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added group2ID

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pmla
2020-02-25 18:05:36 +01:00
parent 3168c1116f
commit 7acba4584d
3 changed files with 19 additions and 8 deletions
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7
doc/src/compute_ptm_atom.rst
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@ -9,12 +9,13 @@ Syntax
.. parsed-literal::
compute ID group-ID ptm/atom structures threshold
compute ID group-ID ptm/atom structures threshold group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* ptm/atom = style name of this compute command
* structures = structure types to search for
* threshold = lattice distortion threshold (RMSD)
* group2-ID determines which group are used for neighbor selection (optional, default "all")
Examples
""""""""
@ -22,8 +23,8 @@ Examples
.. parsed-literal::
compute 1 all ptm/atom default 0.1
compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
compute 1 all ptm/atom default 0.1 all
compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15 all
compute 1 all ptm/atom all 0
Description

19
src/USER-PTM/compute_ptm_atom.cpp
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@ -33,6 +33,7 @@ under
#include "neigh_request.h"
#include "neighbor.h"
#include "update.h"
#include "group.h"
#include "ptm_functions.h"
@ -61,7 +62,7 @@ static const char cite_user_ptm_package[] =
ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
: Compute(lmp, narg, arg), list(NULL), output(NULL) {
if (narg != 5)
if (narg < 5)
error->all(FLERR, "Illegal compute ptm/atom command");
char *structures = arg[3];
@ -122,6 +123,14 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg)
if (rmsd_threshold == 0)
rmsd_threshold = INFINITY;
char* group_name = (char *)"all";
if (narg > 5) {
group_name = arg[5];
}
int igroup = group->find(group_name);
if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
group2bit = group->bitmask[igroup];
peratom_flag = 1;
size_peratom_cols = NUM_COLUMNS;
create_attribute = 1;
@ -169,7 +178,7 @@ typedef struct
int *ilist;
int nlocal;
int *mask;
int groupbit;
int group2bit;
} ptmnbrdata_t;
@ -187,7 +196,7 @@ static int get_neighbours(void* vdata, size_t central_index, size_t atom_index,
{
ptmnbrdata_t* data = (ptmnbrdata_t*)vdata;
int *mask = data->mask;
int groupbit = data->groupbit;
int group2bit = data->group2bit;
double **x = data->x;
double *pos = x[atom_index];
@ -207,7 +216,7 @@ static int get_neighbours(void* vdata, size_t central_index, size_t atom_index,
for (int jj = 0; jj < jnum; jj++) {
int j = jlist[jj];
if (!(mask[j] & groupbit))
if (!(mask[j] & group2bit))
continue;
j &= NEIGHMASK;
@ -272,7 +281,7 @@ void ComputePTMAtom::compute_peratom() {
double **x = atom->x;
int *mask = atom->mask;
ptmnbrdata_t nbrlist = {x, numneigh, firstneigh, ilist, atom->nlocal, mask, groupbit};
ptmnbrdata_t nbrlist = {x, numneigh, firstneigh, ilist, atom->nlocal, mask, group2bit};
for (int ii = 0; ii < inum; ii++) {

1
src/USER-PTM/compute_ptm_atom.h
View File

@ -39,6 +39,7 @@ class ComputePTMAtom : public Compute {
double rmsd_threshold;
class NeighList *list;
double **output;
int group2bit;
};
}