Commit 6f1f40aa authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@935 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 4933685c

src/OPT/pair_eam_opt.h

+36 −31
Original line number Diff line number Diff line
@@ -26,10 +26,9 @@ 
#include "stdlib.h"

#include "pair_eam.h"

#include "atom.h"

#include "update.h"

#include "force.h"

#include "neighbor.h"

#include "comm.h"

#include "force.h"

#include "neigh_list.h"

#include "memory.h"



#define MIN(a,b) ((a) < (b) ? (a) : (b))
@@ -71,7 +70,7 @@ void PairEAMOpt::eval() 
    double _pad[3];

  } fast_gamma_t;

  

  double** __restrict__ f;

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

  double* __restrict__ coeff;

  

  // grow energy array if necessary
@@ -85,12 +84,10 @@ void PairEAMOpt::eval() 
  }

  

  eng_vdwl = 0.0;

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

  

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

  else f = atom->f;

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

  

  double** __restrict__ x = atom->x;

  double** __restrict__ f = atom->f;

  int* __restrict__ type = atom->type;

  int nlocal = atom->nlocal;
@@ -102,15 +99,17 @@ void PairEAMOpt::eval() 
  int nr2 = nr-2;

  int nr1 = nr-1;

  

  int** __restrict__ firstneigh = neighbor->firstneigh;

  int* __restrict__ num = neighbor->numneigh;

  inum = list->inum;

  int* __restrict__ ilist = list->ilist;

  int** __restrict__ firstneigh = list->firstneigh;

  int* __restrict__ numneigh = list->numneigh;

  

  int ntypes = atom->ntypes;

  int ntypes2 = ntypes*ntypes;

  

  fast_alpha_t* __restrict__ fast_alpha = 

    (fast_alpha_t*) malloc(ntypes2*(nr+1)*sizeof(fast_alpha_t));

  for( int i = 0; i < ntypes; i++) for( int j = 0; j < ntypes; j++) {

  for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {

    fast_alpha_t* __restrict__ tab = &fast_alpha[i*ntypes*nr+j*nr];

    for(int m = 1; m <= nr; m++) {

      tab[m].rhor0i =  rhor_spline[type2rhor[i+1][j+1]][m][6];
@@ -127,7 +126,7 @@ void PairEAMOpt::eval() 
  

  fast_gamma_t* __restrict__ fast_gamma = 

    (fast_gamma_t*) malloc(ntypes2*(nr+1)*sizeof(fast_gamma_t));

  for( int i = 0; i < ntypes; i++) for( int j = 0; j < ntypes; j++) {

  for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {

    fast_gamma_t* __restrict__ tab = &fast_gamma[i*ntypes*nr+j*nr];

    for(int m = 1; m <= nr; m++) {

      tab[m].rhor4i =  rhor_spline[type2rhor[i+1][j+1]][m][2];
@@ -151,25 +150,28 @@ void PairEAMOpt::eval() 
  

  if (NEWTON_PAIR) {

    int m = nlocal + atom->nghost;

    for (int i = 0; i < m; i++) rho[i] = 0.0;

  } else for (int i = 0; i < nlocal; i++) rho[i] = 0.0;

    for (i = 0; i < m; i++) rho[i] = 0.0;

  } else for (i = 0; i < nlocal; i++) rho[i] = 0.0;

  

  // rho = density at each atom

  // loop over neighbors of my atoms

  

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

  // loop over neighbors of my atoms

  

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

    i = ilist[ii];

    double xtmp = xx[i].x;

    double ytmp = xx[i].y;

    double ztmp = xx[i].z;

    int itype = type[i] - 1;

    int* __restrict__ neighs = firstneigh[i];

    int numneigh = num[i];

    itype = type[i] - 1;

    int* __restrict__ jlist = firstneigh[i];

    jnum = numneigh[i];

    

    double tmprho = rho[i];

    

    fast_alpha_t* __restrict__ tabeighti = &tabeight[itype*ntypes*nr];

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

      int j = neighs[k];



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

      j = jlist[jj];



      double delx = xtmp - xx[j].x;

      double dely = ytmp - xx[j].y;
@@ -178,7 +180,7 @@ void PairEAMOpt::eval() 
      

      if (rsq < tmp_cutforcesq) {

	

	int jtype = type[j] - 1;

	jtype = type[j] - 1;

	

	double p = sqrt(rsq)*tmp_rdr;

	if ( (int)p <= nr2 ) {
@@ -210,7 +212,8 @@ void PairEAMOpt::eval() 
  // fp = derivative of embedding energy at each atom

  // phi = embedding energy at each atom

  

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

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

    i = ilist[ii];

    double p = rho[i]*rdrho;

    int m = MIN((int)p,nrho-2);

    p -= (double)m;
@@ -227,21 +230,23 @@ void PairEAMOpt::eval() 
  // compute forces on each atom

  // loop over neighbors of my atoms



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

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

    i = ilist[ii];

    double xtmp = xx[i].x;

    double ytmp = xx[i].y;

    double ztmp = xx[i].z;

    int itype1 = type[i] - 1;

    int* __restrict__ neighs = firstneigh[i];

    int numneigh = num[i];

    int* __restrict__ jlist = firstneigh[i];

    jnum = numneigh[i];

    

    double tmpfx = 0.0;

    double tmpfy = 0.0;

    double tmpfz = 0.0;

    

    fast_gamma_t* __restrict__ tabssi = &tabss[itype1*ntypes*nr];

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

      int j = neighs[k];



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

      j = jlist[jj];

      

      double delx = xtmp - xx[j].x;

      double dely = ytmp - xx[j].y;
@@ -249,7 +254,7 @@ void PairEAMOpt::eval() 
      double rsq = delx*delx + dely*dely + delz*delz;

      

      if (rsq < tmp_cutforcesq) {

	int jtype = type[j] - 1;

	jtype = type[j] - 1;

	double r = sqrt(rsq);

	double rhoip,rhojp,z2,z2p;

	double p = r*tmp_rdr;

src/OPT/pair_lj_charmm_coul_long_opt.h

+17 −25
Original line number Diff line number Diff line
@@ -21,21 +21,12 @@ 
#ifndef PAIR_LJ_CHARMM_COUL_LONG_OPT_H

#define PAIR_LJ_CHARMM_COUL_LONG_OPT_H



#include "pair_lj_charmm_coul_long.h"

#include "math.h"

#include "stdio.h"

#include "stdlib.h"

#include "string.h"

#include "pair_lj_charmm_coul_long.h"

#include "atom.h"

#include "comm.h"

#include "force.h"

#include "kspace.h"

#include "update.h"

#include "integrate.h"

#include "respa.h"

#include "memory.h"

#include "neighbor.h"

#include "error.h"

#include "neigh_list.h"



#define MIN(a,b) ((a) < (b) ? (a) : (b))

#define MAX(a,b) ((a) > (b) ? (a) : (b))
@@ -69,24 +60,20 @@ void PairLJCharmmCoulLongOpt::eval() 
    double _pad[2];

  } fast_alpha_t;

  

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

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

  double fraction,table;

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

  double grij,expm2,prefactor,t,erfc;

  double factor,phicoul,philj,switch1,switch2;

  

  double** __restrict__ f;

  

  float rsq;

  int *int_rsq = (int *) &rsq;

  

  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** __restrict__ x = atom->x;

  double** __restrict__ f = atom->f;

  double* __restrict__ q = atom->q;

  int* __restrict__ type = atom->type;

  int nlocal = atom->nlocal;
@@ -94,8 +81,11 @@ void PairLJCharmmCoulLongOpt::eval() 
  double* __restrict__ special_coul = force->special_coul;

  double* __restrict__ special_lj = force->special_lj;

  double qqrd2e = force->qqrd2e;

  int** __restrict__ firstneigh = neighbor->firstneigh;

  int* __restrict__ num = neighbor->numneigh;



  inum = list->inum;

  int* __restrict__ ilist = list->ilist;

  int** __restrict__ firstneigh = list->firstneigh;

  int* __restrict__ numneigh = list->numneigh;

  

  vec3_t* __restrict__ xx = (vec3_t*)x[0];

  vec3_t* __restrict__ ff = (vec3_t*)f[0];
@@ -108,7 +98,7 @@ void PairLJCharmmCoulLongOpt::eval() 
  

  fast_alpha_t* __restrict__ fast_alpha = 

    (fast_alpha_t*)malloc(ntypes2*sizeof(fast_alpha_t));

  for( int i = 0; i < ntypes; i++) for( int j = 0; j < ntypes; j++) {

  for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {

    fast_alpha_t& a = fast_alpha[i*ntypes+j];

    a.cutsq = cutsq[i+1][j+1];

    a.lj1 = lj1[i+1][j+1];
@@ -120,22 +110,24 @@ void PairLJCharmmCoulLongOpt::eval() 
  

  // loop over neighbors of my atoms

  

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

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

    i = ilist[ii];

    double qtmp = q[i];

    double xtmp = xx[i].x;

    double ytmp = xx[i].y;

    double ztmp = xx[i].z;

    itype = type[i] - 1;

    int* __restrict__ neighs = firstneigh[i];

    int numneigh = num[i];

    int* __restrict__ jlist = firstneigh[i];

    jnum = numneigh[i];

    

    double tmpfx = 0.0;

    double tmpfy = 0.0;

    double tmpfz = 0.0;

    

    fast_alpha_t* __restrict__ tabsixi = (fast_alpha_t*) &tabsix[itype*ntypes];

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

      j = neighs[k];



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

      j = jlist[jj];

      

      if (j < nall) {

	double delx = xtmp - xx[j].x;

src/OPT/pair_lj_cut_opt.h

+20 −19
Original line number Diff line number Diff line
@@ -24,9 +24,8 @@ 
#include "stdlib.h"

#include "pair_lj_cut.h"

#include "atom.h"

#include "update.h"

#include "force.h"

#include "neighbor.h"

#include "neigh_list.h"



namespace LAMMPS_NS {
@@ -49,21 +48,22 @@ void PairLJCutOpt::eval() 
    double _pad[2];

  } fast_alpha_t;

  

  double** __restrict__ f;

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

  

  eng_vdwl = 0.0;

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

  

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

  else f = atom->f;

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

  

  double** __restrict__ x = atom->x;

  double** __restrict__ f = atom->f;

  int* __restrict__ type = atom->type;

  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;

  double* __restrict__ special_lj = force->special_lj;

  int** __restrict__ firstneigh = neighbor->firstneigh;

  int* __restrict__ num = neighbor->numneigh;



  inum = list->inum;

  int* __restrict__ ilist = list->ilist;

  int** __restrict__ firstneigh = list->firstneigh;

  int* __restrict__ numneigh = list->numneigh;

  

  vec3_t* __restrict__ xx = (vec3_t*)x[0];

  vec3_t* __restrict__ ff = (vec3_t*)f[0];
@@ -73,7 +73,7 @@ void PairLJCutOpt::eval() 
  

  fast_alpha_t* __restrict__ fast_alpha = 

    (fast_alpha_t*) malloc(ntypes2*sizeof(fast_alpha_t));

  for( int i = 0; i < ntypes; i++) for( int j = 0; j < ntypes; j++) {

  for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {

    fast_alpha_t& a = fast_alpha[i*ntypes+j];

    a.cutsq = cutsq[i+1][j+1];

    a.lj1 = lj1[i+1][j+1];
@@ -86,13 +86,14 @@ void PairLJCutOpt::eval() 
  

  // loop over neighbors of my atoms

  

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

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

    i = ilist[ii];

    double xtmp = xx[i].x;

    double ytmp = xx[i].y;

    double ztmp = xx[i].z;

    int itype = type[i] - 1;

    int* __restrict__ neighs = firstneigh[i];

    int numneigh = num[i];

    itype = type[i] - 1;

    int* __restrict__ jlist = firstneigh[i];

    jnum = numneigh[i];

    

    double tmpfx = 0.0;

    double tmpfy = 0.0;
@@ -100,8 +101,8 @@ void PairLJCutOpt::eval() 
    

    fast_alpha_t* __restrict__ tabsixi = (fast_alpha_t*)&tabsix[itype*ntypes];

    

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

      int j = neighs[k];

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

      j = jlist[jj];

      double factor_lj;



      if (j < nall) {
@@ -110,7 +111,7 @@ void PairLJCutOpt::eval() 
	double delz = ztmp - xx[j].z;

	double rsq = delx*delx + dely*dely + delz*delz;

	

	int jtype = type[j] - 1;

	jtype = type[j] - 1;

	

	fast_alpha_t& a = tabsixi[jtype];
@@ -155,7 +156,7 @@ void PairLJCutOpt::eval() 
	double rsq = delx*delx + dely*dely + delz*delz;

	

	int jtype1 = type[j];

	int jtype = jtype1 - 1;

	jtype = jtype1 - 1;

	

	fast_alpha_t& a = tabsixi[jtype];

	if (rsq < a.cutsq) {

src/OPT/pair_morse_opt.h

+20 −24
Original line number Diff line number Diff line
@@ -22,16 +22,11 @@ 
#define PAIR_MORSE_OPT_H



#include "math.h"

#include "stdio.h"

#include "stdlib.h"

#include "pair_morse.h"

#include "atom.h"

#include "comm.h"

#include "force.h"

#include "update.h"

#include "memory.h"

#include "neighbor.h"

#include "error.h"

#include "neigh_list.h"



namespace LAMMPS_NS {
@@ -54,22 +49,22 @@ void PairMorseOpt::eval() 
    double _pad[2];

  } fast_alpha_t;

  

  double** __restrict__ f;

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

  

  eng_vdwl = 0.0;

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

  

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

  else f = atom->f;

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

  

  double** __restrict__ x = atom->x;

  double** __restrict__ f = atom->f;

  int* __restrict__ type = atom->type;

  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;

  double* __restrict__ special_lj = force->special_lj;

  

  int** __restrict__ firstneigh = neighbor->firstneigh;

  int* __restrict__ num = neighbor->numneigh;

  inum = list->inum;

  int* __restrict__ ilist = list->ilist;

  int** __restrict__ firstneigh = list->firstneigh;

  int* __restrict__ numneigh = list->numneigh;

  

  vec3_t* __restrict__ xx = (vec3_t*)x[0];

  vec3_t* __restrict__ ff = (vec3_t*)f[0];
@@ -79,7 +74,7 @@ void PairMorseOpt::eval() 
  

  fast_alpha_t* __restrict__ fast_alpha = 

    (fast_alpha_t*) malloc(ntypes2*sizeof(fast_alpha_t));

  for( int i = 0; i < ntypes; i++) for( int j = 0; j < ntypes; j++) {

  for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {

    fast_alpha_t& a = fast_alpha[i*ntypes+j];

    a.cutsq = cutsq[i+1][j+1];

    a.r0 = r0[i+1][j+1];
@@ -92,13 +87,14 @@ void PairMorseOpt::eval() 
  

  // loop over neighbors of my atoms

  

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

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

    i = ilist[ii];

    double xtmp = xx[i].x;

    double ytmp = xx[i].y;

    double ztmp = xx[i].z;

    int itype = type[i] - 1;

    int* __restrict__ neighs = firstneigh[i];

    int numneigh = num[i];

    itype = type[i] - 1;

    int* __restrict__ jlist = firstneigh[i];

    jnum = numneigh[i];

    

    double tmpfx = 0.0;

    double tmpfy = 0.0;
@@ -106,17 +102,17 @@ void PairMorseOpt::eval() 
    

    fast_alpha_t* __restrict__ tabsixi = (fast_alpha_t*)&tabsix[itype*ntypes];

   

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

      int j = neighs[k];

      

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

      j = jlist[jj];

      double factor_lj;



      if (j < nall) {

	double delx = xtmp - xx[j].x;

	double dely = ytmp - xx[j].y;

	double delz = ztmp - xx[j].z;

	double rsq = delx*delx + dely*dely + delz*delz;

	

	int jtype = type[j] - 1;

	jtype = type[j] - 1;

	

	fast_alpha_t& a = tabsixi[jtype];

	if (rsq < a.cutsq) {
@@ -161,7 +157,7 @@ void PairMorseOpt::eval() 
	double delz = ztmp - xx[j].z;

	double rsq = delx*delx + dely*dely + delz*delz;

	

	int jtype = type[j] - 1;

	jtype = type[j] - 1;

	

	fast_alpha_t& a = tabsixi[jtype];

	if (rsq < a.cutsq) {

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