Commit 4933685c authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@934 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 9fe0fc37

src/MOLECULE/dump_bond.cpp

+1 −1
Original line number Diff line number Diff line
@@ -30,7 +30,7 @@ DumpBond::DumpBond(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg) 


  size_one = 3;



  char *str = "%d %d %d %d";

  char *str = (char *) "%d %d %d %d";

  int n = strlen(str) + 1;

  format_default = new char[n];

  strcpy(format_default,str);

src/MOLECULE/pair_lj_charmm_coul_charmm.cpp

+44 −38
Original line number Diff line number Diff line
@@ -22,9 +22,9 @@ 
#include "atom.h"

#include "comm.h"

#include "force.h"

#include "update.h"

#include "memory.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "memory.h"

#include "error.h"



using namespace LAMMPS_NS;
@@ -63,19 +63,17 @@ PairLJCharmmCoulCharmm::~PairLJCharmmCoulCharmm() 


void PairLJCharmmCoulCharmm::compute(int eflag, int vflag)

{

  int i,j,k,numneigh,itype,jtype;

  int i,j,ii,jj,inum,jnum,itype,jtype;

  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;

  double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;

  double factor,phicoul,philj,switch1,switch2;

  int *neighs;

  double **f;

  int *ilist,*jlist,*numneigh,**firstneigh;



  eng_vdwl = eng_coul = 0.0;

  if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;



  if (vflag == 2) f = update->f_pair;

  else f = atom->f;

  double **x = atom->x;

  double **f = atom->f;

  double *q = atom->q;

  int *type = atom->type;

  int nlocal = atom->nlocal;
@@ -85,19 +83,25 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag) 
  int newton_pair = force->newton_pair;

  double qqrd2e = force->qqrd2e;



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  // loop over neighbors of my atoms



  for (i = 0; i < nlocal; i++) {

  for (ii = 0; ii < inum; ii++) {

    i = ilist[ii];

    qtmp = q[i];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    itype = type[i];

    neighs = neighbor->firstneigh[i];

    numneigh = neighbor->numneigh[i];

    jlist = firstneigh[i];

    jnum = numneigh[i];



    for (k = 0; k < numneigh; k++) {

      j = neighs[k];

    for (jj = 0; jj < jnum; jj++) {

      j = jlist[jj];



      if (j < nall) factor_coul = factor_lj = 1.0;

      else {
@@ -279,6 +283,34 @@ void PairLJCharmmCoulCharmm::coeff(int narg, char **arg) 
  if (count == 0) error->all("Incorrect args for pair coefficients");

}



/* ----------------------------------------------------------------------

   init specific to this pair style

------------------------------------------------------------------------- */



void PairLJCharmmCoulCharmm::init_style()

{

  if (!atom->q_flag)

    error->all("Pair style lj/charmm/coul/charmm requires atom attribute q");



  int irequest = neighbor->request(this);



  // require cut_lj_inner < cut_lj, cut_coul_inner < cut_coul



  if (cut_lj_inner >= cut_lj || cut_coul_inner >= cut_coul)

    error->all("Pair inner cutoff >= Pair outer cutoff");



  cut_lj_innersq = cut_lj_inner * cut_lj_inner;

  cut_ljsq = cut_lj * cut_lj;

  cut_coul_innersq = cut_coul_inner * cut_coul_inner;

  cut_coulsq = cut_coul * cut_coul;

  cut_bothsq = MAX(cut_ljsq,cut_coulsq);



  denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * 

    (cut_ljsq-cut_lj_innersq);

  denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) * 

    (cut_coulsq-cut_coul_innersq);

}



/* ----------------------------------------------------------------------

   init for one type pair i,j and corresponding j,i

------------------------------------------------------------------------- */
@@ -317,32 +349,6 @@ double PairLJCharmmCoulCharmm::init_one(int i, int j) 
  return cut;

}



/* ----------------------------------------------------------------------

   init specific to this pair style

------------------------------------------------------------------------- */



void PairLJCharmmCoulCharmm::init_style()

{

  if (!atom->q_flag)

    error->all("Pair style lj/charmm/coul/charmm requires atom attribute q");



  // require cut_lj_inner < cut_lj, cut_coul_inner < cut_coul



  if (cut_lj_inner >= cut_lj || cut_coul_inner >= cut_coul)

    error->all("Pair inner cutoff >= Pair outer cutoff");



  cut_lj_innersq = cut_lj_inner * cut_lj_inner;

  cut_ljsq = cut_lj * cut_lj;

  cut_coul_innersq = cut_coul_inner * cut_coul_inner;

  cut_coulsq = cut_coul * cut_coul;

  cut_bothsq = MAX(cut_ljsq,cut_coulsq);



  denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) * 

    (cut_ljsq-cut_lj_innersq);

  denom_coul = (cut_coulsq-cut_coul_innersq) * (cut_coulsq-cut_coul_innersq) * 

    (cut_coulsq-cut_coul_innersq);

}



/* ----------------------------------------------------------------------

  proc 0 writes to restart file

------------------------------------------------------------------------- */

src/MOLECULE/pair_lj_charmm_coul_charmm.h

+1 −1
Original line number Diff line number Diff line
@@ -25,8 +25,8 @@ class PairLJCharmmCoulCharmm : public Pair { 
  virtual void compute(int, int);

  void settings(int, char **);

  void coeff(int, char **);

  double init_one(int, int);

  void init_style();

  double init_one(int, int);

  void write_restart(FILE *);

  void read_restart(FILE *);

  void write_restart_settings(FILE *);

src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp

+15 −12
Original line number Diff line number Diff line
@@ -15,8 +15,7 @@ 
#include "pair_lj_charmm_coul_charmm_implicit.h"

#include "atom.h"

#include "force.h"

#include "update.h"

#include "neighbor.h"

#include "neigh_list.h"



using namespace LAMMPS_NS;
@@ -29,19 +28,17 @@ PairLJCharmmCoulCharmmImplicit::PairLJCharmmCoulCharmmImplicit(LAMMPS *lmp) : 


void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag)

{

  int i,j,k,numneigh,itype,jtype;

  int i,j,ii,jj,inum,jnum,itype,jtype;

  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;

  double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;

  double factor,phicoul,philj,switch1,switch2;

  int *neighs;

  double **f;

  int *ilist,*jlist,*numneigh,**firstneigh;



  eng_vdwl = eng_coul = 0.0;

  if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;



  if (vflag == 2) f = update->f_pair;

  else f = atom->f;

  double **x = atom->x;

  double **f = atom->f;

  double *q = atom->q;

  int *type = atom->type;

  int nlocal = atom->nlocal;
@@ -51,19 +48,25 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag) 
  int newton_pair = force->newton_pair;

  double qqrd2e = force->qqrd2e;



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;

  

  // loop over neighbors of my atoms



  for (i = 0; i < nlocal; i++) {

  for (ii = 0; ii < inum; ii++) {

    i = ilist[ii];

    qtmp = q[i];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    itype = type[i];

    neighs = neighbor->firstneigh[i];

    numneigh = neighbor->numneigh[i];

    jlist = firstneigh[i];

    jnum = numneigh[i];



    for (k = 0; k < numneigh; k++) {

      j = neighs[k];

    for (jj = 0; jj < jnum; jj++) {

      j = jlist[jj];



      if (j < nall) factor_coul = factor_lj = 1.0;

      else {

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