dump grid and compute property/grid
This commit is contained in:
Steve Plimpton
@ -44,7 +44,8 @@ DumpGrid::DumpGrid(LAMMPS *lmp, int narg, char **arg) :
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Dump(lmp, narg, arg), idregion(nullptr), earg(nullptr), vtype(nullptr),
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vformat(nullptr), columns(nullptr), columns_default(nullptr),
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choose(nullptr), dchoose(nullptr), clist(nullptr),
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field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr),
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field2index(nullptr), field2grid(nullptr), field2data(nullptr),
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argindex(nullptr), id_compute(nullptr), compute(nullptr),
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id_fix(nullptr), fix(nullptr), pack_choice(nullptr)
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{
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if (narg == 5) error->all(FLERR,"No dump grid arguments specified");
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@ -67,12 +68,17 @@ DumpGrid::DumpGrid(LAMMPS *lmp, int narg, char **arg) :
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pack_choice = new FnPtrPack[nfield];
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vtype = new int[nfield];
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memory->create(field2index,nfield,"dump:field2index");
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memory->create(argindex,nfield,"dump:argindex");
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field2source = new int[nfield];
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field2index = new int[nfield];
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field2grid = new int[nfield];
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field2data = new int[nfield];
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argindex = new int[nfield];
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buffer_allow = 1;
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buffer_flag = 1;
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dimension = domain->dimension;
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// computes and fixes which the dump accesses
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ncompute = 0;
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@ -144,9 +150,12 @@ DumpGrid::~DumpGrid()
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delete[] pack_choice;
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delete[] vtype;
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memory->destroy(field2index);
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memory->destroy(argindex);
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delete[] field2source;
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delete[] field2index;
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delete[] field2grid;
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delete[] field2data;
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delete[] argindex;
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delete[] idregion;
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for (int i = 0; i < ncompute; i++) delete[] id_compute[i];
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@ -256,6 +265,48 @@ void DumpGrid::init_style()
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error->all(FLERR,"Could not find dump grid fix ID {}", id_fix[i]);
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}
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// check that grid sizes for all fields are the same
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Compute *icompute;
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Fix *ifix;
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Grid2d *grid2d;
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Grid3d *grid3d;
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int nx,ny,nz,nxtmp,nytmp,nztmp;
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for (int i = 1; i < nfield; i++) {
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if (dimension == 2) {
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if (field2source[i] == COMPUTE) {
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icompute = compute[field2index[i]];
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grid2d = (Grid2d *) icompute->get_grid_by_index(field2grid[i]);
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} else {
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ifix = fix[field2index[i]];
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grid2d = (Grid2d *) ifix->get_grid_by_index(field2grid[i]);
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}
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if (i == 0) grid2d->query_global_size(nx,ny);
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else {
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grid2d->query_global_size(nxtmp,nytmp);
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if (nxtmp != nx || nytmp != ny)
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error->all(FLERR,"Dump grid field grid sizes do not match");
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}
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} else {
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if (field2source[0] == COMPUTE) {
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icompute = compute[field2index[i]];
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grid3d = (Grid3d *) icompute->get_grid_by_index(field2grid[i]);
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} else {
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ifix = fix[field2index[i]];
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grid3d = (Grid3d *) ifix->get_grid_by_index(field2grid[i]);
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}
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if (i == 0) grid3d->query_global_size(nx,ny,nz);
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else {
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grid3d->query_global_size(nxtmp,nytmp,nztmp);
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if (nxtmp != nx || nytmp != ny || nztmp != nz)
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error->all(FLERR,"Dump grid field grid sizes do not match");
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}
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}
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}
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// check validity of region
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if (idregion && !domain->get_region_by_id(idregion))
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@ -471,6 +522,30 @@ int DumpGrid::count()
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}
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*/
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// set current size for portion of grid on each proc
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// may change between dump snapshots due to load balancing
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Grid2d *grid2d;
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Grid3d *grid3d;
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if (dimension == 2) {
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if (field2source[0] == COMPUTE)
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grid2d = (Grid2d *)
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compute[field2index[0]]->get_grid_by_index(field2grid[0]);
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else if (field2source[0] == FIX)
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grid2d = (Grid2d *)
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fix[field2index[0]]->get_grid_by_index(field2grid[0]);
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grid2d->query_in_bounds(nxlo_in,nxhi_in,nylo_in,nyhi_in);
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} else {
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if (field2source[0] == COMPUTE)
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grid3d = (Grid3d *)
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compute[field2index[0]]->get_grid_by_index(field2grid[0]);
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else if (field2source[0] == FIX)
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grid3d = (Grid3d *)
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fix[field2index[0]]->get_grid_by_index(field2grid[0]);
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grid3d->query_in_bounds(nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in);
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}
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// invoke Computes for per-grid quantities
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// only if within a run or minimize
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// else require that computes are current
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@ -491,6 +566,16 @@ int DumpGrid::count()
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}
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}
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// return count of grid points I own
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int ngrid;
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if (dimension == 2)
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ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1);
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else
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ngrid = (nxhi_in-nxlo_in+1) * (nyhi_in-nylo_in+1) * (nzhi_in-nzlo_in+1);
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return ngrid;
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// choose all local grid pts for output
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// NOTE: this needs to change
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@ -499,29 +584,29 @@ int DumpGrid::count()
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// un-choose if not in region
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// NOTE: this needs to change
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/*
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if (idregion) {
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auto region = domain->get_region_by_id(idregion);
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region->prematch();
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/*
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double **x = atom->x;
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for (i = 0; i < nlocal; i++)
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if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0)
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choose[i] = 0;
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*/
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}
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*/
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// compress choose flags into clist
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// nchoose = # of selected atoms
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// clist[i] = local index of each selected atom
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// NOTE: this neds to change
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nchoose = 0;
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/*
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nchoose = 0;
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for (i = 0; i < nlocal; i++)
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if (choose[i]) clist[nchoose++] = i;
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*/
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return nchoose;
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*/
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}
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/* ---------------------------------------------------------------------- */
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@ -641,8 +726,10 @@ int DumpGrid::parse_fields(int narg, char **arg)
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// if no trailing [], then arg is set to 0, else arg is int between []
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case ArgInfo::COMPUTE: {
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pack_choice[iarg] = &DumpGrid::pack_compute;
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if (dimension == 2) pack_choice[iarg] = &DumpGrid::pack_grid2d;
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else pack_choice[iarg] = &DumpGrid::pack_grid3d;
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vtype[iarg] = Dump::DOUBLE;
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field2source[iarg] = COMPUTE;
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// name = idcompute:gname:fname, split into 3 strings
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@ -657,13 +744,13 @@ int DumpGrid::parse_fields(int narg, char **arg)
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int n = strlen(name) + 1;
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char *idcompute = new char[n];
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strcpy(idfix,name);
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strcpy(idcompute,name);
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n = strlen(ptr1+1) + 1;
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char *gname = new char[n];
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strcpy(gname,ptr1+1);
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n = strlen(ptr2+1) + 1;
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char *fname = new char[n];
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strcpy(fname,ptr2+1);
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char *dname = new char[n];
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strcpy(dname,ptr2+1);
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*ptr1 = ':';
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*ptr2 = ':';
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@ -676,55 +763,48 @@ int DumpGrid::parse_fields(int narg, char **arg)
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idcompute);
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int dim;
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void *ggrid = icompute->grid_find_name(gname,dim);
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if (!ggrid)
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int igrid = icompute->get_grid_by_name(gname,dim);
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if (igrid < 0)
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error->all(FLERR,"Dump grid compute {} does not recognize grid name {}",
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idcompute,gname);
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Grid2d *grid2d;
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Grid3d *grid3d;
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if (dim == 2) grid2d = (Grid2d *) ggrid;
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if (dim == 3) grid3d = (Grid3d *) ggrid;
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int ncol;
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void *gfield = icompute->grid_find_field(fname,ncol);
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if (!gfield)
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int idata = icompute->get_griddata_by_name(igrid,dname,ncol);
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if (idata < 0)
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error->all(FLERR,
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"Dump grid compute {} does not recognize field name {}",
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idcompute,fname);
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"Dump grid compute {} does not recognize data name {}",
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idcompute,dname);
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if (argi.get_dim() == 0 && ncol)
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error->all(FLERR,"Dump grid compute {} field {} is not per-grid vector",
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idcompute,fname);
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error->all(FLERR,"Dump grid compute {} data {} is not per-grid vector",
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idcompute,dname);
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if (argi.get_dim() > 0 && ncol == 0)
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error->all(FLERR,"Dump grid compute {} field {} is not per-grid array",
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idcompute,fname);
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error->all(FLERR,"Dump grid compute {} data {} is not per-grid array",
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idcompute,dname);
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if (argi.get_dim() > 0 && argi.get_index1() > ncol)
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error->all(FLERR,
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"Dump grid compute {} array {} is accessed out-of-range",
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idcompute,fname);
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idcompute,dname);
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double **vec2d;
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double ***vec3d;
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double ***array2d;
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double ****array3d;
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if (ncol == 0) {
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if (dim == 2) vec2d = (double **) gfield;
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if (dim == 3) vec3d = (double ***) gfield;
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} else if (ncol) {
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if (dim == 2) array2d = (double ***) gfield;
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if (dim == 3) array3d = (double ****) gfield;
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}
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field2index[iarg] = add_compute(idcompute);
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field2grid[iarg] = igrid;
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field2data[iarg] = idata;
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delete [] idcompute;
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delete [] gname;
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delete [] dname;
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} break;
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// fix value = f_ID
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// if no trailing [], then arg is set to 0, else arg is between []
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case ArgInfo::FIX: {
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pack_choice[iarg] = &DumpGrid::pack_fix;
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if (dimension == 2) pack_choice[iarg] = &DumpGrid::pack_grid2d;
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else pack_choice[iarg] = &DumpGrid::pack_grid3d;
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vtype[iarg] = Dump::DOUBLE;
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field2source[iarg] = FIX;
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// name = idfix:gname:fname, split into 3 strings
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@ -744,8 +824,8 @@ int DumpGrid::parse_fields(int narg, char **arg)
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char *gname = new char[n];
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strcpy(gname,ptr1+1);
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n = strlen(ptr2+1) + 1;
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char *fname = new char[n];
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strcpy(fname,ptr2+1);
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char *dname = new char[n];
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strcpy(dname,ptr2+1);
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*ptr1 = ':';
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*ptr2 = ':';
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@ -757,45 +837,35 @@ int DumpGrid::parse_fields(int narg, char **arg)
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idfix);
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int dim;
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void *ggrid = ifix->grid_find_name(gname,dim);
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if (!ggrid)
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int igrid = ifix->get_grid_by_name(gname,dim);
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if (igrid < 0)
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error->all(FLERR,"Dump grid fix {} does not recognize grid name {}",
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idfix,gname);
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Grid2d *grid2d;
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Grid3d *grid3d;
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if (dim == 2) grid2d = (Grid2d *) ggrid;
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if (dim == 3) grid3d = (Grid3d *) ggrid;
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int ncol;
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void *gfield = ifix->grid_find_field(fname,ncol);
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if (!gfield)
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error->all(FLERR,"Dump grid fix {} does not recognize field name {}",
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idfix,fname);
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int idata = ifix->get_griddata_by_name(igrid,dname,ncol);
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if (idata < 0)
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error->all(FLERR,"Dump grid fix {} does not recognize data name {}",
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idfix,dname);
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if (argi.get_dim() == 0 && ncol)
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error->all(FLERR,"Dump grid fix {} field {} is not per-grid vector",
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idfix,fname);
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error->all(FLERR,"Dump grid fix {} data {} is not per-grid vector",
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idfix,dname);
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if (argi.get_dim() > 0 && ncol == 0)
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error->all(FLERR,"Dump grid fix {} field {} is not per-grid array",
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idfix,fname);
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error->all(FLERR,"Dump grid fix {} data {} is not per-grid array",
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idfix,dname);
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if (argi.get_dim() > 0 && argi.get_index1() > ncol)
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error->all(FLERR,"Dump grid fix {} array {} is accessed out-of-range",
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idfix,fname);
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idfix,dname);
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double **vec2d;
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double ***vec3d;
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double ***array2d;
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double ****array3d;
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if (ncol == 0) {
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if (dim == 2) vec2d = (double **) gfield;
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if (dim == 3) vec3d = (double ***) gfield;
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} else if (ncol) {
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if (dim == 2) array2d = (double ***) gfield;
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if (dim == 3) array3d = (double ****) gfield;
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}
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field2index[iarg] = add_fix(idfix);
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field2grid[iarg] = igrid;
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field2data[iarg] = idata;
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delete [] idfix;
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delete [] gname;
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delete [] dname;
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} break;
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// no match
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@ -928,74 +998,86 @@ int DumpGrid::modify_param(int narg, char **arg)
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double DumpGrid::memory_usage()
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{
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double bytes = Dump::memory_usage();
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bytes += memory->usage(choose,maxlocal);
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bytes += memory->usage(dchoose,maxlocal);
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bytes += memory->usage(clist,maxlocal);
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//NOTE: restre if use choose
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//bytes += memory->usage(choose,maxlocal);
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//bytes += memory->usage(dchoose,maxlocal);
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//bytes += memory->usage(clist,maxlocal);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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extraction of Compute and Fix data
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extraction of 2d and 3d grid data
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from either compute or fix
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------------------------------------------------------------------------- */
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void DumpGrid::pack_compute(int n)
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void DumpGrid::pack_grid2d(int n)
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{
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double *vector = compute[field2index[n]]->vector_atom;
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double **array = compute[field2index[n]]->array_atom;
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int index = argindex[n];
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if (index == 0) {
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for (int i = 0; i < nchoose; i++) {
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buf[n] = vector[clist[i]];
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n += size_one;
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}
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double **vec2d;
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if (field2source[n] == COMPUTE)
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vec2d = (double **)
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compute[field2index[n]]->get_griddata_by_index(field2data[n]);
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else if (field2source[n] == FIX)
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vec2d = (double **)
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fix[field2index[n]]->get_griddata_by_index(field2data[n]);
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
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buf[n] = vec2d[iy][ix];
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n += size_one;
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}
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} else {
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double ***array2d;
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if (field2source[n] == COMPUTE)
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array2d = (double ***)
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compute[field2index[n]]->get_griddata_by_index(field2data[n]);
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else if (field2source[n] == FIX)
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array2d = (double ***)
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fix[field2index[n]]->get_griddata_by_index(field2data[n]);
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index--;
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for (int i = 0; i < nchoose; i++) {
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buf[n] = array[clist[i]][index];
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n += size_one;
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}
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for (int iy = nylo_in; iy <= nyhi_in; iy++)
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for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
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buf[n] = array2d[iy][ix][index];
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n += size_one;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpGrid::pack_fix(int n)
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void DumpGrid::pack_grid3d(int n)
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{
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double *vector = fix[field2index[n]]->vector_atom;
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double **array = fix[field2index[n]]->array_atom;
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int index = argindex[n];
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if (index == 0) {
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double ***vec3d;
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if (field2source[n] == COMPUTE)
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vec3d = (double ***)
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compute[field2index[n]]->get_griddata_by_index(field2data[n]);
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else if (field2source[n] == FIX)
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vec3d = (double ***)
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fix[field2index[n]]->get_griddata_by_index(field2data[n]);
|
||||
for (int iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (int iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
buf[n] = vec3d[iz][iy][ix];
|
||||
n += size_one;
|
||||
}
|
||||
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
buf[n] = vec3d[iz][iy][ix];
|
||||
n += size_one;
|
||||
}
|
||||
} else {
|
||||
double ****array3d;
|
||||
if (field2source[n] == COMPUTE)
|
||||
array3d = (double ****)
|
||||
compute[field2index[n]]->get_griddata_by_index(field2data[n]);
|
||||
else if (field2source[n] == FIX)
|
||||
array3d = (double ****)
|
||||
fix[field2index[n]]->get_griddata_by_index(field2data[n]);
|
||||
index--;
|
||||
for (int iz = nzlo_in; iz <= nzhi_in; iz++)
|
||||
for (int iy = nylo_in; iy <= nyhi_in; iy++)
|
||||
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
buf[n] = array3d[iz][iy][ix][index];
|
||||
for (int ix = nxlo_in; ix <= nxhi_in; ix++) {
|
||||
buf[n] = array3d[iz][iy][ix][index];
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
if (index == 0) {
|
||||
for (int i = 0; i < nchoose; i++) {
|
||||
buf[n] = vector[clist[i]];
|
||||
n += size_one;
|
||||
}
|
||||
} else {
|
||||
index--;
|
||||
for (int i = 0; i < nchoose; i++) {
|
||||
buf[n] = array[clist[i]][index];
|
||||
n += size_one;
|
||||
}
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user