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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11644 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-03-19 18:27:22 +00:00
parent 544bf593c5
commit e8154be88c
2 changed files with 15 additions and 6 deletions
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1
src/MANYBODY/pair_airebo.cpp
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@ -25,7 +25,6 @@
#include "pair_airebo.h" #include "pair_airebo.h"
#include "atom.h" #include "atom.h"
#include "neighbor.h" #include "neighbor.h"
#include "neigh_request.h"
#include "force.h" #include "force.h"
#include "comm.h" #include "comm.h"
#include "neighbor.h" #include "neighbor.h"

20
src/MISC/fix_gld.cpp
View File

@ -224,6 +224,8 @@ void FixGLD::initial_integrate(int vflag)
double fran[3], fsum[3], fsumall[3]; double fran[3], fsum[3], fsumall[3];
bigint count; bigint count;
int icoeff;
// update v and x of atoms in group // update v and x of atoms in group
double **x = atom->x; double **x = atom->x;
double **v = atom->v; double **v = atom->v;
@ -231,7 +233,7 @@ void FixGLD::initial_integrate(int vflag)
double *rmass = atom->rmass; double *rmass = atom->rmass;
double *mass = atom->mass; double *mass = atom->mass;
int *type = atom->type; int *type = atom->type;
int *mask = atom->mask; int *mask = atom->mask;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst; if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@ -261,9 +263,10 @@ void FixGLD::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2]; x[i][2] += dtv * v[i][2];
// Advance S by dt // Advance S by dt
icoeff = 0;
for (int k = 0; k < 3*prony_terms; k=k+3) { for (int k = 0; k < 3*prony_terms; k=k+3) {
double theta = exp(-dtv/prony_tau[k]); double theta = exp(-dtv/prony_tau[icoeff]);
double ck = prony_c[k]; double ck = prony_c[icoeff];
double vmult = (theta-1.)*ck/ftm2v; double vmult = (theta-1.)*ck/ftm2v;
double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v; double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
@ -295,6 +298,8 @@ void FixGLD::initial_integrate(int vflag)
s_gld[i][k] += fran[0]; s_gld[i][k] += fran[0];
s_gld[i][k+1] += fran[1]; s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2]; s_gld[i][k+2] += fran[2];
icoeff += 1;
} }
} }
@ -318,9 +323,10 @@ void FixGLD::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2]; x[i][2] += dtv * v[i][2];
// Advance S by dt // Advance S by dt
icoeff = 0;
for (int k = 0; k < 3*prony_terms; k=k+3) { for (int k = 0; k < 3*prony_terms; k=k+3) {
double theta = exp(-dtv/prony_tau[k]); double theta = exp(-dtv/prony_tau[icoeff]);
double ck = prony_c[k]; double ck = prony_c[icoeff];
double vmult = (theta-1.)*ck/ftm2v; double vmult = (theta-1.)*ck/ftm2v;
double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v; double rmult = sqrt(2.0*kT*ck/dtv)*(1.-theta)/ftm2v;
@ -352,6 +358,9 @@ void FixGLD::initial_integrate(int vflag)
s_gld[i][k] += fran[0]; s_gld[i][k] += fran[0];
s_gld[i][k+1] += fran[1]; s_gld[i][k+1] += fran[1];
s_gld[i][k+2] += fran[2]; s_gld[i][k+2] += fran[2];
icoeff += 1;
} }
} }
} }
@ -375,6 +384,7 @@ void FixGLD::initial_integrate(int vflag)
} }
} }
} }
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------