ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Added hexatic bond orientational order parameter

Browse Source 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14234 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
2015-11-05 01:33:46 +00:00
parent a91bbaf7f2
commit 4f71701e4e
5 changed files with 135 additions and 44 deletions
Download Patch File Download Diff File Expand all files Collapse all files

149
src/compute_hexorder_atom.cpp
View File

@ -38,10 +38,7 @@ using namespace LAMMPS_NS;
ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all(FLERR,"Illegal compute hexorder/atom command");
double cutoff = force->numeric(FLERR,arg[3]);
cutsq = cutoff*cutoff;
if (narg != 3) error->all(FLERR,"Illegal compute hexorder/atom command");
ncol = 2;
@ -50,6 +47,10 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
nmax = 0;
q6array = NULL;
maxneigh = 0;
distsq = NULL;
nearest = NULL;
nnn = 6;
}
/* ---------------------------------------------------------------------- */
@ -57,6 +58,8 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
ComputeHexOrderAtom::~ComputeHexOrderAtom()
{
memory->destroy(q6array);
memory->destroy(distsq);
memory->destroy(nearest);
}
/* ---------------------------------------------------------------------- */
@ -65,9 +68,6 @@ void ComputeHexOrderAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute hexorder/atom requires a pair style be defined");
if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,
"Compute hexorder/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
@ -102,7 +102,7 @@ void ComputeHexOrderAtom::compute_peratom()
invoked_peratom = update->ntimestep;
// grow coordination array if necessary
// grow order parameter array if necessary
if (atom->nlocal > nmax) {
memory->destroy(q6array);
@ -120,16 +120,16 @@ void ComputeHexOrderAtom::compute_peratom()
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute order parameter(s) for each atom in group
// compute order parameter for each atom in group
// use full neighbor list to count atoms less than cutoff
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];
double* q6 = q6array[i];
q6[0] = q6[1] = 0.0;
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
@ -137,31 +137,62 @@ void ComputeHexOrderAtom::compute_peratom()
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,"hexcoord/atom:distsq");
memory->create(nearest,maxneigh,"hexcoord/atom:nearest");
}
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// nearest[] = atom indices of neighbors
int ncount = 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[ncount] = rsq;
nearest[ncount++] = j;
}
}
// if not nnn neighbors, order parameter = 0;
if (ncount < nnn) {
q6[0] = q6[1] = 0.0;
continue;
}
// store nnn nearest neighs in 1st nnn locations of distsq and nearest
select2(nnn,ncount,distsq,nearest);
double usum = 0.0;
double vsum = 0.0;
int ncount = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
for (jj = 0; jj < nnn; jj++) {
j = nearest[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) {
double u, v;
calc_q6(delx, dely, u, v);
usum += u;
vsum += v;
ncount++;
}
}
if (ncount > 0) {
double ninv = 1.0/ncount ;
q6[0] = usum*ninv;
q6[1] = vsum*ninv;
double u, v;
calc_q6(delx, dely, u, v);
usum += u;
vsum += v;
}
q6[0] = usum/nnn;
q6[1] = vsum/nnn;
}
}
}
@ -178,6 +209,70 @@ inline void ComputeHexOrderAtom::calc_q6(double delx, double dely, double &u, do
v = ((6*a - 20*b1)*a + 6*b2)*x*y;
}
/* ----------------------------------------------------------------------
select2 routine from Numerical Recipes (slightly modified)
find k smallest values in array of length n
sort 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 ComputeHexOrderAtom::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
------------------------------------------------------------------------- */