forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15082 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
fde2d583e5
commit
7e7450948c
|
|
@ -46,8 +46,6 @@ action pair_lj_cut_soft.cpp
|
|||
action pair_lj_cut_soft.h
|
||||
action pair_lj_cut_tip4p_long_soft.cpp pppm_tip4p.cpp
|
||||
action pair_lj_cut_tip4p_long_soft.h pppm_tip4p.cpp
|
||||
action pair_morse_soft.cpp
|
||||
action pair_morse_soft.h
|
||||
action pair_tip4p_long_soft.cpp pppm_tip4p.cpp
|
||||
action pair_tip4p_long_soft.h pppm_tip4p.cpp
|
||||
|
||||
|
|
|
|||
|
|
@ -11,8 +11,3 @@ There are auxiliary tools for using this package in tools/fep.
|
|||
The person who created this package is Agilio Padua at Université
|
||||
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
|
||||
Contact him directly if you have questions.
|
||||
|
||||
Pair style morse/soft was contributed by Stefan Paquay, s.paquay at tue.nl
|
||||
Applied Physics/Theory of Polymers and Soft Matter,
|
||||
Eindhoven University of Technology (TU/e), The Netherlands
|
||||
Contact him in case of problems with this pair style.
|
||||
|
|
|
|||
|
|
@ -1,350 +0,0 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_morse_soft.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Stefan Paquay (TU/e)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairMorseSoft::~PairMorseSoft()
|
||||
{
|
||||
if(allocated){
|
||||
memory->destroy(lambda);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r,dr,dexp,factor_lj;
|
||||
double dp,la,Vp,Vp2,Vpp;
|
||||
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
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];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
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]) {
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[itype][jtype];
|
||||
dexp = exp(alpha[itype][jtype] * dr); // Careful, 1/(original thing)!
|
||||
|
||||
la = 1.0 - lambda[itype][jtype];
|
||||
la *= la;
|
||||
la *= alpha[itype][jtype];
|
||||
|
||||
Vp = 1.0 / ( la + dexp );
|
||||
Vpp = alpha[itype][jtype]*dexp;
|
||||
Vp2 = Vp*Vp;
|
||||
|
||||
dp = d0[itype][jtype]*pow(lambda[itype][jtype],power);
|
||||
|
||||
fpair = dp*2.0*Vp2*( Vp - 1.0 );
|
||||
fpair *= factor_lj*Vpp/r;
|
||||
|
||||
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) {
|
||||
evdwl = dp*Vp*(Vp - 2.0);
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::allocate()
|
||||
{
|
||||
PairMorse::allocate();
|
||||
int n = atom->ntypes;
|
||||
memory->create(lambda,n+1,n+1,"pair:lambda");
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 6 || narg > 7) 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 d0_one = force->numeric(FLERR,arg[2]);
|
||||
double alpha_one = force->numeric(FLERR,arg[3]);
|
||||
double r0_one = force->numeric(FLERR,arg[4]);
|
||||
double lambda_one = force->numeric(FLERR,arg[5]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 7) cut_one = force->numeric(FLERR,arg[6]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
d0[i][j] = d0_one;
|
||||
alpha[i][j] = alpha_one;
|
||||
r0[i][j] = r0_one;
|
||||
lambda[i][j] = lambda_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Set global stuff.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
power = force->inumeric(FLERR,arg[0]);
|
||||
scale = force->numeric(FLERR,arg[1]);
|
||||
cut_global = force->numeric(FLERR,arg[2]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
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[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairMorseSoft::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
|
||||
|
||||
if (offset_flag) {
|
||||
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
|
||||
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
d0[j][i] = d0[i][j];
|
||||
alpha[j][i] = alpha[i][j];
|
||||
r0[j][i] = r0[i][j];
|
||||
morse1[j][i] = morse1[i][j];
|
||||
lambda[j][i] = lambda[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::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(&d0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&alpha[i][j],sizeof(double),1,fp);
|
||||
fwrite(&r0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&lambda[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::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(&d0[i][j],sizeof(double),1,fp);
|
||||
fread(&alpha[i][j],sizeof(double),1,fp);
|
||||
fread(&r0[i][j],sizeof(double),1,fp);
|
||||
fread(&lambda[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i],
|
||||
lambda[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMorseSoft::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",i,d0[i][j],alpha[i][j],r0[i][j],
|
||||
lambda[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairMorseSoft::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r,dr,dexp,phi;
|
||||
double dp,la,Vp,Vp2,Vpp;
|
||||
|
||||
r = sqrt(rsq);
|
||||
dr = r - r0[itype][jtype];
|
||||
dexp = exp(alpha[itype][jtype] * dr); // Careful, 1/(the original thing)!
|
||||
|
||||
la = 1.0 - lambda[itype][jtype];
|
||||
la *= la;
|
||||
la *= alpha[itype][jtype];
|
||||
|
||||
Vp = 1.0 / ( la + dexp );
|
||||
Vpp = alpha[itype][jtype]*dexp;
|
||||
Vp2 = Vp*Vp;
|
||||
|
||||
dp = d0[itype][jtype]*pow(lambda[itype][jtype],power);
|
||||
|
||||
fforce = dp*2.0*Vp2*( Vp - 1.0 );
|
||||
fforce *= factor_lj*Vpp;
|
||||
|
||||
phi = dp*Vp*(Vp - 2.0);
|
||||
|
||||
return factor_lj*phi;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairMorseSoft::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"d0") == 0) return (void *) d0;
|
||||
if (strcmp(str,"r0") == 0) return (void *) r0;
|
||||
if (strcmp(str,"alpha") == 0) return (void *) alpha;
|
||||
if (strcmp(str,"lambda") == 0) return (void *) lambda;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -1,59 +0,0 @@
|
|||
/* -*- 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.
|
||||
------------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Stefan Paquay (Eindhoven University of Technology)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(morse/soft,PairMorseSoft)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_MORSE_SOFT_H
|
||||
#define LMP_PAIR_MORSE_SOFT_H
|
||||
|
||||
#include "pair_morse.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairMorseSoft : public PairMorse {
|
||||
public:
|
||||
PairMorseSoft(class LAMMPS *lmp) : PairMorse(lmp) {};
|
||||
virtual ~PairMorseSoft();
|
||||
virtual void compute(int, int);
|
||||
|
||||
virtual void settings(int, char **);
|
||||
virtual void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual void write_restart(FILE *);
|
||||
virtual void read_restart(FILE *);
|
||||
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double **lambda;
|
||||
|
||||
int power;
|
||||
double scale;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue