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pair_quip.cpp
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Fri, May 31, 14:23

pair_quip.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, 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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Albert Bartok (Cambridge University)
Aidan Thompson (Sandia, athomps@sandia.gov)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_quip.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairQUIP::PairQUIP(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
one_coeff = 1;
no_virial_fdotr_compute = 1;
manybody_flag = 1;
}
PairQUIP::~PairQUIP()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
delete [] quip_potential;
}
}
void PairQUIP::compute(int eflag, int vflag)
{
int inum, jnum, sum_num_neigh, ii, jj, i, iquip;
int *ilist;
int *jlist;
int *numneigh, **firstneigh;
int *quip_num_neigh, *quip_neigh, *atomic_numbers;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int ntotal = nlocal + nghost;
int *type = atom->type;
tagint *tag = atom->tag;
double **x = atom->x;
double **f = atom->f;
double *quip_local_e, *quip_force, *quip_local_virial, *quip_virial, quip_energy, *lattice;
if (eflag || vflag) ev_setup(eflag,vflag);
else ev_unset();
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
sum_num_neigh = 0;
quip_num_neigh = new int [inum];
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
quip_num_neigh[ii] = numneigh[i];
sum_num_neigh += numneigh[i];
}
quip_neigh = new int [sum_num_neigh];
iquip = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
quip_neigh[iquip] = (jlist[jj] & NEIGHMASK) + 1;
iquip++;
}
}
atomic_numbers = new int[ntotal];
for (ii = 0; ii < ntotal; ii++)
atomic_numbers[ii] = map[type[ii]-1];
quip_local_e = new double [ntotal];
quip_force = new double [ntotal*3];
quip_local_virial = new double [ntotal*9];
quip_virial = new double [9];
lattice = new double [9];
lattice[0] = domain->xprd;
lattice[1] = 0.0;
lattice[2] = 0.0;
lattice[3] = domain->xy;
lattice[4] = domain->yprd;
lattice[5] = 0.0;
lattice[6] = domain->xz;
lattice[7] = domain->yz;
lattice[8] = domain->zprd;
#if defined(LAMMPS_BIGBIG)
int *tmptag = new int[ntotal];
int tmplarge = 0, toolarge = 0;
for (ii = 0; ii < ntotal; ++ii) {
tmptag[ii] = tag[ii];
if (tag[ii] > MAXSMALLINT) tmplarge=1;
}
MPI_Allreduce(&tmplarge,&toolarge,1,MPI_INT,MPI_MAX,world);
if (toolarge > 0)
error->all(FLERR,"Pair style quip does not support 64-bit atom IDs");
quip_lammps_wrapper(&nlocal,&nghost,atomic_numbers,tmptag,
&inum,&sum_num_neigh,ilist,
quip_num_neigh,quip_neigh,lattice,
quip_potential,&n_quip_potential,&x[0][0],
&quip_energy,quip_local_e,quip_virial,
quip_local_virial,quip_force);
delete[] tmptag;
#else
quip_lammps_wrapper(&nlocal,&nghost,atomic_numbers,tag,
&inum,&sum_num_neigh,ilist,
quip_num_neigh,quip_neigh,lattice,
quip_potential,&n_quip_potential,&x[0][0],
&quip_energy,quip_local_e,quip_virial,
quip_local_virial,quip_force);
#endif
iquip = 0;
for (ii = 0; ii < ntotal; ii++) {
for( jj = 0; jj < 3; jj++ ) {
f[ii][jj] += quip_force[iquip];
iquip++;
}
}
if(eflag_global) {
eng_vdwl = quip_energy;
}
if(eflag_atom) {
for (ii = 0; ii < ntotal; ii++) {
eatom[ii] = quip_local_e[ii];
}
}
if (vflag_global) {
virial[0] = quip_virial[0];
virial[1] = quip_virial[4];
virial[2] = quip_virial[8];
virial[3] = (quip_virial[3] + quip_virial[1])*0.5;
virial[4] = (quip_virial[2] + quip_virial[6])*0.5;
virial[5] = (quip_virial[5] + quip_virial[7])*0.5;
}
if(vflag_atom) {
int iatom = 0;
for(ii = 0; ii < ntotal; ii++) {
vatom[ii][0] += quip_local_virial[iatom+0];
vatom[ii][1] += quip_local_virial[iatom+4];
vatom[ii][2] += quip_local_virial[iatom+8];
vatom[ii][3] += (quip_local_virial[iatom+3] +
quip_local_virial[iatom+1])*0.5;
vatom[ii][4] += (quip_local_virial[iatom+2] +
quip_local_virial[iatom+6])*0.5;
vatom[ii][5] += (quip_local_virial[iatom+5] +
quip_local_virial[iatom+7])*0.5;
iatom += 9;
}
}
delete [] atomic_numbers;
delete [] quip_num_neigh;
delete [] quip_neigh;
delete [] quip_local_e;
delete [] quip_force;
delete [] quip_virial;
delete [] quip_local_virial;
delete [] lattice;
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairQUIP::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style,"hybrid") == 0)
error->all(FLERR,"Pair style quip is only compatible with hybrid/overlay");
// check if linked to the correct QUIP library API version
// as of 2017-07-19 this is API_VERSION 1
if (quip_lammps_api_version() != 1)
error->all(FLERR,"QUIP LAMMPS wrapper API version is not compatible "
"with this version of LAMMPS");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairQUIP::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create(setflag,n+1,n+1,"pair:setflag");
cutsq = memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n];
}
void PairQUIP::coeff(int narg, char **arg)
{
if (!allocated) allocate();
int n = atom->ntypes;
// ensure I,J args are * *
for (int i = 1; i <= n; i++){
for (int j = 1; j <= n; j++) {
setflag[i][j] = 1;
}
}
if( narg != (4+n) ) {
char str[1024];
sprintf(str,"Number of arguments %d is not correct, it should be %d", narg, 4+n);
error->all(FLERR,str);
}
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
n_quip_file = strlen(arg[2]);
quip_file = new char[n_quip_file+1];
strcpy(quip_file,arg[2]);
n_quip_string = strlen(arg[3]);
quip_string = new char[n_quip_string+1];
strcpy(quip_string,arg[3]);
for (int i = 4; i < narg; i++) {
if( 0 == sscanf(arg[i],"%d",&map[i-4])) {
char str[1024];
sprintf(str,"Incorrect atomic number %s at position %d",arg[i],i);
error->all(FLERR,str);
}
}
// Initialise potential
// First call initialises potential via the fortran code in memory, and returns the necessary size
// of quip_potential. This behaviour is invoked by setting n_potential_quip to 0.
n_quip_potential = 0;
quip_potential = new int[0];
quip_lammps_potential_initialise(quip_potential,&n_quip_potential,&cutoff,quip_file,&n_quip_file,quip_string,&n_quip_string);
delete [] quip_potential;
// Allocate quip_potential integer array. This initialise call will transfer the location of the
// previously initialised potential to the quip_potential variable, and we will use it as a handle
// when calling the actual calculation routine. We return the cutoff as well.
quip_potential = new int[n_quip_potential];
quip_lammps_potential_initialise(quip_potential,&n_quip_potential,&cutoff,quip_file,&n_quip_file,quip_string,&n_quip_string);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairQUIP::init_style()
{
// Require newton pair on
if (force->newton_pair != 1)
error->all(FLERR,"Pair style quip requires newton pair on");
// Initialise neighbour list
int irequest_full = neighbor->request(this);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
neighbor->requests[irequest_full]->full = 1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairQUIP::init_one(int i, int j)
{
return cutoff;
}

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