added group2ID (7acba458) · Commits · 郑智淋 / lammps

doc/src/compute_ptm_atom.rst

+4 −3

Original line number	Diff line number	Diff line
		@@ -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

src/USER-PTM/compute_ptm_atom.cpp

+14 −5

Original line number	Diff line number	Diff line
		@@ -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++) {

src/USER-PTM/compute_ptm_atom.h

+1 −0

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

		}

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