Merge pull request #1896 from pmla/user-ptm-group-fix (e7665180) · Commits · 郑智淋 / lammps

doc/src/compute_ptm_atom.rst

+8 −4

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 is 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
		@@ -82,7 +83,9 @@ The neighbor list needed to compute this quantity is constructed each
		time the calculation is performed (e.g. each time a snapshot of atoms
		is dumped). Thus it can be inefficient to compute/dump this quantity
		too frequently or to have multiple compute/dump commands, each with a
		ptm/atom style.
		ptm/atom style. By default the compute processes all neighbors
		unless the optional group2-ID argument is given, then only members
		of that group are considered as neighbors.

		Output info:

		@@ -106,6 +109,7 @@ The interatomic distance is computed from the scale factor in the RMSD equation.
		The (qw,qx,qy,qz) parameters represent the orientation of the local structure
		in quaternion form. The reference coordinates for each template (from which the
		orientation is determined) can be found in the ptm\_constants.h file in the PTM source directory.
		For atoms that are not within the compute group-ID, all values are set to zero.

		Restrictions
		""""""""""""

src/USER-PTM/compute_ptm_atom.cpp

+22 −2

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 \|\| narg > 6)
		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;
		@@ -168,6 +177,8 @@ typedef struct
		int **firstneigh;
		int *ilist;
		int nlocal;
		int *mask;
		int group2bit;

		} ptmnbrdata_t;

		@@ -184,6 +195,8 @@ static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) {
		static int get_neighbours(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3])
		{
		ptmnbrdata_t* data = (ptmnbrdata_t*)vdata;
		int *mask = data->mask;
		int group2bit = data->group2bit;

		double **x = data->x;
		double *pos = x[atom_index];
		@@ -203,6 +216,9 @@ 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] & group2bit))
		continue;

		j &= NEIGHMASK;
		if (j == atom_index)
		continue;
		@@ -265,7 +281,11 @@ void ComputePTMAtom::compute_peratom() {

		double **x = atom->x;
		int *mask = atom->mask;
		ptmnbrdata_t nbrlist = {x, numneigh, firstneigh, ilist, atom->nlocal};
		ptmnbrdata_t nbrlist = {x, numneigh, firstneigh, ilist, atom->nlocal, mask, group2bit};

		// zero output

		memset(output,0,nmaxNUM_COLUMNSsizeof(double));

		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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