Actual source code: swarm.c

  1: #define PETSCDM_DLL
  2: #include <petsc/private/dmswarmimpl.h>
  3: #include <petsc/private/hashsetij.h>
  4: #include <petsc/private/petscfeimpl.h>
  5: #include <petscviewer.h>
  6: #include <petscdraw.h>
  7: #include <petscdmplex.h>
  8: #include <petscblaslapack.h>
  9: #include "../src/dm/impls/swarm/data_bucket.h"
 10: #include <petscdmlabel.h>
 11: #include <petscsection.h>

 13: PetscLogEvent DMSWARM_Migrate, DMSWARM_SetSizes, DMSWARM_AddPoints, DMSWARM_RemovePoints, DMSWARM_Sort;
 14: PetscLogEvent DMSWARM_DataExchangerTopologySetup, DMSWARM_DataExchangerBegin, DMSWARM_DataExchangerEnd;
 15: PetscLogEvent DMSWARM_DataExchangerSendCount, DMSWARM_DataExchangerPack;

 17: const char* DMSwarmTypeNames[] = { "basic", "pic", NULL };
 18: const char* DMSwarmMigrateTypeNames[] = { "basic", "dmcellnscatter", "dmcellexact", "user", NULL };
 19: const char* DMSwarmCollectTypeNames[] = { "basic", "boundingbox", "general", "user", NULL  };
 20: const char* DMSwarmPICLayoutTypeNames[] = { "regular", "gauss", "subdivision", NULL  };

 22: const char DMSwarmField_pid[] = "DMSwarm_pid";
 23: const char DMSwarmField_rank[] = "DMSwarm_rank";
 24: const char DMSwarmPICField_coor[] = "DMSwarmPIC_coor";
 25: const char DMSwarmPICField_cellid[] = "DMSwarm_cellid";

 27: PETSC_EXTERN PetscErrorCode VecView_Seq(Vec, PetscViewer);
 28: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);

 30: #if defined(PETSC_HAVE_HDF5)
 31: #include <petscviewerhdf5.h>

 33: PetscErrorCode VecView_Swarm_HDF5_Internal(Vec v, PetscViewer viewer)
 34: {
 35:   DM             dm;
 36:   PetscReal      seqval;
 37:   PetscInt       seqnum, bs;
 38:   PetscBool      isseq;

 42:   VecGetDM(v, &dm);
 43:   VecGetBlockSize(v, &bs);
 44:   PetscViewerHDF5PushGroup(viewer, "/particle_fields");
 45:   PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
 46:   DMGetOutputSequenceNumber(dm, &seqnum, &seqval);
 47:   PetscViewerHDF5SetTimestep(viewer, seqnum);
 48:   /* DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar) seqval, viewer); */
 49:   if (isseq) {VecView_Seq(v, viewer);}
 50:   else       {VecView_MPI(v, viewer);}
 51:   PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) v, "Nc", PETSC_INT, (void *) &bs);
 52:   PetscViewerHDF5PopGroup(viewer);
 53:   return(0);
 54: }

 56: PetscErrorCode DMSwarmView_HDF5(DM dm, PetscViewer viewer)
 57: {
 58:   Vec            coordinates;
 59:   PetscInt       Np;
 60:   PetscBool      isseq;

 64:   DMSwarmGetSize(dm, &Np);
 65:   DMSwarmCreateGlobalVectorFromField(dm, DMSwarmPICField_coor, &coordinates);
 66:   PetscObjectSetName((PetscObject) coordinates, "coordinates");
 67:   PetscViewerHDF5PushGroup(viewer, "/particles");
 68:   PetscObjectTypeCompare((PetscObject) coordinates, VECSEQ, &isseq);
 69:   if (isseq) {VecView_Seq(coordinates, viewer);}
 70:   else       {VecView_MPI(coordinates, viewer);}
 71:   PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject) coordinates, "Np", PETSC_INT, (void *) &Np);
 72:   PetscViewerHDF5PopGroup(viewer);
 73:   DMSwarmDestroyGlobalVectorFromField(dm, DMSwarmPICField_coor, &coordinates);
 74:   return(0);
 75: }
 76: #endif

 78: PetscErrorCode VecView_Swarm(Vec v, PetscViewer viewer)
 79: {
 80:   DM             dm;
 81:   PetscBool      ishdf5;

 85:   VecGetDM(v, &dm);
 86:   if (!dm) SETERRQ(PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
 87:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERHDF5,  &ishdf5);
 88:   if (ishdf5) {
 89: #if defined(PETSC_HAVE_HDF5)
 90:     VecView_Swarm_HDF5_Internal(v, viewer);
 91: #else
 92:     SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5");
 93: #endif
 94:   } else {
 95:     PetscBool isseq;

 97:     PetscObjectTypeCompare((PetscObject) v, VECSEQ, &isseq);
 98:     if (isseq) {VecView_Seq(v, viewer);}
 99:     else       {VecView_MPI(v, viewer);}
100:   }
101:   return(0);
102: }

104: /*@C
105:    DMSwarmVectorDefineField - Sets the field from which to define a Vec object
106:                              when DMCreateLocalVector(), or DMCreateGlobalVector() is called

108:    Collective on dm

110:    Input parameters:
111: +  dm - a DMSwarm
112: -  fieldname - the textual name given to a registered field

114:    Level: beginner

116:    Notes:

118:    The field with name fieldname must be defined as having a data type of PetscScalar.

120:    This function must be called prior to calling DMCreateLocalVector(), DMCreateGlobalVector().
121:    Mutiple calls to DMSwarmVectorDefineField() are permitted.

123: .seealso: DMSwarmRegisterPetscDatatypeField(), DMCreateGlobalVector(), DMCreateLocalVector()
124: @*/
125: PetscErrorCode DMSwarmVectorDefineField(DM dm,const char fieldname[])
126: {
127:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
129:   PetscInt       bs,n;
130:   PetscScalar    *array;
131:   PetscDataType  type;

134:   if (!swarm->issetup) { DMSetUp(dm); }
135:   DMSwarmDataBucketGetSizes(swarm->db,&n,NULL,NULL);
136:   DMSwarmGetField(dm,fieldname,&bs,&type,(void**)&array);

138:   /* Check all fields are of type PETSC_REAL or PETSC_SCALAR */
139:   if (type != PETSC_REAL) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only valid for PETSC_REAL");
140:   PetscSNPrintf(swarm->vec_field_name,PETSC_MAX_PATH_LEN-1,"%s",fieldname);
141:   swarm->vec_field_set = PETSC_TRUE;
142:   swarm->vec_field_bs = bs;
143:   swarm->vec_field_nlocal = n;
144:   DMSwarmRestoreField(dm,fieldname,&bs,&type,(void**)&array);
145:   return(0);
146: }

148: /* requires DMSwarmDefineFieldVector has been called */
149: PetscErrorCode DMCreateGlobalVector_Swarm(DM dm,Vec *vec)
150: {
151:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
153:   Vec            x;
154:   char           name[PETSC_MAX_PATH_LEN];

157:   if (!swarm->issetup) { DMSetUp(dm); }
158:   if (!swarm->vec_field_set) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Must call DMSwarmVectorDefineField first");
159:   if (swarm->vec_field_nlocal != swarm->db->L) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"DMSwarm sizes have changed since last call to VectorDefineField first"); /* Stale data */

161:   PetscSNPrintf(name,PETSC_MAX_PATH_LEN-1,"DMSwarmField_%s",swarm->vec_field_name);
162:   VecCreate(PetscObjectComm((PetscObject)dm),&x);
163:   PetscObjectSetName((PetscObject)x,name);
164:   VecSetSizes(x,swarm->db->L*swarm->vec_field_bs,PETSC_DETERMINE);
165:   VecSetBlockSize(x,swarm->vec_field_bs);
166:   VecSetDM(x,dm);
167:   VecSetFromOptions(x);
168:   VecSetDM(x, dm);
169:   VecSetOperation(x, VECOP_VIEW, (void (*)(void)) VecView_Swarm);
170:   *vec = x;
171:   return(0);
172: }

174: /* requires DMSwarmDefineFieldVector has been called */
175: PetscErrorCode DMCreateLocalVector_Swarm(DM dm,Vec *vec)
176: {
177:   DM_Swarm *swarm = (DM_Swarm*)dm->data;
179:   Vec x;
180:   char name[PETSC_MAX_PATH_LEN];

183:   if (!swarm->issetup) { DMSetUp(dm); }
184:   if (!swarm->vec_field_set) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Must call DMSwarmVectorDefineField first");
185:   if (swarm->vec_field_nlocal != swarm->db->L) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"DMSwarm sizes have changed since last call to VectorDefineField first"); /* Stale data */

187:   PetscSNPrintf(name,PETSC_MAX_PATH_LEN-1,"DMSwarmField_%s",swarm->vec_field_name);
188:   VecCreate(PETSC_COMM_SELF,&x);
189:   PetscObjectSetName((PetscObject)x,name);
190:   VecSetSizes(x,swarm->db->L*swarm->vec_field_bs,PETSC_DETERMINE);
191:   VecSetBlockSize(x,swarm->vec_field_bs);
192:   VecSetDM(x,dm);
193:   VecSetFromOptions(x);
194:   *vec = x;
195:   return(0);
196: }

198: static PetscErrorCode DMSwarmDestroyVectorFromField_Private(DM dm, const char fieldname[], Vec *vec)
199: {
200:   DM_Swarm      *swarm = (DM_Swarm *) dm->data;
201:   DMSwarmDataField      gfield;
202:   void         (*fptr)(void);
203:   PetscInt       bs, nlocal;
204:   char           name[PETSC_MAX_PATH_LEN];

208:   VecGetLocalSize(*vec, &nlocal);
209:   VecGetBlockSize(*vec, &bs);
210:   if (nlocal/bs != swarm->db->L) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"DMSwarm sizes have changed since vector was created - cannot ensure pointers are valid"); /* Stale data */
211:   DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield);
212:   /* check vector is an inplace array */
213:   PetscSNPrintf(name, PETSC_MAX_PATH_LEN-1, "DMSwarm_VecFieldInPlace_%s", fieldname);
214:   PetscObjectQueryFunction((PetscObject) *vec, name, &fptr);
215:   if (!fptr) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_USER, "Vector being destroyed was not created from DMSwarm field(%s)", fieldname);
216:   DMSwarmDataFieldRestoreAccess(gfield);
217:   VecDestroy(vec);
218:   return(0);
219: }

221: static PetscErrorCode DMSwarmCreateVectorFromField_Private(DM dm, const char fieldname[], MPI_Comm comm, Vec *vec)
222: {
223:   DM_Swarm      *swarm = (DM_Swarm *) dm->data;
224:   PetscDataType  type;
225:   PetscScalar   *array;
226:   PetscInt       bs, n;
227:   char           name[PETSC_MAX_PATH_LEN];
228:   PetscMPIInt    size;

232:   if (!swarm->issetup) {DMSetUp(dm);}
233:   DMSwarmDataBucketGetSizes(swarm->db, &n, NULL, NULL);
234:   DMSwarmGetField(dm, fieldname, &bs, &type, (void **) &array);
235:   if (type != PETSC_REAL) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Only valid for PETSC_REAL");

237:   MPI_Comm_size(comm, &size);
238:   if (size == 1) {
239:     VecCreateSeqWithArray(comm, bs, n*bs, array, vec);
240:   } else {
241:     VecCreateMPIWithArray(comm, bs, n*bs, PETSC_DETERMINE, array, vec);
242:   }
243:   PetscSNPrintf(name, PETSC_MAX_PATH_LEN-1, "DMSwarmSharedField_%s", fieldname);
244:   PetscObjectSetName((PetscObject) *vec, name);

246:   /* Set guard */
247:   PetscSNPrintf(name, PETSC_MAX_PATH_LEN-1, "DMSwarm_VecFieldInPlace_%s", fieldname);
248:   PetscObjectComposeFunction((PetscObject) *vec, name, DMSwarmDestroyVectorFromField_Private);

250:   VecSetDM(*vec, dm);
251:   VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Swarm);
252:   return(0);
253: }

255: /* This creates a "mass matrix" between a finite element and particle space. If a finite element interpolant is given by

257:      \hat f = \sum_i f_i \phi_i

259:    and a particle function is given by

261:      f = \sum_i w_i \delta(x - x_i)

263:    then we want to require that

265:      M \hat f = M_p f

267:    where the particle mass matrix is given by

269:      (M_p)_{ij} = \int \phi_i \delta(x - x_j)

271:    The way Dave May does particles, they amount to quadratue weights rather than delta functions, so he has |J| is in
272:    his integral. We allow this with the boolean flag.
273: */
274: static PetscErrorCode DMSwarmComputeMassMatrix_Private(DM dmc, DM dmf, Mat mass, PetscBool useDeltaFunction, void *ctx)
275: {
276:   const char    *name = "Mass Matrix";
277:   MPI_Comm       comm;
278:   PetscDS        prob;
279:   PetscSection   fsection, globalFSection;
280:   PetscHSetIJ    ht;
281:   PetscLayout    rLayout, colLayout;
282:   PetscInt      *dnz, *onz;
283:   PetscInt       locRows, locCols, rStart, colStart, colEnd, *rowIDXs;
284:   PetscReal     *xi, *v0, *J, *invJ, detJ = 1.0, v0ref[3] = {-1.0, -1.0, -1.0};
285:   PetscScalar   *elemMat;
286:   PetscInt       dim, Nf, field, cStart, cEnd, cell, totDim, maxC = 0;

290:   PetscObjectGetComm((PetscObject) mass, &comm);
291:   DMGetCoordinateDim(dmf, &dim);
292:   DMGetDS(dmf, &prob);
293:   PetscDSGetNumFields(prob, &Nf);
294:   PetscDSGetTotalDimension(prob, &totDim);
295:   PetscMalloc3(dim, &v0, dim*dim, &J, dim*dim,&invJ);
296:   DMGetLocalSection(dmf, &fsection);
297:   DMGetGlobalSection(dmf, &globalFSection);
298:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
299:   MatGetLocalSize(mass, &locRows, &locCols);

301:   PetscLayoutCreate(comm, &colLayout);
302:   PetscLayoutSetLocalSize(colLayout, locCols);
303:   PetscLayoutSetBlockSize(colLayout, 1);
304:   PetscLayoutSetUp(colLayout);
305:   PetscLayoutGetRange(colLayout, &colStart, &colEnd);
306:   PetscLayoutDestroy(&colLayout);

308:   PetscLayoutCreate(comm, &rLayout);
309:   PetscLayoutSetLocalSize(rLayout, locRows);
310:   PetscLayoutSetBlockSize(rLayout, 1);
311:   PetscLayoutSetUp(rLayout);
312:   PetscLayoutGetRange(rLayout, &rStart, NULL);
313:   PetscLayoutDestroy(&rLayout);

315:   PetscCalloc2(locRows, &dnz, locRows, &onz);
316:   PetscHSetIJCreate(&ht);

318:   PetscSynchronizedFlush(comm, NULL);
319:   /* count non-zeros */
320:   DMSwarmSortGetAccess(dmc);
321:   for (field = 0; field < Nf; ++field) {
322:     for (cell = cStart; cell < cEnd; ++cell) {
323:       PetscInt  c, i;
324:       PetscInt *findices,   *cindices; /* fine is vertices, coarse is particles */
325:       PetscInt  numFIndices, numCIndices;

327:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
328:       DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices);
329:       maxC = PetscMax(maxC, numCIndices);
330:       {
331:         PetscHashIJKey key;
332:         PetscBool      missing;
333:         for (i = 0; i < numFIndices; ++i) {
334:           key.j = findices[i]; /* global column (from Plex) */
335:           if (key.j >= 0) {
336:             /* Get indices for coarse elements */
337:             for (c = 0; c < numCIndices; ++c) {
338:               key.i = cindices[c] + rStart; /* global cols (from Swarm) */
339:               if (key.i < 0) continue;
340:               PetscHSetIJQueryAdd(ht, key, &missing);
341:               if (missing) {
342:                 if ((key.j >= colStart) && (key.j < colEnd)) ++dnz[key.i - rStart];
343:                 else                                         ++onz[key.i - rStart];
344:               } else SETERRQ2(PetscObjectComm((PetscObject) dmf), PETSC_ERR_SUP, "Set new value at %D,%D", key.i, key.j);
345:             }
346:           }
347:         }
348:         PetscFree(cindices);
349:       }
350:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
351:     }
352:   }
353:   PetscHSetIJDestroy(&ht);
354:   MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);
355:   MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
356:   PetscFree2(dnz, onz);
357:   PetscMalloc3(maxC*totDim, &elemMat, maxC, &rowIDXs, maxC*dim, &xi);
358:   for (field = 0; field < Nf; ++field) {
359:     PetscTabulation Tcoarse;
360:     PetscObject       obj;
361:     PetscReal        *coords;
362:     PetscInt          Nc, i;

364:     PetscDSGetDiscretization(prob, field, &obj);
365:     PetscFEGetNumComponents((PetscFE) obj, &Nc);
366:     if (Nc != 1) SETERRQ1(PetscObjectComm((PetscObject) dmf), PETSC_ERR_SUP, "Can only interpolate a scalar field from particles, Nc = %D", Nc);
367:     DMSwarmGetField(dmc, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);
368:     for (cell = cStart; cell < cEnd; ++cell) {
369:       PetscInt *findices  , *cindices;
370:       PetscInt  numFIndices, numCIndices;
371:       PetscInt  p, c;

373:       /* TODO: Use DMField instead of assuming affine */
374:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
375:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
376:       DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices);
377:       for (p = 0; p < numCIndices; ++p) {
378:         CoordinatesRealToRef(dim, dim, v0ref, v0, invJ, &coords[cindices[p]*dim], &xi[p*dim]);
379:       }
380:       PetscFECreateTabulation((PetscFE) obj, 1, numCIndices, xi, 0, &Tcoarse);
381:       /* Get elemMat entries by multiplying by weight */
382:       PetscArrayzero(elemMat, numCIndices*totDim);
383:       for (i = 0; i < numFIndices; ++i) {
384:         for (p = 0; p < numCIndices; ++p) {
385:           for (c = 0; c < Nc; ++c) {
386:             /* B[(p*pdim + i)*Nc + c] is the value at point p for basis function i and component c */
387:             elemMat[p*numFIndices+i] += Tcoarse->T[0][(p*numFIndices + i)*Nc + c]*(useDeltaFunction ? 1.0 : detJ);
388:           }
389:         }
390:       }
391:       for (p = 0; p < numCIndices; ++p) rowIDXs[p] = cindices[p] + rStart;
392:       if (0) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
393:       MatSetValues(mass, numCIndices, rowIDXs, numFIndices, findices, elemMat, ADD_VALUES);
394:       PetscFree(cindices);
395:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
396:       PetscTabulationDestroy(&Tcoarse);
397:     }
398:     DMSwarmRestoreField(dmc, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);
399:   }
400:   PetscFree3(elemMat, rowIDXs, xi);
401:   DMSwarmSortRestoreAccess(dmc);
402:   PetscFree3(v0, J, invJ);
403:   MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);
404:   MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);
405:   return(0);
406: }

408: /* Returns empty matrix for use with SNES FD */
409: static PetscErrorCode DMCreateMatrix_Swarm(DM sw, Mat* m)
410: {
411:   Vec            field;
412:   PetscInt       size;

416:   DMGetGlobalVector(sw, &field);
417:   VecGetLocalSize(field, &size);
418:   DMRestoreGlobalVector(sw, &field);
419:   MatCreate(PETSC_COMM_WORLD, m);
420:   MatSetFromOptions(*m);
421:   MatSetSizes(*m, PETSC_DECIDE, PETSC_DECIDE, size, size);
422:   MatSeqAIJSetPreallocation(*m, 1, NULL);
423:   MatZeroEntries(*m);
424:   MatAssemblyBegin(*m, MAT_FINAL_ASSEMBLY);
425:   MatAssemblyEnd(*m, MAT_FINAL_ASSEMBLY);
426:   MatShift(*m, 1.0);
427:   MatSetDM(*m, sw);
428:   return(0);
429: }

431: /* FEM cols, Particle rows */
432: static PetscErrorCode DMCreateMassMatrix_Swarm(DM dmCoarse, DM dmFine, Mat *mass)
433: {
434:   PetscSection   gsf;
435:   PetscInt       m, n;
436:   void          *ctx;

440:   DMGetGlobalSection(dmFine, &gsf);
441:   PetscSectionGetConstrainedStorageSize(gsf, &m);
442:   DMSwarmGetLocalSize(dmCoarse, &n);
443:   MatCreate(PetscObjectComm((PetscObject) dmCoarse), mass);
444:   MatSetSizes(*mass, n, m, PETSC_DETERMINE, PETSC_DETERMINE);
445:   MatSetType(*mass, dmCoarse->mattype);
446:   DMGetApplicationContext(dmFine, &ctx);

448:   DMSwarmComputeMassMatrix_Private(dmCoarse, dmFine, *mass, PETSC_TRUE, ctx);
449:   MatViewFromOptions(*mass, NULL, "-mass_mat_view");
450:   return(0);
451: }

453: static PetscErrorCode DMSwarmComputeMassMatrixSquare_Private(DM dmc, DM dmf, Mat mass, PetscBool useDeltaFunction, void *ctx)
454: {
455:   const char    *name = "Mass Matrix Square";
456:   MPI_Comm       comm;
457:   PetscDS        prob;
458:   PetscSection   fsection, globalFSection;
459:   PetscHSetIJ    ht;
460:   PetscLayout    rLayout, colLayout;
461:   PetscInt      *dnz, *onz, *adj, depth, maxConeSize, maxSupportSize, maxAdjSize;
462:   PetscInt       locRows, locCols, rStart, colStart, colEnd, *rowIDXs;
463:   PetscReal     *xi, *v0, *J, *invJ, detJ = 1.0, v0ref[3] = {-1.0, -1.0, -1.0};
464:   PetscScalar   *elemMat, *elemMatSq;
465:   PetscInt       cdim, Nf, field, cStart, cEnd, cell, totDim, maxC = 0;

469:   PetscObjectGetComm((PetscObject) mass, &comm);
470:   DMGetCoordinateDim(dmf, &cdim);
471:   DMGetDS(dmf, &prob);
472:   PetscDSGetNumFields(prob, &Nf);
473:   PetscDSGetTotalDimension(prob, &totDim);
474:   PetscMalloc3(cdim, &v0, cdim*cdim, &J, cdim*cdim,&invJ);
475:   DMGetLocalSection(dmf, &fsection);
476:   DMGetGlobalSection(dmf, &globalFSection);
477:   DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd);
478:   MatGetLocalSize(mass, &locRows, &locCols);

480:   PetscLayoutCreate(comm, &colLayout);
481:   PetscLayoutSetLocalSize(colLayout, locCols);
482:   PetscLayoutSetBlockSize(colLayout, 1);
483:   PetscLayoutSetUp(colLayout);
484:   PetscLayoutGetRange(colLayout, &colStart, &colEnd);
485:   PetscLayoutDestroy(&colLayout);

487:   PetscLayoutCreate(comm, &rLayout);
488:   PetscLayoutSetLocalSize(rLayout, locRows);
489:   PetscLayoutSetBlockSize(rLayout, 1);
490:   PetscLayoutSetUp(rLayout);
491:   PetscLayoutGetRange(rLayout, &rStart, NULL);
492:   PetscLayoutDestroy(&rLayout);

494:   DMPlexGetDepth(dmf, &depth);
495:   DMPlexGetMaxSizes(dmf, &maxConeSize, &maxSupportSize);
496:   maxAdjSize = PetscPowInt(maxConeSize*maxSupportSize, depth);
497:   PetscMalloc1(maxAdjSize, &adj);

499:   PetscCalloc2(locRows, &dnz, locRows, &onz);
500:   PetscHSetIJCreate(&ht);
501:   /* Count nonzeros
502:        This is just FVM++, but we cannot use the Plex P0 allocation since unknowns in a cell will not be contiguous
503:   */
504:   DMSwarmSortGetAccess(dmc);
505:   for (cell = cStart; cell < cEnd; ++cell) {
506:     PetscInt  i;
507:     PetscInt *cindices;
508:     PetscInt  numCIndices;
509:   #if 0
510:     PetscInt  adjSize = maxAdjSize, a, j;
511:   #endif

513:     DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices);
514:     maxC = PetscMax(maxC, numCIndices);
515:     /* Diagonal block */
516:     for (i = 0; i < numCIndices; ++i) {dnz[cindices[i]] += numCIndices;}
517: #if 0
518:     /* Off-diagonal blocks */
519:     DMPlexGetAdjacency(dmf, cell, &adjSize, &adj);
520:     for (a = 0; a < adjSize; ++a) {
521:       if (adj[a] >= cStart && adj[a] < cEnd && adj[a] != cell) {
522:         const PetscInt ncell = adj[a];
523:         PetscInt      *ncindices;
524:         PetscInt       numNCIndices;

526:         DMSwarmSortGetPointsPerCell(dmc, ncell, &numNCIndices, &ncindices);
527:         {
528:           PetscHashIJKey key;
529:           PetscBool      missing;

531:           for (i = 0; i < numCIndices; ++i) {
532:             key.i = cindices[i] + rStart; /* global rows (from Swarm) */
533:             if (key.i < 0) continue;
534:             for (j = 0; j < numNCIndices; ++j) {
535:               key.j = ncindices[j] + rStart; /* global column (from Swarm) */
536:               if (key.j < 0) continue;
537:               PetscHSetIJQueryAdd(ht, key, &missing);
538:               if (missing) {
539:                 if ((key.j >= colStart) && (key.j < colEnd)) ++dnz[key.i - rStart];
540:                 else                                         ++onz[key.i - rStart];
541:               }
542:             }
543:           }
544:         }
545:         PetscFree(ncindices);
546:       }
547:     }
548: #endif
549:     PetscFree(cindices);
550:   }
551:   PetscHSetIJDestroy(&ht);
552:   MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL);
553:   MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
554:   PetscFree2(dnz, onz);
555:   PetscMalloc4(maxC*totDim, &elemMat, maxC*maxC, &elemMatSq, maxC, &rowIDXs, maxC*cdim, &xi);
556:   /* Fill in values
557:        Each entry is a sum of terms \phi_i(x_p) \phi_i(x_q)
558:        Start just by producing block diagonal
559:        Could loop over adjacent cells
560:          Produce neighboring element matrix
561:          TODO Determine which columns and rows correspond to shared dual vector
562:          Do MatMatMult with rectangular matrices
563:          Insert block
564:   */
565:   for (field = 0; field < Nf; ++field) {
566:     PetscTabulation Tcoarse;
567:     PetscObject       obj;
568:     PetscReal        *coords;
569:     PetscInt          Nc, i;

571:     PetscDSGetDiscretization(prob, field, &obj);
572:     PetscFEGetNumComponents((PetscFE) obj, &Nc);
573:     if (Nc != 1) SETERRQ1(PetscObjectComm((PetscObject) dmf), PETSC_ERR_SUP, "Can only interpolate a scalar field from particles, Nc = %D", Nc);
574:     DMSwarmGetField(dmc, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);
575:     for (cell = cStart; cell < cEnd; ++cell) {
576:       PetscInt *findices  , *cindices;
577:       PetscInt  numFIndices, numCIndices;
578:       PetscInt  p, c;

580:       /* TODO: Use DMField instead of assuming affine */
581:       DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ);
582:       DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
583:       DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices);
584:       for (p = 0; p < numCIndices; ++p) {
585:         CoordinatesRealToRef(cdim, cdim, v0ref, v0, invJ, &coords[cindices[p]*cdim], &xi[p*cdim]);
586:       }
587:       PetscFECreateTabulation((PetscFE) obj, 1, numCIndices, xi, 0, &Tcoarse);
588:       /* Get elemMat entries by multiplying by weight */
589:       PetscArrayzero(elemMat, numCIndices*totDim);
590:       for (i = 0; i < numFIndices; ++i) {
591:         for (p = 0; p < numCIndices; ++p) {
592:           for (c = 0; c < Nc; ++c) {
593:             /* B[(p*pdim + i)*Nc + c] is the value at point p for basis function i and component c */
594:             elemMat[p*numFIndices+i] += Tcoarse->T[0][(p*numFIndices + i)*Nc + c]*(useDeltaFunction ? 1.0 : detJ);
595:           }
596:         }
597:       }
598:       PetscTabulationDestroy(&Tcoarse);
599:       for (p = 0; p < numCIndices; ++p) rowIDXs[p] = cindices[p] + rStart;
600:       if (0) {DMPrintCellMatrix(cell, name, 1, numCIndices, elemMat);}
601:       /* Block diagonal */
602:       {
603:         PetscBLASInt blasn, blask;
604:         PetscScalar  one = 1.0, zero = 0.0;

606:         PetscBLASIntCast(numCIndices, &blasn);
607:         PetscBLASIntCast(numFIndices, &blask);
608:         PetscStackCallBLAS("BLASgemm",BLASgemm_("T","N",&blasn,&blasn,&blask,&one,elemMat,&blask,elemMat,&blask,&zero,elemMatSq,&blasn));
609:       }
610:       MatSetValues(mass, numCIndices, rowIDXs, numCIndices, rowIDXs, elemMatSq, ADD_VALUES);
611:       /* TODO Off-diagonal */
612:       PetscFree(cindices);
613:       DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL);
614:     }
615:     DMSwarmRestoreField(dmc, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);
616:   }
617:   PetscFree4(elemMat, elemMatSq, rowIDXs, xi);
618:   PetscFree(adj);
619:   DMSwarmSortRestoreAccess(dmc);
620:   PetscFree3(v0, J, invJ);
621:   MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY);
622:   MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY);
623:   return(0);
624: }

626: /*@C
627:   DMSwarmCreateMassMatrixSquare - Creates the block-diagonal of the square, M^T_p M_p, of the particle mass matrix M_p

629:   Collective on dmCoarse

631:   Input parameters:
632: + dmCoarse - a DMSwarm
633: - dmFine   - a DMPlex

635:   Output parameter:
636: . mass     - the square of the particle mass matrix

638:   Level: advanced

640:   Notes:
641:   We only compute the block diagonal since this provides a good preconditioner and is completely local. It would be possible in the
642:   future to compute the full normal equations.

644: .seealso: DMCreateMassMatrix()
645: @*/
646: PetscErrorCode DMSwarmCreateMassMatrixSquare(DM dmCoarse, DM dmFine, Mat *mass)
647: {
648:   PetscInt       n;
649:   void          *ctx;

653:   DMSwarmGetLocalSize(dmCoarse, &n);
654:   MatCreate(PetscObjectComm((PetscObject) dmCoarse), mass);
655:   MatSetSizes(*mass, n, n, PETSC_DETERMINE, PETSC_DETERMINE);
656:   MatSetType(*mass, dmCoarse->mattype);
657:   DMGetApplicationContext(dmFine, &ctx);

659:   DMSwarmComputeMassMatrixSquare_Private(dmCoarse, dmFine, *mass, PETSC_TRUE, ctx);
660:   MatViewFromOptions(*mass, NULL, "-mass_sq_mat_view");
661:   return(0);
662: }

664: /*@C
665:    DMSwarmCreateGlobalVectorFromField - Creates a Vec object sharing the array associated with a given field

667:    Collective on dm

669:    Input parameters:
670: +  dm - a DMSwarm
671: -  fieldname - the textual name given to a registered field

673:    Output parameter:
674: .  vec - the vector

676:    Level: beginner

678:    Notes:
679:    The vector must be returned using a matching call to DMSwarmDestroyGlobalVectorFromField().

681: .seealso: DMSwarmRegisterPetscDatatypeField(), DMSwarmDestroyGlobalVectorFromField()
682: @*/
683: PetscErrorCode DMSwarmCreateGlobalVectorFromField(DM dm,const char fieldname[],Vec *vec)
684: {
685:   MPI_Comm       comm = PetscObjectComm((PetscObject) dm);

689:   DMSwarmCreateVectorFromField_Private(dm, fieldname, comm, vec);
690:   return(0);
691: }

693: /*@C
694:    DMSwarmDestroyGlobalVectorFromField - Destroys the Vec object which share the array associated with a given field

696:    Collective on dm

698:    Input parameters:
699: +  dm - a DMSwarm
700: -  fieldname - the textual name given to a registered field

702:    Output parameter:
703: .  vec - the vector

705:    Level: beginner

707: .seealso: DMSwarmRegisterPetscDatatypeField(), DMSwarmCreateGlobalVectorFromField()
708: @*/
709: PetscErrorCode DMSwarmDestroyGlobalVectorFromField(DM dm,const char fieldname[],Vec *vec)
710: {

714:   DMSwarmDestroyVectorFromField_Private(dm, fieldname, vec);
715:   return(0);
716: }

718: /*@C
719:    DMSwarmCreateLocalVectorFromField - Creates a Vec object sharing the array associated with a given field

721:    Collective on dm

723:    Input parameters:
724: +  dm - a DMSwarm
725: -  fieldname - the textual name given to a registered field

727:    Output parameter:
728: .  vec - the vector

730:    Level: beginner

732:    Notes:
733:    The vector must be returned using a matching call to DMSwarmDestroyLocalVectorFromField().

735: .seealso: DMSwarmRegisterPetscDatatypeField(), DMSwarmDestroyLocalVectorFromField()
736: @*/
737: PetscErrorCode DMSwarmCreateLocalVectorFromField(DM dm,const char fieldname[],Vec *vec)
738: {
739:   MPI_Comm       comm = PETSC_COMM_SELF;

743:   DMSwarmCreateVectorFromField_Private(dm, fieldname, comm, vec);
744:   return(0);
745: }

747: /*@C
748:    DMSwarmDestroyLocalVectorFromField - Destroys the Vec object which share the array associated with a given field

750:    Collective on dm

752:    Input parameters:
753: +  dm - a DMSwarm
754: -  fieldname - the textual name given to a registered field

756:    Output parameter:
757: .  vec - the vector

759:    Level: beginner

761: .seealso: DMSwarmRegisterPetscDatatypeField(), DMSwarmCreateLocalVectorFromField()
762: @*/
763: PetscErrorCode DMSwarmDestroyLocalVectorFromField(DM dm,const char fieldname[],Vec *vec)
764: {

768:   DMSwarmDestroyVectorFromField_Private(dm, fieldname, vec);
769:   return(0);
770: }

772: /*
773: PetscErrorCode DMSwarmCreateGlobalVectorFromFields(DM dm,const PetscInt nf,const char *fieldnames[],Vec *vec)
774: {
775:   return(0);
776: }

778: PetscErrorCode DMSwarmRestoreGlobalVectorFromFields(DM dm,Vec *vec)
779: {
780:   return(0);
781: }
782: */

784: /*@C
785:    DMSwarmInitializeFieldRegister - Initiates the registration of fields to a DMSwarm

787:    Collective on dm

789:    Input parameter:
790: .  dm - a DMSwarm

792:    Level: beginner

794:    Notes:
795:    After all fields have been registered, you must call DMSwarmFinalizeFieldRegister().

797: .seealso: DMSwarmFinalizeFieldRegister(), DMSwarmRegisterPetscDatatypeField(),
798:  DMSwarmRegisterUserStructField(), DMSwarmRegisterUserDatatypeField()
799: @*/
800: PetscErrorCode DMSwarmInitializeFieldRegister(DM dm)
801: {
802:   DM_Swarm      *swarm = (DM_Swarm *) dm->data;

806:   if (!swarm->field_registration_initialized) {
807:     swarm->field_registration_initialized = PETSC_TRUE;
808:     DMSwarmRegisterPetscDatatypeField(dm,DMSwarmField_pid,1,PETSC_INT64); /* unique identifer */
809:     DMSwarmRegisterPetscDatatypeField(dm,DMSwarmField_rank,1,PETSC_INT); /* used for communication */
810:   }
811:   return(0);
812: }

814: /*@
815:    DMSwarmFinalizeFieldRegister - Finalizes the registration of fields to a DMSwarm

817:    Collective on dm

819:    Input parameter:
820: .  dm - a DMSwarm

822:    Level: beginner

824:    Notes:
825:    After DMSwarmFinalizeFieldRegister() has been called, no new fields can be defined on the DMSwarm.

827: .seealso: DMSwarmInitializeFieldRegister(), DMSwarmRegisterPetscDatatypeField(),
828:  DMSwarmRegisterUserStructField(), DMSwarmRegisterUserDatatypeField()
829: @*/
830: PetscErrorCode DMSwarmFinalizeFieldRegister(DM dm)
831: {
832:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

836:   if (!swarm->field_registration_finalized) {
837:     DMSwarmDataBucketFinalize(swarm->db);
838:   }
839:   swarm->field_registration_finalized = PETSC_TRUE;
840:   return(0);
841: }

843: /*@
844:    DMSwarmSetLocalSizes - Sets the length of all registered fields on the DMSwarm

846:    Not collective

848:    Input parameters:
849: +  dm - a DMSwarm
850: .  nlocal - the length of each registered field
851: -  buffer - the length of the buffer used to efficient dynamic re-sizing

853:    Level: beginner

855: .seealso: DMSwarmGetLocalSize()
856: @*/
857: PetscErrorCode DMSwarmSetLocalSizes(DM dm,PetscInt nlocal,PetscInt buffer)
858: {
859:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

863:   PetscLogEventBegin(DMSWARM_SetSizes,0,0,0,0);
864:   DMSwarmDataBucketSetSizes(swarm->db,nlocal,buffer);
865:   PetscLogEventEnd(DMSWARM_SetSizes,0,0,0,0);
866:   return(0);
867: }

869: /*@
870:    DMSwarmSetCellDM - Attachs a DM to a DMSwarm

872:    Collective on dm

874:    Input parameters:
875: +  dm - a DMSwarm
876: -  dmcell - the DM to attach to the DMSwarm

878:    Level: beginner

880:    Notes:
881:    The attached DM (dmcell) will be queried for point location and
882:    neighbor MPI-rank information if DMSwarmMigrate() is called.

884: .seealso: DMSwarmSetType(), DMSwarmGetCellDM(), DMSwarmMigrate()
885: @*/
886: PetscErrorCode DMSwarmSetCellDM(DM dm,DM dmcell)
887: {
888:   DM_Swarm *swarm = (DM_Swarm*)dm->data;

891:   swarm->dmcell = dmcell;
892:   return(0);
893: }

895: /*@
896:    DMSwarmGetCellDM - Fetches the attached cell DM

898:    Collective on dm

900:    Input parameter:
901: .  dm - a DMSwarm

903:    Output parameter:
904: .  dmcell - the DM which was attached to the DMSwarm

906:    Level: beginner

908: .seealso: DMSwarmSetCellDM()
909: @*/
910: PetscErrorCode DMSwarmGetCellDM(DM dm,DM *dmcell)
911: {
912:   DM_Swarm *swarm = (DM_Swarm*)dm->data;

915:   *dmcell = swarm->dmcell;
916:   return(0);
917: }

919: /*@
920:    DMSwarmGetLocalSize - Retrives the local length of fields registered

922:    Not collective

924:    Input parameter:
925: .  dm - a DMSwarm

927:    Output parameter:
928: .  nlocal - the length of each registered field

930:    Level: beginner

932: .seealso: DMSwarmGetSize(), DMSwarmSetLocalSizes()
933: @*/
934: PetscErrorCode DMSwarmGetLocalSize(DM dm,PetscInt *nlocal)
935: {
936:   DM_Swarm *swarm = (DM_Swarm*)dm->data;

940:   if (nlocal) {DMSwarmDataBucketGetSizes(swarm->db,nlocal,NULL,NULL);}
941:   return(0);
942: }

944: /*@
945:    DMSwarmGetSize - Retrives the total length of fields registered

947:    Collective on dm

949:    Input parameter:
950: .  dm - a DMSwarm

952:    Output parameter:
953: .  n - the total length of each registered field

955:    Level: beginner

957:    Note:
958:    This calls MPI_Allreduce upon each call (inefficient but safe)

960: .seealso: DMSwarmGetLocalSize(), DMSwarmSetLocalSizes()
961: @*/
962: PetscErrorCode DMSwarmGetSize(DM dm,PetscInt *n)
963: {
964:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
966:   PetscInt       nlocal,ng;

969:   DMSwarmDataBucketGetSizes(swarm->db,&nlocal,NULL,NULL);
970:   MPI_Allreduce(&nlocal,&ng,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)dm));
971:   if (n) { *n = ng; }
972:   return(0);
973: }

975: /*@C
976:    DMSwarmRegisterPetscDatatypeField - Register a field to a DMSwarm with a native PETSc data type

978:    Collective on dm

980:    Input parameters:
981: +  dm - a DMSwarm
982: .  fieldname - the textual name to identify this field
983: .  blocksize - the number of each data type
984: -  type - a valid PETSc data type (PETSC_CHAR, PETSC_SHORT, PETSC_INT, PETSC_FLOAT, PETSC_REAL, PETSC_LONG)

986:    Level: beginner

988:    Notes:
989:    The textual name for each registered field must be unique.

991: .seealso: DMSwarmRegisterUserStructField(), DMSwarmRegisterUserDatatypeField()
992: @*/
993: PetscErrorCode DMSwarmRegisterPetscDatatypeField(DM dm,const char fieldname[],PetscInt blocksize,PetscDataType type)
994: {
996:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
997:   size_t         size;

1000:   if (!swarm->field_registration_initialized) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Must call DMSwarmInitializeFieldRegister() first");
1001:   if (swarm->field_registration_finalized) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Cannot register additional fields after calling DMSwarmFinalizeFieldRegister() first");

1003:   if (type == PETSC_OBJECT) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Valid for {char,short,int,long,float,double}");
1004:   if (type == PETSC_FUNCTION) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Valid for {char,short,int,long,float,double}");
1005:   if (type == PETSC_STRING) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Valid for {char,short,int,long,float,double}");
1006:   if (type == PETSC_STRUCT) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Valid for {char,short,int,long,float,double}");
1007:   if (type == PETSC_DATATYPE_UNKNOWN) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Valid for {char,short,int,long,float,double}");

1009:   PetscDataTypeGetSize(type, &size);
1010:   /* Load a specific data type into data bucket, specifying textual name and its size in bytes */
1011:   DMSwarmDataBucketRegisterField(swarm->db,"DMSwarmRegisterPetscDatatypeField",fieldname,blocksize*size,NULL);
1012:   {
1013:     DMSwarmDataField gfield;

1015:     DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db,fieldname,&gfield);
1016:     DMSwarmDataFieldSetBlockSize(gfield,blocksize);
1017:   }
1018:   swarm->db->field[swarm->db->nfields-1]->petsc_type = type;
1019:   return(0);
1020: }

1022: /*@C
1023:    DMSwarmRegisterUserStructField - Register a user defined struct to a DMSwarm

1025:    Collective on dm

1027:    Input parameters:
1028: +  dm - a DMSwarm
1029: .  fieldname - the textual name to identify this field
1030: -  size - the size in bytes of the user struct of each data type

1032:    Level: beginner

1034:    Notes:
1035:    The textual name for each registered field must be unique.

1037: .seealso: DMSwarmRegisterPetscDatatypeField(), DMSwarmRegisterUserDatatypeField()
1038: @*/
1039: PetscErrorCode DMSwarmRegisterUserStructField(DM dm,const char fieldname[],size_t size)
1040: {
1042:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1045:   DMSwarmDataBucketRegisterField(swarm->db,"DMSwarmRegisterUserStructField",fieldname,size,NULL);
1046:   swarm->db->field[swarm->db->nfields-1]->petsc_type = PETSC_STRUCT ;
1047:   return(0);
1048: }

1050: /*@C
1051:    DMSwarmRegisterUserDatatypeField - Register a user defined data type to a DMSwarm

1053:    Collective on dm

1055:    Input parameters:
1056: +  dm - a DMSwarm
1057: .  fieldname - the textual name to identify this field
1058: .  size - the size in bytes of the user data type
1059: -  blocksize - the number of each data type

1061:    Level: beginner

1063:    Notes:
1064:    The textual name for each registered field must be unique.

1066: .seealso: DMSwarmRegisterPetscDatatypeField(), DMSwarmRegisterUserStructField(), DMSwarmRegisterUserDatatypeField()
1067: @*/
1068: PetscErrorCode DMSwarmRegisterUserDatatypeField(DM dm,const char fieldname[],size_t size,PetscInt blocksize)
1069: {
1070:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1074:   DMSwarmDataBucketRegisterField(swarm->db,"DMSwarmRegisterUserDatatypeField",fieldname,blocksize*size,NULL);
1075:   {
1076:     DMSwarmDataField gfield;

1078:     DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db,fieldname,&gfield);
1079:     DMSwarmDataFieldSetBlockSize(gfield,blocksize);
1080:   }
1081:   swarm->db->field[swarm->db->nfields-1]->petsc_type = PETSC_DATATYPE_UNKNOWN;
1082:   return(0);
1083: }

1085: /*@C
1086:    DMSwarmGetField - Get access to the underlying array storing all entries associated with a registered field

1088:    Not collective

1090:    Input parameters:
1091: +  dm - a DMSwarm
1092: -  fieldname - the textual name to identify this field

1094:    Output parameters:
1095: +  blocksize - the number of each data type
1096: .  type - the data type
1097: -  data - pointer to raw array

1099:    Level: beginner

1101:    Notes:
1102:    The array must be returned using a matching call to DMSwarmRestoreField().

1104: .seealso: DMSwarmRestoreField()
1105: @*/
1106: PetscErrorCode DMSwarmGetField(DM dm,const char fieldname[],PetscInt *blocksize,PetscDataType *type,void **data)
1107: {
1108:   DM_Swarm         *swarm = (DM_Swarm*)dm->data;
1109:   DMSwarmDataField gfield;

1113:   if (!swarm->issetup) { DMSetUp(dm); }
1114:   DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db,fieldname,&gfield);
1115:   DMSwarmDataFieldGetAccess(gfield);
1116:   DMSwarmDataFieldGetEntries(gfield,data);
1117:   if (blocksize) {*blocksize = gfield->bs; }
1118:   if (type) { *type = gfield->petsc_type; }
1119:   return(0);
1120: }

1122: /*@C
1123:    DMSwarmRestoreField - Restore access to the underlying array storing all entries associated with a registered field

1125:    Not collective

1127:    Input parameters:
1128: +  dm - a DMSwarm
1129: -  fieldname - the textual name to identify this field

1131:    Output parameters:
1132: +  blocksize - the number of each data type
1133: .  type - the data type
1134: -  data - pointer to raw array

1136:    Level: beginner

1138:    Notes:
1139:    The user must call DMSwarmGetField() prior to calling DMSwarmRestoreField().

1141: .seealso: DMSwarmGetField()
1142: @*/
1143: PetscErrorCode DMSwarmRestoreField(DM dm,const char fieldname[],PetscInt *blocksize,PetscDataType *type,void **data)
1144: {
1145:   DM_Swarm         *swarm = (DM_Swarm*)dm->data;
1146:   DMSwarmDataField gfield;

1150:   DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db,fieldname,&gfield);
1151:   DMSwarmDataFieldRestoreAccess(gfield);
1152:   if (data) *data = NULL;
1153:   return(0);
1154: }

1156: /*@
1157:    DMSwarmAddPoint - Add space for one new point in the DMSwarm

1159:    Not collective

1161:    Input parameter:
1162: .  dm - a DMSwarm

1164:    Level: beginner

1166:    Notes:
1167:    The new point will have all fields initialized to zero.

1169: .seealso: DMSwarmAddNPoints()
1170: @*/
1171: PetscErrorCode DMSwarmAddPoint(DM dm)
1172: {
1173:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1177:   if (!swarm->issetup) {DMSetUp(dm);}
1178:   PetscLogEventBegin(DMSWARM_AddPoints,0,0,0,0);
1179:   DMSwarmDataBucketAddPoint(swarm->db);
1180:   PetscLogEventEnd(DMSWARM_AddPoints,0,0,0,0);
1181:   return(0);
1182: }

1184: /*@
1185:    DMSwarmAddNPoints - Add space for a number of new points in the DMSwarm

1187:    Not collective

1189:    Input parameters:
1190: +  dm - a DMSwarm
1191: -  npoints - the number of new points to add

1193:    Level: beginner

1195:    Notes:
1196:    The new point will have all fields initialized to zero.

1198: .seealso: DMSwarmAddPoint()
1199: @*/
1200: PetscErrorCode DMSwarmAddNPoints(DM dm,PetscInt npoints)
1201: {
1202:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
1204:   PetscInt       nlocal;

1207:   PetscLogEventBegin(DMSWARM_AddPoints,0,0,0,0);
1208:   DMSwarmDataBucketGetSizes(swarm->db,&nlocal,NULL,NULL);
1209:   nlocal = nlocal + npoints;
1210:   DMSwarmDataBucketSetSizes(swarm->db,nlocal,DMSWARM_DATA_BUCKET_BUFFER_DEFAULT);
1211:   PetscLogEventEnd(DMSWARM_AddPoints,0,0,0,0);
1212:   return(0);
1213: }

1215: /*@
1216:    DMSwarmRemovePoint - Remove the last point from the DMSwarm

1218:    Not collective

1220:    Input parameter:
1221: .  dm - a DMSwarm

1223:    Level: beginner

1225: .seealso: DMSwarmRemovePointAtIndex()
1226: @*/
1227: PetscErrorCode DMSwarmRemovePoint(DM dm)
1228: {
1229:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1233:   PetscLogEventBegin(DMSWARM_RemovePoints,0,0,0,0);
1234:   DMSwarmDataBucketRemovePoint(swarm->db);
1235:   PetscLogEventEnd(DMSWARM_RemovePoints,0,0,0,0);
1236:   return(0);
1237: }

1239: /*@
1240:    DMSwarmRemovePointAtIndex - Removes a specific point from the DMSwarm

1242:    Not collective

1244:    Input parameters:
1245: +  dm - a DMSwarm
1246: -  idx - index of point to remove

1248:    Level: beginner

1250: .seealso: DMSwarmRemovePoint()
1251: @*/
1252: PetscErrorCode DMSwarmRemovePointAtIndex(DM dm,PetscInt idx)
1253: {
1254:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1258:   PetscLogEventBegin(DMSWARM_RemovePoints,0,0,0,0);
1259:   DMSwarmDataBucketRemovePointAtIndex(swarm->db,idx);
1260:   PetscLogEventEnd(DMSWARM_RemovePoints,0,0,0,0);
1261:   return(0);
1262: }

1264: /*@
1265:    DMSwarmCopyPoint - Copy point pj to point pi in the DMSwarm

1267:    Not collective

1269:    Input parameters:
1270: +  dm - a DMSwarm
1271: .  pi - the index of the point to copy
1272: -  pj - the point index where the copy should be located

1274:  Level: beginner

1276: .seealso: DMSwarmRemovePoint()
1277: @*/
1278: PetscErrorCode DMSwarmCopyPoint(DM dm,PetscInt pi,PetscInt pj)
1279: {
1280:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1284:   if (!swarm->issetup) {DMSetUp(dm);}
1285:   DMSwarmDataBucketCopyPoint(swarm->db,pi,swarm->db,pj);
1286:   return(0);
1287: }

1289: PetscErrorCode DMSwarmMigrate_Basic(DM dm,PetscBool remove_sent_points)
1290: {

1294:   DMSwarmMigrate_Push_Basic(dm,remove_sent_points);
1295:   return(0);
1296: }

1298: /*@
1299:    DMSwarmMigrate - Relocates points defined in the DMSwarm to other MPI-ranks

1301:    Collective on dm

1303:    Input parameters:
1304: +  dm - the DMSwarm
1305: -  remove_sent_points - flag indicating if sent points should be removed from the current MPI-rank

1307:    Notes:
1308:    The DM will be modified to accomodate received points.
1309:    If remove_sent_points = PETSC_TRUE, any points that were sent will be removed from the DM.
1310:    Different styles of migration are supported. See DMSwarmSetMigrateType().

1312:    Level: advanced

1314: .seealso: DMSwarmSetMigrateType()
1315: @*/
1316: PetscErrorCode DMSwarmMigrate(DM dm,PetscBool remove_sent_points)
1317: {
1318:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1322:   PetscLogEventBegin(DMSWARM_Migrate,0,0,0,0);
1323:   switch (swarm->migrate_type) {
1324:     case DMSWARM_MIGRATE_BASIC:
1325:       DMSwarmMigrate_Basic(dm,remove_sent_points);
1326:       break;
1327:     case DMSWARM_MIGRATE_DMCELLNSCATTER:
1328:       DMSwarmMigrate_CellDMScatter(dm,remove_sent_points);
1329:       break;
1330:     case DMSWARM_MIGRATE_DMCELLEXACT:
1331:       SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DMSWARM_MIGRATE_DMCELLEXACT not implemented");
1332:     case DMSWARM_MIGRATE_USER:
1333:       SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DMSWARM_MIGRATE_USER not implemented");
1334:     default:
1335:       SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DMSWARM_MIGRATE type unknown");
1336:   }
1337:   PetscLogEventEnd(DMSWARM_Migrate,0,0,0,0);
1338:   DMClearGlobalVectors(dm);
1339:   return(0);
1340: }

1342: PetscErrorCode DMSwarmMigrate_GlobalToLocal_Basic(DM dm,PetscInt *globalsize);

1344: /*
1345:  DMSwarmCollectViewCreate

1347:  * Applies a collection method and gathers point neighbour points into dm

1349:  Notes:
1350:  Users should call DMSwarmCollectViewDestroy() after
1351:  they have finished computations associated with the collected points
1352: */

1354: /*@
1355:    DMSwarmCollectViewCreate - Applies a collection method and gathers points
1356:    in neighbour MPI-ranks into the DMSwarm

1358:    Collective on dm

1360:    Input parameter:
1361: .  dm - the DMSwarm

1363:    Notes:
1364:    Users should call DMSwarmCollectViewDestroy() after
1365:    they have finished computations associated with the collected points
1366:    Different collect methods are supported. See DMSwarmSetCollectType().

1368:    Level: advanced

1370: .seealso: DMSwarmCollectViewDestroy(), DMSwarmSetCollectType()
1371: @*/
1372: PetscErrorCode DMSwarmCollectViewCreate(DM dm)
1373: {
1375:   DM_Swarm *swarm = (DM_Swarm*)dm->data;
1376:   PetscInt ng;

1379:   if (swarm->collect_view_active) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"CollectView currently active");
1380:   DMSwarmGetLocalSize(dm,&ng);
1381:   switch (swarm->collect_type) {

1383:     case DMSWARM_COLLECT_BASIC:
1384:       DMSwarmMigrate_GlobalToLocal_Basic(dm,&ng);
1385:       break;
1386:     case DMSWARM_COLLECT_DMDABOUNDINGBOX:
1387:       SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DMSWARM_COLLECT_DMDABOUNDINGBOX not implemented");
1388:     case DMSWARM_COLLECT_GENERAL:
1389:       SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DMSWARM_COLLECT_GENERAL not implemented");
1390:     default:
1391:       SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DMSWARM_COLLECT type unknown");
1392:   }
1393:   swarm->collect_view_active = PETSC_TRUE;
1394:   swarm->collect_view_reset_nlocal = ng;
1395:   return(0);
1396: }

1398: /*@
1399:    DMSwarmCollectViewDestroy - Resets the DMSwarm to the size prior to calling DMSwarmCollectViewCreate()

1401:    Collective on dm

1403:    Input parameters:
1404: .  dm - the DMSwarm

1406:    Notes:
1407:    Users should call DMSwarmCollectViewCreate() before this function is called.

1409:    Level: advanced

1411: .seealso: DMSwarmCollectViewCreate(), DMSwarmSetCollectType()
1412: @*/
1413: PetscErrorCode DMSwarmCollectViewDestroy(DM dm)
1414: {
1416:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1419:   if (!swarm->collect_view_active) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"CollectView is currently not active");
1420:   DMSwarmSetLocalSizes(dm,swarm->collect_view_reset_nlocal,-1);
1421:   swarm->collect_view_active = PETSC_FALSE;
1422:   return(0);
1423: }

1425: PetscErrorCode DMSwarmSetUpPIC(DM dm)
1426: {
1427:   PetscInt       dim;

1431:   DMGetDimension(dm,&dim);
1432:   if (dim < 1) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Dimension must be 1,2,3 - found %D",dim);
1433:   if (dim > 3) SETERRQ1(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Dimension must be 1,2,3 - found %D",dim);
1434:   DMSwarmRegisterPetscDatatypeField(dm,DMSwarmPICField_coor,dim,PETSC_DOUBLE);
1435:   DMSwarmRegisterPetscDatatypeField(dm,DMSwarmPICField_cellid,1,PETSC_INT);
1436:   return(0);
1437: }

1439: /*@
1440:   DMSwarmSetPointCoordinatesRandom - Sets initial coordinates for particles in each cell

1442:   Collective on dm

1444:   Input parameters:
1445: + dm  - the DMSwarm
1446: - Npc - The number of particles per cell in the cell DM

1448:   Notes:
1449:   The user must use DMSwarmSetCellDM() to set the cell DM first. The particles are placed randomly inside each cell. If only
1450:   one particle is in each cell, it is placed at the centroid.

1452:   Level: intermediate

1454: .seealso: DMSwarmSetCellDM()
1455: @*/
1456: PetscErrorCode DMSwarmSetPointCoordinatesRandom(DM dm, PetscInt Npc)
1457: {
1458:   DM             cdm;
1459:   PetscRandom    rnd;
1460:   DMPolytopeType ct;
1461:   PetscBool      simplex;
1462:   PetscReal     *centroid, *coords, *xi0, *v0, *J, *invJ, detJ;
1463:   PetscInt       dim, d, cStart, cEnd, c, p;

1467:   PetscRandomCreate(PetscObjectComm((PetscObject) dm), &rnd);
1468:   PetscRandomSetInterval(rnd, -1.0, 1.0);
1469:   PetscRandomSetType(rnd, PETSCRAND48);

1471:   DMSwarmGetCellDM(dm, &cdm);
1472:   DMGetDimension(cdm, &dim);
1473:   DMPlexGetHeightStratum(cdm, 0, &cStart, &cEnd);
1474:   DMPlexGetCellType(cdm, cStart, &ct);
1475:   simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct)+1 ? PETSC_TRUE : PETSC_FALSE;

1477:   PetscMalloc5(dim, &centroid, dim, &xi0, dim, &v0, dim*dim, &J, dim*dim, &invJ);
1478:   for (d = 0; d < dim; ++d) xi0[d] = -1.0;
1479:   DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);
1480:   for (c = cStart; c < cEnd; ++c) {
1481:     if (Npc == 1) {
1482:       DMPlexComputeCellGeometryFVM(cdm, c, NULL, centroid, NULL);
1483:       for (d = 0; d < dim; ++d) coords[c*dim+d] = centroid[d];
1484:     } else {
1485:       DMPlexComputeCellGeometryFEM(cdm, c, NULL, v0, J, invJ, &detJ); /* affine */
1486:       for (p = 0; p < Npc; ++p) {
1487:         const PetscInt n   = c*Npc + p;
1488:         PetscReal      sum = 0.0, refcoords[3];

1490:         for (d = 0; d < dim; ++d) {
1491:           PetscRandomGetValueReal(rnd, &refcoords[d]);
1492:           sum += refcoords[d];
1493:         }
1494:         if (simplex && sum > 0.0) for (d = 0; d < dim; ++d) refcoords[d] -= PetscSqrtReal(dim)*sum;
1495:         CoordinatesRefToReal(dim, dim, xi0, v0, J, refcoords, &coords[n*dim]);
1496:       }
1497:     }
1498:   }
1499:   DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);
1500:   PetscFree5(centroid, xi0, v0, J, invJ);
1501:   PetscRandomDestroy(&rnd);
1502:   return(0);
1503: }

1505: /*@
1506:    DMSwarmSetType - Set particular flavor of DMSwarm

1508:    Collective on dm

1510:    Input parameters:
1511: +  dm - the DMSwarm
1512: -  stype - the DMSwarm type (e.g. DMSWARM_PIC)

1514:    Level: advanced

1516: .seealso: DMSwarmSetMigrateType(), DMSwarmSetCollectType()
1517: @*/
1518: PetscErrorCode DMSwarmSetType(DM dm,DMSwarmType stype)
1519: {
1520:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1524:   swarm->swarm_type = stype;
1525:   if (swarm->swarm_type == DMSWARM_PIC) {
1526:     DMSwarmSetUpPIC(dm);
1527:   }
1528:   return(0);
1529: }

1531: PetscErrorCode DMSetup_Swarm(DM dm)
1532: {
1533:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
1535:   PetscMPIInt    rank;
1536:   PetscInt       p,npoints,*rankval;

1539:   if (swarm->issetup) return(0);

1541:   swarm->issetup = PETSC_TRUE;

1543:   if (swarm->swarm_type == DMSWARM_PIC) {
1544:     /* check dmcell exists */
1545:     if (!swarm->dmcell) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"DMSWARM_PIC requires you call DMSwarmSetCellDM");

1547:     if (swarm->dmcell->ops->locatepointssubdomain) {
1548:       /* check methods exists for exact ownership identificiation */
1549:       PetscInfo(dm, "DMSWARM_PIC: Using method CellDM->ops->LocatePointsSubdomain\n");
1550:       swarm->migrate_type = DMSWARM_MIGRATE_DMCELLEXACT;
1551:     } else {
1552:       /* check methods exist for point location AND rank neighbor identification */
1553:       if (swarm->dmcell->ops->locatepoints) {
1554:         PetscInfo(dm, "DMSWARM_PIC: Using method CellDM->LocatePoints\n");
1555:       } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"DMSWARM_PIC requires the method CellDM->ops->locatepoints be defined");

1557:       if (swarm->dmcell->ops->getneighbors) {
1558:         PetscInfo(dm, "DMSWARM_PIC: Using method CellDM->GetNeigbors\n");
1559:       } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"DMSWARM_PIC requires the method CellDM->ops->getneighbors be defined");

1561:       swarm->migrate_type = DMSWARM_MIGRATE_DMCELLNSCATTER;
1562:     }
1563:   }

1565:   DMSwarmFinalizeFieldRegister(dm);

1567:   /* check some fields were registered */
1568:   if (swarm->db->nfields <= 2) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"At least one field user must be registered via DMSwarmRegisterXXX()");

1570:   /* check local sizes were set */
1571:   if (swarm->db->L == -1) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Local sizes must be set via DMSwarmSetLocalSizes()");

1573:   /* initialize values in pid and rank placeholders */
1574:   /* TODO: [pid - use MPI_Scan] */
1575:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);
1576:   DMSwarmDataBucketGetSizes(swarm->db,&npoints,NULL,NULL);
1577:   DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);
1578:   for (p=0; p<npoints; p++) {
1579:     rankval[p] = (PetscInt)rank;
1580:   }
1581:   DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);
1582:   return(0);
1583: }

1585: extern PetscErrorCode DMSwarmSortDestroy(DMSwarmSort *_ctx);

1587: PetscErrorCode DMDestroy_Swarm(DM dm)
1588: {
1589:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;

1593:   if (--swarm->refct > 0) return(0);
1594:   DMSwarmDataBucketDestroy(&swarm->db);
1595:   if (swarm->sort_context) {
1596:     DMSwarmSortDestroy(&swarm->sort_context);
1597:   }
1598:   PetscFree(swarm);
1599:   return(0);
1600: }

1602: PetscErrorCode DMSwarmView_Draw(DM dm, PetscViewer viewer)
1603: {
1604:   DM             cdm;
1605:   PetscDraw      draw;
1606:   PetscReal     *coords, oldPause, radius = 0.01;
1607:   PetscInt       Np, p, bs;

1611:   PetscOptionsGetReal(NULL, ((PetscObject) dm)->prefix, "-dm_view_swarm_radius", &radius, NULL);
1612:   PetscViewerDrawGetDraw(viewer, 0, &draw);
1613:   DMSwarmGetCellDM(dm, &cdm);
1614:   PetscDrawGetPause(draw, &oldPause);
1615:   PetscDrawSetPause(draw, 0.0);
1616:   DMView(cdm, viewer);
1617:   PetscDrawSetPause(draw, oldPause);

1619:   DMSwarmGetLocalSize(dm, &Np);
1620:   DMSwarmGetField(dm, DMSwarmPICField_coor, &bs, NULL, (void **) &coords);
1621:   for (p = 0; p < Np; ++p) {
1622:     const PetscInt i = p*bs;

1624:     PetscDrawEllipse(draw, coords[i], coords[i+1], radius, radius, PETSC_DRAW_BLUE);
1625:   }
1626:   DMSwarmRestoreField(dm, DMSwarmPICField_coor, &bs, NULL, (void **) &coords);
1627:   PetscDrawFlush(draw);
1628:   PetscDrawPause(draw);
1629:   PetscDrawSave(draw);
1630:   return(0);
1631: }

1633: PetscErrorCode DMView_Swarm(DM dm, PetscViewer viewer)
1634: {
1635:   DM_Swarm       *swarm = (DM_Swarm*)dm->data;
1636:   PetscBool      iascii,ibinary,ishdf5,isvtk,isdraw;

1642:   PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii);
1643:   PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY,&ibinary);
1644:   PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK,   &isvtk);
1645:   PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5,  &ishdf5);
1646:   PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW,  &isdraw);
1647:   if (iascii) {
1648:     DMSwarmDataBucketView(PetscObjectComm((PetscObject)dm),swarm->db,NULL,DATABUCKET_VIEW_STDOUT);
1649:   } else if (ibinary) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"NO Binary support");
1650: #if defined(PETSC_HAVE_HDF5)
1651:   else if (ishdf5) {
1652:     DMSwarmView_HDF5(dm, viewer);
1653:   }
1654: #else
1655:   else if (ishdf5) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"HDF5 not supported. Please reconfigure using --download-hdf5");
1656: #endif
1657:   else if (isvtk) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"NO VTK support");
1658:   else if (isdraw) {
1659:     DMSwarmView_Draw(dm, viewer);
1660:   }
1661:   return(0);
1662: }

1664: /*@C
1665:    DMSwarmGetCellSwarm - Extracts a single cell from the DMSwarm object, returns it as a single cell DMSwarm.
1666:    The cell DM is filtered for fields of that cell, and the filtered DM is used as the cell DM of the new swarm object.

1668:    Important: Changes to this cell of the swarm will be lost if they are made prior to restoring this cell.

1670:    Noncollective

1672:    Input parameters:
1673: +  sw - the DMSwarm
1674: -  cellID - the integer id of the cell to be extracted and filtered

1676:    Output parameters:
1677: .  cellswarm - The new DMSwarm

1679:    Level: beginner

1681:    Note: This presently only supports DMSWARM_PIC type

1683: .seealso: DMSwarmRestoreCellSwarm()
1684: @*/
1685: PETSC_EXTERN PetscErrorCode DMSwarmGetCellSwarm(DM sw, PetscInt cellID, DM cellswarm)
1686: {
1687:   DM_Swarm      *original = (DM_Swarm*) sw->data;
1688:   DMLabel        label;
1689:   DM             dmc, subdmc;
1690:   PetscInt      *pids, particles, dim;

1694:   /* Configure new swarm */
1695:   DMSetType(cellswarm, DMSWARM);
1696:   DMGetDimension(sw, &dim);
1697:   DMSetDimension(cellswarm, dim);
1698:   DMSwarmSetType(cellswarm, DMSWARM_PIC);
1699:   /* Destroy the unused, unconfigured data bucket to prevent stragglers in memory */
1700:   DMSwarmDataBucketDestroy(&((DM_Swarm*)cellswarm->data)->db);
1701:   DMSwarmSortGetAccess(sw);
1702:   DMSwarmSortGetNumberOfPointsPerCell(sw, cellID, &particles);
1703:   DMSwarmSortGetPointsPerCell(sw, cellID, &particles, &pids);
1704:   DMSwarmDataBucketCreateFromSubset(original->db, particles, pids, &((DM_Swarm*)cellswarm->data)->db);
1705:   DMSwarmSortRestoreAccess(sw);
1706:   PetscFree(pids);
1707:   DMSwarmGetCellDM(sw, &dmc);
1708:   DMLabelCreate(PetscObjectComm((PetscObject)sw), "singlecell", &label);
1709:   DMAddLabel(dmc, label);
1710:   DMLabelSetValue(label, cellID, 1);
1711:   DMPlexFilter(dmc, label, 1, &subdmc);
1712:   DMSwarmSetCellDM(cellswarm, subdmc);
1713:   DMLabelDestroy(&label);
1714:   return(0);
1715: }

1717: /*@C
1718:    DMSwarmRestoreCellSwarm - Restores a DMSwarm object obtained with DMSwarmGetCellSwarm. All fields are copied back into the parent swarm.

1720:    Noncollective

1722:    Input parameters:
1723: +  sw - the parent DMSwarm
1724: .  cellID - the integer id of the cell to be copied back into the parent swarm
1725: -  cellswarm - the cell swarm object

1727:    Level: beginner

1729:    Note: This only supports DMSWARM_PIC types of DMSwarms

1731: .seealso: DMSwarmGetCellSwarm()
1732: @*/
1733: PETSC_EXTERN PetscErrorCode DMSwarmRestoreCellSwarm(DM sw, PetscInt cellID, DM cellswarm)
1734: {
1735:   DM                dmc;
1736:   PetscInt         *pids, particles, p;
1737:   PetscErrorCode    ierr;

1740:   DMSwarmSortGetAccess(sw);
1741:   DMSwarmSortGetPointsPerCell(sw, cellID, &particles, &pids);
1742:   DMSwarmSortRestoreAccess(sw);
1743:   /* Pointwise copy of each particle based on pid. The parent swarm may not be altered during this process. */
1744:   for (p=0; p<particles; ++p) {
1745:     DMSwarmDataBucketCopyPoint(((DM_Swarm*)cellswarm->data)->db,pids[p],((DM_Swarm*)sw->data)->db,pids[p]);
1746:   }
1747:   /* Free memory, destroy cell dm */
1748:   DMSwarmGetCellDM(cellswarm, &dmc);
1749:   DMDestroy(&dmc);
1750:   PetscFree(pids);
1751:   return(0);
1752: }

1754: PETSC_INTERN PetscErrorCode DMClone_Swarm(DM, DM *);

1756: static PetscErrorCode DMInitialize_Swarm(DM sw)
1757: {
1759:   sw->dim  = 0;
1760:   sw->ops->view                            = DMView_Swarm;
1761:   sw->ops->load                            = NULL;
1762:   sw->ops->setfromoptions                  = NULL;
1763:   sw->ops->clone                           = DMClone_Swarm;
1764:   sw->ops->setup                           = DMSetup_Swarm;
1765:   sw->ops->createlocalsection              = NULL;
1766:   sw->ops->createdefaultconstraints        = NULL;
1767:   sw->ops->createglobalvector              = DMCreateGlobalVector_Swarm;
1768:   sw->ops->createlocalvector               = DMCreateLocalVector_Swarm;
1769:   sw->ops->getlocaltoglobalmapping         = NULL;
1770:   sw->ops->createfieldis                   = NULL;
1771:   sw->ops->createcoordinatedm              = NULL;
1772:   sw->ops->getcoloring                     = NULL;
1773:   sw->ops->creatematrix                    = DMCreateMatrix_Swarm;
1774:   sw->ops->createinterpolation             = NULL;
1775:   sw->ops->createinjection                 = NULL;
1776:   sw->ops->createmassmatrix                = DMCreateMassMatrix_Swarm;
1777:   sw->ops->refine                          = NULL;
1778:   sw->ops->coarsen                         = NULL;
1779:   sw->ops->refinehierarchy                 = NULL;
1780:   sw->ops->coarsenhierarchy                = NULL;
1781:   sw->ops->globaltolocalbegin              = NULL;
1782:   sw->ops->globaltolocalend                = NULL;
1783:   sw->ops->localtoglobalbegin              = NULL;
1784:   sw->ops->localtoglobalend                = NULL;
1785:   sw->ops->destroy                         = DMDestroy_Swarm;
1786:   sw->ops->createsubdm                     = NULL;
1787:   sw->ops->getdimpoints                    = NULL;
1788:   sw->ops->locatepoints                    = NULL;
1789:   return(0);
1790: }

1792: PETSC_INTERN PetscErrorCode DMClone_Swarm(DM dm, DM *newdm)
1793: {
1794:   DM_Swarm       *swarm = (DM_Swarm *) dm->data;

1798:   swarm->refct++;
1799:   (*newdm)->data = swarm;
1800:   PetscObjectChangeTypeName((PetscObject) *newdm, DMSWARM);
1801:   DMInitialize_Swarm(*newdm);
1802:   return(0);
1803: }

1805: /*MC

1807:  DMSWARM = "swarm" - A DM object used to represent arrays of data (fields) of arbitrary data type.
1808:  This implementation was designed for particle methods in which the underlying
1809:  data required to be represented is both (i) dynamic in length, (ii) and of arbitrary data type.

1811:  User data can be represented by DMSwarm through a registering "fields".
1812:  To register a field, the user must provide;
1813:  (a) a unique name;
1814:  (b) the data type (or size in bytes);
1815:  (c) the block size of the data.

1817:  For example, suppose the application requires a unique id, energy, momentum and density to be stored
1818:  on a set of particles. Then the following code could be used

1820: $    DMSwarmInitializeFieldRegister(dm)
1821: $    DMSwarmRegisterPetscDatatypeField(dm,"uid",1,PETSC_LONG);
1822: $    DMSwarmRegisterPetscDatatypeField(dm,"energy",1,PETSC_REAL);
1823: $    DMSwarmRegisterPetscDatatypeField(dm,"momentum",3,PETSC_REAL);
1824: $    DMSwarmRegisterPetscDatatypeField(dm,"density",1,PETSC_FLOAT);
1825: $    DMSwarmFinalizeFieldRegister(dm)

1827:  The fields represented by DMSwarm are dynamic and can be re-sized at any time.
1828:  The only restriction imposed by DMSwarm is that all fields contain the same number of points.

1830:  To support particle methods, "migration" techniques are provided. These methods migrate data
1831:  between MPI-ranks.

1833:  DMSwarm supports the methods DMCreateGlobalVector() and DMCreateLocalVector().
1834:  As a DMSwarm may internally define and store values of different data types,
1835:  before calling DMCreateGlobalVector() or DMCreateLocalVector(), the user must inform DMSwarm which
1836:  fields should be used to define a Vec object via
1837:    DMSwarmVectorDefineField()
1838:  The specified field can be changed at any time - thereby permitting vectors
1839:  compatible with different fields to be created.

1841:  A dual representation of fields in the DMSwarm and a Vec object is permitted via
1842:    DMSwarmCreateGlobalVectorFromField()
1843:  Here the data defining the field in the DMSwarm is shared with a Vec.
1844:  This is inherently unsafe if you alter the size of the field at any time between
1845:  calls to DMSwarmCreateGlobalVectorFromField() and DMSwarmDestroyGlobalVectorFromField().
1846:  If the local size of the DMSwarm does not match the local size of the global vector
1847:  when DMSwarmDestroyGlobalVectorFromField() is called, an error is thrown.

1849:  Additional high-level support is provided for Particle-In-Cell methods.
1850:  Please refer to the man page for DMSwarmSetType().

1852:  Level: beginner

1854: .seealso: DMType, DMCreate(), DMSetType()
1855: M*/
1856: PETSC_EXTERN PetscErrorCode DMCreate_Swarm(DM dm)
1857: {
1858:   DM_Swarm      *swarm;

1863:   PetscNewLog(dm,&swarm);
1864:   dm->data = swarm;
1865:   DMSwarmDataBucketCreate(&swarm->db);
1866:   DMSwarmInitializeFieldRegister(dm);
1867:   swarm->refct = 1;
1868:   swarm->vec_field_set = PETSC_FALSE;
1869:   swarm->issetup = PETSC_FALSE;
1870:   swarm->swarm_type = DMSWARM_BASIC;
1871:   swarm->migrate_type = DMSWARM_MIGRATE_BASIC;
1872:   swarm->collect_type = DMSWARM_COLLECT_BASIC;
1873:   swarm->migrate_error_on_missing_point = PETSC_FALSE;
1874:   swarm->dmcell = NULL;
1875:   swarm->collect_view_active = PETSC_FALSE;
1876:   swarm->collect_view_reset_nlocal = -1;
1877:   DMInitialize_Swarm(dm);
1878:   return(0);
1879: }