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lammps/src/compute_centro_atom.cpp
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compute_centro_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: Michel Perez (U Lyon) for non-fcc lattices
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include "compute_centro_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 "math_extra.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
distsq(NULL), nearest(NULL), centro(NULL)
{
if (narg < 4 || narg > 6) error->all(FLERR,"Illegal compute centro/atom command");
if (strcmp(arg[3],"fcc") == 0) nnn = 12;
else if (strcmp(arg[3],"bcc") == 0) nnn = 8;
else nnn = force->inumeric(FLERR,arg[3]);
// default values
axes_flag = 0;
// optional keywords
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"axes") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute centro/atom command3");
if (strcmp(arg[iarg+1],"yes") == 0) axes_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) axes_flag = 0;
else error->all(FLERR,"Illegal compute centro/atom command2");
iarg += 2;
} else error->all(FLERR,"Illegal compute centro/atom command1");
}
if (nnn <= 0 || nnn % 2)
error->all(FLERR,"Illegal neighbor value for compute centro/atom command");
peratom_flag = 1;
if (!axes_flag) size_peratom_cols = 0;
else size_peratom_cols = 10;
nmax = 0;
maxneigh = 0;
}
/* ---------------------------------------------------------------------- */
ComputeCentroAtom::~ComputeCentroAtom()
{
memory->destroy(centro);
memory->destroy(distsq);
memory->destroy(nearest);
if (axes_flag) memory->destroy(array_atom);
}
/* ---------------------------------------------------------------------- */
void ComputeCentroAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute centro/atom requires a pair style be defined");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"centro/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute centro/atom");
// 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;
}
/* ---------------------------------------------------------------------- */
void ComputeCentroAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeCentroAtom::compute_peratom()
{
int i,j,k,ii,jj,kk,n,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
int *ilist,*jlist,*numneigh,**firstneigh;
invoked_peratom = update->ntimestep;
// grow centro array if necessary
// grow array_atom array if axes_flag set
if (atom->nmax > nmax) {
if (!axes_flag) {
memory->destroy(centro);
nmax = atom->nmax;
memory->create(centro,nmax,"centro/atom:centro");
vector_atom = centro;
} else {
memory->destroy(centro);
memory->destroy(array_atom);
nmax = atom->nmax;
memory->create(centro,nmax,"centro/atom:centro");
memory->create(array_atom,nmax,size_peratom_cols,"centro/atom:array_atom");
}
}
// 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;
// npairs = number of unique pairs
int nhalf = nnn/2;
int npairs = nnn * (nnn-1) / 2;
double *pairs = new double[npairs];
// compute centro-symmetry 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];
// insure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
memory->destroy(distsq);
memory->destroy(nearest);
maxneigh = jnum;
memory->create(distsq,maxneigh,"centro/atom:distsq");
memory->create(nearest,maxneigh,"centro/atom:nearest");
}
// 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;
}
}
// check whether to include local crystal symmetry axes
if (!axes_flag) {
// if not nnn neighbors, centro = 0.0
if (n < nnn) {
centro[i] = 0.0;
continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2(nnn,n,distsq,nearest);
// R = Ri + Rj for each of npairs i,j pairs among nnn neighbors
// pairs = squared length of each R
n = 0;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; 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;
}
}
} else {
// calculate local crystal symmetry axes
// rsq1, rsq2 are two smallest values of R^2
// R1, R2 are corresponding vectors Ri - Rj
// R3 is normal to R1, R2
double rsq1,rsq2;
double* r1 = &array_atom[i][1];
double* r2 = &array_atom[i][4];
double* r3 = &array_atom[i][7];
if (n < nnn) {
centro[i] = 0.0;
MathExtra::zero3(r1);
MathExtra::zero3(r2);
MathExtra::zero3(r3);
continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2(nnn,n,distsq,nearest);
n = 0;
rsq1 = rsq2 = cutsq;
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < nnn; 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;
double rsq = delx*delx + dely*dely + delz*delz;
pairs[n++] = rsq;
if (rsq < rsq2) {
if (rsq < rsq1) {
rsq2 = rsq1;
MathExtra::copy3(r1, r2);
rsq1 = rsq;
MathExtra::sub3(x[jj],x[kk],r1);
} else {
rsq2 = rsq;
MathExtra::sub3(x[jj],x[kk],r2);
}
}
}
}
MathExtra::cross3(r1,r2,r3);
MathExtra::norm3(r1);
MathExtra::norm3(r2);
MathExtra::norm3(r3);
}
// store nhalf smallest pair distances in 1st nhalf locations of pairs
select(nhalf,npairs,pairs);
// centrosymmetry = sum of nhalf smallest squared values
value = 0.0;
for (j = 0; j < nhalf; j++) value += pairs[j];
centro[i] = value;
} else {
centro[i] = 0.0;
if (axes_flag) {
MathExtra::zero3(&array_atom[i][1]);
MathExtra::zero3(&array_atom[i][4]);
MathExtra::zero3(&array_atom[i][7]);
}
}
}
delete [] pairs;
if (axes_flag)
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
array_atom[i][0] = centro[i];
}
}
/* ----------------------------------------------------------------------
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 ComputeCentroAtom::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 ComputeCentroAtom::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 ComputeCentroAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}
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