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lammps/src/USER-MISC/compute_ackland_atom.cpp
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compute_ackland_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: G. Ziegenhain, gerolf@ziegenhain.com
Copyright (C) 2007
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_ackland_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.h>
using namespace LAMMPS_NS;
enum{UNKNOWN,BCC,FCC,HCP,ICO};
/* ---------------------------------------------------------------------- */
ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute ackland/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
nmax = 0;
structure = NULL;
maxneigh = 0;
distsq = NULL;
nearest = NULL;
nearest_n0 = NULL;
nearest_n1 = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeAcklandAtom::~ComputeAcklandAtom()
{
memory->destroy(structure);
memory->destroy(distsq);
memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
}
/* ---------------------------------------------------------------------- */
void ComputeAcklandAtom::init()
{
// 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,"ackland/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute ackland/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeAcklandAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeAcklandAtom::compute_peratom()
{
int i,j,ii,jj,k,n,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int chi[8];
invoked_peratom = update->ntimestep;
// grow structure array if necessary
if (atom->nmax > nmax) {
memory->destroy(structure);
nmax = atom->nmax;
memory->create(structure,nmax,"compute/ackland/atom:ackland");
vector_atom = structure;
}
// 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 structure parameter for each atom in group
// use full neighbor list
double **x = atom->x;
int *mask = atom->mask;
double cutsq = force->pair->cutforce * force->pair->cutforce;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
memory->destroy(distsq);
memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
maxneigh = jnum;
memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
}
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// nearest[] = atom indices of neighbors
n = 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[n] = rsq;
nearest[n++] = j;
}
}
// Select 6 nearest neighbors
select2(6,n,distsq,nearest);
// Mean squared separation
double r0_sq = 0.;
for (j = 0; j < 6; j++)
r0_sq += distsq[j];
r0_sq /= 6.;
// n0 near neighbors with: distsq<1.45*r0_sq
// n1 near neighbors with: distsq<1.55*r0_sq
double n0_dist_sq = 1.45*r0_sq,
n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
if (distsq[j] < n1_dist_sq) {
nearest_n1[n1++] = nearest[j];
if (distsq[j] < n0_dist_sq) {
nearest_n0[n0++] = nearest[j];
}
}
}
// Evaluate all angles <(r_ij,rik) forall n0 particles with:
// distsq < 1.45*r0_sq
double bond_angle;
double norm_j, norm_k;
chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik;
for (j = 0; j < n0; j++) {
x_ij = x[i][0]-x[nearest_n0[j]][0];
y_ij = x[i][1]-x[nearest_n0[j]][1];
z_ij = x[i][2]-x[nearest_n0[j]][2];
norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
if (norm_j <= 0.) continue;
for (k = j+1; k < n0; k++) {
x_ik = x[i][0]-x[nearest_n0[k]][0];
y_ik = x[i][1]-x[nearest_n0[k]][1];
z_ik = x[i][2]-x[nearest_n0[k]][2];
norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
if (norm_k <= 0.)
continue;
bond_angle = (x_ij*x_ik + y_ij*y_ik + z_ij*z_ik) / (norm_j*norm_k);
// Histogram for identifying the relevant peaks
if (bond_angle < -0.945) chi[0]++;
else if (bond_angle < -0.915) chi[1]++;
else if (bond_angle < -0.755) chi[2]++;
else if (bond_angle < -0.195) chi[3]++;
else if (bond_angle < 0.195) chi[4]++;
else if (bond_angle < 0.245) chi[5]++;
else if (bond_angle < 0.795) chi[6]++;
else chi[7]++;
}
}
if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
else if (chi[0] == 7) structure[i] = BCC;
else if (chi[0] == 6) structure[i] = FCC;
else if (chi[0] == 3) structure[i] = HCP;
else {
// Deviations from the different lattice structures
double delta_cp = fabs(1.-(double)chi[6]/24.);
// ensure we do not get divide by zero
// and if we will, make delta_bcc irrelevant
double delta_bcc = delta_cp + 1.0;
int chi56m4 = chi[5]+chi[6]-chi[4];
// note that chi[7] presumed zero
if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
+(double)chi[2])/6.0;
double delta_hcp = (fabs((double)chi[0]-3.)+fabs((double)chi[0]
+(double)chi[1]+(double)chi[2]+(double)chi[3]
-9.0))/12.0;
// Identification of the local structure according to the reference
if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
&& delta_hcp >= 0.1) structure[i] = UNKNOWN;
// not part of Ackland-Jones 2006; included for backward compatibility
if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
else {
if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
if (n0 > 12) structure[i] = UNKNOWN;
else {
if (delta_fcc < delta_hcp) structure[i] = FCC;
else
structure[i] = HCP;
}
}
}
}
} else structure[i] = 0.0;
}
}
/* ----------------------------------------------------------------------
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 ComputeAcklandAtom::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 ComputeAcklandAtom::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 ComputeAcklandAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}
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