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lammps/src/MANYBODY/pair_vashishta_table.cpp
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pair_vashishta_table.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 author: Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_vashishta_table.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"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairVashishtaTable::PairVashishtaTable(LAMMPS *lmp) : PairVashishta(lmp)
{
neigh3BodyMax = 0;
neigh3BodyCount = NULL;
neigh3Body = NULL;
forceTable = NULL;
potentialTable = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairVashishtaTable::~PairVashishtaTable()
{
memory->destroy(forceTable);
memory->destroy(potentialTable);
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fj[3],fk[3];
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// reallocate 3-body neighbor list if necessary
// NOTE: using 1000 is inefficient
// could make this a LAMMPS paged neighbor list
if (nlocal > neigh3BodyMax) {
neigh3BodyMax = atom->nmax;
memory->destroy(neigh3BodyCount);
memory->destroy(neigh3Body);
memory->create(neigh3BodyCount,neigh3BodyMax,
"pair:vashishta:neigh3BodyCount");
memory->create(neigh3Body,neigh3BodyMax,1000,
"pair:vashishta:neigh3Body");
}
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// reset the 3-body neighbor list
neigh3BodyCount[i] = 0;
// two-body interactions, skip half of them
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
ijparam = elem2param[itype][jtype][jtype];
if (rsq <= params[ijparam].cutsq2) {
neigh3Body[i][neigh3BodyCount[i]] = j;
neigh3BodyCount[i]++;
}
if (rsq > params[ijparam].cutsq) continue;
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
twobody_table(params[ijparam],rsq,fpair,eflag,evdwl);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
jlist = neigh3Body[i];
jnum = neigh3BodyCount[i];
jnumm1 = jnum - 1;
for (jj = 0; jj < jnumm1; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (rsq1 >= params[ijparam].cutsq2) continue;
for (kk = jj+1; kk < jnum; kk++) {
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (rsq2 >= params[ikparam].cutsq2) continue;
threebody(&params[ijparam],&params[ikparam],&params[ijkparam],
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
f[i][0] -= fj[0] + fk[0];
f[i][1] -= fj[1] + fk[1];
f[i][2] -= fj[2] + fk[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::twobody_table(const Param &param, double rsq,
double &fforce, int eflag, double &eng)
{
// use analytic form if rsq is inside inner cutoff
if (rsq < tabinnersq) {
Param *pparam = const_cast<Param *> (&param);
PairVashishta::twobody(pparam,rsq,fforce,eflag,eng);
return;
}
// double -> int will only keep the 0.xxxx part
const int tableIndex = (rsq - tabinnersq)*oneOverDeltaR2;
const double fraction = (rsq - tabinnersq)*oneOverDeltaR2 - tableIndex;
// force/energy are linearly interpolated between two adjacent values
double force0 = forceTable[param.ielement][param.jelement][tableIndex];
double force1 = forceTable[param.ielement][param.jelement][tableIndex+1];
fforce = (1.0 - fraction)*force0 + fraction*force1;
if (evflag) {
double energy0 = potentialTable[param.ielement][param.jelement][tableIndex];
double energy1 = potentialTable[param.ielement][param.jelement]
[tableIndex+1];
eng = (1.0 - fraction)*energy0 + fraction*energy1;
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairVashishtaTable::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
ntable = force->inumeric(FLERR,arg[0]);
tabinner = force->numeric(FLERR,arg[1]);
if (tabinner <= 0.0)
error->all(FLERR,"Illegal inner cutoff for tabulation");
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::setup_params()
{
PairVashishta::setup_params();
create_tables();
}
/* ---------------------------------------------------------------------- */
void PairVashishtaTable::create_tables()
{
memory->destroy(forceTable);
memory->destroy(potentialTable);
forceTable = NULL;
potentialTable = NULL;
tabinnersq = tabinner*tabinner;
deltaR2 = (cutmax*cutmax - tabinnersq) / (ntable-1);
oneOverDeltaR2 = 1.0/deltaR2;
memory->create(forceTable,nelements,nelements,ntable+1,
"pair:vashishta:forceTable");
memory->create(potentialTable,nelements,nelements,ntable+1,
"pair:vashishta:potentialTable");
// tabulalate energy/force via analytic twobody() in parent
int i,j,idx;
double rsq,fpair,eng;
for (i = 0; i < nelements; i++) {
for (j = 0; j < nelements; j++) {
int ijparam = elem2param[i][j][j];
for (idx = 0; idx <= ntable; idx++) {
rsq = tabinnersq + idx*deltaR2;
PairVashishta::twobody(&params[ijparam],rsq,fpair,1,eng);
forceTable[i][j][idx] = fpair;
potentialTable[i][j][idx] = eng;
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of tabulation arrays
------------------------------------------------------------------------- */
double PairVashishtaTable::memory_usage()
{
double bytes = 2*nelements*nelements*sizeof(double)*ntable;
return bytes;
}
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