Actual source code: swarmpic.c
1: #define PETSCDM_DLL
2: #include <petsc/private/dmswarmimpl.h>
3: #include <petscsf.h>
4: #include <petscdmda.h>
5: #include <petscdmplex.h>
6: #include <petscdt.h>
7: #include "../src/dm/impls/swarm/data_bucket.h"
9: #include <petsc/private/petscfeimpl.h>
11: /* Coordinate insertition/addition API */
12: /*@C
13: DMSwarmSetPointsUniformCoordinates - Set point coordinates in a `DMSWARM` on a regular (ijk) grid
15: Collective
17: Input Parameters:
18: + dm - the `DMSWARM`
19: . min - minimum coordinate values in the x, y, z directions (array of length dim)
20: . max - maximum coordinate values in the x, y, z directions (array of length dim)
21: . npoints - number of points in each spatial direction (array of length dim)
22: - mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`)
24: Level: beginner
26: Notes:
27: When using mode = `INSERT_VALUES`, this method will reset the number of particles in the `DMSWARM`
28: to be `npoints[0]` x `npoints[1]` (2D) or `npoints[0]` x `npoints[1]` x `npoints[2]` (3D). When using mode = `ADD_VALUES`,
29: new points will be appended to any already existing in the `DMSWARM`
31: .seealso: `DM`, `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
32: @*/
33: PETSC_EXTERN PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm, PetscReal min[], PetscReal max[], PetscInt npoints[], InsertMode mode)
34: {
35: PetscReal lmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
36: PetscReal lmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
37: PetscInt i, j, k, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
38: const PetscScalar *_coor;
39: DM celldm;
40: PetscReal dx[3];
41: PetscInt _npoints[] = {0, 0, 1};
42: Vec pos;
43: PetscScalar *_pos;
44: PetscReal *swarm_coor;
45: PetscInt *swarm_cellid;
46: PetscSF sfcell = NULL;
47: const PetscSFNode *LA_sfcell;
49: PetscFunctionBegin;
50: DMSWARMPICVALID(dm);
51: PetscCall(DMSwarmGetCellDM(dm, &celldm));
52: PetscCall(DMGetLocalBoundingBox(celldm, lmin, lmax));
53: PetscCall(DMGetCoordinateDim(celldm, &bs));
55: for (b = 0; b < bs; b++) {
56: if (npoints[b] > 1) {
57: dx[b] = (max[b] - min[b]) / ((PetscReal)(npoints[b] - 1));
58: } else {
59: dx[b] = 0.0;
60: }
61: _npoints[b] = npoints[b];
62: }
64: /* determine number of points living in the bounding box */
65: n_estimate = 0;
66: for (k = 0; k < _npoints[2]; k++) {
67: for (j = 0; j < _npoints[1]; j++) {
68: for (i = 0; i < _npoints[0]; i++) {
69: PetscReal xp[] = {0.0, 0.0, 0.0};
70: PetscInt ijk[3];
71: PetscBool point_inside = PETSC_TRUE;
73: ijk[0] = i;
74: ijk[1] = j;
75: ijk[2] = k;
76: for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b];
77: for (b = 0; b < bs; b++) {
78: if (xp[b] < lmin[b]) point_inside = PETSC_FALSE;
79: if (xp[b] > lmax[b]) point_inside = PETSC_FALSE;
80: }
81: if (point_inside) n_estimate++;
82: }
83: }
84: }
86: /* create candidate list */
87: PetscCall(VecCreate(PETSC_COMM_SELF, &pos));
88: PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE));
89: PetscCall(VecSetBlockSize(pos, bs));
90: PetscCall(VecSetFromOptions(pos));
91: PetscCall(VecGetArray(pos, &_pos));
93: n_estimate = 0;
94: for (k = 0; k < _npoints[2]; k++) {
95: for (j = 0; j < _npoints[1]; j++) {
96: for (i = 0; i < _npoints[0]; i++) {
97: PetscReal xp[] = {0.0, 0.0, 0.0};
98: PetscInt ijk[3];
99: PetscBool point_inside = PETSC_TRUE;
101: ijk[0] = i;
102: ijk[1] = j;
103: ijk[2] = k;
104: for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b];
105: for (b = 0; b < bs; b++) {
106: if (xp[b] < lmin[b]) point_inside = PETSC_FALSE;
107: if (xp[b] > lmax[b]) point_inside = PETSC_FALSE;
108: }
109: if (point_inside) {
110: for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = xp[b];
111: n_estimate++;
112: }
113: }
114: }
115: }
116: PetscCall(VecRestoreArray(pos, &_pos));
118: /* locate points */
119: PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell));
120: PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell));
121: n_found = 0;
122: for (p = 0; p < n_estimate; p++) {
123: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++;
124: }
126: /* adjust size */
127: if (mode == ADD_VALUES) {
128: PetscCall(DMSwarmGetLocalSize(dm, &n_curr));
129: n_new_est = n_curr + n_found;
130: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
131: }
132: if (mode == INSERT_VALUES) {
133: n_curr = 0;
134: n_new_est = n_found;
135: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
136: }
138: /* initialize new coords, cell owners, pid */
139: PetscCall(VecGetArrayRead(pos, &_coor));
140: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
141: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
142: n_found = 0;
143: for (p = 0; p < n_estimate; p++) {
144: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
145: for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]);
146: swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
147: n_found++;
148: }
149: }
150: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
151: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
152: PetscCall(VecRestoreArrayRead(pos, &_coor));
154: PetscCall(PetscSFDestroy(&sfcell));
155: PetscCall(VecDestroy(&pos));
156: PetscFunctionReturn(PETSC_SUCCESS);
157: }
159: /*@C
160: DMSwarmSetPointCoordinates - Set point coordinates in a `DMSWARM` from a user defined list
162: Collective
164: Input Parameters:
165: + dm - the `DMSWARM`
166: . npoints - the number of points to insert
167: . coor - the coordinate values
168: . redundant - if set to `PETSC_TRUE`, it is assumed that `npoints` and `coor` are only valid on rank 0 and should be broadcast to other ranks
169: - mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`)
171: Level: beginner
173: Notes:
174: If the user has specified `redundant` as `PETSC_FALSE`, the cell `DM` will attempt to locate the coordinates provided by `coor` within
175: its sub-domain. If they any values within `coor` are not located in the sub-domain, they will be ignored and will not get
176: added to the `DMSWARM`.
178: .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`, `DMSwarmSetPointsUniformCoordinates()`
179: @*/
180: PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinates(DM dm, PetscInt npoints, PetscReal coor[], PetscBool redundant, InsertMode mode)
181: {
182: PetscReal gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
183: PetscReal gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
184: PetscInt i, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
185: Vec coorlocal;
186: const PetscScalar *_coor;
187: DM celldm;
188: Vec pos;
189: PetscScalar *_pos;
190: PetscReal *swarm_coor;
191: PetscInt *swarm_cellid;
192: PetscSF sfcell = NULL;
193: const PetscSFNode *LA_sfcell;
194: PetscReal *my_coor;
195: PetscInt my_npoints;
196: PetscMPIInt rank;
197: MPI_Comm comm;
199: PetscFunctionBegin;
200: DMSWARMPICVALID(dm);
201: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
202: PetscCallMPI(MPI_Comm_rank(comm, &rank));
204: PetscCall(DMSwarmGetCellDM(dm, &celldm));
205: PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal));
206: PetscCall(VecGetSize(coorlocal, &N));
207: PetscCall(VecGetBlockSize(coorlocal, &bs));
208: N = N / bs;
209: PetscCall(VecGetArrayRead(coorlocal, &_coor));
210: for (i = 0; i < N; i++) {
211: for (b = 0; b < bs; b++) {
212: gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b]));
213: gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b]));
214: }
215: }
216: PetscCall(VecRestoreArrayRead(coorlocal, &_coor));
218: /* broadcast points from rank 0 if requested */
219: if (redundant) {
220: my_npoints = npoints;
221: PetscCallMPI(MPI_Bcast(&my_npoints, 1, MPIU_INT, 0, comm));
223: if (rank > 0) { /* allocate space */
224: PetscCall(PetscMalloc1(bs * my_npoints, &my_coor));
225: } else {
226: my_coor = coor;
227: }
228: PetscCallMPI(MPI_Bcast(my_coor, bs * my_npoints, MPIU_REAL, 0, comm));
229: } else {
230: my_npoints = npoints;
231: my_coor = coor;
232: }
234: /* determine the number of points living in the bounding box */
235: n_estimate = 0;
236: for (i = 0; i < my_npoints; i++) {
237: PetscBool point_inside = PETSC_TRUE;
239: for (b = 0; b < bs; b++) {
240: if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE;
241: if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE;
242: }
243: if (point_inside) n_estimate++;
244: }
246: /* create candidate list */
247: PetscCall(VecCreate(PETSC_COMM_SELF, &pos));
248: PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE));
249: PetscCall(VecSetBlockSize(pos, bs));
250: PetscCall(VecSetFromOptions(pos));
251: PetscCall(VecGetArray(pos, &_pos));
253: n_estimate = 0;
254: for (i = 0; i < my_npoints; i++) {
255: PetscBool point_inside = PETSC_TRUE;
257: for (b = 0; b < bs; b++) {
258: if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE;
259: if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE;
260: }
261: if (point_inside) {
262: for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = my_coor[bs * i + b];
263: n_estimate++;
264: }
265: }
266: PetscCall(VecRestoreArray(pos, &_pos));
268: /* locate points */
269: PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell));
271: PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell));
272: n_found = 0;
273: for (p = 0; p < n_estimate; p++) {
274: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++;
275: }
277: /* adjust size */
278: if (mode == ADD_VALUES) {
279: PetscCall(DMSwarmGetLocalSize(dm, &n_curr));
280: n_new_est = n_curr + n_found;
281: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
282: }
283: if (mode == INSERT_VALUES) {
284: n_curr = 0;
285: n_new_est = n_found;
286: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
287: }
289: /* initialize new coords, cell owners, pid */
290: PetscCall(VecGetArrayRead(pos, &_coor));
291: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
292: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
293: n_found = 0;
294: for (p = 0; p < n_estimate; p++) {
295: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
296: for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]);
297: swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
298: n_found++;
299: }
300: }
301: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
302: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
303: PetscCall(VecRestoreArrayRead(pos, &_coor));
305: if (redundant) {
306: if (rank > 0) PetscCall(PetscFree(my_coor));
307: }
308: PetscCall(PetscSFDestroy(&sfcell));
309: PetscCall(VecDestroy(&pos));
310: PetscFunctionReturn(PETSC_SUCCESS);
311: }
313: extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_DA(DM, DM, DMSwarmPICLayoutType, PetscInt);
314: extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_PLEX(DM, DM, DMSwarmPICLayoutType, PetscInt);
316: /*@C
317: DMSwarmInsertPointsUsingCellDM - Insert point coordinates within each cell
319: Not Collective
321: Input Parameters:
322: + dm - the `DMSWARM`
323: . layout_type - method used to fill each cell with the cell `DM`
324: - fill_param - parameter controlling how many points per cell are added (the meaning of this parameter is dependent on the layout type)
326: Level: beginner
328: Notes:
329: The insert method will reset any previous defined points within the `DMSWARM`.
331: When using a `DMDA` both 2D and 3D are supported for all layout types provided you are using `DMDA_ELEMENT_Q1`.
333: When using a `DMPLEX` the following case are supported\:
334: .vb
335: (i) DMSWARMPIC_LAYOUT_REGULAR: 2D (triangle),
336: (ii) DMSWARMPIC_LAYOUT_GAUSS: 2D and 3D provided the cell is a tri/tet or a quad/hex,
337: (iii) DMSWARMPIC_LAYOUT_SUBDIVISION: 2D and 3D for quad/hex and 2D tri.
338: .ve
340: .seealso: `DMSWARM`, `DMSwarmPICLayoutType`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
341: @*/
342: PETSC_EXTERN PetscErrorCode DMSwarmInsertPointsUsingCellDM(DM dm, DMSwarmPICLayoutType layout_type, PetscInt fill_param)
343: {
344: DM celldm;
345: PetscBool isDA, isPLEX;
347: PetscFunctionBegin;
348: DMSWARMPICVALID(dm);
349: PetscCall(DMSwarmGetCellDM(dm, &celldm));
350: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
351: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
352: if (isDA) {
353: PetscCall(private_DMSwarmInsertPointsUsingCellDM_DA(dm, celldm, layout_type, fill_param));
354: } else if (isPLEX) {
355: PetscCall(private_DMSwarmInsertPointsUsingCellDM_PLEX(dm, celldm, layout_type, fill_param));
356: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
357: PetscFunctionReturn(PETSC_SUCCESS);
358: }
360: extern PetscErrorCode private_DMSwarmSetPointCoordinatesCellwise_PLEX(DM, DM, PetscInt, PetscReal *);
362: /*@C
363: DMSwarmSetPointCoordinatesCellwise - Insert point coordinates (defined over the reference cell) within each cell
365: Not Collective
367: Input Parameters:
368: + dm - the `DMSWARM`
369: . npoints - the number of points to insert in each cell
370: - xi - the coordinates (defined in the local coordinate system for each cell) to insert
372: Level: beginner
374: Notes:
375: The method will reset any previous defined points within the `DMSWARM`.
376: Only supported for `DMPLEX`. If you are using a `DMDA` it is recommended to either use
377: `DMSwarmInsertPointsUsingCellDM()`, or extract and set the coordinates yourself the following code
378: .vb
379: PetscReal *coor;
380: DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
381: // user code to define the coordinates here
382: DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
383: .ve
385: .seealso: `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmInsertPointsUsingCellDM()`
386: @*/
387: PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinatesCellwise(DM dm, PetscInt npoints, PetscReal xi[])
388: {
389: DM celldm;
390: PetscBool isDA, isPLEX;
392: PetscFunctionBegin;
393: DMSWARMPICVALID(dm);
394: PetscCall(DMSwarmGetCellDM(dm, &celldm));
395: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
396: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
397: PetscCheck(!isDA, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMPLEX. Recommended you use DMSwarmInsertPointsUsingCellDM()");
398: if (isPLEX) {
399: PetscCall(private_DMSwarmSetPointCoordinatesCellwise_PLEX(dm, celldm, npoints, xi));
400: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
401: PetscFunctionReturn(PETSC_SUCCESS);
402: }
404: /*@C
405: DMSwarmCreatePointPerCellCount - Count the number of points within all cells in the cell DM
407: Not Collective
409: Input Parameter:
410: . dm - the `DMSWARM`
412: Output Parameters:
413: + ncells - the number of cells in the cell `DM` (optional argument, pass `NULL` to ignore)
414: - count - array of length ncells containing the number of points per cell
416: Level: beginner
418: Notes:
419: The array count is allocated internally and must be free'd by the user.
421: .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
422: @*/
423: PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm, PetscInt *ncells, PetscInt **count)
424: {
425: PetscBool isvalid;
426: PetscInt nel;
427: PetscInt *sum;
429: PetscFunctionBegin;
430: PetscCall(DMSwarmSortGetIsValid(dm, &isvalid));
431: nel = 0;
432: if (isvalid) {
433: PetscInt e;
435: PetscCall(DMSwarmSortGetSizes(dm, &nel, NULL));
437: PetscCall(PetscMalloc1(nel, &sum));
438: for (e = 0; e < nel; e++) PetscCall(DMSwarmSortGetNumberOfPointsPerCell(dm, e, &sum[e]));
439: } else {
440: DM celldm;
441: PetscBool isda, isplex, isshell;
442: PetscInt p, npoints;
443: PetscInt *swarm_cellid;
445: /* get the number of cells */
446: PetscCall(DMSwarmGetCellDM(dm, &celldm));
447: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isda));
448: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isplex));
449: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMSHELL, &isshell));
450: if (isda) {
451: PetscInt _nel, _npe;
452: const PetscInt *_element;
454: PetscCall(DMDAGetElements(celldm, &_nel, &_npe, &_element));
455: nel = _nel;
456: PetscCall(DMDARestoreElements(celldm, &_nel, &_npe, &_element));
457: } else if (isplex) {
458: PetscInt ps, pe;
460: PetscCall(DMPlexGetHeightStratum(celldm, 0, &ps, &pe));
461: nel = pe - ps;
462: } else if (isshell) {
463: PetscErrorCode (*method_DMShellGetNumberOfCells)(DM, PetscInt *);
465: PetscCall(PetscObjectQueryFunction((PetscObject)celldm, "DMGetNumberOfCells_C", &method_DMShellGetNumberOfCells));
466: if (method_DMShellGetNumberOfCells) {
467: PetscCall(method_DMShellGetNumberOfCells(celldm, &nel));
468: } else
469: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot determine the number of cells for the DMSHELL object. User must provide a method via PetscObjectComposeFunction( (PetscObject)shelldm, \"DMGetNumberOfCells_C\", your_function_to_compute_number_of_cells);");
470: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot determine the number of cells for a DM not of type DA, PLEX or SHELL");
472: PetscCall(PetscMalloc1(nel, &sum));
473: PetscCall(PetscArrayzero(sum, nel));
474: PetscCall(DMSwarmGetLocalSize(dm, &npoints));
475: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
476: for (p = 0; p < npoints; p++) {
477: if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) sum[swarm_cellid[p]]++;
478: }
479: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
480: }
481: if (ncells) *ncells = nel;
482: *count = sum;
483: PetscFunctionReturn(PETSC_SUCCESS);
484: }
486: /*@
487: DMSwarmGetNumSpecies - Get the number of particle species
489: Not Collective
491: Input Parameter:
492: . sw - the `DMSWARM`
494: Output Parameters:
495: . Ns - the number of species
497: Level: intermediate
499: .seealso: `DMSWARM`, `DMSwarmSetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType`
500: @*/
501: PetscErrorCode DMSwarmGetNumSpecies(DM sw, PetscInt *Ns)
502: {
503: DM_Swarm *swarm = (DM_Swarm *)sw->data;
505: PetscFunctionBegin;
506: *Ns = swarm->Ns;
507: PetscFunctionReturn(PETSC_SUCCESS);
508: }
510: /*@
511: DMSwarmSetNumSpecies - Set the number of particle species
513: Not Collective
515: Input Parameters:
516: + sw - the `DMSWARM`
517: - Ns - the number of species
519: Level: intermediate
521: .seealso: `DMSWARM`, `DMSwarmGetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType`
522: @*/
523: PetscErrorCode DMSwarmSetNumSpecies(DM sw, PetscInt Ns)
524: {
525: DM_Swarm *swarm = (DM_Swarm *)sw->data;
527: PetscFunctionBegin;
528: swarm->Ns = Ns;
529: PetscFunctionReturn(PETSC_SUCCESS);
530: }
532: /*@C
533: DMSwarmGetCoordinateFunction - Get the function setting initial particle positions, if it exists
535: Not Collective
537: Input Parameter:
538: . sw - the `DMSWARM`
540: Output Parameter:
541: . coordFunc - the function setting initial particle positions, or `NULL`, see `PetscSimplePointFn` for the calling sequence
543: Level: intermediate
545: .seealso: `DMSWARM`, `DMSwarmSetCoordinateFunction()`, `DMSwarmGetVelocityFunction()`, `DMSwarmInitializeCoordinates()`, `PetscSimplePointFn`
546: @*/
547: PetscErrorCode DMSwarmGetCoordinateFunction(DM sw, PetscSimplePointFn **coordFunc)
548: {
549: DM_Swarm *swarm = (DM_Swarm *)sw->data;
551: PetscFunctionBegin;
553: PetscAssertPointer(coordFunc, 2);
554: *coordFunc = swarm->coordFunc;
555: PetscFunctionReturn(PETSC_SUCCESS);
556: }
558: /*@C
559: DMSwarmSetCoordinateFunction - Set the function setting initial particle positions
561: Not Collective
563: Input Parameters:
564: + sw - the `DMSWARM`
565: - coordFunc - the function setting initial particle positions, see `PetscSimplePointFn` for the calling sequence
567: Level: intermediate
569: .seealso: `DMSWARM`, `DMSwarmGetCoordinateFunction()`, `DMSwarmSetVelocityFunction()`, `DMSwarmInitializeCoordinates()`, `PetscSimplePointFn`
570: @*/
571: PetscErrorCode DMSwarmSetCoordinateFunction(DM sw, PetscSimplePointFn *coordFunc)
572: {
573: DM_Swarm *swarm = (DM_Swarm *)sw->data;
575: PetscFunctionBegin;
578: swarm->coordFunc = coordFunc;
579: PetscFunctionReturn(PETSC_SUCCESS);
580: }
582: /*@C
583: DMSwarmGetVelocityFunction - Get the function setting initial particle velocities, if it exists
585: Not Collective
587: Input Parameter:
588: . sw - the `DMSWARM`
590: Output Parameter:
591: . velFunc - the function setting initial particle velocities, or `NULL`, see `PetscSimplePointFn` for the calling sequence
593: Level: intermediate
595: .seealso: `DMSWARM`, `DMSwarmSetVelocityFunction()`, `DMSwarmGetCoordinateFunction()`, `DMSwarmInitializeVelocities()`, `PetscSimplePointFn`
596: @*/
597: PetscErrorCode DMSwarmGetVelocityFunction(DM sw, PetscSimplePointFn **velFunc)
598: {
599: DM_Swarm *swarm = (DM_Swarm *)sw->data;
601: PetscFunctionBegin;
603: PetscAssertPointer(velFunc, 2);
604: *velFunc = swarm->velFunc;
605: PetscFunctionReturn(PETSC_SUCCESS);
606: }
608: /*@C
609: DMSwarmSetVelocityFunction - Set the function setting initial particle velocities
611: Not Collective
613: Input Parameters:
614: + sw - the `DMSWARM`
615: - velFunc - the function setting initial particle velocities, see `PetscSimplePointFn` for the calling sequence
617: Level: intermediate
619: .seealso: `DMSWARM`, `DMSwarmGetVelocityFunction()`, `DMSwarmSetCoordinateFunction()`, `DMSwarmInitializeVelocities()`, `PetscSimplePointFn`
620: @*/
621: PetscErrorCode DMSwarmSetVelocityFunction(DM sw, PetscSimplePointFn *velFunc)
622: {
623: DM_Swarm *swarm = (DM_Swarm *)sw->data;
625: PetscFunctionBegin;
628: swarm->velFunc = velFunc;
629: PetscFunctionReturn(PETSC_SUCCESS);
630: }
632: /*@C
633: DMSwarmComputeLocalSize - Compute the local number and distribution of particles based upon a density function
635: Not Collective
637: Input Parameters:
638: + sw - The `DMSWARM`
639: . N - The target number of particles
640: - density - The density field for the particle layout, normalized to unity
642: Level: advanced
644: Note:
645: One particle will be created for each species.
647: .seealso: `DMSWARM`, `DMSwarmComputeLocalSizeFromOptions()`
648: @*/
649: PetscErrorCode DMSwarmComputeLocalSize(DM sw, PetscInt N, PetscProbFunc density)
650: {
651: DM dm;
652: PetscQuadrature quad;
653: const PetscReal *xq, *wq;
654: PetscReal *n_int;
655: PetscInt *npc_s, *cellid, Ni;
656: PetscReal gmin[3], gmax[3], xi0[3];
657: PetscInt Ns, cStart, cEnd, c, dim, d, Nq, q, Np = 0, p, s;
658: PetscBool simplex;
660: PetscFunctionBegin;
661: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
662: PetscCall(DMSwarmGetCellDM(sw, &dm));
663: PetscCall(DMGetDimension(dm, &dim));
664: PetscCall(DMGetBoundingBox(dm, gmin, gmax));
665: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
666: PetscCall(DMPlexIsSimplex(dm, &simplex));
667: PetscCall(DMGetCoordinatesLocalSetUp(dm));
668: if (simplex) PetscCall(PetscDTStroudConicalQuadrature(dim, 1, 5, -1.0, 1.0, &quad));
669: else PetscCall(PetscDTGaussTensorQuadrature(dim, 1, 5, -1.0, 1.0, &quad));
670: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, &xq, &wq));
671: PetscCall(PetscCalloc2(Ns, &n_int, (cEnd - cStart) * Ns, &npc_s));
672: /* Integrate the density function to get the number of particles in each cell */
673: for (d = 0; d < dim; ++d) xi0[d] = -1.0;
674: for (c = 0; c < cEnd - cStart; ++c) {
675: const PetscInt cell = c + cStart;
676: PetscReal v0[3], J[9], invJ[9], detJ, detJp = 2. / (gmax[0] - gmin[0]), xr[3], den;
678: /* Have to transform quadrature points/weights to cell domain */
679: PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ));
680: PetscCall(PetscArrayzero(n_int, Ns));
681: for (q = 0; q < Nq; ++q) {
682: CoordinatesRefToReal(dim, dim, xi0, v0, J, &xq[q * dim], xr);
683: /* Have to transform mesh to domain of definition of PDF, [-1, 1], and weight PDF by |J|/2 */
684: xr[0] = detJp * (xr[0] - gmin[0]) - 1.;
686: for (s = 0; s < Ns; ++s) {
687: PetscCall(density(xr, NULL, &den));
688: n_int[s] += (detJp * den) * (detJ * wq[q]) / (PetscReal)Ns;
689: }
690: }
691: for (s = 0; s < Ns; ++s) {
692: Ni = N;
693: npc_s[c * Ns + s] += (PetscInt)(Ni * n_int[s]);
694: Np += npc_s[c * Ns + s];
695: }
696: }
697: PetscCall(PetscQuadratureDestroy(&quad));
698: PetscCall(DMSwarmSetLocalSizes(sw, Np, 0));
699: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid));
700: for (c = 0, p = 0; c < cEnd - cStart; ++c) {
701: for (s = 0; s < Ns; ++s) {
702: for (q = 0; q < npc_s[c * Ns + s]; ++q, ++p) cellid[p] = c;
703: }
704: }
705: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid));
706: PetscCall(PetscFree2(n_int, npc_s));
707: PetscFunctionReturn(PETSC_SUCCESS);
708: }
710: /*@
711: DMSwarmComputeLocalSizeFromOptions - Compute the local number and distribution of particles based upon a density function determined by options
713: Not Collective
715: Input Parameter:
716: . sw - The `DMSWARM`
718: Level: advanced
720: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`
721: @*/
722: PetscErrorCode DMSwarmComputeLocalSizeFromOptions(DM sw)
723: {
724: PetscProbFunc pdf;
725: const char *prefix;
726: char funcname[PETSC_MAX_PATH_LEN];
727: PetscInt *N, Ns, dim, n;
728: PetscBool flg;
729: PetscMPIInt size, rank;
731: PetscFunctionBegin;
732: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)sw), &size));
733: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)sw), &rank));
734: PetscCall(PetscCalloc1(size, &N));
735: PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM");
736: n = size;
737: PetscCall(PetscOptionsIntArray("-dm_swarm_num_particles", "The target number of particles", "", N, &n, NULL));
738: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
739: PetscCall(PetscOptionsInt("-dm_swarm_num_species", "The number of species", "DMSwarmSetNumSpecies", Ns, &Ns, &flg));
740: if (flg) PetscCall(DMSwarmSetNumSpecies(sw, Ns));
741: PetscCall(PetscOptionsString("-dm_swarm_coordinate_function", "Function to determine particle coordinates", "DMSwarmSetCoordinateFunction", funcname, funcname, sizeof(funcname), &flg));
742: PetscOptionsEnd();
743: if (flg) {
744: PetscSimplePointFn *coordFunc;
746: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
747: PetscCall(PetscDLSym(NULL, funcname, (void **)&coordFunc));
748: PetscCheck(coordFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname);
749: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
750: PetscCall(DMSwarmSetLocalSizes(sw, N[rank] * Ns, 0));
751: PetscCall(DMSwarmSetCoordinateFunction(sw, coordFunc));
752: } else {
753: PetscCall(DMGetDimension(sw, &dim));
754: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix));
755: PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_coordinate_density", &pdf, NULL, NULL));
756: PetscCall(DMSwarmComputeLocalSize(sw, N[rank], pdf));
757: }
758: PetscCall(PetscFree(N));
759: PetscFunctionReturn(PETSC_SUCCESS);
760: }
762: /*@
763: DMSwarmInitializeCoordinates - Determine the initial coordinates of particles for a PIC method
765: Not Collective
767: Input Parameter:
768: . sw - The `DMSWARM`
770: Level: advanced
772: Note:
773: Currently, we randomly place particles in their assigned cell
775: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeVelocities()`
776: @*/
777: PetscErrorCode DMSwarmInitializeCoordinates(DM sw)
778: {
779: PetscSimplePointFn *coordFunc;
780: PetscScalar *weight;
781: PetscReal *x;
782: PetscInt *species;
783: void *ctx;
784: PetscBool removePoints = PETSC_TRUE;
785: PetscDataType dtype;
786: PetscInt Np, p, Ns, dim, d, bs;
788: PetscFunctionBeginUser;
789: PetscCall(DMGetDimension(sw, &dim));
790: PetscCall(DMSwarmGetLocalSize(sw, &Np));
791: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
792: PetscCall(DMSwarmGetCoordinateFunction(sw, &coordFunc));
794: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, &bs, &dtype, (void **)&x));
795: PetscCall(DMSwarmGetField(sw, "w_q", &bs, &dtype, (void **)&weight));
796: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
797: if (coordFunc) {
798: PetscCall(DMGetApplicationContext(sw, &ctx));
799: for (p = 0; p < Np; ++p) {
800: PetscScalar X[3];
802: PetscCall((*coordFunc)(dim, 0., NULL, p, X, ctx));
803: for (d = 0; d < dim; ++d) x[p * dim + d] = PetscRealPart(X[d]);
804: weight[p] = 1.0;
805: species[p] = p % Ns;
806: }
807: } else {
808: DM dm;
809: PetscRandom rnd;
810: PetscReal xi0[3];
811: PetscInt cStart, cEnd, c;
813: PetscCall(DMSwarmGetCellDM(sw, &dm));
814: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
815: PetscCall(DMGetApplicationContext(sw, &ctx));
817: /* Set particle position randomly in cell, set weights to 1 */
818: PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)dm), &rnd));
819: PetscCall(PetscRandomSetInterval(rnd, -1.0, 1.0));
820: PetscCall(PetscRandomSetFromOptions(rnd));
821: PetscCall(DMSwarmSortGetAccess(sw));
822: for (d = 0; d < dim; ++d) xi0[d] = -1.0;
823: for (c = cStart; c < cEnd; ++c) {
824: PetscReal v0[3], J[9], invJ[9], detJ;
825: PetscInt *pidx, Npc, q;
827: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
828: PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ));
829: for (q = 0; q < Npc; ++q) {
830: const PetscInt p = pidx[q];
831: PetscReal xref[3];
833: for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &xref[d]));
834: CoordinatesRefToReal(dim, dim, xi0, v0, J, xref, &x[p * dim]);
836: weight[p] = 1.0 / Np;
837: species[p] = p % Ns;
838: }
839: PetscCall(PetscFree(pidx));
840: }
841: PetscCall(PetscRandomDestroy(&rnd));
842: PetscCall(DMSwarmSortRestoreAccess(sw));
843: }
844: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
845: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
846: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
848: PetscCall(DMSwarmMigrate(sw, removePoints));
849: PetscCall(DMLocalizeCoordinates(sw));
850: PetscFunctionReturn(PETSC_SUCCESS);
851: }
853: /*@C
854: DMSwarmInitializeVelocities - Set the initial velocities of particles using a distribution.
856: Collective
858: Input Parameters:
859: + sw - The `DMSWARM` object
860: . sampler - A function which uniformly samples the velocity PDF
861: - v0 - The velocity scale for nondimensionalization for each species
863: Level: advanced
865: Note:
866: If `v0` is zero for the first species, all velocities are set to zero. If it is zero for any other species, the effect will be to give that species zero velocity.
868: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocitiesFromOptions()`
869: @*/
870: PetscErrorCode DMSwarmInitializeVelocities(DM sw, PetscProbFunc sampler, const PetscReal v0[])
871: {
872: PetscSimplePointFn *velFunc;
873: PetscReal *v;
874: PetscInt *species;
875: void *ctx;
876: PetscInt dim, Np, p;
878: PetscFunctionBegin;
879: PetscCall(DMSwarmGetVelocityFunction(sw, &velFunc));
881: PetscCall(DMGetDimension(sw, &dim));
882: PetscCall(DMSwarmGetLocalSize(sw, &Np));
883: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v));
884: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
885: if (v0[0] == 0.) {
886: PetscCall(PetscArrayzero(v, Np * dim));
887: } else if (velFunc) {
888: PetscCall(DMGetApplicationContext(sw, &ctx));
889: for (p = 0; p < Np; ++p) {
890: PetscInt s = species[p], d;
891: PetscScalar vel[3];
893: PetscCall((*velFunc)(dim, 0., NULL, p, vel, ctx));
894: for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * PetscRealPart(vel[d]);
895: }
896: } else {
897: PetscRandom rnd;
899: PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)sw), &rnd));
900: PetscCall(PetscRandomSetInterval(rnd, 0, 1.));
901: PetscCall(PetscRandomSetFromOptions(rnd));
903: for (p = 0; p < Np; ++p) {
904: PetscInt s = species[p], d;
905: PetscReal a[3], vel[3];
907: for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &a[d]));
908: PetscCall(sampler(a, NULL, vel));
909: for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * vel[d];
910: }
911: PetscCall(PetscRandomDestroy(&rnd));
912: }
913: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v));
914: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
915: PetscFunctionReturn(PETSC_SUCCESS);
916: }
918: /*@
919: DMSwarmInitializeVelocitiesFromOptions - Set the initial velocities of particles using a distribution determined from options.
921: Collective
923: Input Parameters:
924: + sw - The `DMSWARM` object
925: - v0 - The velocity scale for nondimensionalization for each species
927: Level: advanced
929: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocities()`
930: @*/
931: PetscErrorCode DMSwarmInitializeVelocitiesFromOptions(DM sw, const PetscReal v0[])
932: {
933: PetscProbFunc sampler;
934: PetscInt dim;
935: const char *prefix;
936: char funcname[PETSC_MAX_PATH_LEN];
937: PetscBool flg;
939: PetscFunctionBegin;
940: PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM");
941: PetscCall(PetscOptionsString("-dm_swarm_velocity_function", "Function to determine particle velocities", "DMSwarmSetVelocityFunction", funcname, funcname, sizeof(funcname), &flg));
942: PetscOptionsEnd();
943: if (flg) {
944: PetscSimplePointFn *velFunc;
946: PetscCall(PetscDLSym(NULL, funcname, (void **)&velFunc));
947: PetscCheck(velFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname);
948: PetscCall(DMSwarmSetVelocityFunction(sw, velFunc));
949: }
950: PetscCall(DMGetDimension(sw, &dim));
951: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix));
952: PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_velocity_density", NULL, NULL, &sampler));
953: PetscCall(DMSwarmInitializeVelocities(sw, sampler, v0));
954: PetscFunctionReturn(PETSC_SUCCESS);
955: }