xref: /petsc/src/dm/impls/swarm/swarmpic.c (revision d083f849a86f1f43e18d534ee43954e2786cb29a)
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>
6279f676cSBarry Smith #include "../src/dm/impls/swarm/data_bucket.h"
70e2ec84fSDave May 
80e2ec84fSDave May /*
90e2ec84fSDave May  Error chceking macto to ensure the swarm type is correct and that a cell DM has been set
100e2ec84fSDave May */
110e2ec84fSDave May #define DMSWARMPICVALID(dm) \
120e2ec84fSDave May { \
130e2ec84fSDave May   DM_Swarm *_swarm = (DM_Swarm*)(dm)->data; \
140e2ec84fSDave May   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)"); \
150e2ec84fSDave May   else \
160e2ec84fSDave May     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)"); \
170e2ec84fSDave May }
180e2ec84fSDave May 
190e2ec84fSDave May /* Coordinate insertition/addition API */
200e2ec84fSDave May /*@C
210e2ec84fSDave May    DMSwarmSetPointsUniformCoordinates - Set point coordinates in a DMSwarm on a regular (ijk) grid
220e2ec84fSDave May 
23*d083f849SBarry Smith    Collective on dm
240e2ec84fSDave May 
250e2ec84fSDave May    Input parameters:
260e2ec84fSDave May +  dm - the DMSwarm
270e2ec84fSDave May .  min - minimum coordinate values in the x, y, z directions (array of length dim)
280e2ec84fSDave May .  max - maximum coordinate values in the x, y, z directions (array of length dim)
290e2ec84fSDave May .  npoints - number of points in each spatial direction (array of length dim)
300e2ec84fSDave May -  mode - indicates whether to append points to the swarm (ADD_VALUES), or over-ride existing points (INSERT_VALUES)
310e2ec84fSDave May 
320e2ec84fSDave May    Level: beginner
330e2ec84fSDave May 
340e2ec84fSDave May    Notes:
350e2ec84fSDave May    When using mode = INSERT_VALUES, this method will reset the number of particles in the DMSwarm
360e2ec84fSDave May    to be npoints[0]*npoints[1] (2D) or npoints[0]*npoints[1]*npoints[2] (3D). When using mode = ADD_VALUES,
370e2ec84fSDave May    new points will be appended to any already existing in the DMSwarm
380e2ec84fSDave May 
390e2ec84fSDave May .seealso: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
400e2ec84fSDave May @*/
410e2ec84fSDave May PETSC_EXTERN PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm,PetscReal min[],PetscReal max[],PetscInt npoints[],InsertMode mode)
420e2ec84fSDave May {
430e2ec84fSDave May   PetscErrorCode    ierr;
440e2ec84fSDave May   PetscReal         gmin[] = {PETSC_MAX_REAL ,PETSC_MAX_REAL, PETSC_MAX_REAL};
450e2ec84fSDave May   PetscReal         gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
460e2ec84fSDave May   PetscInt          i,j,k,N,bs,b,n_estimate,n_curr,n_new_est,p,n_found;
470e2ec84fSDave May   Vec               coorlocal;
480e2ec84fSDave May   const PetscScalar *_coor;
490e2ec84fSDave May   DM                celldm;
500e2ec84fSDave May   PetscReal         dx[3];
512e3d3761SDave May   PetscInt          _npoints[] = { 0, 0, 1 };
520e2ec84fSDave May   Vec               pos;
530e2ec84fSDave May   PetscScalar       *_pos;
540e2ec84fSDave May   PetscReal         *swarm_coor;
550e2ec84fSDave May   PetscInt          *swarm_cellid;
560e2ec84fSDave May   PetscSF           sfcell = NULL;
570e2ec84fSDave May   const PetscSFNode *LA_sfcell;
580e2ec84fSDave May 
590e2ec84fSDave May   PetscFunctionBegin;
600e2ec84fSDave May   DMSWARMPICVALID(dm);
610e2ec84fSDave May   ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
620e2ec84fSDave May   ierr = DMGetCoordinatesLocal(celldm,&coorlocal);CHKERRQ(ierr);
630e2ec84fSDave May   ierr = VecGetSize(coorlocal,&N);CHKERRQ(ierr);
640e2ec84fSDave May   ierr = VecGetBlockSize(coorlocal,&bs);CHKERRQ(ierr);
650e2ec84fSDave May   N = N / bs;
660e2ec84fSDave May   ierr = VecGetArrayRead(coorlocal,&_coor);CHKERRQ(ierr);
670e2ec84fSDave May   for (i=0; i<N; i++) {
680e2ec84fSDave May     for (b=0; b<bs; b++) {
69a5f152d1SDave May       gmin[b] = PetscMin(gmin[b],PetscRealPart(_coor[bs*i+b]));
70a5f152d1SDave May       gmax[b] = PetscMax(gmax[b],PetscRealPart(_coor[bs*i+b]));
710e2ec84fSDave May     }
720e2ec84fSDave May   }
730e2ec84fSDave May   ierr = VecRestoreArrayRead(coorlocal,&_coor);CHKERRQ(ierr);
740e2ec84fSDave May 
750e2ec84fSDave May   for (b=0; b<bs; b++) {
7671844bb8SDave May     if (npoints[b] > 1) {
770e2ec84fSDave May       dx[b] = (max[b] - min[b])/((PetscReal)(npoints[b]-1));
7871844bb8SDave May     } else {
7971844bb8SDave May       dx[b] = 0.0;
8071844bb8SDave May     }
812e3d3761SDave 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;
970e2ec84fSDave May         for (b=0; b<bs; b++) {
980e2ec84fSDave May           xp[b] = min[b] + ijk[b] * dx[b];
990e2ec84fSDave May         }
1000e2ec84fSDave May         for (b=0; b<bs; b++) {
1010e2ec84fSDave May           if (xp[b] < gmin[b]) { point_inside = PETSC_FALSE; }
1020e2ec84fSDave May           if (xp[b] > gmax[b]) { point_inside = PETSC_FALSE; }
1030e2ec84fSDave May         }
1040e2ec84fSDave May         if (point_inside) { n_estimate++; }
1050e2ec84fSDave May       }
1060e2ec84fSDave May     }
1070e2ec84fSDave May   }
1080e2ec84fSDave May 
1090e2ec84fSDave May   /* create candidate list */
110c28a3c15SDave May   ierr = VecCreate(PETSC_COMM_SELF,&pos);CHKERRQ(ierr);
1110e2ec84fSDave May   ierr = VecSetSizes(pos,bs*n_estimate,PETSC_DECIDE);CHKERRQ(ierr);
1120e2ec84fSDave May   ierr = VecSetBlockSize(pos,bs);CHKERRQ(ierr);
1130e2ec84fSDave May   ierr = VecSetFromOptions(pos);CHKERRQ(ierr);
1140e2ec84fSDave May   ierr = VecGetArray(pos,&_pos);CHKERRQ(ierr);
1150e2ec84fSDave May 
1160e2ec84fSDave May   n_estimate = 0;
1172e3d3761SDave May   for (k=0; k<_npoints[2]; k++) {
1182e3d3761SDave May     for (j=0; j<_npoints[1]; j++) {
1192e3d3761SDave May       for (i=0; i<_npoints[0]; i++) {
1200e2ec84fSDave May         PetscReal xp[] = {0.0,0.0,0.0};
1210e2ec84fSDave May         PetscInt  ijk[3];
1220e2ec84fSDave May         PetscBool point_inside = PETSC_TRUE;
1230e2ec84fSDave May 
1240e2ec84fSDave May         ijk[0] = i;
1250e2ec84fSDave May         ijk[1] = j;
1260e2ec84fSDave May         ijk[2] = k;
1270e2ec84fSDave May         for (b=0; b<bs; b++) {
1280e2ec84fSDave May           xp[b] = min[b] + ijk[b] * dx[b];
1290e2ec84fSDave May         }
1300e2ec84fSDave May         for (b=0; b<bs; b++) {
1310e2ec84fSDave May           if (xp[b] < gmin[b]) { point_inside = PETSC_FALSE; }
1320e2ec84fSDave May           if (xp[b] > gmax[b]) { point_inside = PETSC_FALSE; }
1330e2ec84fSDave May         }
1340e2ec84fSDave May         if (point_inside) {
1350e2ec84fSDave May           for (b=0; b<bs; b++) {
1360e2ec84fSDave May             _pos[bs*n_estimate+b] = xp[b];
1370e2ec84fSDave May           }
1380e2ec84fSDave May           n_estimate++;
1390e2ec84fSDave May         }
1400e2ec84fSDave May       }
1410e2ec84fSDave May     }
1420e2ec84fSDave May   }
1430e2ec84fSDave May   ierr = VecRestoreArray(pos,&_pos);CHKERRQ(ierr);
1440e2ec84fSDave May 
1450e2ec84fSDave May   /* locate points */
1460e2ec84fSDave May   ierr = DMLocatePoints(celldm,pos,DM_POINTLOCATION_NONE,&sfcell);CHKERRQ(ierr);
1470e2ec84fSDave May 
1480e2ec84fSDave May   ierr = PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell);CHKERRQ(ierr);
1490e2ec84fSDave May   n_found = 0;
1500e2ec84fSDave May   for (p=0; p<n_estimate; p++) {
1510e2ec84fSDave May     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
1520e2ec84fSDave May       n_found++;
1530e2ec84fSDave May     }
1540e2ec84fSDave May   }
1550e2ec84fSDave May 
1560e2ec84fSDave May   /* adjust size */
1570e2ec84fSDave May   if (mode == ADD_VALUES) {
1580e2ec84fSDave May     ierr = DMSwarmGetLocalSize(dm,&n_curr);CHKERRQ(ierr);
1590e2ec84fSDave May     n_new_est = n_curr + n_found;
1600e2ec84fSDave May     ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
1610e2ec84fSDave May   }
1620e2ec84fSDave May   if (mode == INSERT_VALUES) {
1630e2ec84fSDave May     n_curr = 0;
1640e2ec84fSDave May     n_new_est = n_found;
1650e2ec84fSDave May     ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
1660e2ec84fSDave May   }
1670e2ec84fSDave May 
1680e2ec84fSDave May   /* initialize new coords, cell owners, pid */
1690e2ec84fSDave May   ierr = VecGetArrayRead(pos,&_coor);CHKERRQ(ierr);
1700e2ec84fSDave May   ierr = DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
1710e2ec84fSDave May   ierr = DMSwarmGetField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
1720e2ec84fSDave May   n_found = 0;
1730e2ec84fSDave May   for (p=0; p<n_estimate; p++) {
1740e2ec84fSDave May     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
1750e2ec84fSDave May       for (b=0; b<bs; b++) {
1760ca99263SDave May         swarm_coor[bs*(n_curr + n_found) + b] = PetscRealPart(_coor[bs*p+b]);
1770e2ec84fSDave May       }
1780e2ec84fSDave May       swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
1790e2ec84fSDave May       n_found++;
1800e2ec84fSDave May     }
1810e2ec84fSDave May   }
1820e2ec84fSDave May   ierr = DMSwarmRestoreField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
1830e2ec84fSDave May   ierr = DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
1840e2ec84fSDave May   ierr = VecRestoreArrayRead(pos,&_coor);CHKERRQ(ierr);
1850e2ec84fSDave May 
1860e2ec84fSDave May   ierr = PetscSFDestroy(&sfcell);CHKERRQ(ierr);
1870e2ec84fSDave May   ierr = VecDestroy(&pos);CHKERRQ(ierr);
1880e2ec84fSDave May 
1890e2ec84fSDave May   PetscFunctionReturn(0);
1900e2ec84fSDave May }
1910e2ec84fSDave May 
1920e2ec84fSDave May /*@C
1930e2ec84fSDave May    DMSwarmSetPointCoordinates - Set point coordinates in a DMSwarm from a user defined list
1940e2ec84fSDave May 
195*d083f849SBarry Smith    Collective on dm
1960e2ec84fSDave May 
1970e2ec84fSDave May    Input parameters:
1980e2ec84fSDave May +  dm - the DMSwarm
1990e2ec84fSDave May .  npoints - the number of points to insert
2000e2ec84fSDave May .  coor - the coordinate values
2010e2ec84fSDave May .  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
2020e2ec84fSDave May -  mode - indicates whether to append points to the swarm (ADD_VALUES), or over-ride existing points (INSERT_VALUES)
2030e2ec84fSDave May 
2040e2ec84fSDave May    Level: beginner
2050e2ec84fSDave May 
2060e2ec84fSDave May    Notes:
2070e2ec84fSDave May    If the user has specified redundant = PETSC_FALSE, the cell DM will attempt to locate the coordinates provided by coor[] within
2080e2ec84fSDave May    its sub-domain. If they any values within coor[] are not located in the sub-domain, they will be ignored and will not get
2090e2ec84fSDave May    added to the DMSwarm.
2100e2ec84fSDave May 
2110e2ec84fSDave May .seealso: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType, DMSwarmSetPointsUniformCoordinates()
2120e2ec84fSDave May @*/
2130e2ec84fSDave May PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinates(DM dm,PetscInt npoints,PetscReal coor[],PetscBool redundant,InsertMode mode)
2140e2ec84fSDave May {
2150e2ec84fSDave May   PetscErrorCode    ierr;
2160e2ec84fSDave May   PetscReal         gmin[] = {PETSC_MAX_REAL ,PETSC_MAX_REAL, PETSC_MAX_REAL};
2170e2ec84fSDave May   PetscReal         gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
2180e2ec84fSDave May   PetscInt          i,N,bs,b,n_estimate,n_curr,n_new_est,p,n_found;
2190e2ec84fSDave May   Vec               coorlocal;
2200e2ec84fSDave May   const PetscScalar *_coor;
2210e2ec84fSDave May   DM                celldm;
2220e2ec84fSDave May   Vec               pos;
2230e2ec84fSDave May   PetscScalar       *_pos;
2240e2ec84fSDave May   PetscReal         *swarm_coor;
2250e2ec84fSDave May   PetscInt          *swarm_cellid;
2260e2ec84fSDave May   PetscSF           sfcell = NULL;
2270e2ec84fSDave May   const PetscSFNode *LA_sfcell;
2280e2ec84fSDave May   PetscReal         *my_coor;
2290e2ec84fSDave May   PetscInt          my_npoints;
2300e2ec84fSDave May   PetscMPIInt       rank;
2310e2ec84fSDave May   MPI_Comm          comm;
2320e2ec84fSDave May 
2330e2ec84fSDave May   PetscFunctionBegin;
2340e2ec84fSDave May   DMSWARMPICVALID(dm);
2350e2ec84fSDave May   ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
2360e2ec84fSDave May   ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
2370e2ec84fSDave May 
2380e2ec84fSDave May   ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
2390e2ec84fSDave May   ierr = DMGetCoordinatesLocal(celldm,&coorlocal);CHKERRQ(ierr);
2400e2ec84fSDave May   ierr = VecGetSize(coorlocal,&N);CHKERRQ(ierr);
2410e2ec84fSDave May   ierr = VecGetBlockSize(coorlocal,&bs);CHKERRQ(ierr);
2420e2ec84fSDave May   N = N / bs;
2430e2ec84fSDave May   ierr = VecGetArrayRead(coorlocal,&_coor);CHKERRQ(ierr);
2440e2ec84fSDave May   for (i=0; i<N; i++) {
2450e2ec84fSDave May     for (b=0; b<bs; b++) {
246a5f152d1SDave May       gmin[b] = PetscMin(gmin[b],PetscRealPart(_coor[bs*i+b]));
247a5f152d1SDave May       gmax[b] = PetscMax(gmax[b],PetscRealPart(_coor[bs*i+b]));
2480e2ec84fSDave May     }
2490e2ec84fSDave May   }
2500e2ec84fSDave May   ierr = VecRestoreArrayRead(coorlocal,&_coor);CHKERRQ(ierr);
2510e2ec84fSDave May 
2520e2ec84fSDave May   /* broadcast points from rank 0 if requested */
2530e2ec84fSDave May   if (redundant) {
2540e2ec84fSDave May     my_npoints = npoints;
2550e2ec84fSDave May     ierr = MPI_Bcast(&my_npoints,1,MPIU_INT,0,comm);CHKERRQ(ierr);
2560e2ec84fSDave May 
2570e2ec84fSDave May     if (rank > 0) { /* allocate space */
25871844bb8SDave May       ierr = PetscMalloc1(bs*my_npoints,&my_coor);CHKERRQ(ierr);
2590e2ec84fSDave May     } else {
2600e2ec84fSDave May       my_coor = coor;
2610e2ec84fSDave May     }
2620e2ec84fSDave May     ierr = MPI_Bcast(my_coor,bs*my_npoints,MPIU_REAL,0,comm);CHKERRQ(ierr);
2630e2ec84fSDave May   } else {
2640e2ec84fSDave May     my_npoints = npoints;
2650e2ec84fSDave May     my_coor = coor;
2660e2ec84fSDave May   }
2670e2ec84fSDave May 
2680e2ec84fSDave May   /* determine the number of points living in the bounding box */
2690e2ec84fSDave May   n_estimate = 0;
2700e2ec84fSDave May   for (i=0; i<my_npoints; i++) {
2710e2ec84fSDave May     PetscBool point_inside = PETSC_TRUE;
2720e2ec84fSDave May 
2730e2ec84fSDave May     for (b=0; b<bs; b++) {
2740e2ec84fSDave May       if (my_coor[bs*i+b] < gmin[b]) { point_inside = PETSC_FALSE; }
2750e2ec84fSDave May       if (my_coor[bs*i+b] > gmax[b]) { point_inside = PETSC_FALSE; }
2760e2ec84fSDave May     }
2770e2ec84fSDave May     if (point_inside) { n_estimate++; }
2780e2ec84fSDave May   }
2790e2ec84fSDave May 
2800e2ec84fSDave May   /* create candidate list */
281c28a3c15SDave May   ierr = VecCreate(PETSC_COMM_SELF,&pos);CHKERRQ(ierr);
2820e2ec84fSDave May   ierr = VecSetSizes(pos,bs*n_estimate,PETSC_DECIDE);CHKERRQ(ierr);
2830e2ec84fSDave May   ierr = VecSetBlockSize(pos,bs);CHKERRQ(ierr);
2840e2ec84fSDave May   ierr = VecSetFromOptions(pos);CHKERRQ(ierr);
2850e2ec84fSDave May   ierr = VecGetArray(pos,&_pos);CHKERRQ(ierr);
2860e2ec84fSDave May 
2870e2ec84fSDave May   n_estimate = 0;
2880e2ec84fSDave May   for (i=0; i<my_npoints; i++) {
2890e2ec84fSDave May     PetscBool point_inside = PETSC_TRUE;
2900e2ec84fSDave May 
2910e2ec84fSDave May     for (b=0; b<bs; b++) {
2920e2ec84fSDave May       if (my_coor[bs*i+b] < gmin[b]) { point_inside = PETSC_FALSE; }
2930e2ec84fSDave May       if (my_coor[bs*i+b] > gmax[b]) { point_inside = PETSC_FALSE; }
2940e2ec84fSDave May     }
2950e2ec84fSDave May     if (point_inside) {
2960e2ec84fSDave May       for (b=0; b<bs; b++) {
2970e2ec84fSDave May         _pos[bs*n_estimate+b] = my_coor[bs*i+b];
2980e2ec84fSDave May       }
2990e2ec84fSDave May       n_estimate++;
3000e2ec84fSDave May     }
3010e2ec84fSDave May   }
3020e2ec84fSDave May   ierr = VecRestoreArray(pos,&_pos);CHKERRQ(ierr);
3030e2ec84fSDave May 
3040e2ec84fSDave May   /* locate points */
3050e2ec84fSDave May   ierr = DMLocatePoints(celldm,pos,DM_POINTLOCATION_NONE,&sfcell);CHKERRQ(ierr);
3060e2ec84fSDave May 
3070e2ec84fSDave May   ierr = PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell);CHKERRQ(ierr);
3080e2ec84fSDave May   n_found = 0;
3090e2ec84fSDave May   for (p=0; p<n_estimate; p++) {
3100e2ec84fSDave May     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
3110e2ec84fSDave May       n_found++;
3120e2ec84fSDave May     }
3130e2ec84fSDave May   }
3140e2ec84fSDave May 
3150e2ec84fSDave May   /* adjust size */
3160e2ec84fSDave May   if (mode == ADD_VALUES) {
3170e2ec84fSDave May     ierr = DMSwarmGetLocalSize(dm,&n_curr);CHKERRQ(ierr);
3180e2ec84fSDave May     n_new_est = n_curr + n_found;
3190e2ec84fSDave May     ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
3200e2ec84fSDave May   }
3210e2ec84fSDave May   if (mode == INSERT_VALUES) {
3220e2ec84fSDave May     n_curr = 0;
3230e2ec84fSDave May     n_new_est = n_found;
3240e2ec84fSDave May     ierr = DMSwarmSetLocalSizes(dm,n_new_est,-1);CHKERRQ(ierr);
3250e2ec84fSDave May   }
3260e2ec84fSDave May 
3270e2ec84fSDave May   /* initialize new coords, cell owners, pid */
3280e2ec84fSDave May   ierr = VecGetArrayRead(pos,&_coor);CHKERRQ(ierr);
3290e2ec84fSDave May   ierr = DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
3300e2ec84fSDave May   ierr = DMSwarmGetField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
3310e2ec84fSDave May   n_found = 0;
3320e2ec84fSDave May   for (p=0; p<n_estimate; p++) {
3330e2ec84fSDave May     if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
3340e2ec84fSDave May       for (b=0; b<bs; b++) {
3350ca99263SDave May         swarm_coor[bs*(n_curr + n_found) + b] = PetscRealPart(_coor[bs*p+b]);
3360e2ec84fSDave May       }
3370e2ec84fSDave May       swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
3380e2ec84fSDave May       n_found++;
3390e2ec84fSDave May     }
3400e2ec84fSDave May   }
3410e2ec84fSDave May   ierr = DMSwarmRestoreField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
3420e2ec84fSDave May   ierr = DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&swarm_coor);CHKERRQ(ierr);
3430e2ec84fSDave May   ierr = VecRestoreArrayRead(pos,&_coor);CHKERRQ(ierr);
3440e2ec84fSDave May 
3450e2ec84fSDave May   if (redundant) {
3460e2ec84fSDave May     if (rank > 0) {
3470e2ec84fSDave May       ierr = PetscFree(my_coor);CHKERRQ(ierr);
3480e2ec84fSDave May     }
3490e2ec84fSDave May   }
3500e2ec84fSDave May   ierr = PetscSFDestroy(&sfcell);CHKERRQ(ierr);
3510e2ec84fSDave May   ierr = VecDestroy(&pos);CHKERRQ(ierr);
3520e2ec84fSDave May 
3530e2ec84fSDave May   PetscFunctionReturn(0);
3540e2ec84fSDave May }
3550e2ec84fSDave May 
3560e2ec84fSDave May extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_DA(DM,DM,DMSwarmPICLayoutType,PetscInt);
3570e2ec84fSDave May extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_PLEX(DM,DM,DMSwarmPICLayoutType,PetscInt);
3580e2ec84fSDave May 
3590e2ec84fSDave May /*@C
3600e2ec84fSDave May    DMSwarmInsertPointsUsingCellDM - Insert point coordinates within each cell
3610e2ec84fSDave May 
3620e2ec84fSDave May    Not collective
3630e2ec84fSDave May 
3640e2ec84fSDave May    Input parameters:
3650e2ec84fSDave May +  dm - the DMSwarm
3660e2ec84fSDave May .  layout_type - method used to fill each cell with the cell DM
3670e2ec84fSDave May -  fill_param - parameter controlling how many points per cell are added (the meaning of this parameter is dependent on the layout type)
3680e2ec84fSDave May 
3690e2ec84fSDave May    Level: beginner
3700e2ec84fSDave May 
3710e2ec84fSDave May    Notes:
372e7af74c8SDave May 
373e7af74c8SDave May    The insert method will reset any previous defined points within the DMSwarm.
374e7af74c8SDave May 
375e7af74c8SDave May    When using a DMDA both 2D and 3D are supported for all layout types provided you are using DMDA_ELEMENT_Q1.
376e7af74c8SDave May 
377e7af74c8SDave May    When using a DMPLEX the following case are supported:
378ea3d7275SDave May    (i  ) DMSWARMPIC_LAYOUT_REGULAR: 2D (triangle),
379ea3d7275SDave May    (ii ) DMSWARMPIC_LAYOUT_GAUSS: 2D and 3D provided the cell is a tri/tet or a quad/hex,
380ea3d7275SDave May    (iii) DMSWARMPIC_LAYOUT_SUBDIVISION: 2D and 3D for quad/hex and 2D tri.
3810e2ec84fSDave May 
3820e2ec84fSDave May .seealso: DMSwarmPICLayoutType, DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
3830e2ec84fSDave May @*/
3840e2ec84fSDave May PETSC_EXTERN PetscErrorCode DMSwarmInsertPointsUsingCellDM(DM dm,DMSwarmPICLayoutType layout_type,PetscInt fill_param)
3850e2ec84fSDave May {
3860e2ec84fSDave May   PetscErrorCode ierr;
3870e2ec84fSDave May   DM             celldm;
3880e2ec84fSDave May   PetscBool      isDA,isPLEX;
3890e2ec84fSDave May 
3900e2ec84fSDave May   PetscFunctionBegin;
3910e2ec84fSDave May   DMSWARMPICVALID(dm);
3920e2ec84fSDave May   ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
3930e2ec84fSDave May   ierr = PetscObjectTypeCompare((PetscObject)celldm,DMDA,&isDA);CHKERRQ(ierr);
3940e2ec84fSDave May   ierr = PetscObjectTypeCompare((PetscObject)celldm,DMPLEX,&isPLEX);CHKERRQ(ierr);
3950e2ec84fSDave May   if (isDA) {
3960e2ec84fSDave May     ierr = private_DMSwarmInsertPointsUsingCellDM_DA(dm,celldm,layout_type,fill_param);CHKERRQ(ierr);
3970e2ec84fSDave May   } else if (isPLEX) {
3980e2ec84fSDave May     ierr = private_DMSwarmInsertPointsUsingCellDM_PLEX(dm,celldm,layout_type,fill_param);CHKERRQ(ierr);
3990e2ec84fSDave May   } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only supported for cell DMs of type DMDA and DMPLEX");
4000e2ec84fSDave May 
4010e2ec84fSDave May   PetscFunctionReturn(0);
4020e2ec84fSDave May }
4030e2ec84fSDave May 
404431382f2SDave May 
405431382f2SDave May extern PetscErrorCode private_DMSwarmSetPointCoordinatesCellwise_PLEX(DM,DM,PetscInt,PetscReal*);
406431382f2SDave May 
407431382f2SDave May /*@C
408431382f2SDave May    DMSwarmSetPointCoordinatesCellwise - Insert point coordinates (defined over the reference cell) within each cell
409431382f2SDave May 
410431382f2SDave May    Not collective
411431382f2SDave May 
412431382f2SDave May    Input parameters:
413431382f2SDave May +  dm - the DMSwarm
414431382f2SDave May .  celldm - the cell DM
415431382f2SDave May .  npoints - the number of points to insert in each cell
416431382f2SDave May -  xi - the coordinates (defined in the local coordinate system for each cell) to insert
417431382f2SDave May 
418431382f2SDave May  Level: beginner
419431382f2SDave May 
420431382f2SDave May  Notes:
421431382f2SDave May  The method will reset any previous defined points within the DMSwarm.
422ea3d7275SDave May  Only supported for DMPLEX. If you are using a DMDA it is recommended to either use
423e7af74c8SDave May  DMSwarmInsertPointsUsingCellDM(), or extract and set the coordinates yourself the following code
424e7af74c8SDave May 
425e7af74c8SDave May $    PetscReal *coor;
426e7af74c8SDave May $    DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
427e7af74c8SDave May $    // user code to define the coordinates here
428e7af74c8SDave May $    DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
429431382f2SDave May 
430431382f2SDave May .seealso: DMSwarmSetCellDM(), DMSwarmInsertPointsUsingCellDM()
431431382f2SDave May @*/
432431382f2SDave May PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinatesCellwise(DM dm,PetscInt npoints,PetscReal xi[])
4330e2ec84fSDave May {
434431382f2SDave May   PetscErrorCode ierr;
435431382f2SDave May   DM             celldm;
436431382f2SDave May   PetscBool      isDA,isPLEX;
437431382f2SDave May 
4380e2ec84fSDave May   PetscFunctionBegin;
439431382f2SDave May   DMSWARMPICVALID(dm);
440431382f2SDave May   ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
441431382f2SDave May   ierr = PetscObjectTypeCompare((PetscObject)celldm,DMDA,&isDA);CHKERRQ(ierr);
442431382f2SDave May   ierr = PetscObjectTypeCompare((PetscObject)celldm,DMPLEX,&isPLEX);CHKERRQ(ierr);
443431382f2SDave May   if (isDA) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only supported for cell DMs of type DMPLEX. Recommended you use DMSwarmInsertPointsUsingCellDM()");
444431382f2SDave May   else if (isPLEX) {
445431382f2SDave May     ierr = private_DMSwarmSetPointCoordinatesCellwise_PLEX(dm,celldm,npoints,xi);CHKERRQ(ierr);
446431382f2SDave May   } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only supported for cell DMs of type DMDA and DMPLEX");
447431382f2SDave May 
4480e2ec84fSDave May   PetscFunctionReturn(0);
4490e2ec84fSDave May }
450431382f2SDave May 
4510e2ec84fSDave May 
4520e2ec84fSDave May /* Field projection API */
45377048351SPatrick Sanan extern PetscErrorCode private_DMSwarmProjectFields_DA(DM swarm,DM celldm,PetscInt project_type,PetscInt nfields,DMSwarmDataField dfield[],Vec vecs[]);
45477048351SPatrick Sanan extern PetscErrorCode private_DMSwarmProjectFields_PLEX(DM swarm,DM celldm,PetscInt project_type,PetscInt nfields,DMSwarmDataField dfield[],Vec vecs[]);
45594f7d2dcSDave May 
45694f7d2dcSDave May /*@C
45794f7d2dcSDave May    DMSwarmProjectFields - Project a set of swarm fields onto the cell DM
45894f7d2dcSDave May 
459*d083f849SBarry Smith    Collective on dm
46094f7d2dcSDave May 
46194f7d2dcSDave May    Input parameters:
46294f7d2dcSDave May +  dm - the DMSwarm
46394f7d2dcSDave May .  nfields - the number of swarm fields to project
46494f7d2dcSDave May .  fieldnames - the textual names of the swarm fields to project
46594f7d2dcSDave May .  fields - an array of Vec's of length nfields
46694f7d2dcSDave May -  reuse - flag indicating whether the array and contents of fields should be re-used or internally allocated
46794f7d2dcSDave May 
46894f7d2dcSDave May    Currently, the only available projection method consists of
46994f7d2dcSDave May      phi_i = \sum_{p=0}^{np} N_i(x_p) phi_p dJ / \sum_{p=0}^{np} N_i(x_p) dJ
47094f7d2dcSDave May    where phi_p is the swarm field at point p,
47194f7d2dcSDave May      N_i() is the cell DM basis function at vertex i,
47294f7d2dcSDave May      dJ is the determinant of the cell Jacobian and
47394f7d2dcSDave May      phi_i is the projected vertex value of the field phi.
47494f7d2dcSDave May 
47594f7d2dcSDave May    Level: beginner
47694f7d2dcSDave May 
47794f7d2dcSDave May    Notes:
478e7af74c8SDave May 
479e7af74c8SDave May    If reuse = PETSC_FALSE, this function will allocate the array of Vec's, and each individual Vec.
48094f7d2dcSDave May      The user is responsible for destroying both the array and the individual Vec objects.
481e7af74c8SDave May 
482e7af74c8SDave May    Only swarm fields registered with data type = PETSC_REAL can be projected onto the cell DM.
483e7af74c8SDave May 
484e7af74c8SDave May    Only swarm fields of block size = 1 can currently be projected.
485e7af74c8SDave May 
486e7af74c8SDave May    The only projection methods currently only support the DA (2D) and PLEX (triangles 2D).
48794f7d2dcSDave May 
48894f7d2dcSDave May .seealso: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
48994f7d2dcSDave May @*/
49094f7d2dcSDave May PETSC_EXTERN PetscErrorCode DMSwarmProjectFields(DM dm,PetscInt nfields,const char *fieldnames[],Vec **fields,PetscBool reuse)
4910e2ec84fSDave May {
49294f7d2dcSDave May   DM_Swarm         *swarm = (DM_Swarm*)dm->data;
49377048351SPatrick Sanan   DMSwarmDataField *gfield;
49494f7d2dcSDave May   DM               celldm;
49594f7d2dcSDave May   PetscBool        isDA,isPLEX;
49694f7d2dcSDave May   Vec              *vecs;
49794f7d2dcSDave May   PetscInt         f,nvecs;
49894f7d2dcSDave May   PetscInt         project_type = 0;
49994f7d2dcSDave May   PetscErrorCode ierr;
50094f7d2dcSDave May 
5010e2ec84fSDave May   PetscFunctionBegin;
50294f7d2dcSDave May   DMSWARMPICVALID(dm);
50394f7d2dcSDave May   ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
50494f7d2dcSDave May   ierr = PetscMalloc1(nfields,&gfield);CHKERRQ(ierr);
50594f7d2dcSDave May   nvecs = 0;
50694f7d2dcSDave May   for (f=0; f<nfields; f++) {
50777048351SPatrick Sanan     ierr = DMSwarmDataBucketGetDMSwarmDataFieldByName(swarm->db,fieldnames[f],&gfield[f]);CHKERRQ(ierr);
50894f7d2dcSDave May     if (gfield[f]->petsc_type != PETSC_REAL) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Projection only valid for fields using a data type = PETSC_REAL");
50994f7d2dcSDave May     if (gfield[f]->bs != 1) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Projection only valid for fields with block size = 1");
51094f7d2dcSDave May     nvecs += gfield[f]->bs;
51194f7d2dcSDave May   }
51294f7d2dcSDave May   if (!reuse) {
51394f7d2dcSDave May     ierr = PetscMalloc1(nvecs,&vecs);CHKERRQ(ierr);
51494f7d2dcSDave May     for (f=0; f<nvecs; f++) {
51594f7d2dcSDave May       ierr = DMCreateGlobalVector(celldm,&vecs[f]);CHKERRQ(ierr);
51694f7d2dcSDave May       ierr = PetscObjectSetName((PetscObject)vecs[f],gfield[f]->name);CHKERRQ(ierr);
51794f7d2dcSDave May     }
51894f7d2dcSDave May   } else {
51994f7d2dcSDave May     vecs = *fields;
52094f7d2dcSDave May   }
52194f7d2dcSDave May 
52294f7d2dcSDave May   ierr = PetscObjectTypeCompare((PetscObject)celldm,DMDA,&isDA);CHKERRQ(ierr);
52394f7d2dcSDave May   ierr = PetscObjectTypeCompare((PetscObject)celldm,DMPLEX,&isPLEX);CHKERRQ(ierr);
52494f7d2dcSDave May   if (isDA) {
52594f7d2dcSDave May     ierr = private_DMSwarmProjectFields_DA(dm,celldm,project_type,nfields,gfield,vecs);CHKERRQ(ierr);
52694f7d2dcSDave May   } else if (isPLEX) {
52794f7d2dcSDave May     ierr = private_DMSwarmProjectFields_PLEX(dm,celldm,project_type,nfields,gfield,vecs);CHKERRQ(ierr);
52894f7d2dcSDave May   } else SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only supported for cell DMs of type DMDA and DMPLEX");
52994f7d2dcSDave May 
53094f7d2dcSDave May   ierr = PetscFree(gfield);CHKERRQ(ierr);
53194f7d2dcSDave May   if (!reuse) {
53294f7d2dcSDave May     *fields = vecs;
53394f7d2dcSDave May   }
53494f7d2dcSDave May 
5350e2ec84fSDave May   PetscFunctionReturn(0);
5360e2ec84fSDave May }
5370e2ec84fSDave May 
5380e2ec84fSDave May /*@C
539b799feefSDave May    DMSwarmCreatePointPerCellCount - Count the number of points within all cells in the cell DM
5400e2ec84fSDave May 
5410e2ec84fSDave May    Not collective
5420e2ec84fSDave May 
5430e2ec84fSDave May    Input parameter:
5440e2ec84fSDave May .  dm - the DMSwarm
5450e2ec84fSDave May 
5460e2ec84fSDave May    Output parameters:
5470e2ec84fSDave May +  ncells - the number of cells in the cell DM (optional argument, pass NULL to ignore)
548b799feefSDave May -  count - array of length ncells containing the number of points per cell
5490e2ec84fSDave May 
5500e2ec84fSDave May    Level: beginner
5510e2ec84fSDave May 
5520e2ec84fSDave May    Notes:
5530e2ec84fSDave May    The array count is allocated internally and must be free'd by the user.
5540e2ec84fSDave May 
5550e2ec84fSDave May .seealso: DMSwarmSetType(), DMSwarmSetCellDM(), DMSwarmType
5560e2ec84fSDave May @*/
5570e2ec84fSDave May PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm,PetscInt *ncells,PetscInt **count)
5580e2ec84fSDave May {
559b799feefSDave May   PetscErrorCode ierr;
560b799feefSDave May   PetscBool      isvalid;
561b799feefSDave May   PetscInt       nel;
562b799feefSDave May   PetscInt       *sum;
563b799feefSDave May 
5640e2ec84fSDave May   PetscFunctionBegin;
565b799feefSDave May   ierr = DMSwarmSortGetIsValid(dm,&isvalid);CHKERRQ(ierr);
566b799feefSDave May   nel = 0;
567b799feefSDave May   if (isvalid) {
568b799feefSDave May     PetscInt e;
569b799feefSDave May 
570b799feefSDave May     ierr = DMSwarmSortGetSizes(dm,&nel,NULL);CHKERRQ(ierr);
571b799feefSDave May 
572b799feefSDave May     ierr = PetscMalloc1(nel,&sum);CHKERRQ(ierr);
573b799feefSDave May     for (e=0; e<nel; e++) {
574b799feefSDave May       ierr = DMSwarmSortGetNumberOfPointsPerCell(dm,e,&sum[e]);CHKERRQ(ierr);
575b799feefSDave May     }
576b799feefSDave May   } else {
577b799feefSDave May     DM        celldm;
578b799feefSDave May     PetscBool isda,isplex,isshell;
579b799feefSDave May     PetscInt  p,npoints;
580b799feefSDave May     PetscInt *swarm_cellid;
581b799feefSDave May 
582b799feefSDave May     /* get the number of cells */
583b799feefSDave May     ierr = DMSwarmGetCellDM(dm,&celldm);CHKERRQ(ierr);
584b799feefSDave May     ierr = PetscObjectTypeCompare((PetscObject)celldm,DMDA,&isda);CHKERRQ(ierr);
585b799feefSDave May     ierr = PetscObjectTypeCompare((PetscObject)celldm,DMPLEX,&isplex);CHKERRQ(ierr);
586b799feefSDave May     ierr = PetscObjectTypeCompare((PetscObject)celldm,DMSHELL,&isshell);CHKERRQ(ierr);
587b799feefSDave May     if (isda) {
588b799feefSDave May       PetscInt       _nel,_npe;
589b799feefSDave May       const PetscInt *_element;
590b799feefSDave May 
591b799feefSDave May       ierr = DMDAGetElements(celldm,&_nel,&_npe,&_element);CHKERRQ(ierr);
592b799feefSDave May       nel = _nel;
593b799feefSDave May       ierr = DMDARestoreElements(celldm,&_nel,&_npe,&_element);CHKERRQ(ierr);
594b799feefSDave May     } else if (isplex) {
595b799feefSDave May       PetscInt ps,pe;
596b799feefSDave May 
597b799feefSDave May       ierr = DMPlexGetHeightStratum(celldm,0,&ps,&pe);CHKERRQ(ierr);
598b799feefSDave May       nel = pe - ps;
599b799feefSDave May     } else if (isshell) {
600b799feefSDave May       PetscErrorCode (*method_DMShellGetNumberOfCells)(DM,PetscInt*);
601b799feefSDave May 
602b799feefSDave May       ierr = PetscObjectQueryFunction((PetscObject)celldm,"DMGetNumberOfCells_C",&method_DMShellGetNumberOfCells);CHKERRQ(ierr);
603b799feefSDave May       if (method_DMShellGetNumberOfCells) {
604b799feefSDave May         ierr = method_DMShellGetNumberOfCells(celldm,&nel);CHKERRQ(ierr);
605b799feefSDave May       } 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 );");
606b799feefSDave 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");
607b799feefSDave May 
608b799feefSDave May     ierr = PetscMalloc1(nel,&sum);CHKERRQ(ierr);
609b799feefSDave May     ierr = PetscMemzero(sum,sizeof(PetscInt)*nel);CHKERRQ(ierr);
610b799feefSDave May     ierr = DMSwarmGetLocalSize(dm,&npoints);CHKERRQ(ierr);
611b799feefSDave May     ierr = DMSwarmGetField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
612b799feefSDave May     for (p=0; p<npoints; p++) {
613b799feefSDave May       if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) {
614b799feefSDave May         sum[ swarm_cellid[p] ]++;
615b799feefSDave May       }
616b799feefSDave May     }
617b799feefSDave May     ierr = DMSwarmRestoreField(dm,DMSwarmPICField_cellid,NULL,NULL,(void**)&swarm_cellid);CHKERRQ(ierr);
618b799feefSDave May   }
619b799feefSDave May   if (ncells) { *ncells = nel; }
620b799feefSDave May   *count  = sum;
6210e2ec84fSDave May   PetscFunctionReturn(0);
6220e2ec84fSDave May }
623