xref: /petsc/src/dm/impls/swarm/swarmpic.c (revision 2fe279fdf3e687a416e4eadb7d3c7a82d60442c6)
10e2ec84fSDave May #define PETSCDM_DLL
20e2ec84fSDave May #include <petsc/private/dmswarmimpl.h> /*I   "petscdmswarm.h"   I*/
30e2ec84fSDave May #include <petscsf.h>
4b799feefSDave May #include <petscdmda.h>
5b799feefSDave May #include <petscdmplex.h>
635b38c60SMatthew G. Knepley #include <petscdt.h>
7279f676cSBarry Smith #include "../src/dm/impls/swarm/data_bucket.h"
80e2ec84fSDave May 
935b38c60SMatthew G. Knepley #include <petsc/private/petscfeimpl.h> /* For CoordinatesRefToReal() */
1035b38c60SMatthew G. Knepley 
110e2ec84fSDave May /*
125627991aSBarry Smith  Error checking to ensure the swarm type is correct and that a cell DM has been set
130e2ec84fSDave May */
140e2ec84fSDave May #define DMSWARMPICVALID(dm) \
15f7d195e4SLawrence Mitchell   do { \
160e2ec84fSDave May     DM_Swarm *_swarm = (DM_Swarm *)(dm)->data; \
175f80ce2aSJacob Faibussowitsch     PetscCheck(_swarm->swarm_type == DMSWARM_PIC, PetscObjectComm((PetscObject)(dm)), PETSC_ERR_SUP, "Valid only for DMSwarm-PIC. You must call DMSwarmSetType(dm,DMSWARM_PIC)"); \
1828b400f6SJacob Faibussowitsch     PetscCheck(_swarm->dmcell, PetscObjectComm((PetscObject)(dm)), PETSC_ERR_SUP, "Valid only for DMSwarmPIC if the cell DM is set. You must call DMSwarmSetCellDM(dm,celldm)"); \
19f7d195e4SLawrence Mitchell   } while (0)
200e2ec84fSDave May 
210e2ec84fSDave May /* Coordinate insertition/addition API */
220e2ec84fSDave May /*@C
2320f4b53cSBarry Smith    DMSwarmSetPointsUniformCoordinates - Set point coordinates in a `DMSWARM` on a regular (ijk) grid
240e2ec84fSDave May 
2520f4b53cSBarry Smith    Collective
260e2ec84fSDave May 
270e2ec84fSDave May    Input parameters:
2820f4b53cSBarry Smith +  dm - the `DMSWARM`
290e2ec84fSDave May .  min - minimum coordinate values in the x, y, z directions (array of length dim)
300e2ec84fSDave May .  max - maximum coordinate values in the x, y, z directions (array of length dim)
310e2ec84fSDave May .  npoints - number of points in each spatial direction (array of length dim)
3220f4b53cSBarry Smith -  mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`)
330e2ec84fSDave May 
340e2ec84fSDave May    Level: beginner
350e2ec84fSDave May 
360e2ec84fSDave May    Notes:
3720f4b53cSBarry Smith    When using mode = `INSERT_VALUES`, this method will reset the number of particles in the `DMSWARM`
3820f4b53cSBarry Smith    to be npoints[0]*npoints[1] (2D) or npoints[0]*npoints[1]*npoints[2] (3D). When using mode = `ADD_VALUES`,
3920f4b53cSBarry Smith    new points will be appended to any already existing in the `DMSWARM`
400e2ec84fSDave May 
4120f4b53cSBarry Smith .seealso: `DM`, `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
420e2ec84fSDave May @*/
43d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm, PetscReal min[], PetscReal max[], PetscInt npoints[], InsertMode mode)
44d71ae5a4SJacob Faibussowitsch {
450e2ec84fSDave May   PetscReal          gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
460e2ec84fSDave May   PetscReal          gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
470e2ec84fSDave May   PetscInt           i, j, k, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
480e2ec84fSDave May   Vec                coorlocal;
490e2ec84fSDave May   const PetscScalar *_coor;
500e2ec84fSDave May   DM                 celldm;
510e2ec84fSDave May   PetscReal          dx[3];
522e3d3761SDave May   PetscInt           _npoints[] = {0, 0, 1};
530e2ec84fSDave May   Vec                pos;
540e2ec84fSDave May   PetscScalar       *_pos;
550e2ec84fSDave May   PetscReal         *swarm_coor;
560e2ec84fSDave May   PetscInt          *swarm_cellid;
570e2ec84fSDave May   PetscSF            sfcell = NULL;
580e2ec84fSDave May   const PetscSFNode *LA_sfcell;
590e2ec84fSDave May 
600e2ec84fSDave May   PetscFunctionBegin;
610e2ec84fSDave May   DMSWARMPICVALID(dm);
629566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetCellDM(dm, &celldm));
639566063dSJacob Faibussowitsch   PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal));
649566063dSJacob Faibussowitsch   PetscCall(VecGetSize(coorlocal, &N));
659566063dSJacob Faibussowitsch   PetscCall(VecGetBlockSize(coorlocal, &bs));
660e2ec84fSDave May   N = N / bs;
679566063dSJacob Faibussowitsch   PetscCall(VecGetArrayRead(coorlocal, &_coor));
680e2ec84fSDave May   for (i = 0; i < N; i++) {
690e2ec84fSDave May     for (b = 0; b < bs; b++) {
70a5f152d1SDave May       gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b]));
71a5f152d1SDave May       gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b]));
720e2ec84fSDave May     }
730e2ec84fSDave May   }
749566063dSJacob Faibussowitsch   PetscCall(VecRestoreArrayRead(coorlocal, &_coor));
750e2ec84fSDave May 
760e2ec84fSDave May   for (b = 0; b < bs; b++) {
7771844bb8SDave May     if (npoints[b] > 1) {
780e2ec84fSDave May       dx[b] = (max[b] - min[b]) / ((PetscReal)(npoints[b] - 1));
7971844bb8SDave May     } else {
8071844bb8SDave May       dx[b] = 0.0;
8171844bb8SDave May     }
822e3d3761SDave May     _npoints[b] = npoints[b];
830e2ec84fSDave May   }
840e2ec84fSDave May 
850e2ec84fSDave May   /* determine number of points living in the bounding box */
860e2ec84fSDave May   n_estimate = 0;
872e3d3761SDave May   for (k = 0; k < _npoints[2]; k++) {
882e3d3761SDave May     for (j = 0; j < _npoints[1]; j++) {
892e3d3761SDave May       for (i = 0; i < _npoints[0]; i++) {
900e2ec84fSDave May         PetscReal xp[] = {0.0, 0.0, 0.0};
910e2ec84fSDave May         PetscInt  ijk[3];
920e2ec84fSDave May         PetscBool point_inside = PETSC_TRUE;
930e2ec84fSDave May 
940e2ec84fSDave May         ijk[0] = i;
950e2ec84fSDave May         ijk[1] = j;
960e2ec84fSDave May         ijk[2] = k;
97ad540459SPierre Jolivet         for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b];
980e2ec84fSDave May         for (b = 0; b < bs; b++) {
99ad540459SPierre Jolivet           if (xp[b] < gmin[b]) point_inside = PETSC_FALSE;
100ad540459SPierre Jolivet           if (xp[b] > gmax[b]) point_inside = PETSC_FALSE;
1010e2ec84fSDave May         }
102ad540459SPierre Jolivet         if (point_inside) n_estimate++;
1030e2ec84fSDave May       }
1040e2ec84fSDave May     }
1050e2ec84fSDave May   }
1060e2ec84fSDave May 
1070e2ec84fSDave May   /* create candidate list */
1089566063dSJacob Faibussowitsch   PetscCall(VecCreate(PETSC_COMM_SELF, &pos));
1099566063dSJacob Faibussowitsch   PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE));
1109566063dSJacob Faibussowitsch   PetscCall(VecSetBlockSize(pos, bs));
1119566063dSJacob Faibussowitsch   PetscCall(VecSetFromOptions(pos));
1129566063dSJacob Faibussowitsch   PetscCall(VecGetArray(pos, &_pos));
1130e2ec84fSDave May 
1140e2ec84fSDave May   n_estimate = 0;
1152e3d3761SDave May   for (k = 0; k < _npoints[2]; k++) {
1162e3d3761SDave May     for (j = 0; j < _npoints[1]; j++) {
1172e3d3761SDave May       for (i = 0; i < _npoints[0]; i++) {
1180e2ec84fSDave May         PetscReal xp[] = {0.0, 0.0, 0.0};
1190e2ec84fSDave May         PetscInt  ijk[3];
1200e2ec84fSDave May         PetscBool point_inside = PETSC_TRUE;
1210e2ec84fSDave May 
1220e2ec84fSDave May         ijk[0] = i;
1230e2ec84fSDave May         ijk[1] = j;
1240e2ec84fSDave May         ijk[2] = k;
125ad540459SPierre Jolivet         for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b];
1260e2ec84fSDave May         for (b = 0; b < bs; b++) {
127ad540459SPierre Jolivet           if (xp[b] < gmin[b]) point_inside = PETSC_FALSE;
128ad540459SPierre Jolivet           if (xp[b] > gmax[b]) point_inside = PETSC_FALSE;
1290e2ec84fSDave May         }
1300e2ec84fSDave May         if (point_inside) {
131ad540459SPierre Jolivet           for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = xp[b];
1320e2ec84fSDave May           n_estimate++;
1330e2ec84fSDave May         }
1340e2ec84fSDave May       }
1350e2ec84fSDave May     }
1360e2ec84fSDave May   }
1379566063dSJacob Faibussowitsch   PetscCall(VecRestoreArray(pos, &_pos));
1380e2ec84fSDave May 
1390e2ec84fSDave May   /* locate points */
1409566063dSJacob Faibussowitsch   PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell));
1419566063dSJacob Faibussowitsch   PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell));
1420e2ec84fSDave May   n_found = 0;
1430e2ec84fSDave May   for (p = 0; p < n_estimate; p++) {
144ad540459SPierre Jolivet     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++;
1450e2ec84fSDave May   }
1460e2ec84fSDave May 
1470e2ec84fSDave May   /* adjust size */
1480e2ec84fSDave May   if (mode == ADD_VALUES) {
1499566063dSJacob Faibussowitsch     PetscCall(DMSwarmGetLocalSize(dm, &n_curr));
1500e2ec84fSDave May     n_new_est = n_curr + n_found;
1519566063dSJacob Faibussowitsch     PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
1520e2ec84fSDave May   }
1530e2ec84fSDave May   if (mode == INSERT_VALUES) {
1540e2ec84fSDave May     n_curr    = 0;
1550e2ec84fSDave May     n_new_est = n_found;
1569566063dSJacob Faibussowitsch     PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
1570e2ec84fSDave May   }
1580e2ec84fSDave May 
1590e2ec84fSDave May   /* initialize new coords, cell owners, pid */
1609566063dSJacob Faibussowitsch   PetscCall(VecGetArrayRead(pos, &_coor));
1619566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
1629566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
1630e2ec84fSDave May   n_found = 0;
1640e2ec84fSDave May   for (p = 0; p < n_estimate; p++) {
1650e2ec84fSDave May     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
166ad540459SPierre Jolivet       for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]);
1670e2ec84fSDave May       swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
1680e2ec84fSDave May       n_found++;
1690e2ec84fSDave May     }
1700e2ec84fSDave May   }
1719566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
1729566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
1739566063dSJacob Faibussowitsch   PetscCall(VecRestoreArrayRead(pos, &_coor));
1740e2ec84fSDave May 
1759566063dSJacob Faibussowitsch   PetscCall(PetscSFDestroy(&sfcell));
1769566063dSJacob Faibussowitsch   PetscCall(VecDestroy(&pos));
1773ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
1780e2ec84fSDave May }
1790e2ec84fSDave May 
1800e2ec84fSDave May /*@C
18120f4b53cSBarry Smith    DMSwarmSetPointCoordinates - Set point coordinates in a `DMSWARM` from a user defined list
1820e2ec84fSDave May 
18320f4b53cSBarry Smith    Collective
1840e2ec84fSDave May 
1850e2ec84fSDave May    Input parameters:
18620f4b53cSBarry Smith +  dm - the `DMSWARM`
1870e2ec84fSDave May .  npoints - the number of points to insert
1880e2ec84fSDave May .  coor - the coordinate values
18920f4b53cSBarry Smith .  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
19020f4b53cSBarry Smith -  mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`)
1910e2ec84fSDave May 
1920e2ec84fSDave May    Level: beginner
1930e2ec84fSDave May 
1940e2ec84fSDave May    Notes:
19520f4b53cSBarry Smith    If the user has specified `redundant` as `PETSC_FALSE`, the cell `DM` will attempt to locate the coordinates provided by `coor` within
19620f4b53cSBarry Smith    its sub-domain. If they any values within `coor` are not located in the sub-domain, they will be ignored and will not get
19720f4b53cSBarry Smith    added to the `DMSWARM`.
1980e2ec84fSDave May 
19920f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`, `DMSwarmSetPointsUniformCoordinates()`
2000e2ec84fSDave May @*/
201d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinates(DM dm, PetscInt npoints, PetscReal coor[], PetscBool redundant, InsertMode mode)
202d71ae5a4SJacob Faibussowitsch {
2030e2ec84fSDave May   PetscReal          gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
2040e2ec84fSDave May   PetscReal          gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
2050e2ec84fSDave May   PetscInt           i, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
2060e2ec84fSDave May   Vec                coorlocal;
2070e2ec84fSDave May   const PetscScalar *_coor;
2080e2ec84fSDave May   DM                 celldm;
2090e2ec84fSDave May   Vec                pos;
2100e2ec84fSDave May   PetscScalar       *_pos;
2110e2ec84fSDave May   PetscReal         *swarm_coor;
2120e2ec84fSDave May   PetscInt          *swarm_cellid;
2130e2ec84fSDave May   PetscSF            sfcell = NULL;
2140e2ec84fSDave May   const PetscSFNode *LA_sfcell;
2150e2ec84fSDave May   PetscReal         *my_coor;
2160e2ec84fSDave May   PetscInt           my_npoints;
2170e2ec84fSDave May   PetscMPIInt        rank;
2180e2ec84fSDave May   MPI_Comm           comm;
2190e2ec84fSDave May 
2200e2ec84fSDave May   PetscFunctionBegin;
2210e2ec84fSDave May   DMSWARMPICVALID(dm);
2229566063dSJacob Faibussowitsch   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2239566063dSJacob Faibussowitsch   PetscCallMPI(MPI_Comm_rank(comm, &rank));
2240e2ec84fSDave May 
2259566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetCellDM(dm, &celldm));
2269566063dSJacob Faibussowitsch   PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal));
2279566063dSJacob Faibussowitsch   PetscCall(VecGetSize(coorlocal, &N));
2289566063dSJacob Faibussowitsch   PetscCall(VecGetBlockSize(coorlocal, &bs));
2290e2ec84fSDave May   N = N / bs;
2309566063dSJacob Faibussowitsch   PetscCall(VecGetArrayRead(coorlocal, &_coor));
2310e2ec84fSDave May   for (i = 0; i < N; i++) {
2320e2ec84fSDave May     for (b = 0; b < bs; b++) {
233a5f152d1SDave May       gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b]));
234a5f152d1SDave May       gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b]));
2350e2ec84fSDave May     }
2360e2ec84fSDave May   }
2379566063dSJacob Faibussowitsch   PetscCall(VecRestoreArrayRead(coorlocal, &_coor));
2380e2ec84fSDave May 
2390e2ec84fSDave May   /* broadcast points from rank 0 if requested */
2400e2ec84fSDave May   if (redundant) {
2410e2ec84fSDave May     my_npoints = npoints;
2429566063dSJacob Faibussowitsch     PetscCallMPI(MPI_Bcast(&my_npoints, 1, MPIU_INT, 0, comm));
2430e2ec84fSDave May 
2440e2ec84fSDave May     if (rank > 0) { /* allocate space */
2459566063dSJacob Faibussowitsch       PetscCall(PetscMalloc1(bs * my_npoints, &my_coor));
2460e2ec84fSDave May     } else {
2470e2ec84fSDave May       my_coor = coor;
2480e2ec84fSDave May     }
2499566063dSJacob Faibussowitsch     PetscCallMPI(MPI_Bcast(my_coor, bs * my_npoints, MPIU_REAL, 0, comm));
2500e2ec84fSDave May   } else {
2510e2ec84fSDave May     my_npoints = npoints;
2520e2ec84fSDave May     my_coor    = coor;
2530e2ec84fSDave May   }
2540e2ec84fSDave May 
2550e2ec84fSDave May   /* determine the number of points living in the bounding box */
2560e2ec84fSDave May   n_estimate = 0;
2570e2ec84fSDave May   for (i = 0; i < my_npoints; i++) {
2580e2ec84fSDave May     PetscBool point_inside = PETSC_TRUE;
2590e2ec84fSDave May 
2600e2ec84fSDave May     for (b = 0; b < bs; b++) {
261ad540459SPierre Jolivet       if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE;
262ad540459SPierre Jolivet       if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE;
2630e2ec84fSDave May     }
264ad540459SPierre Jolivet     if (point_inside) n_estimate++;
2650e2ec84fSDave May   }
2660e2ec84fSDave May 
2670e2ec84fSDave May   /* create candidate list */
2689566063dSJacob Faibussowitsch   PetscCall(VecCreate(PETSC_COMM_SELF, &pos));
2699566063dSJacob Faibussowitsch   PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE));
2709566063dSJacob Faibussowitsch   PetscCall(VecSetBlockSize(pos, bs));
2719566063dSJacob Faibussowitsch   PetscCall(VecSetFromOptions(pos));
2729566063dSJacob Faibussowitsch   PetscCall(VecGetArray(pos, &_pos));
2730e2ec84fSDave May 
2740e2ec84fSDave May   n_estimate = 0;
2750e2ec84fSDave May   for (i = 0; i < my_npoints; i++) {
2760e2ec84fSDave May     PetscBool point_inside = PETSC_TRUE;
2770e2ec84fSDave May 
2780e2ec84fSDave May     for (b = 0; b < bs; b++) {
279ad540459SPierre Jolivet       if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE;
280ad540459SPierre Jolivet       if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE;
2810e2ec84fSDave May     }
2820e2ec84fSDave May     if (point_inside) {
283ad540459SPierre Jolivet       for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = my_coor[bs * i + b];
2840e2ec84fSDave May       n_estimate++;
2850e2ec84fSDave May     }
2860e2ec84fSDave May   }
2879566063dSJacob Faibussowitsch   PetscCall(VecRestoreArray(pos, &_pos));
2880e2ec84fSDave May 
2890e2ec84fSDave May   /* locate points */
2909566063dSJacob Faibussowitsch   PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell));
2910e2ec84fSDave May 
2929566063dSJacob Faibussowitsch   PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell));
2930e2ec84fSDave May   n_found = 0;
2940e2ec84fSDave May   for (p = 0; p < n_estimate; p++) {
295ad540459SPierre Jolivet     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++;
2960e2ec84fSDave May   }
2970e2ec84fSDave May 
2980e2ec84fSDave May   /* adjust size */
2990e2ec84fSDave May   if (mode == ADD_VALUES) {
3009566063dSJacob Faibussowitsch     PetscCall(DMSwarmGetLocalSize(dm, &n_curr));
3010e2ec84fSDave May     n_new_est = n_curr + n_found;
3029566063dSJacob Faibussowitsch     PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
3030e2ec84fSDave May   }
3040e2ec84fSDave May   if (mode == INSERT_VALUES) {
3050e2ec84fSDave May     n_curr    = 0;
3060e2ec84fSDave May     n_new_est = n_found;
3079566063dSJacob Faibussowitsch     PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
3080e2ec84fSDave May   }
3090e2ec84fSDave May 
3100e2ec84fSDave May   /* initialize new coords, cell owners, pid */
3119566063dSJacob Faibussowitsch   PetscCall(VecGetArrayRead(pos, &_coor));
3129566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
3139566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
3140e2ec84fSDave May   n_found = 0;
3150e2ec84fSDave May   for (p = 0; p < n_estimate; p++) {
3160e2ec84fSDave May     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
317ad540459SPierre Jolivet       for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]);
3180e2ec84fSDave May       swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
3190e2ec84fSDave May       n_found++;
3200e2ec84fSDave May     }
3210e2ec84fSDave May   }
3229566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
3239566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
3249566063dSJacob Faibussowitsch   PetscCall(VecRestoreArrayRead(pos, &_coor));
3250e2ec84fSDave May 
3260e2ec84fSDave May   if (redundant) {
32748a46eb9SPierre Jolivet     if (rank > 0) PetscCall(PetscFree(my_coor));
3280e2ec84fSDave May   }
3299566063dSJacob Faibussowitsch   PetscCall(PetscSFDestroy(&sfcell));
3309566063dSJacob Faibussowitsch   PetscCall(VecDestroy(&pos));
3313ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
3320e2ec84fSDave May }
3330e2ec84fSDave May 
3340e2ec84fSDave May extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_DA(DM, DM, DMSwarmPICLayoutType, PetscInt);
3350e2ec84fSDave May extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_PLEX(DM, DM, DMSwarmPICLayoutType, PetscInt);
3360e2ec84fSDave May 
3370e2ec84fSDave May /*@C
3380e2ec84fSDave May    DMSwarmInsertPointsUsingCellDM - Insert point coordinates within each cell
3390e2ec84fSDave May 
34020f4b53cSBarry Smith    Not Collective
3410e2ec84fSDave May 
3420e2ec84fSDave May    Input parameters:
34320f4b53cSBarry Smith +  dm - the `DMSWARM`
34420f4b53cSBarry Smith .  layout_type - method used to fill each cell with the cell `DM`
3450e2ec84fSDave May -  fill_param - parameter controlling how many points per cell are added (the meaning of this parameter is dependent on the layout type)
3460e2ec84fSDave May 
3470e2ec84fSDave May    Level: beginner
3480e2ec84fSDave May 
3490e2ec84fSDave May    Notes:
35020f4b53cSBarry Smith    The insert method will reset any previous defined points within the `DMSWARM`.
351e7af74c8SDave May 
35220f4b53cSBarry Smith    When using a `DMDA` both 2D and 3D are supported for all layout types provided you are using `DMDA_ELEMENT_Q1`.
353e7af74c8SDave May 
35420f4b53cSBarry Smith    When using a `DMPLEX` the following case are supported:
35520f4b53cSBarry Smith .vb
356ea3d7275SDave May    (i) DMSWARMPIC_LAYOUT_REGULAR: 2D (triangle),
357ea3d7275SDave May    (ii) DMSWARMPIC_LAYOUT_GAUSS: 2D and 3D provided the cell is a tri/tet or a quad/hex,
358ea3d7275SDave May    (iii) DMSWARMPIC_LAYOUT_SUBDIVISION: 2D and 3D for quad/hex and 2D tri.
35920f4b53cSBarry Smith .ve
3600e2ec84fSDave May 
36120f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmPICLayoutType`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
3620e2ec84fSDave May @*/
363d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmInsertPointsUsingCellDM(DM dm, DMSwarmPICLayoutType layout_type, PetscInt fill_param)
364d71ae5a4SJacob Faibussowitsch {
3650e2ec84fSDave May   DM        celldm;
3660e2ec84fSDave May   PetscBool isDA, isPLEX;
3670e2ec84fSDave May 
3680e2ec84fSDave May   PetscFunctionBegin;
3690e2ec84fSDave May   DMSWARMPICVALID(dm);
3709566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetCellDM(dm, &celldm));
3719566063dSJacob Faibussowitsch   PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
3729566063dSJacob Faibussowitsch   PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
3730e2ec84fSDave May   if (isDA) {
3749566063dSJacob Faibussowitsch     PetscCall(private_DMSwarmInsertPointsUsingCellDM_DA(dm, celldm, layout_type, fill_param));
3750e2ec84fSDave May   } else if (isPLEX) {
3769566063dSJacob Faibussowitsch     PetscCall(private_DMSwarmInsertPointsUsingCellDM_PLEX(dm, celldm, layout_type, fill_param));
3770e2ec84fSDave May   } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
3783ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
3790e2ec84fSDave May }
3800e2ec84fSDave May 
381431382f2SDave May extern PetscErrorCode private_DMSwarmSetPointCoordinatesCellwise_PLEX(DM, DM, PetscInt, PetscReal *);
382431382f2SDave May 
383431382f2SDave May /*@C
384431382f2SDave May    DMSwarmSetPointCoordinatesCellwise - Insert point coordinates (defined over the reference cell) within each cell
385431382f2SDave May 
38620f4b53cSBarry Smith    Not Collective
387431382f2SDave May 
388431382f2SDave May    Input parameters:
38920f4b53cSBarry Smith +  dm - the `DMSWARM`
39020f4b53cSBarry Smith .  celldm - the cell `DM`
391431382f2SDave May .  npoints - the number of points to insert in each cell
392431382f2SDave May -  xi - the coordinates (defined in the local coordinate system for each cell) to insert
393431382f2SDave May 
394431382f2SDave May  Level: beginner
395431382f2SDave May 
396431382f2SDave May  Notes:
39720f4b53cSBarry Smith  The method will reset any previous defined points within the `DMSWARM`.
39820f4b53cSBarry Smith  Only supported for `DMPLEX`. If you are using a `DMDA` it is recommended to either use
39920f4b53cSBarry Smith  `DMSwarmInsertPointsUsingCellDM()`, or extract and set the coordinates yourself the following code
40020f4b53cSBarry Smith .vb
40120f4b53cSBarry Smith     PetscReal *coor;
40220f4b53cSBarry Smith     DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
40320f4b53cSBarry Smith     // user code to define the coordinates here
40420f4b53cSBarry Smith     DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
40520f4b53cSBarry Smith .ve
406e7af74c8SDave May 
40720f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmInsertPointsUsingCellDM()`
408431382f2SDave May @*/
409d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinatesCellwise(DM dm, PetscInt npoints, PetscReal xi[])
410d71ae5a4SJacob Faibussowitsch {
411431382f2SDave May   DM        celldm;
412431382f2SDave May   PetscBool isDA, isPLEX;
413431382f2SDave May 
4140e2ec84fSDave May   PetscFunctionBegin;
415431382f2SDave May   DMSWARMPICVALID(dm);
4169566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetCellDM(dm, &celldm));
4179566063dSJacob Faibussowitsch   PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
4189566063dSJacob Faibussowitsch   PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
41928b400f6SJacob Faibussowitsch   PetscCheck(!isDA, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMPLEX. Recommended you use DMSwarmInsertPointsUsingCellDM()");
420f7d195e4SLawrence Mitchell   if (isPLEX) {
4219566063dSJacob Faibussowitsch     PetscCall(private_DMSwarmSetPointCoordinatesCellwise_PLEX(dm, celldm, npoints, xi));
422431382f2SDave May   } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
4233ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
4240e2ec84fSDave May }
425431382f2SDave May 
4260e2ec84fSDave May /* Field projection API */
42777048351SPatrick Sanan extern PetscErrorCode private_DMSwarmProjectFields_DA(DM swarm, DM celldm, PetscInt project_type, PetscInt nfields, DMSwarmDataField dfield[], Vec vecs[]);
42877048351SPatrick Sanan extern PetscErrorCode private_DMSwarmProjectFields_PLEX(DM swarm, DM celldm, PetscInt project_type, PetscInt nfields, DMSwarmDataField dfield[], Vec vecs[]);
42994f7d2dcSDave May 
43094f7d2dcSDave May /*@C
43120f4b53cSBarry Smith    DMSwarmProjectFields - Project a set of swarm fields onto the cell `DM`
43294f7d2dcSDave May 
43320f4b53cSBarry Smith    Collective
43494f7d2dcSDave May 
43594f7d2dcSDave May    Input parameters:
43620f4b53cSBarry Smith +  dm - the `DMSWARM`
43794f7d2dcSDave May .  nfields - the number of swarm fields to project
43894f7d2dcSDave May .  fieldnames - the textual names of the swarm fields to project
43994f7d2dcSDave May .  fields - an array of Vec's of length nfields
44094f7d2dcSDave May -  reuse - flag indicating whether the array and contents of fields should be re-used or internally allocated
44194f7d2dcSDave May 
44220f4b53cSBarry Smith    Level: beginner
44320f4b53cSBarry Smith 
44420f4b53cSBarry Smith    Notes:
44594f7d2dcSDave May    Currently, the only available projection method consists of
44620f4b53cSBarry Smith .vb
44794f7d2dcSDave May      phi_i = \sum_{p=0}^{np} N_i(x_p) phi_p dJ / \sum_{p=0}^{np} N_i(x_p) dJ
44894f7d2dcSDave May    where phi_p is the swarm field at point p,
44994f7d2dcSDave May      N_i() is the cell DM basis function at vertex i,
45094f7d2dcSDave May      dJ is the determinant of the cell Jacobian and
45194f7d2dcSDave May      phi_i is the projected vertex value of the field phi.
45220f4b53cSBarry Smith .ve
45394f7d2dcSDave May 
45420f4b53cSBarry Smith    If `reuse` is `PETSC_FALSE`, this function will allocate the array of `Vec`'s, and each individual `Vec`.
45520f4b53cSBarry Smith      The user is responsible for destroying both the array and the individual `Vec` objects.
45694f7d2dcSDave May 
45720f4b53cSBarry Smith    Only swarm fields registered with data type of `PETSC_REAL` can be projected onto the cell `DM`.
458e7af74c8SDave May 
459e7af74c8SDave May    Only swarm fields of block size = 1 can currently be projected.
460e7af74c8SDave May 
46120f4b53cSBarry Smith    The only projection methods currently only support the `DMDA` (2D) and `DMPLEX` (triangles 2D).
46294f7d2dcSDave May 
46320f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
46494f7d2dcSDave May @*/
465d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmProjectFields(DM dm, PetscInt nfields, const char *fieldnames[], Vec **fields, PetscBool reuse)
466d71ae5a4SJacob Faibussowitsch {
46794f7d2dcSDave May   DM_Swarm         *swarm = (DM_Swarm *)dm->data;
46877048351SPatrick Sanan   DMSwarmDataField *gfield;
46994f7d2dcSDave May   DM                celldm;
47094f7d2dcSDave May   PetscBool         isDA, isPLEX;
47194f7d2dcSDave May   Vec              *vecs;
47294f7d2dcSDave May   PetscInt          f, nvecs;
47394f7d2dcSDave May   PetscInt          project_type = 0;
47494f7d2dcSDave May 
4750e2ec84fSDave May   PetscFunctionBegin;
47694f7d2dcSDave May   DMSWARMPICVALID(dm);
4779566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetCellDM(dm, &celldm));
4789566063dSJacob Faibussowitsch   PetscCall(PetscMalloc1(nfields, &gfield));
47994f7d2dcSDave May   nvecs = 0;
48094f7d2dcSDave May   for (f = 0; f < nfields; f++) {
4819566063dSJacob Faibussowitsch     PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldnames[f], &gfield[f]));
4825f80ce2aSJacob Faibussowitsch     PetscCheck(gfield[f]->petsc_type == PETSC_REAL, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Projection only valid for fields using a data type = PETSC_REAL");
4835f80ce2aSJacob Faibussowitsch     PetscCheck(gfield[f]->bs == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Projection only valid for fields with block size = 1");
48494f7d2dcSDave May     nvecs += gfield[f]->bs;
48594f7d2dcSDave May   }
48694f7d2dcSDave May   if (!reuse) {
4879566063dSJacob Faibussowitsch     PetscCall(PetscMalloc1(nvecs, &vecs));
48894f7d2dcSDave May     for (f = 0; f < nvecs; f++) {
4899566063dSJacob Faibussowitsch       PetscCall(DMCreateGlobalVector(celldm, &vecs[f]));
4909566063dSJacob Faibussowitsch       PetscCall(PetscObjectSetName((PetscObject)vecs[f], gfield[f]->name));
49194f7d2dcSDave May     }
49294f7d2dcSDave May   } else {
49394f7d2dcSDave May     vecs = *fields;
49494f7d2dcSDave May   }
49594f7d2dcSDave May 
4969566063dSJacob Faibussowitsch   PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
4979566063dSJacob Faibussowitsch   PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
49894f7d2dcSDave May   if (isDA) {
4999566063dSJacob Faibussowitsch     PetscCall(private_DMSwarmProjectFields_DA(dm, celldm, project_type, nfields, gfield, vecs));
50094f7d2dcSDave May   } else if (isPLEX) {
5019566063dSJacob Faibussowitsch     PetscCall(private_DMSwarmProjectFields_PLEX(dm, celldm, project_type, nfields, gfield, vecs));
50294f7d2dcSDave May   } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
50394f7d2dcSDave May 
5049566063dSJacob Faibussowitsch   PetscCall(PetscFree(gfield));
5055f80ce2aSJacob Faibussowitsch   if (!reuse) *fields = vecs;
5063ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
5070e2ec84fSDave May }
5080e2ec84fSDave May 
5090e2ec84fSDave May /*@C
510b799feefSDave May    DMSwarmCreatePointPerCellCount - Count the number of points within all cells in the cell DM
5110e2ec84fSDave May 
51220f4b53cSBarry Smith    Not Collective
5130e2ec84fSDave May 
5140e2ec84fSDave May    Input parameter:
51520f4b53cSBarry Smith .  dm - the `DMSWARM`
5160e2ec84fSDave May 
5170e2ec84fSDave May    Output parameters:
51820f4b53cSBarry Smith +  ncells - the number of cells in the cell `DM` (optional argument, pass `NULL` to ignore)
519b799feefSDave May -  count - array of length ncells containing the number of points per cell
5200e2ec84fSDave May 
5210e2ec84fSDave May    Level: beginner
5220e2ec84fSDave May 
5230e2ec84fSDave May    Notes:
5240e2ec84fSDave May    The array count is allocated internally and must be free'd by the user.
5250e2ec84fSDave May 
52620f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
5270e2ec84fSDave May @*/
528d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm, PetscInt *ncells, PetscInt **count)
529d71ae5a4SJacob Faibussowitsch {
530b799feefSDave May   PetscBool isvalid;
531b799feefSDave May   PetscInt  nel;
532b799feefSDave May   PetscInt *sum;
533b799feefSDave May 
5340e2ec84fSDave May   PetscFunctionBegin;
5359566063dSJacob Faibussowitsch   PetscCall(DMSwarmSortGetIsValid(dm, &isvalid));
536b799feefSDave May   nel = 0;
537b799feefSDave May   if (isvalid) {
538b799feefSDave May     PetscInt e;
539b799feefSDave May 
5409566063dSJacob Faibussowitsch     PetscCall(DMSwarmSortGetSizes(dm, &nel, NULL));
541b799feefSDave May 
5429566063dSJacob Faibussowitsch     PetscCall(PetscMalloc1(nel, &sum));
54348a46eb9SPierre Jolivet     for (e = 0; e < nel; e++) PetscCall(DMSwarmSortGetNumberOfPointsPerCell(dm, e, &sum[e]));
544b799feefSDave May   } else {
545b799feefSDave May     DM        celldm;
546b799feefSDave May     PetscBool isda, isplex, isshell;
547b799feefSDave May     PetscInt  p, npoints;
548b799feefSDave May     PetscInt *swarm_cellid;
549b799feefSDave May 
550b799feefSDave May     /* get the number of cells */
5519566063dSJacob Faibussowitsch     PetscCall(DMSwarmGetCellDM(dm, &celldm));
5529566063dSJacob Faibussowitsch     PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isda));
5539566063dSJacob Faibussowitsch     PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isplex));
5549566063dSJacob Faibussowitsch     PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMSHELL, &isshell));
555b799feefSDave May     if (isda) {
556b799feefSDave May       PetscInt        _nel, _npe;
557b799feefSDave May       const PetscInt *_element;
558b799feefSDave May 
5599566063dSJacob Faibussowitsch       PetscCall(DMDAGetElements(celldm, &_nel, &_npe, &_element));
560b799feefSDave May       nel = _nel;
5619566063dSJacob Faibussowitsch       PetscCall(DMDARestoreElements(celldm, &_nel, &_npe, &_element));
562b799feefSDave May     } else if (isplex) {
563b799feefSDave May       PetscInt ps, pe;
564b799feefSDave May 
5659566063dSJacob Faibussowitsch       PetscCall(DMPlexGetHeightStratum(celldm, 0, &ps, &pe));
566b799feefSDave May       nel = pe - ps;
567b799feefSDave May     } else if (isshell) {
568b799feefSDave May       PetscErrorCode (*method_DMShellGetNumberOfCells)(DM, PetscInt *);
569b799feefSDave May 
5709566063dSJacob Faibussowitsch       PetscCall(PetscObjectQueryFunction((PetscObject)celldm, "DMGetNumberOfCells_C", &method_DMShellGetNumberOfCells));
571b799feefSDave May       if (method_DMShellGetNumberOfCells) {
5729566063dSJacob Faibussowitsch         PetscCall(method_DMShellGetNumberOfCells(celldm, &nel));
5739371c9d4SSatish Balay       } else
5749371c9d4SSatish Balay         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);");
575b799feefSDave May     } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot determine the number of cells for a DM not of type DA, PLEX or SHELL");
576b799feefSDave May 
5779566063dSJacob Faibussowitsch     PetscCall(PetscMalloc1(nel, &sum));
5789566063dSJacob Faibussowitsch     PetscCall(PetscArrayzero(sum, nel));
5799566063dSJacob Faibussowitsch     PetscCall(DMSwarmGetLocalSize(dm, &npoints));
5809566063dSJacob Faibussowitsch     PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
581b799feefSDave May     for (p = 0; p < npoints; p++) {
582ad540459SPierre Jolivet       if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) sum[swarm_cellid[p]]++;
583b799feefSDave May     }
5849566063dSJacob Faibussowitsch     PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
585b799feefSDave May   }
586ad540459SPierre Jolivet   if (ncells) *ncells = nel;
587b799feefSDave May   *count = sum;
5883ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
5890e2ec84fSDave May }
59035b38c60SMatthew G. Knepley 
59135b38c60SMatthew G. Knepley /*@
59235b38c60SMatthew G. Knepley   DMSwarmGetNumSpecies - Get the number of particle species
59335b38c60SMatthew G. Knepley 
59420f4b53cSBarry Smith   Not Collective
59535b38c60SMatthew G. Knepley 
59635b38c60SMatthew G. Knepley   Input parameter:
59720f4b53cSBarry Smith . dm - the `DMSWARM`
59835b38c60SMatthew G. Knepley 
59935b38c60SMatthew G. Knepley   Output parameters:
60035b38c60SMatthew G. Knepley . Ns - the number of species
60135b38c60SMatthew G. Knepley 
60235b38c60SMatthew G. Knepley   Level: intermediate
60335b38c60SMatthew G. Knepley 
60420f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType`
60535b38c60SMatthew G. Knepley @*/
606d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmGetNumSpecies(DM sw, PetscInt *Ns)
607d71ae5a4SJacob Faibussowitsch {
60835b38c60SMatthew G. Knepley   DM_Swarm *swarm = (DM_Swarm *)sw->data;
60935b38c60SMatthew G. Knepley 
61035b38c60SMatthew G. Knepley   PetscFunctionBegin;
61135b38c60SMatthew G. Knepley   *Ns = swarm->Ns;
6123ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
61335b38c60SMatthew G. Knepley }
61435b38c60SMatthew G. Knepley 
61535b38c60SMatthew G. Knepley /*@
61635b38c60SMatthew G. Knepley   DMSwarmSetNumSpecies - Set the number of particle species
61735b38c60SMatthew G. Knepley 
61820f4b53cSBarry Smith   Not Collective
61935b38c60SMatthew G. Knepley 
62035b38c60SMatthew G. Knepley   Input parameter:
62120f4b53cSBarry Smith + dm - the `DMSWARM`
62235b38c60SMatthew G. Knepley - Ns - the number of species
62335b38c60SMatthew G. Knepley 
62435b38c60SMatthew G. Knepley   Level: intermediate
62535b38c60SMatthew G. Knepley 
62620f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmGetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType`
62735b38c60SMatthew G. Knepley @*/
628d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmSetNumSpecies(DM sw, PetscInt Ns)
629d71ae5a4SJacob Faibussowitsch {
63035b38c60SMatthew G. Knepley   DM_Swarm *swarm = (DM_Swarm *)sw->data;
63135b38c60SMatthew G. Knepley 
63235b38c60SMatthew G. Knepley   PetscFunctionBegin;
63335b38c60SMatthew G. Knepley   swarm->Ns = Ns;
6343ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
63535b38c60SMatthew G. Knepley }
63635b38c60SMatthew G. Knepley 
63735b38c60SMatthew G. Knepley /*@C
6386c5a79ebSMatthew G. Knepley   DMSwarmGetCoordinateFunction - Get the function setting initial particle positions, if it exists
6396c5a79ebSMatthew G. Knepley 
64020f4b53cSBarry Smith   Not Collective
6416c5a79ebSMatthew G. Knepley 
6426c5a79ebSMatthew G. Knepley   Input parameter:
64320f4b53cSBarry Smith . dm - the `DMSWARM`
6446c5a79ebSMatthew G. Knepley 
6456c5a79ebSMatthew G. Knepley   Output Parameter:
64620f4b53cSBarry Smith . coordFunc - the function setting initial particle positions, or `NULL`
6476c5a79ebSMatthew G. Knepley 
6486c5a79ebSMatthew G. Knepley   Level: intermediate
6496c5a79ebSMatthew G. Knepley 
65020f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetCoordinateFunction()`, `DMSwarmGetVelocityFunction()`, `DMSwarmInitializeCoordinates()`
6516c5a79ebSMatthew G. Knepley @*/
652d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmGetCoordinateFunction(DM sw, PetscSimplePointFunc *coordFunc)
653d71ae5a4SJacob Faibussowitsch {
6546c5a79ebSMatthew G. Knepley   DM_Swarm *swarm = (DM_Swarm *)sw->data;
6556c5a79ebSMatthew G. Knepley 
6566c5a79ebSMatthew G. Knepley   PetscFunctionBegin;
6576c5a79ebSMatthew G. Knepley   PetscValidHeaderSpecific(sw, DM_CLASSID, 1);
6586c5a79ebSMatthew G. Knepley   PetscValidPointer(coordFunc, 2);
6596c5a79ebSMatthew G. Knepley   *coordFunc = swarm->coordFunc;
6603ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
6616c5a79ebSMatthew G. Knepley }
6626c5a79ebSMatthew G. Knepley 
6636c5a79ebSMatthew G. Knepley /*@C
6646c5a79ebSMatthew G. Knepley   DMSwarmSetCoordinateFunction - Set the function setting initial particle positions
6656c5a79ebSMatthew G. Knepley 
66620f4b53cSBarry Smith   Not Collective
6676c5a79ebSMatthew G. Knepley 
6686c5a79ebSMatthew G. Knepley   Input parameters:
66920f4b53cSBarry Smith + dm - the `DMSWARM`
6706c5a79ebSMatthew G. Knepley - coordFunc - the function setting initial particle positions
6716c5a79ebSMatthew G. Knepley 
6726c5a79ebSMatthew G. Knepley   Level: intermediate
6736c5a79ebSMatthew G. Knepley 
67420f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmGetCoordinateFunction()`, `DMSwarmSetVelocityFunction()`, `DMSwarmInitializeCoordinates()`
6756c5a79ebSMatthew G. Knepley @*/
676d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmSetCoordinateFunction(DM sw, PetscSimplePointFunc coordFunc)
677d71ae5a4SJacob Faibussowitsch {
6786c5a79ebSMatthew G. Knepley   DM_Swarm *swarm = (DM_Swarm *)sw->data;
6796c5a79ebSMatthew G. Knepley 
6806c5a79ebSMatthew G. Knepley   PetscFunctionBegin;
6816c5a79ebSMatthew G. Knepley   PetscValidHeaderSpecific(sw, DM_CLASSID, 1);
6826c5a79ebSMatthew G. Knepley   PetscValidFunction(coordFunc, 2);
6836c5a79ebSMatthew G. Knepley   swarm->coordFunc = coordFunc;
6843ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
6856c5a79ebSMatthew G. Knepley }
6866c5a79ebSMatthew G. Knepley 
6876c5a79ebSMatthew G. Knepley /*@C
6886c5a79ebSMatthew G. Knepley   DMSwarmGetCoordinateFunction - Get the function setting initial particle velocities, if it exists
6896c5a79ebSMatthew G. Knepley 
69020f4b53cSBarry Smith   Not Collective
6916c5a79ebSMatthew G. Knepley 
6926c5a79ebSMatthew G. Knepley   Input parameter:
69320f4b53cSBarry Smith . dm - the `DMSWARM`
6946c5a79ebSMatthew G. Knepley 
6956c5a79ebSMatthew G. Knepley   Output Parameter:
69620f4b53cSBarry Smith . velFunc - the function setting initial particle velocities, or `NULL`
6976c5a79ebSMatthew G. Knepley 
6986c5a79ebSMatthew G. Knepley   Level: intermediate
6996c5a79ebSMatthew G. Knepley 
70020f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetVelocityFunction()`, `DMSwarmGetCoordinateFunction()`, `DMSwarmInitializeVelocities()`
7016c5a79ebSMatthew G. Knepley @*/
702d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmGetVelocityFunction(DM sw, PetscSimplePointFunc *velFunc)
703d71ae5a4SJacob Faibussowitsch {
7046c5a79ebSMatthew G. Knepley   DM_Swarm *swarm = (DM_Swarm *)sw->data;
7056c5a79ebSMatthew G. Knepley 
7066c5a79ebSMatthew G. Knepley   PetscFunctionBegin;
7076c5a79ebSMatthew G. Knepley   PetscValidHeaderSpecific(sw, DM_CLASSID, 1);
7086c5a79ebSMatthew G. Knepley   PetscValidPointer(velFunc, 2);
7096c5a79ebSMatthew G. Knepley   *velFunc = swarm->velFunc;
7103ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
7116c5a79ebSMatthew G. Knepley }
7126c5a79ebSMatthew G. Knepley 
7136c5a79ebSMatthew G. Knepley /*@C
7146c5a79ebSMatthew G. Knepley   DMSwarmSetVelocityFunction - Set the function setting initial particle velocities
7156c5a79ebSMatthew G. Knepley 
71620f4b53cSBarry Smith   Not Collective
7176c5a79ebSMatthew G. Knepley 
7186c5a79ebSMatthew G. Knepley   Input parameters:
71920f4b53cSBarry Smith + dm - the `DMSWARM`
7206c5a79ebSMatthew G. Knepley - coordFunc - the function setting initial particle velocities
7216c5a79ebSMatthew G. Knepley 
7226c5a79ebSMatthew G. Knepley   Level: intermediate
7236c5a79ebSMatthew G. Knepley 
72420f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmGetVelocityFunction()`, `DMSwarmSetCoordinateFunction()`, `DMSwarmInitializeVelocities()`
7256c5a79ebSMatthew G. Knepley @*/
726d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmSetVelocityFunction(DM sw, PetscSimplePointFunc velFunc)
727d71ae5a4SJacob Faibussowitsch {
7286c5a79ebSMatthew G. Knepley   DM_Swarm *swarm = (DM_Swarm *)sw->data;
7296c5a79ebSMatthew G. Knepley 
7306c5a79ebSMatthew G. Knepley   PetscFunctionBegin;
7316c5a79ebSMatthew G. Knepley   PetscValidHeaderSpecific(sw, DM_CLASSID, 1);
7326c5a79ebSMatthew G. Knepley   PetscValidFunction(velFunc, 2);
7336c5a79ebSMatthew G. Knepley   swarm->velFunc = velFunc;
7343ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
7356c5a79ebSMatthew G. Knepley }
7366c5a79ebSMatthew G. Knepley 
7376c5a79ebSMatthew G. Knepley /*@C
73835b38c60SMatthew G. Knepley   DMSwarmComputeLocalSize - Compute the local number and distribution of particles based upon a density function
73935b38c60SMatthew G. Knepley 
74020f4b53cSBarry Smith   Not Collective
74135b38c60SMatthew G. Knepley 
74235b38c60SMatthew G. Knepley   Input Parameters:
74320f4b53cSBarry Smith + sw      - The `DMSWARM`
74435b38c60SMatthew G. Knepley . N       - The target number of particles
74535b38c60SMatthew G. Knepley - density - The density field for the particle layout, normalized to unity
74635b38c60SMatthew G. Knepley 
74735b38c60SMatthew G. Knepley   Level: advanced
74835b38c60SMatthew G. Knepley 
74920f4b53cSBarry Smith   Note:
75020f4b53cSBarry Smith   One particle will be created for each species.
75120f4b53cSBarry Smith 
75220f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSizeFromOptions()`
75335b38c60SMatthew G. Knepley @*/
754d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmComputeLocalSize(DM sw, PetscInt N, PetscProbFunc density)
755d71ae5a4SJacob Faibussowitsch {
75635b38c60SMatthew G. Knepley   DM               dm;
75735b38c60SMatthew G. Knepley   PetscQuadrature  quad;
75835b38c60SMatthew G. Knepley   const PetscReal *xq, *wq;
759ea7032a0SMatthew G. Knepley   PetscReal       *n_int;
760ea7032a0SMatthew G. Knepley   PetscInt        *npc_s, *cellid, Ni;
761ea7032a0SMatthew G. Knepley   PetscReal        gmin[3], gmax[3], xi0[3];
762ea7032a0SMatthew G. Knepley   PetscInt         Ns, cStart, cEnd, c, dim, d, Nq, q, Np = 0, p, s;
76335b38c60SMatthew G. Knepley   PetscBool        simplex;
76435b38c60SMatthew G. Knepley 
76535b38c60SMatthew G. Knepley   PetscFunctionBegin;
7669566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
7679566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetCellDM(sw, &dm));
7689566063dSJacob Faibussowitsch   PetscCall(DMGetDimension(dm, &dim));
769ea7032a0SMatthew G. Knepley   PetscCall(DMGetBoundingBox(dm, gmin, gmax));
7709566063dSJacob Faibussowitsch   PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
7719566063dSJacob Faibussowitsch   PetscCall(DMPlexIsSimplex(dm, &simplex));
7726858538eSMatthew G. Knepley   PetscCall(DMGetCoordinatesLocalSetUp(dm));
7739566063dSJacob Faibussowitsch   if (simplex) PetscCall(PetscDTStroudConicalQuadrature(dim, 1, 5, -1.0, 1.0, &quad));
7749566063dSJacob Faibussowitsch   else PetscCall(PetscDTGaussTensorQuadrature(dim, 1, 5, -1.0, 1.0, &quad));
7759566063dSJacob Faibussowitsch   PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, &xq, &wq));
776ea7032a0SMatthew G. Knepley   PetscCall(PetscCalloc2(Ns, &n_int, (cEnd - cStart) * Ns, &npc_s));
77735b38c60SMatthew G. Knepley   /* Integrate the density function to get the number of particles in each cell */
77835b38c60SMatthew G. Knepley   for (d = 0; d < dim; ++d) xi0[d] = -1.0;
77935b38c60SMatthew G. Knepley   for (c = 0; c < cEnd - cStart; ++c) {
78035b38c60SMatthew G. Knepley     const PetscInt cell = c + cStart;
781ea7032a0SMatthew G. Knepley     PetscReal      v0[3], J[9], invJ[9], detJ, detJp = 2. / (gmax[0] - gmin[0]), xr[3], den;
78235b38c60SMatthew G. Knepley 
783ea7032a0SMatthew G. Knepley     /*Have to transform quadrature points/weights to cell domain*/
7849566063dSJacob Faibussowitsch     PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ));
785ea7032a0SMatthew G. Knepley     PetscCall(PetscArrayzero(n_int, Ns));
78635b38c60SMatthew G. Knepley     for (q = 0; q < Nq; ++q) {
78735b38c60SMatthew G. Knepley       CoordinatesRefToReal(dim, dim, xi0, v0, J, &xq[q * dim], xr);
788ea7032a0SMatthew G. Knepley       /* Have to transform mesh to domain of definition of PDF, [-1, 1], and weight PDF by |J|/2 */
789ea7032a0SMatthew G. Knepley       xr[0] = detJp * (xr[0] - gmin[0]) - 1.;
790ea7032a0SMatthew G. Knepley 
791ea7032a0SMatthew G. Knepley       for (s = 0; s < Ns; ++s) {
792ea7032a0SMatthew G. Knepley         PetscCall(density(xr, NULL, &den));
793ea7032a0SMatthew G. Knepley         n_int[s] += (detJp * den) * (detJ * wq[q]) / (PetscReal)Ns;
79435b38c60SMatthew G. Knepley       }
795ea7032a0SMatthew G. Knepley     }
796ea7032a0SMatthew G. Knepley     for (s = 0; s < Ns; ++s) {
797ea7032a0SMatthew G. Knepley       Ni = N;
798ea7032a0SMatthew G. Knepley       npc_s[c * Ns + s] += (PetscInt)(Ni * n_int[s]);
799ea7032a0SMatthew G. Knepley       Np += npc_s[c * Ns + s];
800ea7032a0SMatthew G. Knepley     }
80135b38c60SMatthew G. Knepley   }
8029566063dSJacob Faibussowitsch   PetscCall(PetscQuadratureDestroy(&quad));
8039566063dSJacob Faibussowitsch   PetscCall(DMSwarmSetLocalSizes(sw, Np, 0));
8049566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid));
80535b38c60SMatthew G. Knepley   for (c = 0, p = 0; c < cEnd - cStart; ++c) {
806ea7032a0SMatthew G. Knepley     for (s = 0; s < Ns; ++s) {
807ea7032a0SMatthew G. Knepley       for (q = 0; q < npc_s[c * Ns + s]; ++q, ++p) cellid[p] = c;
808ea7032a0SMatthew G. Knepley     }
80935b38c60SMatthew G. Knepley   }
8109566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid));
811ea7032a0SMatthew G. Knepley   PetscCall(PetscFree2(n_int, npc_s));
8123ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
81335b38c60SMatthew G. Knepley }
81435b38c60SMatthew G. Knepley 
81535b38c60SMatthew G. Knepley /*@
81635b38c60SMatthew G. Knepley   DMSwarmComputeLocalSizeFromOptions - Compute the local number and distribution of particles based upon a density function determined by options
81735b38c60SMatthew G. Knepley 
81820f4b53cSBarry Smith   Not Collective
81935b38c60SMatthew G. Knepley 
820*2fe279fdSBarry Smith   Input Parameter:
821*2fe279fdSBarry Smith . sw - The `DMSWARM`
82235b38c60SMatthew G. Knepley 
82335b38c60SMatthew G. Knepley   Level: advanced
82435b38c60SMatthew G. Knepley 
82520f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`
82635b38c60SMatthew G. Knepley @*/
827d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmComputeLocalSizeFromOptions(DM sw)
828d71ae5a4SJacob Faibussowitsch {
82935b38c60SMatthew G. Knepley   PetscProbFunc pdf;
83035b38c60SMatthew G. Knepley   const char   *prefix;
8316c5a79ebSMatthew G. Knepley   char          funcname[PETSC_MAX_PATH_LEN];
8326c5a79ebSMatthew G. Knepley   PetscInt     *N, Ns, dim, n;
8336c5a79ebSMatthew G. Knepley   PetscBool     flg;
8346c5a79ebSMatthew G. Knepley   PetscMPIInt   size, rank;
83535b38c60SMatthew G. Knepley 
83635b38c60SMatthew G. Knepley   PetscFunctionBegin;
8376c5a79ebSMatthew G. Knepley   PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)sw), &size));
8386c5a79ebSMatthew G. Knepley   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)sw), &rank));
8396c5a79ebSMatthew G. Knepley   PetscCall(PetscCalloc1(size, &N));
840d0609cedSBarry Smith   PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM");
8416c5a79ebSMatthew G. Knepley   n = size;
8426c5a79ebSMatthew G. Knepley   PetscCall(PetscOptionsIntArray("-dm_swarm_num_particles", "The target number of particles", "", N, &n, NULL));
8436c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
8449566063dSJacob Faibussowitsch   PetscCall(PetscOptionsInt("-dm_swarm_num_species", "The number of species", "DMSwarmSetNumSpecies", Ns, &Ns, &flg));
8459566063dSJacob Faibussowitsch   if (flg) PetscCall(DMSwarmSetNumSpecies(sw, Ns));
8466c5a79ebSMatthew G. Knepley   PetscCall(PetscOptionsString("-dm_swarm_coordinate_function", "Function to determine particle coordinates", "DMSwarmSetCoordinateFunction", funcname, funcname, sizeof(funcname), &flg));
847d0609cedSBarry Smith   PetscOptionsEnd();
8486c5a79ebSMatthew G. Knepley   if (flg) {
8496c5a79ebSMatthew G. Knepley     PetscSimplePointFunc coordFunc;
85035b38c60SMatthew G. Knepley 
8516c5a79ebSMatthew G. Knepley     PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
8526c5a79ebSMatthew G. Knepley     PetscCall(PetscDLSym(NULL, funcname, (void **)&coordFunc));
8536c5a79ebSMatthew G. Knepley     PetscCheck(coordFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname);
8546c5a79ebSMatthew G. Knepley     PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
8556c5a79ebSMatthew G. Knepley     PetscCall(DMSwarmSetLocalSizes(sw, N[rank] * Ns, 0));
8566c5a79ebSMatthew G. Knepley     PetscCall(DMSwarmSetCoordinateFunction(sw, coordFunc));
8576c5a79ebSMatthew G. Knepley   } else {
8589566063dSJacob Faibussowitsch     PetscCall(DMGetDimension(sw, &dim));
8599566063dSJacob Faibussowitsch     PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix));
8609566063dSJacob Faibussowitsch     PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_coordinate_density", &pdf, NULL, NULL));
8616c5a79ebSMatthew G. Knepley     PetscCall(DMSwarmComputeLocalSize(sw, N[rank], pdf));
8626c5a79ebSMatthew G. Knepley   }
8636c5a79ebSMatthew G. Knepley   PetscCall(PetscFree(N));
8643ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
86535b38c60SMatthew G. Knepley }
86635b38c60SMatthew G. Knepley 
86735b38c60SMatthew G. Knepley /*@
86835b38c60SMatthew G. Knepley   DMSwarmInitializeCoordinates - Determine the initial coordinates of particles for a PIC method
86935b38c60SMatthew G. Knepley 
87020f4b53cSBarry Smith   Not Collective
87135b38c60SMatthew G. Knepley 
87220f4b53cSBarry Smith   Input Parameter:
87320f4b53cSBarry Smith . sw - The `DMSWARM`
87435b38c60SMatthew G. Knepley 
87535b38c60SMatthew G. Knepley   Level: advanced
87635b38c60SMatthew G. Knepley 
87720f4b53cSBarry Smith   Note:
87820f4b53cSBarry Smith   Currently, we randomly place particles in their assigned cell
87920f4b53cSBarry Smith 
88020f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeVelocities()`
88135b38c60SMatthew G. Knepley @*/
882d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmInitializeCoordinates(DM sw)
883d71ae5a4SJacob Faibussowitsch {
8846c5a79ebSMatthew G. Knepley   PetscSimplePointFunc coordFunc;
88535b38c60SMatthew G. Knepley   PetscScalar         *weight;
8866c5a79ebSMatthew G. Knepley   PetscReal           *x;
88735b38c60SMatthew G. Knepley   PetscInt            *species;
8886c5a79ebSMatthew G. Knepley   void                *ctx;
88935b38c60SMatthew G. Knepley   PetscBool            removePoints = PETSC_TRUE;
89035b38c60SMatthew G. Knepley   PetscDataType        dtype;
8916c5a79ebSMatthew G. Knepley   PetscInt             Np, p, Ns, dim, d, bs;
89235b38c60SMatthew G. Knepley 
89335b38c60SMatthew G. Knepley   PetscFunctionBeginUser;
8946c5a79ebSMatthew G. Knepley   PetscCall(DMGetDimension(sw, &dim));
8956c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetLocalSize(sw, &Np));
8969566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
8976c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetCoordinateFunction(sw, &coordFunc));
8986c5a79ebSMatthew G. Knepley 
8996c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, &bs, &dtype, (void **)&x));
9006c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetField(sw, "w_q", &bs, &dtype, (void **)&weight));
9016c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
9026c5a79ebSMatthew G. Knepley   if (coordFunc) {
9036c5a79ebSMatthew G. Knepley     PetscCall(DMGetApplicationContext(sw, &ctx));
9046c5a79ebSMatthew G. Knepley     for (p = 0; p < Np; ++p) {
9056c5a79ebSMatthew G. Knepley       PetscScalar X[3];
9066c5a79ebSMatthew G. Knepley 
9076c5a79ebSMatthew G. Knepley       PetscCall((*coordFunc)(dim, 0., NULL, p, X, ctx));
9086c5a79ebSMatthew G. Knepley       for (d = 0; d < dim; ++d) x[p * dim + d] = PetscRealPart(X[d]);
9096c5a79ebSMatthew G. Knepley       weight[p]  = 1.0;
9106c5a79ebSMatthew G. Knepley       species[p] = p % Ns;
9116c5a79ebSMatthew G. Knepley     }
9126c5a79ebSMatthew G. Knepley   } else {
9136c5a79ebSMatthew G. Knepley     DM          dm;
9146c5a79ebSMatthew G. Knepley     PetscRandom rnd;
9156c5a79ebSMatthew G. Knepley     PetscReal   xi0[3];
9166c5a79ebSMatthew G. Knepley     PetscInt    cStart, cEnd, c;
9176c5a79ebSMatthew G. Knepley 
9189566063dSJacob Faibussowitsch     PetscCall(DMSwarmGetCellDM(sw, &dm));
9199566063dSJacob Faibussowitsch     PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
920ea7032a0SMatthew G. Knepley     PetscCall(DMGetApplicationContext(sw, &ctx));
92135b38c60SMatthew G. Knepley 
92235b38c60SMatthew G. Knepley     /* Set particle position randomly in cell, set weights to 1 */
9239566063dSJacob Faibussowitsch     PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)dm), &rnd));
9249566063dSJacob Faibussowitsch     PetscCall(PetscRandomSetInterval(rnd, -1.0, 1.0));
9259566063dSJacob Faibussowitsch     PetscCall(PetscRandomSetFromOptions(rnd));
9269566063dSJacob Faibussowitsch     PetscCall(DMSwarmSortGetAccess(sw));
92735b38c60SMatthew G. Knepley     for (d = 0; d < dim; ++d) xi0[d] = -1.0;
92835b38c60SMatthew G. Knepley     for (c = cStart; c < cEnd; ++c) {
92935b38c60SMatthew G. Knepley       PetscReal v0[3], J[9], invJ[9], detJ;
93035b38c60SMatthew G. Knepley       PetscInt *pidx, Npc, q;
93135b38c60SMatthew G. Knepley 
9329566063dSJacob Faibussowitsch       PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
9339566063dSJacob Faibussowitsch       PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ));
93435b38c60SMatthew G. Knepley       for (q = 0; q < Npc; ++q) {
93535b38c60SMatthew G. Knepley         const PetscInt p = pidx[q];
93635b38c60SMatthew G. Knepley         PetscReal      xref[3];
93735b38c60SMatthew G. Knepley 
9389566063dSJacob Faibussowitsch         for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &xref[d]));
93935b38c60SMatthew G. Knepley         CoordinatesRefToReal(dim, dim, xi0, v0, J, xref, &x[p * dim]);
94035b38c60SMatthew G. Knepley 
941ea7032a0SMatthew G. Knepley         weight[p]  = 1.0 / Np;
9426c5a79ebSMatthew G. Knepley         species[p] = p % Ns;
94335b38c60SMatthew G. Knepley       }
9449566063dSJacob Faibussowitsch       PetscCall(PetscFree(pidx));
94535b38c60SMatthew G. Knepley     }
9469566063dSJacob Faibussowitsch     PetscCall(PetscRandomDestroy(&rnd));
9479566063dSJacob Faibussowitsch     PetscCall(DMSwarmSortRestoreAccess(sw));
9486c5a79ebSMatthew G. Knepley   }
9499566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
9506c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
9519566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
9526c5a79ebSMatthew G. Knepley 
9539566063dSJacob Faibussowitsch   PetscCall(DMSwarmMigrate(sw, removePoints));
9549566063dSJacob Faibussowitsch   PetscCall(DMLocalizeCoordinates(sw));
9553ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
95635b38c60SMatthew G. Knepley }
95735b38c60SMatthew G. Knepley 
95835b38c60SMatthew G. Knepley /*@C
95935b38c60SMatthew G. Knepley   DMSwarmInitializeVelocities - Set the initial velocities of particles using a distribution.
96035b38c60SMatthew G. Knepley 
96120f4b53cSBarry Smith   Collective
96235b38c60SMatthew G. Knepley 
96335b38c60SMatthew G. Knepley   Input Parameters:
96420f4b53cSBarry Smith + sw      - The `DMSWARM` object
96535b38c60SMatthew G. Knepley . sampler - A function which uniformly samples the velocity PDF
96635b38c60SMatthew G. Knepley - v0      - The velocity scale for nondimensionalization for each species
96735b38c60SMatthew G. Knepley 
96835b38c60SMatthew G. Knepley   Level: advanced
96935b38c60SMatthew G. Knepley 
97020f4b53cSBarry Smith   Note:
97120f4b53cSBarry Smith   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.
97220f4b53cSBarry Smith 
97320f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocitiesFromOptions()`
97435b38c60SMatthew G. Knepley @*/
975d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmInitializeVelocities(DM sw, PetscProbFunc sampler, const PetscReal v0[])
976d71ae5a4SJacob Faibussowitsch {
9776c5a79ebSMatthew G. Knepley   PetscSimplePointFunc velFunc;
97835b38c60SMatthew G. Knepley   PetscReal           *v;
97935b38c60SMatthew G. Knepley   PetscInt            *species;
9806c5a79ebSMatthew G. Knepley   void                *ctx;
98135b38c60SMatthew G. Knepley   PetscInt             dim, Np, p;
98235b38c60SMatthew G. Knepley 
98335b38c60SMatthew G. Knepley   PetscFunctionBegin;
9846c5a79ebSMatthew G. Knepley   PetscCall(DMSwarmGetVelocityFunction(sw, &velFunc));
98535b38c60SMatthew G. Knepley 
9869566063dSJacob Faibussowitsch   PetscCall(DMGetDimension(sw, &dim));
9879566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetLocalSize(sw, &Np));
9889566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v));
9899566063dSJacob Faibussowitsch   PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
9906c5a79ebSMatthew G. Knepley   if (v0[0] == 0.) {
9916c5a79ebSMatthew G. Knepley     PetscCall(PetscArrayzero(v, Np * dim));
9926c5a79ebSMatthew G. Knepley   } else if (velFunc) {
9936c5a79ebSMatthew G. Knepley     PetscCall(DMGetApplicationContext(sw, &ctx));
9946c5a79ebSMatthew G. Knepley     for (p = 0; p < Np; ++p) {
9956c5a79ebSMatthew G. Knepley       PetscInt    s = species[p], d;
9966c5a79ebSMatthew G. Knepley       PetscScalar vel[3];
9976c5a79ebSMatthew G. Knepley 
9986c5a79ebSMatthew G. Knepley       PetscCall((*velFunc)(dim, 0., NULL, p, vel, ctx));
9996c5a79ebSMatthew G. Knepley       for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * PetscRealPart(vel[d]);
10006c5a79ebSMatthew G. Knepley     }
10016c5a79ebSMatthew G. Knepley   } else {
10026c5a79ebSMatthew G. Knepley     PetscRandom rnd;
10036c5a79ebSMatthew G. Knepley 
10046c5a79ebSMatthew G. Knepley     PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)sw), &rnd));
10056c5a79ebSMatthew G. Knepley     PetscCall(PetscRandomSetInterval(rnd, 0, 1.));
10066c5a79ebSMatthew G. Knepley     PetscCall(PetscRandomSetFromOptions(rnd));
10076c5a79ebSMatthew G. Knepley 
100835b38c60SMatthew G. Knepley     for (p = 0; p < Np; ++p) {
100935b38c60SMatthew G. Knepley       PetscInt  s = species[p], d;
101035b38c60SMatthew G. Knepley       PetscReal a[3], vel[3];
101135b38c60SMatthew G. Knepley 
10129566063dSJacob Faibussowitsch       for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &a[d]));
10139566063dSJacob Faibussowitsch       PetscCall(sampler(a, NULL, vel));
1014ad540459SPierre Jolivet       for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * vel[d];
101535b38c60SMatthew G. Knepley     }
10166c5a79ebSMatthew G. Knepley     PetscCall(PetscRandomDestroy(&rnd));
10176c5a79ebSMatthew G. Knepley   }
10189566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v));
10199566063dSJacob Faibussowitsch   PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
10203ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
102135b38c60SMatthew G. Knepley }
102235b38c60SMatthew G. Knepley 
102335b38c60SMatthew G. Knepley /*@
102435b38c60SMatthew G. Knepley   DMSwarmInitializeVelocitiesFromOptions - Set the initial velocities of particles using a distribution determined from options.
102535b38c60SMatthew G. Knepley 
102620f4b53cSBarry Smith   Collective
102735b38c60SMatthew G. Knepley 
102835b38c60SMatthew G. Knepley   Input Parameters:
102920f4b53cSBarry Smith + sw      - The `DMSWARM` object
103035b38c60SMatthew G. Knepley - v0      - The velocity scale for nondimensionalization for each species
103135b38c60SMatthew G. Knepley 
103235b38c60SMatthew G. Knepley   Level: advanced
103335b38c60SMatthew G. Knepley 
103420f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocities()`
103535b38c60SMatthew G. Knepley @*/
1036d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmInitializeVelocitiesFromOptions(DM sw, const PetscReal v0[])
1037d71ae5a4SJacob Faibussowitsch {
103835b38c60SMatthew G. Knepley   PetscProbFunc sampler;
103935b38c60SMatthew G. Knepley   PetscInt      dim;
104035b38c60SMatthew G. Knepley   const char   *prefix;
10416c5a79ebSMatthew G. Knepley   char          funcname[PETSC_MAX_PATH_LEN];
10426c5a79ebSMatthew G. Knepley   PetscBool     flg;
104335b38c60SMatthew G. Knepley 
104435b38c60SMatthew G. Knepley   PetscFunctionBegin;
1045d0609cedSBarry Smith   PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM");
10466c5a79ebSMatthew G. Knepley   PetscCall(PetscOptionsString("-dm_swarm_velocity_function", "Function to determine particle velocities", "DMSwarmSetVelocityFunction", funcname, funcname, sizeof(funcname), &flg));
1047d0609cedSBarry Smith   PetscOptionsEnd();
10486c5a79ebSMatthew G. Knepley   if (flg) {
10496c5a79ebSMatthew G. Knepley     PetscSimplePointFunc velFunc;
10506c5a79ebSMatthew G. Knepley 
10516c5a79ebSMatthew G. Knepley     PetscCall(PetscDLSym(NULL, funcname, (void **)&velFunc));
10526c5a79ebSMatthew G. Knepley     PetscCheck(velFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname);
10536c5a79ebSMatthew G. Knepley     PetscCall(DMSwarmSetVelocityFunction(sw, velFunc));
10546c5a79ebSMatthew G. Knepley   }
10559566063dSJacob Faibussowitsch   PetscCall(DMGetDimension(sw, &dim));
10569566063dSJacob Faibussowitsch   PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix));
10579566063dSJacob Faibussowitsch   PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_velocity_density", NULL, NULL, &sampler));
10589566063dSJacob Faibussowitsch   PetscCall(DMSwarmInitializeVelocities(sw, sampler, v0));
10593ba16761SJacob Faibussowitsch   PetscFunctionReturn(PETSC_SUCCESS);
106035b38c60SMatthew G. Knepley }
1061