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Adding triclinic patch (except for intel)

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This commit is contained in:
jtclemm
2023-10-22 21:52:43 -06:00
parent b456beb62f 49f08e6231
commit 1571c96480
3033 changed files with 125592 additions and 129201 deletions
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100
src/npair_multi_old.cpp
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@ -18,6 +18,7 @@
#include "atom_vec.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "molecule.h"
#include "my_page.h"
#include "neigh_list.h"
@ -51,12 +52,13 @@ NPairMultiOld<HALF, NEWTON, TRI, SIZE>::NPairMultiOld(LAMMPS *lmp) : NPair(lmp)
template<int HALF, int NEWTON, int TRI, int SIZE>
void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
{
int i,j,jh,k,n,itype,jtype,ibin,bin_start,which,ns,imol,iatom,moltemplate;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radsum,cut,cutsq;
int *neighptr,*s;
double *cutnsq,*distsq;
int i, j, jh, k, n, itype, jtype, ibin, bin_start, which, ns, imol, iatom, moltemplate;
tagint itag, jtag, tagprev;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq, radsum, cut, cutsq;
int *neighptr, *s;
double *cutnsq, *distsq;
const double delta = 0.01 * force->angstrom;
double **x = atom->x;
double *radius = atom->radius;
@ -72,8 +74,10 @@ void NPairMultiOld<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 (molecular == Atom::TEMPLATE)
moltemplate = 1;
else
moltemplate = 0;
int history = list->history;
int mask_history = 1 << HISTBITS;
@ -90,6 +94,7 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
n = 0;
neighptr = ipage->vget();
itag = tag[i];
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
@ -128,16 +133,26 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
if (j <= i) continue;
} else if (TRI) {
// Half neighbor list, newton on, triclinic
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp) {
if (x[j][1] < ytmp) continue;
if (x[j][1] == ytmp) {
if (x[j][0] < xtmp) continue;
if (x[j][0] == xtmp && j <= i) continue;
// for triclinic, bin stencil is full in all 3 dims
// must use itag/jtag to eliminate half the I/J interactions
// cannot use I/J exact coord comparision
// b/c transforming orthog -> lambda -> orthog for ghost atoms
// with an added PBC offset can shift all 3 coords by epsilon
if (j <= i) continue;
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
if ((itag + jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag + jtag) % 2 == 1) continue;
} else {
if (fabs(x[j][2] - ztmp) > delta) {
if (x[j][2] < ztmp) continue;
} else if (fabs(x[j][1] - ytmp) > delta) {
if (x[j][1] < ytmp) continue;
} else {
if (x[j][0] < xtmp) continue;
}
}
}
} else {
@ -160,12 +175,12 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
jtype = type[j];
if (cutnsq[jtype] < distsq[k]) continue;
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
if (SIZE) {
radsum = radius[i] + radius[j];
@ -179,33 +194,39 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
if (molecular != Atom::ATOMIC) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
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))
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 (which > 0) neighptr[n++] = jh ^ (which << SBBITS);
} else 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]);
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))
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 (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;
}
}
}
@ -215,8 +236,7 @@ void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
if (ipage->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
list->inum = inum;