git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@255 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
290
src/compute_centro_atom.cpp
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290
src/compute_centro_atom.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "compute_centro_atom.h"
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#include "atom.h"
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#include "modify.h"
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#include "update.h"
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#include "neighbor.h"
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#include "force.h"
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#include "pair.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal compute centro/atom command");
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peratom_flag = 1;
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size_peratom = 0;
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neigh_full_once = 1;
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nmax = 0;
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centro = NULL;
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maxneigh = 0;
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distsq = NULL;
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nearest = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeCentroAtom::~ComputeCentroAtom()
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{
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memory->sfree(centro);
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memory->sfree(distsq);
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memory->sfree(nearest);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCentroAtom::init()
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{
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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if (strcmp(modify->compute[i]->style,"centro/atom") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning("More than one compute centro/atom defined");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCentroAtom::compute_peratom()
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{
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int j,k,jj,kk,n,numneigh;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
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int *neighs;
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double pairs[66];
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// grow centro array if necessary
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if (atom->nlocal > nmax) {
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memory->sfree(centro);
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nmax = atom->nmax;
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centro = (double *)
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memory->smalloc(nmax*sizeof(double),"compute/centro/atom:centro");
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scalar_atom = centro;
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}
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// if needed, build a full neighbor list
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if (!neighbor->full_every) neighbor->build_full();
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// compute centro-symmetry parameter for each atom in group
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// use full neighbor list
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double **x = atom->x;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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double cutsq = force->pair->cutforce * force->pair->cutforce;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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neighs = neighbor->firstneigh_full[i];
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numneigh = neighbor->numneigh_full[i];
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// insure distsq and nearest arrays are long enough
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if (numneigh > maxneigh) {
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memory->sfree(distsq);
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memory->sfree(nearest);
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maxneigh = numneigh;
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distsq = (double *) memory->smalloc(maxneigh*sizeof(double),
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"compute/centro/atom:distsq");
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nearest = (int *) memory->smalloc(maxneigh*sizeof(int),
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"compute/centro/atom:nearest");
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}
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// loop over list of all neighbors within force cutoff
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// distsq[] = distance sq to each
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// nearest[] = atom indices of neighbors
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n = 0;
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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if (j >= nall) j %= nall;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < cutsq) {
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distsq[n] = rsq;
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nearest[n++] = j;
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}
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}
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// if not 12 neighbors, centro = 0.0
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if (n < 12) {
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centro[i] = 0.0;
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continue;
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}
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// store 12 nearest neighs in 1st 12 locations of distsq and nearest
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select2(12,n,distsq,nearest);
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// R = Ri + Rj for each of 66 i,j pairs among 12 neighbors
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// pairs = squared length of each R
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n = 0;
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for (j = 0; j < 12; j++) {
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jj = nearest[j];
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for (k = j+1; k < 12; k++) {
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kk = nearest[k];
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delx = x[jj][0] + x[kk][0] - 2.0*xtmp;
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dely = x[jj][1] + x[kk][1] - 2.0*ytmp;
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delz = x[jj][2] + x[kk][2] - 2.0*ztmp;
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pairs[n++] = delx*delx + dely*dely + delz*delz;
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}
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}
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// store 6 smallest pair distances in 1st 6 locations of pairs
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select(6,66,pairs);
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// centrosymmetry = sum of 6 smallest squared values
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value = 0.0;
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for (j = 0; j < 6; j++) value += pairs[j];
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centro[i] = value;
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}
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}
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/* ----------------------------------------------------------------------
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2 select routines from Numerical Recipes (slightly modified)
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find k smallest values in array of length n
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2nd routine sorts auxiliary array at same time
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------------------------------------------------------------------------- */
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#define SWAP(a,b) tmp = a; a = b; b = tmp;
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#define ISWAP(a,b) itmp = a; a = b; b = itmp;
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void ComputeCentroAtom::select(int k, int n, double *arr)
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{
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int i,ir,j,l,mid;
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double a,tmp;
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arr--;
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l = 1;
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ir = n;
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for (;;) {
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if (ir <= l+1) {
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if (ir == l+1 && arr[ir] < arr[l]) {
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SWAP(arr[l],arr[ir])
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}
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return;
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} else {
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mid=(l+ir) >> 1;
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SWAP(arr[mid],arr[l+1])
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if (arr[l] > arr[ir]) {
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SWAP(arr[l],arr[ir])
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}
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if (arr[l+1] > arr[ir]) {
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SWAP(arr[l+1],arr[ir])
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}
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if (arr[l] > arr[l+1]) {
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SWAP(arr[l],arr[l+1])
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}
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i = l+1;
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j = ir;
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a = arr[l+1];
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for (;;) {
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do i++; while (arr[i] < a);
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do j--; while (arr[j] > a);
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if (j < i) break;
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SWAP(arr[i],arr[j])
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}
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arr[l+1] = arr[j];
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arr[j] = a;
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if (j >= k) ir = j-1;
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if (j <= k) l = i;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeCentroAtom::select2(int k, int n, double *arr, int *iarr)
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{
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int i,ir,j,l,mid,ia,itmp;
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double a,tmp;
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arr--;
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iarr--;
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l = 1;
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ir = n;
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for (;;) {
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if (ir <= l+1) {
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if (ir == l+1 && arr[ir] < arr[l]) {
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SWAP(arr[l],arr[ir])
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ISWAP(iarr[l],iarr[ir])
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}
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return;
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} else {
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mid=(l+ir) >> 1;
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SWAP(arr[mid],arr[l+1])
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ISWAP(iarr[mid],iarr[l+1])
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if (arr[l] > arr[ir]) {
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SWAP(arr[l],arr[ir])
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ISWAP(iarr[l],iarr[ir])
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}
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if (arr[l+1] > arr[ir]) {
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SWAP(arr[l+1],arr[ir])
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ISWAP(iarr[l+1],iarr[ir])
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}
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if (arr[l] > arr[l+1]) {
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SWAP(arr[l],arr[l+1])
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ISWAP(iarr[l],iarr[l+1])
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}
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i = l+1;
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j = ir;
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a = arr[l+1];
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ia = iarr[l+1];
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for (;;) {
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do i++; while (arr[i] < a);
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do j--; while (arr[j] > a);
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if (j < i) break;
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SWAP(arr[i],arr[j])
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ISWAP(iarr[i],iarr[j])
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}
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arr[l+1] = arr[j];
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arr[j] = a;
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iarr[l+1] = iarr[j];
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iarr[j] = ia;
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if (j >= k) ir = j-1;
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if (j <= k) l = i;
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}
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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int ComputeCentroAtom::memory_usage()
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{
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int bytes = nmax * sizeof(double);
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return bytes;
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}
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