Actual source code: dmmbmg.cxx
1: #include <petsc/private/dmmbimpl.h>
2: #include <petscdmmoab.h>
3: #include <MBTagConventions.hpp>
4: #include <moab/NestedRefine.hpp>
6: /*@C
7: DMMoabGenerateHierarchy - Generate a multi-level uniform refinement hierarchy
8: by succesively refining a coarse mesh, already defined in the DM object
9: provided by the user.
11: Collective
13: Input Parameter:
14: . dmb - The DMMoab object
16: Output Parameters:
17: + nlevels - The number of levels of refinement needed to generate the hierarchy
18: - ldegrees - The degree of refinement at each level in the hierarchy
20: Level: beginner
22: @*/
23: PetscErrorCode DMMoabGenerateHierarchy(DM dm, PetscInt nlevels, PetscInt *ldegrees)
24: {
25: DM_Moab *dmmoab;
26: PetscErrorCode ierr;
27: moab::ErrorCode merr;
28: PetscInt *pdegrees, ilevel;
29: std::vector<moab::EntityHandle> hsets;
33: dmmoab = (DM_Moab*)(dm)->data;
35: if (!ldegrees) {
36: PetscMalloc1(nlevels, &pdegrees);
37: for (ilevel = 0; ilevel < nlevels; ilevel++) pdegrees[ilevel] = 2; /* default = Degree 2 refinement */
38: }
39: else pdegrees = ldegrees;
41: /* initialize set level refinement data for hierarchy */
42: dmmoab->nhlevels = nlevels;
44: /* Instantiate the nested refinement class */
45: #ifdef MOAB_HAVE_MPI
46: dmmoab->hierarchy = new moab::NestedRefine(dynamic_cast<moab::Core*>(dmmoab->mbiface), dmmoab->pcomm, dmmoab->fileset);
47: #else
48: dmmoab->hierarchy = new moab::NestedRefine(dynamic_cast<moab::Core*>(dmmoab->mbiface), NULL, dmmoab->fileset);
49: #endif
51: PetscMalloc1(nlevels + 1, &dmmoab->hsets);
53: /* generate the mesh hierarchy */
54: merr = dmmoab->hierarchy->generate_mesh_hierarchy(nlevels, pdegrees, hsets, false);MBERRNM(merr);
56: #ifdef MOAB_HAVE_MPI
57: if (dmmoab->pcomm->size() > 1) {
58: merr = dmmoab->hierarchy->exchange_ghosts(hsets, dmmoab->nghostrings);MBERRNM(merr);
59: }
60: #endif
62: /* copy the mesh sets for nested refinement hierarchy */
63: dmmoab->hsets[0] = hsets[0];
64: for (ilevel = 1; ilevel <= nlevels; ilevel++)
65: {
66: dmmoab->hsets[ilevel] = hsets[ilevel];
68: #ifdef MOAB_HAVE_MPI
69: merr = dmmoab->pcomm->assign_global_ids(hsets[ilevel], dmmoab->dim, 0, false, true, false);MBERRNM(merr);
70: #endif
72: /* Update material and other geometric tags from parent to child sets */
73: merr = dmmoab->hierarchy->update_special_tags(ilevel, hsets[ilevel]);MBERRNM(merr);
74: }
76: hsets.clear();
77: if (!ldegrees) {
78: PetscFree(pdegrees);
79: }
80: return(0);
81: }
83: /*@C
84: DMRefineHierarchy_Moab - Generate a multi-level DM hierarchy
85: by succesively refining a coarse mesh.
87: Collective
89: Input Parameter:
90: . dm - The DMMoab object
92: Output Parameters:
93: + nlevels - The number of levels of refinement needed to generate the hierarchy
94: - dmf - The DM objects after successive refinement of the hierarchy
96: Level: beginner
98: @*/
99: PETSC_EXTERN PetscErrorCode DMRefineHierarchy_Moab(DM dm, PetscInt nlevels, DM dmf[])
100: {
101: PetscErrorCode ierr;
102: PetscInt i;
106: DMRefine(dm, PetscObjectComm((PetscObject)dm), &dmf[0]);
107: for (i = 1; i < nlevels; i++) {
108: DMRefine(dmf[i - 1], PetscObjectComm((PetscObject)dm), &dmf[i]);
109: }
110: return(0);
111: }
113: /*@C
114: DMCoarsenHierarchy_Moab - Generate a multi-level DM hierarchy
115: by succesively coarsening a refined mesh.
117: Collective
119: Input Parameter:
120: . dm - The DMMoab object
122: Output Parameters:
123: + nlevels - The number of levels of refinement needed to generate the hierarchy
124: - dmc - The DM objects after successive coarsening of the hierarchy
126: Level: beginner
128: @*/
129: PETSC_EXTERN PetscErrorCode DMCoarsenHierarchy_Moab(DM dm, PetscInt nlevels, DM dmc[])
130: {
131: PetscErrorCode ierr;
132: PetscInt i;
136: DMCoarsen(dm, PetscObjectComm((PetscObject)dm), &dmc[0]);
137: for (i = 1; i < nlevels; i++) {
138: DMCoarsen(dmc[i - 1], PetscObjectComm((PetscObject)dm), &dmc[i]);
139: }
140: return(0);
141: }
143: PETSC_EXTERN PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM, PetscInt*, PetscInt*, PetscInt*, PetscInt*, PetscBool);
145: /*@C
146: DMCreateInterpolation_Moab - Generate the interpolation operators to transform
147: operators (matrices, vectors) from parent level to child level as defined by
148: the DM inputs provided by the user.
150: Collective
152: Input Parameters:
153: + dm1 - The DMMoab object
154: - dm2 - the second, finer DMMoab object
156: Output Parameters:
157: + interpl - The interpolation operator for transferring data between the levels
158: - vec - The scaling vector (optional)
160: Level: developer
162: @*/
163: PETSC_EXTERN PetscErrorCode DMCreateInterpolation_Moab(DM dmp, DM dmc, Mat* interpl, Vec* vec)
164: {
165: DM_Moab *dmbp, *dmbc;
166: PetscErrorCode ierr;
167: moab::ErrorCode merr;
168: PetscInt dim;
169: PetscReal factor;
170: PetscInt innz, *nnz, ionz, *onz;
171: PetscInt nlsizp, nlsizc, nlghsizp, ngsizp, ngsizc;
172: const PetscBool use_consistent_bases=PETSC_TRUE;
177: dmbp = (DM_Moab*)(dmp)->data;
178: dmbc = (DM_Moab*)(dmc)->data;
179: nlsizp = dmbp->nloc;// *dmb1->numFields;
180: nlsizc = dmbc->nloc;// *dmb2->numFields;
181: ngsizp = dmbp->n; // *dmb1->numFields;
182: ngsizc = dmbc->n; // *dmb2->numFields;
183: nlghsizp = (dmbp->nloc + dmbp->nghost); // *dmb1->numFields;
185: // Columns = Parent DoFs ; Rows = Child DoFs
186: // Interpolation matrix: \sum_{i=1}^P Owned(Child) * (Owned(Parent) + Ghosted(Parent))
187: // Size: nlsizc * nlghsizp
188: PetscInfo4(NULL, "Creating interpolation matrix %D X %D to apply transformation between levels %D -> %D.\n", ngsizc, nlghsizp, dmbp->hlevel, dmbc->hlevel);
190: DMGetDimension(dmp, &dim);
192: /* allocate the nnz, onz arrays based on block size and local nodes */
193: PetscCalloc2(nlsizc, &nnz, nlsizc, &onz);
195: /* Loop through the local elements and compute the relation between the current parent and the refined_level. */
196: for (moab::Range::iterator iter = dmbc->vowned->begin(); iter != dmbc->vowned->end(); iter++) {
198: const moab::EntityHandle vhandle = *iter;
199: /* define local variables */
200: moab::EntityHandle parent;
201: std::vector<moab::EntityHandle> adjs;
202: moab::Range found;
204: /* store the vertex DoF number */
205: const int ldof = dmbc->lidmap[vhandle - dmbc->seqstart];
207: /* Get adjacency information for current vertex - i.e., all elements of dimension (dim) that connects
208: to the current vertex. We can then decipher if a vertex is ghosted or not and compute the
209: non-zero pattern accordingly. */
210: merr = dmbc->hierarchy->get_adjacencies(vhandle, dmbc->dim, adjs);MBERRNM(merr);
212: /* loop over vertices and update the number of connectivity */
213: for (unsigned jter = 0; jter < adjs.size(); jter++) {
215: const moab::EntityHandle jhandle = adjs[jter];
217: /* Get the relation between the current (coarse) parent and its corresponding (finer) children elements */
218: merr = dmbc->hierarchy->child_to_parent(jhandle, dmbc->hlevel, dmbp->hlevel, &parent);MBERRNM(merr);
220: /* Get connectivity information in canonical ordering for the local element */
221: std::vector<moab::EntityHandle> connp;
222: merr = dmbp->hierarchy->get_connectivity(parent, dmbp->hlevel, connp);MBERRNM(merr);
224: for (unsigned ic=0; ic < connp.size(); ++ic) {
226: /* loop over each element connected to the adjacent vertex and update as needed */
227: /* find the truly user-expected layer of ghosted entities to decipher NNZ pattern */
228: if (found.find(connp[ic]) != found.end()) continue; /* make sure we don't double count shared vertices */
229: if (dmbp->vghost->find(connp[ic]) != dmbp->vghost->end()) onz[ldof]++; /* update out-of-proc onz */
230: else nnz[ldof]++; /* else local vertex */
231: found.insert(connp[ic]);
232: }
233: }
234: }
236: for (int i = 0; i < nlsizc; i++)
237: nnz[i] += 1; /* self count the node */
239: ionz = onz[0];
240: innz = nnz[0];
241: for (int tc = 0; tc < nlsizc; tc++) {
242: // check for maximum allowed sparsity = fully dense
243: nnz[tc] = std::min(nlsizp, nnz[tc]);
244: onz[tc] = std::min(ngsizp - nlsizp, onz[tc]);
246: PetscInfo3(NULL, " %d: NNZ = %d, ONZ = %d\n", tc, nnz[tc], onz[tc]);
248: innz = (innz < nnz[tc] ? nnz[tc] : innz);
249: ionz = (ionz < onz[tc] ? onz[tc] : ionz);
250: }
252: /* create interpolation matrix */
253: MatCreate(PetscObjectComm((PetscObject)dmc), interpl);
254: MatSetSizes(*interpl, nlsizc, nlsizp, ngsizc, ngsizp);
255: MatSetType(*interpl, MATAIJ);
256: MatSetFromOptions(*interpl);
258: MatSeqAIJSetPreallocation(*interpl, innz, nnz);
259: MatMPIAIJSetPreallocation(*interpl, innz, nnz, ionz, onz);
261: /* clean up temporary memory */
262: PetscFree2(nnz, onz);
264: /* set up internal matrix data-structures */
265: MatSetUp(*interpl);
267: /* Define variables for assembly */
268: std::vector<moab::EntityHandle> children;
269: std::vector<moab::EntityHandle> connp, connc;
270: std::vector<PetscReal> pcoords, ccoords, values_phi;
272: if (use_consistent_bases) {
273: const moab::EntityHandle ehandle = dmbp->elocal->front();
275: merr = dmbp->hierarchy->parent_to_child(ehandle, dmbp->hlevel, dmbc->hlevel, children);MBERRNM(merr);
277: /* Get connectivity and coordinates of the parent vertices */
278: merr = dmbp->hierarchy->get_connectivity(ehandle, dmbp->hlevel, connp);MBERRNM(merr);
279: merr = dmbc->mbiface->get_connectivity(&children[0], children.size(), connc);MBERRNM(merr);
281: std::vector<PetscReal> natparam(3*connc.size(), 0.0);
282: pcoords.resize(connp.size() * 3);
283: ccoords.resize(connc.size() * 3);
284: values_phi.resize(connp.size()*connc.size());
285: /* Get coordinates for connectivity entities in canonical order for both coarse and finer levels */
286: merr = dmbp->hierarchy->get_coordinates(&connp[0], connp.size(), dmbp->hlevel, &pcoords[0]);MBERRNM(merr);
287: merr = dmbc->hierarchy->get_coordinates(&connc[0], connc.size(), dmbc->hlevel, &ccoords[0]);MBERRNM(merr);
289: /* Set values: For each DOF in coarse grid cell, set the contribution or PHI evaluated at each fine grid DOF point */
290: for (unsigned tc = 0; tc < connc.size(); tc++) {
291: const PetscInt offset = tc * 3;
293: /* Scale ccoords relative to pcoords */
294: DMMoabPToRMapping(dim, connp.size(), &pcoords[0], &ccoords[offset], &natparam[offset], &values_phi[connp.size()*tc]);
295: }
296: }
297: else {
298: factor = std::pow(2.0 /*degree_P_for_refinement*/, (dmbc->hlevel - dmbp->hlevel) * dmbp->dim * 1.0);
299: }
301: /* TODO: Decipher the correct non-zero pattern. There is still some issue with onz allocation */
302: MatSetOption(*interpl, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
304: /* Loop through the remaining vertices. These vertices appear only on the current refined_level. */
305: for (moab::Range::iterator iter = dmbp->elocal->begin(); iter != dmbp->elocal->end(); iter++) {
307: const moab::EntityHandle ehandle = *iter;
309: /* Get the relation between the current (coarse) parent and its corresponding (finer) children elements */
310: children.clear();
311: connc.clear();
312: merr = dmbp->hierarchy->parent_to_child(ehandle, dmbp->hlevel, dmbc->hlevel, children);MBERRNM(merr);
314: /* Get connectivity and coordinates of the parent vertices */
315: merr = dmbp->hierarchy->get_connectivity(ehandle, dmbp->hlevel, connp);MBERRNM(merr);
316: merr = dmbc->mbiface->get_connectivity(&children[0], children.size(), connc);MBERRNM(merr);
318: pcoords.resize(connp.size() * 3);
319: ccoords.resize(connc.size() * 3);
320: /* Get coordinates for connectivity entities in canonical order for both coarse and finer levels */
321: merr = dmbp->hierarchy->get_coordinates(&connp[0], connp.size(), dmbp->hlevel, &pcoords[0]);MBERRNM(merr);
322: merr = dmbc->hierarchy->get_coordinates(&connc[0], connc.size(), dmbc->hlevel, &ccoords[0]);MBERRNM(merr);
324: std::vector<int> dofsp(connp.size()), dofsc(connc.size());
325: /* TODO: specific to scalar system - use GetDofs */
326: DMMoabGetDofsBlocked(dmp, connp.size(), &connp[0], &dofsp[0]);
327: DMMoabGetDofsBlocked(dmc, connc.size(), &connc[0], &dofsc[0]);
329: /* Compute the actual interpolation weights when projecting solution/residual between levels */
330: if (use_consistent_bases) {
332: /* Use the cached values of natural parameteric coordinates and basis pre-evaluated.
333: We are making an assumption here that UMR used in GMG to generate the hierarchy uses
334: the same template for all elements; This will fail for mixed element meshes (TRI/QUAD).
336: TODO: Fix the above assumption by caching data for families (especially for Tets and mixed meshes)
337: */
339: /* Set values: For each DOF in coarse grid cell, set the contribution or PHI evaluated at each fine grid DOF point */
340: for (unsigned tc = 0; tc < connc.size(); tc++) {
341: /* TODO: Check if we should be using INSERT_VALUES instead */
342: MatSetValues(*interpl, 1, &dofsc[tc], connp.size(), &dofsp[0], &values_phi[connp.size()*tc], ADD_VALUES);
343: }
344: }
345: else {
346: /* Compute the interpolation weights by determining distance of 1-ring
347: neighbor vertices from current vertex
349: This should be used only when FEM basis is not used for the discretization.
350: Else, the consistent interface to compute the basis function for interpolation
351: between the levels should be evaluated correctly to preserve convergence of GMG.
352: Shephard's basis will be terrible for any unsmooth problems.
353: */
354: values_phi.resize(connp.size());
355: for (unsigned tc = 0; tc < connc.size(); tc++) {
357: PetscReal normsum = 0.0;
358: for (unsigned tp = 0; tp < connp.size(); tp++) {
359: values_phi[tp] = 0.0;
360: for (unsigned k = 0; k < 3; k++)
361: values_phi[tp] += std::pow(pcoords[tp * 3 + k] - ccoords[k + tc * 3], dim);
362: if (values_phi[tp] < 1e-12) {
363: values_phi[tp] = 1e12;
364: }
365: else {
366: //values_phi[tp] = std::pow(values_phi[tp], -1.0/dim);
367: values_phi[tp] = std::pow(values_phi[tp], -1.0);
368: normsum += values_phi[tp];
369: }
370: }
371: for (unsigned tp = 0; tp < connp.size(); tp++) {
372: if (values_phi[tp] > 1e11)
373: values_phi[tp] = factor * 0.5 / connp.size();
374: else
375: values_phi[tp] = factor * values_phi[tp] * 0.5 / (connp.size() * normsum);
376: }
377: MatSetValues(*interpl, 1, &dofsc[tc], connp.size(), &dofsp[0], &values_phi[0], ADD_VALUES);
378: }
379: }
380: }
381: if (vec) *vec = NULL;
382: MatAssemblyBegin(*interpl, MAT_FINAL_ASSEMBLY);
383: MatAssemblyEnd(*interpl, MAT_FINAL_ASSEMBLY);
384: return(0);
385: }
387: /*@C
388: DMCreateInjection_Moab - Generate a multi-level uniform refinement hierarchy
389: by succesively refining a coarse mesh, already defined in the DM object
390: provided by the user.
392: Collective
394: Input Parameter:
395: . dmb - The DMMoab object
397: Output Parameters:
398: + nlevels - The number of levels of refinement needed to generate the hierarchy
399: - ldegrees - The degree of refinement at each level in the hierarchy
401: Level: beginner
403: @*/
404: PETSC_EXTERN PetscErrorCode DMCreateInjection_Moab(DM dm1, DM dm2, VecScatter* ctx)
405: {
406: //DM_Moab *dmmoab;
411: //dmmoab = (DM_Moab*)(dm1)->data;
413: PetscPrintf(PETSC_COMM_WORLD, "[DMCreateInjection_Moab] :: Placeholder\n");
414: return(0);
415: }
417: static PetscErrorCode DMMoab_UMR_Private(DM dm, MPI_Comm comm, PetscBool refine, DM *dmref)
418: {
419: PetscErrorCode ierr;
420: PetscInt i, dim;
421: DM dm2;
422: moab::ErrorCode merr;
423: DM_Moab *dmb = (DM_Moab*)dm->data, *dd2;
429: if ((dmb->hlevel == dmb->nhlevels && refine) || (dmb->hlevel == 0 && !refine)) {
430: if (dmb->hlevel + 1 > dmb->nhlevels && refine) PetscInfo2(NULL, "Invalid multigrid refinement hierarchy level specified (%D). MOAB UMR max levels = %D. Creating a NULL object.\n", dmb->hlevel + 1, dmb->nhlevels);
431: if (dmb->hlevel - 1 < 0 && !refine) PetscInfo1(NULL, "Invalid multigrid coarsen hierarchy level specified (%D). Creating a NULL object.\n", dmb->hlevel - 1);
432: *dmref = PETSC_NULL;
433: return(0);
434: }
436: DMMoabCreate(PetscObjectComm((PetscObject)dm), &dm2);
437: dd2 = (DM_Moab*)dm2->data;
439: dd2->mbiface = dmb->mbiface;
440: #ifdef MOAB_HAVE_MPI
441: dd2->pcomm = dmb->pcomm;
442: #endif
443: dd2->icreatedinstance = PETSC_FALSE;
444: dd2->nghostrings = dmb->nghostrings;
446: /* set the new level based on refinement/coarsening */
447: if (refine) {
448: dd2->hlevel = dmb->hlevel + 1;
449: }
450: else {
451: dd2->hlevel = dmb->hlevel - 1;
452: }
454: /* Copy the multilevel hierarchy pointers in MOAB */
455: dd2->hierarchy = dmb->hierarchy;
456: dd2->nhlevels = dmb->nhlevels;
457: PetscMalloc1(dd2->nhlevels + 1, &dd2->hsets);
458: for (i = 0; i <= dd2->nhlevels; i++) {
459: dd2->hsets[i] = dmb->hsets[i];
460: }
461: dd2->fileset = dd2->hsets[dd2->hlevel];
463: /* do the remaining initializations for DMMoab */
464: dd2->bs = dmb->bs;
465: dd2->numFields = dmb->numFields;
466: dd2->rw_dbglevel = dmb->rw_dbglevel;
467: dd2->partition_by_rank = dmb->partition_by_rank;
468: PetscStrcpy(dd2->extra_read_options, dmb->extra_read_options);
469: PetscStrcpy(dd2->extra_write_options, dmb->extra_write_options);
470: dd2->read_mode = dmb->read_mode;
471: dd2->write_mode = dmb->write_mode;
473: /* set global ID tag handle */
474: DMMoabSetLocalToGlobalTag(dm2, dmb->ltog_tag);
476: merr = dd2->mbiface->tag_get_handle(MATERIAL_SET_TAG_NAME, dd2->material_tag);MBERRNM(merr);
478: DMSetOptionsPrefix(dm2, ((PetscObject)dm)->prefix);
479: DMGetDimension(dm, &dim);
480: DMSetDimension(dm2, dim);
482: /* allow overloaded (user replaced) operations to be inherited by refinement clones */
483: dm2->ops->creatematrix = dm->ops->creatematrix;
485: /* copy fill information if given */
486: DMMoabSetBlockFills(dm2, dmb->dfill, dmb->ofill);
488: /* copy vector type information */
489: DMSetMatType(dm2, dm->mattype);
490: DMSetVecType(dm2, dm->vectype);
491: dd2->numFields = dmb->numFields;
492: if (dmb->numFields) {
493: DMMoabSetFieldNames(dm2, dmb->numFields, dmb->fieldNames);
494: }
496: DMSetFromOptions(dm2);
498: /* recreate Dof numbering for the refined DM and make sure the distribution is correctly populated */
499: DMSetUp(dm2);
501: *dmref = dm2;
502: return(0);
503: }
505: /*@C
506: DMRefine_Moab - Generate a multi-level uniform refinement hierarchy
507: by succesively refining a coarse mesh, already defined in the DM object
508: provided by the user.
510: Collective on dm
512: Input Parameters:
513: + dm - The DMMoab object
514: - comm - the communicator to contain the new DM object (or MPI_COMM_NULL)
516: Output Parameter:
517: . dmf - the refined DM, or NULL
519: Note: If no refinement was done, the return value is NULL
521: Level: developer
523: @*/
524: PETSC_EXTERN PetscErrorCode DMRefine_Moab(DM dm, MPI_Comm comm, DM* dmf)
525: {
526: PetscErrorCode ierr;
531: DMMoab_UMR_Private(dm, comm, PETSC_TRUE, dmf);
532: return(0);
533: }
535: /*@C
536: DMCoarsen_Moab - Generate a multi-level uniform refinement hierarchy
537: by succesively refining a coarse mesh, already defined in the DM object
538: provided by the user.
540: Collective on dm
542: Input Parameters:
543: + dm - The DMMoab object
544: - comm - the communicator to contain the new DM object (or MPI_COMM_NULL)
546: Output Parameter:
547: . dmf - the coarsened DM, or NULL
549: Note: If no coarsening was done, the return value is NULL
551: Level: developer
553: @*/
554: PETSC_EXTERN PetscErrorCode DMCoarsen_Moab(DM dm, MPI_Comm comm, DM* dmc)
555: {
556: PetscErrorCode ierr;
561: DMMoab_UMR_Private(dm, comm, PETSC_FALSE, dmc);
562: return(0);
563: }