pair style born/coul/dsf added with its coreshell version
This commit is contained in:
arielzn
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -976,6 +976,8 @@
|
||||
/fix_ttm_mod.h
|
||||
/pair_born_coul_long_cs.cpp
|
||||
/pair_born_coul_long_cs.h
|
||||
/pair_born_coul_dsf_cs.cpp
|
||||
/pair_born_coul_dsf_cs.h
|
||||
/pair_buck_coul_long_cs.cpp
|
||||
/pair_buck_coul_long_cs.h
|
||||
/pair_coul_long_cs.cpp
|
||||
|
||||
@ -31,8 +31,10 @@ action () {
|
||||
action compute_temp_cs.cpp
|
||||
action compute_temp_cs.h
|
||||
action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
|
||||
action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp
|
||||
action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
|
||||
action pair_born_coul_long_cs.h pair_born_coul_long.h
|
||||
action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h
|
||||
action pair_buck_coul_long_cs.h pair_buck_coul_long.h
|
||||
action pair_coul_long_cs.cpp pair_coul_long.cpp
|
||||
action pair_coul_long_cs.h pair_coul_long.h
|
||||
|
||||
162
src/CORESHELL/pair_born_coul_dsf_cs.cpp
Normal file
162
src/CORESHELL/pair_born_coul_dsf_cs.cpp
Normal file
@ -0,0 +1,162 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Ariel Lozano (arielzn@gmail.com)
|
||||
References: Fennell and Gezelter, JCP 124, 234104 (2006)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_born_coul_dsf_cs.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "math_special.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define EPSILON 1.0e-20
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBornCoulDSFCS::PairBornCoulDSFCS(LAMMPS *lmp) : PairBornCoulDSF(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
single_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSFCS::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
|
||||
double prefactor,erfcc,erfcd,arg;
|
||||
double rexp;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
double *special_coul = force->special_coul;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
// self coulombic energy
|
||||
if (eflag) {
|
||||
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
}
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = qqrd2e*qtmp*q[j] / r;
|
||||
arg = alpha * r ;
|
||||
erfcd = MathSpecial::expmsq(arg);
|
||||
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
|
||||
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
|
||||
+ born3[itype][jtype]*r2inv*r6inv;
|
||||
} else forceborn = 0.0;
|
||||
|
||||
fpair = (forcecoul + factor_lj*forceborn) * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
|
||||
d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
59
src/CORESHELL/pair_born_coul_dsf_cs.h
Normal file
59
src/CORESHELL/pair_born_coul_dsf_cs.h
Normal file
@ -0,0 +1,59 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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(born/coul/dsf/cs,PairBornCoulDSFCS)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BORN_COUL_DSF_CS_H
|
||||
#define LMP_PAIR_BORN_COUL_DSF_CS_H
|
||||
|
||||
#include "pair_born_coul_dsf.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBornCoulDSFCS : public PairBornCoulDSF {
|
||||
public:
|
||||
PairBornCoulDSFCS(class LAMMPS *);
|
||||
virtual void compute(int, int);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* 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 style born/coul/dsf requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
*/
|
||||
494
src/pair_born_coul_dsf.cpp
Normal file
494
src/pair_born_coul_dsf.cpp
Normal file
@ -0,0 +1,494 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Ariel Lozano (arielzn@gmail.com)
|
||||
References: Fennell and Gezelter, JCP 124, 234104 (2006)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_born_coul_dsf.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "math_special.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBornCoulDSF::PairBornCoulDSF(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
single_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBornCoulDSF::~PairBornCoulDSF()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(a);
|
||||
memory->destroy(rho);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(c);
|
||||
memory->destroy(d);
|
||||
memory->destroy(rhoinv);
|
||||
memory->destroy(born1);
|
||||
memory->destroy(born2);
|
||||
memory->destroy(born3);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
|
||||
double prefactor,erfcc,erfcd,arg;
|
||||
double rexp;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
double *special_coul = force->special_coul;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
// self coulombic energy
|
||||
if (eflag) {
|
||||
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
}
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
arg = alpha * r ;
|
||||
erfcd = MathSpecial::expmsq(arg);
|
||||
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
|
||||
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
|
||||
+ born3[itype][jtype]*r2inv*r6inv;
|
||||
} else forceborn = 0.0;
|
||||
|
||||
fpair = (forcecoul + factor_lj*forceborn) * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
|
||||
d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::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(a,n+1,n+1,"pair:a");
|
||||
memory->create(rho,n+1,n+1,"pair:rho");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(c,n+1,n+1,"pair:c");
|
||||
memory->create(d,n+1,n+1,"pair:d");
|
||||
memory->create(rhoinv,n+1,n+1,"pair:rhoinv");
|
||||
memory->create(born1,n+1,n+1,"pair:born1");
|
||||
memory->create(born2,n+1,n+1,"pair:born2");
|
||||
memory->create(born3,n+1,n+1,"pair:born3");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
alpha = force->numeric(FLERR,arg[0]);
|
||||
cut_lj_global = force->numeric(FLERR,arg[1]);
|
||||
if (narg == 2) cut_coul = cut_lj_global;
|
||||
else cut_coul = force->numeric(FLERR,arg[2]);
|
||||
|
||||
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 PairBornCoulDSF::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 7 || narg > 8)
|
||||
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 a_one = force->numeric(FLERR,arg[2]);
|
||||
double rho_one = force->numeric(FLERR,arg[3]);
|
||||
double sigma_one = force->numeric(FLERR,arg[4]);
|
||||
if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
double c_one = force->numeric(FLERR,arg[5]);
|
||||
double d_one = force->numeric(FLERR,arg[6]);
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
if (narg == 8) cut_lj_one = force->numeric(FLERR,arg[7]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
a[i][j] = a_one;
|
||||
rho[i][j] = rho_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
c[i][j] = c_one;
|
||||
d[i][j] = d_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style born/coul/dsf requires atom attribute q");
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
|
||||
cut_coulsq = cut_coul * cut_coul;
|
||||
double erfcc = erfc(alpha*cut_coul);
|
||||
double erfcd = exp(-alpha*alpha*cut_coul*cut_coul);
|
||||
f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul);
|
||||
e_shift = erfcc/cut_coul - f_shift*cut_coul;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairBornCoulDSF::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
|
||||
rhoinv[i][j] = 1.0/rho[i][j];
|
||||
born1[i][j] = a[i][j]/rho[i][j];
|
||||
born2[i][j] = 6.0*c[i][j];
|
||||
born3[i][j] = 8.0*d[i][j];
|
||||
|
||||
if (offset_flag) {
|
||||
double rexp = exp((sigma[i][j]-cut_lj[i][j])*rhoinv[i][j]);
|
||||
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0)
|
||||
+ d[i][j]/pow(cut_lj[i][j],8.0);
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
cut_ljsq[j][i] = cut_ljsq[i][j];
|
||||
a[j][i] = a[i][j];
|
||||
c[j][i] = c[i][j];
|
||||
d[j][i] = d[i][j];
|
||||
rhoinv[j][i] = rhoinv[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
born1[j][i] = born1[i][j];
|
||||
born2[j][i] = born2[i][j];
|
||||
born3[j][i] = born3[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::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(&a[i][j],sizeof(double),1,fp);
|
||||
fwrite(&rho[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
fwrite(&c[i][j],sizeof(double),1,fp);
|
||||
fwrite(&d[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::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(&a[i][j],sizeof(double),1,fp);
|
||||
fread(&rho[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
fread(&c[i][j],sizeof(double),1,fp);
|
||||
fread(&d[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&d[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 PairBornCoulDSF::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&alpha,sizeof(double),1,fp);
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&alpha,sizeof(double),1,fp);
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&alpha,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(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g %g\n",i,
|
||||
a[i][i],rho[i][i],sigma[i][i],c[i][i],d[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBornCoulDSF::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j,
|
||||
a[i][j],rho[i][j],sigma[i][j],c[i][j],d[i][j],cut_lj[i][j]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
only the pair part is calculated here
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairBornCoulDSF::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,r,prefactor,rexp;
|
||||
double forcecoul,forceborn,phicoul,phiborn;
|
||||
double erfcc,erfcd,arg;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * force->qqrd2e * atom->q[i]*atom->q[j]/r;
|
||||
|
||||
arg = alpha * r ;
|
||||
erfcd = MathSpecial::expmsq(arg);
|
||||
erfcc = MathSpecial::my_erfcx(arg) * erfcd;
|
||||
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS*erfcd +
|
||||
r*f_shift) * r;
|
||||
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
rexp = exp(-r*rhoinv[itype][jtype]);
|
||||
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
|
||||
+ born3[itype][jtype]*r2inv*r6inv;
|
||||
} else forceborn = 0.0;
|
||||
|
||||
fforce = (forcecoul + factor_lj*forceborn) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq) {
|
||||
phicoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
|
||||
eng += phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
|
||||
+ d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
|
||||
eng += factor_lj*phiborn;
|
||||
}
|
||||
return eng;
|
||||
}
|
||||
81
src/pair_born_coul_dsf.h
Normal file
81
src/pair_born_coul_dsf.h
Normal file
@ -0,0 +1,81 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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(born/coul/dsf,PairBornCoulDSF)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BORN_COUL_DSF_H
|
||||
#define LMP_PAIR_BORN_COUL_DSF_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBornCoulDSF : public Pair {
|
||||
public:
|
||||
PairBornCoulDSF(class LAMMPS *);
|
||||
virtual ~PairBornCoulDSF();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global,alpha;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double cut_coul,cut_coulsq;
|
||||
double **a,**rho,**sigma,**c,**d;
|
||||
double **rhoinv,**born1,**born2,**born3,**offset;
|
||||
double f_shift,e_shift;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* 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 style born/coul/dsf requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user