add option to restrict coordination number by group (27a2d0cb) · Commits · 郑智淋 / lammps

doc/src/compute_coord_atom.txt

+14 −5

Original line number	Diff line number	Diff line
		@@ -15,8 +15,9 @@ compute ID group-ID coord/atom cstyle args ... :pre
		ID, group-ID are documented in "compute"_compute.html command :ulb,l
		coord/atom = style name of this compute command :l
		cstyle = {cutoff} or {orientorder} :l
		{cutoff} args = cutoff typeN
		{cutoff} args = cutoff \[group group2-ID\] typeN
		cutoff = distance within which to count coordination neighbors (distance units)
		group {group2-ID} = select group-ID to restrict which atoms to cound for coordination number (optional)
		typeN = atom type for Nth coordination count (see asterisk form below)
		{orientorder} args = orientorderID threshold
		orientorderID = ID of an orientorder/atom compute
		@@ -28,6 +29,7 @@ cstyle = {cutoff} or {orientorder} :l
		compute 1 all coord/atom cutoff 2.0
		compute 1 all coord/atom cutoff 6.0 1 2
		compute 1 all coord/atom cutoff 6.0 24 58 *
		compute 1 solute coord/atom cutoff 2.0 group solvent
		compute 1 all coord/atom orientorder 2 0.5 :pre

		[Description:]
		@@ -38,9 +40,14 @@ meaning of the resulting value depend on the {cstyle} keyword used.

		The {cutoff} cstyle calculates one or more traditional coordination
		numbers for each atom. A coordination number is defined as the number
		of neighbor atoms with specified atom type(s) that are within the
		specified cutoff distance from the central atom. Atoms not in the
		specified group are included in the coordination number tally.
		of neighbor atoms with specified atom type(s), and optionally within
		the specified group, that are within the specified cutoff distance from
		the central atom. The compute group selects only the central atoms; all
		neighboring atoms, unless selected by type, type range, or group option,
		are included in the coordinations number tally.

		The optional {group} keyword allows to specify from which group atoms
		contribute to the coordination number. Default setting is group 'all'.

		The {typeN} keywords allow specification of which atom types
		contribute to each coordination number. One coordination number is
		@@ -122,7 +129,9 @@ explained above.
		"compute cluster/atom"_compute_cluster_atom.html
		"compute orientorder/atom"_compute_orientorder_atom.html

		[Default:] none
		[Default:]

		group = all

		:line

src/compute_coord_atom.cpp

+28 −11

Original line number	Diff line number	Diff line
		@@ -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);
		@@ -229,6 +244,7 @@ void ComputeCoordAtom::compute_peratom()
		j = jlist[jj];
		j &= NEIGHMASK;

		if (mask[j] & jgroupbit) {
		jtype = type[j];
		delx = xtmp - x[j][0];
		dely = ytmp - x[j][1];
		@@ -237,6 +253,7 @@ void ComputeCoordAtom::compute_peratom()
		if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
		n++;
		}
		}

		cvec[i] = n;
		} else cvec[i] = 0.0;

src/compute_coord_atom.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -45,6 +45,9 @@ class ComputeCoordAtom : public Compute {
		double *cvec;
		double **carray;

		char *group2;
		int jgroup,jgroupbit;

		class ComputeOrientOrderAtom *c_orientorder;
		char *id_orientorder;
		double threshold;

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