Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F90847669
pair_line_lj.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, 07:41
Size
13 KB
Mime Type
text/x-c
Expires
Thu, Nov 7, 07:41 (2 d)
Engine
blob
Format
Raw Data
Handle
22144402
Attached To
rLAMMPS lammps
pair_line_lj.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_line_lj.h"
#include "atom.h"
#include "atom_vec_line.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
PairLineLJ::PairLineLJ(LAMMPS *lmp) : Pair(lmp)
{
dmax = nmax = 0;
discrete = NULL;
dnum = dfirst = NULL;
single_enable = 0;
restartinfo = 0;
}
/* ---------------------------------------------------------------------- */
PairLineLJ::~PairLineLJ()
{
memory->sfree(discrete);
memory->destroy(dnum);
memory->destroy(dfirst);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(subsize);
memory->destroy(cut);
memory->destroy(cutsub);
memory->destroy(cutsubsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
}
}
/* ---------------------------------------------------------------------- */
void PairLineLJ::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int ni,nj,npi,npj,ifirst,jfirst;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj;
double xi[2],xj[2],fi[2],dxi,dxj,dyi,dyj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double **torque = atom->torque;
int *line = atom->line;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// grow discrete list if necessary and initialize
if (nall > nmax) {
nmax = nall;
memory->destroy(dnum);
memory->destroy(dfirst);
memory->create(dnum,nall,"pair:dnum");
memory->create(dfirst,nall,"pair:dfirst");
}
for (i = 0; i < nall; i++) dnum[i] = 0;
ndiscrete = 0;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
// line/line interactions = NxN particles
evdwl = 0.0;
if (line[i] >= 0 && line[j] >= 0) {
if (dnum[i] == 0) discretize(i,subsize[itype]);
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[j] == 0) discretize(j,subsize[jtype]);
npj = dnum[j];
jfirst = dfirst[j];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
// skip this pair of sub-particles if outside sub cutoff
if (rsq >= cutsubsq[itype][jtype]) continue;
sig = sigma[itype][jtype];
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
torque[i][2] += dxi*fi[1] - dyi*fi[0];
if (newton_pair || j < nlocal) {
f[j][0] -= fi[0];
f[j][1] -= fi[1];
torque[j][2] -= dxj*fi[1] - dyj*fi[0];
}
}
}
// line/particle interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[i] >= 0) {
if (dnum[i] == 0) discretize(i,subsize[itype]);
npi = dnum[i];
ifirst = dfirst[i];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xj[0] = x[j][0];
xj[1] = x[j][1];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
// skip this pair of sub-particles if outside sub cutoff
if (rsq >= cutsubsq[itype][jtype]) continue;
sig = sigma[itype][jtype];
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
torque[i][2] += dxi*fi[1] - dyi*fi[0];
if (newton_pair || j < nlocal) {
f[j][0] -= fi[0];
f[j][1] -= fi[1];
}
}
// particle/line interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[j] >= 0) {
if (dnum[j] == 0) discretize(j,subsize[jtype]);
npj = dnum[j];
jfirst = dfirst[j];
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
xi[0] = x[i][0];
xi[1] = x[i][1];
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
// skip this pair of sub-particles if outside sub cutoff
if (rsq >= cutsubsq[itype][jtype]) continue;
sig = sigma[itype][jtype];
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
if (newton_pair || j < nlocal) {
f[j][0] -= fi[0];
f[j][1] -= fi[1];
torque[j][2] -= dxj*fi[1] - dyj*fi[0];
}
}
// particle/particle interaction = 1x1 particles
} else {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = forcelj*r2inv;
if (eflag)
evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLineLJ::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(subsize,n+1,"pair:subsize");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(cutsub,n+1,n+1,"pair:cutsub");
memory->create(cutsubsq,n+1,n+1,"pair:cutsubsq");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLineLJ::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLineLJ::coeff(int narg, char **arg)
{
if (narg < 7 || narg > 8)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double size_itype = force->numeric(FLERR,arg[2]);
double size_jtype = force->numeric(FLERR,arg[3]);
double epsilon_one = force->numeric(FLERR,arg[4]);
double sigma_one = force->numeric(FLERR,arg[5]);
double cutsub_one = force->numeric(FLERR,arg[6]);
double cut_one = cut_global;
if (narg == 8) cut_one = force->numeric(FLERR,arg[7]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
subsize[i] = size_itype;
subsize[j] = size_jtype;
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cutsub[i][j] = cutsub_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLineLJ::init_style()
{
avec = (AtomVecLine *) atom->style_match("line");
if (!avec) error->all(FLERR,"Pair line/lj requires atom style line");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLineLJ::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
cutsubsq[i][j] = cutsub[i][j] * cutsub[i][j];
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
epsilon[j][i] = epsilon[i][j];
sigma[j][i] = sigma[i][j];
cutsubsq[j][i] = cutsubsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
discretize line segment I into N sub-particles with <= size separation
store displacement dx,dy of discrete particles in Discrete list
------------------------------------------------------------------------- */
void PairLineLJ::discretize(int i, double size)
{
AtomVecLine::Bonus *bonus = avec->bonus;
double length = bonus[atom->line[i]].length;
double theta = bonus[atom->line[i]].theta;
int n = static_cast<int> (length/size) + 1;
dnum[i] = n;
dfirst[i] = ndiscrete;
if (ndiscrete + n > dmax) {
dmax += DELTA;
discrete = (Discrete *)
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
}
double delta;
for (int m = 0; m < n; m++) {
delta = -0.5 + (2*m+1)/(2.0*n);
discrete[ndiscrete].dx = delta*length*cos(theta);
discrete[ndiscrete].dy = delta*length*sin(theta);
ndiscrete++;
}
}
Event Timeline
Log In to Comment