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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10289 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-07-23 15:16:11 +00:00
parent fd39535f88
commit 2584cbe902
6 changed files with 73 additions and 4 deletions
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25
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -52,6 +52,7 @@ PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp)
ftable = NULL;
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -920,6 +921,30 @@ void PairLJCharmmCoulLong::read_restart_settings(FILE *fp)
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",
i,epsilon[i][i],sigma[i][i],eps14[i][i],sigma14[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::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\n",i,j,
epsilon[i][j],sigma[i][j],eps14[i][j],sigma14[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,

4
src/KSPACE/pair_lj_charmm_coul_long.h
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@ -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
@ -39,6 +39,8 @@ class PairLJCharmmCoulLong : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
void compute_inner();

15
src/MOLECULE/dihedral_charmm.cpp
View File

@ -41,6 +41,7 @@ using namespace MathConst;
DihedralCharmm::DihedralCharmm(LAMMPS *lmp) : Dihedral(lmp)
{
weightflag = 0;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -394,6 +395,7 @@ void DihedralCharmm::write_restart(FILE *fp)
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
fwrite(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
fwrite(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&weightflag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
@ -409,11 +411,13 @@ void DihedralCharmm::read_restart(FILE *fp)
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&weightflag,sizeof(int),1,fp);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&shift[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&weight[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&weightflag,1,MPI_INT,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
@ -421,3 +425,14 @@ void DihedralCharmm::read_restart(FILE *fp)
sin_shift[i] = sin(MY_PI*shift[i]/180.0);
}
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralCharmm::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
}

3
src/MOLECULE/dihedral_charmm.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
@ -34,6 +34,7 @@ class DihedralCharmm : public Dihedral {
void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
double *k,*weight,*cos_shift,*sin_shift;

26
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
View File

@ -36,6 +36,7 @@ PairLJCharmmCoulCharmm::PairLJCharmmCoulCharmm(LAMMPS *lmp) : Pair(lmp)
{
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -104,6 +105,7 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jtype = type[j];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
@ -129,7 +131,6 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
@ -392,6 +393,29 @@ void PairLJCharmmCoulCharmm::read_restart(FILE *fp)
}
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulCharmm::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",
i,epsilon[i][i],sigma[i][i],eps14[i][i],sigma14[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulCharmm::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\n",i,j,
epsilon[i][j],sigma[i][j],eps14[i][j],sigma14[i][j]);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */

4
src/MOLECULE/pair_lj_charmm_coul_charmm.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 PairLJCharmmCoulCharmm : public Pair {
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
virtual void *extract(const char *, int &);