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