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bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue

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This commit is contained in:
Steve Plimpton
2017-05-16 15:51:41 -06:00
parent 06c151421c
commit 7f9a331c73
47 changed files with 80 additions and 98 deletions
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50
src/npair.cpp
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@ -128,6 +128,7 @@ void NPair::copy_bin_info()
bininvy = nb->bininvy;
bininvz = nb->bininvz;
atom2bin = nb->atom2bin;
bins = nb->bins;
binhead = nb->binhead;
}
@ -198,53 +199,8 @@ int NPair::exclusion(int i, int j, int itype, int jtype,
}
/* ----------------------------------------------------------------------
convert atom coords into local bin #
for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
take special care to insure ghosts are in correct bins even w/ roundoff
hi ghost atoms = nbin,nbin+1,etc
owned atoms = 0 to nbin-1
lo ghost atoms = -1,-2,etc
this is necessary so that both procs on either side of PBC
treat a pair of atoms straddling the PBC in a consistent way
for triclinic, doesn't matter since stencil & neigh list built differently
------------------------------------------------------------------------- */
int NPair::coord2bin(double *x)
{
int ix,iy,iz;
if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
error->one(FLERR,"Non-numeric positions - simulation unstable");
if (x[0] >= bboxhi[0])
ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
else if (x[0] >= bboxlo[0]) {
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
if (x[1] >= bboxhi[1])
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
else if (x[1] >= bboxlo[1]) {
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
if (x[2] >= bboxhi[2])
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
else if (x[2] >= bboxlo[2]) {
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
iz = MIN(iz,nbinz-1);
} else
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
}
/* ----------------------------------------------------------------------
same as coord2bin, but also return ix,iy,iz offsets in each dim
same as coord2bin in Nbin, but also return ix,iy,iz offsets in each dim
used by some of the ghost neighbor lists
------------------------------------------------------------------------- */
int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)