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lammps/src/compute_hexorder_atom.cpp
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compute_hexorder_atom.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
#include <complex>
#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"
#include "math_const.h"
#ifdef DBL_EPSILON
#define MY_EPSILON (10.0*DBL_EPSILON)
#else
#define MY_EPSILON (10.0*2.220446049250313e-16)
#endif
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
distsq(NULL), nearest(NULL), qnarray(NULL)
{
if (narg < 3 ) error->all(FLERR,"Illegal compute hexorder/atom command");
ndegree = 6;
nnn = 6;
cutsq = 0.0;
// process optional args
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"degree") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
ndegree = force->numeric(FLERR,arg[iarg+1]);
if (ndegree < 0)
error->all(FLERR,"Illegal compute hexorder/atom command");
iarg += 2;
} else if (strcmp(arg[iarg],"nnn") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
if (strcmp(arg[iarg+1],"NULL") == 0)
nnn = 0;
else {
nnn = force->numeric(FLERR,arg[iarg+1]);
if (nnn < 0)
error->all(FLERR,"Illegal compute hexorder/atom command");
}
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hexorder/atom command");
double cutoff = force->numeric(FLERR,arg[iarg+1]);
if (cutoff <= 0.0)
error->all(FLERR,"Illegal compute hexorder/atom command");
cutsq = cutoff*cutoff;
iarg += 2;
} else error->all(FLERR,"Illegal compute hexorder/atom command");
}
ncol = 2;
peratom_flag = 1;
size_peratom_cols = ncol;
nmax = 0;
maxneigh = 0;
}
/* ---------------------------------------------------------------------- */
ComputeHexOrderAtom::~ComputeHexOrderAtom()
{
memory->destroy(qnarray);
memory->destroy(distsq);
memory->destroy(nearest);
}
/* ---------------------------------------------------------------------- */
void ComputeHexOrderAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute hexorder/atom requires a pair style be defined");
if (cutsq == 0.0) cutsq = force->pair->cutforce * force->pair->cutforce;
else 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,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
invoked_peratom = update->ntimestep;
// grow order parameter array if necessary
if (atom->nmax > nmax) {
memory->destroy(qnarray);
nmax = atom->nmax;
memory->create(qnarray,nmax,ncol,"hexorder/atom:qnarray");
array_atom = qnarray;
}
// 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 for each atom in group
// use full neighbor list to count atoms less than cutoff
double **x = atom->x;
int *mask = atom->mask;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double* qn = qnarray[i];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// insure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
memory->destroy(distsq);
memory->destroy(nearest);
maxneigh = jnum;
memory->create(distsq,maxneigh,"hexorder/atom:distsq");
memory->create(nearest,maxneigh,"hexorder/atom:nearest");
}
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// nearest[] = atom indices of neighbors
int ncount = 0;
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;
if (rsq < cutsq) {
distsq[ncount] = rsq;
nearest[ncount++] = j;
}
}
// if not nnn neighbors, order parameter = 0;
if (ncount < nnn) {
qn[0] = qn[1] = 0.0;
continue;
}
// if nnn > 0, use only nearest nnn neighbors
if (nnn > 0) {
select2(nnn,ncount,distsq,nearest);
ncount = nnn;
}
double usum = 0.0;
double vsum = 0.0;
for (jj = 0; jj < ncount; jj++) {
j = nearest[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
double u, v;
calc_qn_complex(delx, dely, u, v);
usum += u;
vsum += v;
}
qn[0] = usum/nnn;
qn[1] = vsum/nnn;
}
}
}
// calculate order parameter using std::complex::pow function
inline void ComputeHexOrderAtom::calc_qn_complex(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;
std::complex<double> z(x, y);
std::complex<double> zn = pow(z, nnn);
u = real(zn);
v = imag(zn);
}
// calculate order parameter using trig functions
// this is usually slower, but can be used if <complex> not available
inline void ComputeHexOrderAtom::calc_qn_trig(double delx, double dely, double &u, double &v) {
double ntheta;
if(fabs(delx) <= MY_EPSILON) {
if(dely > 0.0) ntheta = nnn * MY_PI / 2.0;
else ntheta = nnn * 3.0 * MY_PI / 2.0;
} else ntheta = nnn * atan(dely / delx);
u = cos(ntheta);
v = sin(ntheta);
}
/* ----------------------------------------------------------------------
select2 routine from Numerical Recipes (slightly modified)
find k smallest values in array of length n
sort auxiliary array at same time
------------------------------------------------------------------------- */
#define SWAP(a,b) tmp = a; a = b; b = tmp;
#define ISWAP(a,b) itmp = a; a = b; b = itmp;
/* ---------------------------------------------------------------------- */
void ComputeHexOrderAtom::select2(int k, int n, double *arr, int *iarr)
{
int i,ir,j,l,mid,ia,itmp;
double a,tmp;
arr--;
iarr--;
l = 1;
ir = n;
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
ISWAP(iarr[mid],iarr[l+1])
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
}
if (arr[l+1] > arr[ir]) {
SWAP(arr[l+1],arr[ir])
ISWAP(iarr[l+1],iarr[ir])
}
if (arr[l] > arr[l+1]) {
SWAP(arr[l],arr[l+1])
ISWAP(iarr[l],iarr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
ia = iarr[l+1];
for (;;) {
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
ISWAP(iarr[i],iarr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
iarr[l+1] = iarr[j];
iarr[j] = ia;
if (j >= k) ir = j-1;
if (j <= k) l = i;
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeHexOrderAtom::memory_usage()
{
double bytes = ncol*nmax * sizeof(double);
bytes += maxneigh * sizeof(double);
bytes += maxneigh * sizeof(int);
return bytes;
}
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