Added hexatic bond orientational order parameter
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14231 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
263
src/compute_hexorder_atom.cpp
Normal file
263
src/compute_hexorder_atom.cpp
Normal file
@ -0,0 +1,263 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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 author: Aidan Thompson (SNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
#include "compute_hexorder_atom.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal compute hexorder/atom command");
|
||||
|
||||
double cutoff = force->numeric(FLERR,arg[3]);
|
||||
cutsq = cutoff*cutoff;
|
||||
|
||||
ncol = narg-4 + 1;
|
||||
int ntypes = atom->ntypes;
|
||||
typelo = new int[ncol];
|
||||
typehi = new int[ncol];
|
||||
|
||||
if (narg == 4) {
|
||||
ncol = 2;
|
||||
typelo[0] = 1;
|
||||
typehi[0] = ntypes;
|
||||
} else {
|
||||
ncol = 0;
|
||||
int iarg = 4;
|
||||
while (iarg < narg) {
|
||||
force->bounds(arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
|
||||
if (typelo[ncol] > typehi[ncol])
|
||||
error->all(FLERR,"Illegal compute hexorder/atom command");
|
||||
typelo[ncol+1] = typelo[ncol];
|
||||
typehi[ncol+1] = typehi[ncol];
|
||||
ncol+=2;
|
||||
iarg++;
|
||||
}
|
||||
}
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = ncol;
|
||||
|
||||
nmax = 0;
|
||||
q6array = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeHexOrderAtom::~ComputeHexOrderAtom()
|
||||
{
|
||||
delete [] typelo;
|
||||
delete [] typehi;
|
||||
memory->destroy(q6array);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHexOrderAtom::init()
|
||||
{
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"Compute hexorder/atom requires a pair style be defined");
|
||||
if (sqrt(cutsq) > force->pair->cutforce)
|
||||
error->all(FLERR,
|
||||
"Compute hexorder/atom cutoff is longer than pairwise cutoff");
|
||||
|
||||
// need an occasional full neighbor list
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->pair = 0;
|
||||
neighbor->requests[irequest]->compute = 1;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
neighbor->requests[irequest]->occasional = 1;
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->ncompute; i++)
|
||||
if (strcmp(modify->compute[i]->style,"hexorder/atom") == 0) count++;
|
||||
if (count > 1 && comm->me == 0)
|
||||
error->warning(FLERR,"More than one compute hexorder/atom");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHexOrderAtom::init_list(int id, NeighList *ptr)
|
||||
{
|
||||
list = ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeHexOrderAtom::compute_peratom()
|
||||
{
|
||||
int i,j,m,ii,jj,inum,jnum,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
double *count;
|
||||
|
||||
invoked_peratom = update->ntimestep;
|
||||
|
||||
// grow coordination array if necessary
|
||||
|
||||
if (atom->nlocal > nmax) {
|
||||
memory->destroy(q6array);
|
||||
nmax = atom->nmax;
|
||||
memory->create(q6array,nmax,ncol,"hexorder/atom:q6array");
|
||||
array_atom = q6array;
|
||||
}
|
||||
|
||||
// invoke full neighbor list (will copy or build if necessary)
|
||||
|
||||
neighbor->build_one(list);
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// compute order parameter(s) for each atom in group
|
||||
// use full neighbor list to count atoms less than cutoff
|
||||
|
||||
double **x = atom->x;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
|
||||
if (ncol == 2) {
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
double* q6 = q6array[i];
|
||||
q6[0] = q6[1] = 0.0;
|
||||
if (mask[i] & groupbit) {
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
double usum = 0.0;
|
||||
double vsum = 0.0;
|
||||
int ncount = 0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
jtype = type[j];
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0]) {
|
||||
double u, v;
|
||||
calc_q6(delx, dely, u, v);
|
||||
usum += u;
|
||||
vsum += v;
|
||||
ncount++;
|
||||
}
|
||||
}
|
||||
if (ncount > 0) {
|
||||
double ninv = 1.0/ncount ;
|
||||
q6[0] = usum*ninv;
|
||||
q6[1] = vsum*ninv;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
double* q6 = q6array[i];
|
||||
for (m = 0; m < ncol; m++) q6[m] = 0.0;
|
||||
|
||||
if (mask[i] & groupbit) {
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (m = 0; m < ncol; m+=2) {
|
||||
|
||||
double usum = 0.0;
|
||||
double vsum = 0.0;
|
||||
int ncount = 0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
jtype = type[j];
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
if (rsq < cutsq) {
|
||||
if (jtype >= typelo[m] && jtype <= typehi[m]) {
|
||||
double u, v;
|
||||
calc_q6(delx, dely, u, v);
|
||||
usum += u;
|
||||
vsum += v;
|
||||
ncount++;
|
||||
}
|
||||
}
|
||||
if (ncount > 0) {
|
||||
double ninv = 1.0/ncount ;
|
||||
q6[m] = usum*ninv;
|
||||
q6[m+1] = vsum*ninv;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
inline void ComputeHexOrderAtom::calc_q6(double delx, double dely, double &u, double &v) {
|
||||
double rinv = 1.0/sqrt(delx*delx+dely*dely);
|
||||
double x = delx*rinv;
|
||||
double y = dely*rinv;
|
||||
double a = x*x;
|
||||
double b1 = y*y;
|
||||
double b2 = b1*b1;
|
||||
double b3 = b2*b1;
|
||||
u = (( a - 15*b1)*a + 15*b2)*a - b3;
|
||||
v = ((6*a - 20*b1)*a + 6*b2)*x*y;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeHexOrderAtom::memory_usage()
|
||||
{
|
||||
double bytes = ncol*nmax * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
Reference in New Issue
Block a user