xref: /petsc/src/dm/impls/swarm/swarmpic.c (revision 71844bb8d9b6b640b934b4f3526f4bb2bc397e8c)

#define PETSCDM_DLL
#include <petsc/private/dmswarmimpl.h>    /*I   "petscdmswarm.h"   I*/
#include <petscsf.h>
#include <petscdmda.h>
#include <petscdmplex.h>

/*
 Error chceking macto to ensure the swarm type is correct and that a cell DM has been set
*/
#define DMSWARMPICVALID(dm) \
{ \
  DM_Swarm *_swarm = (DM_Swarm*)(dm)->data; \
  if (_swarm->swarm_type != DMSWARM_PIC) SETERRQ(PetscObjectComm((PetscObject)(dm)),PETSC_ERR_SUP,"Only valid for DMSwarm-PIC. You must call DMSwarmSetType(dm,DMSWARM_PIC)"); \
  else \
    if (!_swarm->dmcell) SETERRQ(PetscObjectComm((PetscObject)(dm)),PETSC_ERR_SUP,"Only valid for DMSwarmPIC if the cell DM is set. You must call DMSwarmSetCellDM(dm,celldm)"); \
}

/* Coordinate insertition/addition API */
/*@C
   DMSwarmSetPointsUniformCoordinates - Set point coordinates in a DMSwarm on a regular (ijk) grid

   Collective on DM

   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: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
@*/
PETSC_EXTERN PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm,PetscReal min[],PetscReal max[],PetscInt npoints[],InsertMode mode)
{
  PetscErrorCode ierr;
  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];
  Vec pos;
  PetscScalar *_pos;
  PetscReal *swarm_coor;
  PetscInt *swarm_cellid;
  PetscSF sfcell = NULL;
  const PetscSFNode *LA_sfcell;

  PetscFunctionBegin;
  DMSWARMPICVALID(dm);
  ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(celldm,&coorlocal);CHKERRQ(ierr);
  ierr = VecGetSize(coorlocal,&N);CHKERRQ(ierr);
  ierr = VecGetBlockSize(coorlocal,&bs);CHKERRQ(ierr);
  N = N / bs;
  ierr = VecGetArrayRead(coorlocal,&_coor);CHKERRQ(ierr);
  for (i=0; i<N; i++) {
    for (b=0; b<bs; b++) {
      gmin[b] = PetscMin(gmin[b],_coor[bs*i+b]);
      gmax[b] = PetscMax(gmax[b],_coor[bs*i+b]);
    }
  }
  ierr = VecRestoreArrayRead(coorlocal,&_coor);CHKERRQ(ierr);

  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;
    }
  }

  /* determine number of points living in the bounding box */
  n_estimate = 0;
  if (bs == 2) { npoints[2] = 1; }
  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 */
  ierr = VecCreate(PetscObjectComm((PetscObject)dm),&pos);CHKERRQ(ierr);
  ierr = VecSetSizes(pos,bs*n_estimate,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetBlockSize(pos,bs);CHKERRQ(ierr);
  ierr = VecSetFromOptions(pos);CHKERRQ(ierr);
  ierr = VecGetArray(pos,&_pos);CHKERRQ(ierr);

  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++;
        }
      }
    }
  }
  ierr = VecRestoreArray(pos,&_pos);CHKERRQ(ierr);

  /* locate points */
  ierr = DMLocatePoints(celldm,pos,DM_POINTLOCATION_NONE,&sfcell);CHKERRQ(ierr);

  ierr = PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell);CHKERRQ(ierr);
  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) {
    ierr = DMSwarmGetLocalSize(dm,&n_curr);CHKERRQ(ierr);
    n_new_est = n_curr + n_found;
    ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
  }
  if (mode == INSERT_VALUES) {
    n_curr = 0;
    n_new_est = n_found;
    ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
  }

  /* initialize new coords, cell owners, pid */
  ierr = VecGetArrayRead(pos,&_coor);CHKERRQ(ierr);
  ierr = DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
  ierr = DMSwarmGetField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
  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] = _coor[bs*p+b];
      }
      swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
      n_found++;
    }
  }
  ierr = DMSwarmRestoreField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
  ierr = DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(pos,&_coor);CHKERRQ(ierr);

  ierr = PetscSFDestroy(&sfcell);CHKERRQ(ierr);
  ierr = VecDestroy(&pos);CHKERRQ(ierr);

  PetscFunctionReturn(0);
}

/*@C
   DMSwarmSetPointCoordinates - Set point coordinates in a DMSwarm from a user defined list

   Collective on DM

   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 = 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: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType, DMSwarmSetPointsUniformCoordinates()
@*/
PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinates(DM dm,PetscInt npoints,PetscReal coor[],PetscBool redundant,InsertMode mode)
{
  PetscErrorCode ierr;
  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);
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);

  ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(celldm,&coorlocal);CHKERRQ(ierr);
  ierr = VecGetSize(coorlocal,&N);CHKERRQ(ierr);
  ierr = VecGetBlockSize(coorlocal,&bs);CHKERRQ(ierr);
  N = N / bs;
  ierr = VecGetArrayRead(coorlocal,&_coor);CHKERRQ(ierr);
  for (i=0; i<N; i++) {
    for (b=0; b<bs; b++) {
      gmin[b] = PetscMin(gmin[b],_coor[bs*i+b]);
      gmax[b] = PetscMax(gmax[b],_coor[bs*i+b]);
    }
  }
  ierr = VecRestoreArrayRead(coorlocal,&_coor);CHKERRQ(ierr);

  /* broadcast points from rank 0 if requested */
  if (redundant) {
    my_npoints = npoints;
    ierr = MPI_Bcast(&my_npoints,1,MPIU_INT,0,comm);CHKERRQ(ierr);

    if (rank > 0) { /* allocate space */
      ierr = PetscMalloc1(bs*my_npoints,&my_coor);CHKERRQ(ierr);
    } else {
      my_coor = coor;
    }
    ierr = MPI_Bcast(my_coor,bs*my_npoints,MPIU_REAL,0,comm);CHKERRQ(ierr);
  } 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 */
  ierr = VecCreate(PetscObjectComm((PetscObject)dm),&pos);CHKERRQ(ierr);
  ierr = VecSetSizes(pos,bs*n_estimate,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetBlockSize(pos,bs);CHKERRQ(ierr);
  ierr = VecSetFromOptions(pos);CHKERRQ(ierr);
  ierr = VecGetArray(pos,&_pos);CHKERRQ(ierr);

  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++;
    }
  }
  ierr = VecRestoreArray(pos,&_pos);CHKERRQ(ierr);

  /* locate points */
  ierr = DMLocatePoints(celldm,pos,DM_POINTLOCATION_NONE,&sfcell);CHKERRQ(ierr);

  ierr = PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell);CHKERRQ(ierr);
  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) {
    ierr = DMSwarmGetLocalSize(dm,&n_curr);CHKERRQ(ierr);
    n_new_est = n_curr + n_found;
    ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
  }
  if (mode == INSERT_VALUES) {
    n_curr = 0;
    n_new_est = n_found;
    ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
  }

  /* initialize new coords, cell owners, pid */
  ierr = VecGetArrayRead(pos,&_coor);CHKERRQ(ierr);
  ierr = DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
  ierr = DMSwarmGetField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
  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] = _coor[bs*p+b];
      }
      swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
      n_found++;
    }
  }
  ierr = DMSwarmRestoreField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
  ierr = DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(pos,&_coor);CHKERRQ(ierr);

  if (redundant) {
    if (rank > 0) {
      ierr = PetscFree(my_coor);CHKERRQ(ierr);
    }
  }
  ierr = PetscSFDestroy(&sfcell);CHKERRQ(ierr);
  ierr = VecDestroy(&pos);CHKERRQ(ierr);

  PetscFunctionReturn(0);
}

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

.seealso: DMSwarmPICLayoutType, DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
@*/
PETSC_EXTERN PetscErrorCode DMSwarmInsertPointsUsingCellDM(DM dm,DMSwarmPICLayoutType layout_type,PetscInt fill_param)
{
  PetscErrorCode ierr;
  DM celldm;
  PetscBool isDA,isPLEX;

  PetscFunctionBegin;
  DMSWARMPICVALID(dm);
  ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)celldm,DMDA,&isDA);CHKERRQ(ierr);
  ierr = PetscObjectTypeCompare((PetscObject)celldm,DMPLEX,&isPLEX);CHKERRQ(ierr);
  if (isDA) {
    ierr = private_DMSwarmInsertPointsUsingCellDM_DA(dm,celldm,layout_type,fill_param);CHKERRQ(ierr);
  } else if (isPLEX) {
    ierr = private_DMSwarmInsertPointsUsingCellDM_PLEX(dm,celldm,layout_type,fill_param);CHKERRQ(ierr);
  } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only supported for cell DMs of type DMDA and DMPLEX");

  PetscFunctionReturn(0);
}

/*
PETSC_EXTERN PetscErrorCode DMSwarmAddPointCoordinatesCellWise(DM dm,PetscInt cell,PetscInt npoints,PetscReal xi[],PetscBool proximity_initialization)
{
  PetscFunctionBegin;
  PetscFunctionReturn(0);
}
*/

/* Field projection API */
/*
PETSC_EXTERN PetscErrorCode DMSwarmProjectFields(DM dm,PetscInt project_type,PetscInt nfields,const char *fieldnames[],Vec *fields)
{
  PetscFunctionBegin;
  PetscFunctionReturn(0);
}
*/

/*@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: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
@*/
PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm,PetscInt *ncells,PetscInt **count)
{
  PetscErrorCode ierr;
  PetscBool      isvalid;
  PetscInt       nel;
  PetscInt       *sum;

  PetscFunctionBegin;
  ierr = DMSwarmSortGetIsValid(dm,&isvalid);CHKERRQ(ierr);
  nel = 0;
  if (isvalid) {
    PetscInt e;

    ierr = DMSwarmSortGetSizes(dm,&nel,NULL);CHKERRQ(ierr);

    ierr = PetscMalloc1(nel,&sum);CHKERRQ(ierr);
    for (e=0; e<nel; e++) {
      ierr = DMSwarmSortGetNumberOfPointsPerCell(dm,e,&sum[e]);CHKERRQ(ierr);
    }
  } else {
    DM        celldm;
    PetscBool isda,isplex,isshell;
    PetscInt  p,npoints;
    PetscInt *swarm_cellid;

    /* get the number of cells */
    ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
    ierr = PetscObjectTypeCompare((PetscObject)celldm,DMDA,&isda);CHKERRQ(ierr);
    ierr = PetscObjectTypeCompare((PetscObject)celldm,DMPLEX,&isplex);CHKERRQ(ierr);
    ierr = PetscObjectTypeCompare((PetscObject)celldm,DMSHELL,&isshell);CHKERRQ(ierr);
    if (isda) {
      PetscInt _nel,_npe;
      const PetscInt *_element;

      ierr = DMDAGetElements(celldm,&_nel,&_npe,&_element);CHKERRQ(ierr);
      nel = _nel;
      ierr = DMDARestoreElements(celldm,&_nel,&_npe,&_element);CHKERRQ(ierr);
    } else if (isplex) {
      PetscInt ps,pe;

      ierr = DMPlexGetHeightStratum(celldm,0,&ps,&pe);CHKERRQ(ierr);
      nel = pe - ps;
    } else if (isshell) {
      PetscErrorCode (*method_DMShellGetNumberOfCells)(DM,PetscInt*);

      ierr = PetscObjectQueryFunction((PetscObject)celldm,"DMGetNumberOfCells_C",&method_DMShellGetNumberOfCells);CHKERRQ(ierr);
      if (method_DMShellGetNumberOfCells) {
        ierr = method_DMShellGetNumberOfCells(celldm,&nel);CHKERRQ(ierr);
      } 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");

    ierr = PetscMalloc1(nel,&sum);CHKERRQ(ierr);
    ierr = PetscMemzero(sum,sizeof(PetscInt)*nel);CHKERRQ(ierr);
    ierr = DMSwarmGetLocalSize(dm,&npoints);CHKERRQ(ierr);
    ierr = DMSwarmGetField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
    for (p=0; p<npoints; p++) {
      if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) {
        sum[ swarm_cellid[p] ]++;
      }
    }
    ierr = DMSwarmRestoreField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
  }
  if (ncells) { *ncells = nel; }
  *count  = sum;
  PetscFunctionReturn(0);
}