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pair_body.cpp
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Wed, May 29, 13:37

pair_body.cpp
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/* ----------------------------------------------------------------------
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_body.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "body_nparticle.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
PairBody::PairBody(LAMMPS *lmp) : Pair(lmp)
{
dmax = nmax = 0;
discrete = NULL;
dnum = dfirst = NULL;
single_enable = 0;
restartinfo = 0;
}
/* ---------------------------------------------------------------------- */
PairBody::~PairBody()
{
memory->destroy(discrete);
memory->destroy(dnum);
memory->destroy(dfirst);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
}
}
/* ---------------------------------------------------------------------- */
void PairBody::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,forcelj;
double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3];
double *dxi,*dxj;
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 *body = atom->body;
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;
// body/body interactions = NxM sub-particles
evdwl = 0.0;
if (body[i] >= 0 && body[j] >= 0) {
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[j] == 0) body2space(j);
npj = dnum[j];
jfirst = dfirst[j];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni];
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj];
xi[0] = x[i][0] + dxi[0];
xi[1] = x[i][1] + dxi[1];
xi[2] = x[i][2] + dxi[2];
xj[0] = x[j][0] + dxj[0];
xj[1] = x[j][1] + dxj[1];
xj[2] = x[j][2] + dxj[2];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
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]);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
ti[0] = dxi[1]*fi[2] - dxi[2]*fi[1];
ti[1] = dxi[2]*fi[0] - dxi[0]*fi[2];
ti[2] = dxi[0]*fi[1] - dxi[1]*fi[0];
torque[i][0] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
tj[0] = dxj[1]*fj[2] - dxj[2]*fj[1];
tj[1] = dxj[2]*fj[0] - dxj[0]*fj[2];
tj[2] = dxj[0]*fj[1] - dxj[1]*fj[0];
torque[j][0] += tj[0];
torque[j][1] += tj[1];
torque[j][2] += tj[2];
}
}
}
// body/particle interaction = Nx1 sub-particles
} else if (body[i] >= 0) {
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni];
xi[0] = x[i][0] + dxi[0];
xi[1] = x[i][1] + dxi[1];
xi[2] = x[i][2] + dxi[2];
xj[0] = x[j][0];
xj[1] = x[j][1];
xj[2] = x[j][2];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
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]);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
ti[0] = dxi[1]*fi[2] - dxi[2]*fi[1];
ti[1] = dxi[2]*fi[0] - dxi[0]*fi[2];
ti[2] = dxi[0]*fi[1] - dxi[1]*fi[0];
torque[i][0] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
}
}
// particle/body interaction = Nx1 sub-particles
} else if (body[j] >= 0) {
if (dnum[j] == 0) body2space(j);
npj = dnum[j];
jfirst = dfirst[j];
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj];
xi[0] = x[i][0];
xi[1] = x[i][1];
xi[2] = x[i][2];
xj[0] = x[j][0] + dxj[0];
xj[1] = x[j][1] + dxj[1];
xj[2] = x[j][2] + dxj[2];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
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]);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
tj[0] = dxj[1]*fj[2] - dxj[2]*fj[1];
tj[1] = dxj[2]*fj[0] - dxj[0]*fj[2];
tj[2] = dxj[0]*fj[1] - dxj[1]*fj[0];
torque[j][0] += tj[0];
torque[j][1] += tj[1];
torque[j][2] += tj[2];
}
}
// 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 PairBody::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(cut,n+1,n+1,"pair:cut");
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 PairBody::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; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBody::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double cut_one = cut_global;
if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_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 PairBody::init_style()
{
avec = (AtomVecBody *) atom->style_match("body");
if (!avec) error->all(FLERR,"Pair body requires atom style body");
if (strcmp(avec->bptr->style,"nparticle") != 0)
error->all(FLERR,"Pair body requires body style nparticle");
bptr = (BodyNparticle *) avec->bptr;
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBody::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][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];
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];
}
/* ----------------------------------------------------------------------
convert N sub-particles in body I to space frame using current quaternion
store sub-particle space-frame displacements from COM in discrete list
------------------------------------------------------------------------- */
void PairBody::body2space(int i)
{
int ibonus = atom->body[i];
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
int nsub = bptr->nsub(bonus);
double *coords = bptr->coords(bonus);
dnum[i] = nsub;
dfirst[i] = ndiscrete;
if (ndiscrete + nsub > dmax) {
dmax += DELTA;
memory->grow(discrete,dmax,3,"pair:discrete");
}
double p[3][3];
MathExtra::quat_to_mat(bonus->quat,p);
for (int m = 0; m < nsub; m++) {
MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]);
ndiscrete++;
}
}

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