Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F90916228
pair_morse_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
Tue, Nov 5, 23:22
Size
5 KB
Mime Type
text/x-c++
Expires
Thu, Nov 7, 23:22 (2 d)
Engine
blob
Format
Raw Data
Handle
22118224
Attached To
rLAMMPS lammps
pair_morse_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_morse_opt.h"
#include "atom.h"
#include "force.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMorseOpt::PairMorseOpt(LAMMPS *lmp) : PairMorse(lmp) {}
/* ---------------------------------------------------------------------- */
void PairMorseOpt::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 PairMorseOpt::eval()
{
typedef struct { double x,y,z; } vec3_t;
typedef struct {
double cutsq,r0,alpha,morse1,d0,offset;
double _pad[2];
} fast_alpha_t;
int i,j,ii,jj,inum,jnum,itype,jtype,sbindex;
double factor_lj;
double evdwl = 0.0;
double** __restrict__ x = atom->x;
double** __restrict__ f = atom->f;
int* __restrict__ type = atom->type;
int nlocal = atom->nlocal;
double* __restrict__ special_lj = force->special_lj;
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];
int ntypes = atom->ntypes;
int ntypes2 = ntypes*ntypes;
fast_alpha_t* __restrict__ 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.r0 = r0[i+1][j+1];
a.alpha = alpha[i+1][j+1];
a.morse1 = morse1[i+1][j+1];
a.d0 = d0[i+1][j+1];
a.offset = offset[i+1][j+1];
}
fast_alpha_t* __restrict__ tabsix = fast_alpha;
// 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;
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 (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;
double rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j] - 1;
fast_alpha_t& a = tabsixi[jtype];
if (rsq < a.cutsq) {
double r = sqrt(rsq);
double dr = r - a.r0;
double dexp = exp(-a.alpha * dr);
double fpair = a.morse1 * (dexp*dexp - dexp) / r;
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) evdwl = a.d0 * (dexp*dexp - 2.0*dexp) - a.offset;
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz);
}
} else {
factor_lj = special_lj[sbindex];
j &= NEIGHMASK;
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;
jtype = type[j] - 1;
fast_alpha_t& a = tabsixi[jtype];
if (rsq < a.cutsq) {
double r = sqrt(rsq);
double dr = r - a.r0;
double dexp = exp(-a.alpha * dr);
double fpair = factor_lj * a.morse1 * (dexp*dexp - dexp) / r;
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) {
evdwl = a.d0 * (dexp*dexp - 2.0*dexp) - a.offset;
evdwl *= factor_lj;
}
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,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