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Added hexatic bond orientational order parameter

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14233 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
2015-11-04 23:56:47 +00:00
parent 984132322e
commit a91bbaf7f2
3 changed files with 47 additions and 144 deletions
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146
src/compute_hexorder_atom.cpp
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@ -38,33 +38,12 @@ 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");
if (narg != 4) error->all(FLERR,"Illegal compute hexorder/atom command");
double cutoff = force->numeric(FLERR,arg[3]);
cutsq = cutoff*cutoff;
ncol = narg-4 + 1;
int ntypes = atom->ntypes;
typelo = new int[ncol];
typehi = new int[ncol];
if (narg == 4) {
ncol = 2;
typelo[0] = 1;
typehi[0] = ntypes;
} else {
ncol = 0;
int iarg = 4;
while (iarg < narg) {
force->bounds(arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
if (typelo[ncol] > typehi[ncol])
error->all(FLERR,"Illegal compute hexorder/atom command");
typelo[ncol+1] = typelo[ncol];
typehi[ncol+1] = typehi[ncol];
ncol+=2;
iarg++;
}
}
ncol = 2;
peratom_flag = 1;
size_peratom_cols = ncol;
@ -77,8 +56,6 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) :
ComputeHexOrderAtom::~ComputeHexOrderAtom()
{
delete [] typelo;
delete [] typehi;
memory->destroy(q6array);
}
@ -119,10 +96,9 @@ void ComputeHexOrderAtom::init_list(int id, NeighList *ptr)
void ComputeHexOrderAtom::compute_peratom()
{
int i,j,m,ii,jj,inum,jnum,jtype;
int i,j,m,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
double *count;
invoked_peratom = update->ntimestep;
@ -148,93 +124,43 @@ void ComputeHexOrderAtom::compute_peratom()
// use full neighbor list to count atoms less than cutoff
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
if (ncol == 2) {
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];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
double usum = 0.0;
double vsum = 0.0;
int ncount = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
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 && jtype >= typelo[0] && jtype <= typehi[0]) {
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;
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];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
double usum = 0.0;
double vsum = 0.0;
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) {
double u, v;
calc_q6(delx, dely, u, v);
usum += u;
vsum += v;
ncount++;
}
}
}
} else {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
double* q6 = q6array[i];
for (m = 0; m < ncol; m++) q6[m] = 0.0;
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (m = 0; m < ncol; m+=2) {
double usum = 0.0;
double vsum = 0.0;
int ncount = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
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) {
if (jtype >= typelo[m] && jtype <= typehi[m]) {
double u, v;
calc_q6(delx, dely, u, v);
usum += u;
vsum += v;
ncount++;
}
}
if (ncount > 0) {
double ninv = 1.0/ncount ;
q6[m] = usum*ninv;
q6[m+1] = vsum*ninv;
}
}
}
if (ncount > 0) {
double ninv = 1.0/ncount ;
q6[0] = usum*ninv;
q6[1] = vsum*ninv;
}
}
}