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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3988 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-04-13 15:09:31 +00:00
parent a568e7267b
commit 54b920041d
2 changed files with 71 additions and 63 deletions
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41
src/compute_centro_atom.cpp
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@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "compute_centro_atom.h"
#include "atom.h"
#include "update.h"
@ -32,7 +33,14 @@ using namespace LAMMPS_NS;
ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute centro/atom command");
if (narg != 4) error->all("Illegal compute centro/atom command");
if (strcmp(arg[3],"fcc") == 0) nnn = 12;
else if (strcmp(arg[3],"bcc") == 0) nnn = 8;
else nnn = atoi(arg[3]);
if (nnn <= 0 || nnn % 2)
error->all("Illegal neighbor value for compute centro/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
@ -90,7 +98,6 @@ 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;
double pairs[66];
invoked_peratom = update->ntimestep;
@ -113,6 +120,12 @@ void ComputeCentroAtom::compute_peratom()
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
@ -161,24 +174,24 @@ void ComputeCentroAtom::compute_peratom()
}
}
// if not 12 neighbors, centro = 0.0
// if not nnn neighbors, centro = 0.0
if (n < 12) {
if (n < nnn) {
centro[i] = 0.0;
continue;
}
// store 12 nearest neighs in 1st 12 locations of distsq and nearest
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2(12,n,distsq,nearest);
select2(nnn,n,distsq,nearest);
// R = Ri + Rj for each of 66 i,j pairs among 12 neighbors
// 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 < 12; j++) {
for (j = 0; j < nnn; j++) {
jj = nearest[j];
for (k = j+1; k < 12; k++) {
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;
@ -187,17 +200,19 @@ void ComputeCentroAtom::compute_peratom()
}
}
// store 6 smallest pair distances in 1st 6 locations of pairs
// store nhalf smallest pair distances in 1st nhalf locations of pairs
select(6,66,pairs);
select(nhalf,npairs,pairs);
// centrosymmetry = sum of 6 smallest squared values
// centrosymmetry = sum of nhalf smallest squared values
value = 0.0;
for (j = 0; j < 6; j++) value += pairs[j];
for (j = 0; j < nhalf; j++) value += pairs[j];
centro[i] = value;
} else centro[i] = 0.0;
}
delete [] pairs;
}
/* ----------------------------------------------------------------------