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 2760225df5SJacob Faibussowitsch 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 18560225df5SJacob Faibussowitsch 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 34260225df5SJacob Faibussowitsch 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 354*a4e35b19SJacob Faibussowitsch 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 38860225df5SJacob Faibussowitsch Input Parameters: 38920f4b53cSBarry Smith + dm - the `DMSWARM` 390431382f2SDave May . npoints - the number of points to insert in each cell 391431382f2SDave May - xi - the coordinates (defined in the local coordinate system for each cell) to insert 392431382f2SDave May 393431382f2SDave May Level: beginner 394431382f2SDave May 395431382f2SDave May Notes: 39620f4b53cSBarry Smith The method will reset any previous defined points within the `DMSWARM`. 39720f4b53cSBarry Smith Only supported for `DMPLEX`. If you are using a `DMDA` it is recommended to either use 39820f4b53cSBarry Smith `DMSwarmInsertPointsUsingCellDM()`, or extract and set the coordinates yourself the following code 39920f4b53cSBarry Smith .vb 40020f4b53cSBarry Smith PetscReal *coor; 40120f4b53cSBarry Smith DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor); 40220f4b53cSBarry Smith // user code to define the coordinates here 40320f4b53cSBarry Smith DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor); 40420f4b53cSBarry Smith .ve 405e7af74c8SDave May 40620f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmInsertPointsUsingCellDM()` 407431382f2SDave May @*/ 408d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinatesCellwise(DM dm, PetscInt npoints, PetscReal xi[]) 409d71ae5a4SJacob Faibussowitsch { 410431382f2SDave May DM celldm; 411431382f2SDave May PetscBool isDA, isPLEX; 412431382f2SDave May 4130e2ec84fSDave May PetscFunctionBegin; 414431382f2SDave May DMSWARMPICVALID(dm); 4159566063dSJacob Faibussowitsch PetscCall(DMSwarmGetCellDM(dm, &celldm)); 4169566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA)); 4179566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX)); 41828b400f6SJacob Faibussowitsch PetscCheck(!isDA, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMPLEX. Recommended you use DMSwarmInsertPointsUsingCellDM()"); 419f7d195e4SLawrence Mitchell if (isPLEX) { 4209566063dSJacob Faibussowitsch PetscCall(private_DMSwarmSetPointCoordinatesCellwise_PLEX(dm, celldm, npoints, xi)); 421431382f2SDave May } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX"); 4223ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 4230e2ec84fSDave May } 424431382f2SDave May 4250e2ec84fSDave May /* Field projection API */ 42677048351SPatrick Sanan extern PetscErrorCode private_DMSwarmProjectFields_DA(DM swarm, DM celldm, PetscInt project_type, PetscInt nfields, DMSwarmDataField dfield[], Vec vecs[]); 42777048351SPatrick Sanan extern PetscErrorCode private_DMSwarmProjectFields_PLEX(DM swarm, DM celldm, PetscInt project_type, PetscInt nfields, DMSwarmDataField dfield[], Vec vecs[]); 42894f7d2dcSDave May 42994f7d2dcSDave May /*@C 43020f4b53cSBarry Smith DMSwarmProjectFields - Project a set of swarm fields onto the cell `DM` 43194f7d2dcSDave May 43220f4b53cSBarry Smith Collective 43394f7d2dcSDave May 43460225df5SJacob Faibussowitsch Input Parameters: 43520f4b53cSBarry Smith + dm - the `DMSWARM` 43694f7d2dcSDave May . nfields - the number of swarm fields to project 43794f7d2dcSDave May . fieldnames - the textual names of the swarm fields to project 43894f7d2dcSDave May . fields - an array of Vec's of length nfields 43994f7d2dcSDave May - reuse - flag indicating whether the array and contents of fields should be re-used or internally allocated 44094f7d2dcSDave May 44120f4b53cSBarry Smith Level: beginner 44220f4b53cSBarry Smith 44320f4b53cSBarry Smith Notes: 44494f7d2dcSDave May Currently, the only available projection method consists of 44520f4b53cSBarry Smith .vb 44694f7d2dcSDave May phi_i = \sum_{p=0}^{np} N_i(x_p) phi_p dJ / \sum_{p=0}^{np} N_i(x_p) dJ 44794f7d2dcSDave May where phi_p is the swarm field at point p, 44894f7d2dcSDave May N_i() is the cell DM basis function at vertex i, 44994f7d2dcSDave May dJ is the determinant of the cell Jacobian and 45094f7d2dcSDave May phi_i is the projected vertex value of the field phi. 45120f4b53cSBarry Smith .ve 45294f7d2dcSDave May 45320f4b53cSBarry Smith If `reuse` is `PETSC_FALSE`, this function will allocate the array of `Vec`'s, and each individual `Vec`. 45420f4b53cSBarry Smith The user is responsible for destroying both the array and the individual `Vec` objects. 45594f7d2dcSDave May 45620f4b53cSBarry Smith Only swarm fields registered with data type of `PETSC_REAL` can be projected onto the cell `DM`. 457e7af74c8SDave May 458e7af74c8SDave May Only swarm fields of block size = 1 can currently be projected. 459e7af74c8SDave May 46020f4b53cSBarry Smith The only projection methods currently only support the `DMDA` (2D) and `DMPLEX` (triangles 2D). 46194f7d2dcSDave May 46220f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType` 46394f7d2dcSDave May @*/ 464d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmProjectFields(DM dm, PetscInt nfields, const char *fieldnames[], Vec **fields, PetscBool reuse) 465d71ae5a4SJacob Faibussowitsch { 46694f7d2dcSDave May DM_Swarm *swarm = (DM_Swarm *)dm->data; 46777048351SPatrick Sanan DMSwarmDataField *gfield; 46894f7d2dcSDave May DM celldm; 46994f7d2dcSDave May PetscBool isDA, isPLEX; 47094f7d2dcSDave May Vec *vecs; 47194f7d2dcSDave May PetscInt f, nvecs; 47294f7d2dcSDave May PetscInt project_type = 0; 47394f7d2dcSDave May 4740e2ec84fSDave May PetscFunctionBegin; 47594f7d2dcSDave May DMSWARMPICVALID(dm); 4769566063dSJacob Faibussowitsch PetscCall(DMSwarmGetCellDM(dm, &celldm)); 4779566063dSJacob Faibussowitsch PetscCall(PetscMalloc1(nfields, &gfield)); 47894f7d2dcSDave May nvecs = 0; 47994f7d2dcSDave May for (f = 0; f < nfields; f++) { 4809566063dSJacob Faibussowitsch PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldnames[f], &gfield[f])); 4815f80ce2aSJacob 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"); 4825f80ce2aSJacob Faibussowitsch PetscCheck(gfield[f]->bs == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Projection only valid for fields with block size = 1"); 48394f7d2dcSDave May nvecs += gfield[f]->bs; 48494f7d2dcSDave May } 48594f7d2dcSDave May if (!reuse) { 4869566063dSJacob Faibussowitsch PetscCall(PetscMalloc1(nvecs, &vecs)); 48794f7d2dcSDave May for (f = 0; f < nvecs; f++) { 4889566063dSJacob Faibussowitsch PetscCall(DMCreateGlobalVector(celldm, &vecs[f])); 4899566063dSJacob Faibussowitsch PetscCall(PetscObjectSetName((PetscObject)vecs[f], gfield[f]->name)); 49094f7d2dcSDave May } 49194f7d2dcSDave May } else { 49294f7d2dcSDave May vecs = *fields; 49394f7d2dcSDave May } 49494f7d2dcSDave May 4959566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA)); 4969566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX)); 49794f7d2dcSDave May if (isDA) { 4989566063dSJacob Faibussowitsch PetscCall(private_DMSwarmProjectFields_DA(dm, celldm, project_type, nfields, gfield, vecs)); 49994f7d2dcSDave May } else if (isPLEX) { 5009566063dSJacob Faibussowitsch PetscCall(private_DMSwarmProjectFields_PLEX(dm, celldm, project_type, nfields, gfield, vecs)); 50194f7d2dcSDave May } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX"); 50294f7d2dcSDave May 5039566063dSJacob Faibussowitsch PetscCall(PetscFree(gfield)); 5045f80ce2aSJacob Faibussowitsch if (!reuse) *fields = vecs; 5053ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 5060e2ec84fSDave May } 5070e2ec84fSDave May 5080e2ec84fSDave May /*@C 509b799feefSDave May DMSwarmCreatePointPerCellCount - Count the number of points within all cells in the cell DM 5100e2ec84fSDave May 51120f4b53cSBarry Smith Not Collective 5120e2ec84fSDave May 51360225df5SJacob Faibussowitsch Input Parameter: 51420f4b53cSBarry Smith . dm - the `DMSWARM` 5150e2ec84fSDave May 51660225df5SJacob Faibussowitsch Output Parameters: 51720f4b53cSBarry Smith + ncells - the number of cells in the cell `DM` (optional argument, pass `NULL` to ignore) 518b799feefSDave May - count - array of length ncells containing the number of points per cell 5190e2ec84fSDave May 5200e2ec84fSDave May Level: beginner 5210e2ec84fSDave May 5220e2ec84fSDave May Notes: 5230e2ec84fSDave May The array count is allocated internally and must be free'd by the user. 5240e2ec84fSDave May 52520f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType` 5260e2ec84fSDave May @*/ 527d71ae5a4SJacob Faibussowitsch PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm, PetscInt *ncells, PetscInt **count) 528d71ae5a4SJacob Faibussowitsch { 529b799feefSDave May PetscBool isvalid; 530b799feefSDave May PetscInt nel; 531b799feefSDave May PetscInt *sum; 532b799feefSDave May 5330e2ec84fSDave May PetscFunctionBegin; 5349566063dSJacob Faibussowitsch PetscCall(DMSwarmSortGetIsValid(dm, &isvalid)); 535b799feefSDave May nel = 0; 536b799feefSDave May if (isvalid) { 537b799feefSDave May PetscInt e; 538b799feefSDave May 5399566063dSJacob Faibussowitsch PetscCall(DMSwarmSortGetSizes(dm, &nel, NULL)); 540b799feefSDave May 5419566063dSJacob Faibussowitsch PetscCall(PetscMalloc1(nel, &sum)); 54248a46eb9SPierre Jolivet for (e = 0; e < nel; e++) PetscCall(DMSwarmSortGetNumberOfPointsPerCell(dm, e, &sum[e])); 543b799feefSDave May } else { 544b799feefSDave May DM celldm; 545b799feefSDave May PetscBool isda, isplex, isshell; 546b799feefSDave May PetscInt p, npoints; 547b799feefSDave May PetscInt *swarm_cellid; 548b799feefSDave May 549b799feefSDave May /* get the number of cells */ 5509566063dSJacob Faibussowitsch PetscCall(DMSwarmGetCellDM(dm, &celldm)); 5519566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isda)); 5529566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isplex)); 5539566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMSHELL, &isshell)); 554b799feefSDave May if (isda) { 555b799feefSDave May PetscInt _nel, _npe; 556b799feefSDave May const PetscInt *_element; 557b799feefSDave May 5589566063dSJacob Faibussowitsch PetscCall(DMDAGetElements(celldm, &_nel, &_npe, &_element)); 559b799feefSDave May nel = _nel; 5609566063dSJacob Faibussowitsch PetscCall(DMDARestoreElements(celldm, &_nel, &_npe, &_element)); 561b799feefSDave May } else if (isplex) { 562b799feefSDave May PetscInt ps, pe; 563b799feefSDave May 5649566063dSJacob Faibussowitsch PetscCall(DMPlexGetHeightStratum(celldm, 0, &ps, &pe)); 565b799feefSDave May nel = pe - ps; 566b799feefSDave May } else if (isshell) { 567b799feefSDave May PetscErrorCode (*method_DMShellGetNumberOfCells)(DM, PetscInt *); 568b799feefSDave May 5699566063dSJacob Faibussowitsch PetscCall(PetscObjectQueryFunction((PetscObject)celldm, "DMGetNumberOfCells_C", &method_DMShellGetNumberOfCells)); 570b799feefSDave May if (method_DMShellGetNumberOfCells) { 5719566063dSJacob Faibussowitsch PetscCall(method_DMShellGetNumberOfCells(celldm, &nel)); 5729371c9d4SSatish Balay } else 5739371c9d4SSatish 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);"); 574b799feefSDave 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"); 575b799feefSDave May 5769566063dSJacob Faibussowitsch PetscCall(PetscMalloc1(nel, &sum)); 5779566063dSJacob Faibussowitsch PetscCall(PetscArrayzero(sum, nel)); 5789566063dSJacob Faibussowitsch PetscCall(DMSwarmGetLocalSize(dm, &npoints)); 5799566063dSJacob Faibussowitsch PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); 580b799feefSDave May for (p = 0; p < npoints; p++) { 581ad540459SPierre Jolivet if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) sum[swarm_cellid[p]]++; 582b799feefSDave May } 5839566063dSJacob Faibussowitsch PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); 584b799feefSDave May } 585ad540459SPierre Jolivet if (ncells) *ncells = nel; 586b799feefSDave May *count = sum; 5873ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 5880e2ec84fSDave May } 58935b38c60SMatthew G. Knepley 59035b38c60SMatthew G. Knepley /*@ 59135b38c60SMatthew G. Knepley DMSwarmGetNumSpecies - Get the number of particle species 59235b38c60SMatthew G. Knepley 59320f4b53cSBarry Smith Not Collective 59435b38c60SMatthew G. Knepley 59560225df5SJacob Faibussowitsch Input Parameter: 59660225df5SJacob Faibussowitsch . sw - the `DMSWARM` 59735b38c60SMatthew G. Knepley 59860225df5SJacob Faibussowitsch Output Parameters: 59935b38c60SMatthew G. Knepley . Ns - the number of species 60035b38c60SMatthew G. Knepley 60135b38c60SMatthew G. Knepley Level: intermediate 60235b38c60SMatthew G. Knepley 60320f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType` 60435b38c60SMatthew G. Knepley @*/ 605d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmGetNumSpecies(DM sw, PetscInt *Ns) 606d71ae5a4SJacob Faibussowitsch { 60735b38c60SMatthew G. Knepley DM_Swarm *swarm = (DM_Swarm *)sw->data; 60835b38c60SMatthew G. Knepley 60935b38c60SMatthew G. Knepley PetscFunctionBegin; 61035b38c60SMatthew G. Knepley *Ns = swarm->Ns; 6113ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 61235b38c60SMatthew G. Knepley } 61335b38c60SMatthew G. Knepley 61435b38c60SMatthew G. Knepley /*@ 61535b38c60SMatthew G. Knepley DMSwarmSetNumSpecies - Set the number of particle species 61635b38c60SMatthew G. Knepley 61720f4b53cSBarry Smith Not Collective 61835b38c60SMatthew G. Knepley 61960225df5SJacob Faibussowitsch Input Parameters: 62060225df5SJacob Faibussowitsch + sw - the `DMSWARM` 62135b38c60SMatthew G. Knepley - Ns - the number of species 62235b38c60SMatthew G. Knepley 62335b38c60SMatthew G. Knepley Level: intermediate 62435b38c60SMatthew G. Knepley 62520f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmGetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType` 62635b38c60SMatthew G. Knepley @*/ 627d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmSetNumSpecies(DM sw, PetscInt Ns) 628d71ae5a4SJacob Faibussowitsch { 62935b38c60SMatthew G. Knepley DM_Swarm *swarm = (DM_Swarm *)sw->data; 63035b38c60SMatthew G. Knepley 63135b38c60SMatthew G. Knepley PetscFunctionBegin; 63235b38c60SMatthew G. Knepley swarm->Ns = Ns; 6333ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 63435b38c60SMatthew G. Knepley } 63535b38c60SMatthew G. Knepley 63635b38c60SMatthew G. Knepley /*@C 6376c5a79ebSMatthew G. Knepley DMSwarmGetCoordinateFunction - Get the function setting initial particle positions, if it exists 6386c5a79ebSMatthew G. Knepley 63920f4b53cSBarry Smith Not Collective 6406c5a79ebSMatthew G. Knepley 64160225df5SJacob Faibussowitsch Input Parameter: 64260225df5SJacob Faibussowitsch . sw - the `DMSWARM` 6436c5a79ebSMatthew G. Knepley 6446c5a79ebSMatthew G. Knepley Output Parameter: 64520f4b53cSBarry Smith . coordFunc - the function setting initial particle positions, or `NULL` 6466c5a79ebSMatthew G. Knepley 6476c5a79ebSMatthew G. Knepley Level: intermediate 6486c5a79ebSMatthew G. Knepley 64920f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetCoordinateFunction()`, `DMSwarmGetVelocityFunction()`, `DMSwarmInitializeCoordinates()` 6506c5a79ebSMatthew G. Knepley @*/ 651d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmGetCoordinateFunction(DM sw, PetscSimplePointFunc *coordFunc) 652d71ae5a4SJacob Faibussowitsch { 6536c5a79ebSMatthew G. Knepley DM_Swarm *swarm = (DM_Swarm *)sw->data; 6546c5a79ebSMatthew G. Knepley 6556c5a79ebSMatthew G. Knepley PetscFunctionBegin; 6566c5a79ebSMatthew G. Knepley PetscValidHeaderSpecific(sw, DM_CLASSID, 1); 6574f572ea9SToby Isaac PetscAssertPointer(coordFunc, 2); 6586c5a79ebSMatthew G. Knepley *coordFunc = swarm->coordFunc; 6593ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 6606c5a79ebSMatthew G. Knepley } 6616c5a79ebSMatthew G. Knepley 6626c5a79ebSMatthew G. Knepley /*@C 6636c5a79ebSMatthew G. Knepley DMSwarmSetCoordinateFunction - Set the function setting initial particle positions 6646c5a79ebSMatthew G. Knepley 66520f4b53cSBarry Smith Not Collective 6666c5a79ebSMatthew G. Knepley 66760225df5SJacob Faibussowitsch Input Parameters: 66860225df5SJacob Faibussowitsch + sw - the `DMSWARM` 6696c5a79ebSMatthew G. Knepley - coordFunc - the function setting initial particle positions 6706c5a79ebSMatthew G. Knepley 6716c5a79ebSMatthew G. Knepley Level: intermediate 6726c5a79ebSMatthew G. Knepley 67320f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmGetCoordinateFunction()`, `DMSwarmSetVelocityFunction()`, `DMSwarmInitializeCoordinates()` 6746c5a79ebSMatthew G. Knepley @*/ 675d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmSetCoordinateFunction(DM sw, PetscSimplePointFunc coordFunc) 676d71ae5a4SJacob Faibussowitsch { 6776c5a79ebSMatthew G. Knepley DM_Swarm *swarm = (DM_Swarm *)sw->data; 6786c5a79ebSMatthew G. Knepley 6796c5a79ebSMatthew G. Knepley PetscFunctionBegin; 6806c5a79ebSMatthew G. Knepley PetscValidHeaderSpecific(sw, DM_CLASSID, 1); 6816c5a79ebSMatthew G. Knepley PetscValidFunction(coordFunc, 2); 6826c5a79ebSMatthew G. Knepley swarm->coordFunc = coordFunc; 6833ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 6846c5a79ebSMatthew G. Knepley } 6856c5a79ebSMatthew G. Knepley 6866c5a79ebSMatthew G. Knepley /*@C 68760225df5SJacob Faibussowitsch DMSwarmGetVelocityFunction - Get the function setting initial particle velocities, if it exists 6886c5a79ebSMatthew G. Knepley 68920f4b53cSBarry Smith Not Collective 6906c5a79ebSMatthew G. Knepley 69160225df5SJacob Faibussowitsch Input Parameter: 69260225df5SJacob Faibussowitsch . sw - the `DMSWARM` 6936c5a79ebSMatthew G. Knepley 6946c5a79ebSMatthew G. Knepley Output Parameter: 69520f4b53cSBarry Smith . velFunc - the function setting initial particle velocities, or `NULL` 6966c5a79ebSMatthew G. Knepley 6976c5a79ebSMatthew G. Knepley Level: intermediate 6986c5a79ebSMatthew G. Knepley 69920f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmSetVelocityFunction()`, `DMSwarmGetCoordinateFunction()`, `DMSwarmInitializeVelocities()` 7006c5a79ebSMatthew G. Knepley @*/ 701d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmGetVelocityFunction(DM sw, PetscSimplePointFunc *velFunc) 702d71ae5a4SJacob Faibussowitsch { 7036c5a79ebSMatthew G. Knepley DM_Swarm *swarm = (DM_Swarm *)sw->data; 7046c5a79ebSMatthew G. Knepley 7056c5a79ebSMatthew G. Knepley PetscFunctionBegin; 7066c5a79ebSMatthew G. Knepley PetscValidHeaderSpecific(sw, DM_CLASSID, 1); 7074f572ea9SToby Isaac PetscAssertPointer(velFunc, 2); 7086c5a79ebSMatthew G. Knepley *velFunc = swarm->velFunc; 7093ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 7106c5a79ebSMatthew G. Knepley } 7116c5a79ebSMatthew G. Knepley 7126c5a79ebSMatthew G. Knepley /*@C 7136c5a79ebSMatthew G. Knepley DMSwarmSetVelocityFunction - Set the function setting initial particle velocities 7146c5a79ebSMatthew G. Knepley 71520f4b53cSBarry Smith Not Collective 7166c5a79ebSMatthew G. Knepley 71760225df5SJacob Faibussowitsch Input Parameters: 718*a4e35b19SJacob Faibussowitsch + sw - the `DMSWARM` 719*a4e35b19SJacob Faibussowitsch - velFunc - the function setting initial particle velocities 7206c5a79ebSMatthew G. Knepley 7216c5a79ebSMatthew G. Knepley Level: intermediate 7226c5a79ebSMatthew G. Knepley 72320f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmGetVelocityFunction()`, `DMSwarmSetCoordinateFunction()`, `DMSwarmInitializeVelocities()` 7246c5a79ebSMatthew G. Knepley @*/ 725d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmSetVelocityFunction(DM sw, PetscSimplePointFunc velFunc) 726d71ae5a4SJacob Faibussowitsch { 7276c5a79ebSMatthew G. Knepley DM_Swarm *swarm = (DM_Swarm *)sw->data; 7286c5a79ebSMatthew G. Knepley 7296c5a79ebSMatthew G. Knepley PetscFunctionBegin; 7306c5a79ebSMatthew G. Knepley PetscValidHeaderSpecific(sw, DM_CLASSID, 1); 7316c5a79ebSMatthew G. Knepley PetscValidFunction(velFunc, 2); 7326c5a79ebSMatthew G. Knepley swarm->velFunc = velFunc; 7333ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 7346c5a79ebSMatthew G. Knepley } 7356c5a79ebSMatthew G. Knepley 7366c5a79ebSMatthew G. Knepley /*@C 73735b38c60SMatthew G. Knepley DMSwarmComputeLocalSize - Compute the local number and distribution of particles based upon a density function 73835b38c60SMatthew G. Knepley 73920f4b53cSBarry Smith Not Collective 74035b38c60SMatthew G. Knepley 74135b38c60SMatthew G. Knepley Input Parameters: 74220f4b53cSBarry Smith + sw - The `DMSWARM` 74335b38c60SMatthew G. Knepley . N - The target number of particles 74435b38c60SMatthew G. Knepley - density - The density field for the particle layout, normalized to unity 74535b38c60SMatthew G. Knepley 74635b38c60SMatthew G. Knepley Level: advanced 74735b38c60SMatthew G. Knepley 74820f4b53cSBarry Smith Note: 74920f4b53cSBarry Smith One particle will be created for each species. 75020f4b53cSBarry Smith 75120f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSizeFromOptions()` 75235b38c60SMatthew G. Knepley @*/ 753d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmComputeLocalSize(DM sw, PetscInt N, PetscProbFunc density) 754d71ae5a4SJacob Faibussowitsch { 75535b38c60SMatthew G. Knepley DM dm; 75635b38c60SMatthew G. Knepley PetscQuadrature quad; 75735b38c60SMatthew G. Knepley const PetscReal *xq, *wq; 758ea7032a0SMatthew G. Knepley PetscReal *n_int; 759ea7032a0SMatthew G. Knepley PetscInt *npc_s, *cellid, Ni; 760ea7032a0SMatthew G. Knepley PetscReal gmin[3], gmax[3], xi0[3]; 761ea7032a0SMatthew G. Knepley PetscInt Ns, cStart, cEnd, c, dim, d, Nq, q, Np = 0, p, s; 76235b38c60SMatthew G. Knepley PetscBool simplex; 76335b38c60SMatthew G. Knepley 76435b38c60SMatthew G. Knepley PetscFunctionBegin; 7659566063dSJacob Faibussowitsch PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); 7669566063dSJacob Faibussowitsch PetscCall(DMSwarmGetCellDM(sw, &dm)); 7679566063dSJacob Faibussowitsch PetscCall(DMGetDimension(dm, &dim)); 768ea7032a0SMatthew G. Knepley PetscCall(DMGetBoundingBox(dm, gmin, gmax)); 7699566063dSJacob Faibussowitsch PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 7709566063dSJacob Faibussowitsch PetscCall(DMPlexIsSimplex(dm, &simplex)); 7716858538eSMatthew G. Knepley PetscCall(DMGetCoordinatesLocalSetUp(dm)); 7729566063dSJacob Faibussowitsch if (simplex) PetscCall(PetscDTStroudConicalQuadrature(dim, 1, 5, -1.0, 1.0, &quad)); 7739566063dSJacob Faibussowitsch else PetscCall(PetscDTGaussTensorQuadrature(dim, 1, 5, -1.0, 1.0, &quad)); 7749566063dSJacob Faibussowitsch PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, &xq, &wq)); 775ea7032a0SMatthew G. Knepley PetscCall(PetscCalloc2(Ns, &n_int, (cEnd - cStart) * Ns, &npc_s)); 77635b38c60SMatthew G. Knepley /* Integrate the density function to get the number of particles in each cell */ 77735b38c60SMatthew G. Knepley for (d = 0; d < dim; ++d) xi0[d] = -1.0; 77835b38c60SMatthew G. Knepley for (c = 0; c < cEnd - cStart; ++c) { 77935b38c60SMatthew G. Knepley const PetscInt cell = c + cStart; 780ea7032a0SMatthew G. Knepley PetscReal v0[3], J[9], invJ[9], detJ, detJp = 2. / (gmax[0] - gmin[0]), xr[3], den; 78135b38c60SMatthew G. Knepley 782ea7032a0SMatthew G. Knepley /*Have to transform quadrature points/weights to cell domain*/ 7839566063dSJacob Faibussowitsch PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ)); 784ea7032a0SMatthew G. Knepley PetscCall(PetscArrayzero(n_int, Ns)); 78535b38c60SMatthew G. Knepley for (q = 0; q < Nq; ++q) { 78635b38c60SMatthew G. Knepley CoordinatesRefToReal(dim, dim, xi0, v0, J, &xq[q * dim], xr); 787ea7032a0SMatthew G. Knepley /* Have to transform mesh to domain of definition of PDF, [-1, 1], and weight PDF by |J|/2 */ 788ea7032a0SMatthew G. Knepley xr[0] = detJp * (xr[0] - gmin[0]) - 1.; 789ea7032a0SMatthew G. Knepley 790ea7032a0SMatthew G. Knepley for (s = 0; s < Ns; ++s) { 791ea7032a0SMatthew G. Knepley PetscCall(density(xr, NULL, &den)); 792ea7032a0SMatthew G. Knepley n_int[s] += (detJp * den) * (detJ * wq[q]) / (PetscReal)Ns; 79335b38c60SMatthew G. Knepley } 794ea7032a0SMatthew G. Knepley } 795ea7032a0SMatthew G. Knepley for (s = 0; s < Ns; ++s) { 796ea7032a0SMatthew G. Knepley Ni = N; 797ea7032a0SMatthew G. Knepley npc_s[c * Ns + s] += (PetscInt)(Ni * n_int[s]); 798ea7032a0SMatthew G. Knepley Np += npc_s[c * Ns + s]; 799ea7032a0SMatthew G. Knepley } 80035b38c60SMatthew G. Knepley } 8019566063dSJacob Faibussowitsch PetscCall(PetscQuadratureDestroy(&quad)); 8029566063dSJacob Faibussowitsch PetscCall(DMSwarmSetLocalSizes(sw, Np, 0)); 8039566063dSJacob Faibussowitsch PetscCall(DMSwarmGetField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid)); 80435b38c60SMatthew G. Knepley for (c = 0, p = 0; c < cEnd - cStart; ++c) { 805ea7032a0SMatthew G. Knepley for (s = 0; s < Ns; ++s) { 806ea7032a0SMatthew G. Knepley for (q = 0; q < npc_s[c * Ns + s]; ++q, ++p) cellid[p] = c; 807ea7032a0SMatthew G. Knepley } 80835b38c60SMatthew G. Knepley } 8099566063dSJacob Faibussowitsch PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid)); 810ea7032a0SMatthew G. Knepley PetscCall(PetscFree2(n_int, npc_s)); 8113ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 81235b38c60SMatthew G. Knepley } 81335b38c60SMatthew G. Knepley 81435b38c60SMatthew G. Knepley /*@ 81535b38c60SMatthew G. Knepley DMSwarmComputeLocalSizeFromOptions - Compute the local number and distribution of particles based upon a density function determined by options 81635b38c60SMatthew G. Knepley 81720f4b53cSBarry Smith Not Collective 81835b38c60SMatthew G. Knepley 8192fe279fdSBarry Smith Input Parameter: 8202fe279fdSBarry Smith . sw - The `DMSWARM` 82135b38c60SMatthew G. Knepley 82235b38c60SMatthew G. Knepley Level: advanced 82335b38c60SMatthew G. Knepley 82420f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()` 82535b38c60SMatthew G. Knepley @*/ 826d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmComputeLocalSizeFromOptions(DM sw) 827d71ae5a4SJacob Faibussowitsch { 82835b38c60SMatthew G. Knepley PetscProbFunc pdf; 82935b38c60SMatthew G. Knepley const char *prefix; 8306c5a79ebSMatthew G. Knepley char funcname[PETSC_MAX_PATH_LEN]; 8316c5a79ebSMatthew G. Knepley PetscInt *N, Ns, dim, n; 8326c5a79ebSMatthew G. Knepley PetscBool flg; 8336c5a79ebSMatthew G. Knepley PetscMPIInt size, rank; 83435b38c60SMatthew G. Knepley 83535b38c60SMatthew G. Knepley PetscFunctionBegin; 8366c5a79ebSMatthew G. Knepley PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)sw), &size)); 8376c5a79ebSMatthew G. Knepley PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)sw), &rank)); 8386c5a79ebSMatthew G. Knepley PetscCall(PetscCalloc1(size, &N)); 839d0609cedSBarry Smith PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM"); 8406c5a79ebSMatthew G. Knepley n = size; 8416c5a79ebSMatthew G. Knepley PetscCall(PetscOptionsIntArray("-dm_swarm_num_particles", "The target number of particles", "", N, &n, NULL)); 8426c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); 8439566063dSJacob Faibussowitsch PetscCall(PetscOptionsInt("-dm_swarm_num_species", "The number of species", "DMSwarmSetNumSpecies", Ns, &Ns, &flg)); 8449566063dSJacob Faibussowitsch if (flg) PetscCall(DMSwarmSetNumSpecies(sw, Ns)); 8456c5a79ebSMatthew G. Knepley PetscCall(PetscOptionsString("-dm_swarm_coordinate_function", "Function to determine particle coordinates", "DMSwarmSetCoordinateFunction", funcname, funcname, sizeof(funcname), &flg)); 846d0609cedSBarry Smith PetscOptionsEnd(); 8476c5a79ebSMatthew G. Knepley if (flg) { 8486c5a79ebSMatthew G. Knepley PetscSimplePointFunc coordFunc; 84935b38c60SMatthew G. Knepley 8506c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); 8516c5a79ebSMatthew G. Knepley PetscCall(PetscDLSym(NULL, funcname, (void **)&coordFunc)); 8526c5a79ebSMatthew G. Knepley PetscCheck(coordFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname); 8536c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); 8546c5a79ebSMatthew G. Knepley PetscCall(DMSwarmSetLocalSizes(sw, N[rank] * Ns, 0)); 8556c5a79ebSMatthew G. Knepley PetscCall(DMSwarmSetCoordinateFunction(sw, coordFunc)); 8566c5a79ebSMatthew G. Knepley } else { 8579566063dSJacob Faibussowitsch PetscCall(DMGetDimension(sw, &dim)); 8589566063dSJacob Faibussowitsch PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix)); 8599566063dSJacob Faibussowitsch PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_coordinate_density", &pdf, NULL, NULL)); 8606c5a79ebSMatthew G. Knepley PetscCall(DMSwarmComputeLocalSize(sw, N[rank], pdf)); 8616c5a79ebSMatthew G. Knepley } 8626c5a79ebSMatthew G. Knepley PetscCall(PetscFree(N)); 8633ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 86435b38c60SMatthew G. Knepley } 86535b38c60SMatthew G. Knepley 86635b38c60SMatthew G. Knepley /*@ 86735b38c60SMatthew G. Knepley DMSwarmInitializeCoordinates - Determine the initial coordinates of particles for a PIC method 86835b38c60SMatthew G. Knepley 86920f4b53cSBarry Smith Not Collective 87035b38c60SMatthew G. Knepley 87120f4b53cSBarry Smith Input Parameter: 87220f4b53cSBarry Smith . sw - The `DMSWARM` 87335b38c60SMatthew G. Knepley 87435b38c60SMatthew G. Knepley Level: advanced 87535b38c60SMatthew G. Knepley 87620f4b53cSBarry Smith Note: 87720f4b53cSBarry Smith Currently, we randomly place particles in their assigned cell 87820f4b53cSBarry Smith 87920f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeVelocities()` 88035b38c60SMatthew G. Knepley @*/ 881d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmInitializeCoordinates(DM sw) 882d71ae5a4SJacob Faibussowitsch { 8836c5a79ebSMatthew G. Knepley PetscSimplePointFunc coordFunc; 88435b38c60SMatthew G. Knepley PetscScalar *weight; 8856c5a79ebSMatthew G. Knepley PetscReal *x; 88635b38c60SMatthew G. Knepley PetscInt *species; 8876c5a79ebSMatthew G. Knepley void *ctx; 88835b38c60SMatthew G. Knepley PetscBool removePoints = PETSC_TRUE; 88935b38c60SMatthew G. Knepley PetscDataType dtype; 8906c5a79ebSMatthew G. Knepley PetscInt Np, p, Ns, dim, d, bs; 89135b38c60SMatthew G. Knepley 89235b38c60SMatthew G. Knepley PetscFunctionBeginUser; 8936c5a79ebSMatthew G. Knepley PetscCall(DMGetDimension(sw, &dim)); 8946c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetLocalSize(sw, &Np)); 8959566063dSJacob Faibussowitsch PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); 8966c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetCoordinateFunction(sw, &coordFunc)); 8976c5a79ebSMatthew G. Knepley 8986c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, &bs, &dtype, (void **)&x)); 8996c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetField(sw, "w_q", &bs, &dtype, (void **)&weight)); 9006c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species)); 9016c5a79ebSMatthew G. Knepley if (coordFunc) { 9026c5a79ebSMatthew G. Knepley PetscCall(DMGetApplicationContext(sw, &ctx)); 9036c5a79ebSMatthew G. Knepley for (p = 0; p < Np; ++p) { 9046c5a79ebSMatthew G. Knepley PetscScalar X[3]; 9056c5a79ebSMatthew G. Knepley 9066c5a79ebSMatthew G. Knepley PetscCall((*coordFunc)(dim, 0., NULL, p, X, ctx)); 9076c5a79ebSMatthew G. Knepley for (d = 0; d < dim; ++d) x[p * dim + d] = PetscRealPart(X[d]); 9086c5a79ebSMatthew G. Knepley weight[p] = 1.0; 9096c5a79ebSMatthew G. Knepley species[p] = p % Ns; 9106c5a79ebSMatthew G. Knepley } 9116c5a79ebSMatthew G. Knepley } else { 9126c5a79ebSMatthew G. Knepley DM dm; 9136c5a79ebSMatthew G. Knepley PetscRandom rnd; 9146c5a79ebSMatthew G. Knepley PetscReal xi0[3]; 9156c5a79ebSMatthew G. Knepley PetscInt cStart, cEnd, c; 9166c5a79ebSMatthew G. Knepley 9179566063dSJacob Faibussowitsch PetscCall(DMSwarmGetCellDM(sw, &dm)); 9189566063dSJacob Faibussowitsch PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); 919ea7032a0SMatthew G. Knepley PetscCall(DMGetApplicationContext(sw, &ctx)); 92035b38c60SMatthew G. Knepley 92135b38c60SMatthew G. Knepley /* Set particle position randomly in cell, set weights to 1 */ 9229566063dSJacob Faibussowitsch PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)dm), &rnd)); 9239566063dSJacob Faibussowitsch PetscCall(PetscRandomSetInterval(rnd, -1.0, 1.0)); 9249566063dSJacob Faibussowitsch PetscCall(PetscRandomSetFromOptions(rnd)); 9259566063dSJacob Faibussowitsch PetscCall(DMSwarmSortGetAccess(sw)); 92635b38c60SMatthew G. Knepley for (d = 0; d < dim; ++d) xi0[d] = -1.0; 92735b38c60SMatthew G. Knepley for (c = cStart; c < cEnd; ++c) { 92835b38c60SMatthew G. Knepley PetscReal v0[3], J[9], invJ[9], detJ; 92935b38c60SMatthew G. Knepley PetscInt *pidx, Npc, q; 93035b38c60SMatthew G. Knepley 9319566063dSJacob Faibussowitsch PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx)); 9329566063dSJacob Faibussowitsch PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ)); 93335b38c60SMatthew G. Knepley for (q = 0; q < Npc; ++q) { 93435b38c60SMatthew G. Knepley const PetscInt p = pidx[q]; 93535b38c60SMatthew G. Knepley PetscReal xref[3]; 93635b38c60SMatthew G. Knepley 9379566063dSJacob Faibussowitsch for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &xref[d])); 93835b38c60SMatthew G. Knepley CoordinatesRefToReal(dim, dim, xi0, v0, J, xref, &x[p * dim]); 93935b38c60SMatthew G. Knepley 940ea7032a0SMatthew G. Knepley weight[p] = 1.0 / Np; 9416c5a79ebSMatthew G. Knepley species[p] = p % Ns; 94235b38c60SMatthew G. Knepley } 9439566063dSJacob Faibussowitsch PetscCall(PetscFree(pidx)); 94435b38c60SMatthew G. Knepley } 9459566063dSJacob Faibussowitsch PetscCall(PetscRandomDestroy(&rnd)); 9469566063dSJacob Faibussowitsch PetscCall(DMSwarmSortRestoreAccess(sw)); 9476c5a79ebSMatthew G. Knepley } 9489566063dSJacob Faibussowitsch PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x)); 9496c5a79ebSMatthew G. Knepley PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight)); 9509566063dSJacob Faibussowitsch PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species)); 9516c5a79ebSMatthew G. Knepley 9529566063dSJacob Faibussowitsch PetscCall(DMSwarmMigrate(sw, removePoints)); 9539566063dSJacob Faibussowitsch PetscCall(DMLocalizeCoordinates(sw)); 9543ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 95535b38c60SMatthew G. Knepley } 95635b38c60SMatthew G. Knepley 95735b38c60SMatthew G. Knepley /*@C 95835b38c60SMatthew G. Knepley DMSwarmInitializeVelocities - Set the initial velocities of particles using a distribution. 95935b38c60SMatthew G. Knepley 96020f4b53cSBarry Smith Collective 96135b38c60SMatthew G. Knepley 96235b38c60SMatthew G. Knepley Input Parameters: 96320f4b53cSBarry Smith + sw - The `DMSWARM` object 96435b38c60SMatthew G. Knepley . sampler - A function which uniformly samples the velocity PDF 96535b38c60SMatthew G. Knepley - v0 - The velocity scale for nondimensionalization for each species 96635b38c60SMatthew G. Knepley 96735b38c60SMatthew G. Knepley Level: advanced 96835b38c60SMatthew G. Knepley 96920f4b53cSBarry Smith Note: 97020f4b53cSBarry 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. 97120f4b53cSBarry Smith 97220f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocitiesFromOptions()` 97335b38c60SMatthew G. Knepley @*/ 974d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmInitializeVelocities(DM sw, PetscProbFunc sampler, const PetscReal v0[]) 975d71ae5a4SJacob Faibussowitsch { 9766c5a79ebSMatthew G. Knepley PetscSimplePointFunc velFunc; 97735b38c60SMatthew G. Knepley PetscReal *v; 97835b38c60SMatthew G. Knepley PetscInt *species; 9796c5a79ebSMatthew G. Knepley void *ctx; 98035b38c60SMatthew G. Knepley PetscInt dim, Np, p; 98135b38c60SMatthew G. Knepley 98235b38c60SMatthew G. Knepley PetscFunctionBegin; 9836c5a79ebSMatthew G. Knepley PetscCall(DMSwarmGetVelocityFunction(sw, &velFunc)); 98435b38c60SMatthew G. Knepley 9859566063dSJacob Faibussowitsch PetscCall(DMGetDimension(sw, &dim)); 9869566063dSJacob Faibussowitsch PetscCall(DMSwarmGetLocalSize(sw, &Np)); 9879566063dSJacob Faibussowitsch PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v)); 9889566063dSJacob Faibussowitsch PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species)); 9896c5a79ebSMatthew G. Knepley if (v0[0] == 0.) { 9906c5a79ebSMatthew G. Knepley PetscCall(PetscArrayzero(v, Np * dim)); 9916c5a79ebSMatthew G. Knepley } else if (velFunc) { 9926c5a79ebSMatthew G. Knepley PetscCall(DMGetApplicationContext(sw, &ctx)); 9936c5a79ebSMatthew G. Knepley for (p = 0; p < Np; ++p) { 9946c5a79ebSMatthew G. Knepley PetscInt s = species[p], d; 9956c5a79ebSMatthew G. Knepley PetscScalar vel[3]; 9966c5a79ebSMatthew G. Knepley 9976c5a79ebSMatthew G. Knepley PetscCall((*velFunc)(dim, 0., NULL, p, vel, ctx)); 9986c5a79ebSMatthew G. Knepley for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * PetscRealPart(vel[d]); 9996c5a79ebSMatthew G. Knepley } 10006c5a79ebSMatthew G. Knepley } else { 10016c5a79ebSMatthew G. Knepley PetscRandom rnd; 10026c5a79ebSMatthew G. Knepley 10036c5a79ebSMatthew G. Knepley PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)sw), &rnd)); 10046c5a79ebSMatthew G. Knepley PetscCall(PetscRandomSetInterval(rnd, 0, 1.)); 10056c5a79ebSMatthew G. Knepley PetscCall(PetscRandomSetFromOptions(rnd)); 10066c5a79ebSMatthew G. Knepley 100735b38c60SMatthew G. Knepley for (p = 0; p < Np; ++p) { 100835b38c60SMatthew G. Knepley PetscInt s = species[p], d; 100935b38c60SMatthew G. Knepley PetscReal a[3], vel[3]; 101035b38c60SMatthew G. Knepley 10119566063dSJacob Faibussowitsch for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &a[d])); 10129566063dSJacob Faibussowitsch PetscCall(sampler(a, NULL, vel)); 1013ad540459SPierre Jolivet for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * vel[d]; 101435b38c60SMatthew G. Knepley } 10156c5a79ebSMatthew G. Knepley PetscCall(PetscRandomDestroy(&rnd)); 10166c5a79ebSMatthew G. Knepley } 10179566063dSJacob Faibussowitsch PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v)); 10189566063dSJacob Faibussowitsch PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species)); 10193ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 102035b38c60SMatthew G. Knepley } 102135b38c60SMatthew G. Knepley 102235b38c60SMatthew G. Knepley /*@ 102335b38c60SMatthew G. Knepley DMSwarmInitializeVelocitiesFromOptions - Set the initial velocities of particles using a distribution determined from options. 102435b38c60SMatthew G. Knepley 102520f4b53cSBarry Smith Collective 102635b38c60SMatthew G. Knepley 102735b38c60SMatthew G. Knepley Input Parameters: 102820f4b53cSBarry Smith + sw - The `DMSWARM` object 102935b38c60SMatthew G. Knepley - v0 - The velocity scale for nondimensionalization for each species 103035b38c60SMatthew G. Knepley 103135b38c60SMatthew G. Knepley Level: advanced 103235b38c60SMatthew G. Knepley 103320f4b53cSBarry Smith .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocities()` 103435b38c60SMatthew G. Knepley @*/ 1035d71ae5a4SJacob Faibussowitsch PetscErrorCode DMSwarmInitializeVelocitiesFromOptions(DM sw, const PetscReal v0[]) 1036d71ae5a4SJacob Faibussowitsch { 103735b38c60SMatthew G. Knepley PetscProbFunc sampler; 103835b38c60SMatthew G. Knepley PetscInt dim; 103935b38c60SMatthew G. Knepley const char *prefix; 10406c5a79ebSMatthew G. Knepley char funcname[PETSC_MAX_PATH_LEN]; 10416c5a79ebSMatthew G. Knepley PetscBool flg; 104235b38c60SMatthew G. Knepley 104335b38c60SMatthew G. Knepley PetscFunctionBegin; 1044d0609cedSBarry Smith PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM"); 10456c5a79ebSMatthew G. Knepley PetscCall(PetscOptionsString("-dm_swarm_velocity_function", "Function to determine particle velocities", "DMSwarmSetVelocityFunction", funcname, funcname, sizeof(funcname), &flg)); 1046d0609cedSBarry Smith PetscOptionsEnd(); 10476c5a79ebSMatthew G. Knepley if (flg) { 10486c5a79ebSMatthew G. Knepley PetscSimplePointFunc velFunc; 10496c5a79ebSMatthew G. Knepley 10506c5a79ebSMatthew G. Knepley PetscCall(PetscDLSym(NULL, funcname, (void **)&velFunc)); 10516c5a79ebSMatthew G. Knepley PetscCheck(velFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname); 10526c5a79ebSMatthew G. Knepley PetscCall(DMSwarmSetVelocityFunction(sw, velFunc)); 10536c5a79ebSMatthew G. Knepley } 10549566063dSJacob Faibussowitsch PetscCall(DMGetDimension(sw, &dim)); 10559566063dSJacob Faibussowitsch PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix)); 10569566063dSJacob Faibussowitsch PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_velocity_density", NULL, NULL, &sampler)); 10579566063dSJacob Faibussowitsch PetscCall(DMSwarmInitializeVelocities(sw, sampler, v0)); 10583ba16761SJacob Faibussowitsch PetscFunctionReturn(PETSC_SUCCESS); 105935b38c60SMatthew G. Knepley } 1060