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lammps/src/fix_centro.cpp
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fix_centro.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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 "string.h"
#include "fix_centro.h"
#include "atom.h"
#include "modify.h"
#include "update.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
/* ---------------------------------------------------------------------- */
FixCentro::FixCentro(int narg, char **arg) : Fix(narg, arg)
{
if (narg != 3) error->all("Illegal fix centro command");
neigh_full_once = 1;
nmax = 0;
centro = NULL;
maxneigh = 0;
distsq = NULL;
nearest = NULL;
}
/* ---------------------------------------------------------------------- */
FixCentro::~FixCentro()
{
memory->sfree(centro);
memory->sfree(distsq);
memory->sfree(nearest);
}
/* ---------------------------------------------------------------------- */
int FixCentro::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixCentro::init()
{
// warn if more than one centro fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"CENTRO") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one dump custom with a centro attribute");
}
/* ---------------------------------------------------------------------- */
void FixCentro::dump()
{
int j,k,jj,kk,n,numneigh;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
int *neighs;
double pairs[66];
// grow centro array if necessary
if (atom->nlocal > nmax) {
memory->sfree(centro);
nmax = atom->nmax;
centro = (double *) memory->smalloc(nmax*sizeof(double),"centro:centro");
}
// if needed, build a full neighbor list
if (!neighbor->full_every) neighbor->build_full();
// compute centro-symmetry parameter for each atom in group
// use full neighbor list
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double cutsq = force->pair->cutforce * force->pair->cutforce;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
neighs = neighbor->firstneigh_full[i];
numneigh = neighbor->numneigh_full[i];
// insure distsq and nearest arrays are long enough
if (numneigh > maxneigh) {
memory->sfree(distsq);
memory->sfree(nearest);
maxneigh = numneigh;
distsq = (double *) memory->smalloc(maxneigh*sizeof(double),
"centro:distsq");
nearest = (int *) memory->smalloc(maxneigh*sizeof(int),
"centro:nearest");
}
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// nearest[] = atom indices of neighbors
n = 0;
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j >= nall) j %= nall;
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[n] = rsq;
nearest[n++] = j;
}
}
// if not 12 neighbors, centro = 0.0
if (n < 12) {
centro[i] = 0.0;
continue;
}
// store 12 nearest neighs in 1st 12 locations of distsq and nearest
select2(12,n,distsq,nearest);
// R = Ri + Rj for each of 66 i,j pairs among 12 neighbors
// pairs = squared length of each R
n = 0;
for (j = 0; j < 12; j++) {
jj = nearest[j];
for (k = j+1; k < 12; k++) {
kk = nearest[k];
delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
pairs[n++] = delx*delx + dely*dely + delz*delz;
}
}
// store 6 smallest pair distances in 1st 6 locations of pairs
select(6,66,pairs);
// centrosymmetry = sum of 6 smallest squared values
value = 0.0;
for (j = 0; j < 6; j++) value += pairs[j];
centro[i] = value;
}
}
/* ----------------------------------------------------------------------
2 select routines from Numerical Recipes (slightly modified)
find k smallest values in array of length n
2nd routine sorts 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 FixCentro::select(int k, int n, double *arr)
{
int i,ir,j,l,mid;
double a,tmp;
arr--;
l = 1;
ir = n;
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir])
}
if (arr[l+1] > arr[ir]) {
SWAP(arr[l+1],arr[ir])
}
if (arr[l] > arr[l+1]) {
SWAP(arr[l],arr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
for (;;) {
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
if (j >= k) ir = j-1;
if (j <= k) l = i;
}
}
}
/* ---------------------------------------------------------------------- */
void FixCentro::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
------------------------------------------------------------------------- */
int FixCentro::memory_usage()
{
int bytes = nmax * sizeof(double);
return bytes;
}
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