impls/swarm/swarmpic.c

#define PETSCDM_DLL
#include <petsc/private/dmswarmimpl.h> /*I   "petscdmswarm.h"   I*/
#include <petscsf.h>
#include <petscdmda.h>
#include <petscdmplex.h>
#include <petscdt.h>
#include "../src/dm/impls/swarm/data_bucket.h"

#include <petsc/private/petscfeimpl.h> /* For CoordinatesRefToReal() */

/* Coordinate insertition/addition API */
/*@
  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]` x `npoints[1]` (2D) or `npoints[0]` x `npoints[1]` x `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`
@*/
PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm, PetscReal min[], PetscReal max[], PetscInt npoints[], InsertMode mode)
{
  PetscReal          lmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
  PetscReal          lmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
  PetscInt           i, j, k, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
  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(DMGetLocalBoundingBox(celldm, lmin, lmax));
  PetscCall(DMGetCoordinateDim(celldm, &bs));

  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] < lmin[b]) point_inside = PETSC_FALSE;
          if (xp[b] > lmax[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] < lmin[b]) point_inside = PETSC_FALSE;
          if (xp[b] > lmax[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);
}

/*@
  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()`
@*/
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) {
    PetscMPIInt imy;

    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;
    }
    PetscCall(PetscMPIIntCast(bs * my_npoints, &imy));
    PetscCallMPI(MPI_Bcast(my_coor, imy, 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);

/*@
  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`
@*/
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()`
@*/
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);
}

/*@
  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`
@*/
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`, see `PetscSimplePointFn` for the calling sequence

  Level: intermediate

.seealso: `DMSWARM`, `DMSwarmSetCoordinateFunction()`, `DMSwarmGetVelocityFunction()`, `DMSwarmInitializeCoordinates()`, `PetscSimplePointFn`
@*/
PetscErrorCode DMSwarmGetCoordinateFunction(DM sw, PetscSimplePointFn **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, see `PetscSimplePointFn` for the calling sequence

  Level: intermediate

.seealso: `DMSWARM`, `DMSwarmGetCoordinateFunction()`, `DMSwarmSetVelocityFunction()`, `DMSwarmInitializeCoordinates()`, `PetscSimplePointFn`
@*/
PetscErrorCode DMSwarmSetCoordinateFunction(DM sw, PetscSimplePointFn *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`, see `PetscSimplePointFn` for the calling sequence

  Level: intermediate

.seealso: `DMSWARM`, `DMSwarmSetVelocityFunction()`, `DMSwarmGetCoordinateFunction()`, `DMSwarmInitializeVelocities()`, `PetscSimplePointFn`
@*/
PetscErrorCode DMSwarmGetVelocityFunction(DM sw, PetscSimplePointFn **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, see `PetscSimplePointFn` for the calling sequence

  Level: intermediate

.seealso: `DMSWARM`, `DMSwarmGetVelocityFunction()`, `DMSwarmSetCoordinateFunction()`, `DMSwarmInitializeVelocities()`, `PetscSimplePointFn`
@*/
PetscErrorCode DMSwarmSetVelocityFunction(DM sw, PetscSimplePointFn *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) {
    PetscSimplePointFn *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)
{
  PetscSimplePointFn *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[])
{
  PetscSimplePointFn *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) {
    PetscSimplePointFn *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);
}