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random permulations of both I and J atoms in double loop

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This commit is contained in:
Steve Plimpton
2022-09-12 09:18:06 -06:00
parent d860e9a3ed
commit 572e8cc399
1 changed files with 10 additions and 34 deletions
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44
src/MC/fix_bond_swap.cpp
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@ -244,6 +244,15 @@ void FixBondSwap::post_integrate()
memory->create(alist,nmax,"bondswap:alist");
}
// use randomized permulation of both I and J atoms in double loop below
// this is to avoid any bias in accepted MC swaps based on
// ordering LAMMPS creates on a processor for atoms or their neighbors
// create a random permutation of list of Neligible atoms
// uses one-pass Fisher-Yates shuffle on an initial identity permutation
// output: randomized alist[] vector, used in outer loop to select an I atom
// similar randomized permulation is created for neighbors of each I atom
int neligible = 0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@ -262,6 +271,7 @@ void FixBondSwap::post_integrate()
// examine ntest of my eligible atoms for potential swaps
// atom I is randomly selected via atom list
// look at all J neighbors of atom I
// done in a randomized permutation, via neighbor_permutation()
// J must be on-processor (J < nlocal)
// I,J must be in fix group
// I,J must have same molecule IDs
@ -283,31 +293,6 @@ void FixBondSwap::post_integrate()
neighbor_permutation(jnum);
// DEBUG
int picked[4];
int count = 0;
printf("BSWAP CANDIDATES nstep %ld itag %d jnum %d jtags",
update->ntimestep,atom->tag[i],jnum);
for (jj = 0; jj < jnum; jj++) {
j = jlist[permute[jj]];
j &= NEIGHMASK;
printf(" %d",atom->tag[j]);
if (j >= nlocal) continue;
if ((mask[j] & groupbit) == 0) continue;
if (molecule[i] != molecule[j]) continue;
picked[count++] = atom->tag[j];
}
if (count) {
printf(" picked %d",count);
for (jj = 0; jj < count; jj++) {
printf(" %d",picked[jj]);
}
}
printf("\n");
// END DEBUG
for (jj = 0; jj < jnum; jj++) {
j = jlist[permute[jj]];
j &= NEIGHMASK;
@ -328,8 +313,6 @@ void FixBondSwap::post_integrate()
// already know i != inext, j != jnext
// all 4 old and new bonds must have length < cutoff
printf(" SWAP candidate ijtag %d %d\n",atom->tag[i],atom->tag[j]);
for (ibond = 0; ibond < num_bond[i]; ibond++) {
inext = atom->map(bond_atom[i][ibond]);
if (inext >= nlocal || inext < 0) continue;
@ -349,10 +332,6 @@ void FixBondSwap::post_integrate()
if (dist_rsq(i,jnext) >= cutsq) continue;
if (dist_rsq(j,inext) >= cutsq) continue;
printf(" BOND nstep %ld ijtag %d %d ibondtag %d jbondtag %d\n",
update->ntimestep,
atom->tag[i],atom->tag[j],atom->tag[inext],atom->tag[jnext]);
// if angles are enabled:
// find other atoms i,inext,j,jnext are in angles with
// and angletypes: i/j angletype, i/j nextangletype
@ -471,9 +450,6 @@ void FixBondSwap::post_integrate()
if (random->uniform() < factor) accept = 1;
}
printf(" MC result jtag %d delta %g accept %d\n",
atom->tag[j],delta,accept);
goto done;
}
}