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Adding custom grouping option

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This commit is contained in:
Joel Clemmer
2020-12-26 11:03:29 -07:00
parent b421c3d676
commit 2458eaf4f9
30 changed files with 599 additions and 551 deletions
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57
src/npair_half_multi_newton.cpp
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@ -28,14 +28,14 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
multi-type stencil is itype-jtype dependent
multi stencil is igroup-jgroup dependent
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfMultiNewton::build(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,jbin,which,ns,imol,iatom,moltemplate;
int i,j,k,n,itype,jtype,igroup,jgroup,ibin,jbin,which,ns,imol,iatom,moltemplate;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*s;
@ -68,8 +68,8 @@ void NPairHalfMultiNewton::build(NeighList *list)
for (i = 0; i < nlocal; i++) {
n = 0;
neighptr = ipage->vget();
itype = type[i];
igroup = map_type_multi[itype];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
@ -79,28 +79,28 @@ void NPairHalfMultiNewton::build(NeighList *list)
tagprev = tag[i] - iatom - 1;
}
ibin = atom2bin_multi[itype][i];
ibin = atom2bin_multi[igroup][i];
// loop through stencils for all types
for (jtype = 1; jtype <= atom->ntypes; jtype++) {
// loop through stencils for all groups
for (jgroup = 0; jgroup < n_multi_groups; jgroup++) {
// if same type use own bin
if(itype == jtype) jbin = ibin;
else jbin = coord2bin(x[i], jtype);
// if same group use own bin
if(igroup == jgroup) jbin = ibin;
else jbin = coord2bin(x[i], jgroup);
if(cutneighsq[itype][itype] == cutneighsq[jtype][jtype]){
if(cutmultisq[igroup][igroup] == cutmultisq[jgroup][jgroup]){
// if same size: use half stencil
if(itype == jtype){
if(igroup == jgroup){
// if same type, implement with:
// if same group, implement with:
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above and to the right" of i
js = bins_multi[itype][i];
js = bins_multi[igroup][i];
for (j = js; j >= 0; j = bins_multi[jtype][j]) {
for (j = js; j >= 0; j = bins_multi[jgroup][j]) {
if (j >= nlocal) {
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
@ -109,7 +109,8 @@ void NPairHalfMultiNewton::build(NeighList *list)
}
}
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -134,14 +135,14 @@ void NPairHalfMultiNewton::build(NeighList *list)
}
} else {
// if different types, implement with:
// loop over all atoms in jtype bin
// if different groups, implement with:
// loop over all atoms in jgroup bin
// if j is owned atom, store it if j > i
// if j is ghost, only store if j coords are "above and to the right" of i
js = binhead_multi[jtype][jbin];
js = binhead_multi[jgroup][jbin];
for (j = js; j >= 0; j = bins_multi[jtype][j]) {
for (j = js; j >= 0; j = bins_multi[jgroup][j]) {
if(j < i) continue;
if (j >= nlocal) {
@ -152,7 +153,8 @@ void NPairHalfMultiNewton::build(NeighList *list)
}
}
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@ -178,20 +180,21 @@ void NPairHalfMultiNewton::build(NeighList *list)
}
}
// for all types, loop over all atoms in other bins in stencil, store every pair
// for all groups, loop over all atoms in other bins in stencil, store every pair
// stencil is empty if i larger than j
// stencil is half if i same size as j
// stencil is full if i smaller than j
s = stencil_multi[itype][jtype];
ns = nstencil_multi[itype][jtype];
s = stencil_multi[igroup][jgroup];
ns = nstencil_multi[igroup][jgroup];
for (k = 0; k < ns; k++) {
js = binhead_multi[jtype][jbin + s[k]];
for (j = js; j >= 0; j = bins_multi[jtype][j]) {
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
js = binhead_multi[jgroup][jbin + s[k]];
for (j = js; j >= 0; j = bins_multi[jgroup][j]) {
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];