Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F102370578
pair_lj_charmm_coul_long_opt.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Feb 20, 00:35
Size
10 KB
Mime Type
text/x-c++
Expires
Sat, Feb 22, 00:35 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
24321845
Attached To
rLAMMPS lammps
pair_lj_charmm_coul_long_opt.cpp
View Options
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Fischer, High Performance Technologies, Inc.
David Richie, Stone Ridge Technology
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "pair_lj_charmm_coul_long_opt.h"
#include "atom.h"
#include "force.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define EWALD_A1 0.254829592
#define EWALD_A2 -0.284496736
#define EWALD_A3 1.421413741
#define EWALD_A4 -1.453152027
#define EWALD_A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongOpt::PairLJCharmmCoulLongOpt(LAMMPS *lmp) :
PairLJCharmmCoulLong(lmp) {}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongOpt::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
if (evflag) {
if (eflag) {
if (force->newton_pair) return eval<1,1,1>();
else return eval<1,1,0>();
} else {
if (force->newton_pair) return eval<1,0,1>();
else return eval<1,0,0>();
}
} else {
if (force->newton_pair) return eval<0,0,1>();
else return eval<0,0,0>();
}
}
/* ---------------------------------------------------------------------- */
template < int EVFLAG, int EFLAG, int NEWTON_PAIR >
void PairLJCharmmCoulLongOpt::eval()
{
typedef struct { double x,y,z; } vec3_t;
typedef struct {
double cutsq,lj1,lj2,lj3,lj4,offset;
double _pad[2];
} fast_alpha_t;
int i,j,ii,jj,inum,jnum,itype,jtype,itable,sbindex;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
double rsq;
double evdwl = 0.0;
double ecoul = 0.0;
double** _noalias x = atom->x;
double** _noalias f = atom->f;
double* _noalias q = atom->q;
int* _noalias type = atom->type;
int nlocal = atom->nlocal;
double* _noalias special_coul = force->special_coul;
double* _noalias special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
inum = list->inum;
int* _noalias ilist = list->ilist;
int** _noalias firstneigh = list->firstneigh;
int* _noalias numneigh = list->numneigh;
vec3_t* _noalias xx = (vec3_t*)x[0];
vec3_t* _noalias ff = (vec3_t*)f[0];
int ntypes = atom->ntypes;
int ntypes2 = ntypes*ntypes;
double tmp_coef1 = 1.0/denom_lj;
double tmp_coef2 = cut_ljsq - 3.0*cut_lj_innersq;
fast_alpha_t* _noalias fast_alpha =
(fast_alpha_t*)malloc(ntypes2*sizeof(fast_alpha_t));
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];
a.lj2 = lj2[i+1][j+1];
a.lj3 = lj3[i+1][j+1];
a.lj4 = lj4[i+1][j+1];
}
fast_alpha_t* _noalias tabsix = fast_alpha;
// loop over neighbors of my atoms
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* _noalias jlist = firstneigh[i];
jnum = numneigh[i];
double tmpfx = 0.0;
double tmpfy = 0.0;
double tmpfz = 0.0;
fast_alpha_t* _noalias tabsixi = (fast_alpha_t*) &tabsix[itype*ntypes];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
sbindex = sbmask(j);
if (sbindex == 0) {
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
rsq = delx*delx + dely*dely + delz*delz;
double tmp_coef3 = qtmp*q[j];
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
forcecoul = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t *
(EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) *
expm2;
prefactor = qqrd2e * tmp_coef3/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = tmp_coef3 * table;
}
}
forcelj = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j] - 1;
fast_alpha_t& a = tabsixi[jtype];
forcelj = r6inv * (a.lj1*r6inv - a.lj2);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(tmp_coef2 + 2.0*rsq) * tmp_coef1;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * tmp_coef1;
philj = r6inv * (a.lj3*r6inv - a.lj4);
forcelj = forcelj*switch1 + philj*switch2;
}
}
double fpair = (forcecoul + forcelj) * r2inv;
tmpfx += delx*fpair;
tmpfy += dely*fpair;
tmpfz += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
ff[j].x -= delx*fpair;
ff[j].y -= dely*fpair;
ff[j].z -= delz*fpair;
}
if (EFLAG) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = tmp_coef3 * table;
}
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
fast_alpha_t& a = tabsixi[jtype];
evdwl = r6inv*(a.lj3*r6inv-a.lj4);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(tmp_coef2 + 2.0*rsq) * tmp_coef1;
evdwl *= switch1;
}
} else evdwl = 0.0;
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
}
} else {
factor_lj = special_lj[sbindex];
factor_coul = special_coul[sbindex];
j &= NEIGHMASK;
double delx = xtmp - xx[j].x;
double dely = ytmp - xx[j].y;
double delz = ztmp - xx[j].z;
rsq = delx*delx + dely*dely + delz*delz;
double tmp_coef3 = qtmp*q[j];
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
forcecoul = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t *
(EWALD_A1+t*(EWALD_A2+t*(EWALD_A3+t*(EWALD_A4+t*EWALD_A5)))) *
expm2;
prefactor = qqrd2e * tmp_coef3/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = tmp_coef3 * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = tmp_coef3 * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
}
forcelj = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j] - 1;
fast_alpha_t& a = tabsixi[jtype];
forcelj = r6inv * (a.lj1*r6inv - a.lj2);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(tmp_coef2 + 2.0*rsq) * tmp_coef1;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * tmp_coef1;
fast_alpha_t& a = tabsixi[jtype];
philj = r6inv * (a.lj3*r6inv - a.lj4);
forcelj = forcelj*switch1 + philj*switch2;
}
}
double fpair = (forcecoul + factor_lj*forcelj) * r2inv;
tmpfx += delx*fpair;
tmpfy += dely*fpair;
tmpfz += delz*fpair;
if (NEWTON_PAIR || j < nlocal) {
ff[j].x -= delx*fpair;
ff[j].y -= dely*fpair;
ff[j].z -= delz*fpair;
}
if (EFLAG) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = tmp_coef3 * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
fast_alpha_t& a = tabsixi[jtype];
evdwl = r6inv*(a.lj3*r6inv-a.lj4);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(tmp_coef2 + 2.0*rsq) * tmp_coef1;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
ff[i].x += tmpfx;
ff[i].y += tmpfy;
ff[i].z += tmpfz;
}
free(fast_alpha); fast_alpha = 0;
if (vflag_fdotr) virial_fdotr_compute();
}
Event Timeline
Log In to Comment