merr = mm.merge_using_integer_tag(verts, global_id_tag);MBERR("Can't merge with GLOBAL_ID tag", merr);
710: }
711: else {
712: merr = mm.merge_entities(cells, 0.0001);MBERR("Can't merge with coordinates", merr);
713: }
714: }
716: #ifdef MOAB_HAVE_MPI
717: /* check the handles */
718: merr = pcomm->check_all_shared_handles();MBERRV(mbImpl, merr);
720: /* resolve the shared entities by exchanging information to adjacent processors */
721: merr = pcomm->resolve_shared_ents(dmmoab->fileset, cells, dim, dim - 1, NULL, &global_id_tag);MBERRV(mbImpl, merr);
722: if (dmmoab->fileset) {
723: merr = pcomm->exchange_ghost_cells(dim, 0, nghost, dim, true, false, &dmmoab->fileset);MBERRV(mbImpl, merr);
724: }
725: else {
726: merr = pcomm->exchange_ghost_cells(dim, 0, nghost, dim, true, false);MBERRV(mbImpl, merr);
727: }
729: /* Reassign global IDs on all entities. */
730: merr = pcomm->assign_global_ids(dmmoab->fileset, dim, 1, false, true, false);MBERRNM(merr);
731: #endif
733: PetscLogEventEnd(genCtx.parResolve, 0, 0, 0, 0);
734: }
736: if (!genCtx.keep_skins) { // default is to delete the 1- and 2-dimensional entities
737: // delete all quads and edges
738: moab::Range toDelete;
739: if (genCtx.dim > 1) {
740: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 1, toDelete);MBERR("Can't get edges", merr);
741: }
743: if (genCtx.dim > 2) {
744: merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 2, toDelete);MBERR("Can't get faces", merr);
745: }
747: #ifdef MOAB_HAVE_MPI
748: merr = dmmoab->pcomm->delete_entities(toDelete) ;MBERR("Can't delete entities", merr);
749: #endif
750: }
752: /* set geometric dimension tag for regions */
753: merr = mbImpl->tag_set_data(geom_tag, ®ionset, 1, &dmmoab->dim);MBERRNM(merr);
754: /* set default material ID for regions */
755: int default_material = 1;
756: merr = mbImpl->tag_set_data(mat_tag, ®ionset, 1, &default_material);MBERRNM(merr);
757: /*
758: int default_dbc = 0;
759: merr = mbImpl->tag_set_data(dir_tag, &vertexset, 1, &default_dbc);MBERRNM(merr);
760: */
761: return(0);
762: }
765: 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)
766: {
767: char *ropts;
768: char ropts_par[PETSC_MAX_PATH_LEN], ropts_pargh[PETSC_MAX_PATH_LEN];
769: char ropts_dbg[PETSC_MAX_PATH_LEN];
773: PetscMalloc1(PETSC_MAX_PATH_LEN, &ropts);
774: PetscMemzero(&ropts_par, PETSC_MAX_PATH_LEN);
775: PetscMemzero(&ropts_pargh, PETSC_MAX_PATH_LEN);
776: PetscMemzero(&ropts_dbg, PETSC_MAX_PATH_LEN);
778: /* do parallel read unless using only one processor */
779: if (numproc > 1) {
780: // 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":""));
781: 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;" : ""));
782: if (nghost) {
783: PetscSNPrintf(ropts_pargh, PETSC_MAX_PATH_LEN, "PARALLEL_GHOSTS=%d.0.%d;", dim, nghost);
784: }
785: }
787: if (dbglevel) {
788: if (numproc > 1) {
789: PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "CPUTIME;DEBUG_IO=%d;DEBUG_PIO=%d;", dbglevel, dbglevel);
790: }
791: else {
792: PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "CPUTIME;DEBUG_IO=%d;", dbglevel);
793: }
794: }
796: 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 : ""));
797: *read_opts = ropts;
798: return(0);
799: }
802: /*@
803: DMMoabLoadFromFile - Creates a DM object by loading the mesh from a user specified file.
805: Collective
807: Input Parameters:
808: + comm - The communicator for the DM object
809: . dim - The spatial dimension
810: . filename - The name of the mesh file to be loaded
811: - usrreadopts - The options string to read a MOAB mesh.
813: Reference (Parallel Mesh Initialization: https://www.mcs.anl.gov/~fathom/moab-docs/html/contents.html#fivetwo)
815: Output Parameter:
816: . dm - The DM object
818: Level: beginner
820: .seealso: DMSetType(), DMCreate(), DMMoabCreateBoxMesh()
821: @*/
822: PetscErrorCode DMMoabLoadFromFile(MPI_Comm comm, PetscInt dim, PetscInt nghost, const char* filename, const char* usrreadopts, DM *dm)
823: {
824: moab::ErrorCode merr;
825: PetscInt nprocs;
826: DM_Moab *dmmoab;
827: moab::Interface *mbiface;
828: #ifdef MOAB_HAVE_MPI
829: moab::ParallelComm *pcomm;
830: #endif
831: moab::Range verts, elems;
832: const char *readopts;
833: PetscErrorCode ierr;
838: /* Create the basic DMMoab object and keep the default parameters created by DM impls */
839: DMMoabCreateMoab(comm, NULL, NULL, NULL, dm);
841: /* get all the necessary handles from the private DM object */
842: dmmoab = (DM_Moab*)(*dm)->data;
843: mbiface = dmmoab->mbiface;
844: #ifdef MOAB_HAVE_MPI
845: pcomm = dmmoab->pcomm;
846: nprocs = pcomm->size();
847: #else
848: nprocs = 1;
849: #endif
850: /* TODO: Decipher dimension based on the loaded mesh instead of getting from user */
851: dmmoab->dim = dim;
852: dmmoab->nghostrings = nghost;
853: dmmoab->refct = 1;
855: /* create a file set to associate all entities in current mesh */
856: merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);
858: /* add mesh loading options specific to the DM */
859: DMMoab_GetReadOptions_Private(dmmoab->partition_by_rank, nprocs, dim, nghost, dmmoab->read_mode,
860: dmmoab->rw_dbglevel, dmmoab->extra_read_options, usrreadopts, &readopts);
862: PetscInfo2(*dm, "Reading file %s with options: %s\n", filename, readopts);
864: /* Load the mesh from a file. */
865: if (dmmoab->fileset) {
866: merr = mbiface->load_file(filename, &dmmoab->fileset, readopts);MBERRVM(mbiface, "Reading MOAB file failed.", merr);
867: }
868: else {
869: merr = mbiface->load_file(filename, 0, readopts);MBERRVM(mbiface, "Reading MOAB file failed.", merr);
870: }
872: #ifdef MOAB_HAVE_MPI
873: /* Reassign global IDs on all entities. */
874: /* merr = pcomm->assign_global_ids(dmmoab->fileset, dim, 1, true, true, true);MBERRNM(merr); */
875: #endif
877: /* load the local vertices */
878: merr = mbiface->get_entities_by_type(dmmoab->fileset, moab::MBVERTEX, verts, true);MBERRNM(merr);
879: /* load the local elements */
880: merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, elems, true);MBERRNM(merr);
882: #ifdef MOAB_HAVE_MPI
883: /* Everything is set up, now just do a tag exchange to update tags
884: on all of the ghost vertexes */
885: merr = pcomm->exchange_tags(dmmoab->ltog_tag, verts);MBERRV(mbiface, merr);
886: merr = pcomm->exchange_tags(dmmoab->ltog_tag, elems);MBERRV(mbiface, merr);
887: merr = pcomm->collective_sync_partition();MBERR("Collective sync failed", merr);
888: #endif
890: PetscInfo3(*dm, "MOAB file '%s' was successfully loaded. Found %D vertices and %D elements.\n", filename, verts.size(), elems.size());
891: PetscFree(readopts);
892: return(0);
893: }
896: /*@
897: DMMoabRenumberMeshEntities - Order and number all entities (vertices->elements) to be contiguously ordered
898: in parallel
900: Collective
902: Input Parameters:
903: . dm - The DM object
905: Level: advanced
907: .seealso: DMSetUp(), DMCreate()
908: @*/
909: PetscErrorCode DMMoabRenumberMeshEntities(DM dm)
910: {
911: moab::Range verts;
916: #ifdef MOAB_HAVE_MPI
917: /* Insert new points */
918: moab::ErrorCode merr;
919: merr = ((DM_Moab*) dm->data)->pcomm->assign_global_ids(((DM_Moab*) dm->data)->fileset, 3, 0, false, true, false);MBERRNM(merr);
920: #endif
921: return(0);
922: }