forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1805 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Mark Stevens (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "pair_lj_gromacs.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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PairLJGromacs::PairLJGromacs(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairLJGromacs::~PairLJGromacs()
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{
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if (allocated) {
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memory->destroy_2d_int_array(setflag);
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memory->destroy_2d_double_array(cutsq);
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memory->destroy_2d_double_array(cut);
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memory->destroy_2d_double_array(cut_inner);
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memory->destroy_2d_double_array(cut_inner_sq);
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memory->destroy_2d_double_array(epsilon);
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memory->destroy_2d_double_array(sigma);
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memory->destroy_2d_double_array(lj1);
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memory->destroy_2d_double_array(lj2);
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memory->destroy_2d_double_array(lj3);
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memory->destroy_2d_double_array(lj4);
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memory->destroy_2d_double_array(ljsw1);
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memory->destroy_2d_double_array(ljsw2);
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memory->destroy_2d_double_array(ljsw3);
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memory->destroy_2d_double_array(ljsw4);
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memory->destroy_2d_double_array(ljsw5);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJGromacs::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r2inv,r6inv,forcelj,factor_lj;
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double r,t,fswitch,eswitch;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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double *q = atom->q;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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if (j < nall) factor_lj = 1.0;
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else {
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factor_lj = special_lj[j/nall];
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j %= nall;
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}
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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if (rsq > cut_inner_sq[itype][jtype]) {
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r = sqrt(rsq);
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t = r - cut_inner[itype][jtype];
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fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
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forcelj += fswitch;
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}
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fpair = factor_lj*forcelj*r2inv;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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if (eflag) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
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ljsw5[itype][jtype];
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if (rsq > cut_inner_sq[itype][jtype]) {
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eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
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evdwl += eswitch;
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}
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evdwl *= factor_lj;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairLJGromacs::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
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cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
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cut_inner = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner");
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cut_inner_sq = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner_sq");
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epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon");
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sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
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lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");
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lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");
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lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");
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lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");
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ljsw1 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw1");
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ljsw2 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw2");
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ljsw3 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw3");
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ljsw4 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw4");
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ljsw5 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw5");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairLJGromacs::settings(int narg, char **arg)
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{
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if (narg != 2) error->all("Illegal pair_style command");
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cut_inner_global = atof(arg[0]);
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cut_global = atof(arg[1]);
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if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
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error->all("Illegal pair_style command");
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) {
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cut_inner[i][j] = cut_inner_global;
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cut[i][j] = cut_global;
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}
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairLJGromacs::coeff(int narg, char **arg)
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{
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if (narg != 4 && narg != 6)
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error->all("Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double epsilon_one = atof(arg[2]);
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double sigma_one = atof(arg[3]);
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double cut_inner_one = cut_inner_global;
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double cut_one = cut_global;
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if (narg == 6) {
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cut_inner_one = atof(arg[4]);
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cut_one = atof(arg[5]);
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}
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if (cut_inner_one <= 0.0 || cut_inner_one > cut_one)
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error->all("Incorrect args for pair coefficients");
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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epsilon[i][j] = epsilon_one;
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sigma[i][j] = sigma_one;
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cut_inner[i][j] = cut_inner_one;
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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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if (count == 0) error->all("Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairLJGromacs::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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sigma[i][i],sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
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cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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double r6inv = 1.0/pow(cut[i][j],6.0);
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double r8inv = 1.0/pow(cut[i][j],8.0);
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double t = cut[i][j] - cut_inner[i][j];
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double t2inv = 1.0/(t*t);
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double t3inv = t2inv/t;
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double t3 = 1.0/t3inv;
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double a6 = ( 7.0*cut_inner[i][j] - 10.0*cut[i][j])*r8inv*t2inv;
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double b6 = ( 9.0*cut[i][j] - 7.0*cut_inner[i][j])*r8inv*t3inv;
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double a12 = (13.0*cut_inner[i][j] - 16.0*cut[i][j])*r6inv*r8inv*t2inv;
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double b12 = (15.0*cut[i][j] - 13.0*cut_inner[i][j])*r6inv*r8inv*t3inv;
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double c6 = r6inv - t3*(a6/3.0 + b6*t/4.0);
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double c12 = r6inv*r6inv - t3*(a12/3.0 + b12*t/4.0);
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ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6;
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ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6;
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ljsw3[i][j] =-lj3[i][j]*a12/3.0 + lj4[i][j]*a6/3.0;
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ljsw4[i][j] =-lj3[i][j]*b12/4.0 + lj4[i][j]*b6/4.0;
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ljsw5[i][j] =-lj3[i][j]*c12 + lj4[i][j]*c6;
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cut_inner[j][i] = cut_inner[i][j];
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cut_inner_sq[j][i] = cut_inner_sq[i][j];
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lj1[j][i] = lj1[i][j];
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lj2[j][i] = lj2[i][j];
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lj3[j][i] = lj3[i][j];
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lj4[j][i] = lj4[i][j];
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ljsw1[j][i] = ljsw1[i][j];
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ljsw2[j][i] = ljsw2[i][j];
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ljsw3[j][i] = ljsw3[i][j];
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ljsw4[j][i] = ljsw4[i][j];
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ljsw5[j][i] = ljsw5[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairLJGromacs::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&epsilon[i][j],sizeof(double),1,fp);
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fwrite(&sigma[i][j],sizeof(double),1,fp);
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fwrite(&cut_inner[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairLJGromacs::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (setflag[i][j]) {
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if (me == 0) {
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fread(&epsilon[i][j],sizeof(double),1,fp);
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fread(&sigma[i][j],sizeof(double),1,fp);
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fread(&cut_inner[i][j],sizeof(double),1,fp);
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fread(&cut[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairLJGromacs::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_inner_global,sizeof(double),1,fp);
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairLJGromacs::read_restart_settings(FILE *fp)
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{
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int me = comm->me;
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if (me == 0) {
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fread(&cut_inner_global,sizeof(double),1,fp);
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fread(&cut_global,sizeof(double),1,fp);
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fread(&offset_flag,sizeof(int),1,fp);
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fread(&mix_flag,sizeof(int),1,fp);
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}
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MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ---------------------------------------------------------------------- */
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double PairLJGromacs::single(int i, int j, int itype, int jtype,
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double rsq,
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double factor_coul, double factor_lj,
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double &fforce)
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{
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double r2inv,r6inv,forcelj,philj;
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double r,t,fswitch,phiswitch;
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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if (rsq > cut_inner_sq[itype][jtype]) {
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r = sqrt(rsq);
|
||||
t = r - cut_inner[itype][jtype];
|
||||
fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
|
||||
forcelj += fswitch;
|
||||
}
|
||||
fforce = factor_lj*forcelj*r2inv;
|
||||
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
|
||||
ljsw5[itype][jtype];
|
||||
if (rsq > cut_inner_sq[itype][jtype]) {
|
||||
phiswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
|
||||
philj += phiswitch;
|
||||
}
|
||||
|
||||
return factor_lj*philj;
|
||||
}
|
|
@ -0,0 +1,47 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef PAIR_LJ_GROMACS_H
|
||||
#define PAIR_LJ_GROMACS_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJGromacs : public Pair {
|
||||
public:
|
||||
PairLJGromacs(class LAMMPS *);
|
||||
virtual ~PairLJGromacs();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_inner_global,cut_global;
|
||||
double **cut,**cut_inner,**cut_inner_sq;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
double **ljsw1,**ljsw2,**ljsw3,**ljsw4,**ljsw5;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
|
@ -0,0 +1,491 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: Mark Stevens (SNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_lj_gromacs_coul_gromacs.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJGromacsCoulGromacs::PairLJGromacsCoulGromacs(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJGromacsCoulGromacs::~PairLJGromacsCoulGromacs()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy_2d_int_array(setflag);
|
||||
memory->destroy_2d_double_array(cutsq);
|
||||
|
||||
memory->destroy_2d_double_array(epsilon);
|
||||
memory->destroy_2d_double_array(sigma);
|
||||
memory->destroy_2d_double_array(lj1);
|
||||
memory->destroy_2d_double_array(lj2);
|
||||
memory->destroy_2d_double_array(lj3);
|
||||
memory->destroy_2d_double_array(lj4);
|
||||
memory->destroy_2d_double_array(ljsw1);
|
||||
memory->destroy_2d_double_array(ljsw2);
|
||||
memory->destroy_2d_double_array(ljsw3);
|
||||
memory->destroy_2d_double_array(ljsw4);
|
||||
memory->destroy_2d_double_array(ljsw5);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double r,tlj,tc,fswitch,fswitchcoul,eswitch,ecoulswitch;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int nall = nlocal + atom->nghost;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
|
||||
if (j < nall) factor_coul = factor_lj = 1.0;
|
||||
else {
|
||||
factor_coul = special_coul[j/nall];
|
||||
factor_lj = special_lj[j/nall];
|
||||
j %= nall;
|
||||
}
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
if (rsq < cut_bothsq) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
// skip if qi or qj = 0.0 since this potential may be used as
|
||||
// coarse-grain model with many uncharged atoms
|
||||
|
||||
if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) {
|
||||
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
|
||||
if (rsq > cut_coul_innersq) {
|
||||
r = sqrt(rsq);
|
||||
tc = r - cut_coul_inner;
|
||||
fswitchcoul = qqrd2e * qtmp*q[j]*r*tc*tc*(coulsw1 + coulsw2*tc);
|
||||
forcecoul += fswitchcoul;
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
jtype = type[j];
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
if (rsq > cut_lj_innersq) {
|
||||
r = sqrt(rsq);
|
||||
tlj = r - cut_lj_inner;
|
||||
fswitch = r*tlj*tlj*(ljsw1[itype][jtype] +
|
||||
ljsw2[itype][jtype]*tlj);
|
||||
forcelj += fswitch;
|
||||
}
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5);
|
||||
if (rsq > cut_coul_innersq) {
|
||||
ecoulswitch = tc*tc*tc * (coulsw3 + coulsw4*tc);
|
||||
ecoul += qqrd2e*qtmp*q[j]*ecoulswitch;
|
||||
}
|
||||
ecoul *= factor_coul;
|
||||
} else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
|
||||
ljsw5[itype][jtype];
|
||||
if (rsq > cut_lj_innersq) {
|
||||
eswitch = tlj*tlj*tlj * (ljsw3[itype][jtype] +
|
||||
ljsw4[itype][jtype]*tlj);
|
||||
evdwl += eswitch;
|
||||
}
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
|
||||
|
||||
epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon");
|
||||
sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
|
||||
lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");
|
||||
lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");
|
||||
lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");
|
||||
lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");
|
||||
ljsw1 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw1");
|
||||
ljsw2 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw2");
|
||||
ljsw3 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw3");
|
||||
ljsw4 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw4");
|
||||
ljsw5 = memory->create_2d_double_array(n+1,n+1,"pair:ljsw5");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2 && narg != 4)
|
||||
error->all("Illegal pair_style command");
|
||||
|
||||
cut_lj_inner = atof(arg[0]);
|
||||
cut_lj = atof(arg[1]);
|
||||
if (narg == 2) {
|
||||
cut_coul_inner = cut_lj_inner;
|
||||
cut_coul = cut_lj;
|
||||
} else {
|
||||
cut_coul_inner = atof(arg[2]);
|
||||
cut_coul = atof(arg[3]);
|
||||
}
|
||||
|
||||
if (cut_lj_inner <= 0.0 || cut_coul_inner < 0.0)
|
||||
error->all("Illegal pair_style command");
|
||||
if (cut_lj_inner > cut_lj || cut_coul_inner > cut_coul)
|
||||
error->all("Illegal pair_style command");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all("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);
|
||||
|
||||
double epsilon_one = atof(arg[2]);
|
||||
double sigma_one = atof(arg[3]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all("Pair style lj/gromacs/coul/gromacs requires atom attribute q");
|
||||
|
||||
int irequest = neighbor->request(this);
|
||||
|
||||
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
|
||||
cut_ljsq = cut_lj * cut_lj;
|
||||
cut_coul_innersq = cut_coul_inner * cut_coul_inner;
|
||||
cut_coulsq = cut_coul * cut_coul;
|
||||
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJGromacsCoulGromacs::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||
sigma[i][i],sigma[j][j]);
|
||||
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
|
||||
}
|
||||
|
||||
double cut = MAX(cut_lj,cut_coul);
|
||||
|
||||
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||
|
||||
double r6inv = 1.0/pow(cut_lj,6.0);
|
||||
double r8inv = 1.0/pow(cut_lj,8.0);
|
||||
double t = cut_lj - cut_lj_inner;
|
||||
double t2inv = 1.0/(t*t);
|
||||
double t3inv = t2inv/t;
|
||||
double t3 = 1.0/t3inv;
|
||||
double a6 = (7.0*cut_lj_inner - 10.0*cut_lj)*r8inv*t2inv;
|
||||
double b6 = (9.0*cut_lj - 7.0*cut_lj_inner)*r8inv*t3inv;
|
||||
double a12 = (13.0*cut_lj_inner - 16.0*cut_lj)*r6inv*r8inv*t2inv;
|
||||
double b12 = (15.0*cut_lj - 13.0*cut_lj_inner)*r6inv*r8inv*t3inv;
|
||||
double c6 = r6inv - t3*(a6/3.0 + b6*t/4.0);
|
||||
double c12 = r6inv*r6inv - t3*(a12/3.0 + b12*t/4.0);
|
||||
ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6;
|
||||
ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6;
|
||||
ljsw3[i][j] = -lj3[i][j]*a12/3.0 + lj4[i][j]*a6/3.0;
|
||||
ljsw4[i][j] = -lj3[i][j]*b12/4.0 + lj4[i][j]*b6/4.0;
|
||||
ljsw5[i][j] = -lj3[i][j]*c12 + lj4[i][j]*c6;
|
||||
|
||||
double r3inv = 1.0/pow(cut_coul,3.0);
|
||||
t = cut_coul - cut_coul_inner;
|
||||
t2inv = 1.0/(t*t);
|
||||
t3inv = t2inv/t;
|
||||
double a1 = (2.0*cut_coul_inner - 5.0*cut_coul) * r3inv*t2inv;
|
||||
double b1 = (4.0*cut_coul - 2.0*cut_coul_inner) * r3inv*t3inv;
|
||||
coulsw1 = a1;
|
||||
coulsw2 = b1;
|
||||
coulsw3 = -a1/3.0;
|
||||
coulsw4 = -b1/4.0;
|
||||
coulsw5 = 1.0/cut_coul - t*t*t*(a1/3.0 + b1*t/4.0);
|
||||
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
ljsw1[j][i] = ljsw1[i][j];
|
||||
ljsw2[j][i] = ljsw2[i][j];
|
||||
ljsw3[j][i] = ljsw3[i][j];
|
||||
ljsw4[j][i] = ljsw4[i][j];
|
||||
ljsw5[j][i] = ljsw5[i][j];
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::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(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::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(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_lj_inner,sizeof(double),1,fp);
|
||||
fwrite(&cut_lj,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul_inner,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_lj_inner,sizeof(double),1,fp);
|
||||
fread(&cut_lj,sizeof(double),1,fp);
|
||||
fread(&cut_coul_inner,sizeof(double),1,fp);
|
||||
fread(&cut_coul,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul_inner,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
|
||||
double r,tlj,tc,fswitch,phiswitch,fswitchcoul,phiswitchcoul;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq) {
|
||||
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
|
||||
if (rsq > cut_coul_innersq) {
|
||||
r = sqrt(rsq);
|
||||
tc = r - cut_coul_inner;
|
||||
fswitchcoul = force->qqrd2e *
|
||||
atom->q[i]*atom->q[j] * r*tc*tc * (coulsw1 + coulsw2*tcoul);
|
||||
forcecoul += fswitchcoul;
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
if (rsq > cut_lj_innersq) {
|
||||
r = sqrt(rsq);
|
||||
tlj = r - cut_lj_inner;
|
||||
fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*tlj);
|
||||
forcelj += fswitch;
|
||||
}
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq) {
|
||||
phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * (sqrt(r2inv)-coulsw5);
|
||||
if (rsq > cut_coul_innersq) {
|
||||
phiswitchcoul = force->qqrd2e * atom->q[i]*atom->q[j] *
|
||||
tc*tc*tc * (coulsw3 + coulsw4*tc);
|
||||
phicoul += phiswitchcoul;
|
||||
}
|
||||
eng += factor_coul*phicoul;
|
||||
}
|
||||
|
||||
if (rsq < cut_ljsq) {
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
|
||||
ljsw5[itype][jtype];
|
||||
if (rsq > cut_lj_innersq) {
|
||||
phiswitch = tlj*tlj*tlj * (ljsw3[itype][jtype] +
|
||||
ljsw4[itype][jtype]*tlj);
|
||||
philj += phiswitch;
|
||||
}
|
||||
eng += factor_lj*philj;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
|
@ -0,0 +1,49 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef PAIR_LJ_GROMACS_COUL_GROMACS_H
|
||||
#define PAIR_LJ_GROMACS_COUL_GROMACS_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJGromacsCoulGromacs : public Pair {
|
||||
public:
|
||||
PairLJGromacsCoulGromacs(class LAMMPS *);
|
||||
virtual ~PairLJGromacsCoulGromacs();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_lj_inner,cut_lj,cut_coul_inner,cut_coul;
|
||||
double cut_lj_innersq,cut_ljsq,cut_coul_innersq,cut_coulsq,cut_bothsq;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
double **ljsw1,**ljsw2,**ljsw3,**ljsw4,**ljsw5;
|
||||
double coulsw1,coulsw2,coulsw3,coulsw4,coulsw5;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
|
@ -300,6 +300,8 @@ MinimizeStyle(sd,MinSD)
|
|||
#include "pair_lj_cut_coul_cut.h"
|
||||
#include "pair_lj_cut_coul_debye.h"
|
||||
#include "pair_lj_expand.h"
|
||||
#include "pair_lj_gromacs.h"
|
||||
#include "pair_lj_gromacs_coul_gromacs.h"
|
||||
#include "pair_lj_smooth.h"
|
||||
#include "pair_morse.h"
|
||||
#include "pair_soft.h"
|
||||
|
@ -318,6 +320,8 @@ PairStyle(lj/cut,PairLJCut)
|
|||
PairStyle(lj/cut/coul/cut,PairLJCutCoulCut)
|
||||
PairStyle(lj/cut/coul/debye,PairLJCutCoulDebye)
|
||||
PairStyle(lj/expand,PairLJExpand)
|
||||
PairStyle(lj/gromacs,PairLJGromacs)
|
||||
PairStyle(lj/gromacs/coul/gromacs,PairLJGromacsCoulGromacs)
|
||||
PairStyle(lj/smooth,PairLJSmooth)
|
||||
PairStyle(morse,PairMorse)
|
||||
PairStyle(soft,PairSoft)
|
||||
|
|
Loading…
Reference in New Issue