Commit d31eb1a0 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@932 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent bc528eda

src/MANYBODY/pair_airebo.cpp

+69 −43
Original line number Diff line number Diff line
@@ -22,10 +22,13 @@ 
#include "mpi.h"

#include "pair_airebo.h"

#include "atom.h"

#include "neighbor.h"

#include "neigh_request.h"

#include "force.h"

#include "comm.h"

#include "update.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "neigh_request.h"

#include "memory.h"

#include "error.h"
@@ -43,8 +46,6 @@ using namespace LAMMPS_NS; 


PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp)

{

  neigh_half_every = 0;

  neigh_full_every = 1;

  single_enable = 0;

  one_coeff = 1;
@@ -89,9 +90,7 @@ void PairAIREBO::compute(int eflag, int vflag) 
  eng_vdwl = 0.0;

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



  double **f;

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

  else f = atom->f;

  double **f = atom->f;

	

  REBO_neigh();

  FREBO(eflag,f);
@@ -200,6 +199,30 @@ void PairAIREBO::coeff(int narg, char **arg) 
  if (count == 0) error->all("Incorrect args for pair coefficients");

}



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

   init specific to this pair style

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



void PairAIREBO::init_style()

{

  if (atom->tag_enable == 0)

    error->all("Pair style AIREBO requires atom IDs");

  if (force->newton_pair == 0)

    error->all("Pair style AIREBO requires newton pair on");



  // need a full neighbor list



  int irequest = neighbor->request(this);

  neighbor->requests[irequest]->half = 0;

  neighbor->requests[irequest]->full = 1;



  // local REBO neighbor list memory



  pgsize = neighbor->pgsize;

  oneatom = neighbor->oneatom;

  if (maxlocal == 0) add_pages(0);

}



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

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

------------------------------------------------------------------------- */
@@ -262,31 +285,17 @@ double PairAIREBO::init_one(int i, int j) 
  return cutmax;

}



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

   init specific to this pair style

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



void PairAIREBO::init_style()

{

  if (atom->tag_enable == 0)

    error->all("Pair style AIREBO requires atom IDs");

  if (force->newton_pair == 0)

    error->all("Pair style AIREBO requires newton pair on");



  pgsize = neighbor->pgsize;

  oneatom = neighbor->oneatom;

  if (maxlocal == 0) add_pages(0);

}



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

   create REBO neighbor list from main neighbor list

   REBO neighbor list stores neighbors of ghost atoms

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



void PairAIREBO::REBO_neigh()

{

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

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

  double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;

  int *neighptr,*neighs;

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

  int *neighptr;



  double **x = atom->x;

  int *type = atom->type;
@@ -307,6 +316,11 @@ void PairAIREBO::REBO_neigh() 
    nH = new double[maxlocal];

  }

  

  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  // initialize ghost atom references to -1



  for (i = nlocal; i < nall; i++) REBO_numneigh[i] = -1;
@@ -320,7 +334,9 @@ void PairAIREBO::REBO_neigh() 
  npage = 0;

  int npnt = 0;



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

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

    i = ilist[ii];



    if (pgsize - npnt < oneatom) {

      npnt = 0;

      npage++;
@@ -334,11 +350,11 @@ void PairAIREBO::REBO_neigh() 
    ztmp = x[i][2];

    itype = map[type[i]];

    nC[i] = nH[i] = 0.0;

    neighs = neighbor->firstneigh_full[i];

    numneigh = neighbor->numneigh_full[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];

      jtype = map[type[j]];

      delx = xtmp - x[j][0];

      dely = ytmp - x[j][1];
@@ -399,11 +415,11 @@ void PairAIREBO::REBO_neigh() 
    else

      nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);



    neighs = neighbor->firstneigh_full[m];

    numneigh = neighbor->numneigh_full[m];

    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 == i) continue;

      jtype = map[type[j]];

      delx = xtmp - x[j][0];
@@ -503,14 +519,15 @@ void PairAIREBO::FREBO(int eflag, double **f) 


void PairAIREBO::FLJ(int eflag, double **f)

{

  int i,j,k,m,jj,kk,mm,itype,jtype,ktype,mtype;

  int numneigh,atomi,atomj,atomk,atomm;

  int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype;

  int atomi,atomj,atomk,atomm;

  int testpath,npath,done;

  double rsq,best,wik,wkm,cij,rij,dwij,dwik,dwkj,dwkm,dwmj;

  double delij[3],rijsq,delik[3],rik,delkj[3];

  double rkj,wkj,dC,VLJ,dVLJ,fforce,VA,Str,dStr,Stb;

  double delkm[3],rkm,delmj[3],rmj,wmj,r2inv,r6inv,scale,delscale[3];

  int *neighs,*REBO_neighs_i,*REBO_neighs_k;

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

  int *REBO_neighs_i,*REBO_neighs_k;

  double delikS[3],delkjS[3],delkmS[3],delmjS[3];

  double rikS,rkjS,rkmS,rmjS,wikS,dwikS;

  double wkjS,dwkjS,wkmS,dwkmS,wmjS,dwmjS;
@@ -523,13 +540,22 @@ void PairAIREBO::FLJ(int eflag, double **f) 
  int *type = atom->type;

  int nlocal = atom->nlocal;

  

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

  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  // loop over neighbors of my atoms



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

    i = ilist[ii];

    itype = map[type[i]];

    neighs = neighbor->firstneigh_full[i];

    numneigh = neighbor->numneigh_full[i];

    atomi = i;

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

      j = neighs[jj];

    jlist = firstneigh[i];

    jnum = numneigh[i];



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

      j = jlist[jj];

      atomj = j;

      if (tag[i] > tag[j]) continue;

      jtype = map[type[j]];

src/MANYBODY/pair_airebo.h

+1 −1
Original line number Diff line number Diff line
@@ -25,8 +25,8 @@ class PairAIREBO : public Pair { 
  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/MANYBODY/pair_eam.cpp

+38 −29
Original line number Diff line number Diff line
@@ -22,9 +22,9 @@ 
#include "pair_eam.h"

#include "atom.h"

#include "force.h"

#include "update.h"

#include "comm.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "memory.h"

#include "error.h"
@@ -124,12 +124,11 @@ PairEAM::~PairEAM() 


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

{

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

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

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

  double rsq,r,p,fforce,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;

  double *coeff;

  int *neighs;

  double **f;

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



  // grow energy array if necessary
@@ -144,13 +143,17 @@ void PairEAM::compute(int eflag, int vflag) 
  eng_vdwl = 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;

  int *type = atom->type;

  int nlocal = atom->nlocal;

  int newton_pair = force->newton_pair;



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;

  

  // zero out density



  if (newton_pair) {
@@ -161,16 +164,17 @@ void PairEAM::compute(int eflag, int vflag) 
  // rho = density at each atom

  // loop over neighbors of my atoms



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

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

    i = ilist[ii];

    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];



      delx = xtmp - x[j][0];

      dely = ytmp - x[j][1];
@@ -201,7 +205,8 @@ void PairEAM::compute(int eflag, int vflag) 
  // fp = derivative of embedding energy at each atom

  // phi = embedding energy at each atom



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

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

    i = ilist[ii];

    p = rho[i]*rdrho + 1.0;

    m = static_cast<int> (p);

    m = MAX(1,MIN(m,nrho-1));
@@ -219,16 +224,18 @@ void PairEAM::compute(int eflag, int vflag) 
  // compute forces on each atom

  // loop over neighbors of my atoms



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

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

    i = ilist[ii];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    itype = type[i];

    neighs = neighbor->firstneigh[i];

    numneigh = neighbor->numneigh[i];



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

      j = neighs[k];

    jlist = firstneigh[i];

    jnum = numneigh[i];



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

      j = jlist[jj];



      delx = xtmp - x[j][0];

      dely = ytmp - x[j][1];
@@ -382,6 +389,20 @@ void PairEAM::coeff(int narg, char **arg) 
  if (count == 0) error->all("Incorrect args for pair coefficients");

}



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

   init specific to this pair style

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



void PairEAM::init_style()

{

  // convert read-in file(s) to arrays and spline them



  file2array();

  array2spline();



  int irequest = neighbor->request(this);

}



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

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

------------------------------------------------------------------------- */
@@ -404,18 +425,6 @@ double PairEAM::init_one(int i, int j) 
  return cutmax;

}



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

   init specific to this pair style

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



void PairEAM::init_style()

{

  // convert read-in file(s) to arrays and spline them



  file2array();

  array2spline();

}



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

   read potential values from a DYNAMO single element funcfl file

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

src/MANYBODY/pair_eam.h

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

  void settings(int, char **);

  virtual void coeff(int, char **);

  double init_one(int, int);

  void init_style();

  double init_one(int, int);

  void single(int, int, int, int, double, double, double, int, One &);



  void single_embed(int, int, double &);

src/MANYBODY/pair_sw.cpp

+39 −26
Original line number Diff line number Diff line
@@ -21,11 +21,13 @@ 
#include "string.h"

#include "pair_sw.h"

#include "atom.h"

#include "neighbor.h"

#include "neigh_request.h"

#include "force.h"

#include "comm.h"

#include "update.h"

#include "memory.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "memory.h"

#include "error.h"
@@ -38,8 +40,6 @@ using namespace LAMMPS_NS; 


PairSW::PairSW(LAMMPS *lmp) : Pair(lmp)

{

  neigh_half_every = 0;

  neigh_full_every = 1;

  single_enable = 0;

  one_coeff = 1;
@@ -74,23 +74,26 @@ PairSW::~PairSW() 


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

{

  int i,j,k,m,n,itag,jtag,itype,jtype,ktype,iparam,numneigh;

  int i,j,k,ii,jj,kk,inum,jnum,jnumm1,itag,jtag,itype,jtype,ktype,iparam;

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

  double rsq,rsq1,rsq2,eng,fforce;

  double delr1[3],delr2[3],fj[3],fk[3];

  int *neighs;

  double **f;

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



  eng_vdwl = 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;

  int *tag = atom->tag;

  int *type = atom->type;

  int nlocal = atom->nlocal;



  inum = list->inum;

  ilist = list->ilist;

  numneigh = list->numneigh;

  firstneigh = list->firstneigh;



  // loop over full neighbor list of my atoms



  for (i = 0; i < nlocal; i++) {
@@ -102,11 +105,11 @@ void PairSW::compute(int eflag, int vflag) 


    // two-body interactions, skip half of them



    neighs = neighbor->firstneigh_full[i];

    numneigh = neighbor->numneigh_full[i];

    jlist = firstneigh[i];

    jnum = numneigh[i];



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

      j = neighs[m];

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

      j = jlist[jj];

      jtag = tag[j];



      if (itag > jtag) {
@@ -145,12 +148,14 @@ void PairSW::compute(int eflag, int vflag) 
    // cannot test I-J distance against cutoff outside of 2nd loop

    // b/c must use I-J-K cutoff for both rij and rik



    for (m = 0; m < numneigh-1; m++) {

      j = neighs[m];

    jnumm1 = jnum - 1;



    for (jj = 0; jj < jnumm1; jj++) {

      j = jlist[jj];

      jtype = map[type[j]];



      for (n = m+1; n < numneigh; n++) {

	k = neighs[n];

      for (kk = jj+1; kk < jnum; kk++) {

	k = jlist[kk];

	ktype = map[type[k]];

	iparam = elem2param[itype][jtype][ktype];
@@ -279,24 +284,32 @@ void PairSW::coeff(int narg, char **arg) 
}



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

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

   init specific to this pair style

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



double PairSW::init_one(int i, int j)

{

  if (setflag[i][j] == 0) error->all("All pair coeffs are not set");



  return cutmax;

}



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



void PairSW::init_style()

{

  if (atom->tag_enable == 0)

    error->all("Pair style Stillinger-Weber requires atom IDs");

  if (force->newton_pair == 0)

    error->all("Pair style Stillinger-Weber requires newton pair on");



  // need a full neighbor list



  int irequest = neighbor->request(this);

  neighbor->requests[irequest]->half = 0;

  neighbor->requests[irequest]->full = 1;

}



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

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

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



double PairSW::init_one(int i, int j)

{

  if (setflag[i][j] == 0) error->all("All pair coeffs are not set");



  return cutmax;

}



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

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