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add option to restrict coordination number by group

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This commit is contained in:
Axel Kohlmeyer
2019-05-16 08:55:03 -04:00
parent 267782d689
commit 27a2d0cbd4
3 changed files with 45 additions and 16 deletions
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39
src/compute_coord_atom.cpp
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@ -25,6 +25,7 @@
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "group.h"
#include "memory.h"
#include "error.h"
@ -37,10 +38,12 @@ using namespace LAMMPS_NS;
ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL),
id_orientorder(NULL), normv(NULL)
group2(NULL), id_orientorder(NULL), normv(NULL)
{
if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");
jgroup = group->find("all");
jgroupbit = group->bitmask[jgroup];
cstyle = NONE;
if (strcmp(arg[3],"cutoff") == 0) {
@ -48,18 +51,29 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
double cutoff = force->numeric(FLERR,arg[4]);
cutsq = cutoff*cutoff;
ncol = narg-5 + 1;
int iarg = 5;
if ((narg > 6) && (strcmp(arg[5],"group") == 0)) {
int len = strlen(arg[6])+1;
group2 = new char[len];
strcpy(group2,arg[6]);
iarg += 2;
jgroup = group->find(group2);
if (jgroup == -1)
error->all(FLERR,"Compute coord/atom group2 ID does not exist");
jgroupbit = group->bitmask[jgroup];
}
ncol = narg-iarg + 1;
int ntypes = atom->ntypes;
typelo = new int[ncol];
typehi = new int[ncol];
if (narg == 5) {
if (narg == iarg) {
ncol = 1;
typelo[0] = 1;
typehi[0] = ntypes;
} else {
ncol = 0;
int iarg = 5;
while (iarg < narg) {
force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
if (typelo[ncol] > typehi[ncol])
@ -106,6 +120,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
ComputeCoordAtom::~ComputeCoordAtom()
{
delete [] group2;
delete [] typelo;
delete [] typehi;
memory->destroy(cvec);
@ -229,13 +244,15 @@ void ComputeCoordAtom::compute_peratom()
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])
n++;
if (mask[j] & jgroupbit) {
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])
n++;
}
}
cvec[i] = n;