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lammps/src/ML-SNAP/compute_sna_atom.cpp

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// clang-format off
/* ----------------------------------------------------------------------
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_sna_atom.h"
#include "sna.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <cstring>
using namespace LAMMPS_NS;
ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), sna(nullptr),
radelem(nullptr), wjelem(nullptr), rinnerelem(nullptr), drinnerelem(nullptr)
{
double rmin0, rfac0;
int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
int ntypes = atom->ntypes;
int nargmin = 6+2*ntypes;
if (narg < nargmin) error->all(FLERR,"Illegal compute sna/atom command");
// default values
rmin0 = 0.0;
switchflag = 1;
bzeroflag = 1;
bnormflag = 0;
quadraticflag = 0;
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 0;
nelements = 1;
// offset by 1 to match up with types
memory->create(radelem,ntypes+1,"sna/atom:radelem");
memory->create(wjelem,ntypes+1,"sna/atom: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/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;
}
}
// 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/atom 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/atom 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/atom 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/atom command");
quadraticflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"chem") == 0) {
if (iarg+2+ntypes > narg)
error->all(FLERR,"Illegal compute sna/atom command");
chemflag = 1;
memory->create(map,ntypes+1,"compute_sna_atom: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/atom 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/atom 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/atom command");
wselfallflag = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
if (iarg+1+2*ntypes > narg)
error->all(FLERR,"Illegal compute sna/atom command");
switchinnerflag = 1;
iarg++;
memory->create(rinnerelem,ntypes+1,"sna/atom:rinnerelem");
memory->create(drinnerelem,ntypes+1,"sna/atom:drinnerelem");
for (int i = 0; i < ntypes; i++)
rinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
iarg += ntypes;
for (int i = 0; i < ntypes; i++)
drinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
iarg += ntypes;
} else error->all(FLERR,"Illegal compute sna/atom command");
}
snaptr = new SNA(lmp, rfac0, twojmax,
rmin0, switchflag, bzeroflag,
chemflag, bnormflag, wselfallflag,
nelements, switchinnerflag);
ncoeff = snaptr->ncoeff;
size_peratom_cols = ncoeff;
if (quadraticflag) size_peratom_cols += (ncoeff*(ncoeff+1))/2;
peratom_flag = 1;
nmax = 0;
sna = nullptr;
}
/* ---------------------------------------------------------------------- */
ComputeSNAAtom::~ComputeSNAAtom()
{
memory->destroy(sna);
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
delete snaptr;
if (chemflag) memory->destroy(map);
if (switchinnerflag) {
memory->destroy(rinnerelem);
memory->destroy(drinnerelem);
}
}
/* ---------------------------------------------------------------------- */
void ComputeSNAAtom::init()
{
if (force->pair == nullptr)
error->all(FLERR,"Compute sna/atom requires a pair style be defined");
if (cutmax > force->pair->cutforce)
error->all(FLERR,"Compute sna/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
if (modify->get_compute_by_style("sna/atom").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute sna/atom");
snaptr->init();
}
/* ---------------------------------------------------------------------- */
void ComputeSNAAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeSNAAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow sna array if necessary
if (atom->nmax > nmax) {
memory->destroy(sna);
nmax = atom->nmax;
memory->create(sna,nmax,size_peratom_cols,"sna/atom:sna");
array_atom = sna;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
const int inum = list->inum;
const int* const ilist = list->ilist;
const int* const numneigh = list->numneigh;
int** const firstneigh = list->firstneigh;
int * const type = atom->type;
// compute sna for each atom in group
// use full neighbor list to count atoms less than cutoff
double** const x = atom->x;
const int* const mask = atom->mask;
for (int ii = 0; ii < inum; ii++) {
const int i = ilist[ii];
if (mask[i] & groupbit) {
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
const int itype = type[i];
int ielem = 0;
if (chemflag)
ielem = map[itype];
const double radi = radelem[itype];
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
// insure rij, inside, and typej are of size jnum
snaptr->grow_rij(jnum);
// 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 jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
j &= NEIGHMASK;
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[itype][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] = (radi+radelem[jtype])*rcutfac;
if (switchinnerflag) {
snaptr->rinnerij[ninside] = 0.5*(rinnerelem[itype]+rinnerelem[jtype]);
snaptr->drinnerij[ninside] = 0.5*(drinnerelem[itype]+drinnerelem[jtype]);
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
}
snaptr->compute_ui(ninside, ielem);
snaptr->compute_zi();
snaptr->compute_bi(ielem);
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
sna[i][icoeff] = snaptr->blist[icoeff];
if (quadraticflag) {
int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr->blist[icoeff];
// diagonal element of quadratic matrix
sna[i][ncount++] = 0.5*bi*bi;
// upper-triangular elements of quadratic matrix
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
sna[i][ncount++] = bi*snaptr->blist[jcoeff];
}
}
} else {
for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++)
sna[i][icoeff] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
memory usage
------------------------------------------------------------------------- */
double ComputeSNAAtom::memory_usage()
{
double bytes = (double)nmax*size_peratom_cols * sizeof(double); // sna
bytes += snaptr->memory_usage(); // SNA object
return bytes;
}
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