#define PETSCDM_DLL #include /*I "petscdmswarm.h" I*/ #include #include #include #include #include "../src/dm/impls/swarm/data_bucket.h" #include /* For CoordinatesRefToReal() */ /* Error checking to ensure the swarm type is correct and that a cell DM has been set */ #define DMSWARMPICVALID(dm) \ do { \ DM_Swarm *_swarm = (DM_Swarm *)(dm)->data; \ PetscCheck(_swarm->swarm_type == DMSWARM_PIC, PetscObjectComm((PetscObject)(dm)), PETSC_ERR_SUP, "Valid only for DMSwarm-PIC. You must call DMSwarmSetType(dm,DMSWARM_PIC)"); \ 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)"); \ } while (0) /* Coordinate insertition/addition API */ /*@C DMSwarmSetPointsUniformCoordinates - Set point coordinates in a `DMSWARM` on a regular (ijk) grid Collective Input Parameters: + dm - the `DMSWARM` . min - minimum coordinate values in the x, y, z directions (array of length dim) . max - maximum coordinate values in the x, y, z directions (array of length dim) . npoints - number of points in each spatial direction (array of length dim) - mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`) Level: beginner Notes: When using mode = `INSERT_VALUES`, this method will reset the number of particles in the `DMSWARM` to be npoints[0]*npoints[1] (2D) or npoints[0]*npoints[1]*npoints[2] (3D). When using mode = `ADD_VALUES`, new points will be appended to any already existing in the `DMSWARM` .seealso: `DM`, `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType` @*/ PETSC_EXTERN PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm, PetscReal min[], PetscReal max[], PetscInt npoints[], InsertMode mode) { PetscReal gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL}; PetscReal gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL}; PetscInt i, j, k, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found; Vec coorlocal; const PetscScalar *_coor; DM celldm; PetscReal dx[3]; PetscInt _npoints[] = {0, 0, 1}; Vec pos; PetscScalar *_pos; PetscReal *swarm_coor; PetscInt *swarm_cellid; PetscSF sfcell = NULL; const PetscSFNode *LA_sfcell; PetscFunctionBegin; DMSWARMPICVALID(dm); PetscCall(DMSwarmGetCellDM(dm, &celldm)); PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal)); PetscCall(VecGetSize(coorlocal, &N)); PetscCall(VecGetBlockSize(coorlocal, &bs)); N = N / bs; PetscCall(VecGetArrayRead(coorlocal, &_coor)); for (i = 0; i < N; i++) { for (b = 0; b < bs; b++) { gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b])); gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b])); } } PetscCall(VecRestoreArrayRead(coorlocal, &_coor)); for (b = 0; b < bs; b++) { if (npoints[b] > 1) { dx[b] = (max[b] - min[b]) / ((PetscReal)(npoints[b] - 1)); } else { dx[b] = 0.0; } _npoints[b] = npoints[b]; } /* determine number of points living in the bounding box */ n_estimate = 0; for (k = 0; k < _npoints[2]; k++) { for (j = 0; j < _npoints[1]; j++) { for (i = 0; i < _npoints[0]; i++) { PetscReal xp[] = {0.0, 0.0, 0.0}; PetscInt ijk[3]; PetscBool point_inside = PETSC_TRUE; ijk[0] = i; ijk[1] = j; ijk[2] = k; for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b]; for (b = 0; b < bs; b++) { if (xp[b] < gmin[b]) point_inside = PETSC_FALSE; if (xp[b] > gmax[b]) point_inside = PETSC_FALSE; } if (point_inside) n_estimate++; } } } /* create candidate list */ PetscCall(VecCreate(PETSC_COMM_SELF, &pos)); PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE)); PetscCall(VecSetBlockSize(pos, bs)); PetscCall(VecSetFromOptions(pos)); PetscCall(VecGetArray(pos, &_pos)); n_estimate = 0; for (k = 0; k < _npoints[2]; k++) { for (j = 0; j < _npoints[1]; j++) { for (i = 0; i < _npoints[0]; i++) { PetscReal xp[] = {0.0, 0.0, 0.0}; PetscInt ijk[3]; PetscBool point_inside = PETSC_TRUE; ijk[0] = i; ijk[1] = j; ijk[2] = k; for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b]; for (b = 0; b < bs; b++) { if (xp[b] < gmin[b]) point_inside = PETSC_FALSE; if (xp[b] > gmax[b]) point_inside = PETSC_FALSE; } if (point_inside) { for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = xp[b]; n_estimate++; } } } } PetscCall(VecRestoreArray(pos, &_pos)); /* locate points */ PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell)); PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell)); n_found = 0; for (p = 0; p < n_estimate; p++) { if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++; } /* adjust size */ if (mode == ADD_VALUES) { PetscCall(DMSwarmGetLocalSize(dm, &n_curr)); n_new_est = n_curr + n_found; PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1)); } if (mode == INSERT_VALUES) { n_curr = 0; n_new_est = n_found; PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1)); } /* initialize new coords, cell owners, pid */ PetscCall(VecGetArrayRead(pos, &_coor)); PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor)); PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); n_found = 0; for (p = 0; p < n_estimate; p++) { if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) { for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]); swarm_cellid[n_curr + n_found] = LA_sfcell[p].index; n_found++; } } PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor)); PetscCall(VecRestoreArrayRead(pos, &_coor)); PetscCall(PetscSFDestroy(&sfcell)); PetscCall(VecDestroy(&pos)); PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmSetPointCoordinates - Set point coordinates in a `DMSWARM` from a user defined list Collective Input Parameters: + dm - the `DMSWARM` . npoints - the number of points to insert . coor - the coordinate values . 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 - mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`) Level: beginner Notes: If the user has specified `redundant` as `PETSC_FALSE`, the cell `DM` will attempt to locate the coordinates provided by `coor` within its sub-domain. If they any values within `coor` are not located in the sub-domain, they will be ignored and will not get added to the `DMSWARM`. .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`, `DMSwarmSetPointsUniformCoordinates()` @*/ PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinates(DM dm, PetscInt npoints, PetscReal coor[], PetscBool redundant, InsertMode mode) { PetscReal gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL}; PetscReal gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL}; PetscInt i, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found; Vec coorlocal; const PetscScalar *_coor; DM celldm; Vec pos; PetscScalar *_pos; PetscReal *swarm_coor; PetscInt *swarm_cellid; PetscSF sfcell = NULL; const PetscSFNode *LA_sfcell; PetscReal *my_coor; PetscInt my_npoints; PetscMPIInt rank; MPI_Comm comm; PetscFunctionBegin; DMSWARMPICVALID(dm); PetscCall(PetscObjectGetComm((PetscObject)dm, &comm)); PetscCallMPI(MPI_Comm_rank(comm, &rank)); PetscCall(DMSwarmGetCellDM(dm, &celldm)); PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal)); PetscCall(VecGetSize(coorlocal, &N)); PetscCall(VecGetBlockSize(coorlocal, &bs)); N = N / bs; PetscCall(VecGetArrayRead(coorlocal, &_coor)); for (i = 0; i < N; i++) { for (b = 0; b < bs; b++) { gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b])); gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b])); } } PetscCall(VecRestoreArrayRead(coorlocal, &_coor)); /* broadcast points from rank 0 if requested */ if (redundant) { my_npoints = npoints; PetscCallMPI(MPI_Bcast(&my_npoints, 1, MPIU_INT, 0, comm)); if (rank > 0) { /* allocate space */ PetscCall(PetscMalloc1(bs * my_npoints, &my_coor)); } else { my_coor = coor; } PetscCallMPI(MPI_Bcast(my_coor, bs * my_npoints, MPIU_REAL, 0, comm)); } else { my_npoints = npoints; my_coor = coor; } /* determine the number of points living in the bounding box */ n_estimate = 0; for (i = 0; i < my_npoints; i++) { PetscBool point_inside = PETSC_TRUE; for (b = 0; b < bs; b++) { if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE; if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE; } if (point_inside) n_estimate++; } /* create candidate list */ PetscCall(VecCreate(PETSC_COMM_SELF, &pos)); PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE)); PetscCall(VecSetBlockSize(pos, bs)); PetscCall(VecSetFromOptions(pos)); PetscCall(VecGetArray(pos, &_pos)); n_estimate = 0; for (i = 0; i < my_npoints; i++) { PetscBool point_inside = PETSC_TRUE; for (b = 0; b < bs; b++) { if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE; if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE; } if (point_inside) { for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = my_coor[bs * i + b]; n_estimate++; } } PetscCall(VecRestoreArray(pos, &_pos)); /* locate points */ PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell)); PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell)); n_found = 0; for (p = 0; p < n_estimate; p++) { if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++; } /* adjust size */ if (mode == ADD_VALUES) { PetscCall(DMSwarmGetLocalSize(dm, &n_curr)); n_new_est = n_curr + n_found; PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1)); } if (mode == INSERT_VALUES) { n_curr = 0; n_new_est = n_found; PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1)); } /* initialize new coords, cell owners, pid */ PetscCall(VecGetArrayRead(pos, &_coor)); PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor)); PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); n_found = 0; for (p = 0; p < n_estimate; p++) { if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) { for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]); swarm_cellid[n_curr + n_found] = LA_sfcell[p].index; n_found++; } } PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor)); PetscCall(VecRestoreArrayRead(pos, &_coor)); if (redundant) { if (rank > 0) PetscCall(PetscFree(my_coor)); } PetscCall(PetscSFDestroy(&sfcell)); PetscCall(VecDestroy(&pos)); PetscFunctionReturn(PETSC_SUCCESS); } extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_DA(DM, DM, DMSwarmPICLayoutType, PetscInt); extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_PLEX(DM, DM, DMSwarmPICLayoutType, PetscInt); /*@C DMSwarmInsertPointsUsingCellDM - Insert point coordinates within each cell Not Collective Input Parameters: + dm - the `DMSWARM` . layout_type - method used to fill each cell with the cell `DM` - fill_param - parameter controlling how many points per cell are added (the meaning of this parameter is dependent on the layout type) Level: beginner Notes: The insert method will reset any previous defined points within the `DMSWARM`. When using a `DMDA` both 2D and 3D are supported for all layout types provided you are using `DMDA_ELEMENT_Q1`. When using a `DMPLEX` the following case are supported\: .vb (i) DMSWARMPIC_LAYOUT_REGULAR: 2D (triangle), (ii) DMSWARMPIC_LAYOUT_GAUSS: 2D and 3D provided the cell is a tri/tet or a quad/hex, (iii) DMSWARMPIC_LAYOUT_SUBDIVISION: 2D and 3D for quad/hex and 2D tri. .ve .seealso: `DMSWARM`, `DMSwarmPICLayoutType`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType` @*/ PETSC_EXTERN PetscErrorCode DMSwarmInsertPointsUsingCellDM(DM dm, DMSwarmPICLayoutType layout_type, PetscInt fill_param) { DM celldm; PetscBool isDA, isPLEX; PetscFunctionBegin; DMSWARMPICVALID(dm); PetscCall(DMSwarmGetCellDM(dm, &celldm)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX)); if (isDA) { PetscCall(private_DMSwarmInsertPointsUsingCellDM_DA(dm, celldm, layout_type, fill_param)); } else if (isPLEX) { PetscCall(private_DMSwarmInsertPointsUsingCellDM_PLEX(dm, celldm, layout_type, fill_param)); } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX"); PetscFunctionReturn(PETSC_SUCCESS); } extern PetscErrorCode private_DMSwarmSetPointCoordinatesCellwise_PLEX(DM, DM, PetscInt, PetscReal *); /*@C DMSwarmSetPointCoordinatesCellwise - Insert point coordinates (defined over the reference cell) within each cell Not Collective Input Parameters: + dm - the `DMSWARM` . npoints - the number of points to insert in each cell - xi - the coordinates (defined in the local coordinate system for each cell) to insert Level: beginner Notes: The method will reset any previous defined points within the `DMSWARM`. Only supported for `DMPLEX`. If you are using a `DMDA` it is recommended to either use `DMSwarmInsertPointsUsingCellDM()`, or extract and set the coordinates yourself the following code .vb PetscReal *coor; DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor); // user code to define the coordinates here DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor); .ve .seealso: `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmInsertPointsUsingCellDM()` @*/ PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinatesCellwise(DM dm, PetscInt npoints, PetscReal xi[]) { DM celldm; PetscBool isDA, isPLEX; PetscFunctionBegin; DMSWARMPICVALID(dm); PetscCall(DMSwarmGetCellDM(dm, &celldm)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX)); PetscCheck(!isDA, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMPLEX. Recommended you use DMSwarmInsertPointsUsingCellDM()"); if (isPLEX) { PetscCall(private_DMSwarmSetPointCoordinatesCellwise_PLEX(dm, celldm, npoints, xi)); } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX"); PetscFunctionReturn(PETSC_SUCCESS); } /* Field projection API */ extern PetscErrorCode private_DMSwarmProjectFields_DA(DM swarm, DM celldm, PetscInt project_type, PetscInt nfields, DMSwarmDataField dfield[], Vec vecs[]); extern PetscErrorCode private_DMSwarmProjectFields_PLEX(DM swarm, DM celldm, PetscInt project_type, PetscInt nfields, DMSwarmDataField dfield[], Vec vecs[]); /*@C DMSwarmProjectFields - Project a set of swarm fields onto the cell `DM` Collective Input Parameters: + dm - the `DMSWARM` . nfields - the number of swarm fields to project . fieldnames - the textual names of the swarm fields to project . fields - an array of Vec's of length nfields - reuse - flag indicating whether the array and contents of fields should be re-used or internally allocated Level: beginner Notes: Currently, the only available projection method consists of .vb phi_i = \sum_{p=0}^{np} N_i(x_p) phi_p dJ / \sum_{p=0}^{np} N_i(x_p) dJ where phi_p is the swarm field at point p, N_i() is the cell DM basis function at vertex i, dJ is the determinant of the cell Jacobian and phi_i is the projected vertex value of the field phi. .ve If `reuse` is `PETSC_FALSE`, this function will allocate the array of `Vec`'s, and each individual `Vec`. The user is responsible for destroying both the array and the individual `Vec` objects. Only swarm fields registered with data type of `PETSC_REAL` can be projected onto the cell `DM`. Only swarm fields of block size = 1 can currently be projected. The only projection methods currently only support the `DMDA` (2D) and `DMPLEX` (triangles 2D). .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType` @*/ PETSC_EXTERN PetscErrorCode DMSwarmProjectFields(DM dm, PetscInt nfields, const char *fieldnames[], Vec **fields, PetscBool reuse) { DM_Swarm *swarm = (DM_Swarm *)dm->data; DMSwarmDataField *gfield; DM celldm; PetscBool isDA, isPLEX; Vec *vecs; PetscInt f, nvecs; PetscInt project_type = 0; PetscFunctionBegin; DMSWARMPICVALID(dm); PetscCall(DMSwarmGetCellDM(dm, &celldm)); PetscCall(PetscMalloc1(nfields, &gfield)); nvecs = 0; for (f = 0; f < nfields; f++) { PetscCall(DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db, fieldnames[f], &gfield[f])); PetscCheck(gfield[f]->petsc_type == PETSC_REAL, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Projection only valid for fields using a data type = PETSC_REAL"); PetscCheck(gfield[f]->bs == 1, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Projection only valid for fields with block size = 1"); nvecs += gfield[f]->bs; } if (!reuse) { PetscCall(PetscMalloc1(nvecs, &vecs)); for (f = 0; f < nvecs; f++) { PetscCall(DMCreateGlobalVector(celldm, &vecs[f])); PetscCall(PetscObjectSetName((PetscObject)vecs[f], gfield[f]->name)); } } else { vecs = *fields; } PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX)); if (isDA) { PetscCall(private_DMSwarmProjectFields_DA(dm, celldm, project_type, nfields, gfield, vecs)); } else if (isPLEX) { PetscCall(private_DMSwarmProjectFields_PLEX(dm, celldm, project_type, nfields, gfield, vecs)); } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX"); PetscCall(PetscFree(gfield)); if (!reuse) *fields = vecs; PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmCreatePointPerCellCount - Count the number of points within all cells in the cell DM Not Collective Input Parameter: . dm - the `DMSWARM` Output Parameters: + ncells - the number of cells in the cell `DM` (optional argument, pass `NULL` to ignore) - count - array of length ncells containing the number of points per cell Level: beginner Notes: The array count is allocated internally and must be free'd by the user. .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType` @*/ PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm, PetscInt *ncells, PetscInt **count) { PetscBool isvalid; PetscInt nel; PetscInt *sum; PetscFunctionBegin; PetscCall(DMSwarmSortGetIsValid(dm, &isvalid)); nel = 0; if (isvalid) { PetscInt e; PetscCall(DMSwarmSortGetSizes(dm, &nel, NULL)); PetscCall(PetscMalloc1(nel, &sum)); for (e = 0; e < nel; e++) PetscCall(DMSwarmSortGetNumberOfPointsPerCell(dm, e, &sum[e])); } else { DM celldm; PetscBool isda, isplex, isshell; PetscInt p, npoints; PetscInt *swarm_cellid; /* get the number of cells */ PetscCall(DMSwarmGetCellDM(dm, &celldm)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isda)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isplex)); PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMSHELL, &isshell)); if (isda) { PetscInt _nel, _npe; const PetscInt *_element; PetscCall(DMDAGetElements(celldm, &_nel, &_npe, &_element)); nel = _nel; PetscCall(DMDARestoreElements(celldm, &_nel, &_npe, &_element)); } else if (isplex) { PetscInt ps, pe; PetscCall(DMPlexGetHeightStratum(celldm, 0, &ps, &pe)); nel = pe - ps; } else if (isshell) { PetscErrorCode (*method_DMShellGetNumberOfCells)(DM, PetscInt *); PetscCall(PetscObjectQueryFunction((PetscObject)celldm, "DMGetNumberOfCells_C", &method_DMShellGetNumberOfCells)); if (method_DMShellGetNumberOfCells) { PetscCall(method_DMShellGetNumberOfCells(celldm, &nel)); } else 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);"); } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot determine the number of cells for a DM not of type DA, PLEX or SHELL"); PetscCall(PetscMalloc1(nel, &sum)); PetscCall(PetscArrayzero(sum, nel)); PetscCall(DMSwarmGetLocalSize(dm, &npoints)); PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); for (p = 0; p < npoints; p++) { if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) sum[swarm_cellid[p]]++; } PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid)); } if (ncells) *ncells = nel; *count = sum; PetscFunctionReturn(PETSC_SUCCESS); } /*@ DMSwarmGetNumSpecies - Get the number of particle species Not Collective Input Parameter: . sw - the `DMSWARM` Output Parameters: . Ns - the number of species Level: intermediate .seealso: `DMSWARM`, `DMSwarmSetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType` @*/ PetscErrorCode DMSwarmGetNumSpecies(DM sw, PetscInt *Ns) { DM_Swarm *swarm = (DM_Swarm *)sw->data; PetscFunctionBegin; *Ns = swarm->Ns; PetscFunctionReturn(PETSC_SUCCESS); } /*@ DMSwarmSetNumSpecies - Set the number of particle species Not Collective Input Parameters: + sw - the `DMSWARM` - Ns - the number of species Level: intermediate .seealso: `DMSWARM`, `DMSwarmGetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType` @*/ PetscErrorCode DMSwarmSetNumSpecies(DM sw, PetscInt Ns) { DM_Swarm *swarm = (DM_Swarm *)sw->data; PetscFunctionBegin; swarm->Ns = Ns; PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmGetCoordinateFunction - Get the function setting initial particle positions, if it exists Not Collective Input Parameter: . sw - the `DMSWARM` Output Parameter: . coordFunc - the function setting initial particle positions, or `NULL` Level: intermediate .seealso: `DMSWARM`, `DMSwarmSetCoordinateFunction()`, `DMSwarmGetVelocityFunction()`, `DMSwarmInitializeCoordinates()` @*/ PetscErrorCode DMSwarmGetCoordinateFunction(DM sw, PetscSimplePointFunc *coordFunc) { DM_Swarm *swarm = (DM_Swarm *)sw->data; PetscFunctionBegin; PetscValidHeaderSpecific(sw, DM_CLASSID, 1); PetscAssertPointer(coordFunc, 2); *coordFunc = swarm->coordFunc; PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmSetCoordinateFunction - Set the function setting initial particle positions Not Collective Input Parameters: + sw - the `DMSWARM` - coordFunc - the function setting initial particle positions Level: intermediate .seealso: `DMSWARM`, `DMSwarmGetCoordinateFunction()`, `DMSwarmSetVelocityFunction()`, `DMSwarmInitializeCoordinates()` @*/ PetscErrorCode DMSwarmSetCoordinateFunction(DM sw, PetscSimplePointFunc coordFunc) { DM_Swarm *swarm = (DM_Swarm *)sw->data; PetscFunctionBegin; PetscValidHeaderSpecific(sw, DM_CLASSID, 1); PetscValidFunction(coordFunc, 2); swarm->coordFunc = coordFunc; PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmGetVelocityFunction - Get the function setting initial particle velocities, if it exists Not Collective Input Parameter: . sw - the `DMSWARM` Output Parameter: . velFunc - the function setting initial particle velocities, or `NULL` Level: intermediate .seealso: `DMSWARM`, `DMSwarmSetVelocityFunction()`, `DMSwarmGetCoordinateFunction()`, `DMSwarmInitializeVelocities()` @*/ PetscErrorCode DMSwarmGetVelocityFunction(DM sw, PetscSimplePointFunc *velFunc) { DM_Swarm *swarm = (DM_Swarm *)sw->data; PetscFunctionBegin; PetscValidHeaderSpecific(sw, DM_CLASSID, 1); PetscAssertPointer(velFunc, 2); *velFunc = swarm->velFunc; PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmSetVelocityFunction - Set the function setting initial particle velocities Not Collective Input Parameters: + sw - the `DMSWARM` - velFunc - the function setting initial particle velocities Level: intermediate .seealso: `DMSWARM`, `DMSwarmGetVelocityFunction()`, `DMSwarmSetCoordinateFunction()`, `DMSwarmInitializeVelocities()` @*/ PetscErrorCode DMSwarmSetVelocityFunction(DM sw, PetscSimplePointFunc velFunc) { DM_Swarm *swarm = (DM_Swarm *)sw->data; PetscFunctionBegin; PetscValidHeaderSpecific(sw, DM_CLASSID, 1); PetscValidFunction(velFunc, 2); swarm->velFunc = velFunc; PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmComputeLocalSize - Compute the local number and distribution of particles based upon a density function Not Collective Input Parameters: + sw - The `DMSWARM` . N - The target number of particles - density - The density field for the particle layout, normalized to unity Level: advanced Note: One particle will be created for each species. .seealso: `DMSWARM`, `DMSwarmComputeLocalSizeFromOptions()` @*/ PetscErrorCode DMSwarmComputeLocalSize(DM sw, PetscInt N, PetscProbFunc density) { DM dm; PetscQuadrature quad; const PetscReal *xq, *wq; PetscReal *n_int; PetscInt *npc_s, *cellid, Ni; PetscReal gmin[3], gmax[3], xi0[3]; PetscInt Ns, cStart, cEnd, c, dim, d, Nq, q, Np = 0, p, s; PetscBool simplex; PetscFunctionBegin; PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); PetscCall(DMSwarmGetCellDM(sw, &dm)); PetscCall(DMGetDimension(dm, &dim)); PetscCall(DMGetBoundingBox(dm, gmin, gmax)); PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); PetscCall(DMPlexIsSimplex(dm, &simplex)); PetscCall(DMGetCoordinatesLocalSetUp(dm)); if (simplex) PetscCall(PetscDTStroudConicalQuadrature(dim, 1, 5, -1.0, 1.0, &quad)); else PetscCall(PetscDTGaussTensorQuadrature(dim, 1, 5, -1.0, 1.0, &quad)); PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, &xq, &wq)); PetscCall(PetscCalloc2(Ns, &n_int, (cEnd - cStart) * Ns, &npc_s)); /* Integrate the density function to get the number of particles in each cell */ for (d = 0; d < dim; ++d) xi0[d] = -1.0; for (c = 0; c < cEnd - cStart; ++c) { const PetscInt cell = c + cStart; PetscReal v0[3], J[9], invJ[9], detJ, detJp = 2. / (gmax[0] - gmin[0]), xr[3], den; /*Have to transform quadrature points/weights to cell domain*/ PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ)); PetscCall(PetscArrayzero(n_int, Ns)); for (q = 0; q < Nq; ++q) { CoordinatesRefToReal(dim, dim, xi0, v0, J, &xq[q * dim], xr); /* Have to transform mesh to domain of definition of PDF, [-1, 1], and weight PDF by |J|/2 */ xr[0] = detJp * (xr[0] - gmin[0]) - 1.; for (s = 0; s < Ns; ++s) { PetscCall(density(xr, NULL, &den)); n_int[s] += (detJp * den) * (detJ * wq[q]) / (PetscReal)Ns; } } for (s = 0; s < Ns; ++s) { Ni = N; npc_s[c * Ns + s] += (PetscInt)(Ni * n_int[s]); Np += npc_s[c * Ns + s]; } } PetscCall(PetscQuadratureDestroy(&quad)); PetscCall(DMSwarmSetLocalSizes(sw, Np, 0)); PetscCall(DMSwarmGetField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid)); for (c = 0, p = 0; c < cEnd - cStart; ++c) { for (s = 0; s < Ns; ++s) { for (q = 0; q < npc_s[c * Ns + s]; ++q, ++p) cellid[p] = c; } } PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid)); PetscCall(PetscFree2(n_int, npc_s)); PetscFunctionReturn(PETSC_SUCCESS); } /*@ DMSwarmComputeLocalSizeFromOptions - Compute the local number and distribution of particles based upon a density function determined by options Not Collective Input Parameter: . sw - The `DMSWARM` Level: advanced .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()` @*/ PetscErrorCode DMSwarmComputeLocalSizeFromOptions(DM sw) { PetscProbFunc pdf; const char *prefix; char funcname[PETSC_MAX_PATH_LEN]; PetscInt *N, Ns, dim, n; PetscBool flg; PetscMPIInt size, rank; PetscFunctionBegin; PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)sw), &size)); PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)sw), &rank)); PetscCall(PetscCalloc1(size, &N)); PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM"); n = size; PetscCall(PetscOptionsIntArray("-dm_swarm_num_particles", "The target number of particles", "", N, &n, NULL)); PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); PetscCall(PetscOptionsInt("-dm_swarm_num_species", "The number of species", "DMSwarmSetNumSpecies", Ns, &Ns, &flg)); if (flg) PetscCall(DMSwarmSetNumSpecies(sw, Ns)); PetscCall(PetscOptionsString("-dm_swarm_coordinate_function", "Function to determine particle coordinates", "DMSwarmSetCoordinateFunction", funcname, funcname, sizeof(funcname), &flg)); PetscOptionsEnd(); if (flg) { PetscSimplePointFunc coordFunc; PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); PetscCall(PetscDLSym(NULL, funcname, (void **)&coordFunc)); PetscCheck(coordFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname); PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); PetscCall(DMSwarmSetLocalSizes(sw, N[rank] * Ns, 0)); PetscCall(DMSwarmSetCoordinateFunction(sw, coordFunc)); } else { PetscCall(DMGetDimension(sw, &dim)); PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix)); PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_coordinate_density", &pdf, NULL, NULL)); PetscCall(DMSwarmComputeLocalSize(sw, N[rank], pdf)); } PetscCall(PetscFree(N)); PetscFunctionReturn(PETSC_SUCCESS); } /*@ DMSwarmInitializeCoordinates - Determine the initial coordinates of particles for a PIC method Not Collective Input Parameter: . sw - The `DMSWARM` Level: advanced Note: Currently, we randomly place particles in their assigned cell .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeVelocities()` @*/ PetscErrorCode DMSwarmInitializeCoordinates(DM sw) { PetscSimplePointFunc coordFunc; PetscScalar *weight; PetscReal *x; PetscInt *species; void *ctx; PetscBool removePoints = PETSC_TRUE; PetscDataType dtype; PetscInt Np, p, Ns, dim, d, bs; PetscFunctionBeginUser; PetscCall(DMGetDimension(sw, &dim)); PetscCall(DMSwarmGetLocalSize(sw, &Np)); PetscCall(DMSwarmGetNumSpecies(sw, &Ns)); PetscCall(DMSwarmGetCoordinateFunction(sw, &coordFunc)); PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, &bs, &dtype, (void **)&x)); PetscCall(DMSwarmGetField(sw, "w_q", &bs, &dtype, (void **)&weight)); PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species)); if (coordFunc) { PetscCall(DMGetApplicationContext(sw, &ctx)); for (p = 0; p < Np; ++p) { PetscScalar X[3]; PetscCall((*coordFunc)(dim, 0., NULL, p, X, ctx)); for (d = 0; d < dim; ++d) x[p * dim + d] = PetscRealPart(X[d]); weight[p] = 1.0; species[p] = p % Ns; } } else { DM dm; PetscRandom rnd; PetscReal xi0[3]; PetscInt cStart, cEnd, c; PetscCall(DMSwarmGetCellDM(sw, &dm)); PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd)); PetscCall(DMGetApplicationContext(sw, &ctx)); /* Set particle position randomly in cell, set weights to 1 */ PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)dm), &rnd)); PetscCall(PetscRandomSetInterval(rnd, -1.0, 1.0)); PetscCall(PetscRandomSetFromOptions(rnd)); PetscCall(DMSwarmSortGetAccess(sw)); for (d = 0; d < dim; ++d) xi0[d] = -1.0; for (c = cStart; c < cEnd; ++c) { PetscReal v0[3], J[9], invJ[9], detJ; PetscInt *pidx, Npc, q; PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx)); PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ)); for (q = 0; q < Npc; ++q) { const PetscInt p = pidx[q]; PetscReal xref[3]; for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &xref[d])); CoordinatesRefToReal(dim, dim, xi0, v0, J, xref, &x[p * dim]); weight[p] = 1.0 / Np; species[p] = p % Ns; } PetscCall(PetscFree(pidx)); } PetscCall(PetscRandomDestroy(&rnd)); PetscCall(DMSwarmSortRestoreAccess(sw)); } PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x)); PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight)); PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species)); PetscCall(DMSwarmMigrate(sw, removePoints)); PetscCall(DMLocalizeCoordinates(sw)); PetscFunctionReturn(PETSC_SUCCESS); } /*@C DMSwarmInitializeVelocities - Set the initial velocities of particles using a distribution. Collective Input Parameters: + sw - The `DMSWARM` object . sampler - A function which uniformly samples the velocity PDF - v0 - The velocity scale for nondimensionalization for each species Level: advanced Note: 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. .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocitiesFromOptions()` @*/ PetscErrorCode DMSwarmInitializeVelocities(DM sw, PetscProbFunc sampler, const PetscReal v0[]) { PetscSimplePointFunc velFunc; PetscReal *v; PetscInt *species; void *ctx; PetscInt dim, Np, p; PetscFunctionBegin; PetscCall(DMSwarmGetVelocityFunction(sw, &velFunc)); PetscCall(DMGetDimension(sw, &dim)); PetscCall(DMSwarmGetLocalSize(sw, &Np)); PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v)); PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species)); if (v0[0] == 0.) { PetscCall(PetscArrayzero(v, Np * dim)); } else if (velFunc) { PetscCall(DMGetApplicationContext(sw, &ctx)); for (p = 0; p < Np; ++p) { PetscInt s = species[p], d; PetscScalar vel[3]; PetscCall((*velFunc)(dim, 0., NULL, p, vel, ctx)); for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * PetscRealPart(vel[d]); } } else { PetscRandom rnd; PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)sw), &rnd)); PetscCall(PetscRandomSetInterval(rnd, 0, 1.)); PetscCall(PetscRandomSetFromOptions(rnd)); for (p = 0; p < Np; ++p) { PetscInt s = species[p], d; PetscReal a[3], vel[3]; for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &a[d])); PetscCall(sampler(a, NULL, vel)); for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * vel[d]; } PetscCall(PetscRandomDestroy(&rnd)); } PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v)); PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species)); PetscFunctionReturn(PETSC_SUCCESS); } /*@ DMSwarmInitializeVelocitiesFromOptions - Set the initial velocities of particles using a distribution determined from options. Collective Input Parameters: + sw - The `DMSWARM` object - v0 - The velocity scale for nondimensionalization for each species Level: advanced .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocities()` @*/ PetscErrorCode DMSwarmInitializeVelocitiesFromOptions(DM sw, const PetscReal v0[]) { PetscProbFunc sampler; PetscInt dim; const char *prefix; char funcname[PETSC_MAX_PATH_LEN]; PetscBool flg; PetscFunctionBegin; PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM"); PetscCall(PetscOptionsString("-dm_swarm_velocity_function", "Function to determine particle velocities", "DMSwarmSetVelocityFunction", funcname, funcname, sizeof(funcname), &flg)); PetscOptionsEnd(); if (flg) { PetscSimplePointFunc velFunc; PetscCall(PetscDLSym(NULL, funcname, (void **)&velFunc)); PetscCheck(velFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname); PetscCall(DMSwarmSetVelocityFunction(sw, velFunc)); } PetscCall(DMGetDimension(sw, &dim)); PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix)); PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_velocity_density", NULL, NULL, &sampler)); PetscCall(DMSwarmInitializeVelocities(sw, sampler, v0)); PetscFunctionReturn(PETSC_SUCCESS); }