1029 lines
33 KiB
C++
1029 lines
33 KiB
C++
/* ----------------------------------------------------------------------
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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: Paul Crozier (SNL)
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Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
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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_charmm_coul_long_soft.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 "kspace.h"
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#include "update.h"
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#include "integrate.h"
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#include "respa.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.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 EWALD_F 1.12837917
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#define EWALD_P 0.3275911
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#define A1 0.254829592
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#define A2 -0.284496736
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#define A3 1.421413741
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#define A4 -1.453152027
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#define A5 1.061405429
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/* ---------------------------------------------------------------------- */
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PairLJCharmmCoulLongSoft::PairLJCharmmCoulLongSoft(LAMMPS *lmp) : Pair(lmp)
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{
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respa_enable = 1;
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ewaldflag = pppmflag = 1;
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implicit = 0;
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mix_flag = ARITHMETIC;
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairLJCharmmCoulLongSoft::~PairLJCharmmCoulLongSoft()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(epsilon);
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memory->destroy(sigma);
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memory->destroy(lambda);
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memory->destroy(eps14);
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memory->destroy(sigma14);
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memory->destroy(lj1);
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memory->destroy(lj2);
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memory->destroy(lj3);
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memory->destroy(lj4);
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memory->destroy(lj14_1);
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memory->destroy(lj14_2);
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memory->destroy(lj14_3);
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memory->destroy(lj14_4);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulLongSoft::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 qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double r,rsq,forcecoul,forcelj,factor_coul,factor_lj;
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double grij,expm2,prefactor,t,erfc;
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double philj,switch1,switch2;
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double denc, denlj, r4sig6;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 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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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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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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qtmp = q[i];
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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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factor_lj = special_lj[sbmask(j)];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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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 < cut_bothsq) {
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if (rsq < cut_coulsq) {
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r = sqrt(rsq);
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grij = g_ewald * r;
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expm2 = exp(-grij*grij);
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t = 1.0 / (1.0 + EWALD_P*grij);
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erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
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denc = sqrt(lj4[itype][jtype] + rsq);
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prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
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forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
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} else forcecoul = 0.0;
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if (rsq < cut_ljsq) {
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r4sig6 = rsq*rsq / lj2[itype][jtype];
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denlj = lj3[itype][jtype] + rsq*r4sig6;
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forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
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(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
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(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
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switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
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philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
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(1.0/(denlj*denlj) - 1.0/denlj);
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forcelj = forcelj*switch1 + philj*switch2;
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}
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} else forcelj = 0.0;
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fpair = forcecoul + factor_lj*forcelj;
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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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if (rsq < cut_coulsq) {
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prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
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ecoul = prefactor*erfc;
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if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
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} else ecoul = 0.0;
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if (rsq < cut_ljsq) {
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evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
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(1.0/(denlj*denlj) - 1.0/denlj);
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
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(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
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evdwl *= switch1;
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}
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evdwl *= factor_lj;
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} else evdwl = 0.0;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,ecoul,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulLongSoft::compute_inner()
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
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double rsq,forcecoul,forcelj,factor_coul,factor_lj;
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double rsw;
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double denc, denlj, r4sig6;
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int *ilist,*jlist,*numneigh,**firstneigh;
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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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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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inum = listinner->inum;
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ilist = listinner->ilist;
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numneigh = listinner->numneigh;
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firstneigh = listinner->firstneigh;
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double cut_out_on = cut_respa[0];
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double cut_out_off = cut_respa[1];
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double cut_out_diff = cut_out_off - cut_out_on;
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double cut_out_on_sq = cut_out_on*cut_out_on;
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double cut_out_off_sq = cut_out_off*cut_out_off;
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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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qtmp = q[i];
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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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factor_lj = special_lj[sbmask(j)];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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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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if (rsq < cut_out_off_sq) {
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jtype = type[j];
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denc = sqrt(lj4[itype][jtype] + rsq);
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forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
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r4sig6 = rsq*rsq / lj2[itype][jtype];
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denlj = lj3[itype][jtype] + rsq*r4sig6;
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forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
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(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
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fpair = forcecoul + factor_lj*forcelj;
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if (rsq > cut_out_on_sq) {
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rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
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fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
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}
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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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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulLongSoft::compute_middle()
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
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double rsq,forcecoul,forcelj,factor_coul,factor_lj;
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double philj,switch1,switch2;
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double rsw;
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double denc, denlj, r4sig6;
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int *ilist,*jlist,*numneigh,**firstneigh;
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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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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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inum = listmiddle->inum;
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ilist = listmiddle->ilist;
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numneigh = listmiddle->numneigh;
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firstneigh = listmiddle->firstneigh;
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double cut_in_off = cut_respa[0];
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double cut_in_on = cut_respa[1];
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double cut_out_on = cut_respa[2];
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double cut_out_off = cut_respa[3];
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double cut_in_diff = cut_in_on - cut_in_off;
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double cut_out_diff = cut_out_off - cut_out_on;
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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double cut_out_on_sq = cut_out_on*cut_out_on;
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double cut_out_off_sq = cut_out_off*cut_out_off;
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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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qtmp = q[i];
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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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factor_lj = special_lj[sbmask(j)];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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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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if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
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jtype = type[j];
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denc = sqrt(lj4[itype][jtype] + rsq);
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forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
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r4sig6 = rsq*rsq / lj2[itype][jtype];
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denlj = lj3[itype][jtype] + rsq*r4sig6;
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forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
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(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
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(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
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switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
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philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
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(1.0/(denlj*denlj) - 1.0/denlj);
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forcelj = forcelj*switch1 + philj*switch2;
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}
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fpair = forcecoul + factor_lj*forcelj;
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if (rsq < cut_in_on_sq) {
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rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
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fpair *= rsw*rsw*(3.0 - 2.0*rsw);
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}
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if (rsq > cut_out_on_sq) {
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rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
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fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
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}
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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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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulLongSoft::compute_outer(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 qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double r,rsq,forcecoul,forcelj,factor_coul,factor_lj;
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double grij,expm2,fprefactor,eprefactor,t,erfc;
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double philj,switch1,switch2;
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double rsw;
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double denc, denlj, r4sig6;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 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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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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inum = listouter->inum;
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ilist = listouter->ilist;
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numneigh = listouter->numneigh;
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firstneigh = listouter->firstneigh;
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double cut_in_off = cut_respa[2];
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double cut_in_on = cut_respa[3];
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double cut_in_diff = cut_in_on - cut_in_off;
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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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];
|
|
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];
|
|
factor_lj = special_lj[sbmask(j)];
|
|
factor_coul = special_coul[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;
|
|
|
|
if (rsq < cut_bothsq) {
|
|
jtype = type[j];
|
|
|
|
if (rsq < cut_coulsq) {
|
|
r = sqrt(rsq);
|
|
grij = g_ewald * r;
|
|
expm2 = exp(-grij*grij);
|
|
t = 1.0 / (1.0 + EWALD_P*grij);
|
|
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
|
|
|
denc = sqrt(lj4[itype][jtype] + rsq);
|
|
fprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] /
|
|
(denc*denc*denc);
|
|
|
|
forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
|
|
|
|
if (rsq > cut_in_off_sq) {
|
|
if (rsq < cut_in_on_sq) {
|
|
rsw = (r - cut_in_off)/cut_in_diff;
|
|
forcecoul += fprefactor*rsw*rsw*(3.0 - 2.0*rsw);
|
|
if (factor_coul < 1.0)
|
|
forcecoul -=
|
|
(1.0-factor_coul)*fprefactor*rsw*rsw*(3.0 - 2.0*rsw);
|
|
} else {
|
|
forcecoul += fprefactor;
|
|
if (factor_coul < 1.0)
|
|
forcecoul -= (1.0-factor_coul)*fprefactor;
|
|
}
|
|
}
|
|
} else forcecoul = 0.0;
|
|
|
|
if (rsq < cut_ljsq && rsq > cut_in_off_sq) {
|
|
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
|
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
|
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
|
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
|
|
|
if (rsq > cut_lj_innersq) {
|
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
|
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
|
|
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
|
(1.0/(denlj*denlj) - 1.0/denlj);
|
|
forcelj = forcelj*switch1 + philj*switch2;
|
|
}
|
|
if (rsq < cut_in_on_sq) {
|
|
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
|
|
forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
|
|
}
|
|
} else forcelj = 0.0;
|
|
|
|
fpair = forcecoul + forcelj;
|
|
|
|
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) {
|
|
eprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
|
|
ecoul = eprefactor*erfc;
|
|
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*eprefactor;
|
|
} else ecoul = 0.0;
|
|
|
|
if (rsq < cut_ljsq) {
|
|
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
|
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
|
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
|
(1.0/(denlj*denlj) - 1.0/denlj);
|
|
if (rsq > cut_lj_innersq) {
|
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
|
evdwl *= switch1;
|
|
}
|
|
evdwl *= factor_lj;
|
|
} else evdwl = 0.0;
|
|
}
|
|
|
|
if (vflag) {
|
|
if (rsq < cut_coulsq) {
|
|
forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2);
|
|
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*fprefactor;
|
|
} else forcecoul = 0.0;
|
|
|
|
if (rsq <= cut_in_off_sq) {
|
|
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
|
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
|
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
|
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
|
|
|
if (rsq > cut_lj_innersq) {
|
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
|
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
|
|
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
|
(1.0/(denlj*denlj) - 1.0/denlj);
|
|
forcelj = forcelj*switch1 + philj*switch2;
|
|
}
|
|
} else if (rsq <= cut_in_on_sq) {
|
|
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
|
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
|
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
|
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
|
if (rsq > cut_lj_innersq) {
|
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
|
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
|
|
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
|
(1.0/(denlj*denlj) - 1.0/denlj);
|
|
forcelj = forcelj*switch1 + philj*switch2;
|
|
}
|
|
}
|
|
fpair = forcecoul + factor_lj*forcelj;
|
|
}
|
|
|
|
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
|
evdwl,ecoul,fpair,delx,dely,delz);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
allocate all arrays
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::allocate()
|
|
{
|
|
allocated = 1;
|
|
int n = atom->ntypes;
|
|
|
|
memory->create(setflag,n+1,n+1,"pair:setflag");
|
|
for (int i = 1; i <= n; i++)
|
|
for (int j = i; j <= n; j++)
|
|
setflag[i][j] = 0;
|
|
|
|
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(lambda,n+1,n+1,"pair:lambda");
|
|
memory->create(eps14,n+1,n+1,"pair:eps14");
|
|
memory->create(sigma14,n+1,n+1,"pair:sigma14");
|
|
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(lj14_1,n+1,n+1,"pair:lj14_1");
|
|
memory->create(lj14_2,n+1,n+1,"pair:lj14_2");
|
|
memory->create(lj14_3,n+1,n+1,"pair:lj14_3");
|
|
memory->create(lj14_4,n+1,n+1,"pair:lj14_4");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
global settings
|
|
unlike other pair styles,
|
|
there are no individual pair settings that these override
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::settings(int narg, char **arg)
|
|
{
|
|
if (narg != 5 && narg != 6) error->all(FLERR,"Illegal pair_style command");
|
|
|
|
nlambda = force->numeric(FLERR,arg[0]);
|
|
alphalj = force->numeric(FLERR,arg[1]);
|
|
alphac = force->numeric(FLERR,arg[2]);
|
|
|
|
cut_lj_inner = force->numeric(FLERR,arg[3]);
|
|
cut_lj = force->numeric(FLERR,arg[4]);
|
|
if (narg == 5) cut_coul = cut_lj;
|
|
else cut_coul = force->numeric(FLERR,arg[5]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more type pairs
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::coeff(int narg, char **arg)
|
|
{
|
|
if (narg != 5 && narg != 7) error->all(FLERR,"Illegal pair_coeff command");
|
|
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 = force->numeric(FLERR,arg[2]);
|
|
double sigma_one = force->numeric(FLERR,arg[3]);
|
|
double lambda_one = force->numeric(FLERR,arg[4]);
|
|
|
|
double eps14_one = epsilon_one;
|
|
double sigma14_one = sigma_one;
|
|
if (narg == 7) {
|
|
eps14_one = force->numeric(FLERR,arg[5]);
|
|
sigma14_one = force->numeric(FLERR,arg[6]);
|
|
}
|
|
|
|
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;
|
|
lambda[i][j] = lambda_one;
|
|
eps14[i][j] = eps14_one;
|
|
sigma14[i][j] = sigma14_one;
|
|
setflag[i][j] = 1;
|
|
count++;
|
|
}
|
|
}
|
|
|
|
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init specific to this pair style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::init_style()
|
|
{
|
|
if (!atom->q_flag)
|
|
error->all(FLERR,
|
|
"Pair style lj/charmm/coul/long/soft requires atom attribute q");
|
|
|
|
// request regular or rRESPA neighbor lists
|
|
|
|
int irequest;
|
|
|
|
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
|
|
int respa = 0;
|
|
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
|
|
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
|
|
|
|
if (respa == 0) irequest = neighbor->request(this,instance_me);
|
|
else if (respa == 1) {
|
|
irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->id = 1;
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->respainner = 1;
|
|
irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->id = 3;
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->respaouter = 1;
|
|
} else {
|
|
irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->id = 1;
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->respainner = 1;
|
|
irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->id = 2;
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->respamiddle = 1;
|
|
irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->id = 3;
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->respaouter = 1;
|
|
}
|
|
|
|
} else irequest = neighbor->request(this,instance_me);
|
|
|
|
// require cut_lj_inner < cut_lj
|
|
|
|
if (cut_lj_inner >= cut_lj)
|
|
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
|
|
|
|
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
|
|
cut_ljsq = cut_lj * cut_lj;
|
|
cut_coulsq = cut_coul * cut_coul;
|
|
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
|
|
|
|
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
|
|
(cut_ljsq-cut_lj_innersq);
|
|
|
|
// set & error check interior rRESPA cutoffs
|
|
|
|
if (strstr(update->integrate_style,"respa") &&
|
|
((Respa *) update->integrate)->level_inner >= 0) {
|
|
cut_respa = ((Respa *) update->integrate)->cutoff;
|
|
if (MIN(cut_lj,cut_coul) < cut_respa[3])
|
|
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
|
|
if (cut_lj_inner < cut_respa[1])
|
|
error->all(FLERR,"Pair inner cutoff < Respa interior cutoff");
|
|
} else cut_respa = NULL;
|
|
|
|
// insure use of KSpace long-range solver, set g_ewald
|
|
|
|
if (force->kspace == NULL)
|
|
error->all(FLERR,"Pair style requires a KSpace style");
|
|
g_ewald = force->kspace->g_ewald;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
neighbor callback to inform pair style of neighbor list to use
|
|
regular or rRESPA
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::init_list(int id, NeighList *ptr)
|
|
{
|
|
if (id == 0) list = ptr;
|
|
else if (id == 1) listinner = ptr;
|
|
else if (id == 2) listmiddle = ptr;
|
|
else if (id == 3) listouter = ptr;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init for one type pair i,j and corresponding j,i
|
|
------------------------------------------------------------------------- */
|
|
|
|
double PairLJCharmmCoulLongSoft::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]);
|
|
if (lambda[i][i] != lambda[j][j])
|
|
error->all(FLERR,"Pair lj/charmm/coul/long/soft different lambda values in mix");
|
|
lambda[i][j] = lambda[i][i];
|
|
eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j],
|
|
sigma14[i][i],sigma14[j][j]);
|
|
sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]);
|
|
}
|
|
|
|
double cut = MAX(cut_lj,cut_coul);
|
|
|
|
lj1[i][j] = pow(lambda[i][j], nlambda);
|
|
lj2[i][j] = pow(sigma[i][j], 6.0);
|
|
lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
|
lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
|
|
|
|
// 1-4 interactions unaffected (they're part of the dihedral term)
|
|
lj14_1[i][j] = 48.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
|
|
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
|
|
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
|
|
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
|
|
|
|
epsilon[j][i] = epsilon[i][j];
|
|
sigma[j][i] = sigma[i][j];
|
|
lambda[j][i] = lambda[i][j];
|
|
lj1[j][i] = lj1[i][j];
|
|
lj2[j][i] = lj2[i][j];
|
|
lj3[j][i] = lj3[i][j];
|
|
lj4[j][i] = lj4[i][j];
|
|
lj14_1[j][i] = lj14_1[i][j];
|
|
lj14_2[j][i] = lj14_2[i][j];
|
|
lj14_3[j][i] = lj14_3[i][j];
|
|
lj14_4[j][i] = lj14_4[i][j];
|
|
|
|
return cut;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes to restart file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::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);
|
|
fwrite(&lambda[i][j],sizeof(double),1,fp);
|
|
fwrite(&eps14[i][j],sizeof(double),1,fp);
|
|
fwrite(&sigma14[i][j],sizeof(double),1,fp);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 reads from restart file, bcasts
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::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);
|
|
fread(&lambda[i][j],sizeof(double),1,fp);
|
|
fread(&eps14[i][j],sizeof(double),1,fp);
|
|
fread(&sigma14[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);
|
|
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes to restart file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::write_restart_settings(FILE *fp)
|
|
{
|
|
fwrite(&nlambda,sizeof(double),1,fp);
|
|
fwrite(&alphalj,sizeof(double),1,fp);
|
|
fwrite(&alphac,sizeof(double),1,fp);
|
|
|
|
fwrite(&cut_lj_inner,sizeof(double),1,fp);
|
|
fwrite(&cut_lj,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 PairLJCharmmCoulLongSoft::read_restart_settings(FILE *fp)
|
|
{
|
|
if (comm->me == 0) {
|
|
fread(&nlambda,sizeof(double),1,fp);
|
|
fread(&alphalj,sizeof(double),1,fp);
|
|
fread(&alphac,sizeof(double),1,fp);
|
|
|
|
fread(&cut_lj_inner,sizeof(double),1,fp);
|
|
fread(&cut_lj,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(&nlambda,1,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
|
|
|
|
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
|
|
MPI_Bcast(&cut_lj,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);
|
|
}
|
|
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::write_data(FILE *fp)
|
|
{
|
|
for (int i = 1; i <= atom->ntypes; i++)
|
|
fprintf(fp,"%d %g %g %g %g %g\n",i,epsilon[i][i],sigma[i][i],
|
|
lambda[i][i],eps14[i][i],sigma14[i][i]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 writes all pairs to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairLJCharmmCoulLongSoft::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 %g %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
|
|
lambda[i][j],eps14[i][j],sigma14[i][j]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairLJCharmmCoulLongSoft::single(int i, int j, int itype, int jtype,
|
|
double rsq,
|
|
double factor_coul, double factor_lj,
|
|
double &fforce)
|
|
{
|
|
double r,grij,expm2,t,erfc,prefactor;
|
|
double switch1,switch2,forcecoul,forcelj,phicoul,philj;
|
|
double denc, denlj, r4sig6;
|
|
|
|
if (rsq < cut_coulsq) {
|
|
r = sqrt(rsq);
|
|
grij = g_ewald * r;
|
|
expm2 = exp(-grij*grij);
|
|
t = 1.0 / (1.0 + EWALD_P*grij);
|
|
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
|
|
|
denc = sqrt(lj4[itype][jtype] + rsq);
|
|
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
|
|
(denc*denc*denc);
|
|
|
|
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
|
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
|
} else forcecoul = 0.0;
|
|
|
|
if (rsq < cut_ljsq) {
|
|
r4sig6 = rsq*rsq / lj2[itype][jtype];
|
|
denlj = lj3[itype][jtype] + rsq*r4sig6;
|
|
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
|
|
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
|
|
if (rsq > cut_lj_innersq) {
|
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
|
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
|
|
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
|
(1.0/(denlj*denlj) - 1.0/denlj);
|
|
forcelj = forcelj*switch1 + philj*switch2;
|
|
}
|
|
} else forcelj = 0.0;
|
|
fforce = forcecoul + factor_lj*forcelj;
|
|
|
|
double eng = 0.0;
|
|
if (rsq < cut_coulsq) {
|
|
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
|
|
phicoul = prefactor*erfc;
|
|
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
|
|
eng += phicoul;
|
|
}
|
|
|
|
if (rsq < cut_ljsq) {
|
|
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
|
|
(1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype];
|
|
if (rsq > cut_lj_innersq) {
|
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
|
philj *= switch1;
|
|
}
|
|
eng += factor_lj*philj;
|
|
}
|
|
|
|
return eng;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void *PairLJCharmmCoulLongSoft::extract(const char *str, int &dim)
|
|
{
|
|
dim = 2;
|
|
if (strcmp(str,"lj14_1") == 0) return (void *) lj14_1;
|
|
if (strcmp(str,"lj14_2") == 0) return (void *) lj14_2;
|
|
if (strcmp(str,"lj14_3") == 0) return (void *) lj14_3;
|
|
if (strcmp(str,"lj14_4") == 0) return (void *) lj14_4;
|
|
|
|
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
|
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
|
if (strcmp(str,"lambda") == 0) return (void *) lambda;
|
|
|
|
dim = 0;
|
|
if (strcmp(str,"implicit") == 0) return (void *) &implicit;
|
|
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
|
|
|
return NULL;
|
|
}
|