From c3588f08b741cbfda6462eff62b1361106d772a7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 6 May 2018 19:21:37 -0400
Subject: [PATCH] provide keyword/value option to compute ackland/atom for
selecting legacy or current variant of implementation
---
doc/src/compute_ackland_atom.txt | 21 +++-
src/USER-MISC/compute_ackland_atom.cpp | 163 ++++++++++++++++++-------
src/USER-MISC/compute_ackland_atom.h | 2 +-
3 files changed, 133 insertions(+), 53 deletions(-)
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index b75d100112..41a8d7e6d2 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -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
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index dcf17ca489..a888fdbfc5 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -12,8 +12,9 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing author: G. Ziegenhain, gerolf@ziegenhain.com
- Copyright (C) 2007
+ 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;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -140,13 +158,13 @@ void ComputeAcklandAtom::compute_peratom()
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
- memory->destroy(distsq);
- memory->destroy(nearest);
+ memory->destroy(distsq);
+ memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
- maxneigh = jnum;
- memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
- memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
+ maxneigh = jnum;
+ memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
+ memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
}
@@ -157,14 +175,14 @@ void ComputeAcklandAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
+ j = jlist[jj];
j &= NEIGHMASK;
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
}
@@ -188,12 +206,12 @@ void ComputeAcklandAtom::compute_peratom()
n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
- if (distsq[j] < n1_dist_sq) {
- nearest_n1[n1++] = nearest[j];
- if (distsq[j] < n0_dist_sq) {
- nearest_n0[n0++] = nearest[j];
- }
- }
+ if (distsq[j] < n1_dist_sq) {
+ nearest_n1[n1++] = nearest[j];
+ if (distsq[j] < n0_dist_sq) {
+ nearest_n0[n0++] = nearest[j];
+ }
+ }
}
// Evaluate all angles <(r_ij,rik) forall n0 particles with:
@@ -231,47 +249,98 @@ void ComputeAcklandAtom::compute_peratom()
else chi[7]++;
}
}
+ if (legacy) {
- if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
- else if (chi[0] == 7) structure[i] = BCC;
- else if (chi[0] == 6) structure[i] = FCC;
- else if (chi[0] == 3) structure[i] = HCP;
- else {
+ // 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;
+ else if (chi[0] == 6) structure[i] = FCC;
+ else if (chi[0] == 3) structure[i] = HCP;
+ else {
+ // Deviations from the different lattice structures
- // ensure we do not get divide by zero
- // and if we will, make delta_bcc irrelevant
- double delta_bcc = delta_cp + 1.0;
- int chi56m4 = chi[5]+chi[6]-chi[4];
+ double delta_cp = fabs(1.-(double)chi[6]/24.);
- // note that chi[7] presumed zero
- if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
+ // ensure we do not get divide by zero
+ // and if we will, make delta_bcc irrelevant
+ double delta_bcc = delta_cp + 1.0;
+ int chi56m4 = chi[5]+chi[6]-chi[4];
- double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
- +(double)chi[2])/6.0;
+ // note that chi[7] presumed zero
+ if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
- 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;
+ double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
+ +(double)chi[2])/6.0;
- // Identification of the local structure according to the reference
+ 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;
- if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
- && delta_hcp >= 0.1) structure[i] = UNKNOWN;
+ // Identification of the local structure according to the reference
- // not part of Ackland-Jones 2006; included for backward compatibility
- if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
+ if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
+ && delta_hcp >= 0.1) structure[i] = UNKNOWN;
+
+ // not part of Ackland-Jones 2006; included for backward compatibility
+ if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
- else {
- if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
- if (n0 > 12) structure[i] = UNKNOWN;
+ if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
- if (delta_fcc < delta_hcp) structure[i] = FCC;
- else
- structure[i] = HCP;
+ if (n0 > 12) structure[i] = UNKNOWN;
+ else {
+ if (delta_fcc < delta_hcp) structure[i] = FCC;
+ else
+ structure[i] = HCP;
+ }
}
}
}
diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/USER-MISC/compute_ackland_atom.h
index 5464a10f87..dd70762627 100644
--- a/src/USER-MISC/compute_ackland_atom.h
+++ b/src/USER-MISC/compute_ackland_atom.h
@@ -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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