forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9611 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
080dcf2849
commit
52f09a7bd1
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@ -35,6 +35,7 @@ if (test $1 = 1) then
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cp pair_hbond_dreiding_morse.cpp ..
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cp pair_lj_charmm_coul_charmm.cpp ..
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cp pair_lj_charmm_coul_charmm_implicit.cpp ..
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cp pair_lj_cut_tip4p_cut.cpp ..
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cp angle_charmm.h ..
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cp angle_cosine.h ..
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@ -69,6 +70,7 @@ if (test $1 = 1) then
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cp pair_hbond_dreiding_morse.h ..
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cp pair_lj_charmm_coul_charmm.h ..
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cp pair_lj_charmm_coul_charmm_implicit.h ..
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cp pair_lj_cut_tip4p_cut.h ..
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elif (test $1 = 0) then
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@ -105,6 +107,7 @@ elif (test $1 = 0) then
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rm -f ../pair_hbond_dreiding_morse.cpp
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rm -f ../pair_lj_charmm_coul_charmm.cpp
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rm -f ../pair_lj_charmm_coul_charmm_implicit.cpp
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rm -f ../pair_lj_cut_tip4p_cut.cpp
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rm -f ../angle_charmm.h
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rm -f ../angle_cosine.h
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@ -139,5 +142,6 @@ elif (test $1 = 0) then
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rm -f ../pair_hbond_dreiding_morse.h
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rm -f ../pair_lj_charmm_coul_charmm.h
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rm -f ../pair_lj_charmm_coul_charmm_implicit.h
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rm -f ../pair_lj_cut_tip4p_cut.h
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fi
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@ -0,0 +1,669 @@
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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: Pavel Elkind (Gothenburg University)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "pair_lj_cut_tip4p_cut.h"
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#include "atom.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 "domain.h"
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#include "angle.h"
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#include "bond.h"
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#include "comm.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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/* ---------------------------------------------------------------------- */
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PairLJCutTIP4PCut::PairLJCutTIP4PCut(LAMMPS *lmp) : Pair(lmp)
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{
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single_enable = 0;
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nmax = 0;
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hneigh = NULL;
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newsite = NULL;
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// TIP4P cannot compute virial as F dot r
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// due to finding bonded H atoms which are not near O atom
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no_virial_fdotr_compute = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairLJCutTIP4PCut::~PairLJCutTIP4PCut()
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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(cut_lj);
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memory->destroy(cut_ljsq);
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memory->destroy(epsilon);
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memory->destroy(sigma);
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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(offset);
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}
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memory->destroy(hneigh);
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memory->destroy(newsite);
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCutTIP4PCut::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;
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double rsq,r2inv,r6inv,forcecoul,forcelj,factor_lj,factor_coul;
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int *ilist,*jlist,*numneigh,**firstneigh;
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int key;
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int n,vlist[6];
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int iH1,iH2,jH1,jH2;
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double cforce;
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double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3];
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double *x1,*x2;
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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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// reallocate hneigh & newsite if necessary
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// initialize hneigh[0] to -1 on steps when reneighboring occurred
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// initialize hneigh[2] to 0 every step
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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if (atom->nmax > nmax) {
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nmax = atom->nmax;
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memory->destroy(hneigh);
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memory->create(hneigh,nmax,3,"pair:hneigh");
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memory->destroy(newsite);
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memory->create(newsite,nmax,3,"pair:newsite");
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}
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if (neighbor->ago == 0)
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for (i = 0; i < nall; i++) hneigh[i][0] = -1;
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for (i = 0; i < nall; i++) hneigh[i][2] = 0;
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double **f = atom->f;
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double **x = atom->x;
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double *q = atom->q;
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int *type = atom->type;
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double *special_lj = force->special_lj;
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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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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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if (itype == typeO) {
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if (hneigh[i][0] < 0) {
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hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
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hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
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hneigh[i][2] = 1;
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if (iH1 == -1 || iH2 == -1)
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error->one(FLERR,"TIP4P hydrogen is missing");
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if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
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error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
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compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
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} else {
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iH1 = hneigh[i][0];
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iH2 = hneigh[i][1];
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if (hneigh[i][2] == 0) {
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hneigh[i][2] = 1;
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compute_newsite(x[i],x[iH1],x[iH2],newsite[i]);
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}
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}
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x1 = newsite[i];
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} else x1 = x[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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// LJ interaction based on true rsq
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if (rsq < cut_ljsq[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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forcelj *= factor_lj * r2inv;
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f[i][0] += delx*forcelj;
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f[i][1] += dely*forcelj;
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f[i][2] += delz*forcelj;
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f[j][0] -= delx*forcelj;
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f[j][1] -= dely*forcelj;
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f[j][2] -= delz*forcelj;
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if (eflag) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
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offset[itype][jtype];
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evdwl *= factor_lj;
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} else evdwl = 0.0;
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,forcelj,delx,dely,delz);
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}
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// adjust rsq and delxyz for off-site O charge(s) if necessary
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// but only if they are within reach
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if (rsq < cut_coulsqplus) {
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if (itype == typeO || jtype == typeO) {
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// if atom J = water O, set x2 = offset charge site
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// else x2 = x of atom J
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if (jtype == typeO) {
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if (hneigh[j][0] < 0) {
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hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
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hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
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hneigh[j][2] = 1;
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if (jH1 == -1 || jH2 == -1)
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error->one(FLERR,"TIP4P hydrogen is missing");
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if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
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error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
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compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
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} else {
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jH1 = hneigh[j][0];
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jH2 = hneigh[j][1];
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if (hneigh[j][2] == 0) {
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hneigh[j][2] = 1;
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compute_newsite(x[j],x[jH1],x[jH2],newsite[j]);
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}
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}
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x2 = newsite[j];
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} else x2 = x[j];
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delx = x1[0] - x2[0];
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dely = x1[1] - x2[1];
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delz = x1[2] - x2[2];
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rsq = delx*delx + dely*dely + delz*delz;
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}
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// Coulombic interaction based on modified rsq
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if (rsq < cut_coulsq) {
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r2inv = 1.0 / rsq;
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forcecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv);
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cforce = factor_coul * forcecoul * r2inv;
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// if i,j are not O atoms, force is applied directly;
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// if i or j are O atoms, force is on fictitious atom & partitioned
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// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
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// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
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// preserves total force and torque on water molecule
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// virial = sum(r x F) where each water's atoms are near xi and xj
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// vlist stores 2,4,6 atoms whose forces contribute to virial
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n = 0;
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key = 0;
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if (itype != typeO) {
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f[i][0] += delx * cforce;
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f[i][1] += dely * cforce;
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f[i][2] += delz * cforce;
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if (vflag) {
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v[0] = x[i][0] * delx * cforce;
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v[1] = x[i][1] * dely * cforce;
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v[2] = x[i][2] * delz * cforce;
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v[3] = x[i][0] * dely * cforce;
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v[4] = x[i][0] * delz * cforce;
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v[5] = x[i][1] * delz * cforce;
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}
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vlist[n++] = i;
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} else {
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key++;
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fd[0] = delx*cforce;
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fd[1] = dely*cforce;
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fd[2] = delz*cforce;
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fO[0] = fd[0]*(1.0 - alpha);
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fO[1] = fd[1]*(1.0 - alpha);
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fO[2] = fd[2]*(1.0 - alpha);
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fH[0] = 0.5 * alpha * fd[0];
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fH[1] = 0.5 * alpha * fd[1];
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fH[2] = 0.5 * alpha * fd[2];
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f[i][0] += fO[0];
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f[i][1] += fO[1];
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f[i][2] += fO[2];
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f[iH1][0] += fH[0];
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f[iH1][1] += fH[1];
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f[iH1][2] += fH[2];
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f[iH2][0] += fH[0];
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f[iH2][1] += fH[1];
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f[iH2][2] += fH[2];
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if(vflag) {
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domain->closest_image(x[i],x[iH1],xH1);
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domain->closest_image(x[i],x[iH2],xH2);
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v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
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v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
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v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
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v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
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v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
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v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
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}
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vlist[n++] = i;
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vlist[n++] = iH1;
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vlist[n++] = iH2;
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}
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if (jtype != typeO) {
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f[j][0] -= delx * cforce;
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f[j][1] -= dely * cforce;
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f[j][2] -= delz * cforce;
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if (vflag) {
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v[0] -= x[j][0] * delx * cforce;
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v[1] -= x[j][1] * dely * cforce;
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v[2] -= x[j][2] * delz * cforce;
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v[3] -= x[j][0] * dely * cforce;
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v[4] -= x[j][0] * delz * cforce;
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v[5] -= x[j][1] * delz * cforce;
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}
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vlist[n++] = j;
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} else {
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key += 2;
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fd[0] = -delx*cforce;
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fd[1] = -dely*cforce;
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fd[2] = -delz*cforce;
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fO[0] = fd[0]*(1 - alpha);
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fO[1] = fd[1]*(1 - alpha);
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fO[2] = fd[2]*(1 - alpha);
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fH[0] = 0.5 * alpha * fd[0];
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fH[1] = 0.5 * alpha * fd[1];
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fH[2] = 0.5 * alpha * fd[2];
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f[j][0] += fO[0];
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f[j][1] += fO[1];
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f[j][2] += fO[2];
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f[jH1][0] += fH[0];
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f[jH1][1] += fH[1];
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f[jH1][2] += fH[2];
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f[jH2][0] += fH[0];
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f[jH2][1] += fH[1];
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f[jH2][2] += fH[2];
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if (vflag) {
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domain->closest_image(x[j],x[jH1],xH1);
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domain->closest_image(x[j],x[jH2],xH2);
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v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
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v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
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v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
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v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
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v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
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v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
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}
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vlist[n++] = j;
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vlist[n++] = jH1;
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vlist[n++] = jH2;
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}
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if (eflag) {
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ecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv);
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ecoul *= factor_coul;
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} else ecoul = 0.0;
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if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha);
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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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allocate all arrays
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------------------------------------------------------------------------- */
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void PairLJCutTIP4PCut::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(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 7) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
typeO = force->inumeric(arg[0]);
|
||||
typeH = force->inumeric(arg[1]);
|
||||
typeB = force->inumeric(arg[2]);
|
||||
typeA = force->inumeric(arg[3]);
|
||||
qdist = force->numeric(arg[4]);
|
||||
|
||||
cut_lj_global = force->numeric(arg[5]);
|
||||
cut_coul = force->numeric(arg[6]);
|
||||
cut_coulsq = cut_coul * cut_coul;
|
||||
cut_coulsqplus = (cut_coul + 2.0*qdist) * (cut_coul + 2.0*qdist);
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i+1; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(arg[2]);
|
||||
double sigma_one = force->numeric(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;
|
||||
cut_lj[i][j] = cut_lj_global;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::init_style()
|
||||
{
|
||||
if (atom->tag_enable == 0)
|
||||
error->all(FLERR,"Pair style lj/cut/coul/cut/tip4p requires atom IDs");
|
||||
if (!force->newton_pair)
|
||||
error->all(FLERR,
|
||||
"Pair style lj/cut/coul/cut/tip4p requires newton pair on");
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,
|
||||
"Pair style lj/cut/coul/cut/tip4p requires atom attribute q");
|
||||
if (force->bond == NULL)
|
||||
error->all(FLERR,"Must use a bond style with TIP4P potential");
|
||||
if (force->angle == NULL)
|
||||
error->all(FLERR,"Must use an angle style with TIP4P potential");
|
||||
|
||||
neighbor->request(this);
|
||||
|
||||
// set alpha parameter
|
||||
|
||||
double theta = force->angle->equilibrium_angle(typeA);
|
||||
double blen = force->bond->equilibrium_distance(typeB);
|
||||
alpha = qdist / (cos(0.5*theta) * blen);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutTIP4PCut::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]);
|
||||
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
|
||||
}
|
||||
|
||||
// include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
|
||||
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);
|
||||
|
||||
if (offset_flag) {
|
||||
double ratio = sigma[i][j] / cut_lj[i][j];
|
||||
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
cut_ljsq[j][i] = cut_ljsq[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];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// check that LJ epsilon = 0.0 for water H
|
||||
// set LJ cutoff to 0.0 for any interaction involving water H
|
||||
// so LJ term isn't calculated in compute()
|
||||
|
||||
if ((i == typeH && epsilon[i][i] != 0.0) ||
|
||||
(j == typeH && epsilon[j][j] != 0.0))
|
||||
error->all(FLERR,"Water H epsilon must be 0.0 for "
|
||||
"pair style lj/cut/coul/long/tip4p");
|
||||
|
||||
if (i == typeH || j == typeH)
|
||||
cut_ljsq[j][i] = cut_ljsq[i][j] = 0.0;
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::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(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::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(&cut_lj[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(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&typeO,sizeof(int),1,fp);
|
||||
fwrite(&typeH,sizeof(int),1,fp);
|
||||
fwrite(&typeB,sizeof(int),1,fp);
|
||||
fwrite(&typeA,sizeof(int),1,fp);
|
||||
fwrite(&qdist,sizeof(double),1,fp);
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul,sizeof(double),1,fp);
|
||||
fwrite(&cut_coulsq,sizeof(double),1,fp);
|
||||
fwrite(&cut_coulsqplus,sizeof(double),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&typeO,sizeof(int),1,fp);
|
||||
fread(&typeH,sizeof(int),1,fp);
|
||||
fread(&typeB,sizeof(int),1,fp);
|
||||
fread(&typeA,sizeof(int),1,fp);
|
||||
fread(&qdist,sizeof(double),1,fp);
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul,sizeof(double),1,fp);
|
||||
fread(&cut_coulsq,sizeof(double),1,fp);
|
||||
fread(&cut_coulsqplus,sizeof(double),1,fp);
|
||||
}
|
||||
|
||||
MPI_Bcast(&typeO,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&typeH,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&typeB,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&typeA,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&qdist,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coulsq,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coulsqplus,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute position xM of fictitious charge site for O atom and 2 H atoms
|
||||
return it as xM
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PCut::compute_newsite(double *xO, double *xH1,
|
||||
double *xH2, double *xM)
|
||||
{
|
||||
double delx1 = xH1[0] - xO[0];
|
||||
double dely1 = xH1[1] - xO[1];
|
||||
double delz1 = xH1[2] - xO[2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
double delx2 = xH2[0] - xO[0];
|
||||
double dely2 = xH2[1] - xO[1];
|
||||
double delz2 = xH2[2] - xO[2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2);
|
||||
xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2);
|
||||
xM[2] = xO[2] + alpha * 0.5 * (delz1 + delz2);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of hneigh
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutTIP4PCut::memory_usage()
|
||||
{
|
||||
double bytes = maxeatom * sizeof(double);
|
||||
bytes += maxvatom*6 * sizeof(double);
|
||||
bytes += 2 * nmax * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/tip4p/cut,PairLJCutTIP4PCut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_TIP4P_CUT_H
|
||||
#define LMP_PAIR_LJ_CUT_TIP4P_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutTIP4PCut : public Pair {
|
||||
public:
|
||||
PairLJCutTIP4PCut(class LAMMPS *);
|
||||
virtual ~PairLJCutTIP4PCut();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double memory_usage();
|
||||
|
||||
protected:
|
||||
double cut_lj_global,cut_coul_global;
|
||||
double cut_coul,cut_coulsq;
|
||||
double cut_coulsqplus; // extended value for cut_coulsq
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4,**offset;
|
||||
|
||||
int typeH,typeO; // atom types of TIP4P water H and O atoms
|
||||
int typeA,typeB; // angle and bond types of TIP4P water
|
||||
double alpha; // geometric constraint parameter for TIP4P
|
||||
double qdist;
|
||||
|
||||
int nmax; // info on off-oxygen charge sites
|
||||
int **hneigh; // 0,1 = indices of 2 H associated with O
|
||||
// 2 = 0 if site loc not yet computed, 1 if yes
|
||||
double **newsite; // locations of charge sites
|
||||
|
||||
void allocate();
|
||||
void compute_newsite(double *, double *, double *, double *);
|
||||
};
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue