mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6659 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
6f1c6fe550
commit
d033f60973
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@ -10,6 +10,7 @@ if (test $1 = 1) then
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cp dihedral_cosine_shift_exp.cpp ..
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cp fix_addtorque.cpp ..
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cp pair_dipole_sf.cpp ..
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cp pair_lj_sf.cpp ..
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cp angle_cosine_shift.h ..
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cp angle_cosine_shift_exp.h ..
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@ -19,6 +20,7 @@ if (test $1 = 1) then
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cp dihedral_cosine_shift_exp.h ..
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cp fix_addtorque.h ..
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cp pair_dipole_sf.h ..
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cp pair_lj_sf.h ..
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elif (test $1 = 0) then
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@ -30,6 +32,7 @@ elif (test $1 = 0) then
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rm -f ../dihedral_cosine_shift_exp.cpp
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rm -f ../fix_addtorque.cpp
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rm -f ../pair_dipole_sf.cpp
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rm -f ../pair_lj_sf.cpp
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rm -f ../angle_cosine_shift.h
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rm -f ../angle_cosine_shift_exp.h
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@ -39,5 +42,6 @@ elif (test $1 = 0) then
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rm -f ../dihedral_cosine_shift_exp.h
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rm -f ../fix_addtorque.h
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rm -f ../pair_dipole_sf.h
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rm -f ../pair_lj_sf.h
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fi
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@ -20,7 +20,8 @@ angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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compute temp/rotate, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8 Aug 11
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compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
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dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
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fix addtorque, Laurent Joly (U Lyon, France), ljoly.ulyon at gmail.com, 8 Aug 11
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fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
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pair dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
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pair lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
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@ -0,0 +1,358 @@
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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: Laurent Joly (U Lyon), ljoly.ulyon at gmail.com
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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 "pair_lj_sf.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 "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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PairLJShiftedForce::PairLJShiftedForce(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairLJShiftedForce::~PairLJShiftedForce()
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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);
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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(foffset);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJShiftedForce::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r2inv,r6inv,forcelj,factor_lj;
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double r,t;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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if (j < nall) factor_lj = 1.0;
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else {
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factor_lj = special_lj[j/nall];
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j %= nall;
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}
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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r = sqrt(rsq);
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t = r/cut[itype][jtype];
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
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t*foffset[itype][jtype];
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fpair = factor_lj*forcelj*r2inv;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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if (eflag) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
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(t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
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evdwl *= factor_lj;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairLJShiftedForce::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(cut,n+1,n+1,"pair:cut");
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memory->create(epsilon,n+1,n+1,"pair:epsilon");
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memory->create(sigma,n+1,n+1,"pair:sigma");
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memory->create(lj1,n+1,n+1,"pair:lj1");
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memory->create(lj3,n+1,n+1,"pair:lj2");
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memory->create(lj3,n+1,n+1,"pair:lj3");
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memory->create(lj4,n+1,n+1,"pair:lj4");
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memory->create(foffset,n+1,n+1,"pair:foffset");
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memory->create(offset,n+1,n+1,"pair:offset");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairLJShiftedForce::settings(int narg, char **arg)
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{
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if (narg != 1) error->all("Illegal pair_style command");
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cut_global = force->numeric(arg[0]);
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if (cut_global <= 0.0)
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error->all("Illegal pair_style command");
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairLJShiftedForce::coeff(int narg, char **arg)
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{
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if (narg < 4 || narg > 5) error->all("Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double epsilon_one = force->numeric(arg[2]);
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double sigma_one = force->numeric(arg[3]);
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double cut_one = cut_global;
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if (narg == 5) cut_one = force->numeric(arg[4]);
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if (cut_one <= 0.0)
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error->all("Incorrect args for pair coefficients");
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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epsilon[i][j] = epsilon_one;
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sigma[i][j] = sigma_one;
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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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if (count == 0) error->all("Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairLJShiftedForce::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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sigma[i][i],sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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double ratio = sigma[i][j] / cut[i][j];
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foffset[i][j] = 4.0 * epsilon[i][j] * (12.0 * pow(ratio,12.0) -
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6.0 * pow(ratio,6.0));
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offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
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cut[j][i] = cut[i][j];
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lj1[j][i] = lj1[i][j];
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lj2[j][i] = lj2[i][j];
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lj3[j][i] = lj3[i][j];
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lj4[j][i] = lj4[i][j];
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foffset[j][i] = foffset[i][j];
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offset[j][i] = offset[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairLJShiftedForce::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&epsilon[i][j],sizeof(double),1,fp);
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fwrite(&sigma[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairLJShiftedForce::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (setflag[i][j]) {
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if (me == 0) {
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fread(&epsilon[i][j],sizeof(double),1,fp);
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fread(&sigma[i][j],sizeof(double),1,fp);
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fread(&cut[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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}
|
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}
|
||||
}
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||||
|
||||
/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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||||
------------------------------------------------------------------------- */
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void PairLJShiftedForce::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
|
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}
|
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|
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
|
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------------------------------------------------------------------------- */
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|
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void PairLJShiftedForce::read_restart_settings(FILE *fp)
|
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{
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int me = comm->me;
|
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if (me == 0) {
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fread(&cut_global,sizeof(double),1,fp);
|
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fread(&offset_flag,sizeof(int),1,fp);
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fread(&mix_flag,sizeof(int),1,fp);
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}
|
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
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}
|
||||
|
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/* ---------------------------------------------------------------------- */
|
||||
|
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double PairLJShiftedForce::single(int i, int j, int itype, int jtype, double rsq,
|
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double factor_coul, double factor_lj,
|
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double &fforce)
|
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{
|
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double r2inv,r6inv,forcelj,philj,r,t;
|
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|
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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r = sqrt(rsq);
|
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t = r/cut[itype][jtype];
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) -
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t*foffset[itype][jtype];
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fforce = factor_lj*forcelj*r2inv;
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|
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philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
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(t-1.0)*foffset[itype][jtype] - offset[itype][jtype];
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return factor_lj*philj;
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}
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|
|
@ -0,0 +1,53 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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
|
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|
||||
PairStyle(lj/sf,PairLJShiftedForce)
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|
||||
#else
|
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|
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#ifndef LMP_PAIR_LJ_SF_H
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#define LMP_PAIR_LJ_SF_H
|
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|
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#include "pair.h"
|
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|
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namespace LAMMPS_NS {
|
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|
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class PairLJShiftedForce : public Pair {
|
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public:
|
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PairLJShiftedForce(class LAMMPS *);
|
||||
virtual ~PairLJShiftedForce();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
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double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4,**foffset,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue