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pair_lj_sdk.cpp
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Sun, Nov 10, 21:03

pair_lj_sdk.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: Axel Kohlmeyer (Temple U)
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_sdk.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace LJSDKParms;
/* ---------------------------------------------------------------------- */
PairLJSDK::PairLJSDK(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 0;
single_enable = 1;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairLJSDK::~PairLJSDK()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(lj_type);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
memory->destroy(rminsq);
memory->destroy(emin);
allocated = 0;
}
}
/* ---------------------------------------------------------------------- */
void PairLJSDK::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>();
else eval<1,1,0>();
} else {
if (force->newton_pair) eval<1,0,1>();
else eval<1,0,0>();
}
} else {
if (force->newton_pair) eval<0,0,1>();
else eval<0,0,0>();
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJSDK::eval()
{
int i,j,ii,jj,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,forcelj,factor_lj;
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = atom->f;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_lj = force->special_lj;
double fxtmp,fytmp,fztmp;
const int inum = list->inum;
const int * const ilist = list->ilist;
const int * const numneigh = list->numneigh;
const int * const * const firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
fxtmp=fytmp=fztmp=0.0;
const int itype = type[i];
const int * const jlist = firstneigh[i];
const int jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
const int ljt = lj_type[itype][jtype];
if (ljt == LJ12_4) {
const double r4inv=r2inv*r2inv;
forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
} else if (ljt == LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
forcelj = r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
} else if (ljt == LJ12_6) {
const double r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
} else continue;
fpair = factor_lj*forcelj*r2inv;
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (EFLAG) evdwl *= factor_lj;
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJSDK::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(lj_type,n+1,n+1,"pair:lj_type");
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) {
setflag[i][j] = 0;
lj_type[i][j] = LJ_NOT_SET;
}
}
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(offset,n+1,n+1,"pair:offset");
memory->create(rminsq,n+1,n+1,"pair:rminsq");
memory->create(emin,n+1,n+1,"pair:emin");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJSDK::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJSDK::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
int lj_type_one = find_lj_type(arg[2],lj_type_list);
if (lj_type_one == LJ_NOT_SET)
error->all(FLERR,"Cannot parse LJ type flag.");
double epsilon_one = force->numeric(FLERR,arg[3]);
double sigma_one = force->numeric(FLERR,arg[4]);
double cut_one = cut_global;
if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
lj_type[i][j] = lj_type_one;
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJSDK::init_one(int i, int j)
{
if (setflag[i][j] == 0)
error->all(FLERR,"No mixing support for lj/sdk. "
"Coefficients for all pairs need to be set explicitly.");
const int ljt = lj_type[i][j];
if (ljt == LJ_NOT_SET)
error->all(FLERR,"unrecognized LJ parameter flag");
lj1[i][j] = lj_prefact[ljt] * lj_pow1[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow1[ljt]);
lj2[i][j] = lj_prefact[ljt] * lj_pow2[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow2[ljt]);
lj3[i][j] = lj_prefact[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow1[ljt]);
lj4[i][j] = lj_prefact[ljt] * epsilon[i][j] * pow(sigma[i][j],lj_pow2[ljt]);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = lj_prefact[ljt] * epsilon[i][j] * (pow(ratio,lj_pow1[ljt]) - pow(ratio,lj_pow2[ljt]));
} else offset[i][j] = 0.0;
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
cut[j][i] = cut[i][j];
cutsq[j][i] = cutsq[i][j];
offset[j][i] = offset[i][j];
lj_type[j][i] = lj_type[i][j];
// compute derived parameters for SDK angle potential
const double eps = epsilon[i][j];
const double sig = sigma[i][j];
const double rmin = sig*exp(1.0/(lj_pow1[ljt]-lj_pow2[ljt])
*log(lj_pow1[ljt]/lj_pow2[ljt]) );
rminsq[j][i] = rminsq[i][j] = rmin*rmin;
const double ratio = sig/rmin;
const double emin_one = lj_prefact[ljt] * eps * (pow(ratio,lj_pow1[ljt])
- pow(ratio,lj_pow2[ljt]));
emin[j][i] = emin[i][j] = emin_one;
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag)
error->all(FLERR,"Tail flag not supported by lj/sdk pair style");
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSDK::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&lj_type[i][j],sizeof(int),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJSDK::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&lj_type[i][j],sizeof(int),1,fp);
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&lj_type[i][j],1,MPI_INT,0,world);
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSDK::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJSDK::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
lj/sdk does not support per atom type output with mixing
------------------------------------------------------------------------- */
void PairLJSDK::write_data(FILE *)
{
error->one(FLERR, "Pair style lj/sdk requires using "
"write_data with the 'pair ij' option");
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJSDK::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %s %g %g %g\n",i,j,lj_type_list[lj_type[i][j]],
epsilon[i][j],sigma[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJSDK::single(int, int, int itype, int jtype, double rsq,
double, double factor_lj, double &fforce)
{
if (rsq < cutsq[itype][jtype]) {
const int ljt = lj_type[itype][jtype];
const double ljpow1 = lj_pow1[ljt];
const double ljpow2 = lj_pow2[ljt];
const double ljpref = lj_prefact[ljt];
const double ratio = sigma[itype][jtype]/sqrt(rsq);
const double eps = epsilon[itype][jtype];
fforce = factor_lj * ljpref*eps * (ljpow1*pow(ratio,ljpow1)
- ljpow2*pow(ratio,ljpow2))/rsq;
return factor_lj * (ljpref*eps * (pow(ratio,ljpow1) - pow(ratio,ljpow2))
- offset[itype][jtype]);
} else fforce=0.0;
return 0.0;
}
/* ---------------------------------------------------------------------- */
void *PairLJSDK::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"lj_type") == 0) return (void *) lj_type;
if (strcmp(str,"lj1") == 0) return (void *) lj1;
if (strcmp(str,"lj2") == 0) return (void *) lj2;
if (strcmp(str,"lj3") == 0) return (void *) lj3;
if (strcmp(str,"lj4") == 0) return (void *) lj4;
if (strcmp(str,"rminsq") == 0) return (void *) rminsq;
if (strcmp(str,"emin") == 0) return (void *) emin;
return NULL;
}
/* ---------------------------------------------------------------------- */
double PairLJSDK::memory_usage()
{
double bytes = Pair::memory_usage();
int n = atom->ntypes;
// setflag/lj_type
bytes += 2 * (n+1)*(n+1)*sizeof(int);
// cut/cutsq/epsilon/sigma/offset/lj1/lj2/lj3/lj4/rminsq/emin
bytes += 11 * (n+1)*(n+1)*sizeof(double);
return bytes;
}

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