forked from lijiext/lammps
add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package
This commit is contained in:
vishalkenchan
parent
40147a7a64
commit
71c4edda51
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@ -30,13 +30,19 @@ action () {
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action compute_temp_cs.cpp
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action compute_temp_cs.h
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action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
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action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp
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action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
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action pair_born_coul_long_cs.h pair_born_coul_long.h
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action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h
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action pair_buck_coul_long_cs.h pair_buck_coul_long.h
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action pair_coul_long_cs.cpp pair_coul_long.cpp
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action pair_coul_long_cs.h pair_coul_long.h
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action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
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action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp
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action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
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action pair_born_coul_long_cs.h pair_born_coul_long.h
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action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h
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action pair_buck_coul_long_cs.h pair_buck_coul_long.h
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action pair_coul_long_cs.cpp pair_coul_long.cpp
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action pair_coul_long_cs.h pair_coul_long.h
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action pair_lj_cut_coul_long_cs.cpp pair_lj_cut_coul_long.cpp
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action pair_lj_cut_coul_long_cs.h pair_lj_cut_coul_long.h
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action pair_lj_cut_coul_long_cs.h pair_lj_cut_coul_long.h
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action pair_born_coul_wolf_cs.cpp pair_born_coul_wolf.cpp
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action pair_born_coul_wolf_cs.h pair_born_coul_wolf.h
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action pair_coul_wolf_cs.cpp pair_coul_wolf.cpp
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action pair_coul_wolf_cs.h pair_coul_wolf.h
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@ -0,0 +1,170 @@
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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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#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_born_coul_wolf_cs.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 "math_const.h"
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#include "math_special.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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using namespace MathConst;
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using namespace MathSpecial;
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#define EPSILON 1.0e-20
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/* ---------------------------------------------------------------------- */
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PairBornCoulWolfCS::PairBornCoulWolfCS(LAMMPS *lmp) : PairBornCoulWolf(lmp)
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{
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single_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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void PairBornCoulWolfCS::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 rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
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double prefactor;
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double r,rexp;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;
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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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// self and shifted coulombic energy
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e_self = v_sh = 0.0;
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e_shift = erfc(alf*cut_coul)/cut_coul;
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f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
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cut_coul;
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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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qisq = qtmp*qtmp;
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e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
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if (eflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
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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 < cutsq[itype][jtype]) {
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rsq += EPSILON;
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// Add EPISLON for case: r = 0; Interaction must be removed
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// by special bond
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r2inv = 1.0/rsq;
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if (rsq < cut_coulsq) {
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r = sqrt(rsq);
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prefactor = qqrd2e*qtmp*q[j]/r;
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erfcc = erfc(alf*r);
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erfcd = exp(-alf*alf*r*r);
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v_sh = (erfcc - e_shift*r) * prefactor;
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dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
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forcecoul = dvdrr*rsq*prefactor;
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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[itype][jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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r = sqrt(rsq);
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rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
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forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
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+ born3[itype][jtype]*r2inv*r6inv;
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} else forceborn = 0.0;
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fpair = (forcecoul + factor_lj*forceborn) * 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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if (rsq < cut_coulsq) {
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ecoul = v_sh;
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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[itype][jtype]) {
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evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
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d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
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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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Using erfc and expmsq provided by math_special.h
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See: http://lammps.sandia.gov/threads/msg61934.html
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*/
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@ -0,0 +1,60 @@
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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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#ifdef PAIR_CLASS
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PairStyle(born/coul/wolf/cs,PairBornCoulWolfCS)
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#else
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#ifndef LMP_PAIR_BORN_COUL_WOLF_CS_H
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#define LMP_PAIR_BORN_COUL_WOLF_CS_H
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#include "pair_born_coul_wolf.h"
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namespace LAMMPS_NS {
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class PairBornCoulWolfCS : public PairBornCoulWolf {
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public:
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PairBornCoulWolfCS(class LAMMPS *);
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virtual void compute(int, int);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Incorrect args for pair coefficients
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Self-explanatory. Check the input script or data file.
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E: All pair coeffs are not set
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All pair coefficients must be set in the data file or by the
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pair_coeff command before running a simulation.
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E: Pair style born/coul/wolf/cs requires atom attribute q
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An atom style that defines this attribute must be used.
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*/
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@ -0,0 +1,145 @@
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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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#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_coul_wolf_cs.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 "math_const.h"
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#include "math_special.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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using namespace MathConst;
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using namespace MathSpecial;
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#define EPSILON 1.0e-20
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/* ---------------------------------------------------------------------- */
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PairCoulWolfCS::PairCoulWolfCS(LAMMPS *lmp) : PairCoulWolf( lmp )
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{
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single_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulWolfCS::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
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double rsq,forcecoul,factor_coul;
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double prefactor;
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double r;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq;
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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 nlocal = atom->nlocal;
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double *special_coul = force->special_coul;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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// self and shifted coulombic energy
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e_self = v_sh = 0.0;
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e_shift = erfc(alf*cut_coul)/cut_coul;
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f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) /
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cut_coul;
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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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jlist = firstneigh[i];
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jnum = numneigh[i];
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qisq = qtmp*qtmp;
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e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
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if (evflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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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_coulsq) {
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rsq += EPSILON;
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// Add EPISLON for case: r = 0; Interaction must be removed
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// by special bond
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r = sqrt(rsq);
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prefactor = qqrd2e*qtmp*q[j]/r;
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erfcc = erfc(alf*r);
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erfcd = exp(-alf*alf*r*r);
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v_sh = (erfcc - e_shift*r) * prefactor;
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dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift;
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forcecoul = dvdrr*rsq*prefactor;
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
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fpair = forcecoul / rsq;
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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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ecoul = v_sh;
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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 (evflag) ev_tally(i,j,nlocal,newton_pair,
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0.0,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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/* NOTES
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Using erfc and expmsq provided by math_special.h
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See: http://lammps.sandia.gov/threads/msg61934.html
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*/
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@ -0,0 +1,54 @@
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/* -*- 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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|
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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.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(coul/wolf/cs,PairCoulWolfCS)
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#else
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#ifndef LMP_PAIR_COUL_WOLF_CS_H_
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#define LMP_PAIR_COUL_WOLF_CS_H_
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#include "pair_coul_wolf.h"
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namespace LAMMPS_NS {
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class PairCoulWolfCS : public PairCoulWolf {
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public:
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PairCoulWolfCS( class LAMMPS *);
|
||||
virtual void compute( int, int);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif /* LMP_PAIR_COUL_WOLF_CS_H_ */
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair coul/wolf/cs requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue