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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10277 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-07-22 22:54:22 +00:00
parent bec0c049d8
commit c102c621e3
17 changed files with 220 additions and 15 deletions
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2
src/CLASS2/angle_class2.cpp
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@ -419,7 +419,7 @@ void AngleClass2::write_data(FILE *fp)
fprintf(fp,"\nBondAngle Coeffs\n\n");
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g %g %g %gx\n",i,ba_k1[i],ba_k2[i],ba_r1[i],ba_r2[i]);
fprintf(fp,"%d %g %g %g %g\n",i,ba_k1[i],ba_k2[i],ba_r1[i],ba_r2[i]);
}
/* ---------------------------------------------------------------------- */

44
src/CLASS2/dihedral_class2.cpp
View File

@ -37,7 +37,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
DihedralClass2::DihedralClass2(LAMMPS *lmp) : Dihedral(lmp) {}
DihedralClass2::DihedralClass2(LAMMPS *lmp) : Dihedral(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -913,3 +916,42 @@ void DihedralClass2::read_restart(FILE *fp)
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralClass2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g\n",
i,k1[i],phi1[i],k2[i],phi2[i],k3[i],phi3[i]);
fprintf(fp,"\nAngleAngleTorsion Coeffs\n\n");
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,aat_k[i],
aat_theta0_1[i]*180.0/MY_PI,aat_theta0_2[i]*180.0/MY_PI);
fprintf(fp,"\nEndBondTorsion Coeffs\n\n");
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g %g %g\n",i,
ebt_f1_1[i],ebt_f2_1[i],ebt_f3_1[i],
ebt_f1_2[i],ebt_f2_2[i],ebt_f3_2[i],
ebt_r0_1[i],ebt_r0_2[i]);
fprintf(fp,"\nMiddleBondTorsion Coeffs\n\n");
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,mbt_f1[i],mbt_f2[i],mbt_f3[i],mbt_r0[i]);
fprintf(fp,"\nBondBond13 Coeffs\n\n");
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g\n",i,bb13t_k[i],bb13t_r10[i],bb13t_r30[i]);
fprintf(fp,"\nAngleTorsion Coeffs\n\n");
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g %g %g\n",i,
at_f1_1[i],at_f2_1[i],at_f3_1[i],
at_f1_2[i],at_f2_2[i],at_f3_2[i],
at_theta0_1[i]*180.0/MY_PI,at_theta0_2[i]*180.0/MY_PI);
}

3
src/CLASS2/dihedral_class2.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
@ -33,6 +33,7 @@ class DihedralClass2 : public Dihedral {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
double *k1,*k2,*k3;

21
src/CLASS2/improper_class2.cpp
View File

@ -36,7 +36,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp) {}
ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -835,3 +838,19 @@ double ImproperClass2::dot(double *a, double *b)
{
return (a[0]*b[0] + a[1]*b[1] + a[2]*b[2]);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void ImproperClass2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nimpropertypes; i++)
fprintf(fp,"%d %g %g\n",i,k0[i],chi0[i]);
fprintf(fp,"\nAngleAngle Coeffs\n\n");
for (int i = 1; i <= atom->nimpropertypes; i++)
fprintf(fp,"%d %g %g %g %g %g %g\n",i,aa_k1[i],aa_k2[i],aa_k3[i],
aa_theta0_1[i]*180.0/MY_PI,aa_theta0_2[i]*180.0/MY_PI,
aa_theta0_3[i]*180.0/MY_PI);
}

3
src/CLASS2/improper_class2.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
@ -33,6 +33,7 @@ class ImproperClass2 : public Improper {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
double *k0,*chi0;

27
src/CLASS2/pair_lj_class2.cpp
View File

@ -28,7 +28,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) {}
PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -348,6 +351,28 @@ void PairLJClass2::read_restart_settings(FILE *fp)
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJClass2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJClass2::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\n",i,j,epsilon[i][j],sigma[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,

4
src/CLASS2/pair_lj_class2.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
@ -36,6 +36,8 @@ class PairLJClass2 : 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 *);
double single(int, int, int, int, double, double, double, double &);
protected:

26
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -29,7 +29,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp) {}
PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -406,6 +409,27 @@ void PairLJClass2CoulCut::read_restart_settings(FILE *fp)
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::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\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJClass2CoulCut::single(int i, int j, int itype, int jtype,

4
src/CLASS2/pair_lj_class2_coul_cut.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 PairLJClass2CoulCut : 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 *);
double single(int, int, int, int, double, double, double, double &);
protected:

22
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -42,6 +42,7 @@ using namespace MathConst;
PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
writedata = 1;
ftable = NULL;
}
@ -453,6 +454,27 @@ void PairLJClass2CoulLong::read_restart_settings(FILE *fp)
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::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\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,

4
src/CLASS2/pair_lj_class2_coul_long.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 PairLJClass2CoulLong : 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 *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);

23
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -51,6 +51,7 @@ PairLJCutCoulLong::PairLJCutCoulLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
respa_enable = 1;
writedata = 1;
ftable = NULL;
qdist = 0.0;
}
@ -880,6 +881,28 @@ void PairLJCutCoulLong::read_restart_settings(FILE *fp)
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCutCoulLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCutCoulLong::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\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulLong::single(int i, int j, int itype, int jtype,

4
src/KSPACE/pair_lj_cut_coul_long.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
@ -39,6 +39,8 @@ class PairLJCutCoulLong : public Pair {
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual 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/improper_cvff.cpp
View File

@ -32,7 +32,10 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ImproperCvff::ImproperCvff(LAMMPS *lmp) : Improper(lmp) {}
ImproperCvff::ImproperCvff(LAMMPS *lmp) : Improper(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -343,3 +346,13 @@ void ImproperCvff::read_restart(FILE *fp)
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void ImproperCvff::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nimpropertypes; i++)
fprintf(fp,"%d %g %d %d\n",i,k[i],sign[i],multiplicity[i]);
}

3
src/MOLECULE/improper_cvff.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
@ -33,6 +33,7 @@ class ImproperCvff : public Improper {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
protected:
double *k;

26
src/pair_lj_cut_coul_cut.cpp
View File

@ -30,7 +30,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp) {}
PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
@ -401,6 +404,27 @@ void PairLJCutCoulCut::read_restart_settings(FILE *fp)
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCutCoulCut::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCutCoulCut::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\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulCut::single(int i, int j, int itype, int jtype,

4
src/pair_lj_cut_coul_cut.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 PairLJCutCoulCut : public Pair {
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual 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 *extract(const char *, int &);