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lammps/src/USER-MISC/pair_agni.cpp
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pair_agni.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: Axel Kohlmeyer (Temple U), Venkatesh Botu
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_agni.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
#include "math_special.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathSpecial;
static const char cite_pair_agni[] =
"pair agni command:\n\n"
"@article{botu2015adaptive,\n"
" author = {Botu, Venkatesh and Ramprasad, Rampi},\n"
" title = {Adaptive machine learning framework to"
" accelerate ab initio molecular dynamics},\n"
" journal = {International Journal of Quantum Chemistry},\n"
" volume = {115},\n"
" number = {16},\n"
" pages = {1074--1083},\n"
" year = {2015},\n"
" publisher = {Wiley Online Library}\n"
"}\n\n"
"@article{botu2015learning,\n"
" author = {Botu, Venkatesh and Ramprasad, Rampi},\n"
" title = {Learning scheme to predict atomic forces"
" and accelerate materials simulations},\n"
" journal = {Physical Review B},\n"
" volume = {92},\n"
" number = {9},\n"
" pages = {094306},\n"
" year = {2015},\n"
" publisher = {APS}\n"
"}\n\n";
#define AGNI_VERSION 1
#define MAXLINE 10240
#define MAXWORD 40
/* ---------------------------------------------------------------------- */
PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_agni);
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
no_virial_fdotr_compute = 1;
nelements = 0;
elements = NULL;
elem2param = NULL;
nparams = 0;
params = NULL;
map = NULL;
cutmax = 0.0;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairAGNI::~PairAGNI()
{
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
if (params) {
for (int i = 0; i < nparams; ++i) {
int n = params[i].numeta;
for (int j = 0; j < n; ++j) {
delete [] params[i].xU[j];
}
delete [] params[i].eta;
delete [] params[i].alpha;
delete [] params[i].xU;
delete [] params[i].yU;
}
memory->destroy(params);
params = NULL;
}
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
}
}
/* ---------------------------------------------------------------------- */
void PairAGNI::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,inum,jnum,itype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
double fxtmp,fytmp,fztmp;
double *Vx, *Vy, *Vz;
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
fxtmp = fytmp = fztmp = 0.0;
const Param &iparam = params[elem2param[itype]];
Vx = new double[iparam.numeta];
Vy = new double[iparam.numeta];
Vz = new double[iparam.numeta];
memset(Vx,0,iparam.numeta*sizeof(double));
memset(Vy,0,iparam.numeta*sizeof(double));
memset(Vz,0,iparam.numeta*sizeof(double));
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if ((rsq > 0.0) && (rsq < iparam.cutsq)) {
const double r = sqrt(rsq);
const double cF = 0.5*(cos((MathConst::MY_PI*r)/iparam.cut)+1.0);
const double wX = cF*delx/r;
const double wY = cF*dely/r;
const double wZ = cF*delz/r;
for (k = 0; k < iparam.numeta; ++k) {
const double e = exp(-(iparam.eta[k]*rsq));
Vx[k] += wX*e;
Vy[k] += wY*e;
Vz[k] += wZ*e;
}
}
}
for (j = 0; j < iparam.numtrain; ++j) {
double kx = 0.0;
double ky = 0.0;
double kz = 0.0;
for(int k = 0; k < iparam.numeta; ++k) {
const double xu = iparam.xU[k][j];
kx += square(Vx[k] - xu);
ky += square(Vy[k] - xu);
kz += square(Vz[k] - xu);
}
const double e = -0.5/(square(iparam.sigma));
fxtmp += iparam.alpha[j]*exp(kx*e);
fytmp += iparam.alpha[j]*exp(ky*e);
fztmp += iparam.alpha[j]*exp(kz*e);
}
fxtmp += iparam.b;
fytmp += iparam.b;
fztmp += iparam.b;
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
if (evflag) ev_tally_xyz_full(i,0.0,0.0,fxtmp,fytmp,fztmp,delx,dely,delz);
delete [] Vx;
delete [] Vy;
delete [] Vz;
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairAGNI::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairAGNI::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairAGNI::coeff(int narg, char **arg)
{
int i,j,n;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
// read potential file and initialize potential parameters
read_file(arg[2]);
setup_params();
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairAGNI::init_style()
{
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairAGNI::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairAGNI::read_file(char *file)
{
memory->sfree(params);
params = NULL;
nparams = 0;
// open file on proc 0 only
// then read line by line and broadcast the line to all MPI ranks
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open AGNI potential file %s",file);
error->one(FLERR,str);
}
}
int i,j,n,nwords,curparam,wantdata;
char line[MAXLINE],*ptr;
int eof = 0;
char **words = new char*[MAXWORD+1];
while (1) {
n = 0;
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
if (nwords > MAXWORD)
error->all(FLERR,"Increase MAXWORD and recompile");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
--nwords;
if ((nwords == 2) && (strcmp(words[0],"generation") == 0)) {
int ver = atoi(words[1]);
if (ver != AGNI_VERSION)
error->all(FLERR,"Incompatible AGNI potential file version");
if ((ver == 1) && (nelements != 1))
error->all(FLERR,"Cannot handle multi-element systems with this potential");
} else if ((nwords == 2) && (strcmp(words[0],"n_elements") == 0)) {
nparams = atoi(words[1]);
if ((nparams < 1) || params) // sanity check
error->all(FLERR,"Invalid AGNI potential file");
params = memory->create(params,nparams,"pair:params");
memset(params,0,nparams*sizeof(Param));
curparam = -1;
} else if (params && (nwords == nparams+1) && (strcmp(words[0],"element") == 0)) {
wantdata = -1;
for (i = 0; i < nparams; ++i) {
for (j = 0; j < nelements; ++j)
if (strcmp(words[i+1],elements[j]) == 0) break;
if (j == nelements)
error->all(FLERR,"No suitable parameters for requested element found");
else params[i].ielement = j;
}
} else if (params && (nwords == 2) && (strcmp(words[0],"interaction") == 0)) {
for (i = 0; i < nparams; ++i)
if (strcmp(words[1],elements[params[i].ielement]) == 0) curparam = i;
} else if ((curparam >=0) && (nwords == 1) && (strcmp(words[0],"endVar") == 0)) {
int numtrain = params[curparam].numtrain;
int numeta = params[curparam].numeta;
params[curparam].alpha = new double[numtrain];
params[curparam].yU = new double[numtrain];
params[curparam].xU = new double*[numeta];
for (i = 0; i < numeta; ++i)
params[curparam].xU[i] = new double[numtrain];
wantdata = curparam;
curparam = -1;
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rc") == 0)) {
params[curparam].cut = atof(words[1]);
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rs") == 0)) {
; // ignored
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"neighbors") == 0)) {
; // ignored
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"sigma") == 0)) {
params[curparam].sigma = atof(words[1]);
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"lambda") == 0)) {
params[curparam].lambda = atof(words[1]);
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"b") == 0)) {
params[curparam].b = atof(words[1]);
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"n_train") == 0)) {
params[curparam].numtrain = atoi(words[1]);
} else if ((curparam >=0) && (nwords > 1) && (strcmp(words[0],"eta") == 0)) {
params[curparam].numeta = nwords-1;
params[curparam].eta = new double[nwords-1];
for (i = 0, j = 1 ; j < nwords; ++i, ++j)
params[curparam].eta[i] = atof(words[j]);
} else if (params && (wantdata >=0) && (nwords == params[wantdata].numeta+3)) {
n = (int) atof(words[0]);
for (i = 0; i < params[wantdata].numeta; ++i) {
params[wantdata].xU[i][n] = atof(words[i+1]);
}
params[wantdata].yU[n] = atof(words[params[wantdata].numeta+1]);
params[wantdata].alpha[n] = atof(words[params[wantdata].numeta+2]);
} else {
if (comm->me == 0)
error->warning(FLERR,"Ignoring unknown content in AGNI potential file.");
}
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairAGNI::setup_params()
{
int i,m,n;
double rtmp;
// set elem2param for all elements
memory->destroy(elem2param);
memory->create(elem2param,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i] = n;
}
// compute parameter values derived from inputs
// set cutsq using shortcut to reduce neighbor list for accelerated
// calculations. cut must remain unchanged as it is a potential parameter
// (cut = a*sigma)
cutmax = 0.0;
for (m = 0; m < nparams; m++) {
rtmp = params[m].cut;
params[m].cutsq = rtmp * rtmp;
if (rtmp > cutmax) cutmax = rtmp;
}
}
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