mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@932 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
bc528eda85
commit
d31eb1a080
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@ -22,10 +22,13 @@
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#include "mpi.h"
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#include "pair_airebo.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "comm.h"
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#include "update.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "memory.h"
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#include "error.h"
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@ -43,8 +46,6 @@ using namespace LAMMPS_NS;
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PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp)
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{
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neigh_half_every = 0;
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neigh_full_every = 1;
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single_enable = 0;
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one_coeff = 1;
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@ -89,9 +90,7 @@ void PairAIREBO::compute(int eflag, int vflag)
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eng_vdwl = 0.0;
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if (vflag) for (int i = 0; i < 6; i++) virial[i] = 0.0;
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double **f;
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if (vflag == 2) f = update->f_pair;
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else f = atom->f;
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double **f = atom->f;
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REBO_neigh();
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FREBO(eflag,f);
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@ -200,6 +199,30 @@ void PairAIREBO::coeff(int narg, char **arg)
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if (count == 0) error->all("Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairAIREBO::init_style()
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{
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if (atom->tag_enable == 0)
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error->all("Pair style AIREBO requires atom IDs");
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if (force->newton_pair == 0)
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error->all("Pair style AIREBO requires newton pair on");
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// need a full neighbor list
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int irequest = neighbor->request(this);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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// local REBO neighbor list memory
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pgsize = neighbor->pgsize;
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oneatom = neighbor->oneatom;
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if (maxlocal == 0) add_pages(0);
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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@ -262,31 +285,17 @@ double PairAIREBO::init_one(int i, int j)
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return cutmax;
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairAIREBO::init_style()
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{
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if (atom->tag_enable == 0)
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error->all("Pair style AIREBO requires atom IDs");
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if (force->newton_pair == 0)
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error->all("Pair style AIREBO requires newton pair on");
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pgsize = neighbor->pgsize;
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oneatom = neighbor->oneatom;
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if (maxlocal == 0) add_pages(0);
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}
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/* ----------------------------------------------------------------------
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create REBO neighbor list from main neighbor list
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REBO neighbor list stores neighbors of ghost atoms
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------------------------------------------------------------------------- */
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void PairAIREBO::REBO_neigh()
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{
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int i,j,k,n,itype,jtype,m,numneigh;
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int i,j,ii,jj,m,n,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;
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int *neighptr,*neighs;
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int *ilist,*jlist,*numneigh,**firstneigh;
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int *neighptr;
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double **x = atom->x;
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int *type = atom->type;
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@ -307,6 +316,11 @@ void PairAIREBO::REBO_neigh()
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nH = new double[maxlocal];
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}
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// initialize ghost atom references to -1
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for (i = nlocal; i < nall; i++) REBO_numneigh[i] = -1;
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@ -320,7 +334,9 @@ void PairAIREBO::REBO_neigh()
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npage = 0;
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int npnt = 0;
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for (i = 0; i < nlocal; i++) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (pgsize - npnt < oneatom) {
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npnt = 0;
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npage++;
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@ -334,11 +350,11 @@ void PairAIREBO::REBO_neigh()
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ztmp = x[i][2];
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itype = map[type[i]];
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nC[i] = nH[i] = 0.0;
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neighs = neighbor->firstneigh_full[i];
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numneigh = neighbor->numneigh_full[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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jtype = map[type[j]];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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@ -399,11 +415,11 @@ void PairAIREBO::REBO_neigh()
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else
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nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
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neighs = neighbor->firstneigh_full[m];
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numneigh = neighbor->numneigh_full[m];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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if (j == i) continue;
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jtype = map[type[j]];
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delx = xtmp - x[j][0];
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@ -503,14 +519,15 @@ void PairAIREBO::FREBO(int eflag, double **f)
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void PairAIREBO::FLJ(int eflag, double **f)
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{
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int i,j,k,m,jj,kk,mm,itype,jtype,ktype,mtype;
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int numneigh,atomi,atomj,atomk,atomm;
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int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype;
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int atomi,atomj,atomk,atomm;
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int testpath,npath,done;
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double rsq,best,wik,wkm,cij,rij,dwij,dwik,dwkj,dwkm,dwmj;
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double delij[3],rijsq,delik[3],rik,delkj[3];
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double rkj,wkj,dC,VLJ,dVLJ,fforce,VA,Str,dStr,Stb;
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double delkm[3],rkm,delmj[3],rmj,wmj,r2inv,r6inv,scale,delscale[3];
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int *neighs,*REBO_neighs_i,*REBO_neighs_k;
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int *ilist,*jlist,*numneigh,**firstneigh;
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int *REBO_neighs_i,*REBO_neighs_k;
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double delikS[3],delkjS[3],delkmS[3],delmjS[3];
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double rikS,rkjS,rkmS,rmjS,wikS,dwikS;
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double wkjS,dwkjS,wkmS,dwkmS,wmjS,dwmjS;
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@ -523,14 +540,23 @@ void PairAIREBO::FLJ(int eflag, double **f)
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int *type = atom->type;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++) {
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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itype = map[type[i]];
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neighs = neighbor->firstneigh_full[i];
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numneigh = neighbor->numneigh_full[i];
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atomi=i;
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for (jj = 0; jj < numneigh; jj++) {
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j = neighs[jj];
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atomj=j;
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atomi = i;
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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atomj = j;
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if (tag[i] > tag[j]) continue;
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jtype = map[type[j]];
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@ -25,8 +25,8 @@ class PairAIREBO : public Pair {
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void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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double init_one(int, int);
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void init_style();
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double init_one(int, int);
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void write_restart(FILE *) {}
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void read_restart(FILE *) {}
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void write_restart_settings(FILE *) {}
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@ -22,9 +22,9 @@
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#include "pair_eam.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "comm.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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@ -124,12 +124,11 @@ PairEAM::~PairEAM()
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void PairEAM::compute(int eflag, int vflag)
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{
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int i,j,k,m,numneigh,itype,jtype;
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int i,j,ii,jj,m,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double rsq,r,p,fforce,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
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double *coeff;
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int *neighs;
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double **f;
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int *ilist,*jlist,*numneigh,**firstneigh;
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// grow energy array if necessary
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@ -144,13 +143,17 @@ void PairEAM::compute(int eflag, int vflag)
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eng_vdwl = 0.0;
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if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
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if (vflag == 2) f = update->f_pair;
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else f = atom->f;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// zero out density
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if (newton_pair) {
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@ -161,16 +164,17 @@ void PairEAM::compute(int eflag, int vflag)
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// rho = density at each atom
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// loop over neighbors of my atoms
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for (i = 0; i < nlocal; i++) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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@ -201,7 +205,8 @@ void PairEAM::compute(int eflag, int vflag)
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// fp = derivative of embedding energy at each atom
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// phi = embedding energy at each atom
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for (i = 0; i < nlocal; i++) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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p = rho[i]*rdrho + 1.0;
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m = static_cast<int> (p);
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m = MAX(1,MIN(m,nrho-1));
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@ -219,16 +224,18 @@ void PairEAM::compute(int eflag, int vflag)
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// compute forces on each atom
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// loop over neighbors of my atoms
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for (i = 0; i < nlocal; i++) {
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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@ -382,6 +389,20 @@ void PairEAM::coeff(int narg, char **arg)
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if (count == 0) error->all("Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairEAM::init_style()
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{
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// convert read-in file(s) to arrays and spline them
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file2array();
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array2spline();
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int irequest = neighbor->request(this);
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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@ -404,18 +425,6 @@ double PairEAM::init_one(int i, int j)
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return cutmax;
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairEAM::init_style()
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{
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// convert read-in file(s) to arrays and spline them
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file2array();
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array2spline();
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}
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/* ----------------------------------------------------------------------
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read potential values from a DYNAMO single element funcfl file
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------------------------------------------------------------------------- */
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@ -25,8 +25,8 @@ class PairEAM : public Pair {
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void compute(int, int);
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void settings(int, char **);
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virtual void coeff(int, char **);
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double init_one(int, int);
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void init_style();
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double init_one(int, int);
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void single(int, int, int, int, double, double, double, int, One &);
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void single_embed(int, int, double &);
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@ -21,11 +21,13 @@
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#include "string.h"
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#include "pair_sw.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "comm.h"
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#include "update.h"
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#include "memory.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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@ -38,8 +40,6 @@ using namespace LAMMPS_NS;
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PairSW::PairSW(LAMMPS *lmp) : Pair(lmp)
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{
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neigh_half_every = 0;
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neigh_full_every = 1;
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single_enable = 0;
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one_coeff = 1;
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@ -74,23 +74,26 @@ PairSW::~PairSW()
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void PairSW::compute(int eflag, int vflag)
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{
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int i,j,k,m,n,itag,jtag,itype,jtype,ktype,iparam,numneigh;
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int i,j,k,ii,jj,kk,inum,jnum,jnumm1,itag,jtag,itype,jtype,ktype,iparam;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double rsq,rsq1,rsq2,eng,fforce;
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double delr1[3],delr2[3],fj[3],fk[3];
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int *neighs;
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double **f;
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int *ilist,*jlist,*numneigh,**firstneigh;
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eng_vdwl = 0.0;
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if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
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if (vflag == 2) f = update->f_pair;
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else f = atom->f;
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double **x = atom->x;
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double **f = atom->f;
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int *tag = atom->tag;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over full neighbor list of my atoms
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for (i = 0; i < nlocal; i++) {
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@ -102,11 +105,11 @@ void PairSW::compute(int eflag, int vflag)
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// two-body interactions, skip half of them
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neighs = neighbor->firstneigh_full[i];
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numneigh = neighbor->numneigh_full[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (m = 0; m < numneigh; m++) {
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j = neighs[m];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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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];
|
||||
|
||||
|
|
@ -278,6 +283,24 @@ void PairSW::coeff(int narg, char **arg)
|
|||
if (count == 0) error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
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
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
@ -291,16 +314,6 @@ double PairSW::init_one(int i, int j)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
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");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSW::read_file(char *file)
|
||||
{
|
||||
int params_per_line = 13;
|
||||
|
|
|
|||
|
|
@ -21,11 +21,11 @@
|
|||
#include "string.h"
|
||||
#include "pair_tersoff.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "update.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
|
|
@ -38,8 +38,6 @@ using namespace LAMMPS_NS;
|
|||
|
||||
PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
neigh_half_every = 0;
|
||||
neigh_full_every = 1;
|
||||
single_enable = 0;
|
||||
one_coeff = 1;
|
||||
|
||||
|
|
@ -77,27 +75,32 @@ PairTersoff::~PairTersoff()
|
|||
|
||||
void PairTersoff::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,k,m,n,itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk,numneigh;
|
||||
int i,j,k,ii,jj,kk,inum,jnum;
|
||||
int itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz;
|
||||
double rsq,rsq1,rsq2,eng,fforce;
|
||||
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
|
||||
double zeta_ij,prefactor;
|
||||
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++) {
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itag = tag[i];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i][0];
|
||||
|
|
@ -106,11 +109,11 @@ void PairTersoff::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) {
|
||||
|
|
@ -148,8 +151,8 @@ void PairTersoff::compute(int eflag, int vflag)
|
|||
// three-body interactions
|
||||
// skip immediately if I-J is not within cutoff
|
||||
|
||||
for (m = 0; m < numneigh; m++) {
|
||||
j = neighs[m];
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
jtype = map[type[j]];
|
||||
iparam_ij = elem2param[itype][jtype][jtype];
|
||||
|
||||
|
|
@ -162,9 +165,10 @@ void PairTersoff::compute(int eflag, int vflag)
|
|||
// accumulate bondorder zeta for each i-j interaction via loop over k
|
||||
|
||||
zeta_ij = 0.0;
|
||||
for (n = 0; n < numneigh; n++) {
|
||||
if (n == m) continue;
|
||||
k = neighs[n];
|
||||
|
||||
for (kk = 0; kk < jnum; kk++) {
|
||||
if (jj == kk) continue;
|
||||
k = jlist[kk];
|
||||
ktype = map[type[k]];
|
||||
iparam_ijk = elem2param[itype][jtype][ktype];
|
||||
|
||||
|
|
@ -191,9 +195,9 @@ void PairTersoff::compute(int eflag, int vflag)
|
|||
|
||||
// attractive term via loop over k
|
||||
|
||||
for (n = 0; n < numneigh; n++) {
|
||||
if (n == m) continue;
|
||||
k = neighs[n];
|
||||
for (kk = 0; kk < jnum; kk++) {
|
||||
if (jj == kk) continue;
|
||||
k = jlist[kk];
|
||||
ktype = map[type[k]];
|
||||
iparam_ijk = elem2param[itype][jtype][ktype];
|
||||
|
||||
|
|
@ -315,6 +319,24 @@ void PairTersoff::coeff(int narg, char **arg)
|
|||
if (count == 0) error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoff::init_style()
|
||||
{
|
||||
if (atom->tag_enable == 0)
|
||||
error->all("Pair style Tersoff requires atom IDs");
|
||||
if (force->newton_pair == 0)
|
||||
error->all("Pair style Tersoff 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
|
||||
------------------------------------------------------------------------- */
|
||||
|
|
@ -328,16 +350,6 @@ double PairTersoff::init_one(int i, int j)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoff::init_style()
|
||||
{
|
||||
if (atom->tag_enable == 0)
|
||||
error->all("Pair style Tersoff requires atom IDs");
|
||||
if (force->newton_pair == 0)
|
||||
error->all("Pair style Tersoff requires newton pair on");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoff::read_file(char *file)
|
||||
{
|
||||
int params_per_line = 15;
|
||||
|
|
|
|||
Loading…
Reference in New Issue