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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5567 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2011-01-19 16:49:59 +00:00
parent 4b8beadb2f
commit 460976db71
3 changed files with 28 additions and 8 deletions
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1
src/force.cpp
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@ -105,7 +105,6 @@ void Force::init()
if (kspace) kspace->init(); // kspace must come before pair if (kspace) kspace->init(); // kspace must come before pair
if (pair) pair->init(); // so g_ewald is defined if (pair) pair->init(); // so g_ewald is defined
if (bond) bond->init();
if (angle) angle->init(); if (angle) angle->init();
if (dihedral) dihedral->init(); if (dihedral) dihedral->init();
if (improper) improper->init(); if (improper) improper->init();

27
src/neighbor.cpp
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@ -208,6 +208,10 @@ void Neighbor::init()
// cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0 // cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0
triggersq = 0.25*skin*skin; triggersq = 0.25*skin*skin;
shrinkcheck = 0;
if (domain->box_change && (domain->xperiodic || domain->yperiodic ||
(dimension == 3 && domain->zperiodic)))
shrinkcheck = 1;
n = atom->ntypes; n = atom->ntypes;
if (cutneighsq == NULL) { if (cutneighsq == NULL) {
@ -996,11 +1000,23 @@ int Neighbor::decide()
} else return 0; } 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() 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; double **x = atom->x;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
@ -1012,7 +1028,7 @@ int Neighbor::check_distance()
dely = x[i][1] - xhold[i][1]; dely = x[i][1] - xhold[i][1];
delz = x[i][2] - xhold[i][2]; delz = x[i][2] - xhold[i][2];
rsq = delx*delx + dely*dely + delz*delz; rsq = delx*delx + dely*dely + delz*delz;
if (rsq > triggersq) flag = 1; if (rsq > deltasq) flag = 1;
} }
int flagall; int flagall;
@ -1033,7 +1049,7 @@ void Neighbor::build()
ago = 0; ago = 0;
ncalls++; ncalls++;
// store current atom positions if needed // store current atom positions and box size if needed
if (dist_check) { if (dist_check) {
double **x = atom->x; double **x = atom->x;
@ -1049,6 +1065,9 @@ void Neighbor::build()
xhold[i][1] = x[i][1]; xhold[i][1] = x[i][1];
xhold[i][2] = x[i][2]; xhold[i][2] = x[i][2];
} }
xprdhold = domain->xprd;
yprdhold = domain->yprd;
zprdhold = domain->zprd;
} }
// if necessary, extend atom arrays in pairwise lists // if necessary, extend atom arrays in pairwise lists

6
src/neighbor.h
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@ -91,8 +91,10 @@ class Neighbor : protected Pointers {
double triggersq; // trigger = build when atom moves this dist double triggersq; // trigger = build when atom moves this dist
double **xhold; // atom coords at last neighbor build double **xhold; // atom coords at last neighbor build
int maxhold; // size of xhold array 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 nbinx,nbiny,nbinz; // # of global bins
int *bins; // ptr to next atom in each bin int *bins; // ptr to next atom in each bin