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

This commit is contained in:
sjplimp 2007-10-03 16:16:21 +00:00
parent 4933685cd7
commit 6f1f40aa6e
4 changed files with 93 additions and 99 deletions
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67
src/OPT/pair_eam_opt.h
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@ -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];
@ -151,26 +150,29 @@ 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;
double delz = ztmp - xx[j].z;
@ -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;
@ -226,22 +229,24 @@ 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;

42
src/OPT/pair_lj_charmm_coul_long_opt.h
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@ -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;

39
src/OPT/pair_lj_cut_opt.h
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@ -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;
@ -100,17 +101,17 @@ 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) {
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];
@ -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) {

44
src/OPT/pair_morse_opt.h
View File

@ -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];
@ -92,31 +87,32 @@ 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;
double tmpfz = 0.0;
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) {