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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
Steve Plimpton, sjplimp@sandia.gov
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_grid_local.h"
#include "compute_sna_grid_local.h"
#include "sna.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
ComputeSNAGridLocal::ComputeSNAGridLocal(LAMMPS *lmp, int narg, char **arg) :
ComputeGridLocal(lmp, narg, arg), cutsq(nullptr),
radelem(nullptr), wjelem(nullptr)
{
double rfac0, rmin0;
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
// skip over arguments used by base class
// so that argument positions are identical to
// regular per-atom compute
arg += nargbase;
narg -= nargbase;
int ntypes = atom->ntypes;
int nargmin = 6+2*ntypes;
if (narg < nargmin) error->all(FLERR,"Illegal compute sna/grid/local command");
// default values
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
quadraticflag = 0;
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
// set local input checks
int sinnerflag = 0;
int dinnerflag = 0;
// process required arguments
memory->create(radelem,ntypes+1,"sna/grid/local:radelem"); // offset by 1 to match up with types
memory->create(wjelem,ntypes+1,"sna/grid/local:wjelem");
rcutfac = atof(arg[3]);
rfac0 = atof(arg[4]);
twojmax = atoi(arg[5]);
for(int i = 0; i < ntypes; i++)
radelem[i+1] = atof(arg[6+i]);
for(int i = 0; i < ntypes; i++)
wjelem[i+1] = atof(arg[6+ntypes+i]);
// construct cutsq
double cut;
cutmax = 0.0;
memory->create(cutsq,ntypes+1,ntypes+1,"sna/grid/local: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;
}
}
// process optional args
int iarg = nargmin;
while (iarg < narg) {
if (strcmp(arg[iarg],"rmin0") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
rmin0 = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
bzeroflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
quadraticflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"chem") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
chemflag = 1;
memory->create(map,ntypes+1,"compute_sna_grid_local: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 sna/grid/local command");
map[i+1] = jelem;
}
iarg += 2+ntypes;
} else if (strcmp(arg[iarg],"bnormflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
bnormflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
wselfallflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
switchinnerflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"sinner") == 0) {
iarg++;
if (iarg+ntypes > narg)
error->all(FLERR,"Illegal compute sna/grid/local command");
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 sna/grid/local command");
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 sna/grid/local command");
}
if (switchinnerflag && !(sinnerflag && dinnerflag))
error->all(FLERR,"Illegal compute sna/grid/local command: switchinnerflag = 1, missing sinner/dinner keyword");
if (!switchinnerflag && (sinnerflag || dinnerflag))
error->all(FLERR,"Illegal compute sna/grid/local command: switchinnerflag = 0, unexpected sinner/dinner keyword");
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;
size_local_cols = size_local_cols_base + nvalues;
}
/* ---------------------------------------------------------------------- */
ComputeSNAGridLocal::~ComputeSNAGridLocal()
{
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
delete snaptr;
if (chemflag) memory->destroy(map);
}
/* ---------------------------------------------------------------------- */
void ComputeSNAGridLocal::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"sna/grid/local") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute sna/grid/local");
snaptr->init();
}
/* ---------------------------------------------------------------------- */
void ComputeSNAGridLocal::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeSNAGridLocal::compute_local()
{
invoked_array = 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;
// insure 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
const int itype = 1;
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[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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