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import updated pair lj/sf/dipole/sf files from sam genheden 

(cherry picked from commit ae691ab786)
This commit is contained in:
Axel Kohlmeyer 2016-08-09 09:33:15 -04:00
parent c3e8cb2f30
commit 8b1ef1c686
2 changed files with 124 additions and 8 deletions
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127
src/USER-MISC/pair_lj_sf_dipole_sf.cpp
View File

@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mario Orsi (U Southampton), orsimario@gmail.com
Contributing authors: Mario Orsi (QMUL), m.orsi@qmul.ac.uk
Samuel Genheden (University of Southampton)
------------------------------------------------------------------------- */
#include <math.h>
@ -34,7 +35,6 @@ using namespace LAMMPS_NS;
PairLJSFDipoleSF::PairLJSFDipoleSF(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
}
/* ---------------------------------------------------------------------- */
@ -55,6 +55,7 @@ PairLJSFDipoleSF::~PairLJSFDipoleSF()
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(scale);
}
}
@ -86,6 +87,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
double **torque = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
// The global scaling parameters aren't used anymore
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
@ -234,7 +236,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
// total force
fq = factor_coul*qqrd2e;
fq = factor_coul*qqrd2e*scale[itype][jtype];
fx = fq*forcecoulx + delx*forcelj;
fy = fq*forcecouly + dely*forcelj;
fz = fq*forcecoulz + delz*forcelj;
@ -268,7 +270,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag)
ecoul += -q[j] * r3inv * pqfac * pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp * r3inv * qpfac * pjdotr;
ecoul *= factor_coul*qqrd2e;
ecoul *= factor_coul*qqrd2e*scale[itype][jtype];
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
@ -315,6 +317,7 @@ void PairLJSFDipoleSF::allocate()
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(scale,n+1,n+1,"pair:scale");
}
/* ----------------------------------------------------------------------
@ -352,7 +355,7 @@ void PairLJSFDipoleSF::settings(int narg, char **arg)
void PairLJSFDipoleSF::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 6)
if (narg < 4 || narg > 7)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@ -363,10 +366,13 @@ void PairLJSFDipoleSF::coeff(int narg, char **arg)
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double scale_one = 1.0;
if (narg >= 5) scale_one = force->numeric(FLERR,arg[4]);
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
if (narg >= 5) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[4]);
if (narg == 6) cut_coul_one = force->numeric(FLERR,arg[5]);
if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]);
if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
@ -376,6 +382,7 @@ void PairLJSFDipoleSF::coeff(int narg, char **arg)
cut_lj[i][j] = cut_lj_one;
cut_coul[i][j] = cut_coul_one;
setflag[i][j] = 1;
scale[i][j] = scale_one;
count++;
}
}
@ -424,6 +431,7 @@ double PairLJSFDipoleSF::init_one(int i, int j)
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
scale[j][i] = scale[i][j];
return cut;
}
@ -445,6 +453,7 @@ void PairLJSFDipoleSF::write_restart(FILE *fp)
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
fwrite(&scale[i][j],sizeof(double),1,fp);
}
}
}
@ -471,11 +480,13 @@ void PairLJSFDipoleSF::read_restart(FILE *fp)
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
fread(&scale[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);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -506,3 +517,105 @@ void PairLJSFDipoleSF::read_restart_settings(FILE *fp)
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
// PairLJSFDipoleSF: calculation of force is missing (to be implemented)
double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv;
double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv;
double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl;
double **x = atom->x;
double *q = atom->q;
double **mu = atom->mu;
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
fforce = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
// if (qtmp != 0.0 && q[j] != 0.0) {
// pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
// forcecoulx += pre1*delx;
// forcecouly += pre1*dely;
// forcecoulz += pre1*delz;
// }
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
}
if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
}
if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
}
}
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
}
double eng = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = (1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype]));
ecoul *= ecoul;
ecoul *= qtmp * q[j] * rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j] * r3inv * pqfac * pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp * r3inv * qpfac * pjdotr;
ecoul *= factor_coul*force->qqrd2e*scale[itype][jtype];
eng += ecoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
rsq*rcutlj2inv+
rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
eng += evdwl*factor_lj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairLJSFDipoleSF::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"scale") == 0) return (void *) scale;
return NULL;
}

5
src/USER-MISC/pair_lj_sf_dipole_sf.h
View File

@ -1,4 +1,4 @@
/* -*- c++ -*- ----------------------------------------------------------
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@ -37,6 +37,8 @@ class PairLJSFDipoleSF : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
protected:
double cut_lj_global,cut_coul_global;
@ -44,6 +46,7 @@ class PairLJSFDipoleSF : public Pair {
double **cut_coul,**cut_coulsq;
double **epsilon,**sigma;
double **lj1,**lj2,**lj3,**lj4;
double **scale;
void allocate();
};