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lammps/src/ML-SNAP/compute_sna_grid_local.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "compute_sna_grid_local.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "memory.h"
#include "modify.h"
#include "sna.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
ComputeGridLocal(lmp, narg, arg), cutsq(nullptr), radelem(nullptr), wjelem(nullptr)
{
// skip over arguments used by base class
// so that argument positions are identical to
// regular per-atom compute
arg += nargbase;
narg -= nargbase;
// begin code common to all SNAP computes
//double rfac0, rmin0;
//int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
int ntypes = atom->ntypes;
int nargmin = 6 + 2 * ntypes;
if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
// default values
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
quadraticflag = 0;
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
chunksize = 32768;
parallel_thresh = 8192;
// process required arguments
memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types
memory->create(wjelem, ntypes + 1, "sna/atom:wjelem");
rcutfac = utils::numeric(FLERR, arg[3], false, lmp);
rfac0 = utils::numeric(FLERR, arg[4], false, lmp);
twojmax = utils::inumeric(FLERR, arg[5], false, lmp);
for (int i = 0; i < ntypes; i++) radelem[i + 1] = utils::numeric(FLERR, arg[6 + i], false, lmp);
for (int i = 0; i < ntypes; i++)
wjelem[i + 1] = utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp);
// construct cutsq
double cut;
cutmax = 0.0;
memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq");
for (int i = 1; i <= ntypes; i++) {
cut = 2.0 * radelem[i] * rcutfac;
if (cut > cutmax) cutmax = cut;
cutsq[i][i] = cut * cut;
for (int j = i + 1; j <= ntypes; j++) {
cut = (radelem[i] + radelem[j]) * rcutfac;
cutsq[i][j] = cutsq[j][i] = cut * cut;
}
}
// set local input checks
int sinnerflag = 0;
int dinnerflag = 0;
// process optional args
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg], "rmin0") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "switchflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "bzeroflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "quadraticflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "chem") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
chemflag = 1;
memory->create(map, ntypes + 1, "compute_sna_grid:map");
nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
for (int i = 0; i < ntypes; i++) {
int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp);
if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style);
map[i + 1] = jelem;
}
iarg += 2 + ntypes;
} else if (strcmp(arg[iarg], "bnormflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "wselfallflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "switchinnerflag") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "sinner") == 0) {
iarg++;
if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style);
memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem");
for (int i = 0; i < ntypes; i++)
sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
sinnerflag = 1;
iarg += ntypes;
} else if (strcmp(arg[iarg], "dinner") == 0) {
iarg++;
if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style);
memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem");
for (int i = 0; i < ntypes; i++)
dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
dinnerflag = 1;
iarg += ntypes;
} else
error->all(FLERR, "Illegal compute {} command", style);
}
if (switchinnerflag && !(sinnerflag && dinnerflag))
error->all(FLERR,
"Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword",
style);
if (!switchinnerflag && (sinnerflag || dinnerflag))
error->all(FLERR,
"Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword",
style);
snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag,
wselfallflag, nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
nvalues = ncoeff;
if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2;
// end code common to all SNAP computes
size_local_cols = size_local_cols_base + nvalues;
}
/* ---------------------------------------------------------------------- */
ComputeSNAGridLocal::~ComputeSNAGridLocal()
{
if (copymode) return;
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
delete snaptr;
if (chemflag) memory->destroy(map);
}
/* ---------------------------------------------------------------------- */
void ComputeSNAGridLocal::init()
{
if ((modify->get_compute_by_style("^sna/grid/local$").size() > 1) && (comm->me == 0))
error->warning(FLERR, "More than one instance of compute sna/grid/local");
snaptr->init();
}
/* ---------------------------------------------------------------------- */
void ComputeSNAGridLocal::compute_local()
{
invoked_local = update->ntimestep;
// compute sna for each gridpoint
double **const x = atom->x;
const int *const mask = atom->mask;
int *const type = atom->type;
const int ntotal = atom->nlocal + atom->nghost;
// ensure rij, inside, and typej are of size jnum
snaptr->grow_rij(ntotal);
int igrid = 0;
for (int iz = nzlo; iz <= nzhi; iz++)
for (int iy = nylo; iy <= nyhi; iy++)
for (int ix = nxlo; ix <= nxhi; ix++) {
double xgrid[3];
grid2x(ix, iy, iz, xgrid);
const double xtmp = xgrid[0];
const double ytmp = xgrid[1];
const double ztmp = xgrid[2];
// currently, all grid points are type 1
// not clear what a better choice would be
const int itype = 1;
int ielem = 0;
if (chemflag) ielem = map[itype];
// rij[][3] = displacements between atom I and those neighbors
// inside = indices of neighbors of I within cutoff
// typej = types of neighbors of I within cutoff
int ninside = 0;
for (int j = 0; j < ntotal; j++) {
// check that j is in compute group
if (!(mask[j] & groupbit)) continue;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx * delx + dely * dely + delz * delz;
int jtype = type[j];
int jelem = 0;
if (chemflag) jelem = map[jtype];
if (rsq < cutsq[jtype][jtype] && rsq > 1e-20) {
snaptr->rij[ninside][0] = delx;
snaptr->rij[ninside][1] = dely;
snaptr->rij[ninside][2] = delz;
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jtype];
snaptr->rcutij[ninside] = 2.0 * radelem[jtype] * rcutfac;
if (switchinnerflag) {
snaptr->sinnerij[ninside] = sinnerelem[jelem];
snaptr->dinnerij[ninside] = dinnerelem[jelem];
}
if (chemflag)
snaptr->element[ninside] = jelem; // element index for multi-element snap
ninside++;
}
}
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
// linear contributions
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
alocal[igrid][size_local_cols_base + icoeff] = snaptr->blist[icoeff];
// quadratic contributions
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->blist[icoeff];
alocal[igrid][size_local_cols_base + ncount++] = 0.5 * bveci * bveci;
for (int jcoeff = icoeff + 1; jcoeff < ncoeff; jcoeff++)
alocal[igrid][size_local_cols_base + ncount++] = bveci * snaptr->blist[jcoeff];
}
}
igrid++;
}
}
/* ----------------------------------------------------------------------
memory usage
------------------------------------------------------------------------- */
double ComputeSNAGridLocal::memory_usage()
{
double nbytes = snaptr->memory_usage(); // SNA object
int n = atom->ntypes + 1;
nbytes += (double) n * sizeof(int); // map
return nbytes;
}
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