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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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112
src/pair_beck.cpp
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@ -5,7 +5,7 @@
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
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.
@ -59,7 +59,7 @@ void PairBeck::compute(int eflag, int vflag)
double aaij,alphaij,betaij;
double term1,term1inv,term2,term3,term4,term5,term6;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
@ -70,12 +70,12 @@ void PairBeck::compute(int eflag, int vflag)
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++) {
@ -97,10 +97,10 @@ void PairBeck::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
r5 = rsq*rsq*r;
r5 = rsq*rsq*r;
aaij = aa[itype][jtype];
alphaij = alpha[itype][jtype];
betaij = beta[itype][jtype];
@ -108,31 +108,31 @@ void PairBeck::compute(int eflag, int vflag)
term2 = 1.0/pow(term1,5.0);
term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq;
term4 = alphaij + r5*betaij;
term5 = alphaij + 6.0*r5*betaij;
term5 = alphaij + 6.0*r5*betaij;
rinv = 1.0/r;
force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
force_beck -= BB[itype][jtype]*r*term2*term3;
fpair = factor_lj*force_beck*rinv;
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) {
force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5;
force_beck -= BB[itype][jtype]*r*term2*term3;
fpair = factor_lj*force_beck*rinv;
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) {
term6 = 1.0/pow(term1,3.0);
term1inv = 1.0/term1;
evdwl = AA[itype][jtype]*exp(-1.0*r*term4);
evdwl -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv);
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@ -141,7 +141,7 @@ void PairBeck::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairBeck::allocate()
@ -165,7 +165,7 @@ void PairBeck::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairBeck::settings(int narg, char **arg)
@ -180,9 +180,9 @@ void PairBeck::settings(int narg, char **arg)
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;
}
if (setflag[i][j]) {
cut[i][j] = cut_global;
}
}
}
@ -205,7 +205,7 @@ void PairBeck::coeff(int narg, char **arg)
double aa_one = atof(arg[4]);
double alpha_one = atof(arg[5]);
double beta_one = atof(arg[6]);
double cut_one = cut_global;
if (narg == 8) cut_one = atof(arg[7]);
@ -245,7 +245,7 @@ double PairBeck::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBeck::write_restart(FILE *fp)
@ -257,12 +257,12 @@ void PairBeck::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&AA[i][j],sizeof(double),1,fp);
fwrite(&BB[i][j],sizeof(double),1,fp);
fwrite(&aa[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&beta[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&AA[i][j],sizeof(double),1,fp);
fwrite(&BB[i][j],sizeof(double),1,fp);
fwrite(&aa[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&beta[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@ -283,20 +283,20 @@ void PairBeck::read_restart(FILE *fp)
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(&AA[i][j],sizeof(double),1,fp);
fread(&BB[i][j],sizeof(double),1,fp);
fread(&aa[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&beta[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&aa[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&AA[i][j],sizeof(double),1,fp);
fread(&BB[i][j],sizeof(double),1,fp);
fread(&aa[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&beta[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&aa[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -328,10 +328,10 @@ void PairBeck::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairBeck::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
double PairBeck::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double phi_beck,r,rinv;
double r5,force_beck;