From 460976db717ea0353574c76f8ef587120fca1a79 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 19 Jan 2011 16:49:59 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5567
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/force.cpp | 1 -
src/neighbor.cpp | 29 ++++++++++++++++++++++++-----
src/neighbor.h | 6 ++++--
3 files changed, 28 insertions(+), 8 deletions(-)
diff --git a/src/force.cpp b/src/force.cpp
index f70d67413e..7b890302e3 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -105,7 +105,6 @@ void Force::init()
if (kspace) kspace->init(); // kspace must come before pair
if (pair) pair->init(); // so g_ewald is defined
- if (bond) bond->init();
if (angle) angle->init();
if (dihedral) dihedral->init();
if (improper) improper->init();
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index eed5a92203..1b6cbccad5 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -208,7 +208,11 @@ void Neighbor::init()
// cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0
triggersq = 0.25*skin*skin;
-
+ shrinkcheck = 0;
+ if (domain->box_change && (domain->xperiodic || domain->yperiodic ||
+ (dimension == 3 && domain->zperiodic)))
+ shrinkcheck = 1;
+
n = atom->ntypes;
if (cutneighsq == NULL) {
cutneighsq = memory->create_2d_double_array(n+1,n+1,"neigh:cutneighsq");
@@ -996,11 +1000,23 @@ int Neighbor::decide()
} else return 0;
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ if any atom moved trigger distance (half of neighbor skin) return 1
+ shrink trigger distance if periodic box dimension has decreased
+------------------------------------------------------------------------- */
int Neighbor::check_distance()
{
- double delx,dely,delz,rsq;
+ double delx,dely,delz,rsq,deltasq;
+
+ if (shrinkcheck) {
+ double delta = 0.0;
+ if (domain->xperiodic) delta = MIN(delta,domain->xprd-xprdhold);
+ if (domain->yperiodic) delta = MIN(delta,domain->yprd-yprdhold);
+ if (domain->zperiodic) delta = MIN(delta,domain->zprd-zprdhold);
+ delta = 0.5*skin - delta;
+ deltasq = delta*delta;
+ } else deltasq = triggersq;
double **x = atom->x;
int nlocal = atom->nlocal;
@@ -1012,7 +1028,7 @@ int Neighbor::check_distance()
dely = x[i][1] - xhold[i][1];
delz = x[i][2] - xhold[i][2];
rsq = delx*delx + dely*dely + delz*delz;
- if (rsq > triggersq) flag = 1;
+ if (rsq > deltasq) flag = 1;
}
int flagall;
@@ -1033,7 +1049,7 @@ void Neighbor::build()
ago = 0;
ncalls++;
- // store current atom positions if needed
+ // store current atom positions and box size if needed
if (dist_check) {
double **x = atom->x;
@@ -1049,6 +1065,9 @@ void Neighbor::build()
xhold[i][1] = x[i][1];
xhold[i][2] = x[i][2];
}
+ xprdhold = domain->xprd;
+ yprdhold = domain->yprd;
+ zprdhold = domain->zprd;
}
// if necessary, extend atom arrays in pairwise lists
diff --git a/src/neighbor.h b/src/neighbor.h
index fcf7600a05..3185e6563c 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -91,8 +91,10 @@ class Neighbor : protected Pointers {
double triggersq; // trigger = build when atom moves this dist
- double **xhold; // atom coords at last neighbor build
- int maxhold; // size of xhold array
+ double **xhold; // atom coords at last neighbor build
+ int maxhold; // size of xhold array
+ double xprdhold,yprdhold,zprdhold; // box size at last neighbor build
+ int shrinkcheck;
int nbinx,nbiny,nbinz; // # of global bins
int *bins; // ptr to next atom in each bin
--
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