Actual source code: swarm.c
1: #include "petscdmswarm.h"
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 *DMSwarmRemapTypeNames[] = {"none", "pfak", "colella", "DMSwarmRemapType", "DMSWARM_REMAP_", NULL};
21: const char *DMSwarmPICLayoutTypeNames[] = {"regular", "gauss", "subdivision", NULL};
23: const char DMSwarmField_pid[] = "DMSwarm_pid";
24: const char DMSwarmField_rank[] = "DMSwarm_rank";
25: const char DMSwarmPICField_coor[] = "DMSwarmPIC_coor";
27: PetscInt SwarmDataFieldId = -1;
29: #if PetscDefined(HAVE_HDF5)
30: #include <petscviewerhdf5.h>
32: static PetscErrorCode VecView_Swarm_HDF5_Internal(Vec v, PetscViewer viewer)
33: {
34: DM dm;
35: PetscReal seqval;
36: PetscInt seqnum, bs;
37: PetscBool isseq, ists;
39: PetscFunctionBegin;
40: PetscCall(VecGetDM(v, &dm));
41: PetscCall(VecGetBlockSize(v, &bs));
42: PetscCall(PetscViewerHDF5PushGroup(viewer, "/particle_fields"));
43: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
44: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
45: PetscCall(PetscViewerHDF5IsTimestepping(viewer, &ists));
46: if (ists) PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
47: /* PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar) seqval, viewer)); */
48: PetscCall(VecViewNative(v, viewer));
49: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)v, "Nc", PETSC_INT, (void *)&bs));
50: PetscCall(PetscViewerHDF5PopGroup(viewer));
51: PetscFunctionReturn(PETSC_SUCCESS);
52: }
54: static PetscErrorCode DMSwarmView_HDF5(DM dm, PetscViewer viewer)
55: {
56: DMSwarmCellDM celldm;
57: Vec coordinates;
58: PetscInt Np, Nfc;
59: PetscBool isseq;
60: const char **coordFields;
62: PetscFunctionBegin;
63: PetscCall(DMSwarmGetCellDMActive(dm, &celldm));
64: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Nfc, &coordFields));
65: PetscCheck(Nfc == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support a single coordinate field right now, not %" PetscInt_FMT, Nfc);
66: PetscCall(DMSwarmGetSize(dm, &Np));
67: PetscCall(DMSwarmCreateGlobalVectorFromField(dm, coordFields[0], &coordinates));
68: PetscCall(PetscObjectSetName((PetscObject)coordinates, "coordinates"));
69: PetscCall(PetscViewerHDF5PushGroup(viewer, "/particles"));
70: PetscCall(PetscObjectTypeCompare((PetscObject)coordinates, VECSEQ, &isseq));
71: PetscCall(VecViewNative(coordinates, viewer));
72: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)coordinates, "Np", PETSC_INT, (void *)&Np));
73: PetscCall(PetscViewerHDF5PopGroup(viewer));
74: PetscCall(DMSwarmDestroyGlobalVectorFromField(dm, coordFields[0], &coordinates));
75: PetscFunctionReturn(PETSC_SUCCESS);
76: }
77: #endif
79: static PetscErrorCode VecView_Swarm(Vec v, PetscViewer viewer)
80: {
81: DM dm;
82: #if PetscDefined(HAVE_HDF5)
83: PetscBool ishdf5;
84: #endif
86: PetscFunctionBegin;
87: PetscCall(VecGetDM(v, &dm));
88: PetscCheck(dm, PetscObjectComm((PetscObject)v), PETSC_ERR_ARG_WRONG, "Vector not generated from a DM");
89: #if PetscDefined(HAVE_HDF5)
90: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
91: if (ishdf5) {
92: PetscCall(VecView_Swarm_HDF5_Internal(v, viewer));
93: PetscFunctionReturn(PETSC_SUCCESS);
94: }
95: #endif
96: PetscCall(VecViewNative(v, viewer));
97: PetscFunctionReturn(PETSC_SUCCESS);
98: }
100: /*@
101: DMSwarmVectorGetField - Gets the fields from which to define a `Vec` object
102: when `DMCreateLocalVector()`, or `DMCreateGlobalVector()` is called
104: Not collective
106: Input Parameter:
107: . sw - a `DMSWARM`
109: Output Parameters:
110: + Nf - the number of fields
111: - fieldnames - the textual name given to each registered field, or NULL if it has not been set
113: Level: beginner
115: .seealso: `DM`, `DMSWARM`, `DMSwarmVectorDefineField()`, `DMSwarmRegisterPetscDatatypeField()`, `DMCreateGlobalVector()`, `DMCreateLocalVector()`
116: @*/
117: PetscErrorCode DMSwarmVectorGetField(DM sw, PetscInt *Nf, const char **fieldnames[])
118: {
119: DMSwarmCellDM celldm;
121: PetscFunctionBegin;
123: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
124: PetscCall(DMSwarmCellDMGetFields(celldm, Nf, fieldnames));
125: PetscFunctionReturn(PETSC_SUCCESS);
126: }
128: /*@
129: DMSwarmVectorDefineField - Sets the field from which to define a `Vec` object
130: when `DMCreateLocalVector()`, or `DMCreateGlobalVector()` is called
132: Collective
134: Input Parameters:
135: + dm - a `DMSWARM`
136: - fieldname - the textual name given to each registered field
138: Level: beginner
140: Notes:
141: The field with name `fieldname` must have data type `PETSC_REAL` or `PETSC_SCALAR`.
143: This function must be called prior to calling `DMCreateLocalVector()`, `DMCreateGlobalVector()`.
144: Multiple calls to `DMSwarmVectorDefineField()` are permitted.
146: .seealso: `DM`, `DMSWARM`, `DMSwarmVectorDefineFields()`, `DMSwarmVectorGetField()`, `DMSwarmRegisterPetscDatatypeField()`, `DMCreateGlobalVector()`, `DMCreateLocalVector()`
147: @*/
148: PetscErrorCode DMSwarmVectorDefineField(DM dm, const char fieldname[])
149: {
150: PetscFunctionBegin;
151: PetscCall(DMSwarmVectorDefineFields(dm, 1, &fieldname));
152: PetscFunctionReturn(PETSC_SUCCESS);
153: }
155: /*@
156: DMSwarmVectorDefineFields - Sets the fields from which to define a `Vec` object
157: when `DMCreateLocalVector()`, or `DMCreateGlobalVector()` is called
159: Collective, No Fortran support
161: Input Parameters:
162: + sw - a `DMSWARM`
163: . Nf - the number of fields
164: - fieldnames - the textual name given to each registered field
166: Level: beginner
168: Notes:
169: Each field with name in `fieldnames` must have data type `PETSC_REAL` or `PETSC_SCALAR`.
171: This function must be called prior to calling `DMCreateLocalVector()`, `DMCreateGlobalVector()`.
172: Multiple calls to `DMSwarmVectorDefineField()` are permitted.
174: .seealso: `DM`, `DMSWARM`, `DMSwarmVectorDefineField()`, `DMSwarmVectorGetField()`, `DMSwarmRegisterPetscDatatypeField()`, `DMCreateGlobalVector()`, `DMCreateLocalVector()`
175: @*/
176: PetscErrorCode DMSwarmVectorDefineFields(DM sw, PetscInt Nf, const char *fieldnames[])
177: {
178: DM_Swarm *swarm = (DM_Swarm *)sw->data;
179: DMSwarmCellDM celldm;
181: PetscFunctionBegin;
183: if (fieldnames) PetscAssertPointer(fieldnames, 3);
184: if (!swarm->issetup) PetscCall(DMSetUp(sw));
185: PetscCheck(Nf >= 0, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_OUTOFRANGE, "Number of fields must be non-negative, not %" PetscInt_FMT, Nf);
186: for (PetscInt f = 0; f < Nf; ++f) {
187: PetscDataType type;
189: PetscCall(DMSwarmGetFieldInfo(sw, fieldnames[f], NULL, &type));
190: PetscCheck(type == PETSC_REAL || type == PETSC_SCALAR, PetscObjectComm((PetscObject)sw), PETSC_ERR_SUP, "Field %s must have type PETSC_REAL or PETSC_SCALAR, not %s", fieldnames[f], PetscDataTypes[type]);
191: }
192: // Create a dummy cell DM if none has been specified (I think we should not support this mode)
193: if (!swarm->activeCellDM) {
194: DM dm;
195: DMSwarmCellDM celldm;
197: PetscCall(DMCreate(PetscObjectComm((PetscObject)sw), &dm));
198: PetscCall(DMSetType(dm, DMSHELL));
199: PetscCall(PetscObjectSetName((PetscObject)dm, "dummy"));
200: PetscCall(DMSwarmCellDMCreate(dm, 0, NULL, 0, NULL, &celldm));
201: PetscCall(DMDestroy(&dm));
202: PetscCall(DMSwarmAddCellDM(sw, celldm));
203: PetscCall(DMSwarmCellDMDestroy(&celldm));
204: PetscCall(DMSwarmSetCellDMActive(sw, "dummy"));
205: }
206: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
207: for (PetscInt f = 0; f < celldm->Nf; ++f) PetscCall(PetscFree(celldm->dmFields[f]));
208: PetscCall(PetscFree(celldm->dmFields));
210: celldm->Nf = Nf;
211: PetscCall(PetscMalloc1(Nf, &celldm->dmFields));
212: for (PetscInt f = 0; f < Nf; ++f) PetscCall(PetscStrallocpy(fieldnames[f], (char **)&celldm->dmFields[f]));
213: PetscFunctionReturn(PETSC_SUCCESS);
214: }
216: /* requires DMSwarmDefineFieldVector has been called */
217: static PetscErrorCode DMCreateGlobalVector_Swarm(DM sw, Vec *vec)
218: {
219: DM_Swarm *swarm = (DM_Swarm *)sw->data;
220: DMSwarmCellDM celldm;
221: Vec x;
222: char name[PETSC_MAX_PATH_LEN];
223: PetscInt bs = 0, n;
225: PetscFunctionBegin;
226: if (!swarm->issetup) PetscCall(DMSetUp(sw));
227: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
228: PetscCheck(celldm->Nf, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "Active cell DM does not define any fields");
229: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, &n, NULL, NULL));
231: PetscCall(PetscStrncpy(name, "DMSwarmField", PETSC_MAX_PATH_LEN));
232: for (PetscInt f = 0; f < celldm->Nf; ++f) {
233: PetscInt fbs;
234: PetscCall(PetscStrlcat(name, "_", PETSC_MAX_PATH_LEN));
235: PetscCall(PetscStrlcat(name, celldm->dmFields[f], PETSC_MAX_PATH_LEN));
236: PetscCall(DMSwarmGetFieldInfo(sw, celldm->dmFields[f], &fbs, NULL));
237: bs += fbs;
238: }
239: PetscCall(VecCreate(PetscObjectComm((PetscObject)sw), &x));
240: PetscCall(PetscObjectSetName((PetscObject)x, name));
241: PetscCall(VecSetSizes(x, n * bs, PETSC_DETERMINE));
242: PetscCall(VecSetBlockSize(x, bs));
243: PetscCall(VecSetDM(x, sw));
244: PetscCall(VecSetFromOptions(x));
245: PetscCall(VecSetOperation(x, VECOP_VIEW, (PetscErrorCodeFn *)VecView_Swarm));
246: *vec = x;
247: PetscFunctionReturn(PETSC_SUCCESS);
248: }
250: /* requires DMSwarmDefineFieldVector has been called */
251: static PetscErrorCode DMCreateLocalVector_Swarm(DM sw, Vec *vec)
252: {
253: DM_Swarm *swarm = (DM_Swarm *)sw->data;
254: DMSwarmCellDM celldm;
255: Vec x;
256: char name[PETSC_MAX_PATH_LEN];
257: PetscInt bs = 0, n;
259: PetscFunctionBegin;
260: if (!swarm->issetup) PetscCall(DMSetUp(sw));
261: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
262: PetscCheck(celldm->Nf, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "Active cell DM does not define any fields");
263: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, &n, NULL, NULL));
265: PetscCall(PetscStrncpy(name, "DMSwarmField", PETSC_MAX_PATH_LEN));
266: for (PetscInt f = 0; f < celldm->Nf; ++f) {
267: PetscInt fbs;
268: PetscCall(PetscStrlcat(name, "_", PETSC_MAX_PATH_LEN));
269: PetscCall(PetscStrlcat(name, celldm->dmFields[f], PETSC_MAX_PATH_LEN));
270: PetscCall(DMSwarmGetFieldInfo(sw, celldm->dmFields[f], &fbs, NULL));
271: bs += fbs;
272: }
273: PetscCall(VecCreate(PETSC_COMM_SELF, &x));
274: PetscCall(PetscObjectSetName((PetscObject)x, name));
275: PetscCall(VecSetSizes(x, n * bs, PETSC_DETERMINE));
276: PetscCall(VecSetBlockSize(x, bs));
277: PetscCall(VecSetDM(x, sw));
278: PetscCall(VecSetFromOptions(x));
279: *vec = x;
280: PetscFunctionReturn(PETSC_SUCCESS);
281: }
283: static PetscErrorCode DMSwarmDestroyVectorFromField_Private(DM dm, const char fieldname[], Vec *vec)
284: {
285: DM_Swarm *swarm = (DM_Swarm *)dm->data;
286: DMSwarmDataField gfield;
287: PetscInt bs, nlocal, fid = -1, cfid = -2;
288: PetscBool flg;
290: PetscFunctionBegin;
291: /* check vector is an inplace array */
292: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldIdByName(swarm->db, fieldname, &fid));
293: PetscCall(PetscObjectComposedDataGetInt((PetscObject)*vec, SwarmDataFieldId, cfid, flg));
294: (void)flg; /* avoid compiler warning */
295: PetscCheck(cfid == fid, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "Vector being destroyed was not created from DMSwarm field(%s)! %" PetscInt_FMT " != %" PetscInt_FMT, fieldname, cfid, fid);
296: PetscCall(VecGetLocalSize(*vec, &nlocal));
297: PetscCall(VecGetBlockSize(*vec, &bs));
298: PetscCheck(nlocal / bs == swarm->db->L, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "DMSwarm sizes have changed since vector was created - cannot ensure pointers are valid");
299: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield));
300: PetscCall(DMSwarmDataFieldRestoreAccess(gfield));
301: PetscCall(VecResetArray(*vec));
302: PetscCall(VecDestroy(vec));
303: PetscFunctionReturn(PETSC_SUCCESS);
304: }
306: static PetscErrorCode DMSwarmCreateVectorFromField_Private(DM dm, const char fieldname[], MPI_Comm comm, Vec *vec)
307: {
308: DM_Swarm *swarm = (DM_Swarm *)dm->data;
309: PetscDataType type;
310: PetscScalar *array;
311: PetscInt bs, n, fid;
312: char name[PETSC_MAX_PATH_LEN];
313: PetscMPIInt size;
314: PetscBool iscuda, iskokkos, iship;
316: PetscFunctionBegin;
317: if (!swarm->issetup) PetscCall(DMSetUp(dm));
318: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, &n, NULL, NULL));
319: PetscCall(DMSwarmGetFieldInfo(dm, fieldname, &bs, &type));
320: PetscCheck(type == PETSC_SCALAR, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Field %s must have type PETSC_SCALAR, not %s", fieldname, PetscDataTypes[type]);
321: PetscCall(DMSwarmGetField(dm, fieldname, NULL, NULL, (void **)&array));
323: PetscCallMPI(MPI_Comm_size(comm, &size));
324: PetscCall(PetscStrcmp(dm->vectype, VECKOKKOS, &iskokkos));
325: PetscCall(PetscStrcmp(dm->vectype, VECCUDA, &iscuda));
326: PetscCall(PetscStrcmp(dm->vectype, VECHIP, &iship));
327: PetscCall(VecCreate(comm, vec));
328: PetscCall(VecSetSizes(*vec, n * bs, PETSC_DETERMINE));
329: PetscCall(VecSetBlockSize(*vec, bs));
330: if (iskokkos) PetscCall(VecSetType(*vec, VECKOKKOS));
331: else if (iscuda) PetscCall(VecSetType(*vec, VECCUDA));
332: else if (iship) PetscCall(VecSetType(*vec, VECHIP));
333: else PetscCall(VecSetType(*vec, VECSTANDARD));
334: PetscCall(VecPlaceArray(*vec, array));
336: PetscCall(PetscSNPrintf(name, PETSC_MAX_PATH_LEN - 1, "DMSwarmSharedField_%s", fieldname));
337: PetscCall(PetscObjectSetName((PetscObject)*vec, name));
339: /* Set guard */
340: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldIdByName(swarm->db, fieldname, &fid));
341: PetscCall(PetscObjectComposedDataSetInt((PetscObject)*vec, SwarmDataFieldId, fid));
343: PetscCall(VecSetDM(*vec, dm));
344: PetscCall(VecSetOperation(*vec, VECOP_VIEW, (PetscErrorCodeFn *)VecView_Swarm));
345: PetscFunctionReturn(PETSC_SUCCESS);
346: }
348: static PetscErrorCode DMSwarmDestroyVectorFromFields_Private(DM sw, PetscInt Nf, const char *fieldnames[], Vec *vec)
349: {
350: DM_Swarm *swarm = (DM_Swarm *)sw->data;
351: const PetscScalar *array;
352: PetscInt bs, n, id = 0, cid = -2;
353: PetscBool flg;
355: PetscFunctionBegin;
356: for (PetscInt f = 0; f < Nf; ++f) {
357: PetscInt fid;
359: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldIdByName(swarm->db, fieldnames[f], &fid));
360: id += fid;
361: }
362: PetscCall(PetscObjectComposedDataGetInt((PetscObject)*vec, SwarmDataFieldId, cid, flg));
363: (void)flg; /* avoid compiler warning */
364: PetscCheck(cid == id, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "Vector being destroyed was not created from DMSwarm field(%s)! %" PetscInt_FMT " != %" PetscInt_FMT, fieldnames[0], cid, id);
365: PetscCall(VecGetLocalSize(*vec, &n));
366: PetscCall(VecGetBlockSize(*vec, &bs));
367: n /= bs;
368: PetscCheck(n == swarm->db->L, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "DMSwarm sizes have changed since vector was created - cannot ensure pointers are valid");
369: PetscCall(VecGetArrayRead(*vec, &array));
370: for (PetscInt f = 0, off = 0; f < Nf; ++f) {
371: void *farray;
372: PetscDataType ftype;
373: PetscInt fbs;
375: PetscCall(DMSwarmGetFieldInfo(sw, fieldnames[f], &fbs, &ftype));
376: PetscCheck(ftype == PETSC_REAL || ftype == PETSC_SCALAR, PetscObjectComm((PetscObject)sw), PETSC_ERR_SUP, "Field %s must have type PETSC_REAL or PETSC_SCALAR, not %s", fieldnames[f], PetscDataTypes[ftype]);
377: PetscCall(DMSwarmGetField(sw, fieldnames[f], NULL, NULL, &farray));
378: PetscCheck(off + fbs <= bs, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid blocksize %" PetscInt_FMT " < %" PetscInt_FMT, bs, off + fbs);
379: if (ftype == PETSC_REAL) {
380: PetscReal *rarray = (PetscReal *)farray;
382: for (PetscInt i = 0; i < n; ++i) {
383: for (PetscInt b = 0; b < fbs; ++b) rarray[i * fbs + b] = PetscRealPart(array[i * bs + off + b]);
384: }
385: } else {
386: PetscScalar *sarray = (PetscScalar *)farray;
388: for (PetscInt i = 0; i < n; ++i) {
389: for (PetscInt b = 0; b < fbs; ++b) sarray[i * fbs + b] = array[i * bs + off + b];
390: }
391: }
392: off += fbs;
393: PetscCall(DMSwarmRestoreField(sw, fieldnames[f], NULL, NULL, &farray));
394: }
395: PetscCall(VecRestoreArrayRead(*vec, &array));
396: PetscCall(VecDestroy(vec));
397: PetscFunctionReturn(PETSC_SUCCESS);
398: }
400: static PetscErrorCode DMSwarmCreateVectorFromFields_Private(DM sw, PetscInt Nf, const char *fieldnames[], MPI_Comm comm, Vec *vec)
401: {
402: DM_Swarm *swarm = (DM_Swarm *)sw->data;
403: PetscScalar *array;
404: PetscInt n, bs = 0, id = 0;
405: char name[PETSC_MAX_PATH_LEN];
407: PetscFunctionBegin;
408: if (!swarm->issetup) PetscCall(DMSetUp(sw));
409: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, &n, NULL, NULL));
410: for (PetscInt f = 0; f < Nf; ++f) {
411: PetscDataType ftype;
412: PetscInt fbs;
414: PetscCall(DMSwarmGetFieldInfo(sw, fieldnames[f], &fbs, &ftype));
415: PetscCheck(ftype == PETSC_REAL || ftype == PETSC_SCALAR, PetscObjectComm((PetscObject)sw), PETSC_ERR_SUP, "Field %s must have type PETSC_REAL or PETSC_SCALAR, not %s", fieldnames[f], PetscDataTypes[ftype]);
416: bs += fbs;
417: }
419: PetscCall(VecCreate(comm, vec));
420: PetscCall(VecSetSizes(*vec, n * bs, PETSC_DETERMINE));
421: PetscCall(VecSetBlockSize(*vec, bs));
422: PetscCall(VecSetType(*vec, sw->vectype));
424: PetscCall(VecGetArrayWrite(*vec, &array));
425: for (PetscInt f = 0, off = 0; f < Nf; ++f) {
426: void *farray;
427: PetscDataType ftype;
428: PetscInt fbs;
430: PetscCall(DMSwarmGetField(sw, fieldnames[f], &fbs, &ftype, &farray));
431: if (ftype == PETSC_REAL) {
432: const PetscReal *rarray = (const PetscReal *)farray;
434: for (PetscInt i = 0; i < n; ++i) {
435: for (PetscInt b = 0; b < fbs; ++b) array[i * bs + off + b] = rarray[i * fbs + b];
436: }
437: } else {
438: const PetscScalar *sarray = (const PetscScalar *)farray;
440: for (PetscInt i = 0; i < n; ++i) {
441: for (PetscInt b = 0; b < fbs; ++b) array[i * bs + off + b] = sarray[i * fbs + b];
442: }
443: }
444: off += fbs;
445: PetscCall(DMSwarmRestoreField(sw, fieldnames[f], &fbs, &ftype, &farray));
446: }
447: PetscCall(VecRestoreArrayWrite(*vec, &array));
449: PetscCall(PetscStrncpy(name, "DMSwarmField", PETSC_MAX_PATH_LEN));
450: for (PetscInt f = 0; f < Nf; ++f) {
451: PetscCall(PetscStrlcat(name, "_", PETSC_MAX_PATH_LEN));
452: PetscCall(PetscStrlcat(name, fieldnames[f], PETSC_MAX_PATH_LEN));
453: }
454: PetscCall(PetscObjectSetName((PetscObject)*vec, name));
456: for (PetscInt f = 0; f < Nf; ++f) {
457: PetscInt fid;
459: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldIdByName(swarm->db, fieldnames[f], &fid));
460: id += fid;
461: }
462: PetscCall(PetscObjectComposedDataSetInt((PetscObject)*vec, SwarmDataFieldId, id));
464: PetscCall(VecSetDM(*vec, sw));
465: PetscCall(VecSetOperation(*vec, VECOP_VIEW, (PetscErrorCodeFn *)VecView_Swarm));
466: PetscFunctionReturn(PETSC_SUCCESS);
467: }
469: /*@
470: DMSwarmPreallocateMassMatrix - Preallocate particle mass matrix between a `DMSWARM` and a `DMPLEX`
472: Collective
474: Input Parameters:
475: + dmc - The `DMSWARM` object
476: . dmf - The `DMPLEX` object
477: . mass - The mass matrix to preallocate
478: . rStart - The starting row index for this process
479: . maxC - The maximum number of columns per row
480: - ctx - The user context
482: Level: developer
484: .seealso: [](ch_unstructured), `DM`, `DMSWARM`, `DMPLEX`, `DMCreateMassMatrix()`, `DMSwarmFillMassMatrix()`
485: @*/
486: PetscErrorCode DMSwarmPreallocateMassMatrix(DM dmc, DM dmf, Mat mass, PetscInt *rStart, PetscInt *maxC, PetscCtx ctx)
487: {
488: MPI_Comm comm;
489: PetscHSetIJ ht;
490: PetscDS ds;
491: PetscSection fsection, globalFSection;
492: PetscLayout rLayout, colLayout;
493: PetscInt *dnz, *onz;
494: PetscInt cStart, cEnd, locRows, locCols, colStart, colEnd, Nf, totNc = 0;
496: PetscFunctionBegin;
500: PetscAssertPointer(rStart, 4);
501: PetscAssertPointer(maxC, 5);
502: PetscCall(PetscObjectGetComm((PetscObject)mass, &comm));
503: PetscCall(DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd));
504: PetscCall(DMGetLocalSection(dmf, &fsection));
505: PetscCall(DMGetGlobalSection(dmf, &globalFSection));
506: PetscCall(DMGetDS(dmf, &ds));
507: PetscCall(PetscDSGetNumFields(ds, &Nf));
508: PetscCall(MatGetLocalSize(mass, &locRows, &locCols));
509: PetscCall(PetscCalloc2(locRows, &dnz, locRows, &onz));
510: PetscCall(PetscHSetIJCreate(&ht));
512: PetscCall(PetscLayoutCreate(comm, &colLayout));
513: PetscCall(PetscLayoutSetLocalSize(colLayout, locCols));
514: PetscCall(PetscLayoutSetBlockSize(colLayout, 1));
515: PetscCall(PetscLayoutSetUp(colLayout));
516: PetscCall(PetscLayoutGetRange(colLayout, &colStart, &colEnd));
517: PetscCall(PetscLayoutDestroy(&colLayout));
519: PetscCall(PetscLayoutCreate(comm, &rLayout));
520: PetscCall(PetscLayoutSetLocalSize(rLayout, locRows));
521: PetscCall(PetscLayoutSetBlockSize(rLayout, 1));
522: PetscCall(PetscLayoutSetUp(rLayout));
523: PetscCall(PetscLayoutGetRange(rLayout, rStart, NULL));
524: PetscCall(PetscLayoutDestroy(&rLayout));
526: for (PetscInt field = 0; field < Nf; ++field) {
527: PetscObject obj;
528: PetscClassId id;
529: PetscInt Nc;
531: PetscCall(PetscDSGetDiscretization(ds, field, &obj));
532: PetscCall(PetscObjectGetClassId(obj, &id));
533: if (id == PETSCFE_CLASSID) PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
534: else PetscCall(PetscFVGetNumComponents((PetscFV)obj, &Nc));
535: totNc += Nc;
536: }
537: PetscCall(DMSwarmSortGetAccess(dmc));
538: for (PetscInt field = 0; field < Nf; ++field) {
539: PetscObject obj;
540: PetscClassId id;
541: PetscInt Nc;
543: PetscCall(PetscDSGetDiscretization(ds, field, &obj));
544: PetscCall(PetscObjectGetClassId(obj, &id));
545: if (id == PETSCFE_CLASSID) PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
546: else PetscCall(PetscFVGetNumComponents((PetscFV)obj, &Nc));
548: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
549: PetscInt *findices, *cindices; /* fine is vertices, coarse is particles */
550: PetscInt numFIndices, numCIndices;
552: PetscCall(DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
553: PetscCall(DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices));
554: *maxC = PetscMax(*maxC, numCIndices);
555: {
556: PetscHashIJKey key;
557: PetscBool missing;
558: for (PetscInt i = 0; i < numFIndices; ++i) {
559: key.j = findices[i]; /* global column (from Plex) */
560: if (key.j >= 0) {
561: /* Get indices for coarse elements */
562: for (PetscInt j = 0; j < numCIndices; ++j) {
563: for (PetscInt c = 0; c < Nc; ++c) {
564: // TODO Need field offset on particle here
565: key.i = cindices[j] * totNc + c + *rStart; /* global cols (from Swarm) */
566: if (key.i < 0) continue;
567: PetscCall(PetscHSetIJQueryAdd(ht, key, &missing));
568: PetscCheck(missing, PetscObjectComm((PetscObject)dmf), PETSC_ERR_SUP, "Set new value at %" PetscInt_FMT ",%" PetscInt_FMT, key.i, key.j);
569: if (key.j >= colStart && key.j < colEnd) ++dnz[key.i - *rStart];
570: else ++onz[key.i - *rStart];
571: }
572: }
573: }
574: }
575: PetscCall(DMSwarmSortRestorePointsPerCell(dmc, cell, &numCIndices, &cindices));
576: }
577: PetscCall(DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
578: }
579: }
580: PetscCall(DMSwarmSortRestoreAccess(dmc));
581: PetscCall(PetscHSetIJDestroy(&ht));
582: PetscCall(MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL));
583: PetscCall(MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE));
584: PetscCall(PetscFree2(dnz, onz));
585: PetscFunctionReturn(PETSC_SUCCESS);
586: }
588: /*@
589: DMSwarmFillMassMatrix - Assemble the particle mass matrix between a `DMSWARM` and a `DMPLEX`
591: Collective
593: Input Parameters:
594: + dmc - The `DMSWARM` object
595: . dmf - The `DMPLEX` object
596: . mass - The mass matrix to fill up
597: . rStart - The starting row index for this process
598: . maxC - The maximum number of columns per row
599: . useDeltaFunction - Flag to use a delta function for the particle shape function
600: . Nfc - The number of swarm coordinate fields
601: . bs - The block size for each swarm coordinate field
602: . coordVals - The values for each particle for each swarm coordinate field
603: - ctx - The user context
605: Level: developer
607: .seealso: [](ch_unstructured), `DM`, `DMSWARM`, `DMPLEX`, `DMCreateMassMatrix()`, `DMSwarmPreallocateMassMatrix()`
608: @*/
609: PetscErrorCode DMSwarmFillMassMatrix(DM dmc, DM dmf, Mat mass, PetscInt rStart, PetscInt maxC, PetscBool useDeltaFunction, PetscInt Nfc, const PetscInt bs[], PetscReal *coordVals[], PetscCtx ctx)
610: {
611: PetscDS ds;
612: PetscSection fsection, globalFSection;
613: PetscInt dim, cStart, cEnd, Nf, totDim, totNc = 0, *rowIDXs;
614: PetscReal *xi, *v0, *J, *invJ, detJ = 1.0, v0ref[3] = {-1.0, -1.0, -1.0};
615: PetscScalar *elemMat;
617: PetscFunctionBegin;
621: PetscCall(DMGetCoordinateDim(dmf, &dim));
622: PetscCall(DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd));
623: PetscCall(DMGetLocalSection(dmf, &fsection));
624: PetscCall(DMGetGlobalSection(dmf, &globalFSection));
625: PetscCall(DMGetDS(dmf, &ds));
626: PetscCall(PetscDSGetNumFields(ds, &Nf));
627: PetscCall(PetscDSGetTotalDimension(ds, &totDim));
628: for (PetscInt field = 0; field < Nf; ++field) {
629: PetscObject obj;
630: PetscClassId id;
631: PetscInt Nc;
633: PetscCall(PetscDSGetDiscretization(ds, field, &obj));
634: PetscCall(PetscObjectGetClassId(obj, &id));
635: if (id == PETSCFE_CLASSID) PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
636: else PetscCall(PetscFVGetNumComponents((PetscFV)obj, &Nc));
637: totNc += Nc;
638: }
640: PetscCall(PetscMalloc3(maxC * totNc * totDim, &elemMat, maxC * totNc, &rowIDXs, maxC * dim, &xi));
641: PetscCall(PetscMalloc3(dim, &v0, dim * dim, &J, dim * dim, &invJ));
642: PetscCall(DMSwarmSortGetAccess(dmc));
643: for (PetscInt field = 0; field < Nf; ++field) {
644: PetscTabulation Tcoarse;
645: PetscObject obj;
646: PetscClassId id;
647: PetscInt Nc;
649: PetscCall(PetscDSGetDiscretization(ds, field, &obj));
650: PetscCall(PetscObjectGetClassId(obj, &id));
651: if (id == PETSCFE_CLASSID) PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
652: else PetscCall(PetscFVGetNumComponents((PetscFV)obj, &Nc));
654: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
655: PetscInt *findices, *cindices;
656: PetscInt numFIndices, numCIndices;
658: /* TODO: Use DMField instead of assuming affine */
659: PetscCall(DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ));
660: PetscCall(DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
661: PetscCall(DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices));
662: for (PetscInt j = 0; j < numCIndices; ++j) {
663: PetscReal xr[8];
664: PetscInt off = 0;
666: for (PetscInt i = 0; i < Nfc; ++i) {
667: for (PetscInt b = 0; b < bs[i]; ++b, ++off) xr[off] = coordVals[i][cindices[j] * bs[i] + b];
668: }
669: PetscCheck(off == dim, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The total block size of coordinates is %" PetscInt_FMT " != %" PetscInt_FMT " the DM coordinate dimension", off, dim);
670: CoordinatesRealToRef(dim, dim, v0ref, v0, invJ, xr, &xi[j * dim]);
671: }
672: if (id == PETSCFE_CLASSID) PetscCall(PetscFECreateTabulation((PetscFE)obj, 1, numCIndices, xi, 0, &Tcoarse));
673: else PetscCall(PetscFVCreateTabulation((PetscFV)obj, 1, numCIndices, xi, 0, &Tcoarse));
674: /* Get elemMat entries by multiplying by weight */
675: PetscCall(PetscArrayzero(elemMat, numCIndices * Nc * totDim));
676: for (PetscInt i = 0; i < numFIndices / Nc; ++i) {
677: for (PetscInt j = 0; j < numCIndices; ++j) {
678: for (PetscInt c = 0; c < Nc; ++c) {
679: // TODO Need field offset on particle and field here
680: /* B[(p*pdim + i)*Nc + c] is the value at point p for basis function i and component c */
681: elemMat[(j * totNc + c) * numFIndices + i * Nc + c] += Tcoarse->T[0][(j * numFIndices + i * Nc + c) * Nc + c] * (useDeltaFunction ? 1.0 : detJ);
682: }
683: }
684: }
685: for (PetscInt j = 0; j < numCIndices; ++j)
686: // TODO Need field offset on particle here
687: for (PetscInt c = 0; c < Nc; ++c) rowIDXs[j * Nc + c] = cindices[j] * totNc + c + rStart;
688: if (0) PetscCall(DMPrintCellMatrix(cell, "Mass Matrix", numCIndices * Nc, numFIndices, elemMat));
689: PetscCall(MatSetValues(mass, numCIndices * Nc, rowIDXs, numFIndices, findices, elemMat, ADD_VALUES));
690: PetscCall(DMSwarmSortRestorePointsPerCell(dmc, cell, &numCIndices, &cindices));
691: PetscCall(DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
692: PetscCall(PetscTabulationDestroy(&Tcoarse));
693: }
694: }
695: PetscCall(DMSwarmSortRestoreAccess(dmc));
696: PetscCall(PetscFree3(elemMat, rowIDXs, xi));
697: PetscCall(PetscFree3(v0, J, invJ));
698: PetscFunctionReturn(PETSC_SUCCESS);
699: }
701: /* This creates a "mass matrix" between a finite element and particle space. If a finite element interpolant is given by
703: \hat f = \sum_i f_i \phi_i
705: and a particle function is given by
707: f = \sum_i w_i \delta(x - x_i)
709: then we want to require that
711: M \hat f = M_p f
713: where the particle mass matrix is given by
715: (M_p)_{ij} = \int \phi_i \delta(x - x_j)
717: The way Dave May does particles, they amount to quadratue weights rather than delta functions, so he has |J| is in
718: his integral. We allow this with the boolean flag.
719: */
720: static PetscErrorCode DMSwarmComputeMassMatrix_Private(DM dmc, DM dmf, Mat mass, PetscBool useDeltaFunction, PetscCtx ctx)
721: {
722: DMSwarmCellDM celldm;
723: PetscInt rStart, maxC = 0;
724: PetscInt Nfc;
725: const char **coordFields;
726: PetscReal **coordVals;
727: PetscInt *bs;
729: PetscFunctionBegin;
730: PetscCall(DMSwarmPreallocateMassMatrix(dmc, dmf, mass, &rStart, &maxC, ctx));
732: PetscCall(DMSwarmGetCellDMActive(dmc, &celldm));
733: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Nfc, &coordFields));
734: PetscCall(PetscMalloc2(Nfc, &coordVals, Nfc, &bs));
735: for (PetscInt i = 0; i < Nfc; ++i) PetscCall(DMSwarmGetField(dmc, coordFields[i], &bs[i], NULL, (void **)&coordVals[i]));
736: PetscCall(DMSwarmFillMassMatrix(dmc, dmf, mass, rStart, maxC, useDeltaFunction, Nfc, bs, coordVals, ctx));
737: for (PetscInt i = 0; i < Nfc; ++i) PetscCall(DMSwarmRestoreField(dmc, coordFields[i], &bs[i], NULL, (void **)&coordVals[i]));
738: PetscCall(PetscFree2(coordVals, bs));
740: PetscCall(MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY));
741: PetscCall(MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY));
742: PetscFunctionReturn(PETSC_SUCCESS);
743: }
745: /* Returns empty matrix for use with SNES FD */
746: static PetscErrorCode DMCreateMatrix_Swarm(DM sw, Mat *m)
747: {
748: Vec field;
749: PetscInt size;
751: PetscFunctionBegin;
752: PetscCall(DMGetGlobalVector(sw, &field));
753: PetscCall(VecGetLocalSize(field, &size));
754: PetscCall(DMRestoreGlobalVector(sw, &field));
755: PetscCall(MatCreate(PETSC_COMM_WORLD, m));
756: PetscCall(MatSetFromOptions(*m));
757: PetscCall(MatSetSizes(*m, PETSC_DECIDE, PETSC_DECIDE, size, size));
758: PetscCall(MatSeqAIJSetPreallocation(*m, 1, NULL));
759: PetscCall(MatZeroEntries(*m));
760: PetscCall(MatAssemblyBegin(*m, MAT_FINAL_ASSEMBLY));
761: PetscCall(MatAssemblyEnd(*m, MAT_FINAL_ASSEMBLY));
762: PetscCall(MatShift(*m, 1.0));
763: PetscCall(MatSetDM(*m, sw));
764: PetscFunctionReturn(PETSC_SUCCESS);
765: }
767: /* FEM cols, Particle rows */
768: static PetscErrorCode DMCreateMassMatrix_Swarm(DM dmCoarse, DM dmFine, Mat *mass)
769: {
770: DMSwarmCellDM celldm;
771: PetscSection gsf;
772: PetscInt m, n, Np, bs;
773: void *ctx;
775: PetscFunctionBegin;
776: PetscCall(DMSwarmGetCellDMActive(dmCoarse, &celldm));
777: PetscCheck(celldm->Nf, PetscObjectComm((PetscObject)dmCoarse), PETSC_ERR_USER, "Active cell DM does not define any fields");
778: PetscCall(DMGetGlobalSection(dmFine, &gsf));
779: PetscCall(PetscSectionGetConstrainedStorageSize(gsf, &m));
780: PetscCall(DMSwarmGetLocalSize(dmCoarse, &Np));
781: PetscCall(DMSwarmCellDMGetBlockSize(celldm, dmCoarse, &bs));
782: n = Np * bs;
783: PetscCall(MatCreate(PetscObjectComm((PetscObject)dmCoarse), mass));
784: PetscCall(MatSetSizes(*mass, n, m, PETSC_DETERMINE, PETSC_DETERMINE));
785: PetscCall(MatSetType(*mass, dmCoarse->mattype));
786: PetscCall(DMGetApplicationContext(dmFine, &ctx));
788: PetscCall(DMSwarmComputeMassMatrix_Private(dmCoarse, dmFine, *mass, PETSC_TRUE, ctx));
789: PetscCall(MatViewFromOptions(*mass, NULL, "-mass_mat_view"));
790: PetscFunctionReturn(PETSC_SUCCESS);
791: }
793: static PetscErrorCode DMSwarmComputeMassMatrixSquare_Private(DM dmc, DM dmf, Mat mass, PetscBool useDeltaFunction, PetscCtx ctx)
794: {
795: MPI_Comm comm;
796: DMSwarmCellDM celldm;
797: PetscDS prob;
798: PetscSection fsection, globalFSection;
799: PetscHSetIJ ht;
800: PetscLayout rLayout, colLayout;
801: PetscInt *dnz, *onz, *adj, depth, maxConeSize, maxSupportSize, maxAdjSize;
802: PetscInt locRows, locCols, rStart, colStart, colEnd, *rowIDXs;
803: PetscReal *xi, *v0, *J, *invJ, detJ = 1.0, v0ref[3] = {-1.0, -1.0, -1.0};
804: PetscScalar *elemMat, *elemMatSq;
805: PetscInt cdim, Nf, Nfc, cStart, cEnd, totDim, maxC = 0;
806: const char **coordFields;
807: PetscReal **coordVals;
808: PetscInt *bs;
810: PetscFunctionBegin;
811: PetscCall(PetscObjectGetComm((PetscObject)mass, &comm));
812: PetscCall(DMGetCoordinateDim(dmf, &cdim));
813: PetscCall(DMGetDS(dmf, &prob));
814: PetscCall(PetscDSGetNumFields(prob, &Nf));
815: PetscCall(PetscDSGetTotalDimension(prob, &totDim));
816: PetscCall(PetscMalloc3(cdim, &v0, cdim * cdim, &J, cdim * cdim, &invJ));
817: PetscCall(DMGetLocalSection(dmf, &fsection));
818: PetscCall(DMGetGlobalSection(dmf, &globalFSection));
819: PetscCall(DMPlexGetHeightStratum(dmf, 0, &cStart, &cEnd));
820: PetscCall(MatGetLocalSize(mass, &locRows, &locCols));
822: PetscCall(DMSwarmGetCellDMActive(dmc, &celldm));
823: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Nfc, &coordFields));
824: PetscCall(PetscMalloc2(Nfc, &coordVals, Nfc, &bs));
826: PetscCall(PetscLayoutCreate(comm, &colLayout));
827: PetscCall(PetscLayoutSetLocalSize(colLayout, locCols));
828: PetscCall(PetscLayoutSetBlockSize(colLayout, 1));
829: PetscCall(PetscLayoutSetUp(colLayout));
830: PetscCall(PetscLayoutGetRange(colLayout, &colStart, &colEnd));
831: PetscCall(PetscLayoutDestroy(&colLayout));
833: PetscCall(PetscLayoutCreate(comm, &rLayout));
834: PetscCall(PetscLayoutSetLocalSize(rLayout, locRows));
835: PetscCall(PetscLayoutSetBlockSize(rLayout, 1));
836: PetscCall(PetscLayoutSetUp(rLayout));
837: PetscCall(PetscLayoutGetRange(rLayout, &rStart, NULL));
838: PetscCall(PetscLayoutDestroy(&rLayout));
840: PetscCall(DMPlexGetDepth(dmf, &depth));
841: PetscCall(DMPlexGetMaxSizes(dmf, &maxConeSize, &maxSupportSize));
842: maxAdjSize = PetscPowInt(maxConeSize * maxSupportSize, depth);
843: PetscCall(PetscMalloc1(maxAdjSize, &adj));
845: PetscCall(PetscCalloc2(locRows, &dnz, locRows, &onz));
846: PetscCall(PetscHSetIJCreate(&ht));
847: /* Count nonzeros
848: This is just FVM++, but we cannot use the Plex P0 allocation since unknowns in a cell will not be contiguous
849: */
850: PetscCall(DMSwarmSortGetAccess(dmc));
851: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
852: PetscInt *cindices;
853: PetscInt numCIndices;
854: #if 0
855: PetscInt adjSize = maxAdjSize, a, j;
856: #endif
858: PetscCall(DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices));
859: maxC = PetscMax(maxC, numCIndices);
860: /* Diagonal block */
861: for (PetscInt i = 0; i < numCIndices; ++i) dnz[cindices[i]] += numCIndices;
862: #if 0
863: /* Off-diagonal blocks */
864: PetscCall(DMPlexGetAdjacency(dmf, cell, &adjSize, &adj));
865: for (a = 0; a < adjSize; ++a) {
866: if (adj[a] >= cStart && adj[a] < cEnd && adj[a] != cell) {
867: const PetscInt ncell = adj[a];
868: PetscInt *ncindices;
869: PetscInt numNCIndices;
871: PetscCall(DMSwarmSortGetPointsPerCell(dmc, ncell, &numNCIndices, &ncindices));
872: {
873: PetscHashIJKey key;
874: PetscBool missing;
876: for (i = 0; i < numCIndices; ++i) {
877: key.i = cindices[i] + rStart; /* global rows (from Swarm) */
878: if (key.i < 0) continue;
879: for (j = 0; j < numNCIndices; ++j) {
880: key.j = ncindices[j] + rStart; /* global column (from Swarm) */
881: if (key.j < 0) continue;
882: PetscCall(PetscHSetIJQueryAdd(ht, key, &missing));
883: if (missing) {
884: if (key.j >= colStart && key.j < colEnd) ++dnz[key.i - rStart];
885: else ++onz[key.i - rStart];
886: }
887: }
888: }
889: }
890: PetscCall(DMSwarmSortRestorePointsPerCell(dmc, ncell, &numNCIndices, &ncindices));
891: }
892: }
893: #endif
894: PetscCall(DMSwarmSortRestorePointsPerCell(dmc, cell, &numCIndices, &cindices));
895: }
896: PetscCall(PetscHSetIJDestroy(&ht));
897: PetscCall(MatXAIJSetPreallocation(mass, 1, dnz, onz, NULL, NULL));
898: PetscCall(MatSetOption(mass, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE));
899: PetscCall(PetscFree2(dnz, onz));
900: PetscCall(PetscMalloc4(maxC * totDim, &elemMat, maxC * maxC, &elemMatSq, maxC, &rowIDXs, maxC * cdim, &xi));
901: /* Fill in values
902: Each entry is a sum of terms \phi_i(x_p) \phi_i(x_q)
903: Start just by producing block diagonal
904: Could loop over adjacent cells
905: Produce neighboring element matrix
906: TODO Determine which columns and rows correspond to shared dual vector
907: Do MatMatMult with rectangular matrices
908: Insert block
909: */
910: for (PetscInt field = 0; field < Nf; ++field) {
911: PetscTabulation Tcoarse;
912: PetscObject obj;
913: PetscInt Nc;
915: PetscCall(PetscDSGetDiscretization(prob, field, &obj));
916: PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
917: PetscCheck(Nc == 1, PetscObjectComm((PetscObject)dmf), PETSC_ERR_SUP, "Can only interpolate a scalar field from particles, Nc = %" PetscInt_FMT, Nc);
918: for (PetscInt i = 0; i < Nfc; ++i) PetscCall(DMSwarmGetField(dmc, coordFields[i], &bs[i], NULL, (void **)&coordVals[i]));
919: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
920: PetscInt *findices, *cindices;
921: PetscInt numFIndices, numCIndices;
923: /* TODO: Use DMField instead of assuming affine */
924: PetscCall(DMPlexComputeCellGeometryFEM(dmf, cell, NULL, v0, J, invJ, &detJ));
925: PetscCall(DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
926: PetscCall(DMSwarmSortGetPointsPerCell(dmc, cell, &numCIndices, &cindices));
927: for (PetscInt p = 0; p < numCIndices; ++p) {
928: PetscReal xr[8];
929: PetscInt off = 0;
931: for (PetscInt i = 0; i < Nfc; ++i) {
932: for (PetscInt b = 0; b < bs[i]; ++b, ++off) xr[off] = coordVals[i][cindices[p] * bs[i] + b];
933: }
934: PetscCheck(off == cdim, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The total block size of coordinates is %" PetscInt_FMT " != %" PetscInt_FMT " the DM coordinate dimension", off, cdim);
935: CoordinatesRealToRef(cdim, cdim, v0ref, v0, invJ, xr, &xi[p * cdim]);
936: }
937: PetscCall(PetscFECreateTabulation((PetscFE)obj, 1, numCIndices, xi, 0, &Tcoarse));
938: /* Get elemMat entries by multiplying by weight */
939: PetscCall(PetscArrayzero(elemMat, numCIndices * totDim));
940: for (PetscInt i = 0; i < numFIndices; ++i) {
941: for (PetscInt p = 0; p < numCIndices; ++p) {
942: for (PetscInt c = 0; c < Nc; ++c) {
943: /* B[(p*pdim + i)*Nc + c] is the value at point p for basis function i and component c */
944: elemMat[p * numFIndices + i] += Tcoarse->T[0][(p * numFIndices + i) * Nc + c] * (useDeltaFunction ? 1.0 : detJ);
945: }
946: }
947: }
948: PetscCall(PetscTabulationDestroy(&Tcoarse));
949: for (PetscInt p = 0; p < numCIndices; ++p) rowIDXs[p] = cindices[p] + rStart;
950: if (0) PetscCall(DMPrintCellMatrix(cell, "Mass Matrix Square", 1, numCIndices, elemMat));
951: /* Block diagonal */
952: if (numCIndices) {
953: PetscBLASInt blasn, blask;
954: PetscScalar one = 1.0, zero = 0.0;
956: PetscCall(PetscBLASIntCast(numCIndices, &blasn));
957: PetscCall(PetscBLASIntCast(numFIndices, &blask));
958: PetscCallBLAS("BLASgemm", BLASgemm_("T", "N", &blasn, &blasn, &blask, &one, elemMat, &blask, elemMat, &blask, &zero, elemMatSq, &blasn));
959: }
960: PetscCall(MatSetValues(mass, numCIndices, rowIDXs, numCIndices, rowIDXs, elemMatSq, ADD_VALUES));
961: /* TODO off-diagonal */
962: PetscCall(DMSwarmSortRestorePointsPerCell(dmc, cell, &numCIndices, &cindices));
963: PetscCall(DMPlexRestoreClosureIndices(dmf, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
964: }
965: for (PetscInt i = 0; i < Nfc; ++i) PetscCall(DMSwarmRestoreField(dmc, coordFields[i], &bs[i], NULL, (void **)&coordVals[i]));
966: }
967: PetscCall(PetscFree4(elemMat, elemMatSq, rowIDXs, xi));
968: PetscCall(PetscFree(adj));
969: PetscCall(DMSwarmSortRestoreAccess(dmc));
970: PetscCall(PetscFree3(v0, J, invJ));
971: PetscCall(PetscFree2(coordVals, bs));
972: PetscCall(MatAssemblyBegin(mass, MAT_FINAL_ASSEMBLY));
973: PetscCall(MatAssemblyEnd(mass, MAT_FINAL_ASSEMBLY));
974: PetscFunctionReturn(PETSC_SUCCESS);
975: }
977: /*@
978: DMSwarmCreateMassMatrixSquare - Creates the block-diagonal of the square, M^T_p M_p, of the particle mass matrix M_p
980: Collective
982: Input Parameters:
983: + dmCoarse - a `DMSWARM`
984: - dmFine - a `DMPLEX`
986: Output Parameter:
987: . mass - the square of the particle mass matrix
989: Level: advanced
991: Note:
992: We only compute the block diagonal since this provides a good preconditioner and is completely local. It would be possible in the
993: future to compute the full normal equations.
995: .seealso: `DM`, `DMSWARM`, `DMCreateMassMatrix()`
996: @*/
997: PetscErrorCode DMSwarmCreateMassMatrixSquare(DM dmCoarse, DM dmFine, Mat *mass)
998: {
999: PetscInt n;
1000: void *ctx;
1002: PetscFunctionBegin;
1003: PetscCall(DMSwarmGetLocalSize(dmCoarse, &n));
1004: PetscCall(MatCreate(PetscObjectComm((PetscObject)dmCoarse), mass));
1005: PetscCall(MatSetSizes(*mass, n, n, PETSC_DETERMINE, PETSC_DETERMINE));
1006: PetscCall(MatSetType(*mass, dmCoarse->mattype));
1007: PetscCall(DMGetApplicationContext(dmFine, &ctx));
1009: PetscCall(DMSwarmComputeMassMatrixSquare_Private(dmCoarse, dmFine, *mass, PETSC_TRUE, ctx));
1010: PetscCall(MatViewFromOptions(*mass, NULL, "-mass_sq_mat_view"));
1011: PetscFunctionReturn(PETSC_SUCCESS);
1012: }
1014: /* This creates a "gradient matrix" between a finite element and particle space, which is meant to enforce a weak divergence condition on the particle space. We are looking for a finite element field that has the same divergence as our particle field, so that
1016: \int_X \psi_i \nabla \cdot \hat f = \int_X \psi_i \nabla \cdot f
1018: and then integrate by parts
1020: \int_X \nabla \psi_i \cdot \hat f = \int_X \nabla \psi_i \cdot f
1022: where \psi is from a scalar FE space. If a finite element interpolant is given by
1024: \hat f^c = \sum_i f_i \phi^c_i
1026: and a particle function is given by
1028: f^c = \sum_p f^c_p \delta(x - x_p)
1030: then we want to require that
1032: D_f \hat f = D_p f
1034: where the gradient matrices are given by
1036: (D_f)_{i(jc)} = \int \partial_c \psi_i \phi_j
1037: (D_p)_{i(jc)} = \int \partial_c \psi_i \delta(x - x_j)
1039: Thus we need two finite element spaces, a scalar and a vector. The vector space holds the representer for the
1040: vector particle field. The scalar space holds the output of D_p or D_f, which is the weak divergence of the field.
1042: The way Dave May does particles, they amount to quadratue weights rather than delta functions, so he has |J| is in
1043: his integral. We allow this with the boolean flag.
1044: */
1045: static PetscErrorCode DMSwarmComputeGradientMatrix_Private(DM sw, DM dm, Mat derv, PetscBool useDeltaFunction, PetscCtx ctx)
1046: {
1047: MPI_Comm comm;
1048: DMSwarmCellDM celldm;
1049: PetscDS ds;
1050: PetscSection fsection, globalFSection;
1051: PetscLayout rLayout;
1052: PetscInt locRows, rStart, *rowIDXs;
1053: PetscReal *xi, *v0, *J, *invJ, detJ = 1.0, v0ref[3] = {-1.0, -1.0, -1.0};
1054: PetscScalar *elemMat;
1055: PetscInt cdim, Nf, Nfc, cStart, cEnd, totDim, maxNpc = 0, totNc = 0;
1056: const char **coordFields;
1057: PetscReal **coordVals;
1058: PetscInt *bs;
1060: PetscFunctionBegin;
1061: PetscCall(PetscObjectGetComm((PetscObject)derv, &comm));
1062: PetscCall(DMGetCoordinateDim(dm, &cdim));
1063: PetscCall(DMGetDS(dm, &ds));
1064: PetscCall(PetscDSGetNumFields(ds, &Nf));
1065: PetscCheck(Nf == 1, comm, PETSC_ERR_SUP, "Currently, we only support a single field");
1066: PetscCall(PetscDSGetTotalDimension(ds, &totDim));
1067: PetscCall(PetscMalloc3(cdim, &v0, cdim * cdim, &J, cdim * cdim, &invJ));
1068: PetscCall(DMGetLocalSection(dm, &fsection));
1069: PetscCall(DMGetGlobalSection(dm, &globalFSection));
1070: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
1071: PetscCall(MatGetLocalSize(derv, &locRows, NULL));
1073: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
1074: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Nfc, &coordFields));
1075: PetscCheck(Nfc == 1, comm, PETSC_ERR_SUP, "Currently, we only support a single field");
1076: PetscCall(PetscMalloc2(Nfc, &coordVals, Nfc, &bs));
1078: PetscCall(PetscLayoutCreate(comm, &rLayout));
1079: PetscCall(PetscLayoutSetLocalSize(rLayout, locRows));
1080: PetscCall(PetscLayoutSetBlockSize(rLayout, cdim));
1081: PetscCall(PetscLayoutSetUp(rLayout));
1082: PetscCall(PetscLayoutGetRange(rLayout, &rStart, NULL));
1083: PetscCall(PetscLayoutDestroy(&rLayout));
1085: for (PetscInt field = 0; field < Nf; ++field) {
1086: PetscObject obj;
1087: PetscInt Nc;
1089: PetscCall(PetscDSGetDiscretization(ds, field, &obj));
1090: PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
1091: totNc += Nc;
1092: }
1093: PetscCheck(totNc == 1, comm, PETSC_ERR_ARG_WRONG, "The number of field components %" PetscInt_FMT " != 1", totNc);
1094: /* count non-zeros */
1095: PetscCall(DMSwarmSortGetAccess(sw));
1096: for (PetscInt field = 0; field < Nf; ++field) {
1097: PetscObject obj;
1098: PetscInt Nc;
1100: PetscCall(PetscDSGetDiscretization(ds, field, &obj));
1101: PetscCall(PetscFEGetNumComponents((PetscFE)obj, &Nc));
1102: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
1103: PetscInt *pind;
1104: PetscInt Npc;
1106: PetscCall(DMSwarmSortGetPointsPerCell(sw, cell, &Npc, &pind));
1107: maxNpc = PetscMax(maxNpc, Npc);
1108: PetscCall(DMSwarmSortRestorePointsPerCell(sw, cell, &Npc, &pind));
1109: }
1110: }
1111: PetscCall(PetscMalloc3(maxNpc * cdim * totDim, &elemMat, maxNpc * cdim, &rowIDXs, maxNpc * cdim, &xi));
1112: for (PetscInt field = 0; field < Nf; ++field) {
1113: PetscTabulation Tcoarse;
1114: PetscFE fe;
1116: PetscCall(PetscDSGetDiscretization(ds, field, (PetscObject *)&fe));
1117: for (PetscInt i = 0; i < Nfc; ++i) PetscCall(DMSwarmGetField(sw, coordFields[i], &bs[i], NULL, (void **)&coordVals[i]));
1118: for (PetscInt cell = cStart; cell < cEnd; ++cell) {
1119: PetscInt *findices, *pind;
1120: PetscInt numFIndices, Npc;
1122: /* TODO: Use DMField instead of assuming affine */
1123: PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ));
1124: PetscCall(DMPlexGetClosureIndices(dm, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
1125: PetscCall(DMSwarmSortGetPointsPerCell(sw, cell, &Npc, &pind));
1126: for (PetscInt j = 0; j < Npc; ++j) {
1127: PetscReal xr[8];
1128: PetscInt off = 0;
1130: for (PetscInt i = 0; i < Nfc; ++i) {
1131: for (PetscInt b = 0; b < bs[i]; ++b, ++off) xr[off] = coordVals[i][pind[j] * bs[i] + b];
1132: }
1133: PetscCheck(off == cdim, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The total block size of coordinates is %" PetscInt_FMT " != %" PetscInt_FMT " the DM coordinate dimension", off, cdim);
1134: CoordinatesRealToRef(cdim, cdim, v0ref, v0, invJ, xr, &xi[j * cdim]);
1135: }
1136: PetscCall(PetscFECreateTabulation(fe, 1, Npc, xi, 1, &Tcoarse));
1137: /* Get elemMat entries by multiplying by weight */
1138: PetscCall(PetscArrayzero(elemMat, Npc * cdim * totDim));
1139: for (PetscInt i = 0; i < numFIndices; ++i) {
1140: for (PetscInt j = 0; j < Npc; ++j) {
1141: /* D[((p*pdim + i)*Nc + c)*cdim + d] is the value at point p for basis function i, component c, derivative d */
1142: for (PetscInt d = 0; d < cdim; ++d) {
1143: xi[d] = 0.;
1144: for (PetscInt e = 0; e < cdim; ++e) xi[d] += invJ[e * cdim + d] * Tcoarse->T[1][(j * numFIndices + i) * cdim + e];
1145: elemMat[(j * cdim + d) * numFIndices + i] += xi[d] * (useDeltaFunction ? 1.0 : detJ);
1146: }
1147: }
1148: }
1149: for (PetscInt j = 0; j < Npc; ++j)
1150: for (PetscInt d = 0; d < cdim; ++d) rowIDXs[j * cdim + d] = pind[j] * cdim + d + rStart;
1151: if (0) PetscCall(DMPrintCellMatrix(cell, "Derivative Matrix", Npc * cdim, numFIndices, elemMat));
1152: PetscCall(MatSetValues(derv, Npc * cdim, rowIDXs, numFIndices, findices, elemMat, ADD_VALUES));
1153: PetscCall(DMSwarmSortRestorePointsPerCell(sw, cell, &Npc, &pind));
1154: PetscCall(DMPlexRestoreClosureIndices(dm, fsection, globalFSection, cell, PETSC_FALSE, &numFIndices, &findices, NULL, NULL));
1155: PetscCall(PetscTabulationDestroy(&Tcoarse));
1156: }
1157: for (PetscInt i = 0; i < Nfc; ++i) PetscCall(DMSwarmRestoreField(sw, coordFields[i], &bs[i], NULL, (void **)&coordVals[i]));
1158: }
1159: PetscCall(PetscFree3(elemMat, rowIDXs, xi));
1160: PetscCall(DMSwarmSortRestoreAccess(sw));
1161: PetscCall(PetscFree3(v0, J, invJ));
1162: PetscCall(PetscFree2(coordVals, bs));
1163: PetscCall(MatAssemblyBegin(derv, MAT_FINAL_ASSEMBLY));
1164: PetscCall(MatAssemblyEnd(derv, MAT_FINAL_ASSEMBLY));
1165: PetscFunctionReturn(PETSC_SUCCESS);
1166: }
1168: /* FEM cols: this is a scalar space
1169: Particle rows: this is a vector space that contracts with the derivative
1170: */
1171: static PetscErrorCode DMCreateGradientMatrix_Swarm(DM sw, DM dm, Mat *derv)
1172: {
1173: DMSwarmCellDM celldm;
1174: PetscSection gs;
1175: PetscInt cdim, m, n, Np, bs;
1176: void *ctx;
1177: MPI_Comm comm;
1179: PetscFunctionBegin;
1180: PetscCall(PetscObjectGetComm((PetscObject)sw, &comm));
1181: PetscCall(DMGetCoordinateDim(dm, &cdim));
1182: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
1183: PetscCheck(celldm->Nf, comm, PETSC_ERR_USER, "Active cell DM does not define any fields");
1184: PetscCall(DMGetGlobalSection(dm, &gs));
1185: PetscCall(PetscSectionGetConstrainedStorageSize(gs, &n));
1186: PetscCall(DMSwarmGetLocalSize(sw, &Np));
1187: PetscCall(DMSwarmCellDMGetBlockSize(celldm, sw, &bs));
1188: PetscCheck(cdim == bs, comm, PETSC_ERR_ARG_WRONG, "Coordinate dimension %" PetscInt_FMT " != %" PetscInt_FMT " swarm field block size", cdim, bs);
1189: m = Np * bs;
1190: PetscCall(MatCreate(PetscObjectComm((PetscObject)sw), derv));
1191: PetscCall(PetscObjectSetName((PetscObject)*derv, "Swarm Derivative Matrix"));
1192: PetscCall(MatSetSizes(*derv, m, n, PETSC_DETERMINE, PETSC_DETERMINE));
1193: PetscCall(MatSetType(*derv, sw->mattype));
1194: PetscCall(DMGetApplicationContext(dm, &ctx));
1196: PetscCall(DMSwarmComputeGradientMatrix_Private(sw, dm, *derv, PETSC_TRUE, ctx));
1197: PetscCall(MatViewFromOptions(*derv, NULL, "-gradient_mat_view"));
1198: PetscFunctionReturn(PETSC_SUCCESS);
1199: }
1201: /*@
1202: DMSwarmCreateGlobalVectorFromField - Creates a `Vec` object sharing the array associated with a given field
1204: Collective
1206: Input Parameters:
1207: + dm - a `DMSWARM`
1208: - fieldname - the textual name given to a registered field
1210: Output Parameter:
1211: . vec - the vector
1213: Level: beginner
1215: Note:
1216: The vector must be returned using a matching call to `DMSwarmDestroyGlobalVectorFromField()`.
1218: The field must have data type `PETSC_SCALAR`.
1220: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmDestroyGlobalVectorFromField()`
1221: @*/
1222: PetscErrorCode DMSwarmCreateGlobalVectorFromField(DM dm, const char fieldname[], Vec *vec)
1223: {
1224: MPI_Comm comm = PetscObjectComm((PetscObject)dm);
1226: PetscFunctionBegin;
1228: PetscCall(DMSwarmCreateVectorFromField_Private(dm, fieldname, comm, vec));
1229: PetscFunctionReturn(PETSC_SUCCESS);
1230: }
1232: /*@
1233: DMSwarmDestroyGlobalVectorFromField - Destroys the `Vec` object which share the array associated with a given field
1235: Collective
1237: Input Parameters:
1238: + dm - a `DMSWARM`
1239: - fieldname - the textual name given to a registered field
1241: Output Parameter:
1242: . vec - the vector
1244: Level: beginner
1246: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmCreateGlobalVectorFromField()`
1247: @*/
1248: PetscErrorCode DMSwarmDestroyGlobalVectorFromField(DM dm, const char fieldname[], Vec *vec)
1249: {
1250: PetscFunctionBegin;
1252: PetscCall(DMSwarmDestroyVectorFromField_Private(dm, fieldname, vec));
1253: PetscFunctionReturn(PETSC_SUCCESS);
1254: }
1256: /*@
1257: DMSwarmCreateLocalVectorFromField - Creates a `Vec` object sharing the array associated with a given field
1259: Collective
1261: Input Parameters:
1262: + dm - a `DMSWARM`
1263: - fieldname - the textual name given to a registered field
1265: Output Parameter:
1266: . vec - the vector
1268: Level: beginner
1270: Note:
1271: The vector must be returned using a matching call to DMSwarmDestroyLocalVectorFromField().
1273: The field must have data type `PETSC_SCALAR`.
1275: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmDestroyLocalVectorFromField()`
1276: @*/
1277: PetscErrorCode DMSwarmCreateLocalVectorFromField(DM dm, const char fieldname[], Vec *vec)
1278: {
1279: PetscFunctionBegin;
1280: PetscCall(DMSwarmCreateVectorFromField_Private(dm, fieldname, PETSC_COMM_SELF, vec));
1281: PetscFunctionReturn(PETSC_SUCCESS);
1282: }
1284: /*@
1285: DMSwarmDestroyLocalVectorFromField - Destroys the `Vec` object which share the array associated with a given field
1287: Collective
1289: Input Parameters:
1290: + dm - a `DMSWARM`
1291: - fieldname - the textual name given to a registered field
1293: Output Parameter:
1294: . vec - the vector
1296: Level: beginner
1298: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmCreateLocalVectorFromField()`
1299: @*/
1300: PetscErrorCode DMSwarmDestroyLocalVectorFromField(DM dm, const char fieldname[], Vec *vec)
1301: {
1302: PetscFunctionBegin;
1304: PetscCall(DMSwarmDestroyVectorFromField_Private(dm, fieldname, vec));
1305: PetscFunctionReturn(PETSC_SUCCESS);
1306: }
1308: /*@
1309: DMSwarmCreateGlobalVectorFromFields - Creates a `Vec` object sharing the array associated with a given field set
1311: Collective
1313: Input Parameters:
1314: + dm - a `DMSWARM`
1315: . Nf - the number of fields
1316: - fieldnames - the textual names given to the registered fields
1318: Output Parameter:
1319: . vec - the vector
1321: Level: beginner
1323: Notes:
1324: The vector must be returned using a matching call to `DMSwarmDestroyGlobalVectorFromFields()`.
1326: All fields must have data type `PETSC_REAL` or `PETSC_SCALAR`. When PETSc is configured with complex scalars,
1327: only the real part of vector entries is copied back to `PETSC_REAL` fields.
1329: This vector is copyin-copyout, rather than a direct pointer like `DMSwarmCreateGlobalVectorFromField()`
1331: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmDestroyGlobalVectorFromFields()`
1332: @*/
1333: PetscErrorCode DMSwarmCreateGlobalVectorFromFields(DM dm, PetscInt Nf, const char *fieldnames[], Vec *vec)
1334: {
1335: MPI_Comm comm = PetscObjectComm((PetscObject)dm);
1337: PetscFunctionBegin;
1339: PetscCall(DMSwarmCreateVectorFromFields_Private(dm, Nf, fieldnames, comm, vec));
1340: PetscFunctionReturn(PETSC_SUCCESS);
1341: }
1343: /*@
1344: DMSwarmDestroyGlobalVectorFromFields - Destroys the `Vec` object which share the array associated with a given field set
1346: Collective
1348: Input Parameters:
1349: + dm - a `DMSWARM`
1350: . Nf - the number of fields
1351: - fieldnames - the textual names given to the registered fields
1353: Output Parameter:
1354: . vec - the vector
1356: Level: beginner
1358: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmCreateGlobalVectorFromField()`
1359: @*/
1360: PetscErrorCode DMSwarmDestroyGlobalVectorFromFields(DM dm, PetscInt Nf, const char *fieldnames[], Vec *vec)
1361: {
1362: PetscFunctionBegin;
1364: PetscCall(DMSwarmDestroyVectorFromFields_Private(dm, Nf, fieldnames, vec));
1365: PetscFunctionReturn(PETSC_SUCCESS);
1366: }
1368: /*@
1369: DMSwarmCreateLocalVectorFromFields - Creates a `Vec` object sharing the array associated with a given field set
1371: Collective
1373: Input Parameters:
1374: + dm - a `DMSWARM`
1375: . Nf - the number of fields
1376: - fieldnames - the textual names given to the registered fields
1378: Output Parameter:
1379: . vec - the vector
1381: Level: beginner
1383: Notes:
1384: The vector must be returned using a matching call to DMSwarmDestroyLocalVectorFromField().
1386: All fields must have data type `PETSC_REAL` or `PETSC_SCALAR`. When PETSc is configured with complex scalars,
1387: only the real part of vector entries is copied back to `PETSC_REAL` fields.
1389: This vector is copyin-copyout, rather than a direct pointer like `DMSwarmCreateLocalVectorFromField()`
1391: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmDestroyLocalVectorFromField()`
1392: @*/
1393: PetscErrorCode DMSwarmCreateLocalVectorFromFields(DM dm, PetscInt Nf, const char *fieldnames[], Vec *vec)
1394: {
1395: PetscFunctionBegin;
1396: PetscCall(DMSwarmCreateVectorFromFields_Private(dm, Nf, fieldnames, PETSC_COMM_SELF, vec));
1397: PetscFunctionReturn(PETSC_SUCCESS);
1398: }
1400: /*@
1401: DMSwarmDestroyLocalVectorFromFields - Destroys the `Vec` object which share the array associated with a given field set
1403: Collective
1405: Input Parameters:
1406: + dm - a `DMSWARM`
1407: . Nf - the number of fields
1408: - fieldnames - the textual names given to the registered fields
1410: Output Parameter:
1411: . vec - the vector
1413: Level: beginner
1415: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmCreateLocalVectorFromFields()`
1416: @*/
1417: PetscErrorCode DMSwarmDestroyLocalVectorFromFields(DM dm, PetscInt Nf, const char *fieldnames[], Vec *vec)
1418: {
1419: PetscFunctionBegin;
1421: PetscCall(DMSwarmDestroyVectorFromFields_Private(dm, Nf, fieldnames, vec));
1422: PetscFunctionReturn(PETSC_SUCCESS);
1423: }
1425: /*@
1426: DMSwarmInitializeFieldRegister - Initiates the registration of fields to a `DMSWARM`
1428: Collective
1430: Input Parameter:
1431: . dm - a `DMSWARM`
1433: Level: beginner
1435: Note:
1436: After all fields have been registered, you must call `DMSwarmFinalizeFieldRegister()`.
1438: .seealso: `DM`, `DMSWARM`, `DMSwarmFinalizeFieldRegister()`, `DMSwarmRegisterPetscDatatypeField()`,
1439: `DMSwarmRegisterUserStructField()`, `DMSwarmRegisterUserDatatypeField()`
1440: @*/
1441: PetscErrorCode DMSwarmInitializeFieldRegister(DM dm)
1442: {
1443: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1445: PetscFunctionBegin;
1446: if (!swarm->field_registration_initialized) {
1447: swarm->field_registration_initialized = PETSC_TRUE;
1448: PetscCall(DMSwarmRegisterPetscDatatypeField(dm, DMSwarmField_pid, 1, PETSC_INT64)); /* unique identifier */
1449: PetscCall(DMSwarmRegisterPetscDatatypeField(dm, DMSwarmField_rank, 1, PETSC_INT)); /* used for communication */
1450: }
1451: PetscFunctionReturn(PETSC_SUCCESS);
1452: }
1454: /*@
1455: DMSwarmFinalizeFieldRegister - Finalizes the registration of fields to a `DMSWARM`
1457: Collective
1459: Input Parameter:
1460: . dm - a `DMSWARM`
1462: Level: beginner
1464: Note:
1465: After `DMSwarmFinalizeFieldRegister()` has been called, no new fields can be defined on the `DMSWARM`.
1467: .seealso: `DM`, `DMSWARM`, `DMSwarmInitializeFieldRegister()`, `DMSwarmRegisterPetscDatatypeField()`,
1468: `DMSwarmRegisterUserStructField()`, `DMSwarmRegisterUserDatatypeField()`
1469: @*/
1470: PetscErrorCode DMSwarmFinalizeFieldRegister(DM dm)
1471: {
1472: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1474: PetscFunctionBegin;
1475: if (!swarm->field_registration_finalized) PetscCall(DMSwarmDataBucketFinalize(swarm->db));
1476: swarm->field_registration_finalized = PETSC_TRUE;
1477: PetscFunctionReturn(PETSC_SUCCESS);
1478: }
1480: /*@
1481: DMSwarmSetLocalSizes - Sets the length of all registered fields on the `DMSWARM`
1483: Not Collective
1485: Input Parameters:
1486: + sw - a `DMSWARM`
1487: . nlocal - the length of each registered field
1488: - buffer - the length of the buffer used to efficient dynamic re-sizing
1490: Level: beginner
1492: .seealso: `DM`, `DMSWARM`, `DMSwarmGetLocalSize()`
1493: @*/
1494: PetscErrorCode DMSwarmSetLocalSizes(DM sw, PetscInt nlocal, PetscInt buffer)
1495: {
1496: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1497: PetscMPIInt rank;
1498: PetscInt *rankval;
1500: PetscFunctionBegin;
1501: PetscCall(PetscLogEventBegin(DMSWARM_SetSizes, 0, 0, 0, 0));
1502: PetscCall(DMSwarmDataBucketSetSizes(swarm->db, nlocal, buffer));
1503: PetscCall(PetscLogEventEnd(DMSWARM_SetSizes, 0, 0, 0, 0));
1505: // Initialize values in pid and rank placeholders
1506: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)sw), &rank));
1507: PetscCall(DMSwarmGetField(sw, DMSwarmField_rank, NULL, NULL, (void **)&rankval));
1508: for (PetscInt p = 0; p < nlocal; p++) rankval[p] = rank;
1509: PetscCall(DMSwarmRestoreField(sw, DMSwarmField_rank, NULL, NULL, (void **)&rankval));
1510: /* TODO: [pid - use MPI_Scan] */
1511: PetscFunctionReturn(PETSC_SUCCESS);
1512: }
1514: /*@
1515: DMSwarmSetCellDM - Attaches a `DM` to a `DMSWARM`
1517: Collective
1519: Input Parameters:
1520: + sw - a `DMSWARM`
1521: - dm - the `DM` to attach to the `DMSWARM`
1523: Level: beginner
1525: Note:
1526: The attached `DM` (dm) will be queried for point location and
1527: neighbor MPI-rank information if `DMSwarmMigrate()` is called.
1529: .seealso: `DM`, `DMSWARM`, `DMSwarmSetType()`, `DMSwarmGetCellDM()`, `DMSwarmMigrate()`
1530: @*/
1531: PetscErrorCode DMSwarmSetCellDM(DM sw, DM dm)
1532: {
1533: DMSwarmCellDM celldm;
1534: const char *name;
1535: char *coordName;
1537: PetscFunctionBegin;
1540: PetscCall(PetscStrallocpy(DMSwarmPICField_coor, &coordName));
1541: PetscCall(DMSwarmCellDMCreate(dm, 0, NULL, 1, (const char **)&coordName, &celldm));
1542: PetscCall(PetscFree(coordName));
1543: PetscCall(PetscObjectGetName((PetscObject)celldm, &name));
1544: PetscCall(DMSwarmAddCellDM(sw, celldm));
1545: PetscCall(DMSwarmCellDMDestroy(&celldm));
1546: PetscCall(DMSwarmSetCellDMActive(sw, name));
1547: PetscFunctionReturn(PETSC_SUCCESS);
1548: }
1550: /*@
1551: DMSwarmGetCellDM - Fetches the active cell `DM`
1553: Collective
1555: Input Parameter:
1556: . sw - a `DMSWARM`
1558: Output Parameter:
1559: . dm - the active `DM` for the `DMSWARM`
1561: Level: beginner
1563: .seealso: `DM`, `DMSWARM`, `DMSwarmSetCellDM()`
1564: @*/
1565: PetscErrorCode DMSwarmGetCellDM(DM sw, DM *dm)
1566: {
1567: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1568: DMSwarmCellDM celldm;
1570: PetscFunctionBegin;
1572: PetscCall(PetscObjectListFind(swarm->cellDMs, swarm->activeCellDM, (PetscObject *)&celldm));
1573: PetscCheck(celldm, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "There is no cell DM named %s in this Swarm", swarm->activeCellDM);
1574: PetscCall(DMSwarmCellDMGetDM(celldm, dm));
1575: PetscFunctionReturn(PETSC_SUCCESS);
1576: }
1578: /*@
1579: DMSwarmGetCellDMNames - Get the list of cell `DM` names
1581: Not collective
1583: Input Parameter:
1584: . sw - a `DMSWARM`
1586: Output Parameters:
1587: + Ndm - the number of `DMSwarmCellDM` in the `DMSWARM`
1588: - celldms - the name of each `DMSwarmCellDM`
1590: Level: beginner
1592: .seealso: `DM`, `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmGetCellDMByName()`
1593: @*/
1594: PetscErrorCode DMSwarmGetCellDMNames(DM sw, PetscInt *Ndm, const char **celldms[])
1595: {
1596: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1597: PetscObjectList next = swarm->cellDMs;
1598: PetscInt n = 0;
1600: PetscFunctionBegin;
1602: PetscAssertPointer(Ndm, 2);
1603: PetscAssertPointer(celldms, 3);
1604: while (next) {
1605: next = next->next;
1606: ++n;
1607: }
1608: PetscCall(PetscMalloc1(n, celldms));
1609: next = swarm->cellDMs;
1610: n = 0;
1611: while (next) {
1612: (*celldms)[n] = (const char *)next->obj->name;
1613: next = next->next;
1614: ++n;
1615: }
1616: *Ndm = n;
1617: PetscFunctionReturn(PETSC_SUCCESS);
1618: }
1620: /*@
1621: DMSwarmSetCellDMActive - Activates a cell `DM` for a `DMSWARM`
1623: Collective
1625: Input Parameters:
1626: + sw - a `DMSWARM`
1627: - name - name of the cell `DM` to active for the `DMSWARM`
1629: Level: beginner
1631: Note:
1632: The attached `DM` (dmcell) will be queried for point location and
1633: neighbor MPI-rank information if `DMSwarmMigrate()` is called.
1635: .seealso: `DM`, `DMSWARM`, `DMSwarmCellDM`, `DMSwarmSetType()`, `DMSwarmAddCellDM()`, `DMSwarmSetCellDM()`, `DMSwarmMigrate()`
1636: @*/
1637: PetscErrorCode DMSwarmSetCellDMActive(DM sw, const char name[])
1638: {
1639: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1640: DMSwarmCellDM celldm;
1642: PetscFunctionBegin;
1644: PetscCall(PetscInfo(sw, "Setting cell DM to %s\n", name));
1645: PetscCall(PetscFree(swarm->activeCellDM));
1646: PetscCall(PetscStrallocpy(name, (char **)&swarm->activeCellDM));
1647: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
1648: PetscFunctionReturn(PETSC_SUCCESS);
1649: }
1651: /*@
1652: DMSwarmGetCellDMActive - Returns the active cell `DM` for a `DMSWARM`
1654: Collective
1656: Input Parameter:
1657: . sw - a `DMSWARM`
1659: Output Parameter:
1660: . celldm - the active `DMSwarmCellDM`
1662: Level: beginner
1664: .seealso: `DM`, `DMSWARM`, `DMSwarmCellDM`, `DMSwarmSetType()`, `DMSwarmAddCellDM()`, `DMSwarmSetCellDM()`, `DMSwarmMigrate()`
1665: @*/
1666: PetscErrorCode DMSwarmGetCellDMActive(DM sw, DMSwarmCellDM *celldm)
1667: {
1668: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1670: PetscFunctionBegin;
1672: PetscAssertPointer(celldm, 2);
1673: PetscCheck(swarm->activeCellDM, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONGSTATE, "Swarm has no active cell DM");
1674: PetscCall(PetscObjectListFind(swarm->cellDMs, swarm->activeCellDM, (PetscObject *)celldm));
1675: PetscCheck(*celldm, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONGSTATE, "Swarm has no valid cell DM for %s", swarm->activeCellDM);
1676: PetscFunctionReturn(PETSC_SUCCESS);
1677: }
1679: /*@
1680: DMSwarmGetCellDMByName - Get a `DMSwarmCellDM` from its name
1682: Not collective
1684: Input Parameters:
1685: + sw - a `DMSWARM`
1686: - name - the name
1688: Output Parameter:
1689: . celldm - the `DMSwarmCellDM`, or `NULL` if the name is unknown
1691: Level: beginner
1693: .seealso: `DM`, `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmGetCellDMNames()`
1694: @*/
1695: PetscErrorCode DMSwarmGetCellDMByName(DM sw, const char name[], DMSwarmCellDM *celldm)
1696: {
1697: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1699: PetscFunctionBegin;
1701: PetscAssertPointer(name, 2);
1702: PetscAssertPointer(celldm, 3);
1703: PetscCall(PetscObjectListFind(swarm->cellDMs, name, (PetscObject *)celldm));
1704: PetscFunctionReturn(PETSC_SUCCESS);
1705: }
1707: /*@
1708: DMSwarmAddCellDM - Adds a cell `DM` to the `DMSWARM`
1710: Collective
1712: Input Parameters:
1713: + sw - a `DMSWARM`
1714: - celldm - the `DMSwarmCellDM`
1716: Level: beginner
1718: Note:
1719: Cell DMs with the same name will share the cellid field
1721: .seealso: `DM`, `DMSWARM`, `DMSwarmSetType()`, `DMSwarmPushCellDM()`, `DMSwarmSetCellDM()`, `DMSwarmMigrate()`
1722: @*/
1723: PetscErrorCode DMSwarmAddCellDM(DM sw, DMSwarmCellDM celldm)
1724: {
1725: DM_Swarm *swarm = (DM_Swarm *)sw->data;
1726: const char *name;
1727: PetscInt dim;
1728: PetscBool flg;
1729: MPI_Comm comm;
1731: PetscFunctionBegin;
1733: PetscCall(PetscObjectGetComm((PetscObject)sw, &comm));
1735: PetscCall(PetscObjectGetName((PetscObject)celldm, &name));
1736: PetscCall(PetscObjectListAdd(&swarm->cellDMs, name, (PetscObject)celldm));
1737: PetscCall(DMGetDimension(sw, &dim));
1738: for (PetscInt f = 0; f < celldm->Nfc; ++f) {
1739: PetscCall(DMSwarmDataFieldStringInList(celldm->coordFields[f], swarm->db->nfields, (const DMSwarmDataField *)swarm->db->field, &flg));
1740: if (!flg) {
1741: PetscCall(DMSwarmRegisterPetscDatatypeField(sw, celldm->coordFields[f], dim, PETSC_REAL));
1742: } else {
1743: PetscDataType dt;
1744: PetscInt bs;
1746: PetscCall(DMSwarmGetFieldInfo(sw, celldm->coordFields[f], &bs, &dt));
1747: PetscCheck(bs == dim, comm, PETSC_ERR_ARG_WRONG, "Coordinate field %s has blocksize %" PetscInt_FMT " != %" PetscInt_FMT " spatial dimension", celldm->coordFields[f], bs, dim);
1748: PetscCheck(dt == PETSC_REAL, comm, PETSC_ERR_ARG_WRONG, "Coordinate field %s has datatype %s != PETSC_REAL", celldm->coordFields[f], PetscDataTypes[dt]);
1749: }
1750: }
1751: // Assume that DMs with the same name share the cellid field
1752: PetscCall(DMSwarmDataFieldStringInList(celldm->cellid, swarm->db->nfields, (const DMSwarmDataField *)swarm->db->field, &flg));
1753: if (!flg) {
1754: PetscBool isShell, isDummy;
1755: const char *name;
1757: // Allow dummy DMSHELL (I don't think we should support this mode)
1758: PetscCall(PetscObjectTypeCompare((PetscObject)celldm->dm, DMSHELL, &isShell));
1759: PetscCall(PetscObjectGetName((PetscObject)celldm->dm, &name));
1760: PetscCall(PetscStrcmp(name, "dummy", &isDummy));
1761: if (!isShell || !isDummy) PetscCall(DMSwarmRegisterPetscDatatypeField(sw, celldm->cellid, 1, PETSC_INT));
1762: }
1763: PetscCall(DMSwarmSetCellDMActive(sw, name));
1764: PetscFunctionReturn(PETSC_SUCCESS);
1765: }
1767: /*@
1768: DMSwarmGetLocalSize - Retrieves the local length of fields registered
1770: Not Collective
1772: Input Parameter:
1773: . dm - a `DMSWARM`
1775: Output Parameter:
1776: . nlocal - the length of each registered field
1778: Level: beginner
1780: .seealso: `DM`, `DMSWARM`, `DMSwarmGetSize()`, `DMSwarmSetLocalSizes()`
1781: @*/
1782: PetscErrorCode DMSwarmGetLocalSize(DM dm, PetscInt *nlocal)
1783: {
1784: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1786: PetscFunctionBegin;
1787: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, nlocal, NULL, NULL));
1788: PetscFunctionReturn(PETSC_SUCCESS);
1789: }
1791: /*@
1792: DMSwarmGetSize - Retrieves the total length of fields registered
1794: Collective
1796: Input Parameter:
1797: . dm - a `DMSWARM`
1799: Output Parameter:
1800: . n - the total length of each registered field
1802: Level: beginner
1804: Note:
1805: This calls `MPI_Allreduce()` upon each call (inefficient but safe)
1807: .seealso: `DM`, `DMSWARM`, `DMSwarmGetLocalSize()`, `DMSwarmSetLocalSizes()`
1808: @*/
1809: PetscErrorCode DMSwarmGetSize(DM dm, PetscInt *n)
1810: {
1811: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1813: PetscFunctionBegin;
1814: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, n, NULL, NULL));
1815: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, n, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)dm)));
1816: PetscFunctionReturn(PETSC_SUCCESS);
1817: }
1819: /*@
1820: DMSwarmRegisterPetscDatatypeField - Register a field to a `DMSWARM` with a native PETSc data type
1822: Collective
1824: Input Parameters:
1825: + dm - a `DMSWARM`
1826: . fieldname - the textual name to identify this field
1827: . blocksize - the number of each data type
1828: - type - a valid PETSc data type (`PETSC_CHAR`, `PETSC_SHORT`, `PETSC_INT`, `PETSC_FLOAT`, `PETSC_REAL`, `PETSC_LONG`)
1830: Level: beginner
1832: Notes:
1833: The textual name for each registered field must be unique.
1835: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterUserStructField()`, `DMSwarmRegisterUserDatatypeField()`
1836: @*/
1837: PetscErrorCode DMSwarmRegisterPetscDatatypeField(DM dm, const char fieldname[], PetscInt blocksize, PetscDataType type)
1838: {
1839: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1840: size_t size;
1842: PetscFunctionBegin;
1843: PetscCheck(swarm->field_registration_initialized, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "Must call DMSwarmInitializeFieldRegister() first");
1844: PetscCheck(!swarm->field_registration_finalized, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "Cannot register additional fields after calling DMSwarmFinalizeFieldRegister() first");
1846: PetscCheck(type != PETSC_OBJECT, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Valid for {char,short,int,long,float,double}");
1847: PetscCheck(type != PETSC_FUNCTION, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Valid for {char,short,int,long,float,double}");
1848: PetscCheck(type != PETSC_STRING, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Valid for {char,short,int,long,float,double}");
1849: PetscCheck(type != PETSC_STRUCT, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Valid for {char,short,int,long,float,double}");
1850: PetscCheck(type != PETSC_DATATYPE_UNKNOWN, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Valid for {char,short,int,long,float,double}");
1852: PetscCall(PetscDataTypeGetSize(type, &size));
1853: /* Load a specific data type into data bucket, specifying textual name and its size in bytes */
1854: PetscCall(DMSwarmDataBucketRegisterField(swarm->db, "DMSwarmRegisterPetscDatatypeField", fieldname, blocksize * size, NULL));
1855: {
1856: DMSwarmDataField gfield;
1858: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield));
1859: PetscCall(DMSwarmDataFieldSetBlockSize(gfield, blocksize));
1860: }
1861: swarm->db->field[swarm->db->nfields - 1]->petsc_type = type;
1862: PetscFunctionReturn(PETSC_SUCCESS);
1863: }
1865: /*@
1866: DMSwarmRegisterUserStructField - Register a user defined struct to a `DMSWARM`
1868: Collective
1870: Input Parameters:
1871: + dm - a `DMSWARM`
1872: . fieldname - the textual name to identify this field
1873: - size - the size in bytes of the user struct of each data type
1875: Level: beginner
1877: Note:
1878: The textual name for each registered field must be unique.
1880: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmRegisterUserDatatypeField()`
1881: @*/
1882: PetscErrorCode DMSwarmRegisterUserStructField(DM dm, const char fieldname[], size_t size)
1883: {
1884: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1886: PetscFunctionBegin;
1887: PetscCall(DMSwarmDataBucketRegisterField(swarm->db, "DMSwarmRegisterUserStructField", fieldname, size, NULL));
1888: swarm->db->field[swarm->db->nfields - 1]->petsc_type = PETSC_STRUCT;
1889: PetscFunctionReturn(PETSC_SUCCESS);
1890: }
1892: /*@
1893: DMSwarmRegisterUserDatatypeField - Register a user defined data type to a `DMSWARM`
1895: Collective
1897: Input Parameters:
1898: + dm - a `DMSWARM`
1899: . fieldname - the textual name to identify this field
1900: . size - the size in bytes of the user data type
1901: - blocksize - the number of each data type
1903: Level: beginner
1905: Note:
1906: The textual name for each registered field must be unique.
1908: .seealso: `DM`, `DMSWARM`, `DMSwarmRegisterPetscDatatypeField()`, `DMSwarmRegisterUserStructField()`
1909: @*/
1910: PetscErrorCode DMSwarmRegisterUserDatatypeField(DM dm, const char fieldname[], size_t size, PetscInt blocksize)
1911: {
1912: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1914: PetscFunctionBegin;
1915: PetscCall(DMSwarmDataBucketRegisterField(swarm->db, "DMSwarmRegisterUserDatatypeField", fieldname, blocksize * size, NULL));
1916: {
1917: DMSwarmDataField gfield;
1919: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield));
1920: PetscCall(DMSwarmDataFieldSetBlockSize(gfield, blocksize));
1921: }
1922: swarm->db->field[swarm->db->nfields - 1]->petsc_type = PETSC_DATATYPE_UNKNOWN;
1923: PetscFunctionReturn(PETSC_SUCCESS);
1924: }
1926: /*@
1927: DMSwarmGetField - Get access to the underlying array storing all entries associated with a registered field
1929: Not Collective, No Fortran Support
1931: Input Parameters:
1932: + dm - a `DMSWARM`
1933: - fieldname - the textual name to identify this field
1935: Output Parameters:
1936: + blocksize - the number of each data type
1937: . type - the data type
1938: - data - pointer to raw array
1940: Level: beginner
1942: Notes:
1943: The array must be returned using a matching call to `DMSwarmRestoreField()`.
1945: Fortran Note:
1946: Only works for `type` of `PETSC_SCALAR`
1948: .seealso: `DM`, `DMSWARM`, `DMSwarmRestoreField()`
1949: @*/
1950: PetscErrorCode DMSwarmGetField(DM dm, const char fieldname[], PetscInt *blocksize, PetscDataType *type, void **data) PeNS
1951: {
1952: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1953: DMSwarmDataField gfield;
1955: PetscFunctionBegin;
1957: if (!swarm->issetup) PetscCall(DMSetUp(dm));
1958: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield));
1959: PetscCall(DMSwarmDataFieldGetAccess(gfield));
1960: PetscCall(DMSwarmDataFieldGetEntries(gfield, data));
1961: if (blocksize) *blocksize = gfield->bs;
1962: if (type) *type = gfield->petsc_type;
1963: PetscFunctionReturn(PETSC_SUCCESS);
1964: }
1966: /*@
1967: DMSwarmRestoreField - Restore access to the underlying array storing all entries associated with a registered field
1969: Not Collective
1971: Input Parameters:
1972: + dm - a `DMSWARM`
1973: - fieldname - the textual name to identify this field
1975: Output Parameters:
1976: + blocksize - the number of each data type
1977: . type - the data type
1978: - data - pointer to raw array
1980: Level: beginner
1982: Notes:
1983: The user must call `DMSwarmGetField()` prior to calling `DMSwarmRestoreField()`.
1985: Fortran Note:
1986: Only works for `type` of `PETSC_SCALAR`
1988: .seealso: `DM`, `DMSWARM`, `DMSwarmGetField()`
1989: @*/
1990: PetscErrorCode DMSwarmRestoreField(DM dm, const char fieldname[], PetscInt *blocksize, PetscDataType *type, void **data) PeNS
1991: {
1992: DM_Swarm *swarm = (DM_Swarm *)dm->data;
1993: DMSwarmDataField gfield;
1995: PetscFunctionBegin;
1997: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield));
1998: PetscCall(DMSwarmDataFieldRestoreAccess(gfield));
1999: if (data) *data = NULL;
2000: PetscFunctionReturn(PETSC_SUCCESS);
2001: }
2003: /*@
2004: DMSwarmGetFieldInfo - Return the block size and data type of a registered `DMSWARM` field without accessing its data.
2006: Not Collective
2008: Input Parameters:
2009: + dm - a `DMSWARM`
2010: - fieldname - the name of the registered field
2012: Output Parameters:
2013: + blocksize - the number of entries of `type` per particle, or `NULL`
2014: - type - the `PetscDataType` of a single entry, or `NULL`
2016: Level: intermediate
2018: .seealso: `DM`, `DMSWARM`, `DMSwarmGetField()`, `DMSwarmRestoreField()`, `DMSwarmRegisterPetscDatatypeField()`
2019: @*/
2020: PetscErrorCode DMSwarmGetFieldInfo(DM dm, const char fieldname[], PetscInt *blocksize, PetscDataType *type)
2021: {
2022: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2023: DMSwarmDataField gfield;
2025: PetscFunctionBegin;
2027: PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldname, &gfield));
2028: if (blocksize) *blocksize = gfield->bs;
2029: if (type) *type = gfield->petsc_type;
2030: PetscFunctionReturn(PETSC_SUCCESS);
2031: }
2033: /*@
2034: DMSwarmAddPoint - Add space for one new point in the `DMSWARM`
2036: Not Collective
2038: Input Parameter:
2039: . dm - a `DMSWARM`
2041: Level: beginner
2043: Notes:
2044: The new point will have all fields initialized to zero.
2046: .seealso: `DM`, `DMSWARM`, `DMSwarmAddNPoints()`
2047: @*/
2048: PetscErrorCode DMSwarmAddPoint(DM dm)
2049: {
2050: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2052: PetscFunctionBegin;
2053: if (!swarm->issetup) PetscCall(DMSetUp(dm));
2054: PetscCall(PetscLogEventBegin(DMSWARM_AddPoints, 0, 0, 0, 0));
2055: PetscCall(DMSwarmDataBucketAddPoint(swarm->db));
2056: PetscCall(PetscLogEventEnd(DMSWARM_AddPoints, 0, 0, 0, 0));
2057: PetscFunctionReturn(PETSC_SUCCESS);
2058: }
2060: /*@
2061: DMSwarmAddNPoints - Add space for a number of new points in the `DMSWARM`
2063: Not Collective
2065: Input Parameters:
2066: + dm - a `DMSWARM`
2067: - npoints - the number of new points to add
2069: Level: beginner
2071: Notes:
2072: The new point will have all fields initialized to zero.
2074: .seealso: `DM`, `DMSWARM`, `DMSwarmAddPoint()`
2075: @*/
2076: PetscErrorCode DMSwarmAddNPoints(DM dm, PetscInt npoints)
2077: {
2078: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2079: PetscInt nlocal;
2081: PetscFunctionBegin;
2082: PetscCall(PetscLogEventBegin(DMSWARM_AddPoints, 0, 0, 0, 0));
2083: PetscCall(DMSwarmDataBucketGetSizes(swarm->db, &nlocal, NULL, NULL));
2084: nlocal = PetscMax(nlocal, 0) + npoints;
2085: PetscCall(DMSwarmDataBucketSetSizes(swarm->db, nlocal, DMSWARM_DATA_BUCKET_BUFFER_DEFAULT));
2086: PetscCall(PetscLogEventEnd(DMSWARM_AddPoints, 0, 0, 0, 0));
2087: PetscFunctionReturn(PETSC_SUCCESS);
2088: }
2090: /*@
2091: DMSwarmRemovePoint - Remove the last point from the `DMSWARM`
2093: Not Collective
2095: Input Parameter:
2096: . dm - a `DMSWARM`
2098: Level: beginner
2100: .seealso: `DM`, `DMSWARM`, `DMSwarmRemovePointAtIndex()`
2101: @*/
2102: PetscErrorCode DMSwarmRemovePoint(DM dm)
2103: {
2104: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2106: PetscFunctionBegin;
2107: PetscCall(PetscLogEventBegin(DMSWARM_RemovePoints, 0, 0, 0, 0));
2108: PetscCall(DMSwarmDataBucketRemovePoint(swarm->db));
2109: PetscCall(PetscLogEventEnd(DMSWARM_RemovePoints, 0, 0, 0, 0));
2110: PetscFunctionReturn(PETSC_SUCCESS);
2111: }
2113: /*@
2114: DMSwarmRemovePointAtIndex - Removes a specific point from the `DMSWARM`
2116: Not Collective
2118: Input Parameters:
2119: + dm - a `DMSWARM`
2120: - idx - index of point to remove
2122: Level: beginner
2124: .seealso: `DM`, `DMSWARM`, `DMSwarmRemovePoint()`
2125: @*/
2126: PetscErrorCode DMSwarmRemovePointAtIndex(DM dm, PetscInt idx)
2127: {
2128: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2130: PetscFunctionBegin;
2131: PetscCall(PetscLogEventBegin(DMSWARM_RemovePoints, 0, 0, 0, 0));
2132: PetscCall(DMSwarmDataBucketRemovePointAtIndex(swarm->db, idx));
2133: PetscCall(PetscLogEventEnd(DMSWARM_RemovePoints, 0, 0, 0, 0));
2134: PetscFunctionReturn(PETSC_SUCCESS);
2135: }
2137: /*@
2138: DMSwarmCopyPoint - Copy point pj to point pi in the `DMSWARM`
2140: Not Collective
2142: Input Parameters:
2143: + dm - a `DMSWARM`
2144: . pi - the index of the point to copy
2145: - pj - the point index where the copy should be located
2147: Level: beginner
2149: .seealso: `DM`, `DMSWARM`, `DMSwarmRemovePoint()`
2150: @*/
2151: PetscErrorCode DMSwarmCopyPoint(DM dm, PetscInt pi, PetscInt pj)
2152: {
2153: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2155: PetscFunctionBegin;
2156: if (!swarm->issetup) PetscCall(DMSetUp(dm));
2157: PetscCall(DMSwarmDataBucketCopyPoint(swarm->db, pi, swarm->db, pj));
2158: PetscFunctionReturn(PETSC_SUCCESS);
2159: }
2161: static PetscErrorCode DMSwarmMigrate_Basic(DM dm, PetscBool remove_sent_points)
2162: {
2163: PetscFunctionBegin;
2164: PetscCall(DMSwarmMigrate_Push_Basic(dm, remove_sent_points));
2165: PetscFunctionReturn(PETSC_SUCCESS);
2166: }
2168: /*@
2169: DMSwarmMigrate - Relocates points defined in the `DMSWARM` to other MPI-ranks
2171: Collective
2173: Input Parameters:
2174: + dm - the `DMSWARM`
2175: - remove_sent_points - flag indicating if sent points should be removed from the current MPI-rank
2177: Level: advanced
2179: Notes:
2180: The `DM` will be modified to accommodate received points.
2181: If `remove_sent_points` is `PETSC_TRUE`, any points that were sent will be removed from the `DM`.
2182: Different styles of migration are supported. See `DMSwarmSetMigrateType()`.
2184: .seealso: `DM`, `DMSWARM`, `DMSwarmSetMigrateType()`
2185: @*/
2186: PetscErrorCode DMSwarmMigrate(DM dm, PetscBool remove_sent_points)
2187: {
2188: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2190: PetscFunctionBegin;
2191: PetscCall(PetscLogEventBegin(DMSWARM_Migrate, 0, 0, 0, 0));
2192: switch (swarm->migrate_type) {
2193: case DMSWARM_MIGRATE_BASIC:
2194: PetscCall(DMSwarmMigrate_Basic(dm, remove_sent_points));
2195: break;
2196: case DMSWARM_MIGRATE_DMCELLNSCATTER:
2197: PetscCall(DMSwarmMigrate_CellDMScatter(dm, remove_sent_points));
2198: break;
2199: case DMSWARM_MIGRATE_DMCELLEXACT:
2200: SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "DMSWARM_MIGRATE_DMCELLEXACT not implemented");
2201: case DMSWARM_MIGRATE_USER:
2202: SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "DMSWARM_MIGRATE_USER not implemented");
2203: default:
2204: SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "DMSWARM_MIGRATE type unknown");
2205: }
2206: PetscCall(PetscLogEventEnd(DMSWARM_Migrate, 0, 0, 0, 0));
2207: PetscCall(DMClearGlobalVectors(dm));
2208: PetscFunctionReturn(PETSC_SUCCESS);
2209: }
2211: PetscErrorCode DMSwarmMigrate_GlobalToLocal_Basic(DM dm, PetscInt *globalsize);
2213: /*
2214: DMSwarmCollectViewCreate
2216: * Applies a collection method and gathers point neighbour points into dm
2218: Notes:
2219: Users should call DMSwarmCollectViewDestroy() after
2220: they have finished computations associated with the collected points
2221: */
2223: /*@
2224: DMSwarmCollectViewCreate - Applies a collection method and gathers points
2225: in neighbour ranks into the `DMSWARM`
2227: Collective
2229: Input Parameter:
2230: . dm - the `DMSWARM`
2232: Level: advanced
2234: Notes:
2235: Users should call `DMSwarmCollectViewDestroy()` after
2236: they have finished computations associated with the collected points
2238: Different collect methods are supported. See `DMSwarmSetCollectType()`.
2240: Developer Note:
2241: Create and Destroy routines create new objects that can get destroyed, they do not change the state
2242: of the current object.
2244: .seealso: `DM`, `DMSWARM`, `DMSwarmCollectViewDestroy()`, `DMSwarmSetCollectType()`
2245: @*/
2246: PetscErrorCode DMSwarmCollectViewCreate(DM dm)
2247: {
2248: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2249: PetscInt ng;
2251: PetscFunctionBegin;
2252: PetscCheck(!swarm->collect_view_active, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "CollectView currently active");
2253: PetscCall(DMSwarmGetLocalSize(dm, &ng));
2254: switch (swarm->collect_type) {
2255: case DMSWARM_COLLECT_BASIC:
2256: PetscCall(DMSwarmMigrate_GlobalToLocal_Basic(dm, &ng));
2257: break;
2258: case DMSWARM_COLLECT_DMDABOUNDINGBOX:
2259: SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "DMSWARM_COLLECT_DMDABOUNDINGBOX not implemented");
2260: case DMSWARM_COLLECT_GENERAL:
2261: SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "DMSWARM_COLLECT_GENERAL not implemented");
2262: default:
2263: SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_SUP, "DMSWARM_COLLECT type unknown");
2264: }
2265: swarm->collect_view_active = PETSC_TRUE;
2266: swarm->collect_view_reset_nlocal = ng;
2267: PetscFunctionReturn(PETSC_SUCCESS);
2268: }
2270: /*@
2271: DMSwarmCollectViewDestroy - Resets the `DMSWARM` to the size prior to calling `DMSwarmCollectViewCreate()`
2273: Collective
2275: Input Parameters:
2276: . dm - the `DMSWARM`
2278: Notes:
2279: Users should call `DMSwarmCollectViewCreate()` before this function is called.
2281: Level: advanced
2283: Developer Note:
2284: Create and Destroy routines create new objects that can get destroyed, they do not change the state
2285: of the current object.
2287: .seealso: `DM`, `DMSWARM`, `DMSwarmCollectViewCreate()`, `DMSwarmSetCollectType()`
2288: @*/
2289: PetscErrorCode DMSwarmCollectViewDestroy(DM dm)
2290: {
2291: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2293: PetscFunctionBegin;
2294: PetscCheck(swarm->collect_view_active, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "CollectView is currently not active");
2295: PetscCall(DMSwarmSetLocalSizes(dm, swarm->collect_view_reset_nlocal, -1));
2296: swarm->collect_view_active = PETSC_FALSE;
2297: PetscFunctionReturn(PETSC_SUCCESS);
2298: }
2300: static PetscErrorCode DMSwarmSetUpPIC(DM dm)
2301: {
2302: PetscInt dim;
2304: PetscFunctionBegin;
2305: PetscCall(DMSwarmSetNumSpecies(dm, 1));
2306: PetscCall(DMGetDimension(dm, &dim));
2307: PetscCheck(dim >= 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "Dimension must be 1,2,3 - found %" PetscInt_FMT, dim);
2308: PetscCheck(dim <= 3, PetscObjectComm((PetscObject)dm), PETSC_ERR_USER, "Dimension must be 1,2,3 - found %" PetscInt_FMT, dim);
2309: PetscFunctionReturn(PETSC_SUCCESS);
2310: }
2312: /*@
2313: DMSwarmSetPointCoordinatesRandom - Sets initial coordinates for particles in each cell
2315: Collective
2317: Input Parameters:
2318: + dm - the `DMSWARM`
2319: - Npc - The number of particles per cell in the cell `DM`
2321: Level: intermediate
2323: Notes:
2324: The user must use `DMSwarmSetCellDM()` to set the cell `DM` first. The particles are placed randomly inside each cell. If only
2325: one particle is in each cell, it is placed at the centroid.
2327: .seealso: `DM`, `DMSWARM`, `DMSwarmSetCellDM()`
2328: @*/
2329: PetscErrorCode DMSwarmSetPointCoordinatesRandom(DM dm, PetscInt Npc)
2330: {
2331: DM cdm;
2332: DMSwarmCellDM celldm;
2333: PetscRandom rnd;
2334: DMPolytopeType ct;
2335: PetscBool simplex;
2336: PetscReal *centroid, *coords, *xi0, *v0, *J, *invJ, detJ;
2337: PetscInt dim, d, cStart, cEnd, c, p, Nfc;
2338: const char **coordFields;
2340: PetscFunctionBeginUser;
2341: PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)dm), &rnd));
2342: PetscCall(PetscRandomSetInterval(rnd, -1.0, 1.0));
2343: PetscCall(PetscRandomSetType(rnd, PETSCRAND48));
2345: PetscCall(DMSwarmGetCellDMActive(dm, &celldm));
2346: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Nfc, &coordFields));
2347: PetscCheck(Nfc == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support a single coordinate field right now, not %" PetscInt_FMT, Nfc);
2348: PetscCall(DMSwarmGetCellDM(dm, &cdm));
2349: PetscCall(DMGetDimension(cdm, &dim));
2350: PetscCall(DMPlexGetHeightStratum(cdm, 0, &cStart, &cEnd));
2351: PetscCall(DMPlexGetCellType(cdm, cStart, &ct));
2352: simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct) + 1 ? PETSC_TRUE : PETSC_FALSE;
2354: PetscCall(PetscMalloc5(dim, ¢roid, dim, &xi0, dim, &v0, dim * dim, &J, dim * dim, &invJ));
2355: for (d = 0; d < dim; ++d) xi0[d] = -1.0;
2356: PetscCall(DMSwarmGetField(dm, coordFields[0], NULL, NULL, (void **)&coords));
2357: for (c = cStart; c < cEnd; ++c) {
2358: if (Npc == 1) {
2359: PetscCall(DMPlexComputeCellGeometryFVM(cdm, c, NULL, centroid, NULL));
2360: for (d = 0; d < dim; ++d) coords[c * dim + d] = centroid[d];
2361: } else {
2362: PetscCall(DMPlexComputeCellGeometryFEM(cdm, c, NULL, v0, J, invJ, &detJ)); /* affine */
2363: for (p = 0; p < Npc; ++p) {
2364: const PetscInt n = c * Npc + p;
2365: PetscReal sum = 0.0, refcoords[3];
2367: for (d = 0; d < dim; ++d) {
2368: PetscCall(PetscRandomGetValueReal(rnd, &refcoords[d]));
2369: sum += refcoords[d];
2370: }
2371: if (simplex && sum > 0.0)
2372: for (d = 0; d < dim; ++d) refcoords[d] -= PetscSqrtReal(dim) * sum;
2373: CoordinatesRefToReal(dim, dim, xi0, v0, J, refcoords, &coords[n * dim]);
2374: }
2375: }
2376: }
2377: PetscCall(DMSwarmRestoreField(dm, coordFields[0], NULL, NULL, (void **)&coords));
2378: PetscCall(PetscFree5(centroid, xi0, v0, J, invJ));
2379: PetscCall(PetscRandomDestroy(&rnd));
2380: PetscFunctionReturn(PETSC_SUCCESS);
2381: }
2383: /*@
2384: DMSwarmGetType - Get particular flavor of `DMSWARM`
2386: Collective
2388: Input Parameter:
2389: . sw - the `DMSWARM`
2391: Output Parameter:
2392: . stype - the `DMSWARM` type (e.g. `DMSWARM_PIC`)
2394: Level: advanced
2396: .seealso: `DM`, `DMSWARM`, `DMSwarmSetMigrateType()`, `DMSwarmSetCollectType()`, `DMSwarmType`, `DMSWARM_PIC`, `DMSWARM_BASIC`
2397: @*/
2398: PetscErrorCode DMSwarmGetType(DM sw, DMSwarmType *stype)
2399: {
2400: DM_Swarm *swarm = (DM_Swarm *)sw->data;
2402: PetscFunctionBegin;
2404: PetscAssertPointer(stype, 2);
2405: *stype = swarm->swarm_type;
2406: PetscFunctionReturn(PETSC_SUCCESS);
2407: }
2409: /*@
2410: DMSwarmSetType - Set particular flavor of `DMSWARM`
2412: Collective
2414: Input Parameters:
2415: + sw - the `DMSWARM`
2416: - stype - the `DMSWARM` type (e.g. `DMSWARM_PIC`)
2418: Level: advanced
2420: .seealso: `DM`, `DMSWARM`, `DMSwarmSetMigrateType()`, `DMSwarmSetCollectType()`, `DMSwarmType`, `DMSWARM_PIC`, `DMSWARM_BASIC`
2421: @*/
2422: PetscErrorCode DMSwarmSetType(DM sw, DMSwarmType stype)
2423: {
2424: DM_Swarm *swarm = (DM_Swarm *)sw->data;
2426: PetscFunctionBegin;
2428: swarm->swarm_type = stype;
2429: if (swarm->swarm_type == DMSWARM_PIC) PetscCall(DMSwarmSetUpPIC(sw));
2430: PetscFunctionReturn(PETSC_SUCCESS);
2431: }
2433: static PetscErrorCode DMSwarmCreateRemapDM_Private(DM sw, DM *rdm)
2434: {
2435: PetscFE fe;
2436: DMPolytopeType ct;
2437: PetscInt dim, cStart;
2438: const char *prefix = "remap_";
2440: PetscFunctionBegin;
2441: PetscCall(DMCreate(PetscObjectComm((PetscObject)sw), rdm));
2442: PetscCall(DMSetType(*rdm, DMPLEX));
2443: PetscCall(DMPlexSetOptionsPrefix(*rdm, prefix));
2444: PetscCall(DMSetFromOptions(*rdm));
2445: PetscCall(PetscObjectSetName((PetscObject)*rdm, "remap"));
2446: PetscCall(DMViewFromOptions(*rdm, NULL, "-dm_view"));
2448: PetscCall(DMGetDimension(*rdm, &dim));
2449: PetscCall(DMPlexGetHeightStratum(*rdm, 0, &cStart, NULL));
2450: PetscCall(DMPlexGetCellType(*rdm, cStart, &ct));
2451: PetscCall(PetscFECreateByCell(PETSC_COMM_SELF, dim, 1, ct, prefix, PETSC_DETERMINE, &fe));
2452: PetscCall(PetscObjectSetName((PetscObject)fe, "distribution"));
2453: PetscCall(DMSetField(*rdm, 0, NULL, (PetscObject)fe));
2454: PetscCall(DMCreateDS(*rdm));
2455: PetscCall(PetscFEDestroy(&fe));
2456: PetscFunctionReturn(PETSC_SUCCESS);
2457: }
2459: static PetscErrorCode DMSetup_Swarm(DM sw)
2460: {
2461: DM_Swarm *swarm = (DM_Swarm *)sw->data;
2463: PetscFunctionBegin;
2464: if (swarm->issetup) PetscFunctionReturn(PETSC_SUCCESS);
2465: swarm->issetup = PETSC_TRUE;
2467: if (swarm->remap_type != DMSWARM_REMAP_NONE) {
2468: DMSwarmCellDM celldm;
2470: PetscCall(DMSwarmGetCellDMByName(sw, "remap", &celldm));
2471: if (!celldm) {
2472: DM rdm;
2473: const char *fieldnames[2] = {DMSwarmPICField_coor, "velocity"};
2474: const char *vfieldnames[1] = {"w_q"};
2476: PetscCall(DMSwarmCreateRemapDM_Private(sw, &rdm));
2477: PetscCall(DMSwarmCellDMCreate(rdm, 1, vfieldnames, 2, fieldnames, &celldm));
2478: PetscCall(DMSwarmAddCellDM(sw, celldm));
2479: PetscCall(DMSwarmCellDMDestroy(&celldm));
2480: PetscCall(DMDestroy(&rdm));
2481: }
2482: }
2484: if (swarm->swarm_type == DMSWARM_PIC) {
2485: DMSwarmCellDM celldm;
2487: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
2488: PetscCheck(celldm, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "No active cell DM. DMSWARM_PIC requires you call DMSwarmSetCellDM() or DMSwarmAddCellDM()");
2489: if (celldm->dm->ops->locatepointssubdomain) {
2490: /* check methods exists for exact ownership identificiation */
2491: PetscCall(PetscInfo(sw, "DMSWARM_PIC: Using method CellDM->ops->LocatePointsSubdomain\n"));
2492: swarm->migrate_type = DMSWARM_MIGRATE_DMCELLEXACT;
2493: } else {
2494: /* check methods exist for point location AND rank neighbor identification */
2495: PetscCheck(celldm->dm->ops->locatepoints, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "DMSWARM_PIC requires the method CellDM->ops->locatepoints be defined");
2496: PetscCall(PetscInfo(sw, "DMSWARM_PIC: Using method CellDM->LocatePoints\n"));
2498: PetscCheck(celldm->dm->ops->getneighbors, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "DMSWARM_PIC requires the method CellDM->ops->getneighbors be defined");
2499: PetscCall(PetscInfo(sw, "DMSWARM_PIC: Using method CellDM->GetNeigbors\n"));
2501: swarm->migrate_type = DMSWARM_MIGRATE_DMCELLNSCATTER;
2502: }
2503: }
2505: PetscCall(DMSwarmFinalizeFieldRegister(sw));
2507: /* check some fields were registered */
2508: PetscCheck(swarm->db->nfields > 2, PetscObjectComm((PetscObject)sw), PETSC_ERR_USER, "At least one field user must be registered via DMSwarmRegisterXXX()");
2509: PetscFunctionReturn(PETSC_SUCCESS);
2510: }
2512: static PetscErrorCode DMDestroy_Swarm(DM dm)
2513: {
2514: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2516: PetscFunctionBegin;
2517: if (--swarm->refct > 0) PetscFunctionReturn(PETSC_SUCCESS);
2518: PetscCall(PetscObjectListDestroy(&swarm->cellDMs));
2519: PetscCall(PetscFree(swarm->activeCellDM));
2520: PetscCall(DMSwarmDataBucketDestroy(&swarm->db));
2521: PetscCall(PetscFree(swarm));
2522: PetscFunctionReturn(PETSC_SUCCESS);
2523: }
2525: static PetscErrorCode DMSwarmView_Draw(DM dm, PetscViewer viewer)
2526: {
2527: DM cdm;
2528: DMSwarmCellDM celldm;
2529: PetscDraw draw;
2530: PetscReal *coords, oldPause, radius = 0.01;
2531: PetscInt Np, p, bs, Nfc;
2532: const char **coordFields;
2534: PetscFunctionBegin;
2535: PetscCall(PetscOptionsGetReal(NULL, ((PetscObject)dm)->prefix, "-dm_view_swarm_radius", &radius, NULL));
2536: PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw));
2537: PetscCall(DMSwarmGetCellDM(dm, &cdm));
2538: PetscCall(PetscDrawGetPause(draw, &oldPause));
2539: PetscCall(PetscDrawSetPause(draw, 0.0));
2540: PetscCall(DMView(cdm, viewer));
2541: PetscCall(PetscDrawSetPause(draw, oldPause));
2543: PetscCall(DMSwarmGetCellDMActive(dm, &celldm));
2544: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Nfc, &coordFields));
2545: PetscCheck(Nfc == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support a single coordinate field right now, not %" PetscInt_FMT, Nfc);
2546: PetscCall(DMSwarmGetLocalSize(dm, &Np));
2547: PetscCall(DMSwarmGetField(dm, coordFields[0], &bs, NULL, (void **)&coords));
2548: for (p = 0; p < Np; ++p) {
2549: const PetscInt i = p * bs;
2551: PetscCall(PetscDrawEllipse(draw, coords[i], coords[i + 1], radius, radius, PETSC_DRAW_BLUE));
2552: }
2553: PetscCall(DMSwarmRestoreField(dm, coordFields[0], &bs, NULL, (void **)&coords));
2554: PetscCall(PetscDrawFlush(draw));
2555: PetscCall(PetscDrawPause(draw));
2556: PetscCall(PetscDrawSave(draw));
2557: PetscFunctionReturn(PETSC_SUCCESS);
2558: }
2560: static PetscErrorCode DMView_Swarm_Ascii(DM dm, PetscViewer viewer)
2561: {
2562: PetscViewerFormat format;
2563: PetscDataType wtype = PETSC_DATATYPE_UNKNOWN;
2564: PetscInt *sizes;
2565: PetscInt dim, Np, wbs = 0, maxSize = 17;
2566: MPI_Comm comm;
2567: PetscMPIInt rank, size;
2568: const char *name, *cellid;
2570: PetscFunctionBegin;
2571: PetscCall(PetscViewerGetFormat(viewer, &format));
2572: PetscCall(DMGetDimension(dm, &dim));
2573: PetscCall(DMSwarmGetLocalSize(dm, &Np));
2574: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2575: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2576: PetscCallMPI(MPI_Comm_size(comm, &size));
2577: PetscCall(PetscObjectGetName((PetscObject)dm, &name));
2578: if (name) PetscCall(PetscViewerASCIIPrintf(viewer, "%s in %" PetscInt_FMT " dimension%s:\n", name, dim, dim == 1 ? "" : "s"));
2579: else PetscCall(PetscViewerASCIIPrintf(viewer, "Swarm in %" PetscInt_FMT " dimension%s:\n", dim, dim == 1 ? "" : "s"));
2580: if (size < maxSize) PetscCall(PetscCalloc1(size, &sizes));
2581: else PetscCall(PetscCalloc1(3, &sizes));
2582: if (size < maxSize) {
2583: PetscCallMPI(MPI_Gather(&Np, 1, MPIU_INT, sizes, 1, MPIU_INT, 0, comm));
2584: PetscCall(PetscViewerASCIIPrintf(viewer, " Number of particles per rank:"));
2585: for (PetscInt p = 0; p < size; ++p) {
2586: if (rank == 0) PetscCall(PetscViewerASCIIPrintf(viewer, " %" PetscInt_FMT, sizes[p]));
2587: }
2588: } else {
2589: PetscInt locMinMax[2] = {Np, Np};
2591: PetscCall(PetscGlobalMinMaxInt(comm, locMinMax, sizes));
2592: PetscCall(PetscViewerASCIIPrintf(viewer, " Min/Max of particles per rank: %" PetscInt_FMT "/%" PetscInt_FMT, sizes[0], sizes[1]));
2593: }
2594: PetscCall(PetscViewerASCIIPrintf(viewer, "\n"));
2595: PetscCall(PetscFree(sizes));
2596: if (format == PETSC_VIEWER_ASCII_INFO) {
2597: DM_Swarm *sw = (DM_Swarm *)dm->data;
2598: DMSwarmCellDM celldm;
2599: PetscInt *cell;
2600: PetscBool hasWeight;
2601: const char *fname = "w_q";
2603: PetscCall(DMSwarmDataFieldStringInList(fname, sw->db->nfields, (const DMSwarmDataField *)sw->db->field, &hasWeight));
2604: if (hasWeight) {
2605: PetscCall(DMSwarmGetFieldInfo(dm, fname, &wbs, &wtype));
2606: PetscCheck(wtype == PETSC_REAL || wtype == PETSC_SCALAR, comm, PETSC_ERR_SUP, "Weight field %s must have type PETSC_REAL or PETSC_SCALAR, not %s", fname, PetscDataTypes[wtype]);
2607: PetscCheck(wbs == 1, comm, PETSC_ERR_ARG_WRONG, "Weight field %s must have block size 1, not %" PetscInt_FMT, fname, wbs);
2608: }
2609: PetscCall(PetscViewerASCIIPrintf(viewer, " Cells containing each particle:\n"));
2610: PetscCall(PetscViewerASCIIPushSynchronized(viewer));
2611: PetscCall(DMSwarmGetCellDMActive(dm, &celldm));
2612: PetscCall(DMSwarmCellDMGetCellID(celldm, &cellid));
2613: PetscCall(DMSwarmGetField(dm, cellid, NULL, NULL, (void **)&cell));
2614: if (hasWeight) {
2615: PetscReal **coords;
2616: void *weight;
2617: PetscInt Ncf, *bsC;
2618: const char **coordNames;
2620: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Ncf, &coordNames));
2621: PetscCall(PetscMalloc2(Ncf, &coords, Ncf, &bsC));
2622: for (PetscInt n = 0; n < Ncf; ++n) PetscCall(DMSwarmGetField(dm, coordNames[n], &bsC[n], NULL, (void **)&coords[n]));
2623: PetscCall(DMSwarmGetField(dm, fname, NULL, NULL, &weight));
2624: for (PetscInt p = 0; p < Np; ++p) {
2625: PetscReal wp;
2627: if (wtype == PETSC_REAL) wp = ((PetscReal *)weight)[p];
2628: else wp = PetscRealPart(((PetscScalar *)weight)[p]);
2629: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " p%" PetscInt_FMT ": %" PetscInt_FMT " wt: %g x: (", p, cell[p], (double)wp));
2630: for (PetscInt n = 0; n < Ncf; ++n) {
2631: if (n > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ", "));
2632: for (PetscInt d = 0; d < bsC[n]; ++d) {
2633: if (d > 0) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ", "));
2634: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%g", (double)coords[n][p * bsC[n] + d]));
2635: }
2636: }
2637: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ")\n"));
2638: }
2639: PetscCall(DMSwarmRestoreField(dm, fname, NULL, NULL, &weight));
2640: for (PetscInt n = 0; n < Ncf; ++n) PetscCall(DMSwarmRestoreField(dm, coordNames[n], &bsC[n], NULL, (void **)&coords[n]));
2641: PetscCall(PetscFree2(coords, bsC));
2642: } else {
2643: for (PetscInt p = 0; p < Np; ++p) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " p%" PetscInt_FMT ": %" PetscInt_FMT "\n", p, cell[p]));
2644: }
2645: PetscCall(DMSwarmRestoreField(dm, cellid, NULL, NULL, (void **)&cell));
2646: PetscCall(PetscViewerFlush(viewer));
2647: PetscCall(PetscViewerASCIIPopSynchronized(viewer));
2648: }
2649: PetscFunctionReturn(PETSC_SUCCESS);
2650: }
2652: static PetscErrorCode DMView_Swarm(DM dm, PetscViewer viewer)
2653: {
2654: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2655: PetscBool isascii, ibinary, isvtk, isdraw, ispython;
2656: #if PetscDefined(HAVE_HDF5)
2657: PetscBool ishdf5;
2658: #endif
2660: PetscFunctionBegin;
2663: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &isascii));
2664: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &ibinary));
2665: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk));
2666: #if PetscDefined(HAVE_HDF5)
2667: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
2668: #endif
2669: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw));
2670: PetscCall(PetscObjectHasFunction((PetscObject)viewer, "PetscViewerPythonViewObject_C", &ispython));
2671: if (isascii) {
2672: PetscViewerFormat format;
2674: PetscCall(PetscViewerGetFormat(viewer, &format));
2675: switch (format) {
2676: case PETSC_VIEWER_ASCII_INFO_DETAIL:
2677: PetscCall(DMSwarmDataBucketView(PetscObjectComm((PetscObject)dm), swarm->db, NULL, DATABUCKET_VIEW_STDOUT));
2678: break;
2679: default:
2680: PetscCall(DMView_Swarm_Ascii(dm, viewer));
2681: }
2682: } else {
2683: #if PetscDefined(HAVE_HDF5)
2684: if (ishdf5) PetscCall(DMSwarmView_HDF5(dm, viewer));
2685: #endif
2686: if (isdraw) PetscCall(DMSwarmView_Draw(dm, viewer));
2687: if (ispython) PetscCall(PetscViewerPythonViewObject(viewer, (PetscObject)dm));
2688: }
2689: PetscFunctionReturn(PETSC_SUCCESS);
2690: }
2692: /*@
2693: DMSwarmGetCellSwarm - Extracts a single cell from the `DMSWARM` object, returns it as a single cell `DMSWARM`.
2694: 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.
2696: Noncollective
2698: Input Parameters:
2699: + sw - the `DMSWARM`
2700: . cellID - the integer id of the cell to be extracted and filtered
2701: - cellswarm - The `DMSWARM` to receive the cell
2703: Level: beginner
2705: Notes:
2706: This presently only supports `DMSWARM_PIC` type
2708: Should be restored with `DMSwarmRestoreCellSwarm()`
2710: Changes to this cell of the swarm will be lost if they are made prior to restoring this cell.
2712: .seealso: `DM`, `DMSWARM`, `DMSwarmRestoreCellSwarm()`
2713: @*/
2714: PetscErrorCode DMSwarmGetCellSwarm(DM sw, PetscInt cellID, DM cellswarm)
2715: {
2716: DM_Swarm *original = (DM_Swarm *)sw->data;
2717: DMLabel label;
2718: DM dmc, subdmc;
2719: PetscInt *pids, particles, dim;
2720: const char *name;
2722: PetscFunctionBegin;
2723: /* Configure new swarm */
2724: PetscCall(DMSetType(cellswarm, DMSWARM));
2725: PetscCall(DMGetDimension(sw, &dim));
2726: PetscCall(DMSetDimension(cellswarm, dim));
2727: PetscCall(DMSwarmSetType(cellswarm, DMSWARM_PIC));
2728: /* Destroy the unused, unconfigured data bucket to prevent stragglers in memory */
2729: PetscCall(DMSwarmDataBucketDestroy(&((DM_Swarm *)cellswarm->data)->db));
2730: PetscCall(DMSwarmSortGetAccess(sw));
2731: PetscCall(DMSwarmSortGetNumberOfPointsPerCell(sw, cellID, &particles));
2732: PetscCall(DMSwarmSortGetPointsPerCell(sw, cellID, &particles, &pids));
2733: PetscCall(DMSwarmDataBucketCreateFromSubset(original->db, particles, pids, &((DM_Swarm *)cellswarm->data)->db));
2734: PetscCall(DMSwarmSortRestoreAccess(sw));
2735: PetscCall(DMSwarmSortRestorePointsPerCell(sw, cellID, &particles, &pids));
2736: PetscCall(DMSwarmGetCellDM(sw, &dmc));
2737: PetscCall(DMLabelCreate(PetscObjectComm((PetscObject)sw), "singlecell", &label));
2738: PetscCall(DMAddLabel(dmc, label));
2739: PetscCall(DMLabelSetValue(label, cellID, 1));
2740: PetscCall(DMPlexFilter(dmc, label, 1, PETSC_FALSE, PETSC_FALSE, PetscObjectComm((PetscObject)dmc), NULL, &subdmc));
2741: PetscCall(PetscObjectGetName((PetscObject)dmc, &name));
2742: PetscCall(PetscObjectSetName((PetscObject)subdmc, name));
2743: PetscCall(DMSwarmSetCellDM(cellswarm, subdmc));
2744: PetscCall(DMLabelDestroy(&label));
2745: PetscFunctionReturn(PETSC_SUCCESS);
2746: }
2748: /*@
2749: DMSwarmRestoreCellSwarm - Restores a `DMSWARM` object obtained with `DMSwarmGetCellSwarm()`. All fields are copied back into the parent swarm.
2751: Noncollective
2753: Input Parameters:
2754: + sw - the parent `DMSWARM`
2755: . cellID - the integer id of the cell to be copied back into the parent swarm
2756: - cellswarm - the cell swarm object
2758: Level: beginner
2760: Note:
2761: This only supports `DMSWARM_PIC` types of `DMSWARM`s
2763: .seealso: `DM`, `DMSWARM`, `DMSwarmGetCellSwarm()`
2764: @*/
2765: PetscErrorCode DMSwarmRestoreCellSwarm(DM sw, PetscInt cellID, DM cellswarm)
2766: {
2767: DM dmc;
2768: PetscInt *pids, particles, p;
2770: PetscFunctionBegin;
2771: PetscCall(DMSwarmSortGetAccess(sw));
2772: PetscCall(DMSwarmSortGetPointsPerCell(sw, cellID, &particles, &pids));
2773: PetscCall(DMSwarmSortRestoreAccess(sw));
2774: /* Pointwise copy of each particle based on pid. The parent swarm may not be altered during this process. */
2775: for (p = 0; p < particles; ++p) PetscCall(DMSwarmDataBucketCopyPoint(((DM_Swarm *)cellswarm->data)->db, pids[p], ((DM_Swarm *)sw->data)->db, pids[p]));
2776: /* Free memory, destroy cell dm */
2777: PetscCall(DMSwarmGetCellDM(cellswarm, &dmc));
2778: PetscCall(DMDestroy(&dmc));
2779: PetscCall(DMSwarmSortRestorePointsPerCell(sw, cellID, &particles, &pids));
2780: PetscFunctionReturn(PETSC_SUCCESS);
2781: }
2783: /*@
2784: DMSwarmComputeMoments - Compute the first three particle moments for a given field
2786: Noncollective
2788: Input Parameters:
2789: + sw - the `DMSWARM`
2790: . coordinate - the coordinate field name
2791: - weight - the weight field name
2793: Output Parameter:
2794: . moments - the field moments
2796: Level: intermediate
2798: Notes:
2799: The `moments` array should be of length bs + 2, where bs is the block size of the coordinate field.
2801: The weight field must have blocksize 1 and data type `PETSC_REAL` or `PETSC_SCALAR`. For complex scalars,
2802: only the real part of each weight is used.
2804: .seealso: `DM`, `DMSWARM`, `DMPlexComputeMoments()`
2805: @*/
2806: PetscErrorCode DMSwarmComputeMoments(DM sw, const char coordinate[], const char weight[], PetscReal moments[])
2807: {
2808: const PetscReal *coords;
2809: void *weights;
2810: PetscDataType dtc, dtw;
2811: PetscInt bsc, bsw, Np;
2812: MPI_Comm comm;
2814: PetscFunctionBegin;
2816: PetscAssertPointer(coordinate, 2);
2817: PetscAssertPointer(weight, 3);
2818: PetscAssertPointer(moments, 4);
2819: PetscCall(PetscObjectGetComm((PetscObject)sw, &comm));
2820: PetscCall(DMSwarmGetFieldInfo(sw, coordinate, &bsc, &dtc));
2821: PetscCall(DMSwarmGetFieldInfo(sw, weight, &bsw, &dtw));
2822: PetscCheck(dtc == PETSC_REAL, comm, PETSC_ERR_ARG_WRONG, "Coordinate field %s must be real, not %s", coordinate, PetscDataTypes[dtc]);
2823: PetscCheck(dtw == PETSC_REAL || dtw == PETSC_SCALAR, comm, PETSC_ERR_ARG_WRONG, "Weight field %s must have type PETSC_REAL or PETSC_SCALAR, not %s", weight, PetscDataTypes[dtw]);
2824: PetscCheck(bsw == 1, comm, PETSC_ERR_ARG_WRONG, "Weight field %s must be a scalar, not blocksize %" PetscInt_FMT, weight, bsw);
2825: PetscCall(DMSwarmGetField(sw, coordinate, NULL, NULL, (void **)&coords));
2826: PetscCall(DMSwarmGetField(sw, weight, NULL, NULL, &weights));
2827: PetscCall(DMSwarmGetLocalSize(sw, &Np));
2828: PetscCall(PetscArrayzero(moments, bsc + 2));
2829: for (PetscInt p = 0; p < Np; ++p) {
2830: const PetscReal *c = &coords[p * bsc];
2831: PetscReal wp;
2833: if (dtw == PETSC_REAL) wp = ((PetscReal *)weights)[p];
2834: else wp = PetscRealPart(((PetscScalar *)weights)[p]);
2835: moments[0] += wp;
2836: for (PetscInt d = 0; d < bsc; ++d) {
2837: moments[d + 1] += wp * c[d];
2838: moments[bsc + 1] += wp * PetscSqr(c[d]);
2839: }
2840: }
2841: PetscCall(DMSwarmRestoreField(sw, coordinate, NULL, NULL, (void **)&coords));
2842: PetscCall(DMSwarmRestoreField(sw, weight, NULL, NULL, &weights));
2843: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, moments, bsc + 2, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)sw)));
2844: PetscFunctionReturn(PETSC_SUCCESS);
2845: }
2847: static PetscErrorCode DMSetFromOptions_Swarm(DM dm, PetscOptionItems PetscOptionsObject)
2848: {
2849: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2851: PetscFunctionBegin;
2852: PetscOptionsHeadBegin(PetscOptionsObject, "DMSwarm Options");
2853: PetscCall(PetscOptionsEnum("-dm_swarm_remap_type", "Remap algorithm", "DMSwarmSetRemapType", DMSwarmRemapTypeNames, (PetscEnum)swarm->remap_type, (PetscEnum *)&swarm->remap_type, NULL));
2854: PetscOptionsHeadEnd();
2855: PetscFunctionReturn(PETSC_SUCCESS);
2856: }
2858: PETSC_INTERN PetscErrorCode DMClone_Swarm(DM, DM *);
2860: static PetscErrorCode DMInitialize_Swarm(DM sw)
2861: {
2862: PetscFunctionBegin;
2863: sw->ops->view = DMView_Swarm;
2864: sw->ops->load = NULL;
2865: sw->ops->setfromoptions = DMSetFromOptions_Swarm;
2866: sw->ops->clone = DMClone_Swarm;
2867: sw->ops->setup = DMSetup_Swarm;
2868: sw->ops->createlocalsection = NULL;
2869: sw->ops->createsectionpermutation = NULL;
2870: sw->ops->createdefaultconstraints = NULL;
2871: sw->ops->createglobalvector = DMCreateGlobalVector_Swarm;
2872: sw->ops->createlocalvector = DMCreateLocalVector_Swarm;
2873: sw->ops->getlocaltoglobalmapping = NULL;
2874: sw->ops->createfieldis = NULL;
2875: sw->ops->createcoordinatedm = NULL;
2876: sw->ops->createcellcoordinatedm = NULL;
2877: sw->ops->getcoloring = NULL;
2878: sw->ops->creatematrix = DMCreateMatrix_Swarm;
2879: sw->ops->createinterpolation = NULL;
2880: sw->ops->createinjection = NULL;
2881: sw->ops->createmassmatrix = DMCreateMassMatrix_Swarm;
2882: sw->ops->creategradientmatrix = DMCreateGradientMatrix_Swarm;
2883: sw->ops->refine = NULL;
2884: sw->ops->coarsen = NULL;
2885: sw->ops->refinehierarchy = NULL;
2886: sw->ops->coarsenhierarchy = NULL;
2887: sw->ops->globaltolocalbegin = DMGlobalToLocalBegin_Swarm;
2888: sw->ops->globaltolocalend = DMGlobalToLocalEnd_Swarm;
2889: sw->ops->localtoglobalbegin = DMLocalToGlobalBegin_Swarm;
2890: sw->ops->localtoglobalend = DMLocalToGlobalEnd_Swarm;
2891: sw->ops->destroy = DMDestroy_Swarm;
2892: sw->ops->createsubdm = NULL;
2893: sw->ops->getdimpoints = NULL;
2894: sw->ops->locatepoints = NULL;
2895: sw->ops->projectfieldlocal = DMProjectFieldLocal_Swarm;
2896: PetscFunctionReturn(PETSC_SUCCESS);
2897: }
2899: PETSC_INTERN PetscErrorCode DMClone_Swarm(DM dm, DM *newdm)
2900: {
2901: DM_Swarm *swarm = (DM_Swarm *)dm->data;
2903: PetscFunctionBegin;
2904: swarm->refct++;
2905: (*newdm)->data = swarm;
2906: PetscCall(PetscObjectChangeTypeName((PetscObject)*newdm, DMSWARM));
2907: PetscCall(DMInitialize_Swarm(*newdm));
2908: (*newdm)->dim = dm->dim;
2909: PetscFunctionReturn(PETSC_SUCCESS);
2910: }
2912: /*MC
2913: DMSWARM = "swarm" - A `DM` object for particle methods, such as particle-in-cell (PIC), in which the underlying
2914: data is both (i) dynamic in length, (ii) and of arbitrary data type.
2916: Level: intermediate
2918: Notes:
2919: User data can be represented by `DMSWARM` through a registering "fields" which are to be stored on particles.
2920: To register a field, the user must provide;
2921: (a) a unique name;
2922: (b) the data type (or size in bytes);
2923: (c) the block size of the data.
2925: For example, suppose the application requires a unique id, energy, momentum and density to be stored
2926: on a set of particles. Then the following code could be used
2927: .vb
2928: DMSwarmInitializeFieldRegister(dm)
2929: DMSwarmRegisterPetscDatatypeField(dm,"uid",1,PETSC_LONG);
2930: DMSwarmRegisterPetscDatatypeField(dm,"energy",1,PETSC_REAL);
2931: DMSwarmRegisterPetscDatatypeField(dm,"momentum",3,PETSC_REAL);
2932: DMSwarmRegisterPetscDatatypeField(dm,"density",1,PETSC_FLOAT);
2933: DMSwarmFinalizeFieldRegister(dm)
2934: .ve
2936: The fields represented by `DMSWARM` are dynamic and can be re-sized at any time.
2937: The only restriction imposed by `DMSWARM` is that all fields contain the same number of particles.
2939: To support particle methods, "migration" techniques are provided. These methods migrate data
2940: between ranks.
2942: `DMSWARM` supports the methods `DMCreateGlobalVector()` and `DMCreateLocalVector()`.
2943: As a `DMSWARM` may internally define and store values of different data types,
2944: before calling `DMCreateGlobalVector()` or `DMCreateLocalVector()`, the user must inform `DMSWARM` which
2945: fields should be used to define a `Vec` object via `DMSwarmVectorDefineField()`
2946: The specified field can be changed at any time - thereby permitting vectors
2947: compatible with different fields to be created.
2949: A dual representation of fields in the `DMSWARM` and a Vec object is permitted via `DMSwarmCreateGlobalVectorFromField()`
2950: Here the data defining the field in the `DMSWARM` is shared with a `Vec`.
2951: This is inherently unsafe if you alter the size of the field at any time between
2952: calls to `DMSwarmCreateGlobalVectorFromField()` and `DMSwarmDestroyGlobalVectorFromField()`.
2953: If the local size of the `DMSWARM` does not match the local size of the global vector
2954: when `DMSwarmDestroyGlobalVectorFromField()` is called, an error is thrown.
2956: Additional high-level support is provided for Particle-In-Cell methods. Refer to `DMSwarmSetType()`.
2958: .seealso: `DM`, `DMSWARM`, `DMType`, `DMCreate()`, `DMSetType()`, `DMSwarmSetType()`, `DMSwarmType`, `DMSwarmCreateGlobalVectorFromField()`,
2959: `DMCreateGlobalVector()`, `DMCreateLocalVector()`
2960: M*/
2962: PETSC_EXTERN PetscErrorCode DMCreate_Swarm(DM dm)
2963: {
2964: DM_Swarm *swarm;
2966: PetscFunctionBegin;
2968: PetscCall(PetscNew(&swarm));
2969: dm->data = swarm;
2970: PetscCall(DMSwarmDataBucketCreate(&swarm->db));
2971: PetscCall(DMSwarmInitializeFieldRegister(dm));
2972: dm->dim = 0;
2973: swarm->refct = 1;
2974: swarm->issetup = PETSC_FALSE;
2975: swarm->swarm_type = DMSWARM_BASIC;
2976: swarm->migrate_type = DMSWARM_MIGRATE_BASIC;
2977: swarm->collect_type = DMSWARM_COLLECT_BASIC;
2978: swarm->migrate_error_on_missing_point = PETSC_FALSE;
2979: swarm->collect_view_active = PETSC_FALSE;
2980: swarm->collect_view_reset_nlocal = -1;
2981: PetscCall(DMInitialize_Swarm(dm));
2982: if (SwarmDataFieldId == -1) PetscCall(PetscObjectComposedDataRegister(&SwarmDataFieldId));
2983: PetscFunctionReturn(PETSC_SUCCESS);
2984: }
2986: /* Replace dm with the contents of ndm, and then destroy ndm
2987: - Share the DM_Swarm structure
2988: */
2989: /*@
2990: DMSwarmReplace - Replace the internal state of a `DMSWARM` with that of another `DMSWARM`, sharing the underlying particle data and destroying the source `DM`.
2992: Collective
2994: Input Parameters:
2995: + dm - the destination `DMSWARM`, whose current contents are discarded
2996: - ndm - pointer to the source `DMSWARM`; destroyed and set to `NULL` on return
2998: Level: developer
3000: Note:
3001: The dimension, periodicity, name, and shared reference to the underlying particle bucket are transferred from the source to the destination.
3003: .seealso: `DM`, `DMSWARM`, `DMSwarmDuplicate()`, `DMDestroy()`
3004: @*/
3005: PetscErrorCode DMSwarmReplace(DM dm, DM *ndm)
3006: {
3007: DM dmNew = *ndm;
3008: const PetscReal *maxCell, *Lstart, *L;
3009: PetscInt dim;
3011: PetscFunctionBegin;
3012: if (dm == dmNew) {
3013: PetscCall(DMDestroy(ndm));
3014: PetscFunctionReturn(PETSC_SUCCESS);
3015: }
3016: dm->setupcalled = dmNew->setupcalled;
3017: if (!dm->hdr.name) {
3018: const char *name;
3020: PetscCall(PetscObjectGetName((PetscObject)*ndm, &name));
3021: PetscCall(PetscObjectSetName((PetscObject)dm, name));
3022: }
3023: PetscCall(DMGetDimension(dmNew, &dim));
3024: PetscCall(DMSetDimension(dm, dim));
3025: PetscCall(DMGetPeriodicity(dmNew, &maxCell, &Lstart, &L));
3026: PetscCall(DMSetPeriodicity(dm, maxCell, Lstart, L));
3027: PetscCall(DMDestroy_Swarm(dm));
3028: PetscCall(DMInitialize_Swarm(dm));
3029: dm->data = dmNew->data;
3030: ((DM_Swarm *)dmNew->data)->refct++;
3031: PetscCall(DMDestroy(ndm));
3032: PetscFunctionReturn(PETSC_SUCCESS);
3033: }
3035: /*@
3036: DMSwarmDuplicate - Creates a new `DMSWARM` with the same fields and cell `DM`s but no particles
3038: Collective
3040: Input Parameter:
3041: . sw - the `DMSWARM`
3043: Output Parameter:
3044: . nsw - the new `DMSWARM`
3046: Level: beginner
3048: .seealso: `DM`, `DMSWARM`, `DMSwarmCreate()`, `DMClone()`
3049: @*/
3050: PetscErrorCode DMSwarmDuplicate(DM sw, DM *nsw)
3051: {
3052: DM_Swarm *swarm = (DM_Swarm *)sw->data;
3053: DMSwarmDataField *fields;
3054: DMSwarmCellDM celldm, ncelldm;
3055: DMSwarmType stype;
3056: const char *name, **celldmnames;
3057: void *ctx;
3058: PetscInt dim, Nf, Ndm;
3059: PetscBool flg;
3061: PetscFunctionBegin;
3062: PetscCall(DMCreate(PetscObjectComm((PetscObject)sw), nsw));
3063: PetscCall(DMSetType(*nsw, DMSWARM));
3064: PetscCall(PetscObjectGetName((PetscObject)sw, &name));
3065: PetscCall(PetscObjectSetName((PetscObject)*nsw, name));
3066: PetscCall(DMGetDimension(sw, &dim));
3067: PetscCall(DMSetDimension(*nsw, dim));
3068: PetscCall(DMSwarmGetType(sw, &stype));
3069: PetscCall(DMSwarmSetType(*nsw, stype));
3070: PetscCall(DMGetApplicationContext(sw, &ctx));
3071: PetscCall(DMSetApplicationContext(*nsw, ctx));
3073: PetscCall(DMSwarmDataBucketGetDMSwarmDataFields(swarm->db, &Nf, &fields));
3074: for (PetscInt f = 0; f < Nf; ++f) {
3075: PetscCall(DMSwarmDataFieldStringInList(fields[f]->name, ((DM_Swarm *)(*nsw)->data)->db->nfields, (const DMSwarmDataField *)((DM_Swarm *)(*nsw)->data)->db->field, &flg));
3076: if (!flg) PetscCall(DMSwarmRegisterPetscDatatypeField(*nsw, fields[f]->name, fields[f]->bs, fields[f]->petsc_type));
3077: }
3079: PetscCall(DMSwarmGetCellDMNames(sw, &Ndm, &celldmnames));
3080: for (PetscInt c = 0; c < Ndm; ++c) {
3081: DM dm;
3082: PetscInt Ncf;
3083: const char **coordfields, **fields;
3085: PetscCall(DMSwarmGetCellDMByName(sw, celldmnames[c], &celldm));
3086: PetscCall(DMSwarmCellDMGetDM(celldm, &dm));
3087: PetscCall(DMSwarmCellDMGetCoordinateFields(celldm, &Ncf, &coordfields));
3088: PetscCall(DMSwarmCellDMGetFields(celldm, &Nf, &fields));
3089: PetscCall(DMSwarmCellDMCreate(dm, Nf, fields, Ncf, coordfields, &ncelldm));
3090: PetscCall(DMSwarmAddCellDM(*nsw, ncelldm));
3091: PetscCall(DMSwarmCellDMDestroy(&ncelldm));
3092: }
3093: PetscCall(PetscFree(celldmnames));
3095: PetscCall(DMSetFromOptions(*nsw));
3096: PetscCall(DMSetUp(*nsw));
3097: PetscCall(DMSwarmGetCellDMActive(sw, &celldm));
3098: PetscCall(PetscObjectGetName((PetscObject)celldm, &name));
3099: PetscCall(DMSwarmSetCellDMActive(*nsw, name));
3100: PetscFunctionReturn(PETSC_SUCCESS);
3101: }
3103: PetscErrorCode DMLocalToGlobalBegin_Swarm(DM dm, Vec l, InsertMode mode, Vec g)
3104: {
3105: PetscFunctionBegin;
3106: PetscFunctionReturn(PETSC_SUCCESS);
3107: }
3109: PetscErrorCode DMLocalToGlobalEnd_Swarm(DM dm, Vec l, InsertMode mode, Vec g)
3110: {
3111: PetscFunctionBegin;
3112: switch (mode) {
3113: case INSERT_VALUES:
3114: PetscCall(VecCopy(l, g));
3115: break;
3116: case ADD_VALUES:
3117: PetscCall(VecAXPY(g, 1., l));
3118: break;
3119: default:
3120: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Mode not supported: %d", mode);
3121: }
3122: PetscFunctionReturn(PETSC_SUCCESS);
3123: }
3125: PetscErrorCode DMGlobalToLocalBegin_Swarm(DM dm, Vec g, InsertMode mode, Vec l)
3126: {
3127: PetscFunctionBegin;
3128: PetscFunctionReturn(PETSC_SUCCESS);
3129: }
3131: PetscErrorCode DMGlobalToLocalEnd_Swarm(DM dm, Vec g, InsertMode mode, Vec l)
3132: {
3133: PetscFunctionBegin;
3134: PetscCall(DMLocalToGlobalEnd_Swarm(dm, g, mode, l));
3135: PetscFunctionReturn(PETSC_SUCCESS);
3136: }