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Merging atomonly npair styles, minor fixes

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This commit is contained in:
jtclemm
2023-10-23 16:14:56 -06:00
parent 3536cf9db9
commit 51577eff2c
17 changed files with 540 additions and 821 deletions
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143
src/npair_bin.cpp
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@ -28,8 +28,8 @@ using namespace NeighConst;
/* ---------------------------------------------------------------------- */
template<int HALF, int NEWTON, int TRI, int SIZE>
NPairBin<HALF, NEWTON, TRI, SIZE>::NPairBin(LAMMPS *lmp) : NPair(lmp) {}
template<int HALF, int NEWTON, int TRI, int SIZE, int ATOMONLY>
NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::NPairBin(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
Full:
@ -46,8 +46,8 @@ NPairBin<HALF, NEWTON, TRI, SIZE>::NPairBin(LAMMPS *lmp) : NPair(lmp) {}
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
template<int HALF, int NEWTON, int TRI, int SIZE>
void NPairBin<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
template<int HALF, int NEWTON, int TRI, int SIZE, int ATOMONLY>
void NPairBin<HALF, NEWTON, TRI, SIZE, ATOMONLY>::build(NeighList *list)
{
int i, j, jh, k, n, itype, jtype, ibin, bin_start, which, imol, iatom, moltemplate;
tagint itag, jtag, tagprev;
@ -70,10 +70,12 @@ void NPairBin<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
if (molecular == Atom::TEMPLATE)
moltemplate = 1;
else
moltemplate = 0;
if (!ATOMONLY) {
if (molecular == Atom::TEMPLATE)
moltemplate = 1;
else
moltemplate = 0;
}
int history = list->history;
int mask_history = 1 << HISTBITS;
@ -95,18 +97,20 @@ void NPairBin<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
if (!ATOMONLY) {
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
}
ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
bin_start = binhead[ibin + stencil[k]];
if (stencil[k] == 0) {
if (HALF && NEWTON && (!TRI)) {
if (HALF && NEWTON && (!TRI)) {
if (stencil[k] == 0) {
// Half neighbor list, newton on, orthonormal
// loop over rest of atoms in i's bin, ghosts are at end of linked list
bin_start = bins[i];
@ -149,7 +153,7 @@ void NPairBin<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
}
} else {
// Half neighbor list, newton on, orthonormal
// store every pair for every bin in stencil,except for i's bin
// store every pair for every bin in stencil, except for i's bin
if (stencil[k] == 0) {
// if j is owned atom, store it, since j is beyond i in linked list
@ -177,46 +181,59 @@ void NPairBin<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
cut = radsum + skin;
cutsq = cut * cut;
if (rsq <= cutsq) {
jh = j;
if (history && rsq < radsum * radsum)
jh = jh ^ mask_history;
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev);
else
which = 0;
if (which == 0)
neighptr[n++] = jh;
else if (domain->minimum_image_check(delx, dely, delz))
neighptr[n++] = jh;
else if (which > 0)
neighptr[n++] = jh ^ (which << SBBITS);
} else
if (ATOMONLY) {
if (rsq <= cutsq) {
jh = j;
if (history && rsq < (radsum * radsum))
jh = jh ^ mask_history;
neighptr[n++] = jh;
}
} else {
if (rsq <= cutsq) {
jh = j;
if (history && rsq < (radsum * radsum))
jh = jh ^ mask_history;
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom],
tag[j] - tagprev);
else
which = 0;
if (which == 0)
neighptr[n++] = jh;
else if (domain->minimum_image_check(delx, dely, delz))
neighptr[n++] = jh;
else if (which > 0)
neighptr[n++] = jh ^ (which << SBBITS);
} else
neighptr[n++] = jh;
}
}
} else {
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
tag[j] - tagprev);
else
which = 0;
if (which == 0)
if (ATOMONLY) {
if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
} else {
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i], nspecial[i], tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom], onemols [imol]->nspecial[iatom],
tag[j] - tagprev);
else
which = 0;
if (which == 0)
neighptr[n++] = j;
else if (domain->minimum_image_check(delx, dely, delz))
neighptr[n++] = j;
else if (which > 0)
neighptr[n++] = j ^ (which << SBBITS);
} else
neighptr[n++] = j;
else if (domain->minimum_image_check(delx, dely, delz))
neighptr[n++] = j;
else if (which > 0)
neighptr[n++] = j ^ (which << SBBITS);
} else
neighptr[n++] = j;
}
}
}
}
@ -234,12 +251,20 @@ void NPairBin<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
}
namespace LAMMPS_NS {
template class NPairBin<0,1,0,0>;
template class NPairBin<1,0,0,0>;
template class NPairBin<1,1,0,0>;
template class NPairBin<1,1,1,0>;
template class NPairBin<0,1,0,1>;
template class NPairBin<1,0,0,1>;
template class NPairBin<1,1,0,1>;
template class NPairBin<1,1,1,1>;
template class NPairBin<0,1,0,0,0>;
template class NPairBin<1,0,0,0,0>;
template class NPairBin<1,1,0,0,0>;
template class NPairBin<1,1,1,0,0>;
template class NPairBin<0,1,0,1,0>;
template class NPairBin<1,0,0,1,0>;
template class NPairBin<1,1,0,1,0>;
template class NPairBin<1,1,1,1,0>;
template class NPairBin<0,1,0,0,1>;
template class NPairBin<1,0,0,0,1>;
template class NPairBin<1,1,0,0,1>;
template class NPairBin<1,1,1,0,1>;
template class NPairBin<0,1,0,1,1>;
template class NPairBin<1,0,0,1,1>;
template class NPairBin<1,1,0,1,1>;
template class NPairBin<1,1,1,1,1>;
}