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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@371 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-03-08 00:54:02 +00:00
parent a70ee2eadc
commit 9e1f8bcd6a
64 changed files with 1785 additions and 772 deletions
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127
src/neighbor.cpp
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@ -206,6 +206,7 @@ void Neighbor::init()
int i,j,m,n;
ncalls = ndanger = 0;
triclinic = domain->triclinic;
// error check
@ -544,7 +545,7 @@ void Neighbor::init()
cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
}
// set ptrs to correct half and full build functions
// set ptrs to correct half, full, triclinic build functions
// cannot combine granular and rRESPA
if (half) {
@ -556,6 +557,8 @@ void Neighbor::init()
} else if (style == 1) {
if (force->newton_pair == 0)
half_build = &Neighbor::granular_bin_no_newton;
else if (triclinic)
half_build = &Neighbor::granular_bin_newton_tri;
else half_build = &Neighbor::granular_bin_newton;
}
} else if (respa) {
@ -566,6 +569,8 @@ void Neighbor::init()
} else if (style == 1) {
if (force->newton_pair == 0)
half_build = &Neighbor::respa_bin_no_newton;
else if (triclinic)
half_build = &Neighbor::respa_bin_newton_tri;
else half_build = &Neighbor::respa_bin_newton;
}
} else {
@ -583,6 +588,8 @@ void Neighbor::init()
else half_build = &Neighbor::half_bin_no_newton;
} else {
if (full_every) half_build = &Neighbor::half_full_newton;
else if (triclinic)
half_build = &Neighbor::half_bin_newton_tri;
else half_build = &Neighbor::half_bin_newton;
}
}
@ -869,6 +876,7 @@ void Neighbor::build_full()
binsize = 1/2 of cutoff is roughly optimal
prd must be filled exactly by integer # of bins
so procs on both sides of PBC see same bin boundary
triclinic is an exception, since stencil & neigh list built differently
mbinlo = lowest global bin any of my ghost atoms could fall into
mbinhi = highest global bin any of my ghost atoms could fall into
mbin = number of bins I need in a dimension
@ -878,31 +886,53 @@ void Neighbor::build_full()
void Neighbor::setup_bins()
{
double cutneighinv = 1.0/cutneigh;
// bbox = bounding box of entire domain
// bboxlo,bboxhi = bounding box of proc's sub-domain
// for triclinic, bounding box surrounds all 8 corner pts
double bbox[3];
double *bboxlo,*bboxhi;
if (triclinic == 0) {
boxlo = domain->boxlo;
boxhi = domain->boxhi;
bboxlo = domain->sublo;
bboxhi = domain->subhi;
} else {
boxlo = domain->boxlo_bound;
boxhi = domain->boxhi_bound;
bboxlo = domain->sublo_bound;
bboxhi = domain->subhi_bound;
}
bbox[0] = boxhi[0] - boxlo[0];
bbox[1] = boxhi[1] - boxlo[1];
bbox[2] = boxhi[2] - boxlo[2];
// test for too many global bins in any dimension due to huge domain
if (2.0*domain->xprd*cutneighinv > INT_MAX ||
2.0*domain->yprd*cutneighinv > INT_MAX ||
2.0*domain->zprd*cutneighinv > INT_MAX)
double cutneighinv = 1.0/cutneigh;
if (2.0*bbox[0]*cutneighinv > INT_MAX || 2.0*bbox[1]*cutneighinv > INT_MAX ||
2.0*bbox[2]*cutneighinv > INT_MAX)
error->all("Domain too large for neighbor bins");
// divide box into bins
// optimal size is roughly 1/2 the cutoff
nbinx = static_cast<int> (2.0*domain->xprd*cutneighinv);
nbiny = static_cast<int> (2.0*domain->yprd*cutneighinv);
nbinx = static_cast<int> (2.0*bbox[0]*cutneighinv);
nbiny = static_cast<int> (2.0*bbox[1]*cutneighinv);
if (force->dimension == 3)
nbinz = static_cast<int> (2.0*domain->zprd*cutneighinv);
nbinz = static_cast<int> (2.0*bbox[2]*cutneighinv);
else nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
binsizex = domain->xprd/nbinx;
binsizey = domain->yprd/nbiny;
binsizez = domain->zprd/nbinz;
binsizex = bbox[0]/nbinx;
binsizey = bbox[1]/nbiny;
binsizez = bbox[2]/nbinz;
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
@ -915,23 +945,23 @@ void Neighbor::setup_bins()
double coord;
int mbinxhi,mbinyhi,mbinzhi;
coord = domain->subxlo - cutneigh - SMALL*domain->xprd;
mbinxlo = static_cast<int> ((coord-domain->boxxlo)*bininvx);
coord = bboxlo[0] - cutneigh - SMALL*bbox[0];
mbinxlo = static_cast<int> ((coord-boxlo[0])*bininvx);
if (coord < 0.0) mbinxlo = mbinxlo - 1;
coord = domain->subxhi + cutneigh + SMALL*domain->xprd;
mbinxhi = static_cast<int> ((coord-domain->boxxlo)*bininvx);
coord = bboxhi[0] + cutneigh + SMALL*bbox[0];
mbinxhi = static_cast<int> ((coord-boxlo[0])*bininvx);
coord = domain->subylo - cutneigh - SMALL*domain->yprd;
mbinylo = static_cast<int> ((coord-domain->boxylo)*bininvy);
coord = bboxlo[1] - cutneigh - SMALL*bbox[1];
mbinylo = static_cast<int> ((coord-boxlo[1])*bininvy);
if (coord < 0.0) mbinylo = mbinylo - 1;
coord = domain->subyhi + cutneigh + SMALL*domain->yprd;
mbinyhi = static_cast<int> ((coord-domain->boxylo)*bininvy);
coord = bboxhi[1] + cutneigh + SMALL*bbox[1];
mbinyhi = static_cast<int> ((coord-boxlo[1])*bininvy);
coord = domain->subzlo - cutneigh - SMALL*domain->zprd;
mbinzlo = static_cast<int> ((coord-domain->boxzlo)*bininvz);
coord = bboxlo[2] - cutneigh - SMALL*bbox[2];
mbinzlo = static_cast<int> ((coord-boxlo[2])*bininvz);
if (coord < 0.0) mbinzlo = mbinzlo - 1;
coord = domain->subzhi + cutneigh + SMALL*domain->zprd;
mbinzhi = static_cast<int> ((coord-domain->boxzlo)*bininvz);
coord = bboxhi[2] + cutneigh + SMALL*bbox[2];
mbinzhi = static_cast<int> ((coord-boxlo[2])*bininvz);
// extend bins by 1 to insure stencil extent is included
@ -965,10 +995,15 @@ void Neighbor::setup_bins()
// is within neighbor cutoff
// next(xyz) = how far the stencil could possibly extend
// for partial Newton (newton = 0)
// stencil is all surrounding bins including self
// stencil is all surrounding bins
// stencil includes self
// for triclinic
// stencil is all bins in z-plane of self and above, but not below
// in 2d is all bins in y-plane of self and above, but not below
// stencil includes self
// for full Newton (newton = 1)
// stencil is bins to the "upper right" of central bin
// stencil does NOT include self
// stencil does not include self
// for full neighbor list (full = 1)
// stencil is all surrounding bins including self, regardless of Newton
// stored in stencil_full
@ -999,6 +1034,12 @@ void Neighbor::setup_bins()
for (i = -nextx; i <= nextx; i++)
if (bin_distance(i,j,k) < cutsq)
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
} else if (triclinic) {
for (k = 0; k <= nextz; k++)
for (j = -nexty; j <= nexty; j++)
for (i = -nextx; i <= nextx; i++)
if (bin_distance(i,j,k) < cutsq)
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
} else {
for (k = 0; k <= nextz; k++)
for (j = -nexty; j <= nexty; j++)
@ -1013,6 +1054,11 @@ void Neighbor::setup_bins()
for (i = -nextx; i <= nextx; i++)
if (bin_distance(i,j,0) < cutsq)
stencil[nstencil++] = j*mbinx + i;
} else if (triclinic) {
for (j = 0; j <= nexty; j++)
for (i = -nextx; i <= nextx; i++)
if (bin_distance(i,j,0) < cutsq)
stencil[nstencil++] = j*mbinx + i;
} else {
for (j = 0; j <= nexty; j++)
for (i = -nextx; i <= nextx; i++)
@ -1373,32 +1419,33 @@ void Neighbor::bin_atoms()
take special care to insure ghosts are put in correct bins
this is necessary so that both procs on either side of PBC
treat a pair of atoms straddling the PBC in a consistent way
triclinic is an exception, since stencil & neigh list built differently
------------------------------------------------------------------------- */
int Neighbor::coord2bin(double *x)
{
int ix,iy,iz;
if (x[0] >= domain->boxxhi)
ix = static_cast<int> ((x[0]-domain->boxxhi)*bininvx) + nbinx - mbinxlo;
else if (x[0] >= domain->boxxlo)
ix = static_cast<int> ((x[0]-domain->boxxlo)*bininvx) - mbinxlo;
if (x[0] >= boxhi[0])
ix = static_cast<int> ((x[0]-boxhi[0])*bininvx) + nbinx - mbinxlo;
else if (x[0] >= boxlo[0])
ix = static_cast<int> ((x[0]-boxlo[0])*bininvx) - mbinxlo;
else
ix = static_cast<int> ((x[0]-domain->boxxlo)*bininvx) - mbinxlo - 1;
ix = static_cast<int> ((x[0]-boxlo[0])*bininvx) - mbinxlo - 1;
if (x[1] >= domain->boxyhi)
iy = static_cast<int> ((x[1]-domain->boxyhi)*bininvy) + nbiny - mbinylo;
else if (x[1] >= domain->boxylo)
iy = static_cast<int> ((x[1]-domain->boxylo)*bininvy) - mbinylo;
if (x[1] >= boxhi[1])
iy = static_cast<int> ((x[1]-boxhi[1])*bininvy) + nbiny - mbinylo;
else if (x[1] >= boxlo[1])
iy = static_cast<int> ((x[1]-boxlo[1])*bininvy) - mbinylo;
else
iy = static_cast<int> ((x[1]-domain->boxylo)*bininvy) - mbinylo - 1;
iy = static_cast<int> ((x[1]-boxlo[1])*bininvy) - mbinylo - 1;
if (x[2] >= domain->boxzhi)
iz = static_cast<int> ((x[2]-domain->boxzhi)*bininvz) + nbinz - mbinzlo;
else if (x[2] >= domain->boxzlo)
iz = static_cast<int> ((x[2]-domain->boxzlo)*bininvz) - mbinzlo;
if (x[2] >= boxhi[2])
iz = static_cast<int> ((x[2]-boxhi[2])*bininvz) + nbinz - mbinzlo;
else if (x[2] >= boxlo[2])
iz = static_cast<int> ((x[2]-boxlo[2])*bininvz) - mbinzlo;
else
iz = static_cast<int> ((x[2]-domain->boxzlo)*bininvz) - mbinzlo - 1;
iz = static_cast<int> ((x[2]-boxlo[2])*bininvz) - mbinzlo - 1;
return (iz*mbiny*mbinx + iy*mbinx + ix + 1);
}