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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@790 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-08-10 22:59:04 +00:00
parent 2736f0e9b8
commit a8bc4c1805
6 changed files with 4193 additions and 45 deletions
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115
src/neighbor.cpp
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@ -44,6 +44,7 @@ using namespace LAMMPS_NS;
#define SMALL 1.0e-6
#define EXDELTA 1
#define BIG 1.0e20
#define CUT2BIN_RATIO 100
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -239,6 +240,7 @@ void Neighbor::init()
int i,j,m,n;
ncalls = ndanger = 0;
dimension = domain->dimension;
triclinic = domain->triclinic;
// error check
@ -520,19 +522,19 @@ void Neighbor::init()
} else if (style == BIN) {
if (force->newton_pair == 0) {
half_build = &Neighbor::granular_bin_no_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton;
} else if (triclinic) {
half_build = &Neighbor::granular_bin_newton_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
} else {
half_build = &Neighbor::granular_bin_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton;
else
half_stencil = &Neighbor::stencil_half_2d_newton;
@ -547,19 +549,19 @@ void Neighbor::init()
} else if (style == BIN) {
if (force->newton_pair == 0) {
half_build = &Neighbor::respa_bin_no_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton;
} else if (triclinic) {
half_build = &Neighbor::respa_bin_newton_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
} else {
half_build = &Neighbor::respa_bin_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton;
else
half_stencil = &Neighbor::stencil_half_2d_newton;
@ -582,7 +584,7 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else {
half_build = &Neighbor::half_bin_no_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton;
@ -593,13 +595,13 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else if (triclinic) {
half_build = &Neighbor::half_bin_newton_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
} else {
half_build = &Neighbor::half_bin_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton;
else
half_stencil = &Neighbor::stencil_half_2d_newton;
@ -612,7 +614,7 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else {
half_build = &Neighbor::half_bin_no_newton_multi;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton_multi;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton_multi;
@ -623,13 +625,13 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else if (triclinic) {
half_build = &Neighbor::half_bin_newton_multi_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_multi_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_multi_tri;
} else {
half_build = &Neighbor::half_bin_newton_multi;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_multi;
else
half_stencil = &Neighbor::stencil_half_2d_newton_multi;
@ -644,13 +646,13 @@ void Neighbor::init()
if (style == NSQ) full_build = &Neighbor::full_nsq;
else if (style == BIN) {
full_build = &Neighbor::full_bin;
if (domain->dimension == 3)
if (dimension == 3)
full_stencil = &Neighbor::stencil_full_3d;
else
full_stencil = &Neighbor::stencil_full_2d;
} else {
full_build = &Neighbor::full_bin_multi;
if (domain->dimension == 3)
if (dimension == 3)
full_stencil = &Neighbor::stencil_full_3d_multi;
else
full_stencil = &Neighbor::stencil_full_2d_multi;
@ -922,16 +924,19 @@ void Neighbor::build_full()
/* ----------------------------------------------------------------------
setup neighbor binning parameters
bin numbering is global: 0 = 0.0 to binsize, 1 = binsize to 2*binsize
nbin-1 = bbox-binsize to binsize
nbin = bbox to bbox+binsize
-1,-2,etc = -binsize to 0.0, -2*size to -size, etc
bin numbering in each dimension is global:
0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
nbin-1,nbin,etc = bbox-binsize to binsize, bbox to bbox+binsize, etc
-1,-2,etc = -binsize to 0.0, -2*size to -size, etc
code will work for any binsize
since next(xyz) and stencil extend as far as necessary
binsize = 1/2 of cutoff is roughly optimal
for orthogonal boxes, prd must be filled exactly by integer # of bins
so procs on both sides of PBC see same bin boundary
for triclinic, tilted simulation box cannot contain integer # of bins
for orthogonal boxes:
a dim must be filled exactly by integer # of bins
in periodic, procs on both sides of PBC must see same bin boundary
in non-periodic, coord2bin() still assumes this by use of nbin xyz
for triclinic boxes:
tilted simulation box cannot contain integer # of bins
stencil & neigh list built differently to account for this
mbinlo = lowest global bin any of my ghost atoms could fall into
mbinhi = highest global bin any of my ghost atoms could fall into
@ -979,36 +984,42 @@ void Neighbor::setup_bins()
bbox[1] = bboxhi[1] - bboxlo[1];
bbox[2] = bboxhi[2] - bboxlo[2];
// optimal bin size is roughly 1/2 the cutoff
// for BIN style, binsize = 1/2 of max neighbor cutoff
// for MULTI style, binsize = 1/2 of min neighbor cutoff
// special case of all cutoffs = 0.0, binsize = box size
double binsize;
if (style == BIN) binsize = 0.5*cutneighmax;
else binsize = 0.5*cutneighmin;
if (binsize == 0.0) binsize = bbox[0];
double binsize_optimal;
if (style == BIN) binsize_optimal = 0.5*cutneighmax;
else binsize_optimal = 0.5*cutneighmin;
if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
double binsizeinv = 1.0/binsize_optimal;
// test for too many global bins in any dimension due to huge domain
// test for too many global bins in any dimension due to huge global domain
double binsizeinv = 1.0/binsize;
if (bbox[0]*binsizeinv > INT_MAX || bbox[1]*binsizeinv > INT_MAX ||
bbox[2]*binsizeinv > INT_MAX)
error->all("Domain too large for neighbor bins");
// divide box into bins
// optimal size is roughly 1/2 the cutoff
// use one bin even if cutoff >> bbox
// create actual bins
// always have one bin even if cutoff > bbox
// for 2d, nbinz = 1
nbinx = static_cast<int> (bbox[0]*binsizeinv);
nbiny = static_cast<int> (bbox[1]*binsizeinv);
if (domain->dimension == 3)
nbinz = static_cast<int> (bbox[2]*binsizeinv);
if (dimension == 3) nbinz = static_cast<int> (bbox[2]*binsizeinv);
else nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
// compute actual bin size for nbins to fit into box exactly
// error if actual bin size << cutoff, since will create a zillion bins
// this happens when nbin = 1 and box size << cutoff
// typically due to non-periodic, flat system in a particular dim
// in that extreme case, should use NSQ not BIN neighbor style
binsizex = bbox[0]/nbinx;
binsizey = bbox[1]/nbiny;
binsizez = bbox[2]/nbinz;
@ -1016,7 +1027,12 @@ void Neighbor::setup_bins()
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
bininvz = 1.0 / binsizez;
if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
binsize_optimal*bininvy > CUT2BIN_RATIO ||
binsize_optimal*bininvz > CUT2BIN_RATIO)
error->all("Cannot use neighbor bins - box size << cutoff");
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in
// coord = lowest and highest values of coords for my ghost atoms
// static_cast(-1.5) = -1, so subract additional -1
@ -1037,13 +1053,16 @@ void Neighbor::setup_bins()
coord = bsubboxhi[1] + SMALL*bbox[1];
mbinyhi = static_cast<int> ((coord-bboxlo[1])*bininvy);
coord = bsubboxlo[2] - SMALL*bbox[2];
mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
coord = bsubboxhi[2] + SMALL*bbox[2];
mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (dimension == 3) {
coord = bsubboxlo[2] - SMALL*bbox[2];
mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
coord = bsubboxhi[2] + SMALL*bbox[2];
mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
}
// extend bins by 1 to insure stencil extent is included
// if 2d, only 1 bin in z
mbinxlo = mbinxlo - 1;
mbinxhi = mbinxhi + 1;
@ -1053,15 +1072,12 @@ void Neighbor::setup_bins()
mbinyhi = mbinyhi + 1;
mbiny = mbinyhi - mbinylo + 1;
mbinzlo = mbinzlo - 1;
mbinzhi = mbinzhi + 1;
if (dimension == 3) {
mbinzlo = mbinzlo - 1;
mbinzhi = mbinzhi + 1;
} else mbinzlo = mbinzhi = 0;
mbinz = mbinzhi - mbinzlo + 1;
// test for too many total local bins due to huge domain
if (1.0*mbinx*mbiny*mbinz > INT_MAX)
error->all("Domain too large for neighbor bins");
// memory for bin ptrs
mbins = mbinx*mbiny*mbinz;
@ -1081,6 +1097,7 @@ void Neighbor::setup_bins()
if (sy*binsizey < cutneighmax) sy++;
int sz = static_cast<int> (cutneighmax*bininvz);
if (sz*binsizez < cutneighmax) sz++;
if (dimension == 2) sz = 0;
// allocate stencil memory and create stencil(s)
// check half/full instead of half_every/full_every so stencils will be
@ -1456,6 +1473,14 @@ void Neighbor::bin_atoms()
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
/*
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
*/
}
/* ----------------------------------------------------------------------