provide keyword/value option to compute ackland/atom for selecting legacy or... (c3588f08) · Commits · 郑智淋 / lammps

doc/src/compute_ackland_atom.txt

+16 −5

Original line number	Diff line number	Diff line
		@@ -10,19 +10,29 @@ compute ackland/atom command :h3

		[Syntax:]

		compute ID group-ID ackland/atom :pre
		compute ID group-ID ackland/atom keyword/value :pre

		ID, group-ID are documented in "compute"_compute.html command
		ackland/atom = style name of this compute command :ul
		ID, group-ID are documented in "compute"_compute.html command :ulb,l
		ackland/atom = style name of this compute command :l

		zero or more keyword/value pairs may be appended :l
		keyword = {legacy} :l
		{legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
		:ule

		[Examples:]

		compute 1 all ackland/atom :pre
		compute 1 all ackland/atom
		compute 1 all ackland/atom legacy yes :pre

		[Description:]

		Defines a computation that calculates the local lattice structure
		according to the formulation given in "(Ackland)"_#Ackland.
		Historically, LAMMPS had two, slightly different implementations of
		the algorithm from the paper. With the {legacy} keyword, it is
		possible to switch between the pre-2015 ({legacy yes}) and post-2015
		implemention ({legacy no}). The post-2015 variant is the default.

		In contrast to the "centro-symmetry
		parameter"_compute_centro_atom.html this method is stable against
		@@ -66,7 +76,8 @@ integers defined above.

		"compute centro/atom"_compute_centro_atom.html

		[Default:] none
		[Default:]
		The keyword {legacy} defaults to {no}.

		:line

src/USER-MISC/compute_ackland_atom.cpp

+116 −47

Original line number	Diff line number	Diff line
		@@ -14,6 +14,7 @@
		/* ----------------------------------------------------------------------
		Contributing author: G. Ziegenhain, gerolf@ziegenhain.com
		Copyright (C) 2007
		Updated algorithm by: Brian Barnes, brian.c.barnes11.civ@mail.mil
		------------------------------------------------------------------------- */

		#include <cmath>
		@@ -40,7 +41,8 @@ enum{UNKNOWN,BCC,FCC,HCP,ICO};
		ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS lmp, int narg, char *arg) :
		Compute(lmp, narg, arg)
		{
		if (narg != 3) error->all(FLERR,"Illegal compute ackland/atom command");
		if ((narg < 3) \|\| (narg > 5))
		error->all(FLERR,"Illegal compute ackland/atom command");

		peratom_flag = 1;
		size_peratom_cols = 0;
		@@ -48,10 +50,26 @@ ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS lmp, int narg, char *arg) :
		nmax = 0;
		structure = NULL;
		maxneigh = 0;
		legacy = 0;
		distsq = NULL;
		nearest = NULL;
		nearest_n0 = NULL;
		nearest_n1 = NULL;

		int iarg = 3;
		while (narg > iarg) {
		if (strcmp("legacy",arg[iarg]) == 0) {
		++iarg;
		if (iarg >= narg)
		error->all(FLERR,"Invalid compute ackland/atom command");
		if (strcmp("yes",arg[iarg]) == 0)
		legacy = 1;
		else if (strcmp("no",arg[iarg]) == 0)
		legacy = 0;
		else error->all(FLERR,"Invalid compute ackland/atom command");
		}
		++iarg;
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -231,6 +249,53 @@ void ComputeAcklandAtom::compute_peratom()
		else chi[7]++;
		}
		}
		if (legacy) {

		// This is the original implementation by Gerolf Ziegenhain
		// Deviations from the different lattice structures

		double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]);
		double delta_cp = fabs(1.-(double)chi[6]/24.);
		double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+
		(double)chi[2])/6.0;
		double delta_hcp = (fabs((double)chi[0]-3.)+
		fabs((double)chi[0]+(double)chi[1]+
		(double)chi[2]+(double)chi[3]-9.0))/12.0;

		// Identification of the local structure according to the reference

		if (chi[0] == 7) { delta_bcc = 0.; }
		else if (chi[0] == 6) { delta_fcc = 0.; }
		else if (chi[0] <= 3) { delta_hcp = 0.; }

		if (chi[7] > 0.)
		structure[i] = UNKNOWN;
		else
		if (chi[4] < 3.)
		{
		if (n1 > 13 \|\| n1 < 11)
		structure[i] = UNKNOWN;
		else
		structure[i] = ICO;
		} else
		if (delta_bcc <= delta_cp)
		{
		if (n1 < 11)
		structure[i] = UNKNOWN;
		else
		structure[i] = BCC;
		} else
		if (n1 > 12 \|\| n1 < 11)
		structure[i] = UNKNOWN;
		else
		if (delta_fcc < delta_hcp)
		structure[i] = FCC;
		else
		structure[i] = HCP;

		} else {

		// This is the updated implementation by Brian Barnes

		if (chi[7] > 0 \|\| n0 < 11) structure[i] = UNKNOWN;
		else if (chi[0] == 7) structure[i] = BCC;
		@@ -252,8 +317,11 @@ void ComputeAcklandAtom::compute_peratom()
		double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
		+(double)chi[2])/6.0;

		double delta_hcp = (fabs((double)chi[0]-3.)+fabs((double)chi[0]
		+(double)chi[1]+(double)chi[2]+(double)chi[3]
		double delta_hcp = (fabs((double)chi[0]-3.)
		+fabs((double)chi[0]
		+(double)chi[1]
		+(double)chi[2]
		+(double)chi[3]
		-9.0))/12.0;

		// Identification of the local structure according to the reference
		@@ -276,6 +344,7 @@ void ComputeAcklandAtom::compute_peratom()
		}
		}
		}
		}
		} else structure[i] = 0.0;
		}
		}

src/USER-MISC/compute_ackland_atom.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -34,7 +34,7 @@ class ComputeAcklandAtom : public Compute {
		double memory_usage();

		private:
		int nmax,maxneigh;
		int nmax,maxneigh,legacy;
		double *distsq;
		int nearest, nearest_n0, *nearest_n1;
		double *structure;

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