Actual source code: plextree.c
petsc-3.13.6 2020-09-29
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/petscfeimpl.h>
4: #include <petscsf.h>
5: #include <petscds.h>
7: /** hierarchy routines */
9: /*@
10: DMPlexSetReferenceTree - set the reference tree for hierarchically non-conforming meshes.
12: Not collective
14: Input Parameters:
15: + dm - The DMPlex object
16: - ref - The reference tree DMPlex object
18: Level: intermediate
20: .seealso: DMPlexGetReferenceTree(), DMPlexCreateDefaultReferenceTree()
21: @*/
22: PetscErrorCode DMPlexSetReferenceTree(DM dm, DM ref)
23: {
24: DM_Plex *mesh = (DM_Plex *)dm->data;
25: PetscErrorCode ierr;
30: PetscObjectReference((PetscObject)ref);
31: DMDestroy(&mesh->referenceTree);
32: mesh->referenceTree = ref;
33: return(0);
34: }
36: /*@
37: DMPlexGetReferenceTree - get the reference tree for hierarchically non-conforming meshes.
39: Not collective
41: Input Parameters:
42: . dm - The DMPlex object
44: Output Parameters:
45: . ref - The reference tree DMPlex object
47: Level: intermediate
49: .seealso: DMPlexSetReferenceTree(), DMPlexCreateDefaultReferenceTree()
50: @*/
51: PetscErrorCode DMPlexGetReferenceTree(DM dm, DM *ref)
52: {
53: DM_Plex *mesh = (DM_Plex *)dm->data;
58: *ref = mesh->referenceTree;
59: return(0);
60: }
62: static PetscErrorCode DMPlexReferenceTreeGetChildSymmetry_Default(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
63: {
64: PetscInt coneSize, dStart, dEnd, dim, ABswap, oAvert, oBvert, ABswapVert;
68: if (parentOrientA == parentOrientB) {
69: if (childOrientB) *childOrientB = childOrientA;
70: if (childB) *childB = childA;
71: return(0);
72: }
73: for (dim = 0; dim < 3; dim++) {
74: DMPlexGetDepthStratum(dm,dim,&dStart,&dEnd);
75: if (parent >= dStart && parent <= dEnd) {
76: break;
77: }
78: }
79: if (dim > 2) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot perform child symmetry for %d-cells",dim);
80: if (!dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A vertex has no children");
81: if (childA < dStart || childA >= dEnd) {
82: /* this is a lower-dimensional child: bootstrap */
83: PetscInt size, i, sA = -1, sB, sOrientB, sConeSize;
84: const PetscInt *supp, *coneA, *coneB, *oA, *oB;
86: DMPlexGetSupportSize(dm,childA,&size);
87: DMPlexGetSupport(dm,childA,&supp);
89: /* find a point sA in supp(childA) that has the same parent */
90: for (i = 0; i < size; i++) {
91: PetscInt sParent;
93: sA = supp[i];
94: if (sA == parent) continue;
95: DMPlexGetTreeParent(dm,sA,&sParent,NULL);
96: if (sParent == parent) {
97: break;
98: }
99: }
100: if (i == size) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"could not find support in children");
101: /* find out which point sB is in an equivalent position to sA under
102: * parentOrientB */
103: DMPlexReferenceTreeGetChildSymmetry_Default(dm,parent,parentOrientA,0,sA,parentOrientB,&sOrientB,&sB);
104: DMPlexGetConeSize(dm,sA,&sConeSize);
105: DMPlexGetCone(dm,sA,&coneA);
106: DMPlexGetCone(dm,sB,&coneB);
107: DMPlexGetConeOrientation(dm,sA,&oA);
108: DMPlexGetConeOrientation(dm,sB,&oB);
109: /* step through the cone of sA in natural order */
110: for (i = 0; i < sConeSize; i++) {
111: if (coneA[i] == childA) {
112: /* if childA is at position i in coneA,
113: * then we want the point that is at sOrientB*i in coneB */
114: PetscInt j = (sOrientB >= 0) ? ((sOrientB + i) % sConeSize) : ((sConeSize -(sOrientB+1) - i) % sConeSize);
115: if (childB) *childB = coneB[j];
116: if (childOrientB) {
117: PetscInt oBtrue;
119: DMPlexGetConeSize(dm,childA,&coneSize);
120: /* compose sOrientB and oB[j] */
121: if (coneSize != 0 && coneSize != 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected a vertex or an edge");
122: /* we may have to flip an edge */
123: oBtrue = coneSize ? ((sOrientB >= 0) ? oB[j] : -(oB[j] + 2)) : 0;
124: ABswap = DihedralSwap(coneSize,oA[i],oBtrue);
125: *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
126: }
127: break;
128: }
129: }
130: if (i == sConeSize) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"support cone mismatch");
131: return(0);
132: }
133: /* get the cone size and symmetry swap */
134: DMPlexGetConeSize(dm,parent,&coneSize);
135: ABswap = DihedralSwap(coneSize, parentOrientA, parentOrientB);
136: if (dim == 2) {
137: /* orientations refer to cones: we want them to refer to vertices:
138: * if it's a rotation, they are the same, but if the order is reversed, a
139: * permutation that puts side i first does *not* put vertex i first */
140: oAvert = (parentOrientA >= 0) ? parentOrientA : -((-parentOrientA % coneSize) + 1);
141: oBvert = (parentOrientB >= 0) ? parentOrientB : -((-parentOrientB % coneSize) + 1);
142: ABswapVert = DihedralSwap(coneSize, oAvert, oBvert);
143: } else {
144: ABswapVert = ABswap;
145: }
146: if (childB) {
147: /* assume that each child corresponds to a vertex, in the same order */
148: PetscInt p, posA = -1, numChildren, i;
149: const PetscInt *children;
151: /* count which position the child is in */
152: DMPlexGetTreeChildren(dm,parent,&numChildren,&children);
153: for (i = 0; i < numChildren; i++) {
154: p = children[i];
155: if (p == childA) {
156: posA = i;
157: break;
158: }
159: }
160: if (posA >= coneSize) {
161: /* this is the triangle in the middle of a uniformly refined triangle: it
162: * is invariant */
163: if (dim != 2 || posA != 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Expected a middle triangle, got something else");
164: *childB = childA;
165: }
166: else {
167: /* figure out position B by applying ABswapVert */
168: PetscInt posB;
170: posB = (ABswapVert >= 0) ? ((ABswapVert + posA) % coneSize) : ((coneSize -(ABswapVert + 1) - posA) % coneSize);
171: if (childB) *childB = children[posB];
172: }
173: }
174: if (childOrientB) *childOrientB = DihedralCompose(coneSize,childOrientA,ABswap);
175: return(0);
176: }
178: /*@
179: DMPlexReferenceTreeGetChildSymmetry - Given a reference tree, transform a childid and orientation from one parent frame to another
181: Input Parameters:
182: + dm - the reference tree DMPlex object
183: . parent - the parent point
184: . parentOrientA - the reference orientation for describing the parent
185: . childOrientA - the reference orientation for describing the child
186: . childA - the reference childID for describing the child
187: - parentOrientB - the new orientation for describing the parent
189: Output Parameters:
190: + childOrientB - if not NULL, set to the new oreintation for describing the child
191: - childB - if not NULL, the new childID for describing the child
193: Level: developer
195: .seealso: DMPlexGetReferenceTree(), DMPlexSetReferenceTree(), DMPlexSetTree()
196: @*/
197: PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM dm, PetscInt parent, PetscInt parentOrientA, PetscInt childOrientA, PetscInt childA, PetscInt parentOrientB, PetscInt *childOrientB, PetscInt *childB)
198: {
199: DM_Plex *mesh = (DM_Plex *)dm->data;
204: if (!mesh->getchildsymmetry) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"DMPlexReferenceTreeGetChildSymmetry not implemented");
205: mesh->getchildsymmetry(dm,parent,parentOrientA,childOrientA,childA,parentOrientB,childOrientB,childB);
206: return(0);
207: }
209: static PetscErrorCode DMPlexSetTree_Internal(DM,PetscSection,PetscInt*,PetscInt*,PetscBool,PetscBool);
211: PetscErrorCode DMPlexCreateReferenceTree_SetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[])
212: {
216: DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_TRUE,PETSC_FALSE);
217: return(0);
218: }
220: PetscErrorCode DMPlexCreateReferenceTree_Union(DM K, DM Kref, const char *labelName, DM *ref)
221: {
222: MPI_Comm comm;
223: PetscInt dim, p, pStart, pEnd, pRefStart, pRefEnd, d, offset, parentSize, *parents, *childIDs;
224: PetscInt *permvals, *unionCones, *coneSizes, *unionOrientations, numUnionPoints, *numDimPoints, numCones, numVerts;
225: DMLabel identity, identityRef;
226: PetscSection unionSection, unionConeSection, parentSection;
227: PetscScalar *unionCoords;
228: IS perm;
232: comm = PetscObjectComm((PetscObject)K);
233: DMGetDimension(K, &dim);
234: DMPlexGetChart(K, &pStart, &pEnd);
235: DMGetLabel(K, labelName, &identity);
236: DMGetLabel(Kref, labelName, &identityRef);
237: DMPlexGetChart(Kref, &pRefStart, &pRefEnd);
238: PetscSectionCreate(comm, &unionSection);
239: PetscSectionSetChart(unionSection, 0, (pEnd - pStart) + (pRefEnd - pRefStart));
240: /* count points that will go in the union */
241: for (p = pStart; p < pEnd; p++) {
242: PetscSectionSetDof(unionSection, p - pStart, 1);
243: }
244: for (p = pRefStart; p < pRefEnd; p++) {
245: PetscInt q, qSize;
246: DMLabelGetValue(identityRef, p, &q);
247: DMLabelGetStratumSize(identityRef, q, &qSize);
248: if (qSize > 1) {
249: PetscSectionSetDof(unionSection, p - pRefStart + (pEnd - pStart), 1);
250: }
251: }
252: PetscMalloc1(pEnd - pStart + pRefEnd - pRefStart,&permvals);
253: offset = 0;
254: /* stratify points in the union by topological dimension */
255: for (d = 0; d <= dim; d++) {
256: PetscInt cStart, cEnd, c;
258: DMPlexGetHeightStratum(K, d, &cStart, &cEnd);
259: for (c = cStart; c < cEnd; c++) {
260: permvals[offset++] = c;
261: }
263: DMPlexGetHeightStratum(Kref, d, &cStart, &cEnd);
264: for (c = cStart; c < cEnd; c++) {
265: permvals[offset++] = c + (pEnd - pStart);
266: }
267: }
268: ISCreateGeneral(comm, (pEnd - pStart) + (pRefEnd - pRefStart), permvals, PETSC_OWN_POINTER, &perm);
269: PetscSectionSetPermutation(unionSection,perm);
270: PetscSectionSetUp(unionSection);
271: PetscSectionGetStorageSize(unionSection,&numUnionPoints);
272: PetscMalloc2(numUnionPoints,&coneSizes,dim+1,&numDimPoints);
273: /* count dimension points */
274: for (d = 0; d <= dim; d++) {
275: PetscInt cStart, cOff, cOff2;
276: DMPlexGetHeightStratum(K,d,&cStart,NULL);
277: PetscSectionGetOffset(unionSection,cStart-pStart,&cOff);
278: if (d < dim) {
279: DMPlexGetHeightStratum(K,d+1,&cStart,NULL);
280: PetscSectionGetOffset(unionSection,cStart-pStart,&cOff2);
281: }
282: else {
283: cOff2 = numUnionPoints;
284: }
285: numDimPoints[dim - d] = cOff2 - cOff;
286: }
287: PetscSectionCreate(comm, &unionConeSection);
288: PetscSectionSetChart(unionConeSection, 0, numUnionPoints);
289: /* count the cones in the union */
290: for (p = pStart; p < pEnd; p++) {
291: PetscInt dof, uOff;
293: DMPlexGetConeSize(K, p, &dof);
294: PetscSectionGetOffset(unionSection, p - pStart,&uOff);
295: PetscSectionSetDof(unionConeSection, uOff, dof);
296: coneSizes[uOff] = dof;
297: }
298: for (p = pRefStart; p < pRefEnd; p++) {
299: PetscInt dof, uDof, uOff;
301: DMPlexGetConeSize(Kref, p, &dof);
302: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
303: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
304: if (uDof) {
305: PetscSectionSetDof(unionConeSection, uOff, dof);
306: coneSizes[uOff] = dof;
307: }
308: }
309: PetscSectionSetUp(unionConeSection);
310: PetscSectionGetStorageSize(unionConeSection,&numCones);
311: PetscMalloc2(numCones,&unionCones,numCones,&unionOrientations);
312: /* write the cones in the union */
313: for (p = pStart; p < pEnd; p++) {
314: PetscInt dof, uOff, c, cOff;
315: const PetscInt *cone, *orientation;
317: DMPlexGetConeSize(K, p, &dof);
318: DMPlexGetCone(K, p, &cone);
319: DMPlexGetConeOrientation(K, p, &orientation);
320: PetscSectionGetOffset(unionSection, p - pStart,&uOff);
321: PetscSectionGetOffset(unionConeSection,uOff,&cOff);
322: for (c = 0; c < dof; c++) {
323: PetscInt e, eOff;
324: e = cone[c];
325: PetscSectionGetOffset(unionSection, e - pStart, &eOff);
326: unionCones[cOff + c] = eOff;
327: unionOrientations[cOff + c] = orientation[c];
328: }
329: }
330: for (p = pRefStart; p < pRefEnd; p++) {
331: PetscInt dof, uDof, uOff, c, cOff;
332: const PetscInt *cone, *orientation;
334: DMPlexGetConeSize(Kref, p, &dof);
335: DMPlexGetCone(Kref, p, &cone);
336: DMPlexGetConeOrientation(Kref, p, &orientation);
337: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
338: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
339: if (uDof) {
340: PetscSectionGetOffset(unionConeSection,uOff,&cOff);
341: for (c = 0; c < dof; c++) {
342: PetscInt e, eOff, eDof;
344: e = cone[c];
345: PetscSectionGetDof(unionSection, e - pRefStart + (pEnd - pStart),&eDof);
346: if (eDof) {
347: PetscSectionGetOffset(unionSection, e - pRefStart + (pEnd - pStart), &eOff);
348: }
349: else {
350: DMLabelGetValue(identityRef, e, &e);
351: PetscSectionGetOffset(unionSection, e - pStart, &eOff);
352: }
353: unionCones[cOff + c] = eOff;
354: unionOrientations[cOff + c] = orientation[c];
355: }
356: }
357: }
358: /* get the coordinates */
359: {
360: PetscInt vStart, vEnd, vRefStart, vRefEnd, v, vDof, vOff;
361: PetscSection KcoordsSec, KrefCoordsSec;
362: Vec KcoordsVec, KrefCoordsVec;
363: PetscScalar *Kcoords;
365: DMGetCoordinateSection(K, &KcoordsSec);
366: DMGetCoordinatesLocal(K, &KcoordsVec);
367: DMGetCoordinateSection(Kref, &KrefCoordsSec);
368: DMGetCoordinatesLocal(Kref, &KrefCoordsVec);
370: numVerts = numDimPoints[0];
371: PetscMalloc1(numVerts * dim,&unionCoords);
372: DMPlexGetDepthStratum(K,0,&vStart,&vEnd);
374: offset = 0;
375: for (v = vStart; v < vEnd; v++) {
376: PetscSectionGetOffset(unionSection,v - pStart,&vOff);
377: VecGetValuesSection(KcoordsVec, KcoordsSec, v, &Kcoords);
378: for (d = 0; d < dim; d++) {
379: unionCoords[offset * dim + d] = Kcoords[d];
380: }
381: offset++;
382: }
383: DMPlexGetDepthStratum(Kref,0,&vRefStart,&vRefEnd);
384: for (v = vRefStart; v < vRefEnd; v++) {
385: PetscSectionGetDof(unionSection,v - pRefStart + (pEnd - pStart),&vDof);
386: PetscSectionGetOffset(unionSection,v - pRefStart + (pEnd - pStart),&vOff);
387: VecGetValuesSection(KrefCoordsVec, KrefCoordsSec, v, &Kcoords);
388: if (vDof) {
389: for (d = 0; d < dim; d++) {
390: unionCoords[offset * dim + d] = Kcoords[d];
391: }
392: offset++;
393: }
394: }
395: }
396: DMCreate(comm,ref);
397: DMSetType(*ref,DMPLEX);
398: DMSetDimension(*ref,dim);
399: DMPlexCreateFromDAG(*ref,dim,numDimPoints,coneSizes,unionCones,unionOrientations,unionCoords);
400: /* set the tree */
401: PetscSectionCreate(comm,&parentSection);
402: PetscSectionSetChart(parentSection,0,numUnionPoints);
403: for (p = pRefStart; p < pRefEnd; p++) {
404: PetscInt uDof, uOff;
406: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
407: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
408: if (uDof) {
409: PetscSectionSetDof(parentSection,uOff,1);
410: }
411: }
412: PetscSectionSetUp(parentSection);
413: PetscSectionGetStorageSize(parentSection,&parentSize);
414: PetscMalloc2(parentSize,&parents,parentSize,&childIDs);
415: for (p = pRefStart; p < pRefEnd; p++) {
416: PetscInt uDof, uOff;
418: PetscSectionGetDof(unionSection, p - pRefStart + (pEnd - pStart),&uDof);
419: PetscSectionGetOffset(unionSection, p - pRefStart + (pEnd - pStart),&uOff);
420: if (uDof) {
421: PetscInt pOff, parent, parentU;
422: PetscSectionGetOffset(parentSection,uOff,&pOff);
423: DMLabelGetValue(identityRef,p,&parent);
424: PetscSectionGetOffset(unionSection, parent - pStart,&parentU);
425: parents[pOff] = parentU;
426: childIDs[pOff] = uOff;
427: }
428: }
429: DMPlexCreateReferenceTree_SetTree(*ref,parentSection,parents,childIDs);
430: PetscSectionDestroy(&parentSection);
431: PetscFree2(parents,childIDs);
433: /* clean up */
434: PetscSectionDestroy(&unionSection);
435: PetscSectionDestroy(&unionConeSection);
436: ISDestroy(&perm);
437: PetscFree(unionCoords);
438: PetscFree2(unionCones,unionOrientations);
439: PetscFree2(coneSizes,numDimPoints);
440: return(0);
441: }
443: /*@
444: DMPlexCreateDefaultReferenceTree - create a reference tree for isotropic hierarchical mesh refinement.
446: Collective
448: Input Parameters:
449: + comm - the MPI communicator
450: . dim - the spatial dimension
451: - simplex - Flag for simplex, otherwise use a tensor-product cell
453: Output Parameters:
454: . ref - the reference tree DMPlex object
456: Level: intermediate
458: .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree()
459: @*/
460: PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *ref)
461: {
462: DM_Plex *mesh;
463: DM K, Kref;
464: PetscInt p, pStart, pEnd;
465: DMLabel identity;
469: #if 1
470: comm = PETSC_COMM_SELF;
471: #endif
472: /* create a reference element */
473: DMPlexCreateReferenceCell(comm, dim, simplex, &K);
474: DMCreateLabel(K, "identity");
475: DMGetLabel(K, "identity", &identity);
476: DMPlexGetChart(K, &pStart, &pEnd);
477: for (p = pStart; p < pEnd; p++) {
478: DMLabelSetValue(identity, p, p);
479: }
480: /* refine it */
481: DMRefine(K,comm,&Kref);
483: /* the reference tree is the union of these two, without duplicating
484: * points that appear in both */
485: DMPlexCreateReferenceTree_Union(K, Kref, "identity", ref);
486: mesh = (DM_Plex *) (*ref)->data;
487: mesh->getchildsymmetry = DMPlexReferenceTreeGetChildSymmetry_Default;
488: DMDestroy(&K);
489: DMDestroy(&Kref);
490: return(0);
491: }
493: static PetscErrorCode DMPlexTreeSymmetrize(DM dm)
494: {
495: DM_Plex *mesh = (DM_Plex *)dm->data;
496: PetscSection childSec, pSec;
497: PetscInt p, pSize, cSize, parMax = PETSC_MIN_INT, parMin = PETSC_MAX_INT;
498: PetscInt *offsets, *children, pStart, pEnd;
503: PetscSectionDestroy(&mesh->childSection);
504: PetscFree(mesh->children);
505: pSec = mesh->parentSection;
506: if (!pSec) return(0);
507: PetscSectionGetStorageSize(pSec,&pSize);
508: for (p = 0; p < pSize; p++) {
509: PetscInt par = mesh->parents[p];
511: parMax = PetscMax(parMax,par+1);
512: parMin = PetscMin(parMin,par);
513: }
514: if (parMin > parMax) {
515: parMin = -1;
516: parMax = -1;
517: }
518: PetscSectionCreate(PetscObjectComm((PetscObject)pSec),&childSec);
519: PetscSectionSetChart(childSec,parMin,parMax);
520: for (p = 0; p < pSize; p++) {
521: PetscInt par = mesh->parents[p];
523: PetscSectionAddDof(childSec,par,1);
524: }
525: PetscSectionSetUp(childSec);
526: PetscSectionGetStorageSize(childSec,&cSize);
527: PetscMalloc1(cSize,&children);
528: PetscCalloc1(parMax-parMin,&offsets);
529: PetscSectionGetChart(pSec,&pStart,&pEnd);
530: for (p = pStart; p < pEnd; p++) {
531: PetscInt dof, off, i;
533: PetscSectionGetDof(pSec,p,&dof);
534: PetscSectionGetOffset(pSec,p,&off);
535: for (i = 0; i < dof; i++) {
536: PetscInt par = mesh->parents[off + i], cOff;
538: PetscSectionGetOffset(childSec,par,&cOff);
539: children[cOff + offsets[par-parMin]++] = p;
540: }
541: }
542: mesh->childSection = childSec;
543: mesh->children = children;
544: PetscFree(offsets);
545: return(0);
546: }
548: static PetscErrorCode AnchorsFlatten (PetscSection section, IS is, PetscSection *sectionNew, IS *isNew)
549: {
550: PetscInt pStart, pEnd, size, sizeNew, i, p, *valsNew = NULL;
551: const PetscInt *vals;
552: PetscSection secNew;
553: PetscBool anyNew, globalAnyNew;
554: PetscBool compress;
558: PetscSectionGetChart(section,&pStart,&pEnd);
559: ISGetLocalSize(is,&size);
560: ISGetIndices(is,&vals);
561: PetscSectionCreate(PetscObjectComm((PetscObject)section),&secNew);
562: PetscSectionSetChart(secNew,pStart,pEnd);
563: for (i = 0; i < size; i++) {
564: PetscInt dof;
566: p = vals[i];
567: if (p < pStart || p >= pEnd) continue;
568: PetscSectionGetDof(section, p, &dof);
569: if (dof) break;
570: }
571: if (i == size) {
572: PetscSectionSetUp(secNew);
573: anyNew = PETSC_FALSE;
574: compress = PETSC_FALSE;
575: sizeNew = 0;
576: }
577: else {
578: anyNew = PETSC_TRUE;
579: for (p = pStart; p < pEnd; p++) {
580: PetscInt dof, off;
582: PetscSectionGetDof(section, p, &dof);
583: PetscSectionGetOffset(section, p, &off);
584: for (i = 0; i < dof; i++) {
585: PetscInt q = vals[off + i], qDof = 0;
587: if (q >= pStart && q < pEnd) {
588: PetscSectionGetDof(section, q, &qDof);
589: }
590: if (qDof) {
591: PetscSectionAddDof(secNew, p, qDof);
592: }
593: else {
594: PetscSectionAddDof(secNew, p, 1);
595: }
596: }
597: }
598: PetscSectionSetUp(secNew);
599: PetscSectionGetStorageSize(secNew,&sizeNew);
600: PetscMalloc1(sizeNew,&valsNew);
601: compress = PETSC_FALSE;
602: for (p = pStart; p < pEnd; p++) {
603: PetscInt dof, off, count, offNew, dofNew;
605: PetscSectionGetDof(section, p, &dof);
606: PetscSectionGetOffset(section, p, &off);
607: PetscSectionGetDof(secNew, p, &dofNew);
608: PetscSectionGetOffset(secNew, p, &offNew);
609: count = 0;
610: for (i = 0; i < dof; i++) {
611: PetscInt q = vals[off + i], qDof = 0, qOff = 0, j;
613: if (q >= pStart && q < pEnd) {
614: PetscSectionGetDof(section, q, &qDof);
615: PetscSectionGetOffset(section, q, &qOff);
616: }
617: if (qDof) {
618: PetscInt oldCount = count;
620: for (j = 0; j < qDof; j++) {
621: PetscInt k, r = vals[qOff + j];
623: for (k = 0; k < oldCount; k++) {
624: if (valsNew[offNew + k] == r) {
625: break;
626: }
627: }
628: if (k == oldCount) {
629: valsNew[offNew + count++] = r;
630: }
631: }
632: }
633: else {
634: PetscInt k, oldCount = count;
636: for (k = 0; k < oldCount; k++) {
637: if (valsNew[offNew + k] == q) {
638: break;
639: }
640: }
641: if (k == oldCount) {
642: valsNew[offNew + count++] = q;
643: }
644: }
645: }
646: if (count < dofNew) {
647: PetscSectionSetDof(secNew, p, count);
648: compress = PETSC_TRUE;
649: }
650: }
651: }
652: ISRestoreIndices(is,&vals);
653: MPIU_Allreduce(&anyNew,&globalAnyNew,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
654: if (!globalAnyNew) {
655: PetscSectionDestroy(&secNew);
656: *sectionNew = NULL;
657: *isNew = NULL;
658: }
659: else {
660: PetscBool globalCompress;
662: MPIU_Allreduce(&compress,&globalCompress,1,MPIU_BOOL,MPI_LOR,PetscObjectComm((PetscObject)secNew));
663: if (compress) {
664: PetscSection secComp;
665: PetscInt *valsComp = NULL;
667: PetscSectionCreate(PetscObjectComm((PetscObject)section),&secComp);
668: PetscSectionSetChart(secComp,pStart,pEnd);
669: for (p = pStart; p < pEnd; p++) {
670: PetscInt dof;
672: PetscSectionGetDof(secNew, p, &dof);
673: PetscSectionSetDof(secComp, p, dof);
674: }
675: PetscSectionSetUp(secComp);
676: PetscSectionGetStorageSize(secComp,&sizeNew);
677: PetscMalloc1(sizeNew,&valsComp);
678: for (p = pStart; p < pEnd; p++) {
679: PetscInt dof, off, offNew, j;
681: PetscSectionGetDof(secNew, p, &dof);
682: PetscSectionGetOffset(secNew, p, &off);
683: PetscSectionGetOffset(secComp, p, &offNew);
684: for (j = 0; j < dof; j++) {
685: valsComp[offNew + j] = valsNew[off + j];
686: }
687: }
688: PetscSectionDestroy(&secNew);
689: secNew = secComp;
690: PetscFree(valsNew);
691: valsNew = valsComp;
692: }
693: ISCreateGeneral(PetscObjectComm((PetscObject)is),sizeNew,valsNew,PETSC_OWN_POINTER,isNew);
694: }
695: return(0);
696: }
698: static PetscErrorCode DMPlexCreateAnchors_Tree(DM dm)
699: {
700: PetscInt p, pStart, pEnd, *anchors, size;
701: PetscInt aMin = PETSC_MAX_INT, aMax = PETSC_MIN_INT;
702: PetscSection aSec;
703: DMLabel canonLabel;
704: IS aIS;
709: DMPlexGetChart(dm,&pStart,&pEnd);
710: DMGetLabel(dm,"canonical",&canonLabel);
711: for (p = pStart; p < pEnd; p++) {
712: PetscInt parent;
714: if (canonLabel) {
715: PetscInt canon;
717: DMLabelGetValue(canonLabel,p,&canon);
718: if (p != canon) continue;
719: }
720: DMPlexGetTreeParent(dm,p,&parent,NULL);
721: if (parent != p) {
722: aMin = PetscMin(aMin,p);
723: aMax = PetscMax(aMax,p+1);
724: }
725: }
726: if (aMin > aMax) {
727: aMin = -1;
728: aMax = -1;
729: }
730: PetscSectionCreate(PETSC_COMM_SELF,&aSec);
731: PetscSectionSetChart(aSec,aMin,aMax);
732: for (p = aMin; p < aMax; p++) {
733: PetscInt parent, ancestor = p;
735: if (canonLabel) {
736: PetscInt canon;
738: DMLabelGetValue(canonLabel,p,&canon);
739: if (p != canon) continue;
740: }
741: DMPlexGetTreeParent(dm,p,&parent,NULL);
742: while (parent != ancestor) {
743: ancestor = parent;
744: DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
745: }
746: if (ancestor != p) {
747: PetscInt closureSize, *closure = NULL;
749: DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
750: PetscSectionSetDof(aSec,p,closureSize);
751: DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
752: }
753: }
754: PetscSectionSetUp(aSec);
755: PetscSectionGetStorageSize(aSec,&size);
756: PetscMalloc1(size,&anchors);
757: for (p = aMin; p < aMax; p++) {
758: PetscInt parent, ancestor = p;
760: if (canonLabel) {
761: PetscInt canon;
763: DMLabelGetValue(canonLabel,p,&canon);
764: if (p != canon) continue;
765: }
766: DMPlexGetTreeParent(dm,p,&parent,NULL);
767: while (parent != ancestor) {
768: ancestor = parent;
769: DMPlexGetTreeParent(dm,ancestor,&parent,NULL);
770: }
771: if (ancestor != p) {
772: PetscInt j, closureSize, *closure = NULL, aOff;
774: PetscSectionGetOffset(aSec,p,&aOff);
776: DMPlexGetTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
777: for (j = 0; j < closureSize; j++) {
778: anchors[aOff + j] = closure[2*j];
779: }
780: DMPlexRestoreTransitiveClosure(dm,ancestor,PETSC_TRUE,&closureSize,&closure);
781: }
782: }
783: ISCreateGeneral(PETSC_COMM_SELF,size,anchors,PETSC_OWN_POINTER,&aIS);
784: {
785: PetscSection aSecNew = aSec;
786: IS aISNew = aIS;
788: PetscObjectReference((PetscObject)aSec);
789: PetscObjectReference((PetscObject)aIS);
790: while (aSecNew) {
791: PetscSectionDestroy(&aSec);
792: ISDestroy(&aIS);
793: aSec = aSecNew;
794: aIS = aISNew;
795: aSecNew = NULL;
796: aISNew = NULL;
797: AnchorsFlatten(aSec,aIS,&aSecNew,&aISNew);
798: }
799: }
800: DMPlexSetAnchors(dm,aSec,aIS);
801: PetscSectionDestroy(&aSec);
802: ISDestroy(&aIS);
803: return(0);
804: }
806: static PetscErrorCode DMPlexGetTrueSupportSize(DM dm,PetscInt p,PetscInt *dof,PetscInt *numTrueSupp)
807: {
811: if (numTrueSupp[p] == -1) {
812: PetscInt i, alldof;
813: const PetscInt *supp;
814: PetscInt count = 0;
816: DMPlexGetSupportSize(dm,p,&alldof);
817: DMPlexGetSupport(dm,p,&supp);
818: for (i = 0; i < alldof; i++) {
819: PetscInt q = supp[i], numCones, j;
820: const PetscInt *cone;
822: DMPlexGetConeSize(dm,q,&numCones);
823: DMPlexGetCone(dm,q,&cone);
824: for (j = 0; j < numCones; j++) {
825: if (cone[j] == p) break;
826: }
827: if (j < numCones) count++;
828: }
829: numTrueSupp[p] = count;
830: }
831: *dof = numTrueSupp[p];
832: return(0);
833: }
835: static PetscErrorCode DMPlexTreeExchangeSupports(DM dm)
836: {
837: DM_Plex *mesh = (DM_Plex *)dm->data;
838: PetscSection newSupportSection;
839: PetscInt newSize, *newSupports, pStart, pEnd, p, d, depth;
840: PetscInt *numTrueSupp;
841: PetscInt *offsets;
846: /* symmetrize the hierarchy */
847: DMPlexGetDepth(dm,&depth);
848: PetscSectionCreate(PetscObjectComm((PetscObject)(mesh->supportSection)),&newSupportSection);
849: DMPlexGetChart(dm,&pStart,&pEnd);
850: PetscSectionSetChart(newSupportSection,pStart,pEnd);
851: PetscCalloc1(pEnd,&offsets);
852: PetscMalloc1(pEnd,&numTrueSupp);
853: for (p = 0; p < pEnd; p++) numTrueSupp[p] = -1;
854: /* if a point is in the (true) support of q, it should be in the support of
855: * parent(q) */
856: for (d = 0; d <= depth; d++) {
857: DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
858: for (p = pStart; p < pEnd; ++p) {
859: PetscInt dof, q, qdof, parent;
861: DMPlexGetTrueSupportSize(dm,p,&dof,numTrueSupp);
862: PetscSectionAddDof(newSupportSection, p, dof);
863: q = p;
864: DMPlexGetTreeParent(dm,q,&parent,NULL);
865: while (parent != q && parent >= pStart && parent < pEnd) {
866: q = parent;
868: DMPlexGetTrueSupportSize(dm,q,&qdof,numTrueSupp);
869: PetscSectionAddDof(newSupportSection,p,qdof);
870: PetscSectionAddDof(newSupportSection,q,dof);
871: DMPlexGetTreeParent(dm,q,&parent,NULL);
872: }
873: }
874: }
875: PetscSectionSetUp(newSupportSection);
876: PetscSectionGetStorageSize(newSupportSection,&newSize);
877: PetscMalloc1(newSize,&newSupports);
878: for (d = 0; d <= depth; d++) {
879: DMPlexGetHeightStratum(dm,d,&pStart,&pEnd);
880: for (p = pStart; p < pEnd; p++) {
881: PetscInt dof, off, q, qdof, qoff, newDof, newOff, newqOff, i, parent;
883: PetscSectionGetDof(mesh->supportSection, p, &dof);
884: PetscSectionGetOffset(mesh->supportSection, p, &off);
885: PetscSectionGetDof(newSupportSection, p, &newDof);
886: PetscSectionGetOffset(newSupportSection, p, &newOff);
887: for (i = 0; i < dof; i++) {
888: PetscInt numCones, j;
889: const PetscInt *cone;
890: PetscInt q = mesh->supports[off + i];
892: DMPlexGetConeSize(dm,q,&numCones);
893: DMPlexGetCone(dm,q,&cone);
894: for (j = 0; j < numCones; j++) {
895: if (cone[j] == p) break;
896: }
897: if (j < numCones) newSupports[newOff+offsets[p]++] = q;
898: }
899: mesh->maxSupportSize = PetscMax(mesh->maxSupportSize,newDof);
901: q = p;
902: DMPlexGetTreeParent(dm,q,&parent,NULL);
903: while (parent != q && parent >= pStart && parent < pEnd) {
904: q = parent;
905: PetscSectionGetDof(mesh->supportSection, q, &qdof);
906: PetscSectionGetOffset(mesh->supportSection, q, &qoff);
907: PetscSectionGetOffset(newSupportSection, q, &newqOff);
908: for (i = 0; i < qdof; i++) {
909: PetscInt numCones, j;
910: const PetscInt *cone;
911: PetscInt r = mesh->supports[qoff + i];
913: DMPlexGetConeSize(dm,r,&numCones);
914: DMPlexGetCone(dm,r,&cone);
915: for (j = 0; j < numCones; j++) {
916: if (cone[j] == q) break;
917: }
918: if (j < numCones) newSupports[newOff+offsets[p]++] = r;
919: }
920: for (i = 0; i < dof; i++) {
921: PetscInt numCones, j;
922: const PetscInt *cone;
923: PetscInt r = mesh->supports[off + i];
925: DMPlexGetConeSize(dm,r,&numCones);
926: DMPlexGetCone(dm,r,&cone);
927: for (j = 0; j < numCones; j++) {
928: if (cone[j] == p) break;
929: }
930: if (j < numCones) newSupports[newqOff+offsets[q]++] = r;
931: }
932: DMPlexGetTreeParent(dm,q,&parent,NULL);
933: }
934: }
935: }
936: PetscSectionDestroy(&mesh->supportSection);
937: mesh->supportSection = newSupportSection;
938: PetscFree(mesh->supports);
939: mesh->supports = newSupports;
940: PetscFree(offsets);
941: PetscFree(numTrueSupp);
943: return(0);
944: }
946: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM,PetscSection,PetscSection,Mat);
947: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM,PetscSection,PetscSection,Mat);
949: static PetscErrorCode DMPlexSetTree_Internal(DM dm, PetscSection parentSection, PetscInt *parents, PetscInt *childIDs, PetscBool computeCanonical, PetscBool exchangeSupports)
950: {
951: DM_Plex *mesh = (DM_Plex *)dm->data;
952: DM refTree;
953: PetscInt size;
959: PetscObjectReference((PetscObject)parentSection);
960: PetscSectionDestroy(&mesh->parentSection);
961: mesh->parentSection = parentSection;
962: PetscSectionGetStorageSize(parentSection,&size);
963: if (parents != mesh->parents) {
964: PetscFree(mesh->parents);
965: PetscMalloc1(size,&mesh->parents);
966: PetscArraycpy(mesh->parents, parents, size);
967: }
968: if (childIDs != mesh->childIDs) {
969: PetscFree(mesh->childIDs);
970: PetscMalloc1(size,&mesh->childIDs);
971: PetscArraycpy(mesh->childIDs, childIDs, size);
972: }
973: DMPlexGetReferenceTree(dm,&refTree);
974: if (refTree) {
975: DMLabel canonLabel;
977: DMGetLabel(refTree,"canonical",&canonLabel);
978: if (canonLabel) {
979: PetscInt i;
981: for (i = 0; i < size; i++) {
982: PetscInt canon;
983: DMLabelGetValue(canonLabel, mesh->childIDs[i], &canon);
984: if (canon >= 0) {
985: mesh->childIDs[i] = canon;
986: }
987: }
988: }
989: mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_FromReference;
990: } else {
991: mesh->computeanchormatrix = DMPlexComputeAnchorMatrix_Tree_Direct;
992: }
993: DMPlexTreeSymmetrize(dm);
994: if (computeCanonical) {
995: PetscInt d, dim;
997: /* add the canonical label */
998: DMGetDimension(dm,&dim);
999: DMCreateLabel(dm,"canonical");
1000: for (d = 0; d <= dim; d++) {
1001: PetscInt p, dStart, dEnd, canon = -1, cNumChildren;
1002: const PetscInt *cChildren;
1004: DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
1005: for (p = dStart; p < dEnd; p++) {
1006: DMPlexGetTreeChildren(dm,p,&cNumChildren,&cChildren);
1007: if (cNumChildren) {
1008: canon = p;
1009: break;
1010: }
1011: }
1012: if (canon == -1) continue;
1013: for (p = dStart; p < dEnd; p++) {
1014: PetscInt numChildren, i;
1015: const PetscInt *children;
1017: DMPlexGetTreeChildren(dm,p,&numChildren,&children);
1018: if (numChildren) {
1019: if (numChildren != cNumChildren) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"All parent points in a stratum should have the same number of children: %d != %d", numChildren, cNumChildren);
1020: DMSetLabelValue(dm,"canonical",p,canon);
1021: for (i = 0; i < numChildren; i++) {
1022: DMSetLabelValue(dm,"canonical",children[i],cChildren[i]);
1023: }
1024: }
1025: }
1026: }
1027: }
1028: if (exchangeSupports) {
1029: DMPlexTreeExchangeSupports(dm);
1030: }
1031: mesh->createanchors = DMPlexCreateAnchors_Tree;
1032: /* reset anchors */
1033: DMPlexSetAnchors(dm,NULL,NULL);
1034: return(0);
1035: }
1037: /*@
1038: DMPlexSetTree - set the tree that describes the hierarchy of non-conforming mesh points. This routine also creates
1039: the point-to-point constraints determined by the tree: a point is constained to the points in the closure of its
1040: tree root.
1042: Collective on dm
1044: Input Parameters:
1045: + dm - the DMPlex object
1046: . parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
1047: offset indexes the parent and childID list; the reference count of parentSection is incremented
1048: . parents - a list of the point parents; copied, can be destroyed
1049: - childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
1050: the child corresponds to the point in the reference tree with index childIDs; copied, can be destroyed
1052: Level: intermediate
1054: .seealso: DMPlexGetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
1055: @*/
1056: PetscErrorCode DMPlexSetTree(DM dm, PetscSection parentSection, PetscInt parents[], PetscInt childIDs[])
1057: {
1061: DMPlexSetTree_Internal(dm,parentSection,parents,childIDs,PETSC_FALSE,PETSC_TRUE);
1062: return(0);
1063: }
1065: /*@
1066: DMPlexGetTree - get the tree that describes the hierarchy of non-conforming mesh points.
1067: Collective on dm
1069: Input Parameters:
1070: . dm - the DMPlex object
1072: Output Parameters:
1073: + parentSection - a section describing the tree: a point has a parent if it has 1 dof in the section; the section
1074: offset indexes the parent and childID list
1075: . parents - a list of the point parents
1076: . childIDs - identifies the relationship of the child point to the parent point; if there is a reference tree, then
1077: the child corresponds to the point in the reference tree with index childID
1078: . childSection - the inverse of the parent section
1079: - children - a list of the point children
1081: Level: intermediate
1083: .seealso: DMPlexSetTree(), DMPlexSetReferenceTree(), DMPlexSetAnchors(), DMPlexGetTreeParent(), DMPlexGetTreeChildren()
1084: @*/
1085: PetscErrorCode DMPlexGetTree(DM dm, PetscSection *parentSection, PetscInt *parents[], PetscInt *childIDs[], PetscSection *childSection, PetscInt *children[])
1086: {
1087: DM_Plex *mesh = (DM_Plex *)dm->data;
1091: if (parentSection) *parentSection = mesh->parentSection;
1092: if (parents) *parents = mesh->parents;
1093: if (childIDs) *childIDs = mesh->childIDs;
1094: if (childSection) *childSection = mesh->childSection;
1095: if (children) *children = mesh->children;
1096: return(0);
1097: }
1099: /*@
1100: DMPlexGetTreeParent - get the parent of a point in the tree describing the point hierarchy (not the DAG)
1102: Input Parameters:
1103: + dm - the DMPlex object
1104: - point - the query point
1106: Output Parameters:
1107: + parent - if not NULL, set to the parent of the point, or the point itself if the point does not have a parent
1108: - childID - if not NULL, set to the child ID of the point with respect to its parent, or 0 if the point
1109: does not have a parent
1111: Level: intermediate
1113: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeChildren()
1114: @*/
1115: PetscErrorCode DMPlexGetTreeParent(DM dm, PetscInt point, PetscInt *parent, PetscInt *childID)
1116: {
1117: DM_Plex *mesh = (DM_Plex *)dm->data;
1118: PetscSection pSec;
1123: pSec = mesh->parentSection;
1124: if (pSec && point >= pSec->pStart && point < pSec->pEnd) {
1125: PetscInt dof;
1127: PetscSectionGetDof (pSec, point, &dof);
1128: if (dof) {
1129: PetscInt off;
1131: PetscSectionGetOffset (pSec, point, &off);
1132: if (parent) *parent = mesh->parents[off];
1133: if (childID) *childID = mesh->childIDs[off];
1134: return(0);
1135: }
1136: }
1137: if (parent) {
1138: *parent = point;
1139: }
1140: if (childID) {
1141: *childID = 0;
1142: }
1143: return(0);
1144: }
1146: /*@C
1147: DMPlexGetTreeChildren - get the children of a point in the tree describing the point hierarchy (not the DAG)
1149: Input Parameters:
1150: + dm - the DMPlex object
1151: - point - the query point
1153: Output Parameters:
1154: + numChildren - if not NULL, set to the number of children
1155: - children - if not NULL, set to a list children, or set to NULL if the point has no children
1157: Level: intermediate
1159: Fortran Notes:
1160: Since it returns an array, this routine is only available in Fortran 90, and you must
1161: include petsc.h90 in your code.
1163: .seealso: DMPlexSetTree(), DMPlexGetTree(), DMPlexGetTreeParent()
1164: @*/
1165: PetscErrorCode DMPlexGetTreeChildren(DM dm, PetscInt point, PetscInt *numChildren, const PetscInt *children[])
1166: {
1167: DM_Plex *mesh = (DM_Plex *)dm->data;
1168: PetscSection childSec;
1169: PetscInt dof = 0;
1174: childSec = mesh->childSection;
1175: if (childSec && point >= childSec->pStart && point < childSec->pEnd) {
1176: PetscSectionGetDof (childSec, point, &dof);
1177: }
1178: if (numChildren) *numChildren = dof;
1179: if (children) {
1180: if (dof) {
1181: PetscInt off;
1183: PetscSectionGetOffset (childSec, point, &off);
1184: *children = &mesh->children[off];
1185: }
1186: else {
1187: *children = NULL;
1188: }
1189: }
1190: return(0);
1191: }
1193: static PetscErrorCode EvaluateBasis(PetscSpace space, PetscInt nBasis, PetscInt nFunctionals, PetscInt nComps, PetscInt nPoints, const PetscInt *pointsPerFn, const PetscReal *points, const PetscReal *weights, PetscReal *work, Mat basisAtPoints)
1194: {
1195: PetscInt f, b, p, c, offset, qPoints;
1199: PetscSpaceEvaluate(space,nPoints,points,work,NULL,NULL);
1200: for (f = 0, offset = 0; f < nFunctionals; f++) {
1201: qPoints = pointsPerFn[f];
1202: for (b = 0; b < nBasis; b++) {
1203: PetscScalar val = 0.;
1205: for (p = 0; p < qPoints; p++) {
1206: for (c = 0; c < nComps; c++) {
1207: val += work[((offset + p) * nBasis + b) * nComps + c] * weights[(offset + p) * nComps + c];
1208: }
1209: }
1210: MatSetValue(basisAtPoints,b,f,val,INSERT_VALUES);
1211: }
1212: offset += qPoints;
1213: }
1214: MatAssemblyBegin(basisAtPoints,MAT_FINAL_ASSEMBLY);
1215: MatAssemblyEnd(basisAtPoints,MAT_FINAL_ASSEMBLY);
1216: return(0);
1217: }
1219: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_Direct(DM dm, PetscSection section, PetscSection cSec, Mat cMat)
1220: {
1221: PetscDS ds;
1222: PetscInt spdim;
1223: PetscInt numFields, f, c, cStart, cEnd, pStart, pEnd, conStart, conEnd;
1224: const PetscInt *anchors;
1225: PetscSection aSec;
1226: PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJparent, detJ, detJparent;
1227: IS aIS;
1231: DMPlexGetChart(dm,&pStart,&pEnd);
1232: DMGetDS(dm,&ds);
1233: PetscDSGetNumFields(ds,&numFields);
1234: DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);
1235: DMPlexGetAnchors(dm,&aSec,&aIS);
1236: ISGetIndices(aIS,&anchors);
1237: PetscSectionGetChart(cSec,&conStart,&conEnd);
1238: DMGetDimension(dm,&spdim);
1239: PetscMalloc6(spdim,&v0,spdim,&v0parent,spdim,&vtmp,spdim*spdim,&J,spdim*spdim,&Jparent,spdim*spdim,&invJparent);
1241: for (f = 0; f < numFields; f++) {
1242: PetscObject disc;
1243: PetscClassId id;
1244: PetscSpace bspace;
1245: PetscDualSpace dspace;
1246: PetscInt i, j, k, nPoints, Nc, offset;
1247: PetscInt fSize, maxDof;
1248: PetscReal *weights, *pointsRef, *pointsReal, *work;
1249: PetscScalar *scwork;
1250: const PetscScalar *X;
1251: PetscInt *sizes, *workIndRow, *workIndCol;
1252: Mat Amat, Bmat, Xmat;
1253: const PetscInt *numDof = NULL;
1254: const PetscInt ***perms = NULL;
1255: const PetscScalar ***flips = NULL;
1257: PetscDSGetDiscretization(ds,f,&disc);
1258: PetscObjectGetClassId(disc,&id);
1259: if (id == PETSCFE_CLASSID) {
1260: PetscFE fe = (PetscFE) disc;
1262: PetscFEGetBasisSpace(fe,&bspace);
1263: PetscFEGetDualSpace(fe,&dspace);
1264: PetscDualSpaceGetDimension(dspace,&fSize);
1265: PetscFEGetNumComponents(fe,&Nc);
1266: }
1267: else if (id == PETSCFV_CLASSID) {
1268: PetscFV fv = (PetscFV) disc;
1270: PetscFVGetNumComponents(fv,&Nc);
1271: PetscSpaceCreate(PetscObjectComm((PetscObject)fv),&bspace);
1272: PetscSpaceSetType(bspace,PETSCSPACEPOLYNOMIAL);
1273: PetscSpaceSetDegree(bspace,0,PETSC_DETERMINE);
1274: PetscSpaceSetNumComponents(bspace,Nc);
1275: PetscSpaceSetNumVariables(bspace,spdim);
1276: PetscSpaceSetUp(bspace);
1277: PetscFVGetDualSpace(fv,&dspace);
1278: PetscDualSpaceGetDimension(dspace,&fSize);
1279: }
1280: else SETERRQ1(PetscObjectComm(disc),PETSC_ERR_ARG_UNKNOWN_TYPE, "PetscDS discretization id %d not recognized.", id);
1281: PetscDualSpaceGetNumDof(dspace,&numDof);
1282: for (i = 0, maxDof = 0; i <= spdim; i++) {maxDof = PetscMax(maxDof,numDof[i]);}
1283: PetscDualSpaceGetSymmetries(dspace,&perms,&flips);
1285: MatCreate(PETSC_COMM_SELF,&Amat);
1286: MatSetSizes(Amat,fSize,fSize,fSize,fSize);
1287: MatSetType(Amat,MATSEQDENSE);
1288: MatSetUp(Amat);
1289: MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Bmat);
1290: MatDuplicate(Amat,MAT_DO_NOT_COPY_VALUES,&Xmat);
1291: nPoints = 0;
1292: for (i = 0; i < fSize; i++) {
1293: PetscInt qPoints, thisNc;
1294: PetscQuadrature quad;
1296: PetscDualSpaceGetFunctional(dspace,i,&quad);
1297: PetscQuadratureGetData(quad,NULL,&thisNc,&qPoints,NULL,NULL);
1298: if (thisNc != Nc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Functional dim %D does not much basis dim %D\n",thisNc,Nc);
1299: nPoints += qPoints;
1300: }
1301: PetscMalloc7(fSize,&sizes,nPoints*Nc,&weights,spdim*nPoints,&pointsRef,spdim*nPoints,&pointsReal,nPoints*fSize*Nc,&work,maxDof,&workIndRow,maxDof,&workIndCol);
1302: PetscMalloc1(maxDof * maxDof,&scwork);
1303: offset = 0;
1304: for (i = 0; i < fSize; i++) {
1305: PetscInt qPoints;
1306: const PetscReal *p, *w;
1307: PetscQuadrature quad;
1309: PetscDualSpaceGetFunctional(dspace,i,&quad);
1310: PetscQuadratureGetData(quad,NULL,NULL,&qPoints,&p,&w);
1311: PetscArraycpy(weights+Nc*offset,w,Nc*qPoints);
1312: PetscArraycpy(pointsRef+spdim*offset,p,spdim*qPoints);
1313: sizes[i] = qPoints;
1314: offset += qPoints;
1315: }
1316: EvaluateBasis(bspace,fSize,fSize,Nc,nPoints,sizes,pointsRef,weights,work,Amat);
1317: MatLUFactor(Amat,NULL,NULL,NULL);
1318: for (c = cStart; c < cEnd; c++) {
1319: PetscInt parent;
1320: PetscInt closureSize, closureSizeP, *closure = NULL, *closureP = NULL;
1321: PetscInt *childOffsets, *parentOffsets;
1323: DMPlexGetTreeParent(dm,c,&parent,NULL);
1324: if (parent == c) continue;
1325: DMPlexGetTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
1326: for (i = 0; i < closureSize; i++) {
1327: PetscInt p = closure[2*i];
1328: PetscInt conDof;
1330: if (p < conStart || p >= conEnd) continue;
1331: if (numFields) {
1332: PetscSectionGetFieldDof(cSec,p,f,&conDof);
1333: }
1334: else {
1335: PetscSectionGetDof(cSec,p,&conDof);
1336: }
1337: if (conDof) break;
1338: }
1339: if (i == closureSize) {
1340: DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
1341: continue;
1342: }
1344: DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, NULL, &detJ);
1345: DMPlexComputeCellGeometryFEM(dm, parent, NULL, v0parent, Jparent, invJparent, &detJparent);
1346: for (i = 0; i < nPoints; i++) {
1347: const PetscReal xi0[3] = {-1.,-1.,-1.};
1349: CoordinatesRefToReal(spdim, spdim, xi0, v0, J, &pointsRef[i*spdim],vtmp);
1350: CoordinatesRealToRef(spdim, spdim, xi0, v0parent, invJparent, vtmp, &pointsReal[i*spdim]);
1351: }
1352: EvaluateBasis(bspace,fSize,fSize,Nc,nPoints,sizes,pointsReal,weights,work,Bmat);
1353: MatMatSolve(Amat,Bmat,Xmat);
1354: MatDenseGetArrayRead(Xmat,&X);
1355: DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
1356: PetscMalloc2(closureSize+1,&childOffsets,closureSizeP+1,&parentOffsets);
1357: childOffsets[0] = 0;
1358: for (i = 0; i < closureSize; i++) {
1359: PetscInt p = closure[2*i];
1360: PetscInt dof;
1362: if (numFields) {
1363: PetscSectionGetFieldDof(section,p,f,&dof);
1364: }
1365: else {
1366: PetscSectionGetDof(section,p,&dof);
1367: }
1368: childOffsets[i+1]=childOffsets[i]+dof;
1369: }
1370: parentOffsets[0] = 0;
1371: for (i = 0; i < closureSizeP; i++) {
1372: PetscInt p = closureP[2*i];
1373: PetscInt dof;
1375: if (numFields) {
1376: PetscSectionGetFieldDof(section,p,f,&dof);
1377: }
1378: else {
1379: PetscSectionGetDof(section,p,&dof);
1380: }
1381: parentOffsets[i+1]=parentOffsets[i]+dof;
1382: }
1383: for (i = 0; i < closureSize; i++) {
1384: PetscInt conDof, conOff, aDof, aOff, nWork;
1385: PetscInt p = closure[2*i];
1386: PetscInt o = closure[2*i+1];
1387: const PetscInt *perm;
1388: const PetscScalar *flip;
1390: if (p < conStart || p >= conEnd) continue;
1391: if (numFields) {
1392: PetscSectionGetFieldDof(cSec,p,f,&conDof);
1393: PetscSectionGetFieldOffset(cSec,p,f,&conOff);
1394: }
1395: else {
1396: PetscSectionGetDof(cSec,p,&conDof);
1397: PetscSectionGetOffset(cSec,p,&conOff);
1398: }
1399: if (!conDof) continue;
1400: perm = (perms && perms[i]) ? perms[i][o] : NULL;
1401: flip = (flips && flips[i]) ? flips[i][o] : NULL;
1402: PetscSectionGetDof(aSec,p,&aDof);
1403: PetscSectionGetOffset(aSec,p,&aOff);
1404: nWork = childOffsets[i+1]-childOffsets[i];
1405: for (k = 0; k < aDof; k++) {
1406: PetscInt a = anchors[aOff + k];
1407: PetscInt aSecDof, aSecOff;
1409: if (numFields) {
1410: PetscSectionGetFieldDof(section,a,f,&aSecDof);
1411: PetscSectionGetFieldOffset(section,a,f,&aSecOff);
1412: }
1413: else {
1414: PetscSectionGetDof(section,a,&aSecDof);
1415: PetscSectionGetOffset(section,a,&aSecOff);
1416: }
1417: if (!aSecDof) continue;
1419: for (j = 0; j < closureSizeP; j++) {
1420: PetscInt q = closureP[2*j];
1421: PetscInt oq = closureP[2*j+1];
1423: if (q == a) {
1424: PetscInt r, s, nWorkP;
1425: const PetscInt *permP;
1426: const PetscScalar *flipP;
1428: permP = (perms && perms[j]) ? perms[j][oq] : NULL;
1429: flipP = (flips && flips[j]) ? flips[j][oq] : NULL;
1430: nWorkP = parentOffsets[j+1]-parentOffsets[j];
1431: /* get a copy of the child-to-anchor portion of the matrix, and transpose so that rows correspond to the
1432: * child and columns correspond to the anchor: BUT the maxrix returned by MatDenseGetArrayRead() is
1433: * column-major, so transpose-transpose = do nothing */
1434: for (r = 0; r < nWork; r++) {
1435: for (s = 0; s < nWorkP; s++) {
1436: scwork[r * nWorkP + s] = X[fSize * (r + childOffsets[i]) + (s + parentOffsets[j])];
1437: }
1438: }
1439: for (r = 0; r < nWork; r++) {workIndRow[perm ? perm[r] : r] = conOff + r;}
1440: for (s = 0; s < nWorkP; s++) {workIndCol[permP ? permP[s] : s] = aSecOff + s;}
1441: if (flip) {
1442: for (r = 0; r < nWork; r++) {
1443: for (s = 0; s < nWorkP; s++) {
1444: scwork[r * nWorkP + s] *= flip[r];
1445: }
1446: }
1447: }
1448: if (flipP) {
1449: for (r = 0; r < nWork; r++) {
1450: for (s = 0; s < nWorkP; s++) {
1451: scwork[r * nWorkP + s] *= flipP[s];
1452: }
1453: }
1454: }
1455: MatSetValues(cMat,nWork,workIndRow,nWorkP,workIndCol,scwork,INSERT_VALUES);
1456: break;
1457: }
1458: }
1459: }
1460: }
1461: MatDenseRestoreArrayRead(Xmat,&X);
1462: PetscFree2(childOffsets,parentOffsets);
1463: DMPlexRestoreTransitiveClosure(dm,c,PETSC_TRUE,&closureSize,&closure);
1464: DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSizeP,&closureP);
1465: }
1466: MatDestroy(&Amat);
1467: MatDestroy(&Bmat);
1468: MatDestroy(&Xmat);
1469: PetscFree(scwork);
1470: PetscFree7(sizes,weights,pointsRef,pointsReal,work,workIndRow,workIndCol);
1471: if (id == PETSCFV_CLASSID) {
1472: PetscSpaceDestroy(&bspace);
1473: }
1474: }
1475: MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
1476: MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
1477: PetscFree6(v0,v0parent,vtmp,J,Jparent,invJparent);
1478: ISRestoreIndices(aIS,&anchors);
1480: return(0);
1481: }
1483: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
1484: {
1485: Mat refCmat;
1486: PetscDS ds;
1487: PetscInt numFields, maxFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof, maxAnDof, **refPointFieldN;
1488: PetscScalar ***refPointFieldMats;
1489: PetscSection refConSec, refAnSec, refSection;
1490: IS refAnIS;
1491: const PetscInt *refAnchors;
1492: const PetscInt **perms;
1493: const PetscScalar **flips;
1494: PetscErrorCode ierr;
1497: DMGetDS(refTree,&ds);
1498: PetscDSGetNumFields(ds,&numFields);
1499: maxFields = PetscMax(1,numFields);
1500: DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
1501: DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
1502: ISGetIndices(refAnIS,&refAnchors);
1503: DMGetLocalSection(refTree,&refSection);
1504: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
1505: PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
1506: PetscMalloc1(pRefEnd-pRefStart,&refPointFieldN);
1507: PetscSectionGetMaxDof(refConSec,&maxDof);
1508: PetscSectionGetMaxDof(refAnSec,&maxAnDof);
1509: PetscMalloc1(maxDof,&rows);
1510: PetscMalloc1(maxDof*maxAnDof,&cols);
1511: for (p = pRefStart; p < pRefEnd; p++) {
1512: PetscInt parent, closureSize, *closure = NULL, pDof;
1514: DMPlexGetTreeParent(refTree,p,&parent,NULL);
1515: PetscSectionGetDof(refConSec,p,&pDof);
1516: if (!pDof || parent == p) continue;
1518: PetscMalloc1(maxFields,&refPointFieldMats[p-pRefStart]);
1519: PetscCalloc1(maxFields,&refPointFieldN[p-pRefStart]);
1520: DMPlexGetTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
1521: for (f = 0; f < maxFields; f++) {
1522: PetscInt cDof, cOff, numCols, r, i;
1524: if (f < numFields) {
1525: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
1526: PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
1527: PetscSectionGetFieldPointSyms(refSection,f,closureSize,closure,&perms,&flips);
1528: } else {
1529: PetscSectionGetDof(refConSec,p,&cDof);
1530: PetscSectionGetOffset(refConSec,p,&cOff);
1531: PetscSectionGetPointSyms(refSection,closureSize,closure,&perms,&flips);
1532: }
1534: for (r = 0; r < cDof; r++) {
1535: rows[r] = cOff + r;
1536: }
1537: numCols = 0;
1538: for (i = 0; i < closureSize; i++) {
1539: PetscInt q = closure[2*i];
1540: PetscInt aDof, aOff, j;
1541: const PetscInt *perm = perms ? perms[i] : NULL;
1543: if (numFields) {
1544: PetscSectionGetFieldDof(refSection,q,f,&aDof);
1545: PetscSectionGetFieldOffset(refSection,q,f,&aOff);
1546: }
1547: else {
1548: PetscSectionGetDof(refSection,q,&aDof);
1549: PetscSectionGetOffset(refSection,q,&aOff);
1550: }
1552: for (j = 0; j < aDof; j++) {
1553: cols[numCols++] = aOff + (perm ? perm[j] : j);
1554: }
1555: }
1556: refPointFieldN[p-pRefStart][f] = numCols;
1557: PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
1558: MatGetValues(refCmat,cDof,rows,numCols,cols,refPointFieldMats[p-pRefStart][f]);
1559: if (flips) {
1560: PetscInt colOff = 0;
1562: for (i = 0; i < closureSize; i++) {
1563: PetscInt q = closure[2*i];
1564: PetscInt aDof, aOff, j;
1565: const PetscScalar *flip = flips ? flips[i] : NULL;
1567: if (numFields) {
1568: PetscSectionGetFieldDof(refSection,q,f,&aDof);
1569: PetscSectionGetFieldOffset(refSection,q,f,&aOff);
1570: }
1571: else {
1572: PetscSectionGetDof(refSection,q,&aDof);
1573: PetscSectionGetOffset(refSection,q,&aOff);
1574: }
1575: if (flip) {
1576: PetscInt k;
1577: for (k = 0; k < cDof; k++) {
1578: for (j = 0; j < aDof; j++) {
1579: refPointFieldMats[p-pRefStart][f][k * numCols + colOff + j] *= flip[j];
1580: }
1581: }
1582: }
1583: colOff += aDof;
1584: }
1585: }
1586: if (numFields) {
1587: PetscSectionRestoreFieldPointSyms(refSection,f,closureSize,closure,&perms,&flips);
1588: } else {
1589: PetscSectionRestorePointSyms(refSection,closureSize,closure,&perms,&flips);
1590: }
1591: }
1592: DMPlexRestoreTransitiveClosure(refTree,parent,PETSC_TRUE,&closureSize,&closure);
1593: }
1594: *childrenMats = refPointFieldMats;
1595: *childrenN = refPointFieldN;
1596: ISRestoreIndices(refAnIS,&refAnchors);
1597: PetscFree(rows);
1598: PetscFree(cols);
1599: return(0);
1600: }
1602: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices(DM refTree, PetscScalar ****childrenMats, PetscInt ***childrenN)
1603: {
1604: PetscDS ds;
1605: PetscInt **refPointFieldN;
1606: PetscScalar ***refPointFieldMats;
1607: PetscInt numFields, maxFields, pRefStart, pRefEnd, p, f;
1608: PetscSection refConSec;
1612: refPointFieldN = *childrenN;
1613: *childrenN = NULL;
1614: refPointFieldMats = *childrenMats;
1615: *childrenMats = NULL;
1616: DMGetDS(refTree,&ds);
1617: PetscDSGetNumFields(ds,&numFields);
1618: maxFields = PetscMax(1,numFields);
1619: DMGetDefaultConstraints(refTree,&refConSec,NULL);
1620: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
1621: for (p = pRefStart; p < pRefEnd; p++) {
1622: PetscInt parent, pDof;
1624: DMPlexGetTreeParent(refTree,p,&parent,NULL);
1625: PetscSectionGetDof(refConSec,p,&pDof);
1626: if (!pDof || parent == p) continue;
1628: for (f = 0; f < maxFields; f++) {
1629: PetscInt cDof;
1631: if (numFields) {
1632: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
1633: }
1634: else {
1635: PetscSectionGetDof(refConSec,p,&cDof);
1636: }
1638: PetscFree(refPointFieldMats[p - pRefStart][f]);
1639: }
1640: PetscFree(refPointFieldMats[p - pRefStart]);
1641: PetscFree(refPointFieldN[p - pRefStart]);
1642: }
1643: PetscFree(refPointFieldMats);
1644: PetscFree(refPointFieldN);
1645: return(0);
1646: }
1648: static PetscErrorCode DMPlexComputeAnchorMatrix_Tree_FromReference(DM dm, PetscSection section, PetscSection conSec, Mat cMat)
1649: {
1650: DM refTree;
1651: PetscDS ds;
1652: Mat refCmat;
1653: PetscInt numFields, maxFields, f, pRefStart, pRefEnd, p, maxDof, maxAnDof, *perm, *iperm, pStart, pEnd, conStart, conEnd, **refPointFieldN;
1654: PetscScalar ***refPointFieldMats, *pointWork;
1655: PetscSection refConSec, refAnSec, anSec;
1656: IS refAnIS, anIS;
1657: const PetscInt *anchors;
1662: DMGetDS(dm,&ds);
1663: PetscDSGetNumFields(ds,&numFields);
1664: maxFields = PetscMax(1,numFields);
1665: DMPlexGetReferenceTree(dm,&refTree);
1666: DMCopyDisc(dm,refTree);
1667: DMGetDefaultConstraints(refTree,&refConSec,&refCmat);
1668: DMPlexGetAnchors(refTree,&refAnSec,&refAnIS);
1669: DMPlexGetAnchors(dm,&anSec,&anIS);
1670: ISGetIndices(anIS,&anchors);
1671: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
1672: PetscSectionGetChart(conSec,&conStart,&conEnd);
1673: PetscSectionGetMaxDof(refConSec,&maxDof);
1674: PetscSectionGetMaxDof(refAnSec,&maxAnDof);
1675: PetscMalloc1(maxDof*maxDof*maxAnDof,&pointWork);
1677: /* step 1: get submats for every constrained point in the reference tree */
1678: DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
1680: /* step 2: compute the preorder */
1681: DMPlexGetChart(dm,&pStart,&pEnd);
1682: PetscMalloc2(pEnd-pStart,&perm,pEnd-pStart,&iperm);
1683: for (p = pStart; p < pEnd; p++) {
1684: perm[p - pStart] = p;
1685: iperm[p - pStart] = p-pStart;
1686: }
1687: for (p = 0; p < pEnd - pStart;) {
1688: PetscInt point = perm[p];
1689: PetscInt parent;
1691: DMPlexGetTreeParent(dm,point,&parent,NULL);
1692: if (parent == point) {
1693: p++;
1694: }
1695: else {
1696: PetscInt size, closureSize, *closure = NULL, i;
1698: DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1699: for (i = 0; i < closureSize; i++) {
1700: PetscInt q = closure[2*i];
1701: if (iperm[q-pStart] > iperm[point-pStart]) {
1702: /* swap */
1703: perm[p] = q;
1704: perm[iperm[q-pStart]] = point;
1705: iperm[point-pStart] = iperm[q-pStart];
1706: iperm[q-pStart] = p;
1707: break;
1708: }
1709: }
1710: size = closureSize;
1711: DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1712: if (i == size) {
1713: p++;
1714: }
1715: }
1716: }
1718: /* step 3: fill the constraint matrix */
1719: /* we are going to use a preorder progressive fill strategy. Mat doesn't
1720: * allow progressive fill without assembly, so we are going to set up the
1721: * values outside of the Mat first.
1722: */
1723: {
1724: PetscInt nRows, row, nnz;
1725: PetscBool done;
1726: const PetscInt *ia, *ja;
1727: PetscScalar *vals;
1729: MatGetRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
1730: if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not get RowIJ of constraint matrix");
1731: nnz = ia[nRows];
1732: /* malloc and then zero rows right before we fill them: this way valgrind
1733: * can tell if we are doing progressive fill in the wrong order */
1734: PetscMalloc1(nnz,&vals);
1735: for (p = 0; p < pEnd - pStart; p++) {
1736: PetscInt parent, childid, closureSize, *closure = NULL;
1737: PetscInt point = perm[p], pointDof;
1739: DMPlexGetTreeParent(dm,point,&parent,&childid);
1740: if ((point < conStart) || (point >= conEnd) || (parent == point)) continue;
1741: PetscSectionGetDof(conSec,point,&pointDof);
1742: if (!pointDof) continue;
1743: DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1744: for (f = 0; f < maxFields; f++) {
1745: PetscInt cDof, cOff, numCols, numFillCols, i, r, matOffset, offset;
1746: PetscScalar *pointMat;
1747: const PetscInt **perms;
1748: const PetscScalar **flips;
1750: if (numFields) {
1751: PetscSectionGetFieldDof(conSec,point,f,&cDof);
1752: PetscSectionGetFieldOffset(conSec,point,f,&cOff);
1753: }
1754: else {
1755: PetscSectionGetDof(conSec,point,&cDof);
1756: PetscSectionGetOffset(conSec,point,&cOff);
1757: }
1758: if (!cDof) continue;
1759: if (numFields) {PetscSectionGetFieldPointSyms(section,f,closureSize,closure,&perms,&flips);}
1760: else {PetscSectionGetPointSyms(section,closureSize,closure,&perms,&flips);}
1762: /* make sure that every row for this point is the same size */
1763: #if defined(PETSC_USE_DEBUG)
1764: for (r = 0; r < cDof; r++) {
1765: if (cDof > 1 && r) {
1766: if ((ia[cOff+r+1]-ia[cOff+r]) != (ia[cOff+r]-ia[cOff+r-1])) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Two point rows have different nnz: %D vs. %D", (ia[cOff+r+1]-ia[cOff+r]), (ia[cOff+r]-ia[cOff+r-1]));
1767: }
1768: }
1769: #endif
1770: /* zero rows */
1771: for (i = ia[cOff] ; i< ia[cOff+cDof];i++) {
1772: vals[i] = 0.;
1773: }
1774: matOffset = ia[cOff];
1775: numFillCols = ia[cOff+1] - matOffset;
1776: pointMat = refPointFieldMats[childid-pRefStart][f];
1777: numCols = refPointFieldN[childid-pRefStart][f];
1778: offset = 0;
1779: for (i = 0; i < closureSize; i++) {
1780: PetscInt q = closure[2*i];
1781: PetscInt aDof, aOff, j, k, qConDof, qConOff;
1782: const PetscInt *perm = perms ? perms[i] : NULL;
1783: const PetscScalar *flip = flips ? flips[i] : NULL;
1785: qConDof = qConOff = 0;
1786: if (numFields) {
1787: PetscSectionGetFieldDof(section,q,f,&aDof);
1788: PetscSectionGetFieldOffset(section,q,f,&aOff);
1789: if (q >= conStart && q < conEnd) {
1790: PetscSectionGetFieldDof(conSec,q,f,&qConDof);
1791: PetscSectionGetFieldOffset(conSec,q,f,&qConOff);
1792: }
1793: }
1794: else {
1795: PetscSectionGetDof(section,q,&aDof);
1796: PetscSectionGetOffset(section,q,&aOff);
1797: if (q >= conStart && q < conEnd) {
1798: PetscSectionGetDof(conSec,q,&qConDof);
1799: PetscSectionGetOffset(conSec,q,&qConOff);
1800: }
1801: }
1802: if (!aDof) continue;
1803: if (qConDof) {
1804: /* this point has anchors: its rows of the matrix should already
1805: * be filled, thanks to preordering */
1806: /* first multiply into pointWork, then set in matrix */
1807: PetscInt aMatOffset = ia[qConOff];
1808: PetscInt aNumFillCols = ia[qConOff + 1] - aMatOffset;
1809: for (r = 0; r < cDof; r++) {
1810: for (j = 0; j < aNumFillCols; j++) {
1811: PetscScalar inVal = 0;
1812: for (k = 0; k < aDof; k++) {
1813: PetscInt col = perm ? perm[k] : k;
1815: inVal += pointMat[r * numCols + offset + col] * vals[aMatOffset + aNumFillCols * k + j] * (flip ? flip[col] : 1.);
1816: }
1817: pointWork[r * aNumFillCols + j] = inVal;
1818: }
1819: }
1820: /* assume that the columns are sorted, spend less time searching */
1821: for (j = 0, k = 0; j < aNumFillCols; j++) {
1822: PetscInt col = ja[aMatOffset + j];
1823: for (;k < numFillCols; k++) {
1824: if (ja[matOffset + k] == col) {
1825: break;
1826: }
1827: }
1828: if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, col);
1829: for (r = 0; r < cDof; r++) {
1830: vals[matOffset + numFillCols * r + k] = pointWork[r * aNumFillCols + j];
1831: }
1832: }
1833: }
1834: else {
1835: /* find where to put this portion of pointMat into the matrix */
1836: for (k = 0; k < numFillCols; k++) {
1837: if (ja[matOffset + k] == aOff) {
1838: break;
1839: }
1840: }
1841: if (k == numFillCols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No nonzero space for (%d, %d)", cOff, aOff);
1842: for (r = 0; r < cDof; r++) {
1843: for (j = 0; j < aDof; j++) {
1844: PetscInt col = perm ? perm[j] : j;
1846: vals[matOffset + numFillCols * r + k + col] += pointMat[r * numCols + offset + j] * (flip ? flip[col] : 1.);
1847: }
1848: }
1849: }
1850: offset += aDof;
1851: }
1852: if (numFields) {
1853: PetscSectionRestoreFieldPointSyms(section,f,closureSize,closure,&perms,&flips);
1854: } else {
1855: PetscSectionRestorePointSyms(section,closureSize,closure,&perms,&flips);
1856: }
1857: }
1858: DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1859: }
1860: for (row = 0; row < nRows; row++) {
1861: MatSetValues(cMat,1,&row,ia[row+1]-ia[row],&ja[ia[row]],&vals[ia[row]],INSERT_VALUES);
1862: }
1863: MatRestoreRowIJ(cMat,0,PETSC_FALSE,PETSC_FALSE,&nRows,&ia,&ja,&done);
1864: if (!done) SETERRQ(PetscObjectComm((PetscObject)cMat),PETSC_ERR_PLIB,"Could not restore RowIJ of constraint matrix");
1865: MatAssemblyBegin(cMat,MAT_FINAL_ASSEMBLY);
1866: MatAssemblyEnd(cMat,MAT_FINAL_ASSEMBLY);
1867: PetscFree(vals);
1868: }
1870: /* clean up */
1871: ISRestoreIndices(anIS,&anchors);
1872: PetscFree2(perm,iperm);
1873: PetscFree(pointWork);
1874: DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
1875: return(0);
1876: }
1878: /* refine a single cell on rank 0: this is not intended to provide good local refinement, only to create an example of
1879: * a non-conforming mesh. Local refinement comes later */
1880: PetscErrorCode DMPlexTreeRefineCell (DM dm, PetscInt cell, DM *ncdm)
1881: {
1882: DM K;
1883: PetscMPIInt rank;
1884: PetscInt dim, *pNewStart, *pNewEnd, *pNewCount, *pOldStart, *pOldEnd, offset, d, pStart, pEnd;
1885: PetscInt numNewCones, *newConeSizes, *newCones, *newOrientations;
1886: PetscInt *Kembedding;
1887: PetscInt *cellClosure=NULL, nc;
1888: PetscScalar *newVertexCoords;
1889: PetscInt numPointsWithParents, *parents, *childIDs, *perm, *iperm, *preOrient, pOffset;
1890: PetscSection parentSection;
1894: MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);
1895: DMGetDimension(dm,&dim);
1896: DMPlexCreate(PetscObjectComm((PetscObject)dm), ncdm);
1897: DMSetDimension(*ncdm,dim);
1899: DMPlexGetChart(dm, &pStart, &pEnd);
1900: PetscSectionCreate(PetscObjectComm((PetscObject)dm),&parentSection);
1901: DMPlexGetReferenceTree(dm,&K);
1902: if (!rank) {
1903: /* compute the new charts */
1904: PetscMalloc5(dim+1,&pNewCount,dim+1,&pNewStart,dim+1,&pNewEnd,dim+1,&pOldStart,dim+1,&pOldEnd);
1905: offset = 0;
1906: for (d = 0; d <= dim; d++) {
1907: PetscInt pOldCount, kStart, kEnd, k;
1909: pNewStart[d] = offset;
1910: DMPlexGetHeightStratum(dm,d,&pOldStart[d],&pOldEnd[d]);
1911: DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
1912: pOldCount = pOldEnd[d] - pOldStart[d];
1913: /* adding the new points */
1914: pNewCount[d] = pOldCount + kEnd - kStart;
1915: if (!d) {
1916: /* removing the cell */
1917: pNewCount[d]--;
1918: }
1919: for (k = kStart; k < kEnd; k++) {
1920: PetscInt parent;
1921: DMPlexGetTreeParent(K,k,&parent,NULL);
1922: if (parent == k) {
1923: /* avoid double counting points that won't actually be new */
1924: pNewCount[d]--;
1925: }
1926: }
1927: pNewEnd[d] = pNewStart[d] + pNewCount[d];
1928: offset = pNewEnd[d];
1930: }
1931: if (cell < pOldStart[0] || cell >= pOldEnd[0]) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"%d not in cell range [%d, %d)", cell, pOldStart[0], pOldEnd[0]);
1932: /* get the current closure of the cell that we are removing */
1933: DMPlexGetTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);
1935: PetscMalloc1(pNewEnd[dim],&newConeSizes);
1936: {
1937: PetscInt kStart, kEnd, k, closureSizeK, *closureK = NULL, j;
1939: DMPlexGetChart(K,&kStart,&kEnd);
1940: PetscMalloc4(kEnd-kStart,&Kembedding,kEnd-kStart,&perm,kEnd-kStart,&iperm,kEnd-kStart,&preOrient);
1942: for (k = kStart; k < kEnd; k++) {
1943: perm[k - kStart] = k;
1944: iperm [k - kStart] = k - kStart;
1945: preOrient[k - kStart] = 0;
1946: }
1948: DMPlexGetTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
1949: for (j = 1; j < closureSizeK; j++) {
1950: PetscInt parentOrientA = closureK[2*j+1];
1951: PetscInt parentOrientB = cellClosure[2*j+1];
1952: PetscInt p, q;
1954: p = closureK[2*j];
1955: q = cellClosure[2*j];
1956: for (d = 0; d <= dim; d++) {
1957: if (q >= pOldStart[d] && q < pOldEnd[d]) {
1958: Kembedding[p] = (q - pOldStart[d]) + pNewStart[d];
1959: }
1960: }
1961: if (parentOrientA != parentOrientB) {
1962: PetscInt numChildren, i;
1963: const PetscInt *children;
1965: DMPlexGetTreeChildren(K,p,&numChildren,&children);
1966: for (i = 0; i < numChildren; i++) {
1967: PetscInt kPerm, oPerm;
1969: k = children[i];
1970: DMPlexReferenceTreeGetChildSymmetry(K,p,parentOrientA,0,k,parentOrientB,&oPerm,&kPerm);
1971: /* perm = what refTree position I'm in */
1972: perm[kPerm-kStart] = k;
1973: /* iperm = who is at this position */
1974: iperm[k-kStart] = kPerm-kStart;
1975: preOrient[kPerm-kStart] = oPerm;
1976: }
1977: }
1978: }
1979: DMPlexRestoreTransitiveClosure(K,0,PETSC_TRUE,&closureSizeK,&closureK);
1980: }
1981: PetscSectionSetChart(parentSection,0,pNewEnd[dim]);
1982: offset = 0;
1983: numNewCones = 0;
1984: for (d = 0; d <= dim; d++) {
1985: PetscInt kStart, kEnd, k;
1986: PetscInt p;
1987: PetscInt size;
1989: for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
1990: /* skip cell 0 */
1991: if (p == cell) continue;
1992: /* old cones to new cones */
1993: DMPlexGetConeSize(dm,p,&size);
1994: newConeSizes[offset++] = size;
1995: numNewCones += size;
1996: }
1998: DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
1999: for (k = kStart; k < kEnd; k++) {
2000: PetscInt kParent;
2002: DMPlexGetTreeParent(K,k,&kParent,NULL);
2003: if (kParent != k) {
2004: Kembedding[k] = offset;
2005: DMPlexGetConeSize(K,k,&size);
2006: newConeSizes[offset++] = size;
2007: numNewCones += size;
2008: if (kParent != 0) {
2009: PetscSectionSetDof(parentSection,Kembedding[k],1);
2010: }
2011: }
2012: }
2013: }
2015: PetscSectionSetUp(parentSection);
2016: PetscSectionGetStorageSize(parentSection,&numPointsWithParents);
2017: PetscMalloc2(numNewCones,&newCones,numNewCones,&newOrientations);
2018: PetscMalloc2(numPointsWithParents,&parents,numPointsWithParents,&childIDs);
2020: /* fill new cones */
2021: offset = 0;
2022: for (d = 0; d <= dim; d++) {
2023: PetscInt kStart, kEnd, k, l;
2024: PetscInt p;
2025: PetscInt size;
2026: const PetscInt *cone, *orientation;
2028: for (p = pOldStart[d]; p < pOldEnd[d]; p++) {
2029: /* skip cell 0 */
2030: if (p == cell) continue;
2031: /* old cones to new cones */
2032: DMPlexGetConeSize(dm,p,&size);
2033: DMPlexGetCone(dm,p,&cone);
2034: DMPlexGetConeOrientation(dm,p,&orientation);
2035: for (l = 0; l < size; l++) {
2036: newCones[offset] = (cone[l] - pOldStart[d + 1]) + pNewStart[d + 1];
2037: newOrientations[offset++] = orientation[l];
2038: }
2039: }
2041: DMPlexGetHeightStratum(K,d,&kStart,&kEnd);
2042: for (k = kStart; k < kEnd; k++) {
2043: PetscInt kPerm = perm[k], kParent;
2044: PetscInt preO = preOrient[k];
2046: DMPlexGetTreeParent(K,k,&kParent,NULL);
2047: if (kParent != k) {
2048: /* embed new cones */
2049: DMPlexGetConeSize(K,k,&size);
2050: DMPlexGetCone(K,kPerm,&cone);
2051: DMPlexGetConeOrientation(K,kPerm,&orientation);
2052: for (l = 0; l < size; l++) {
2053: PetscInt q, m = (preO >= 0) ? ((preO + l) % size) : ((size -(preO + 1) - l) % size);
2054: PetscInt newO, lSize, oTrue;
2056: q = iperm[cone[m]];
2057: newCones[offset] = Kembedding[q];
2058: DMPlexGetConeSize(K,q,&lSize);
2059: oTrue = orientation[m];
2060: oTrue = ((!lSize) || (preOrient[k] >= 0)) ? oTrue : -(oTrue + 2);
2061: newO = DihedralCompose(lSize,oTrue,preOrient[q]);
2062: newOrientations[offset++] = newO;
2063: }
2064: if (kParent != 0) {
2065: PetscInt newPoint = Kembedding[kParent];
2066: PetscSectionGetOffset(parentSection,Kembedding[k],&pOffset);
2067: parents[pOffset] = newPoint;
2068: childIDs[pOffset] = k;
2069: }
2070: }
2071: }
2072: }
2074: PetscMalloc1(dim*(pNewEnd[dim]-pNewStart[dim]),&newVertexCoords);
2076: /* fill coordinates */
2077: offset = 0;
2078: {
2079: PetscInt kStart, kEnd, l;
2080: PetscSection vSection;
2081: PetscInt v;
2082: Vec coords;
2083: PetscScalar *coordvals;
2084: PetscInt dof, off;
2085: PetscReal v0[3], J[9], detJ;
2087: #if defined(PETSC_USE_DEBUG)
2088: {
2089: PetscInt k;
2090: DMPlexGetHeightStratum(K,0,&kStart,&kEnd);
2091: for (k = kStart; k < kEnd; k++) {
2092: DMPlexComputeCellGeometryFEM(K, k, NULL, v0, J, NULL, &detJ);
2093: if (detJ <= 0.) SETERRQ1 (PETSC_COMM_SELF,PETSC_ERR_PLIB,"reference tree cell %d has bad determinant",k);
2094: }
2095: }
2096: #endif
2097: DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, NULL, &detJ);
2098: DMGetCoordinateSection(dm,&vSection);
2099: DMGetCoordinatesLocal(dm,&coords);
2100: VecGetArray(coords,&coordvals);
2101: for (v = pOldStart[dim]; v < pOldEnd[dim]; v++) {
2103: PetscSectionGetDof(vSection,v,&dof);
2104: PetscSectionGetOffset(vSection,v,&off);
2105: for (l = 0; l < dof; l++) {
2106: newVertexCoords[offset++] = coordvals[off + l];
2107: }
2108: }
2109: VecRestoreArray(coords,&coordvals);
2111: DMGetCoordinateSection(K,&vSection);
2112: DMGetCoordinatesLocal(K,&coords);
2113: VecGetArray(coords,&coordvals);
2114: DMPlexGetDepthStratum(K,0,&kStart,&kEnd);
2115: for (v = kStart; v < kEnd; v++) {
2116: PetscReal coord[3], newCoord[3];
2117: PetscInt vPerm = perm[v];
2118: PetscInt kParent;
2119: const PetscReal xi0[3] = {-1.,-1.,-1.};
2121: DMPlexGetTreeParent(K,v,&kParent,NULL);
2122: if (kParent != v) {
2123: /* this is a new vertex */
2124: PetscSectionGetOffset(vSection,vPerm,&off);
2125: for (l = 0; l < dim; ++l) coord[l] = PetscRealPart(coordvals[off+l]);
2126: CoordinatesRefToReal(dim, dim, xi0, v0, J, coord, newCoord);
2127: for (l = 0; l < dim; ++l) newVertexCoords[offset+l] = newCoord[l];
2128: offset += dim;
2129: }
2130: }
2131: VecRestoreArray(coords,&coordvals);
2132: }
2134: /* need to reverse the order of pNewCount: vertices first, cells last */
2135: for (d = 0; d < (dim + 1) / 2; d++) {
2136: PetscInt tmp;
2138: tmp = pNewCount[d];
2139: pNewCount[d] = pNewCount[dim - d];
2140: pNewCount[dim - d] = tmp;
2141: }
2143: DMPlexCreateFromDAG(*ncdm,dim,pNewCount,newConeSizes,newCones,newOrientations,newVertexCoords);
2144: DMPlexSetReferenceTree(*ncdm,K);
2145: DMPlexSetTree(*ncdm,parentSection,parents,childIDs);
2147: /* clean up */
2148: DMPlexRestoreTransitiveClosure(dm,cell,PETSC_TRUE,&nc,&cellClosure);
2149: PetscFree5(pNewCount,pNewStart,pNewEnd,pOldStart,pOldEnd);
2150: PetscFree(newConeSizes);
2151: PetscFree2(newCones,newOrientations);
2152: PetscFree(newVertexCoords);
2153: PetscFree2(parents,childIDs);
2154: PetscFree4(Kembedding,perm,iperm,preOrient);
2155: }
2156: else {
2157: PetscInt p, counts[4];
2158: PetscInt *coneSizes, *cones, *orientations;
2159: Vec coordVec;
2160: PetscScalar *coords;
2162: for (d = 0; d <= dim; d++) {
2163: PetscInt dStart, dEnd;
2165: DMPlexGetDepthStratum(dm,d,&dStart,&dEnd);
2166: counts[d] = dEnd - dStart;
2167: }
2168: PetscMalloc1(pEnd-pStart,&coneSizes);
2169: for (p = pStart; p < pEnd; p++) {
2170: DMPlexGetConeSize(dm,p,&coneSizes[p-pStart]);
2171: }
2172: DMPlexGetCones(dm, &cones);
2173: DMPlexGetConeOrientations(dm, &orientations);
2174: DMGetCoordinatesLocal(dm,&coordVec);
2175: VecGetArray(coordVec,&coords);
2177: PetscSectionSetChart(parentSection,pStart,pEnd);
2178: PetscSectionSetUp(parentSection);
2179: DMPlexCreateFromDAG(*ncdm,dim,counts,coneSizes,cones,orientations,NULL);
2180: DMPlexSetReferenceTree(*ncdm,K);
2181: DMPlexSetTree(*ncdm,parentSection,NULL,NULL);
2182: VecRestoreArray(coordVec,&coords);
2183: }
2184: PetscSectionDestroy(&parentSection);
2186: return(0);
2187: }
2189: PetscErrorCode DMPlexComputeInterpolatorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
2190: {
2191: PetscSF coarseToFineEmbedded;
2192: PetscSection globalCoarse, globalFine;
2193: PetscSection localCoarse, localFine;
2194: PetscSection aSec, cSec;
2195: PetscSection rootIndicesSec, rootMatricesSec;
2196: PetscSection leafIndicesSec, leafMatricesSec;
2197: PetscInt *rootIndices, *leafIndices;
2198: PetscScalar *rootMatrices, *leafMatrices;
2199: IS aIS;
2200: const PetscInt *anchors;
2201: Mat cMat;
2202: PetscInt numFields, maxFields;
2203: PetscInt pStartC, pEndC, pStartF, pEndF, p;
2204: PetscInt aStart, aEnd, cStart, cEnd;
2205: PetscInt *maxChildIds;
2206: PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;
2207: const PetscInt ***perms;
2208: const PetscScalar ***flips;
2209: PetscErrorCode ierr;
2212: DMPlexGetChart(coarse,&pStartC,&pEndC);
2213: DMPlexGetChart(fine,&pStartF,&pEndF);
2214: DMGetGlobalSection(fine,&globalFine);
2215: { /* winnow fine points that don't have global dofs out of the sf */
2216: PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, nleaves, l;
2217: const PetscInt *leaves;
2219: PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
2220: for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
2221: p = leaves ? leaves[l] : l;
2222: PetscSectionGetDof(globalFine,p,&dof);
2223: PetscSectionGetConstraintDof(globalFine,p,&cdof);
2224: if ((dof - cdof) > 0) {
2225: numPointsWithDofs++;
2226: }
2227: }
2228: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
2229: for (l = 0, offset = 0; l < nleaves; l++) {
2230: p = leaves ? leaves[l] : l;
2231: PetscSectionGetDof(globalFine,p,&dof);
2232: PetscSectionGetConstraintDof(globalFine,p,&cdof);
2233: if ((dof - cdof) > 0) {
2234: pointsWithDofs[offset++] = l;
2235: }
2236: }
2237: PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
2238: PetscFree(pointsWithDofs);
2239: }
2240: /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
2241: PetscMalloc1(pEndC-pStartC,&maxChildIds);
2242: for (p = pStartC; p < pEndC; p++) {
2243: maxChildIds[p - pStartC] = -2;
2244: }
2245: PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);
2246: PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,childIds,maxChildIds,MPIU_MAX);
2248: DMGetLocalSection(coarse,&localCoarse);
2249: DMGetGlobalSection(coarse,&globalCoarse);
2251: DMPlexGetAnchors(coarse,&aSec,&aIS);
2252: ISGetIndices(aIS,&anchors);
2253: PetscSectionGetChart(aSec,&aStart,&aEnd);
2255: DMGetDefaultConstraints(coarse,&cSec,&cMat);
2256: PetscSectionGetChart(cSec,&cStart,&cEnd);
2258: /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
2259: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
2260: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootMatricesSec);
2261: PetscSectionSetChart(rootIndicesSec,pStartC,pEndC);
2262: PetscSectionSetChart(rootMatricesSec,pStartC,pEndC);
2263: PetscSectionGetNumFields(localCoarse,&numFields);
2264: maxFields = PetscMax(1,numFields);
2265: PetscMalloc7(maxFields+1,&offsets,maxFields+1,&offsetsCopy,maxFields+1,&newOffsets,maxFields+1,&newOffsetsCopy,maxFields+1,&rowOffsets,maxFields+1,&numD,maxFields+1,&numO);
2266: PetscMalloc2(maxFields+1,(PetscInt****)&perms,maxFields+1,(PetscScalar****)&flips);
2267: PetscMemzero((void *) perms, (maxFields+1) * sizeof(const PetscInt **));
2268: PetscMemzero((void *) flips, (maxFields+1) * sizeof(const PetscScalar **));
2270: for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
2271: PetscInt dof, matSize = 0;
2272: PetscInt aDof = 0;
2273: PetscInt cDof = 0;
2274: PetscInt maxChildId = maxChildIds[p - pStartC];
2275: PetscInt numRowIndices = 0;
2276: PetscInt numColIndices = 0;
2277: PetscInt f;
2279: PetscSectionGetDof(globalCoarse,p,&dof);
2280: if (dof < 0) {
2281: dof = -(dof + 1);
2282: }
2283: if (p >= aStart && p < aEnd) {
2284: PetscSectionGetDof(aSec,p,&aDof);
2285: }
2286: if (p >= cStart && p < cEnd) {
2287: PetscSectionGetDof(cSec,p,&cDof);
2288: }
2289: for (f = 0; f <= numFields; f++) offsets[f] = 0;
2290: for (f = 0; f <= numFields; f++) newOffsets[f] = 0;
2291: if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
2292: PetscInt *closure = NULL, closureSize, cl;
2294: DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
2295: for (cl = 0; cl < closureSize; cl++) { /* get the closure */
2296: PetscInt c = closure[2 * cl], clDof;
2298: PetscSectionGetDof(localCoarse,c,&clDof);
2299: numRowIndices += clDof;
2300: for (f = 0; f < numFields; f++) {
2301: PetscSectionGetFieldDof(localCoarse,c,f,&clDof);
2302: offsets[f + 1] += clDof;
2303: }
2304: }
2305: for (f = 0; f < numFields; f++) {
2306: offsets[f + 1] += offsets[f];
2307: newOffsets[f + 1] = offsets[f + 1];
2308: }
2309: /* get the number of indices needed and their field offsets */
2310: DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,NULL,NULL,NULL,&numColIndices,NULL,NULL,newOffsets,PETSC_FALSE);
2311: DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
2312: if (!numColIndices) { /* there are no hanging constraint modifications, so the matrix is just the identity: do not send it */
2313: numColIndices = numRowIndices;
2314: matSize = 0;
2315: }
2316: else if (numFields) { /* we send one submat for each field: sum their sizes */
2317: matSize = 0;
2318: for (f = 0; f < numFields; f++) {
2319: PetscInt numRow, numCol;
2321: numRow = offsets[f + 1] - offsets[f];
2322: numCol = newOffsets[f + 1] - newOffsets[f];
2323: matSize += numRow * numCol;
2324: }
2325: }
2326: else {
2327: matSize = numRowIndices * numColIndices;
2328: }
2329: } else if (maxChildId == -1) {
2330: if (cDof > 0) { /* this point's dofs are interpolated via cMat: get the submatrix of cMat */
2331: PetscInt aOff, a;
2333: PetscSectionGetOffset(aSec,p,&aOff);
2334: for (f = 0; f < numFields; f++) {
2335: PetscInt fDof;
2337: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
2338: offsets[f+1] = fDof;
2339: }
2340: for (a = 0; a < aDof; a++) {
2341: PetscInt anchor = anchors[a + aOff], aLocalDof;
2343: PetscSectionGetDof(localCoarse,anchor,&aLocalDof);
2344: numColIndices += aLocalDof;
2345: for (f = 0; f < numFields; f++) {
2346: PetscInt fDof;
2348: PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
2349: newOffsets[f+1] += fDof;
2350: }
2351: }
2352: if (numFields) {
2353: matSize = 0;
2354: for (f = 0; f < numFields; f++) {
2355: matSize += offsets[f+1] * newOffsets[f+1];
2356: }
2357: }
2358: else {
2359: matSize = numColIndices * dof;
2360: }
2361: }
2362: else { /* no children, and no constraints on dofs: just get the global indices */
2363: numColIndices = dof;
2364: matSize = 0;
2365: }
2366: }
2367: /* we will pack the column indices with the field offsets */
2368: PetscSectionSetDof(rootIndicesSec,p,numColIndices ? numColIndices+2*numFields : 0);
2369: PetscSectionSetDof(rootMatricesSec,p,matSize);
2370: }
2371: PetscSectionSetUp(rootIndicesSec);
2372: PetscSectionSetUp(rootMatricesSec);
2373: {
2374: PetscInt numRootIndices, numRootMatrices;
2376: PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
2377: PetscSectionGetStorageSize(rootMatricesSec,&numRootMatrices);
2378: PetscMalloc2(numRootIndices,&rootIndices,numRootMatrices,&rootMatrices);
2379: for (p = pStartC; p < pEndC; p++) {
2380: PetscInt numRowIndices, numColIndices, matSize, dof;
2381: PetscInt pIndOff, pMatOff, f;
2382: PetscInt *pInd;
2383: PetscInt maxChildId = maxChildIds[p - pStartC];
2384: PetscScalar *pMat = NULL;
2386: PetscSectionGetDof(rootIndicesSec,p,&numColIndices);
2387: if (!numColIndices) {
2388: continue;
2389: }
2390: for (f = 0; f <= numFields; f++) {
2391: offsets[f] = 0;
2392: newOffsets[f] = 0;
2393: offsetsCopy[f] = 0;
2394: newOffsetsCopy[f] = 0;
2395: }
2396: numColIndices -= 2 * numFields;
2397: PetscSectionGetOffset(rootIndicesSec,p,&pIndOff);
2398: pInd = &(rootIndices[pIndOff]);
2399: PetscSectionGetDof(rootMatricesSec,p,&matSize);
2400: if (matSize) {
2401: PetscSectionGetOffset(rootMatricesSec,p,&pMatOff);
2402: pMat = &rootMatrices[pMatOff];
2403: }
2404: PetscSectionGetDof(globalCoarse,p,&dof);
2405: if (dof < 0) {
2406: dof = -(dof + 1);
2407: }
2408: if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
2409: PetscInt i, j;
2410: PetscInt numRowIndices = matSize / numColIndices;
2412: if (!numRowIndices) { /* don't need to calculate the mat, just the indices */
2413: PetscInt numIndices, *indices;
2414: DMPlexGetClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
2415: if (numIndices != numColIndices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"mismatching constraint indices calculations");
2416: for (i = 0; i < numColIndices; i++) {
2417: pInd[i] = indices[i];
2418: }
2419: for (i = 0; i < numFields; i++) {
2420: pInd[numColIndices + i] = offsets[i+1];
2421: pInd[numColIndices + numFields + i] = offsets[i+1];
2422: }
2423: DMPlexRestoreClosureIndices(coarse,localCoarse,globalCoarse,p,&numIndices,&indices,offsets);
2424: }
2425: else {
2426: PetscInt closureSize, *closure = NULL, cl;
2427: PetscScalar *pMatIn, *pMatModified;
2428: PetscInt numPoints,*points;
2430: DMGetWorkArray(coarse,numRowIndices * numRowIndices,MPIU_SCALAR,&pMatIn);
2431: for (i = 0; i < numRowIndices; i++) { /* initialize to the identity */
2432: for (j = 0; j < numRowIndices; j++) {
2433: pMatIn[i * numRowIndices + j] = (i == j) ? 1. : 0.;
2434: }
2435: }
2436: DMPlexGetTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
2437: for (f = 0; f < maxFields; f++) {
2438: if (numFields) {PetscSectionGetFieldPointSyms(localCoarse,f,closureSize,closure,&perms[f],&flips[f]);}
2439: else {PetscSectionGetPointSyms(localCoarse,closureSize,closure,&perms[f],&flips[f]);}
2440: }
2441: if (numFields) {
2442: for (cl = 0; cl < closureSize; cl++) {
2443: PetscInt c = closure[2 * cl];
2445: for (f = 0; f < numFields; f++) {
2446: PetscInt fDof;
2448: PetscSectionGetFieldDof(localCoarse,c,f,&fDof);
2449: offsets[f + 1] += fDof;
2450: }
2451: }
2452: for (f = 0; f < numFields; f++) {
2453: offsets[f + 1] += offsets[f];
2454: newOffsets[f + 1] = offsets[f + 1];
2455: }
2456: }
2457: /* TODO : flips here ? */
2458: /* apply hanging node constraints on the right, get the new points and the new offsets */
2459: DMPlexAnchorsModifyMat(coarse,localCoarse,closureSize,numRowIndices,closure,perms,pMatIn,&numPoints,NULL,&points,&pMatModified,newOffsets,PETSC_FALSE);
2460: for (f = 0; f < maxFields; f++) {
2461: if (numFields) {PetscSectionRestoreFieldPointSyms(localCoarse,f,closureSize,closure,&perms[f],&flips[f]);}
2462: else {PetscSectionRestorePointSyms(localCoarse,closureSize,closure,&perms[f],&flips[f]);}
2463: }
2464: for (f = 0; f < maxFields; f++) {
2465: if (numFields) {PetscSectionGetFieldPointSyms(localCoarse,f,numPoints,points,&perms[f],&flips[f]);}
2466: else {PetscSectionGetPointSyms(localCoarse,numPoints,points,&perms[f],&flips[f]);}
2467: }
2468: if (!numFields) {
2469: for (i = 0; i < numRowIndices * numColIndices; i++) {
2470: pMat[i] = pMatModified[i];
2471: }
2472: }
2473: else {
2474: PetscInt i, j, count;
2475: for (f = 0, count = 0; f < numFields; f++) {
2476: for (i = offsets[f]; i < offsets[f+1]; i++) {
2477: for (j = newOffsets[f]; j < newOffsets[f+1]; j++, count++) {
2478: pMat[count] = pMatModified[i * numColIndices + j];
2479: }
2480: }
2481: }
2482: }
2483: DMRestoreWorkArray(coarse,numRowIndices * numColIndices,MPIU_SCALAR,&pMatModified);
2484: DMPlexRestoreTransitiveClosure(coarse, p, PETSC_TRUE, &closureSize, &closure);
2485: DMRestoreWorkArray(coarse,numRowIndices * numColIndices,MPIU_SCALAR,&pMatIn);
2486: if (numFields) {
2487: for (f = 0; f < numFields; f++) {
2488: pInd[numColIndices + f] = offsets[f+1];
2489: pInd[numColIndices + numFields + f] = newOffsets[f+1];
2490: }
2491: for (cl = 0; cl < numPoints; cl++) {
2492: PetscInt globalOff, c = points[2*cl];
2493: PetscSectionGetOffset(globalCoarse, c, &globalOff);
2494: DMPlexGetIndicesPointFields_Internal(localCoarse, PETSC_FALSE, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, perms, cl, NULL, pInd);
2495: }
2496: } else {
2497: for (cl = 0; cl < numPoints; cl++) {
2498: PetscInt c = points[2*cl], globalOff;
2499: const PetscInt *perm = perms[0] ? perms[0][cl] : NULL;
2501: PetscSectionGetOffset(globalCoarse, c, &globalOff);
2502: DMPlexGetIndicesPoint_Internal(localCoarse, PETSC_FALSE, c, globalOff < 0 ? -(globalOff+1) : globalOff, newOffsets, PETSC_FALSE, perm, NULL, pInd);
2503: }
2504: }
2505: for (f = 0; f < maxFields; f++) {
2506: if (numFields) {PetscSectionRestoreFieldPointSyms(localCoarse,f,numPoints,points,&perms[f],&flips[f]);}
2507: else {PetscSectionRestorePointSyms(localCoarse,numPoints,points,&perms[f],&flips[f]);}
2508: }
2509: DMRestoreWorkArray(coarse,numPoints,MPIU_SCALAR,&points);
2510: }
2511: }
2512: else if (matSize) {
2513: PetscInt cOff;
2514: PetscInt *rowIndices, *colIndices, a, aDof, aOff;
2516: numRowIndices = matSize / numColIndices;
2517: if (numRowIndices != dof) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Miscounted dofs");
2518: DMGetWorkArray(coarse,numRowIndices,MPIU_INT,&rowIndices);
2519: DMGetWorkArray(coarse,numColIndices,MPIU_INT,&colIndices);
2520: PetscSectionGetOffset(cSec,p,&cOff);
2521: PetscSectionGetDof(aSec,p,&aDof);
2522: PetscSectionGetOffset(aSec,p,&aOff);
2523: if (numFields) {
2524: for (f = 0; f < numFields; f++) {
2525: PetscInt fDof;
2527: PetscSectionGetFieldDof(cSec,p,f,&fDof);
2528: offsets[f + 1] = fDof;
2529: for (a = 0; a < aDof; a++) {
2530: PetscInt anchor = anchors[a + aOff];
2531: PetscSectionGetFieldDof(localCoarse,anchor,f,&fDof);
2532: newOffsets[f + 1] += fDof;
2533: }
2534: }
2535: for (f = 0; f < numFields; f++) {
2536: offsets[f + 1] += offsets[f];
2537: offsetsCopy[f + 1] = offsets[f + 1];
2538: newOffsets[f + 1] += newOffsets[f];
2539: newOffsetsCopy[f + 1] = newOffsets[f + 1];
2540: }
2541: DMPlexGetIndicesPointFields_Internal(cSec,PETSC_TRUE,p,cOff,offsetsCopy,PETSC_TRUE,NULL,-1, NULL,rowIndices);
2542: for (a = 0; a < aDof; a++) {
2543: PetscInt anchor = anchors[a + aOff], lOff;
2544: PetscSectionGetOffset(localCoarse,anchor,&lOff);
2545: DMPlexGetIndicesPointFields_Internal(localCoarse,PETSC_TRUE,anchor,lOff,newOffsetsCopy,PETSC_TRUE,NULL,-1, NULL,colIndices);
2546: }
2547: }
2548: else {
2549: DMPlexGetIndicesPoint_Internal(cSec,PETSC_TRUE,p,cOff,offsetsCopy,PETSC_TRUE,NULL, NULL,rowIndices);
2550: for (a = 0; a < aDof; a++) {
2551: PetscInt anchor = anchors[a + aOff], lOff;
2552: PetscSectionGetOffset(localCoarse,anchor,&lOff);
2553: DMPlexGetIndicesPoint_Internal(localCoarse,PETSC_TRUE,anchor,lOff,newOffsetsCopy,PETSC_TRUE,NULL, NULL,colIndices);
2554: }
2555: }
2556: if (numFields) {
2557: PetscInt count, a;
2559: for (f = 0, count = 0; f < numFields; f++) {
2560: PetscInt iSize = offsets[f + 1] - offsets[f];
2561: PetscInt jSize = newOffsets[f + 1] - newOffsets[f];
2562: MatGetValues(cMat,iSize,&rowIndices[offsets[f]],jSize,&colIndices[newOffsets[f]],&pMat[count]);
2563: count += iSize * jSize;
2564: pInd[numColIndices + f] = offsets[f+1];
2565: pInd[numColIndices + numFields + f] = newOffsets[f+1];
2566: }
2567: for (a = 0; a < aDof; a++) {
2568: PetscInt anchor = anchors[a + aOff];
2569: PetscInt gOff;
2570: PetscSectionGetOffset(globalCoarse,anchor,&gOff);
2571: DMPlexGetIndicesPointFields_Internal(localCoarse,PETSC_FALSE,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,NULL,-1, NULL,pInd);
2572: }
2573: }
2574: else {
2575: PetscInt a;
2576: MatGetValues(cMat,numRowIndices,rowIndices,numColIndices,colIndices,pMat);
2577: for (a = 0; a < aDof; a++) {
2578: PetscInt anchor = anchors[a + aOff];
2579: PetscInt gOff;
2580: PetscSectionGetOffset(globalCoarse,anchor,&gOff);
2581: DMPlexGetIndicesPoint_Internal(localCoarse,PETSC_FALSE,anchor,gOff < 0 ? -(gOff + 1) : gOff,newOffsets,PETSC_FALSE,NULL, NULL,pInd);
2582: }
2583: }
2584: DMRestoreWorkArray(coarse,numColIndices,MPIU_INT,&colIndices);
2585: DMRestoreWorkArray(coarse,numRowIndices,MPIU_INT,&rowIndices);
2586: }
2587: else {
2588: PetscInt gOff;
2590: PetscSectionGetOffset(globalCoarse,p,&gOff);
2591: if (numFields) {
2592: for (f = 0; f < numFields; f++) {
2593: PetscInt fDof;
2594: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
2595: offsets[f + 1] = fDof + offsets[f];
2596: }
2597: for (f = 0; f < numFields; f++) {
2598: pInd[numColIndices + f] = offsets[f+1];
2599: pInd[numColIndices + numFields + f] = offsets[f+1];
2600: }
2601: DMPlexGetIndicesPointFields_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,-1, NULL,pInd);
2602: } else {
2603: DMPlexGetIndicesPoint_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL, NULL,pInd);
2604: }
2605: }
2606: }
2607: PetscFree(maxChildIds);
2608: }
2609: {
2610: PetscSF indicesSF, matricesSF;
2611: PetscInt *remoteOffsetsIndices, *remoteOffsetsMatrices, numLeafIndices, numLeafMatrices;
2613: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
2614: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafMatricesSec);
2615: PetscSFDistributeSection(coarseToFineEmbedded,rootIndicesSec,&remoteOffsetsIndices,leafIndicesSec);
2616: PetscSFDistributeSection(coarseToFineEmbedded,rootMatricesSec,&remoteOffsetsMatrices,leafMatricesSec);
2617: PetscSFCreateSectionSF(coarseToFineEmbedded,rootIndicesSec,remoteOffsetsIndices,leafIndicesSec,&indicesSF);
2618: PetscSFCreateSectionSF(coarseToFineEmbedded,rootMatricesSec,remoteOffsetsMatrices,leafMatricesSec,&matricesSF);
2619: PetscSFDestroy(&coarseToFineEmbedded);
2620: PetscFree(remoteOffsetsIndices);
2621: PetscFree(remoteOffsetsMatrices);
2622: PetscSectionGetStorageSize(leafIndicesSec,&numLeafIndices);
2623: PetscSectionGetStorageSize(leafMatricesSec,&numLeafMatrices);
2624: PetscMalloc2(numLeafIndices,&leafIndices,numLeafMatrices,&leafMatrices);
2625: PetscSFBcastBegin(indicesSF,MPIU_INT,rootIndices,leafIndices);
2626: PetscSFBcastBegin(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
2627: PetscSFBcastEnd(indicesSF,MPIU_INT,rootIndices,leafIndices);
2628: PetscSFBcastEnd(matricesSF,MPIU_SCALAR,rootMatrices,leafMatrices);
2629: PetscSFDestroy(&matricesSF);
2630: PetscSFDestroy(&indicesSF);
2631: PetscFree2(rootIndices,rootMatrices);
2632: PetscSectionDestroy(&rootIndicesSec);
2633: PetscSectionDestroy(&rootMatricesSec);
2634: }
2635: /* count to preallocate */
2636: DMGetLocalSection(fine,&localFine);
2637: {
2638: PetscInt nGlobal;
2639: PetscInt *dnnz, *onnz;
2640: PetscLayout rowMap, colMap;
2641: PetscInt rowStart, rowEnd, colStart, colEnd;
2642: PetscInt maxDof;
2643: PetscInt *rowIndices;
2644: DM refTree;
2645: PetscInt **refPointFieldN;
2646: PetscScalar ***refPointFieldMats;
2647: PetscSection refConSec, refAnSec;
2648: PetscInt pRefStart,pRefEnd,maxConDof,maxColumns,leafStart,leafEnd;
2649: PetscScalar *pointWork;
2651: PetscSectionGetConstrainedStorageSize(globalFine,&nGlobal);
2652: PetscCalloc2(nGlobal,&dnnz,nGlobal,&onnz);
2653: MatGetLayouts(mat,&rowMap,&colMap);
2654: PetscLayoutSetUp(rowMap);
2655: PetscLayoutSetUp(colMap);
2656: PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
2657: PetscLayoutGetRange(colMap,&colStart,&colEnd);
2658: PetscSectionGetMaxDof(globalFine,&maxDof);
2659: PetscSectionGetChart(leafIndicesSec,&leafStart,&leafEnd);
2660: DMGetWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
2661: for (p = leafStart; p < leafEnd; p++) {
2662: PetscInt gDof, gcDof, gOff;
2663: PetscInt numColIndices, pIndOff, *pInd;
2664: PetscInt matSize;
2665: PetscInt i;
2667: PetscSectionGetDof(globalFine,p,&gDof);
2668: PetscSectionGetConstraintDof(globalFine,p,&gcDof);
2669: if ((gDof - gcDof) <= 0) {
2670: continue;
2671: }
2672: PetscSectionGetOffset(globalFine,p,&gOff);
2673: if (gOff < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I though having global dofs meant a non-negative offset");
2674: if ((gOff < rowStart) || ((gOff + gDof - gcDof) > rowEnd)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"I thought the row map would constrain the global dofs");
2675: PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
2676: PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
2677: numColIndices -= 2 * numFields;
2678: if (numColIndices <= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"global fine dof with no dofs to interpolate from");
2679: pInd = &leafIndices[pIndOff];
2680: offsets[0] = 0;
2681: offsetsCopy[0] = 0;
2682: newOffsets[0] = 0;
2683: newOffsetsCopy[0] = 0;
2684: if (numFields) {
2685: PetscInt f;
2686: for (f = 0; f < numFields; f++) {
2687: PetscInt rowDof;
2689: PetscSectionGetFieldDof(localFine,p,f,&rowDof);
2690: offsets[f + 1] = offsets[f] + rowDof;
2691: offsetsCopy[f + 1] = offsets[f + 1];
2692: newOffsets[f + 1] = pInd[numColIndices + numFields + f];
2693: numD[f] = 0;
2694: numO[f] = 0;
2695: }
2696: DMPlexGetIndicesPointFields_Internal(localFine,PETSC_FALSE,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1, NULL,rowIndices);
2697: for (f = 0; f < numFields; f++) {
2698: PetscInt colOffset = newOffsets[f];
2699: PetscInt numFieldCols = newOffsets[f + 1] - newOffsets[f];
2701: for (i = 0; i < numFieldCols; i++) {
2702: PetscInt gInd = pInd[i + colOffset];
2704: if (gInd >= colStart && gInd < colEnd) {
2705: numD[f]++;
2706: }
2707: else if (gInd >= 0) { /* negative means non-entry */
2708: numO[f]++;
2709: }
2710: }
2711: }
2712: }
2713: else {
2714: DMPlexGetIndicesPoint_Internal(localFine,PETSC_FALSE,p,gOff,offsetsCopy,PETSC_FALSE,NULL, NULL,rowIndices);
2715: numD[0] = 0;
2716: numO[0] = 0;
2717: for (i = 0; i < numColIndices; i++) {
2718: PetscInt gInd = pInd[i];
2720: if (gInd >= colStart && gInd < colEnd) {
2721: numD[0]++;
2722: }
2723: else if (gInd >= 0) { /* negative means non-entry */
2724: numO[0]++;
2725: }
2726: }
2727: }
2728: PetscSectionGetDof(leafMatricesSec,p,&matSize);
2729: if (!matSize) { /* incoming matrix is identity */
2730: PetscInt childId;
2732: childId = childIds[p-pStartF];
2733: if (childId < 0) { /* no child interpolation: one nnz per */
2734: if (numFields) {
2735: PetscInt f;
2736: for (f = 0; f < numFields; f++) {
2737: PetscInt numRows = offsets[f+1] - offsets[f], row;
2738: for (row = 0; row < numRows; row++) {
2739: PetscInt gIndCoarse = pInd[newOffsets[f] + row];
2740: PetscInt gIndFine = rowIndices[offsets[f] + row];
2741: if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
2742: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2743: dnnz[gIndFine - rowStart] = 1;
2744: }
2745: else if (gIndCoarse >= 0) { /* remote */
2746: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2747: onnz[gIndFine - rowStart] = 1;
2748: }
2749: else { /* constrained */
2750: if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2751: }
2752: }
2753: }
2754: }
2755: else {
2756: PetscInt i;
2757: for (i = 0; i < gDof; i++) {
2758: PetscInt gIndCoarse = pInd[i];
2759: PetscInt gIndFine = rowIndices[i];
2760: if (gIndCoarse >= colStart && gIndCoarse < colEnd) { /* local */
2761: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2762: dnnz[gIndFine - rowStart] = 1;
2763: }
2764: else if (gIndCoarse >= 0) { /* remote */
2765: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2766: onnz[gIndFine - rowStart] = 1;
2767: }
2768: else { /* constrained */
2769: if (gIndFine >= 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2770: }
2771: }
2772: }
2773: }
2774: else { /* interpolate from all */
2775: if (numFields) {
2776: PetscInt f;
2777: for (f = 0; f < numFields; f++) {
2778: PetscInt numRows = offsets[f+1] - offsets[f], row;
2779: for (row = 0; row < numRows; row++) {
2780: PetscInt gIndFine = rowIndices[offsets[f] + row];
2781: if (gIndFine >= 0) {
2782: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2783: dnnz[gIndFine - rowStart] = numD[f];
2784: onnz[gIndFine - rowStart] = numO[f];
2785: }
2786: }
2787: }
2788: }
2789: else {
2790: PetscInt i;
2791: for (i = 0; i < gDof; i++) {
2792: PetscInt gIndFine = rowIndices[i];
2793: if (gIndFine >= 0) {
2794: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2795: dnnz[gIndFine - rowStart] = numD[0];
2796: onnz[gIndFine - rowStart] = numO[0];
2797: }
2798: }
2799: }
2800: }
2801: }
2802: else { /* interpolate from all */
2803: if (numFields) {
2804: PetscInt f;
2805: for (f = 0; f < numFields; f++) {
2806: PetscInt numRows = offsets[f+1] - offsets[f], row;
2807: for (row = 0; row < numRows; row++) {
2808: PetscInt gIndFine = rowIndices[offsets[f] + row];
2809: if (gIndFine >= 0) {
2810: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2811: dnnz[gIndFine - rowStart] = numD[f];
2812: onnz[gIndFine - rowStart] = numO[f];
2813: }
2814: }
2815: }
2816: }
2817: else { /* every dof get a full row */
2818: PetscInt i;
2819: for (i = 0; i < gDof; i++) {
2820: PetscInt gIndFine = rowIndices[i];
2821: if (gIndFine >= 0) {
2822: if (gIndFine < rowStart || gIndFine >= rowEnd) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Mismatched number of constrained dofs");
2823: dnnz[gIndFine - rowStart] = numD[0];
2824: onnz[gIndFine - rowStart] = numO[0];
2825: }
2826: }
2827: }
2828: }
2829: }
2830: MatXAIJSetPreallocation(mat,1,dnnz,onnz,NULL,NULL);
2831: PetscFree2(dnnz,onnz);
2833: DMPlexGetReferenceTree(fine,&refTree);
2834: DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
2835: DMGetDefaultConstraints(refTree,&refConSec,NULL);
2836: DMPlexGetAnchors(refTree,&refAnSec,NULL);
2837: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
2838: PetscSectionGetMaxDof(refConSec,&maxConDof);
2839: PetscSectionGetMaxDof(leafIndicesSec,&maxColumns);
2840: PetscMalloc1(maxConDof*maxColumns,&pointWork);
2841: for (p = leafStart; p < leafEnd; p++) {
2842: PetscInt gDof, gcDof, gOff;
2843: PetscInt numColIndices, pIndOff, *pInd;
2844: PetscInt matSize;
2845: PetscInt childId;
2847: PetscSectionGetDof(globalFine,p,&gDof);
2848: PetscSectionGetConstraintDof(globalFine,p,&gcDof);
2849: if ((gDof - gcDof) <= 0) {
2850: continue;
2851: }
2852: childId = childIds[p-pStartF];
2853: PetscSectionGetOffset(globalFine,p,&gOff);
2854: PetscSectionGetDof(leafIndicesSec,p,&numColIndices);
2855: PetscSectionGetOffset(leafIndicesSec,p,&pIndOff);
2856: numColIndices -= 2 * numFields;
2857: pInd = &leafIndices[pIndOff];
2858: offsets[0] = 0;
2859: offsetsCopy[0] = 0;
2860: newOffsets[0] = 0;
2861: newOffsetsCopy[0] = 0;
2862: rowOffsets[0] = 0;
2863: if (numFields) {
2864: PetscInt f;
2865: for (f = 0; f < numFields; f++) {
2866: PetscInt rowDof;
2868: PetscSectionGetFieldDof(localFine,p,f,&rowDof);
2869: offsets[f + 1] = offsets[f] + rowDof;
2870: offsetsCopy[f + 1] = offsets[f + 1];
2871: rowOffsets[f + 1] = pInd[numColIndices + f];
2872: newOffsets[f + 1] = pInd[numColIndices + numFields + f];
2873: }
2874: DMPlexGetIndicesPointFields_Internal(localFine,PETSC_FALSE,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1, NULL,rowIndices);
2875: }
2876: else {
2877: DMPlexGetIndicesPoint_Internal(localFine,PETSC_FALSE,p,gOff,offsetsCopy,PETSC_FALSE,NULL, NULL,rowIndices);
2878: }
2879: PetscSectionGetDof(leafMatricesSec,p,&matSize);
2880: if (!matSize) { /* incoming matrix is identity */
2881: if (childId < 0) { /* no child interpolation: scatter */
2882: if (numFields) {
2883: PetscInt f;
2884: for (f = 0; f < numFields; f++) {
2885: PetscInt numRows = offsets[f+1] - offsets[f], row;
2886: for (row = 0; row < numRows; row++) {
2887: MatSetValue(mat,rowIndices[offsets[f]+row],pInd[newOffsets[f]+row],1.,INSERT_VALUES);
2888: }
2889: }
2890: }
2891: else {
2892: PetscInt numRows = gDof, row;
2893: for (row = 0; row < numRows; row++) {
2894: MatSetValue(mat,rowIndices[row],pInd[row],1.,INSERT_VALUES);
2895: }
2896: }
2897: }
2898: else { /* interpolate from all */
2899: if (numFields) {
2900: PetscInt f;
2901: for (f = 0; f < numFields; f++) {
2902: PetscInt numRows = offsets[f+1] - offsets[f];
2903: PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
2904: MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],refPointFieldMats[childId - pRefStart][f],INSERT_VALUES);
2905: }
2906: }
2907: else {
2908: MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,refPointFieldMats[childId - pRefStart][0],INSERT_VALUES);
2909: }
2910: }
2911: }
2912: else { /* interpolate from all */
2913: PetscInt pMatOff;
2914: PetscScalar *pMat;
2916: PetscSectionGetOffset(leafMatricesSec,p,&pMatOff);
2917: pMat = &leafMatrices[pMatOff];
2918: if (childId < 0) { /* copy the incoming matrix */
2919: if (numFields) {
2920: PetscInt f, count;
2921: for (f = 0, count = 0; f < numFields; f++) {
2922: PetscInt numRows = offsets[f+1]-offsets[f];
2923: PetscInt numCols = newOffsets[f+1]-newOffsets[f];
2924: PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
2925: PetscScalar *inMat = &pMat[count];
2927: MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],inMat,INSERT_VALUES);
2928: count += numCols * numInRows;
2929: }
2930: }
2931: else {
2932: MatSetValues(mat,gDof,rowIndices,numColIndices,pInd,pMat,INSERT_VALUES);
2933: }
2934: }
2935: else { /* multiply the incoming matrix by the child interpolation */
2936: if (numFields) {
2937: PetscInt f, count;
2938: for (f = 0, count = 0; f < numFields; f++) {
2939: PetscInt numRows = offsets[f+1]-offsets[f];
2940: PetscInt numCols = newOffsets[f+1]-newOffsets[f];
2941: PetscInt numInRows = rowOffsets[f+1]-rowOffsets[f];
2942: PetscScalar *inMat = &pMat[count];
2943: PetscInt i, j, k;
2944: if (refPointFieldN[childId - pRefStart][f] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
2945: for (i = 0; i < numRows; i++) {
2946: for (j = 0; j < numCols; j++) {
2947: PetscScalar val = 0.;
2948: for (k = 0; k < numInRows; k++) {
2949: val += refPointFieldMats[childId - pRefStart][f][i * numInRows + k] * inMat[k * numCols + j];
2950: }
2951: pointWork[i * numCols + j] = val;
2952: }
2953: }
2954: MatSetValues(mat,numRows,&rowIndices[offsets[f]],numCols,&pInd[newOffsets[f]],pointWork,INSERT_VALUES);
2955: count += numCols * numInRows;
2956: }
2957: }
2958: else { /* every dof gets a full row */
2959: PetscInt numRows = gDof;
2960: PetscInt numCols = numColIndices;
2961: PetscInt numInRows = matSize / numColIndices;
2962: PetscInt i, j, k;
2963: if (refPointFieldN[childId - pRefStart][0] != numInRows) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Point constraint matrix multiply dimension mismatch");
2964: for (i = 0; i < numRows; i++) {
2965: for (j = 0; j < numCols; j++) {
2966: PetscScalar val = 0.;
2967: for (k = 0; k < numInRows; k++) {
2968: val += refPointFieldMats[childId - pRefStart][0][i * numInRows + k] * pMat[k * numCols + j];
2969: }
2970: pointWork[i * numCols + j] = val;
2971: }
2972: }
2973: MatSetValues(mat,numRows,rowIndices,numCols,pInd,pointWork,INSERT_VALUES);
2974: }
2975: }
2976: }
2977: }
2978: DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
2979: DMRestoreWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
2980: PetscFree(pointWork);
2981: }
2982: MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
2983: MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
2984: PetscSectionDestroy(&leafIndicesSec);
2985: PetscSectionDestroy(&leafMatricesSec);
2986: PetscFree2(leafIndices,leafMatrices);
2987: PetscFree2(*(PetscInt****)&perms,*(PetscScalar****)&flips);
2988: PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
2989: ISRestoreIndices(aIS,&anchors);
2990: return(0);
2991: }
2993: /*
2994: * Assuming a nodal basis (w.r.t. the dual basis) basis:
2995: *
2996: * for each coarse dof \phi^c_i:
2997: * for each quadrature point (w_l,x_l) in the dual basis definition of \phi^c_i:
2998: * for each fine dof \phi^f_j;
2999: * a_{i,j} = 0;
3000: * for each fine dof \phi^f_k:
3001: * a_{i,j} += interp_{i,k} * \phi^f_k(x_l) * \phi^f_j(x_l) * w_l
3002: * [^^^ this is = \phi^c_i ^^^]
3003: */
3004: PetscErrorCode DMPlexComputeInjectorReferenceTree(DM refTree, Mat *inj)
3005: {
3006: PetscDS ds;
3007: PetscSection section, cSection;
3008: DMLabel canonical, depth;
3009: Mat cMat, mat;
3010: PetscInt *nnz;
3011: PetscInt f, dim, numFields, numSecFields, p, pStart, pEnd, cStart, cEnd;
3012: PetscInt m, n;
3013: PetscScalar *pointScalar;
3014: PetscReal *v0, *v0parent, *vtmp, *J, *Jparent, *invJ, *pointRef, detJ, detJparent;
3018: DMGetLocalSection(refTree,§ion);
3019: DMGetDimension(refTree, &dim);
3020: PetscMalloc6(dim,&v0,dim,&v0parent,dim,&vtmp,dim*dim,&J,dim*dim,&Jparent,dim*dim,&invJ);
3021: PetscMalloc2(dim,&pointScalar,dim,&pointRef);
3022: DMGetDS(refTree,&ds);
3023: PetscDSGetNumFields(ds,&numFields);
3024: PetscSectionGetNumFields(section,&numSecFields);
3025: DMGetLabel(refTree,"canonical",&canonical);
3026: DMGetLabel(refTree,"depth",&depth);
3027: DMGetDefaultConstraints(refTree,&cSection,&cMat);
3028: DMPlexGetChart(refTree, &pStart, &pEnd);
3029: DMPlexGetHeightStratum(refTree, 0, &cStart, &cEnd);
3030: MatGetSize(cMat,&n,&m); /* the injector has transpose sizes from the constraint matrix */
3031: /* Step 1: compute non-zero pattern. A proper subset of constraint matrix non-zero */
3032: PetscCalloc1(m,&nnz);
3033: for (p = pStart; p < pEnd; p++) { /* a point will have non-zeros if it is canonical, it has dofs, and its children have dofs */
3034: const PetscInt *children;
3035: PetscInt numChildren;
3036: PetscInt i, numChildDof, numSelfDof;
3038: if (canonical) {
3039: PetscInt pCanonical;
3040: DMLabelGetValue(canonical,p,&pCanonical);
3041: if (p != pCanonical) continue;
3042: }
3043: DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
3044: if (!numChildren) continue;
3045: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3046: PetscInt child = children[i];
3047: PetscInt dof;
3049: PetscSectionGetDof(section,child,&dof);
3050: numChildDof += dof;
3051: }
3052: PetscSectionGetDof(section,p,&numSelfDof);
3053: if (!numChildDof || !numSelfDof) continue;
3054: for (f = 0; f < numFields; f++) {
3055: PetscInt selfOff;
3057: if (numSecFields) { /* count the dofs for just this field */
3058: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3059: PetscInt child = children[i];
3060: PetscInt dof;
3062: PetscSectionGetFieldDof(section,child,f,&dof);
3063: numChildDof += dof;
3064: }
3065: PetscSectionGetFieldDof(section,p,f,&numSelfDof);
3066: PetscSectionGetFieldOffset(section,p,f,&selfOff);
3067: }
3068: else {
3069: PetscSectionGetOffset(section,p,&selfOff);
3070: }
3071: for (i = 0; i < numSelfDof; i++) {
3072: nnz[selfOff + i] = numChildDof;
3073: }
3074: }
3075: }
3076: MatCreateAIJ(PETSC_COMM_SELF,m,n,m,n,-1,nnz,-1,NULL,&mat);
3077: PetscFree(nnz);
3078: /* Setp 2: compute entries */
3079: for (p = pStart; p < pEnd; p++) {
3080: const PetscInt *children;
3081: PetscInt numChildren;
3082: PetscInt i, numChildDof, numSelfDof;
3084: /* same conditions about when entries occur */
3085: if (canonical) {
3086: PetscInt pCanonical;
3087: DMLabelGetValue(canonical,p,&pCanonical);
3088: if (p != pCanonical) continue;
3089: }
3090: DMPlexGetTreeChildren(refTree,p,&numChildren,&children);
3091: if (!numChildren) continue;
3092: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3093: PetscInt child = children[i];
3094: PetscInt dof;
3096: PetscSectionGetDof(section,child,&dof);
3097: numChildDof += dof;
3098: }
3099: PetscSectionGetDof(section,p,&numSelfDof);
3100: if (!numChildDof || !numSelfDof) continue;
3102: for (f = 0; f < numFields; f++) {
3103: PetscInt pI = -1, cI = -1;
3104: PetscInt selfOff, Nc, parentCell;
3105: PetscInt cellShapeOff;
3106: PetscObject disc;
3107: PetscDualSpace dsp;
3108: PetscClassId classId;
3109: PetscScalar *pointMat;
3110: PetscInt *matRows, *matCols;
3111: PetscInt pO = PETSC_MIN_INT;
3112: const PetscInt *depthNumDof;
3114: if (numSecFields) {
3115: for (i = 0, numChildDof = 0; i < numChildren; i++) {
3116: PetscInt child = children[i];
3117: PetscInt dof;
3119: PetscSectionGetFieldDof(section,child,f,&dof);
3120: numChildDof += dof;
3121: }
3122: PetscSectionGetFieldDof(section,p,f,&numSelfDof);
3123: PetscSectionGetFieldOffset(section,p,f,&selfOff);
3124: }
3125: else {
3126: PetscSectionGetOffset(section,p,&selfOff);
3127: }
3129: /* find a cell whose closure contains p */
3130: if (p >= cStart && p < cEnd) {
3131: parentCell = p;
3132: }
3133: else {
3134: PetscInt *star = NULL;
3135: PetscInt numStar;
3137: parentCell = -1;
3138: DMPlexGetTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
3139: for (i = numStar - 1; i >= 0; i--) {
3140: PetscInt c = star[2 * i];
3142: if (c >= cStart && c < cEnd) {
3143: parentCell = c;
3144: break;
3145: }
3146: }
3147: DMPlexRestoreTransitiveClosure(refTree,p,PETSC_FALSE,&numStar,&star);
3148: }
3149: /* determine the offset of p's shape functions withing parentCell's shape functions */
3150: PetscDSGetDiscretization(ds,f,&disc);
3151: PetscObjectGetClassId(disc,&classId);
3152: if (classId == PETSCFE_CLASSID) {
3153: PetscFEGetDualSpace((PetscFE)disc,&dsp);
3154: }
3155: else if (classId == PETSCFV_CLASSID) {
3156: PetscFVGetDualSpace((PetscFV)disc,&dsp);
3157: }
3158: else {
3159: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported discretization object");
3160: }
3161: PetscDualSpaceGetNumDof(dsp,&depthNumDof);
3162: PetscDualSpaceGetNumComponents(dsp,&Nc);
3163: {
3164: PetscInt *closure = NULL;
3165: PetscInt numClosure;
3167: DMPlexGetTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
3168: for (i = 0, pI = -1, cellShapeOff = 0; i < numClosure; i++) {
3169: PetscInt point = closure[2 * i], pointDepth;
3171: pO = closure[2 * i + 1];
3172: if (point == p) {
3173: pI = i;
3174: break;
3175: }
3176: DMLabelGetValue(depth,point,&pointDepth);
3177: cellShapeOff += depthNumDof[pointDepth];
3178: }
3179: DMPlexRestoreTransitiveClosure(refTree,parentCell,PETSC_TRUE,&numClosure,&closure);
3180: }
3182: DMGetWorkArray(refTree, numSelfDof * numChildDof, MPIU_SCALAR,&pointMat);
3183: DMGetWorkArray(refTree, numSelfDof + numChildDof, MPIU_INT,&matRows);
3184: matCols = matRows + numSelfDof;
3185: for (i = 0; i < numSelfDof; i++) {
3186: matRows[i] = selfOff + i;
3187: }
3188: for (i = 0; i < numSelfDof * numChildDof; i++) pointMat[i] = 0.;
3189: {
3190: PetscInt colOff = 0;
3192: for (i = 0; i < numChildren; i++) {
3193: PetscInt child = children[i];
3194: PetscInt dof, off, j;
3196: if (numSecFields) {
3197: PetscSectionGetFieldDof(cSection,child,f,&dof);
3198: PetscSectionGetFieldOffset(cSection,child,f,&off);
3199: }
3200: else {
3201: PetscSectionGetDof(cSection,child,&dof);
3202: PetscSectionGetOffset(cSection,child,&off);
3203: }
3205: for (j = 0; j < dof; j++) {
3206: matCols[colOff++] = off + j;
3207: }
3208: }
3209: }
3210: if (classId == PETSCFE_CLASSID) {
3211: PetscFE fe = (PetscFE) disc;
3212: PetscInt fSize;
3213: const PetscInt ***perms;
3214: const PetscScalar ***flips;
3215: const PetscInt *pperms;
3218: PetscFEGetDualSpace(fe,&dsp);
3219: PetscDualSpaceGetDimension(dsp,&fSize);
3220: PetscDualSpaceGetSymmetries(dsp, &perms, &flips);
3221: pperms = perms ? perms[pI] ? perms[pI][pO] : NULL : NULL;
3222: for (i = 0; i < numSelfDof; i++) { /* for every shape function */
3223: PetscQuadrature q;
3224: PetscInt dim, thisNc, numPoints, j, k;
3225: const PetscReal *points;
3226: const PetscReal *weights;
3227: PetscInt *closure = NULL;
3228: PetscInt numClosure;
3229: PetscInt iCell = pperms ? pperms[i] : i;
3230: PetscInt parentCellShapeDof = cellShapeOff + iCell;
3231: PetscTabulation Tparent;
3233: PetscDualSpaceGetFunctional(dsp,parentCellShapeDof,&q);
3234: PetscQuadratureGetData(q,&dim,&thisNc,&numPoints,&points,&weights);
3235: if (thisNc != Nc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Functional dim %D does not much basis dim %D\n",thisNc,Nc);
3236: PetscFECreateTabulation(fe,1,numPoints,points,0,&Tparent); /* I'm expecting a nodal basis: weights[:]' * Bparent[:,cellShapeDof] = 1. */
3237: for (j = 0; j < numPoints; j++) {
3238: PetscInt childCell = -1;
3239: PetscReal *parentValAtPoint;
3240: const PetscReal xi0[3] = {-1.,-1.,-1.};
3241: const PetscReal *pointReal = &points[dim * j];
3242: const PetscScalar *point;
3243: PetscTabulation Tchild;
3244: PetscInt childCellShapeOff, pointMatOff;
3245: #if defined(PETSC_USE_COMPLEX)
3246: PetscInt d;
3248: for (d = 0; d < dim; d++) {
3249: pointScalar[d] = points[dim * j + d];
3250: }
3251: point = pointScalar;
3252: #else
3253: point = pointReal;
3254: #endif
3256: parentValAtPoint = &Tparent->T[0][(fSize * j + parentCellShapeDof) * Nc];
3258: for (k = 0; k < numChildren; k++) { /* locate the point in a child's star cell*/
3259: PetscInt child = children[k];
3260: PetscInt *star = NULL;
3261: PetscInt numStar, s;
3263: DMPlexGetTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
3264: for (s = numStar - 1; s >= 0; s--) {
3265: PetscInt c = star[2 * s];
3267: if (c < cStart || c >= cEnd) continue;
3268: DMPlexLocatePoint_Internal(refTree,dim,point,c,&childCell);
3269: if (childCell >= 0) break;
3270: }
3271: DMPlexRestoreTransitiveClosure(refTree,child,PETSC_FALSE,&numStar,&star);
3272: if (childCell >= 0) break;
3273: }
3274: if (childCell < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Could not locate quadrature point");
3275: DMPlexComputeCellGeometryFEM(refTree, childCell, NULL, v0, J, invJ, &detJ);
3276: DMPlexComputeCellGeometryFEM(refTree, parentCell, NULL, v0parent, Jparent, NULL, &detJparent);
3277: CoordinatesRefToReal(dim, dim, xi0, v0parent, Jparent, pointReal, vtmp);
3278: CoordinatesRealToRef(dim, dim, xi0, v0, invJ, vtmp, pointRef);
3280: PetscFECreateTabulation(fe,1,1,pointRef,0,&Tchild);
3281: DMPlexGetTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
3282: for (k = 0, pointMatOff = 0; k < numChildren; k++) { /* point is located in cell => child dofs support at point are in closure of cell */
3283: PetscInt child = children[k], childDepth, childDof, childO = PETSC_MIN_INT;
3284: PetscInt l;
3285: const PetscInt *cperms;
3287: DMLabelGetValue(depth,child,&childDepth);
3288: childDof = depthNumDof[childDepth];
3289: for (l = 0, cI = -1, childCellShapeOff = 0; l < numClosure; l++) {
3290: PetscInt point = closure[2 * l];
3291: PetscInt pointDepth;
3293: childO = closure[2 * l + 1];
3294: if (point == child) {
3295: cI = l;
3296: break;
3297: }
3298: DMLabelGetValue(depth,point,&pointDepth);
3299: childCellShapeOff += depthNumDof[pointDepth];
3300: }
3301: if (l == numClosure) {
3302: pointMatOff += childDof;
3303: continue; /* child is not in the closure of the cell: has nothing to contribute to this point */
3304: }
3305: cperms = perms ? perms[cI] ? perms[cI][childO] : NULL : NULL;
3306: for (l = 0; l < childDof; l++) {
3307: PetscInt lCell = cperms ? cperms[l] : l;
3308: PetscInt childCellDof = childCellShapeOff + lCell;
3309: PetscReal *childValAtPoint;
3310: PetscReal val = 0.;
3312: childValAtPoint = &Tchild->T[0][childCellDof * Nc];
3313: for (m = 0; m < Nc; m++) {
3314: val += weights[j * Nc + m] * parentValAtPoint[m] * childValAtPoint[m];
3315: }
3317: pointMat[i * numChildDof + pointMatOff + l] += val;
3318: }
3319: pointMatOff += childDof;
3320: }
3321: DMPlexRestoreTransitiveClosure(refTree,childCell,PETSC_TRUE,&numClosure,&closure);
3322: PetscTabulationDestroy(&Tchild);
3323: }
3324: PetscTabulationDestroy(&Tparent);
3325: }
3326: }
3327: else { /* just the volume-weighted averages of the children */
3328: PetscReal parentVol;
3329: PetscInt childCell;
3331: DMPlexComputeCellGeometryFVM(refTree, p, &parentVol, NULL, NULL);
3332: for (i = 0, childCell = 0; i < numChildren; i++) {
3333: PetscInt child = children[i], j;
3334: PetscReal childVol;
3336: if (child < cStart || child >= cEnd) continue;
3337: DMPlexComputeCellGeometryFVM(refTree, child, &childVol, NULL, NULL);
3338: for (j = 0; j < Nc; j++) {
3339: pointMat[j * numChildDof + Nc * childCell + j] = childVol / parentVol;
3340: }
3341: childCell++;
3342: }
3343: }
3344: /* Insert pointMat into mat */
3345: MatSetValues(mat,numSelfDof,matRows,numChildDof,matCols,pointMat,INSERT_VALUES);
3346: DMRestoreWorkArray(refTree, numSelfDof + numChildDof, MPIU_INT,&matRows);
3347: DMRestoreWorkArray(refTree, numSelfDof * numChildDof, MPIU_SCALAR,&pointMat);
3348: }
3349: }
3350: PetscFree6(v0,v0parent,vtmp,J,Jparent,invJ);
3351: PetscFree2(pointScalar,pointRef);
3352: MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
3353: MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
3354: *inj = mat;
3355: return(0);
3356: }
3358: static PetscErrorCode DMPlexReferenceTreeGetChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
3359: {
3360: PetscDS ds;
3361: PetscInt numFields, f, pRefStart, pRefEnd, p, *rows, *cols, maxDof;
3362: PetscScalar ***refPointFieldMats;
3363: PetscSection refConSec, refSection;
3367: DMGetDS(refTree,&ds);
3368: PetscDSGetNumFields(ds,&numFields);
3369: DMGetDefaultConstraints(refTree,&refConSec,NULL);
3370: DMGetLocalSection(refTree,&refSection);
3371: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
3372: PetscMalloc1(pRefEnd-pRefStart,&refPointFieldMats);
3373: PetscSectionGetMaxDof(refConSec,&maxDof);
3374: PetscMalloc1(maxDof,&rows);
3375: PetscMalloc1(maxDof*maxDof,&cols);
3376: for (p = pRefStart; p < pRefEnd; p++) {
3377: PetscInt parent, pDof, parentDof;
3379: DMPlexGetTreeParent(refTree,p,&parent,NULL);
3380: PetscSectionGetDof(refConSec,p,&pDof);
3381: PetscSectionGetDof(refSection,parent,&parentDof);
3382: if (!pDof || !parentDof || parent == p) continue;
3384: PetscMalloc1(numFields,&refPointFieldMats[p-pRefStart]);
3385: for (f = 0; f < numFields; f++) {
3386: PetscInt cDof, cOff, numCols, r;
3388: if (numFields > 1) {
3389: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
3390: PetscSectionGetFieldOffset(refConSec,p,f,&cOff);
3391: }
3392: else {
3393: PetscSectionGetDof(refConSec,p,&cDof);
3394: PetscSectionGetOffset(refConSec,p,&cOff);
3395: }
3397: for (r = 0; r < cDof; r++) {
3398: rows[r] = cOff + r;
3399: }
3400: numCols = 0;
3401: {
3402: PetscInt aDof, aOff, j;
3404: if (numFields > 1) {
3405: PetscSectionGetFieldDof(refSection,parent,f,&aDof);
3406: PetscSectionGetFieldOffset(refSection,parent,f,&aOff);
3407: }
3408: else {
3409: PetscSectionGetDof(refSection,parent,&aDof);
3410: PetscSectionGetOffset(refSection,parent,&aOff);
3411: }
3413: for (j = 0; j < aDof; j++) {
3414: cols[numCols++] = aOff + j;
3415: }
3416: }
3417: PetscMalloc1(cDof*numCols,&refPointFieldMats[p-pRefStart][f]);
3418: /* transpose of constraint matrix */
3419: MatGetValues(inj,numCols,cols,cDof,rows,refPointFieldMats[p-pRefStart][f]);
3420: }
3421: }
3422: *childrenMats = refPointFieldMats;
3423: PetscFree(rows);
3424: PetscFree(cols);
3425: return(0);
3426: }
3428: static PetscErrorCode DMPlexReferenceTreeRestoreChildrenMatrices_Injection(DM refTree, Mat inj, PetscScalar ****childrenMats)
3429: {
3430: PetscDS ds;
3431: PetscScalar ***refPointFieldMats;
3432: PetscInt numFields, pRefStart, pRefEnd, p, f;
3433: PetscSection refConSec, refSection;
3437: refPointFieldMats = *childrenMats;
3438: *childrenMats = NULL;
3439: DMGetDS(refTree,&ds);
3440: DMGetLocalSection(refTree,&refSection);
3441: PetscDSGetNumFields(ds,&numFields);
3442: DMGetDefaultConstraints(refTree,&refConSec,NULL);
3443: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
3444: for (p = pRefStart; p < pRefEnd; p++) {
3445: PetscInt parent, pDof, parentDof;
3447: DMPlexGetTreeParent(refTree,p,&parent,NULL);
3448: PetscSectionGetDof(refConSec,p,&pDof);
3449: PetscSectionGetDof(refSection,parent,&parentDof);
3450: if (!pDof || !parentDof || parent == p) continue;
3452: for (f = 0; f < numFields; f++) {
3453: PetscInt cDof;
3455: if (numFields > 1) {
3456: PetscSectionGetFieldDof(refConSec,p,f,&cDof);
3457: }
3458: else {
3459: PetscSectionGetDof(refConSec,p,&cDof);
3460: }
3462: PetscFree(refPointFieldMats[p - pRefStart][f]);
3463: }
3464: PetscFree(refPointFieldMats[p - pRefStart]);
3465: }
3466: PetscFree(refPointFieldMats);
3467: return(0);
3468: }
3470: static PetscErrorCode DMPlexReferenceTreeGetInjector(DM refTree,Mat *injRef)
3471: {
3472: Mat cMatRef;
3473: PetscObject injRefObj;
3477: DMGetDefaultConstraints(refTree,NULL,&cMatRef);
3478: PetscObjectQuery((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",&injRefObj);
3479: *injRef = (Mat) injRefObj;
3480: if (!*injRef) {
3481: DMPlexComputeInjectorReferenceTree(refTree,injRef);
3482: PetscObjectCompose((PetscObject)cMatRef,"DMPlexComputeInjectorTree_refTree",(PetscObject)*injRef);
3483: /* there is now a reference in cMatRef, which should be the only one for symmetry with the above case */
3484: PetscObjectDereference((PetscObject)*injRef);
3485: }
3486: return(0);
3487: }
3489: static PetscErrorCode DMPlexTransferInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, const PetscInt *childIds, Vec fineVec, PetscInt numFields, PetscInt *offsets, PetscSection *rootMultiSec, PetscSection *multiLeafSec, PetscInt **gatheredIndices, PetscScalar **gatheredValues)
3490: {
3491: PetscInt pStartF, pEndF, pStartC, pEndC, p, maxDof, numMulti;
3492: PetscSection globalCoarse, globalFine;
3493: PetscSection localCoarse, localFine, leafIndicesSec;
3494: PetscSection multiRootSec, rootIndicesSec;
3495: PetscInt *leafInds, *rootInds = NULL;
3496: const PetscInt *rootDegrees;
3497: PetscScalar *leafVals = NULL, *rootVals = NULL;
3498: PetscSF coarseToFineEmbedded;
3502: DMPlexGetChart(coarse,&pStartC,&pEndC);
3503: DMPlexGetChart(fine,&pStartF,&pEndF);
3504: DMGetLocalSection(fine,&localFine);
3505: DMGetGlobalSection(fine,&globalFine);
3506: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafIndicesSec);
3507: PetscSectionSetChart(leafIndicesSec,pStartF, pEndF);
3508: PetscSectionGetMaxDof(localFine,&maxDof);
3509: { /* winnow fine points that don't have global dofs out of the sf */
3510: PetscInt l, nleaves, dof, cdof, numPointsWithDofs, offset, *pointsWithDofs, numIndices;
3511: const PetscInt *leaves;
3513: PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
3514: for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
3515: p = leaves ? leaves[l] : l;
3516: PetscSectionGetDof(globalFine,p,&dof);
3517: PetscSectionGetConstraintDof(globalFine,p,&cdof);
3518: if ((dof - cdof) > 0) {
3519: numPointsWithDofs++;
3521: PetscSectionGetDof(localFine,p,&dof);
3522: PetscSectionSetDof(leafIndicesSec,p,dof + 1);
3523: }
3524: }
3525: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
3526: PetscSectionSetUp(leafIndicesSec);
3527: PetscSectionGetStorageSize(leafIndicesSec,&numIndices);
3528: PetscMalloc1(gatheredIndices ? numIndices : (maxDof + 1),&leafInds);
3529: if (gatheredValues) {PetscMalloc1(numIndices,&leafVals);}
3530: for (l = 0, offset = 0; l < nleaves; l++) {
3531: p = leaves ? leaves[l] : l;
3532: PetscSectionGetDof(globalFine,p,&dof);
3533: PetscSectionGetConstraintDof(globalFine,p,&cdof);
3534: if ((dof - cdof) > 0) {
3535: PetscInt off, gOff;
3536: PetscInt *pInd;
3537: PetscScalar *pVal = NULL;
3539: pointsWithDofs[offset++] = l;
3541: PetscSectionGetOffset(leafIndicesSec,p,&off);
3543: pInd = gatheredIndices ? (&leafInds[off + 1]) : leafInds;
3544: if (gatheredValues) {
3545: PetscInt i;
3547: pVal = &leafVals[off + 1];
3548: for (i = 0; i < dof; i++) pVal[i] = 0.;
3549: }
3550: PetscSectionGetOffset(globalFine,p,&gOff);
3552: offsets[0] = 0;
3553: if (numFields) {
3554: PetscInt f;
3556: for (f = 0; f < numFields; f++) {
3557: PetscInt fDof;
3558: PetscSectionGetFieldDof(localFine,p,f,&fDof);
3559: offsets[f + 1] = fDof + offsets[f];
3560: }
3561: DMPlexGetIndicesPointFields_Internal(localFine,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL,-1, NULL,pInd);
3562: } else {
3563: DMPlexGetIndicesPoint_Internal(localFine,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsets,PETSC_FALSE,NULL, NULL,pInd);
3564: }
3565: if (gatheredValues) {VecGetValues(fineVec,dof,pInd,pVal);}
3566: }
3567: }
3568: PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
3569: PetscFree(pointsWithDofs);
3570: }
3572: DMPlexGetChart(coarse,&pStartC,&pEndC);
3573: DMGetLocalSection(coarse,&localCoarse);
3574: DMGetGlobalSection(coarse,&globalCoarse);
3576: { /* there may be the case where an sf root has a parent: broadcast parents back to children */
3577: MPI_Datatype threeInt;
3578: PetscMPIInt rank;
3579: PetscInt (*parentNodeAndIdCoarse)[3];
3580: PetscInt (*parentNodeAndIdFine)[3];
3581: PetscInt p, nleaves, nleavesToParents;
3582: PetscSF pointSF, sfToParents;
3583: const PetscInt *ilocal;
3584: const PetscSFNode *iremote;
3585: PetscSFNode *iremoteToParents;
3586: PetscInt *ilocalToParents;
3588: MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);
3589: MPI_Type_contiguous(3,MPIU_INT,&threeInt);
3590: MPI_Type_commit(&threeInt);
3591: PetscMalloc2(pEndC-pStartC,&parentNodeAndIdCoarse,pEndF-pStartF,&parentNodeAndIdFine);
3592: DMGetPointSF(coarse,&pointSF);
3593: PetscSFGetGraph(pointSF,NULL,&nleaves,&ilocal,&iremote);
3594: for (p = pStartC; p < pEndC; p++) {
3595: PetscInt parent, childId;
3596: DMPlexGetTreeParent(coarse,p,&parent,&childId);
3597: parentNodeAndIdCoarse[p - pStartC][0] = rank;
3598: parentNodeAndIdCoarse[p - pStartC][1] = parent - pStartC;
3599: parentNodeAndIdCoarse[p - pStartC][2] = (p == parent) ? -1 : childId;
3600: if (nleaves > 0) {
3601: PetscInt leaf = -1;
3603: if (ilocal) {
3604: PetscFindInt(parent,nleaves,ilocal,&leaf);
3605: }
3606: else {
3607: leaf = p - pStartC;
3608: }
3609: if (leaf >= 0) {
3610: parentNodeAndIdCoarse[p - pStartC][0] = iremote[leaf].rank;
3611: parentNodeAndIdCoarse[p - pStartC][1] = iremote[leaf].index;
3612: }
3613: }
3614: }
3615: for (p = pStartF; p < pEndF; p++) {
3616: parentNodeAndIdFine[p - pStartF][0] = -1;
3617: parentNodeAndIdFine[p - pStartF][1] = -1;
3618: parentNodeAndIdFine[p - pStartF][2] = -1;
3619: }
3620: PetscSFBcastBegin(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
3621: PetscSFBcastEnd(coarseToFineEmbedded,threeInt,parentNodeAndIdCoarse,parentNodeAndIdFine);
3622: for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
3623: PetscInt dof;
3625: PetscSectionGetDof(leafIndicesSec,p,&dof);
3626: if (dof) {
3627: PetscInt off;
3629: PetscSectionGetOffset(leafIndicesSec,p,&off);
3630: if (gatheredIndices) {
3631: leafInds[off] = PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
3632: } else if (gatheredValues) {
3633: leafVals[off] = (PetscScalar) PetscMax(childIds[p-pStartF],parentNodeAndIdFine[p-pStartF][2]);
3634: }
3635: }
3636: if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
3637: nleavesToParents++;
3638: }
3639: }
3640: PetscMalloc1(nleavesToParents,&ilocalToParents);
3641: PetscMalloc1(nleavesToParents,&iremoteToParents);
3642: for (p = pStartF, nleavesToParents = 0; p < pEndF; p++) {
3643: if (parentNodeAndIdFine[p-pStartF][0] >= 0) {
3644: ilocalToParents[nleavesToParents] = p - pStartF;
3645: iremoteToParents[nleavesToParents].rank = parentNodeAndIdFine[p-pStartF][0];
3646: iremoteToParents[nleavesToParents].index = parentNodeAndIdFine[p-pStartF][1];
3647: nleavesToParents++;
3648: }
3649: }
3650: PetscSFCreate(PetscObjectComm((PetscObject)coarse),&sfToParents);
3651: PetscSFSetGraph(sfToParents,pEndC-pStartC,nleavesToParents,ilocalToParents,PETSC_OWN_POINTER,iremoteToParents,PETSC_OWN_POINTER);
3652: PetscSFDestroy(&coarseToFineEmbedded);
3654: coarseToFineEmbedded = sfToParents;
3656: PetscFree2(parentNodeAndIdCoarse,parentNodeAndIdFine);
3657: MPI_Type_free(&threeInt);
3658: }
3660: { /* winnow out coarse points that don't have dofs */
3661: PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;
3662: PetscSF sfDofsOnly;
3664: for (p = pStartC, numPointsWithDofs = 0; p < pEndC; p++) {
3665: PetscSectionGetDof(globalCoarse,p,&dof);
3666: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3667: if ((dof - cdof) > 0) {
3668: numPointsWithDofs++;
3669: }
3670: }
3671: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
3672: for (p = pStartC, offset = 0; p < pEndC; p++) {
3673: PetscSectionGetDof(globalCoarse,p,&dof);
3674: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3675: if ((dof - cdof) > 0) {
3676: pointsWithDofs[offset++] = p - pStartC;
3677: }
3678: }
3679: PetscSFCreateEmbeddedSF(coarseToFineEmbedded, numPointsWithDofs, pointsWithDofs, &sfDofsOnly);
3680: PetscSFDestroy(&coarseToFineEmbedded);
3681: PetscFree(pointsWithDofs);
3682: coarseToFineEmbedded = sfDofsOnly;
3683: }
3685: /* communicate back to the coarse mesh which coarse points have children (that may require injection) */
3686: PetscSFComputeDegreeBegin(coarseToFineEmbedded,&rootDegrees);
3687: PetscSFComputeDegreeEnd(coarseToFineEmbedded,&rootDegrees);
3688: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&multiRootSec);
3689: PetscSectionSetChart(multiRootSec,pStartC,pEndC);
3690: for (p = pStartC; p < pEndC; p++) {
3691: PetscSectionSetDof(multiRootSec,p,rootDegrees[p-pStartC]);
3692: }
3693: PetscSectionSetUp(multiRootSec);
3694: PetscSectionGetStorageSize(multiRootSec,&numMulti);
3695: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootIndicesSec);
3696: { /* distribute the leaf section */
3697: PetscSF multi, multiInv, indicesSF;
3698: PetscInt *remoteOffsets, numRootIndices;
3700: PetscSFGetMultiSF(coarseToFineEmbedded,&multi);
3701: PetscSFCreateInverseSF(multi,&multiInv);
3702: PetscSFDistributeSection(multiInv,leafIndicesSec,&remoteOffsets,rootIndicesSec);
3703: PetscSFCreateSectionSF(multiInv,leafIndicesSec,remoteOffsets,rootIndicesSec,&indicesSF);
3704: PetscFree(remoteOffsets);
3705: PetscSFDestroy(&multiInv);
3706: PetscSectionGetStorageSize(rootIndicesSec,&numRootIndices);
3707: if (gatheredIndices) {
3708: PetscMalloc1(numRootIndices,&rootInds);
3709: PetscSFBcastBegin(indicesSF,MPIU_INT,leafInds,rootInds);
3710: PetscSFBcastEnd(indicesSF,MPIU_INT,leafInds,rootInds);
3711: }
3712: if (gatheredValues) {
3713: PetscMalloc1(numRootIndices,&rootVals);
3714: PetscSFBcastBegin(indicesSF,MPIU_SCALAR,leafVals,rootVals);
3715: PetscSFBcastEnd(indicesSF,MPIU_SCALAR,leafVals,rootVals);
3716: }
3717: PetscSFDestroy(&indicesSF);
3718: }
3719: PetscSectionDestroy(&leafIndicesSec);
3720: PetscFree(leafInds);
3721: PetscFree(leafVals);
3722: PetscSFDestroy(&coarseToFineEmbedded);
3723: *rootMultiSec = multiRootSec;
3724: *multiLeafSec = rootIndicesSec;
3725: if (gatheredIndices) *gatheredIndices = rootInds;
3726: if (gatheredValues) *gatheredValues = rootVals;
3727: return(0);
3728: }
3730: PetscErrorCode DMPlexComputeInjectorTree(DM coarse, DM fine, PetscSF coarseToFine, PetscInt *childIds, Mat mat)
3731: {
3732: DM refTree;
3733: PetscSection multiRootSec, rootIndicesSec;
3734: PetscSection globalCoarse, globalFine;
3735: PetscSection localCoarse, localFine;
3736: PetscSection cSecRef;
3737: PetscInt *rootIndices = NULL, *parentIndices, pRefStart, pRefEnd;
3738: Mat injRef;
3739: PetscInt numFields, maxDof;
3740: PetscInt pStartC, pEndC, pStartF, pEndF, p;
3741: PetscInt *offsets, *offsetsCopy, *rowOffsets;
3742: PetscLayout rowMap, colMap;
3743: PetscInt rowStart, rowEnd, colStart, colEnd, *nnzD, *nnzO;
3744: PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */
3749: /* get the templates for the fine-to-coarse injection from the reference tree */
3750: DMPlexGetReferenceTree(coarse,&refTree);
3751: DMGetDefaultConstraints(refTree,&cSecRef,NULL);
3752: PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
3753: DMPlexReferenceTreeGetInjector(refTree,&injRef);
3755: DMPlexGetChart(fine,&pStartF,&pEndF);
3756: DMGetLocalSection(fine,&localFine);
3757: DMGetGlobalSection(fine,&globalFine);
3758: PetscSectionGetNumFields(localFine,&numFields);
3759: DMPlexGetChart(coarse,&pStartC,&pEndC);
3760: DMGetLocalSection(coarse,&localCoarse);
3761: DMGetGlobalSection(coarse,&globalCoarse);
3762: PetscSectionGetMaxDof(localCoarse,&maxDof);
3763: {
3764: PetscInt maxFields = PetscMax(1,numFields) + 1;
3765: PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
3766: }
3768: DMPlexTransferInjectorTree(coarse,fine,coarseToFine,childIds,NULL,numFields,offsets,&multiRootSec,&rootIndicesSec,&rootIndices,NULL);
3770: PetscMalloc1(maxDof,&parentIndices);
3772: /* count indices */
3773: MatGetLayouts(mat,&rowMap,&colMap);
3774: PetscLayoutSetUp(rowMap);
3775: PetscLayoutSetUp(colMap);
3776: PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
3777: PetscLayoutGetRange(colMap,&colStart,&colEnd);
3778: PetscCalloc2(rowEnd-rowStart,&nnzD,rowEnd-rowStart,&nnzO);
3779: for (p = pStartC; p < pEndC; p++) {
3780: PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
3782: PetscSectionGetDof(globalCoarse,p,&dof);
3783: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3784: if ((dof - cdof) <= 0) continue;
3785: PetscSectionGetOffset(globalCoarse,p,&gOff);
3787: rowOffsets[0] = 0;
3788: offsetsCopy[0] = 0;
3789: if (numFields) {
3790: PetscInt f;
3792: for (f = 0; f < numFields; f++) {
3793: PetscInt fDof;
3794: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
3795: rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
3796: }
3797: DMPlexGetIndicesPointFields_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1, NULL,parentIndices);
3798: } else {
3799: DMPlexGetIndicesPoint_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL, NULL,parentIndices);
3800: rowOffsets[1] = offsetsCopy[0];
3801: }
3803: PetscSectionGetDof(multiRootSec,p,&numLeaves);
3804: PetscSectionGetOffset(multiRootSec,p,&leafStart);
3805: leafEnd = leafStart + numLeaves;
3806: for (l = leafStart; l < leafEnd; l++) {
3807: PetscInt numIndices, childId, offset;
3808: const PetscInt *childIndices;
3810: PetscSectionGetDof(rootIndicesSec,l,&numIndices);
3811: PetscSectionGetOffset(rootIndicesSec,l,&offset);
3812: childId = rootIndices[offset++];
3813: childIndices = &rootIndices[offset];
3814: numIndices--;
3816: if (childId == -1) { /* equivalent points: scatter */
3817: PetscInt i;
3819: for (i = 0; i < numIndices; i++) {
3820: PetscInt colIndex = childIndices[i];
3821: PetscInt rowIndex = parentIndices[i];
3822: if (rowIndex < 0) continue;
3823: if (colIndex < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unconstrained fine and constrained coarse");
3824: if (colIndex >= colStart && colIndex < colEnd) {
3825: nnzD[rowIndex - rowStart] = 1;
3826: }
3827: else {
3828: nnzO[rowIndex - rowStart] = 1;
3829: }
3830: }
3831: }
3832: else {
3833: PetscInt parentId, f, lim;
3835: DMPlexGetTreeParent(refTree,childId,&parentId,NULL);
3837: lim = PetscMax(1,numFields);
3838: offsets[0] = 0;
3839: if (numFields) {
3840: PetscInt f;
3842: for (f = 0; f < numFields; f++) {
3843: PetscInt fDof;
3844: PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);
3846: offsets[f + 1] = fDof + offsets[f];
3847: }
3848: }
3849: else {
3850: PetscInt cDof;
3852: PetscSectionGetDof(cSecRef,childId,&cDof);
3853: offsets[1] = cDof;
3854: }
3855: for (f = 0; f < lim; f++) {
3856: PetscInt parentStart = rowOffsets[f], parentEnd = rowOffsets[f + 1];
3857: PetscInt childStart = offsets[f], childEnd = offsets[f + 1];
3858: PetscInt i, numD = 0, numO = 0;
3860: for (i = childStart; i < childEnd; i++) {
3861: PetscInt colIndex = childIndices[i];
3863: if (colIndex < 0) continue;
3864: if (colIndex >= colStart && colIndex < colEnd) {
3865: numD++;
3866: }
3867: else {
3868: numO++;
3869: }
3870: }
3871: for (i = parentStart; i < parentEnd; i++) {
3872: PetscInt rowIndex = parentIndices[i];
3874: if (rowIndex < 0) continue;
3875: nnzD[rowIndex - rowStart] += numD;
3876: nnzO[rowIndex - rowStart] += numO;
3877: }
3878: }
3879: }
3880: }
3881: }
3882: /* preallocate */
3883: MatXAIJSetPreallocation(mat,1,nnzD,nnzO,NULL,NULL);
3884: PetscFree2(nnzD,nnzO);
3885: /* insert values */
3886: DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
3887: for (p = pStartC; p < pEndC; p++) {
3888: PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
3890: PetscSectionGetDof(globalCoarse,p,&dof);
3891: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
3892: if ((dof - cdof) <= 0) continue;
3893: PetscSectionGetOffset(globalCoarse,p,&gOff);
3895: rowOffsets[0] = 0;
3896: offsetsCopy[0] = 0;
3897: if (numFields) {
3898: PetscInt f;
3900: for (f = 0; f < numFields; f++) {
3901: PetscInt fDof;
3902: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
3903: rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
3904: }
3905: DMPlexGetIndicesPointFields_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1, NULL,parentIndices);
3906: } else {
3907: DMPlexGetIndicesPoint_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL, NULL,parentIndices);
3908: rowOffsets[1] = offsetsCopy[0];
3909: }
3911: PetscSectionGetDof(multiRootSec,p,&numLeaves);
3912: PetscSectionGetOffset(multiRootSec,p,&leafStart);
3913: leafEnd = leafStart + numLeaves;
3914: for (l = leafStart; l < leafEnd; l++) {
3915: PetscInt numIndices, childId, offset;
3916: const PetscInt *childIndices;
3918: PetscSectionGetDof(rootIndicesSec,l,&numIndices);
3919: PetscSectionGetOffset(rootIndicesSec,l,&offset);
3920: childId = rootIndices[offset++];
3921: childIndices = &rootIndices[offset];
3922: numIndices--;
3924: if (childId == -1) { /* equivalent points: scatter */
3925: PetscInt i;
3927: for (i = 0; i < numIndices; i++) {
3928: MatSetValue(mat,parentIndices[i],childIndices[i],1.,INSERT_VALUES);
3929: }
3930: }
3931: else {
3932: PetscInt parentId, f, lim;
3934: DMPlexGetTreeParent(refTree,childId,&parentId,NULL);
3936: lim = PetscMax(1,numFields);
3937: offsets[0] = 0;
3938: if (numFields) {
3939: PetscInt f;
3941: for (f = 0; f < numFields; f++) {
3942: PetscInt fDof;
3943: PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);
3945: offsets[f + 1] = fDof + offsets[f];
3946: }
3947: }
3948: else {
3949: PetscInt cDof;
3951: PetscSectionGetDof(cSecRef,childId,&cDof);
3952: offsets[1] = cDof;
3953: }
3954: for (f = 0; f < lim; f++) {
3955: PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0];
3956: PetscInt *rowIndices = &parentIndices[rowOffsets[f]];
3957: const PetscInt *colIndices = &childIndices[offsets[f]];
3959: MatSetValues(mat,rowOffsets[f+1]-rowOffsets[f],rowIndices,offsets[f+1]-offsets[f],colIndices,childMat,INSERT_VALUES);
3960: }
3961: }
3962: }
3963: }
3964: PetscSectionDestroy(&multiRootSec);
3965: PetscSectionDestroy(&rootIndicesSec);
3966: PetscFree(parentIndices);
3967: DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
3968: PetscFree(rootIndices);
3969: PetscFree3(offsets,offsetsCopy,rowOffsets);
3971: MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
3972: MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);
3973: return(0);
3974: }
3976: static PetscErrorCode DMPlexTransferVecTree_Interpolate(DM coarse, Vec vecCoarseLocal, DM fine, Vec vecFine, PetscSF coarseToFine, PetscInt *cids, Vec grad, Vec cellGeom)
3977: {
3978: PetscSF coarseToFineEmbedded;
3979: PetscSection globalCoarse, globalFine;
3980: PetscSection localCoarse, localFine;
3981: PetscSection aSec, cSec;
3982: PetscSection rootValuesSec;
3983: PetscSection leafValuesSec;
3984: PetscScalar *rootValues, *leafValues;
3985: IS aIS;
3986: const PetscInt *anchors;
3987: Mat cMat;
3988: PetscInt numFields;
3989: PetscInt pStartC, pEndC, pStartF, pEndF, p, cellStart, cellEnd;
3990: PetscInt aStart, aEnd, cStart, cEnd;
3991: PetscInt *maxChildIds;
3992: PetscInt *offsets, *newOffsets, *offsetsCopy, *newOffsetsCopy, *rowOffsets, *numD, *numO;
3993: PetscFV fv = NULL;
3994: PetscInt dim, numFVcomps = -1, fvField = -1;
3995: DM cellDM = NULL, gradDM = NULL;
3996: const PetscScalar *cellGeomArray = NULL;
3997: const PetscScalar *gradArray = NULL;
3998: PetscErrorCode ierr;
4001: VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
4002: DMPlexGetChart(coarse,&pStartC,&pEndC);
4003: DMPlexGetSimplexOrBoxCells(coarse,0,&cellStart,&cellEnd);
4004: DMPlexGetChart(fine,&pStartF,&pEndF);
4005: DMGetGlobalSection(fine,&globalFine);
4006: DMGetCoordinateDim(coarse,&dim);
4007: { /* winnow fine points that don't have global dofs out of the sf */
4008: PetscInt nleaves, l;
4009: const PetscInt *leaves;
4010: PetscInt dof, cdof, numPointsWithDofs, offset, *pointsWithDofs;
4012: PetscSFGetGraph(coarseToFine,NULL,&nleaves,&leaves,NULL);
4014: for (l = 0, numPointsWithDofs = 0; l < nleaves; l++) {
4015: PetscInt p = leaves ? leaves[l] : l;
4017: PetscSectionGetDof(globalFine,p,&dof);
4018: PetscSectionGetConstraintDof(globalFine,p,&cdof);
4019: if ((dof - cdof) > 0) {
4020: numPointsWithDofs++;
4021: }
4022: }
4023: PetscMalloc1(numPointsWithDofs,&pointsWithDofs);
4024: for (l = 0, offset = 0; l < nleaves; l++) {
4025: PetscInt p = leaves ? leaves[l] : l;
4027: PetscSectionGetDof(globalFine,p,&dof);
4028: PetscSectionGetConstraintDof(globalFine,p,&cdof);
4029: if ((dof - cdof) > 0) {
4030: pointsWithDofs[offset++] = l;
4031: }
4032: }
4033: PetscSFCreateEmbeddedLeafSF(coarseToFine, numPointsWithDofs, pointsWithDofs, &coarseToFineEmbedded);
4034: PetscFree(pointsWithDofs);
4035: }
4036: /* communicate back to the coarse mesh which coarse points have children (that may require interpolation) */
4037: PetscMalloc1(pEndC-pStartC,&maxChildIds);
4038: for (p = pStartC; p < pEndC; p++) {
4039: maxChildIds[p - pStartC] = -2;
4040: }
4041: PetscSFReduceBegin(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);
4042: PetscSFReduceEnd(coarseToFineEmbedded,MPIU_INT,cids,maxChildIds,MPIU_MAX);
4044: DMGetLocalSection(coarse,&localCoarse);
4045: DMGetGlobalSection(coarse,&globalCoarse);
4047: DMPlexGetAnchors(coarse,&aSec,&aIS);
4048: ISGetIndices(aIS,&anchors);
4049: PetscSectionGetChart(aSec,&aStart,&aEnd);
4051: DMGetDefaultConstraints(coarse,&cSec,&cMat);
4052: PetscSectionGetChart(cSec,&cStart,&cEnd);
4054: /* create sections that will send to children the indices and matrices they will need to construct the interpolator */
4055: PetscSectionCreate(PetscObjectComm((PetscObject)coarse),&rootValuesSec);
4056: PetscSectionSetChart(rootValuesSec,pStartC,pEndC);
4057: PetscSectionGetNumFields(localCoarse,&numFields);
4058: {
4059: PetscInt maxFields = PetscMax(1,numFields) + 1;
4060: PetscMalloc7(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&newOffsets,maxFields,&newOffsetsCopy,maxFields,&rowOffsets,maxFields,&numD,maxFields,&numO);
4061: }
4062: if (grad) {
4063: PetscInt i;
4065: VecGetDM(cellGeom,&cellDM);
4066: VecGetArrayRead(cellGeom,&cellGeomArray);
4067: VecGetDM(grad,&gradDM);
4068: VecGetArrayRead(grad,&gradArray);
4069: for (i = 0; i < PetscMax(1,numFields); i++) {
4070: PetscObject obj;
4071: PetscClassId id;
4073: DMGetField(coarse, i, NULL, &obj);
4074: PetscObjectGetClassId(obj,&id);
4075: if (id == PETSCFV_CLASSID) {
4076: fv = (PetscFV) obj;
4077: PetscFVGetNumComponents(fv,&numFVcomps);
4078: fvField = i;
4079: break;
4080: }
4081: }
4082: }
4084: for (p = pStartC; p < pEndC; p++) { /* count the sizes of the indices and matrices */
4085: PetscInt dof;
4086: PetscInt maxChildId = maxChildIds[p - pStartC];
4087: PetscInt numValues = 0;
4089: PetscSectionGetDof(globalCoarse,p,&dof);
4090: if (dof < 0) {
4091: dof = -(dof + 1);
4092: }
4093: offsets[0] = 0;
4094: newOffsets[0] = 0;
4095: if (maxChildId >= 0) { /* this point has children (with dofs) that will need to be interpolated from the closure of p */
4096: PetscInt *closure = NULL, closureSize, cl;
4098: DMPlexGetTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
4099: for (cl = 0; cl < closureSize; cl++) { /* get the closure */
4100: PetscInt c = closure[2 * cl], clDof;
4102: PetscSectionGetDof(localCoarse,c,&clDof);
4103: numValues += clDof;
4104: }
4105: DMPlexRestoreTransitiveClosure(coarse,p,PETSC_TRUE,&closureSize,&closure);
4106: }
4107: else if (maxChildId == -1) {
4108: PetscSectionGetDof(localCoarse,p,&numValues);
4109: }
4110: /* we will pack the column indices with the field offsets */
4111: if (maxChildId >= 0 && grad && p >= cellStart && p < cellEnd) {
4112: /* also send the centroid, and the gradient */
4113: numValues += dim * (1 + numFVcomps);
4114: }
4115: PetscSectionSetDof(rootValuesSec,p,numValues);
4116: }
4117: PetscSectionSetUp(rootValuesSec);
4118: {
4119: PetscInt numRootValues;
4120: const PetscScalar *coarseArray;
4122: PetscSectionGetStorageSize(rootValuesSec,&numRootValues);
4123: PetscMalloc1(numRootValues,&rootValues);
4124: VecGetArrayRead(vecCoarseLocal,&coarseArray);
4125: for (p = pStartC; p < pEndC; p++) {
4126: PetscInt numValues;
4127: PetscInt pValOff;
4128: PetscScalar *pVal;
4129: PetscInt maxChildId = maxChildIds[p - pStartC];
4131: PetscSectionGetDof(rootValuesSec,p,&numValues);
4132: if (!numValues) {
4133: continue;
4134: }
4135: PetscSectionGetOffset(rootValuesSec,p,&pValOff);
4136: pVal = &(rootValues[pValOff]);
4137: if (maxChildId >= 0) { /* build an identity matrix, apply matrix constraints on the right */
4138: PetscInt closureSize = numValues;
4139: DMPlexVecGetClosure(coarse,NULL,vecCoarseLocal,p,&closureSize,&pVal);
4140: if (grad && p >= cellStart && p < cellEnd) {
4141: PetscFVCellGeom *cg;
4142: PetscScalar *gradVals = NULL;
4143: PetscInt i;
4145: pVal += (numValues - dim * (1 + numFVcomps));
4147: DMPlexPointLocalRead(cellDM,p,cellGeomArray,(void *) &cg);
4148: for (i = 0; i < dim; i++) pVal[i] = cg->centroid[i];
4149: pVal += dim;
4150: DMPlexPointGlobalRead(gradDM,p,gradArray,(void *) &gradVals);
4151: for (i = 0; i < dim * numFVcomps; i++) pVal[i] = gradVals[i];
4152: }
4153: }
4154: else if (maxChildId == -1) {
4155: PetscInt lDof, lOff, i;
4157: PetscSectionGetDof(localCoarse,p,&lDof);
4158: PetscSectionGetOffset(localCoarse,p,&lOff);
4159: for (i = 0; i < lDof; i++) pVal[i] = coarseArray[lOff + i];
4160: }
4161: }
4162: VecRestoreArrayRead(vecCoarseLocal,&coarseArray);
4163: PetscFree(maxChildIds);
4164: }
4165: {
4166: PetscSF valuesSF;
4167: PetscInt *remoteOffsetsValues, numLeafValues;
4169: PetscSectionCreate(PetscObjectComm((PetscObject)fine),&leafValuesSec);
4170: PetscSFDistributeSection(coarseToFineEmbedded,rootValuesSec,&remoteOffsetsValues,leafValuesSec);
4171: PetscSFCreateSectionSF(coarseToFineEmbedded,rootValuesSec,remoteOffsetsValues,leafValuesSec,&valuesSF);
4172: PetscSFDestroy(&coarseToFineEmbedded);
4173: PetscFree(remoteOffsetsValues);
4174: PetscSectionGetStorageSize(leafValuesSec,&numLeafValues);
4175: PetscMalloc1(numLeafValues,&leafValues);
4176: PetscSFBcastBegin(valuesSF,MPIU_SCALAR,rootValues,leafValues);
4177: PetscSFBcastEnd(valuesSF,MPIU_SCALAR,rootValues,leafValues);
4178: PetscSFDestroy(&valuesSF);
4179: PetscFree(rootValues);
4180: PetscSectionDestroy(&rootValuesSec);
4181: }
4182: DMGetLocalSection(fine,&localFine);
4183: {
4184: PetscInt maxDof;
4185: PetscInt *rowIndices;
4186: DM refTree;
4187: PetscInt **refPointFieldN;
4188: PetscScalar ***refPointFieldMats;
4189: PetscSection refConSec, refAnSec;
4190: PetscInt pRefStart,pRefEnd,leafStart,leafEnd;
4191: PetscScalar *pointWork;
4193: PetscSectionGetMaxDof(localFine,&maxDof);
4194: DMGetWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
4195: DMGetWorkArray(fine,maxDof,MPIU_SCALAR,&pointWork);
4196: DMPlexGetReferenceTree(fine,&refTree);
4197: DMCopyDisc(fine,refTree);
4198: DMPlexReferenceTreeGetChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
4199: DMGetDefaultConstraints(refTree,&refConSec,NULL);
4200: DMPlexGetAnchors(refTree,&refAnSec,NULL);
4201: PetscSectionGetChart(refConSec,&pRefStart,&pRefEnd);
4202: PetscSectionGetChart(leafValuesSec,&leafStart,&leafEnd);
4203: DMPlexGetSimplexOrBoxCells(fine,0,&cellStart,&cellEnd);
4204: for (p = leafStart; p < leafEnd; p++) {
4205: PetscInt gDof, gcDof, gOff, lDof;
4206: PetscInt numValues, pValOff;
4207: PetscInt childId;
4208: const PetscScalar *pVal;
4209: const PetscScalar *fvGradData = NULL;
4211: PetscSectionGetDof(globalFine,p,&gDof);
4212: PetscSectionGetDof(localFine,p,&lDof);
4213: PetscSectionGetConstraintDof(globalFine,p,&gcDof);
4214: if ((gDof - gcDof) <= 0) {
4215: continue;
4216: }
4217: PetscSectionGetOffset(globalFine,p,&gOff);
4218: PetscSectionGetDof(leafValuesSec,p,&numValues);
4219: if (!numValues) continue;
4220: PetscSectionGetOffset(leafValuesSec,p,&pValOff);
4221: pVal = &leafValues[pValOff];
4222: offsets[0] = 0;
4223: offsetsCopy[0] = 0;
4224: newOffsets[0] = 0;
4225: newOffsetsCopy[0] = 0;
4226: childId = cids[p - pStartF];
4227: if (numFields) {
4228: PetscInt f;
4229: for (f = 0; f < numFields; f++) {
4230: PetscInt rowDof;
4232: PetscSectionGetFieldDof(localFine,p,f,&rowDof);
4233: offsets[f + 1] = offsets[f] + rowDof;
4234: offsetsCopy[f + 1] = offsets[f + 1];
4235: /* TODO: closure indices */
4236: newOffsets[f + 1] = newOffsets[f] + ((childId == -1) ? rowDof : refPointFieldN[childId - pRefStart][f]);
4237: }
4238: DMPlexGetIndicesPointFields_Internal(localFine,PETSC_FALSE,p,gOff,offsetsCopy,PETSC_FALSE,NULL,-1,NULL,rowIndices);
4239: }
4240: else {
4241: offsets[0] = 0;
4242: offsets[1] = lDof;
4243: newOffsets[0] = 0;
4244: newOffsets[1] = (childId == -1) ? lDof : refPointFieldN[childId - pRefStart][0];
4245: DMPlexGetIndicesPoint_Internal(localFine,PETSC_FALSE,p,gOff,offsetsCopy,PETSC_FALSE,NULL,NULL,rowIndices);
4246: }
4247: if (childId == -1) { /* no child interpolation: one nnz per */
4248: VecSetValues(vecFine,numValues,rowIndices,pVal,INSERT_VALUES);
4249: } else {
4250: PetscInt f;
4252: if (grad && p >= cellStart && p < cellEnd) {
4253: numValues -= (dim * (1 + numFVcomps));
4254: fvGradData = &pVal[numValues];
4255: }
4256: for (f = 0; f < PetscMax(1,numFields); f++) {
4257: const PetscScalar *childMat = refPointFieldMats[childId - pRefStart][f];
4258: PetscInt numRows = offsets[f+1] - offsets[f];
4259: PetscInt numCols = newOffsets[f + 1] - newOffsets[f];
4260: const PetscScalar *cVal = &pVal[newOffsets[f]];
4261: PetscScalar *rVal = &pointWork[offsets[f]];
4262: PetscInt i, j;
4264: #if 0
4265: PetscInfo5(coarse,"childId %D, numRows %D, numCols %D, refPointFieldN %D maxDof %D\n",childId,numRows,numCols,refPointFieldN[childId - pRefStart][f], maxDof);
4266: #endif
4267: for (i = 0; i < numRows; i++) {
4268: PetscScalar val = 0.;
4269: for (j = 0; j < numCols; j++) {
4270: val += childMat[i * numCols + j] * cVal[j];
4271: }
4272: rVal[i] = val;
4273: }
4274: if (f == fvField && p >= cellStart && p < cellEnd) {
4275: PetscReal centroid[3];
4276: PetscScalar diff[3];
4277: const PetscScalar *parentCentroid = &fvGradData[0];
4278: const PetscScalar *gradient = &fvGradData[dim];
4280: DMPlexComputeCellGeometryFVM(fine,p,NULL,centroid,NULL);
4281: for (i = 0; i < dim; i++) {
4282: diff[i] = centroid[i] - parentCentroid[i];
4283: }
4284: for (i = 0; i < numFVcomps; i++) {
4285: PetscScalar val = 0.;
4287: for (j = 0; j < dim; j++) {
4288: val += gradient[dim * i + j] * diff[j];
4289: }
4290: rVal[i] += val;
4291: }
4292: }
4293: VecSetValues(vecFine,numRows,&rowIndices[offsets[f]],rVal,INSERT_VALUES);
4294: }
4295: }
4296: }
4297: DMPlexReferenceTreeRestoreChildrenMatrices(refTree,&refPointFieldMats,&refPointFieldN);
4298: DMRestoreWorkArray(fine,maxDof,MPIU_SCALAR,&pointWork);
4299: DMRestoreWorkArray(fine,maxDof,MPIU_INT,&rowIndices);
4300: }
4301: PetscFree(leafValues);
4302: PetscSectionDestroy(&leafValuesSec);
4303: PetscFree7(offsets,offsetsCopy,newOffsets,newOffsetsCopy,rowOffsets,numD,numO);
4304: ISRestoreIndices(aIS,&anchors);
4305: return(0);
4306: }
4308: static PetscErrorCode DMPlexTransferVecTree_Inject(DM fine, Vec vecFine, DM coarse, Vec vecCoarse, PetscSF coarseToFine, PetscInt *cids)
4309: {
4310: DM refTree;
4311: PetscSection multiRootSec, rootIndicesSec;
4312: PetscSection globalCoarse, globalFine;
4313: PetscSection localCoarse, localFine;
4314: PetscSection cSecRef;
4315: PetscInt *parentIndices, pRefStart, pRefEnd;
4316: PetscScalar *rootValues, *parentValues;
4317: Mat injRef;
4318: PetscInt numFields, maxDof;
4319: PetscInt pStartC, pEndC, pStartF, pEndF, p;
4320: PetscInt *offsets, *offsetsCopy, *rowOffsets;
4321: PetscLayout rowMap, colMap;
4322: PetscInt rowStart, rowEnd, colStart, colEnd;
4323: PetscScalar ***childrenMats=NULL ; /* gcc -O gives 'may be used uninitialized' warning'. Initializing to suppress this warning */
4328: /* get the templates for the fine-to-coarse injection from the reference tree */
4329: VecSetOption(vecFine,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
4330: VecSetOption(vecCoarse,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
4331: DMPlexGetReferenceTree(coarse,&refTree);
4332: DMCopyDisc(coarse,refTree);
4333: DMGetDefaultConstraints(refTree,&cSecRef,NULL);
4334: PetscSectionGetChart(cSecRef,&pRefStart,&pRefEnd);
4335: DMPlexReferenceTreeGetInjector(refTree,&injRef);
4337: DMPlexGetChart(fine,&pStartF,&pEndF);
4338: DMGetLocalSection(fine,&localFine);
4339: DMGetGlobalSection(fine,&globalFine);
4340: PetscSectionGetNumFields(localFine,&numFields);
4341: DMPlexGetChart(coarse,&pStartC,&pEndC);
4342: DMGetLocalSection(coarse,&localCoarse);
4343: DMGetGlobalSection(coarse,&globalCoarse);
4344: PetscSectionGetMaxDof(localCoarse,&maxDof);
4345: {
4346: PetscInt maxFields = PetscMax(1,numFields) + 1;
4347: PetscMalloc3(maxFields,&offsets,maxFields,&offsetsCopy,maxFields,&rowOffsets);
4348: }
4350: DMPlexTransferInjectorTree(coarse,fine,coarseToFine,cids,vecFine,numFields,offsets,&multiRootSec,&rootIndicesSec,NULL,&rootValues);
4352: PetscMalloc2(maxDof,&parentIndices,maxDof,&parentValues);
4354: /* count indices */
4355: VecGetLayout(vecFine,&colMap);
4356: VecGetLayout(vecCoarse,&rowMap);
4357: PetscLayoutSetUp(rowMap);
4358: PetscLayoutSetUp(colMap);
4359: PetscLayoutGetRange(rowMap,&rowStart,&rowEnd);
4360: PetscLayoutGetRange(colMap,&colStart,&colEnd);
4361: /* insert values */
4362: DMPlexReferenceTreeGetChildrenMatrices_Injection(refTree,injRef,&childrenMats);
4363: for (p = pStartC; p < pEndC; p++) {
4364: PetscInt numLeaves, leafStart, leafEnd, l, dof, cdof, gOff;
4365: PetscBool contribute = PETSC_FALSE;
4367: PetscSectionGetDof(globalCoarse,p,&dof);
4368: PetscSectionGetConstraintDof(globalCoarse,p,&cdof);
4369: if ((dof - cdof) <= 0) continue;
4370: PetscSectionGetDof(localCoarse,p,&dof);
4371: PetscSectionGetOffset(globalCoarse,p,&gOff);
4373: rowOffsets[0] = 0;
4374: offsetsCopy[0] = 0;
4375: if (numFields) {
4376: PetscInt f;
4378: for (f = 0; f < numFields; f++) {
4379: PetscInt fDof;
4380: PetscSectionGetFieldDof(localCoarse,p,f,&fDof);
4381: rowOffsets[f + 1] = offsetsCopy[f + 1] = fDof + rowOffsets[f];
4382: }
4383: DMPlexGetIndicesPointFields_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,-1,NULL,parentIndices);
4384: } else {
4385: DMPlexGetIndicesPoint_Internal(localCoarse,PETSC_FALSE,p,gOff < 0 ? -(gOff + 1) : gOff,offsetsCopy,PETSC_FALSE,NULL,NULL,parentIndices);
4386: rowOffsets[1] = offsetsCopy[0];
4387: }
4389: PetscSectionGetDof(multiRootSec,p,&numLeaves);
4390: PetscSectionGetOffset(multiRootSec,p,&leafStart);
4391: leafEnd = leafStart + numLeaves;
4392: for (l = 0; l < dof; l++) parentValues[l] = 0.;
4393: for (l = leafStart; l < leafEnd; l++) {
4394: PetscInt numIndices, childId, offset;
4395: const PetscScalar *childValues;
4397: PetscSectionGetDof(rootIndicesSec,l,&numIndices);
4398: PetscSectionGetOffset(rootIndicesSec,l,&offset);
4399: childId = (PetscInt) PetscRealPart(rootValues[offset++]);
4400: childValues = &rootValues[offset];
4401: numIndices--;
4403: if (childId == -2) { /* skip */
4404: continue;
4405: } else if (childId == -1) { /* equivalent points: scatter */
4406: PetscInt m;
4408: contribute = PETSC_TRUE;
4409: for (m = 0; m < numIndices; m++) parentValues[m] = childValues[m];
4410: } else { /* contributions from children: sum with injectors from reference tree */
4411: PetscInt parentId, f, lim;
4413: contribute = PETSC_TRUE;
4414: DMPlexGetTreeParent(refTree,childId,&parentId,NULL);
4416: lim = PetscMax(1,numFields);
4417: offsets[0] = 0;
4418: if (numFields) {
4419: PetscInt f;
4421: for (f = 0; f < numFields; f++) {
4422: PetscInt fDof;
4423: PetscSectionGetFieldDof(cSecRef,childId,f,&fDof);
4425: offsets[f + 1] = fDof + offsets[f];
4426: }
4427: }
4428: else {
4429: PetscInt cDof;
4431: PetscSectionGetDof(cSecRef,childId,&cDof);
4432: offsets[1] = cDof;
4433: }
4434: for (f = 0; f < lim; f++) {
4435: PetscScalar *childMat = &childrenMats[childId - pRefStart][f][0];
4436: PetscInt n = offsets[f+1]-offsets[f];
4437: PetscInt m = rowOffsets[f+1]-rowOffsets[f];
4438: PetscInt i, j;
4439: const PetscScalar *colValues = &childValues[offsets[f]];
4441: for (i = 0; i < m; i++) {
4442: PetscScalar val = 0.;
4443: for (j = 0; j < n; j++) {
4444: val += childMat[n * i + j] * colValues[j];
4445: }
4446: parentValues[rowOffsets[f] + i] += val;
4447: }
4448: }
4449: }
4450: }
4451: if (contribute) {VecSetValues(vecCoarse,dof,parentIndices,parentValues,INSERT_VALUES);}
4452: }
4453: PetscSectionDestroy(&multiRootSec);
4454: PetscSectionDestroy(&rootIndicesSec);
4455: PetscFree2(parentIndices,parentValues);
4456: DMPlexReferenceTreeRestoreChildrenMatrices_Injection(refTree,injRef,&childrenMats);
4457: PetscFree(rootValues);
4458: PetscFree3(offsets,offsetsCopy,rowOffsets);
4459: return(0);
4460: }
4462: /*@
4463: DMPlexTransferVecTree - transfer a vector between two meshes that differ from each other by refinement/coarsening
4464: that can be represented by a common reference tree used by both. This routine can be used for a combination of
4465: coarsening and refinement at the same time.
4467: collective
4469: Input Parameters:
4470: + dmIn - The DMPlex mesh for the input vector
4471: . vecIn - The input vector
4472: . sfRefine - A star forest indicating points in the mesh dmIn (roots in the star forest) that are parents to points in
4473: the mesh dmOut (leaves in the star forest), i.e. where dmOut is more refined than dmIn
4474: . sfCoarsen - A star forest indicating points in the mesh dmOut (roots in the star forest) that are parents to points in
4475: the mesh dmIn (leaves in the star forest), i.e. where dmOut is more coarsened than dmIn
4476: . cidsRefine - The childIds of the points in dmOut. These childIds relate back to the reference tree: childid[j] = k implies
4477: that mesh point j of dmOut was refined from a point in dmIn just as the mesh point k in the reference
4478: tree was refined from its parent. childid[j] = -1 indicates that the point j in dmOut is exactly
4479: equivalent to its root in dmIn, so no interpolation is necessary. childid[j] = -2 indicates that this
4480: point j in dmOut is not a leaf of sfRefine.
4481: . cidsCoarsen - The childIds of the points in dmIn. These childIds relate back to the reference tree: childid[j] = k implies
4482: that mesh point j of dmIn coarsens to a point in dmOut just as the mesh point k in the reference
4483: tree coarsens to its parent. childid[j] = -2 indicates that point j in dmOut is not a leaf in sfCoarsen.
4484: . useBCs - PETSC_TRUE indicates that boundary values should be inserted into vecIn before transfer.
4485: - time - Used if boundary values are time dependent.
4487: Output Parameters:
4488: . vecOut - Using interpolation and injection operators calculated on the reference tree, the transferred
4489: projection of vecIn from dmIn to dmOut. Note that any field discretized with a PetscFV finite volume
4490: method that uses gradient reconstruction will use reconstructed gradients when interpolating from
4491: coarse points to fine points.
4493: Level: developer
4495: .seealso: DMPlexSetReferenceTree(), DMPlexGetReferenceTree(), PetscFVGetComputeGradients()
4496: @*/
4497: PetscErrorCode DMPlexTransferVecTree(DM dmIn, Vec vecIn, DM dmOut, Vec vecOut, PetscSF sfRefine, PetscSF sfCoarsen, PetscInt *cidsRefine, PetscInt *cidsCoarsen, PetscBool useBCs, PetscReal time)
4498: {
4502: VecSet(vecOut,0.0);
4503: if (sfRefine) {
4504: Vec vecInLocal;
4505: DM dmGrad = NULL;
4506: Vec faceGeom = NULL, cellGeom = NULL, grad = NULL;
4508: DMGetLocalVector(dmIn,&vecInLocal);
4509: VecSet(vecInLocal,0.0);
4510: {
4511: PetscInt numFields, i;
4513: DMGetNumFields(dmIn, &numFields);
4514: for (i = 0; i < numFields; i++) {
4515: PetscObject obj;
4516: PetscClassId classid;
4518: DMGetField(dmIn, i, NULL, &obj);
4519: PetscObjectGetClassId(obj, &classid);
4520: if (classid == PETSCFV_CLASSID) {
4521: DMPlexGetDataFVM(dmIn,(PetscFV)obj,&cellGeom,&faceGeom,&dmGrad);
4522: break;
4523: }
4524: }
4525: }
4526: if (useBCs) {
4527: DMPlexInsertBoundaryValues(dmIn,PETSC_TRUE,vecInLocal,time,faceGeom,cellGeom,NULL);
4528: }
4529: DMGlobalToLocalBegin(dmIn,vecIn,INSERT_VALUES,vecInLocal);
4530: DMGlobalToLocalEnd(dmIn,vecIn,INSERT_VALUES,vecInLocal);
4531: if (dmGrad) {
4532: DMGetGlobalVector(dmGrad,&grad);
4533: DMPlexReconstructGradientsFVM(dmIn,vecInLocal,grad);
4534: }
4535: DMPlexTransferVecTree_Interpolate(dmIn,vecInLocal,dmOut,vecOut,sfRefine,cidsRefine,grad,cellGeom);
4536: DMRestoreLocalVector(dmIn,&vecInLocal);
4537: if (dmGrad) {
4538: DMRestoreGlobalVector(dmGrad,&grad);
4539: }
4540: }
4541: if (sfCoarsen) {
4542: DMPlexTransferVecTree_Inject(dmIn,vecIn,dmOut,vecOut,sfCoarsen,cidsCoarsen);
4543: }
4544: VecAssemblyBegin(vecOut);
4545: VecAssemblyEnd(vecOut);
4546: return(0);
4547: }