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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2090 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2008-08-21 13:53:19 +00:00
parent 9897ee73bf
commit 4fbc6f42c0
5 changed files with 41 additions and 35 deletions
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40
src/neighbor.cpp
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@ -201,15 +201,9 @@ void Neighbor::init()
// set neighbor cutoffs (force cutoff + skin)
// trigger determines when atoms migrate and neighbor lists are rebuilt
// cutneigh and cutneighsq determine what pairs go into neighbor list
// set to 0 if cutforce = 0
// cutneighmin/max used for neighbor bin sizes
// cutghost determines comm distance = max of cutneigh & skin
// skin is only > cutneighmax when cutneighmax = 0.0 due to pair = NULL
// in this case, are running a bond-only simulation
// still need ghost atom communication for bonds and atom exchange
// triggered by atoms moving 1/2 skin distance, but no neigh lists formed
// user should set skin big enough to find all bonds
// needs to be non-zero for migration distance check
// even if pair = NULL and no neighbor lists are used
// cutneigh = force cutoff + skin if cutforce > 0, else cutneigh = 0
triggersq = 0.25*skin*skin;
@ -240,7 +234,6 @@ void Neighbor::init()
cutneighmax = MAX(cutneighmax,cut);
}
}
cutghost = MAX(cutneighmax,skin);
cutneighmaxsq = cutneighmax * cutneighmax;
// check other classes that can induce reneighboring in decide()
@ -1053,7 +1046,7 @@ void Neighbor::setup_bins()
{
// bbox lo/hi = bounding box of entire domain
// bbox = size of bbox of entire domain
// bsubbox lo/hi = bounding box of my subdomain extended by ghost atoms
// bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
// for triclinic:
// bbox bounds all 8 corners of tilted box
// subdomain is in lamda coords
@ -1061,26 +1054,27 @@ void Neighbor::setup_bins()
// domain->bbox() converts lamda extent to box coords and computes bbox
double bbox[3],bsubboxlo[3],bsubboxhi[3];
double *cutghost = comm->cutghost;
if (triclinic == 0) {
bboxlo = domain->boxlo;
bboxhi = domain->boxhi;
bsubboxlo[0] = domain->sublo[0] - cutghost;
bsubboxlo[1] = domain->sublo[1] - cutghost;
bsubboxlo[2] = domain->sublo[2] - cutghost;
bsubboxhi[0] = domain->subhi[0] + cutghost;
bsubboxhi[1] = domain->subhi[1] + cutghost;
bsubboxhi[2] = domain->subhi[2] + cutghost;
bsubboxlo[0] = domain->sublo[0] - cutghost[0];
bsubboxlo[1] = domain->sublo[1] - cutghost[1];
bsubboxlo[2] = domain->sublo[2] - cutghost[2];
bsubboxhi[0] = domain->subhi[0] + cutghost[0];
bsubboxhi[1] = domain->subhi[1] + cutghost[1];
bsubboxhi[2] = domain->subhi[2] + cutghost[2];
} else {
bboxlo = domain->boxlo_bound;
bboxhi = domain->boxhi_bound;
double lo[3],hi[3];
lo[0] = domain->sublo_lamda[0] - comm->cutghost[0];
lo[1] = domain->sublo_lamda[1] - comm->cutghost[1];
lo[2] = domain->sublo_lamda[2] - comm->cutghost[2];
hi[0] = domain->subhi_lamda[0] + comm->cutghost[0];
hi[1] = domain->subhi_lamda[1] + comm->cutghost[1];
hi[2] = domain->subhi_lamda[2] + comm->cutghost[2];
lo[0] = domain->sublo_lamda[0] - cutghost[0];
lo[1] = domain->sublo_lamda[1] - cutghost[1];
lo[2] = domain->sublo_lamda[2] - cutghost[2];
hi[0] = domain->subhi_lamda[0] + cutghost[0];
hi[1] = domain->subhi_lamda[1] + cutghost[1];
hi[2] = domain->subhi_lamda[2] + cutghost[2];
domain->bbox(lo,hi,bsubboxlo,bsubboxhi);
}