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Merge pull request #2888 from lammps/sticker-bonds

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Sticker bonds
This commit is contained in:
Axel Kohlmeyer
2021-08-20 14:28:57 -04:00
committed by GitHub
parent 3404920e98 fcc6cc628e
commit 1eb506002b
2 changed files with 138 additions and 76 deletions
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43
src/MC/fix_bond_swap.cpp
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@ -148,7 +148,8 @@ void FixBondSwap::init()
error->all(FLERR,"Pair style does not support fix bond/swap");
if (force->angle == nullptr && atom->nangles > 0 && comm->me == 0)
error->warning(FLERR,"Fix bond/swap will ignore defined angles");
error->warning(FLERR,"Fix bond/swap will not preserve correct angle "
"topology because no angle_style is defined");
if (force->dihedral || force->improper)
error->all(FLERR,"Fix bond/swap cannot use dihedral or improper styles");
@ -255,12 +256,18 @@ 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
// atom j must be on-processor (j < nlocal)
// atom j must be in fix group
// i and j must be same distance from chain end (mol[i] = mol[j])
// NOTE: must use extra parens in if test on mask[j] & groupbit
// atom I is randomly selected via atom list
// look at all J neighbors of atom I
// J must be on-processor (J < nlocal)
// I,J must be in fix group
// I,J must have same molecule IDs
// use case 1 (see doc page):
// if user defines mol IDs appropriately for linear chains,
// this will mean they are same distance from (either) chain end
// use case 2 (see doc page):
// if user defines a unique mol ID for desired bond sites (on any chain)
// and defines the fix group as these sites,
// this will mean they are eligible bond sites
int ntest = static_cast<int> (fraction * neligible);
int accept = 0;
@ -277,23 +284,29 @@ void FixBondSwap::post_integrate()
if ((mask[j] & groupbit) == 0) continue;
if (molecule[i] != molecule[j]) continue;
// look at all bond partners of atoms i and j
// use num_bond for this, not special list, so also find bondtypes
// inext,jnext = bonded atoms
// loop over all bond partners of atoms I and J
// use num_bond for this, not special list, so also have bondtypes
// inext,jnext = atoms bonded to I,J
// inext,jnext must be on-processor (inext,jnext < nlocal)
// inext,jnext must be same dist from chain end (mol[inext] = mol[jnext])
// since swaps may occur between two ends of a single chain, insure
// the 4 atoms are unique (no duplicates): inext != jnext, inext != j
// inext,jnext must be in fix group
// inext,jnext must have same molecule IDs
// in use cases above ...
// for case 1: this insures chain length is preserved
// for case 2: always satisfied b/c fix group = bond-able atoms
// 4 atoms must be unique (no duplicates): inext != jnext, inext != j
// already know i != inext, j != jnext
// all 4 old and new bonds must have length < cutoff
for (ibond = 0; ibond < num_bond[i]; ibond++) {
inext = atom->map(bond_atom[i][ibond]);
if (inext >= nlocal || inext < 0) continue;
if ((mask[inext] & groupbit) == 0) continue;
ibondtype = bond_type[i][ibond];
for (jbond = 0; jbond < num_bond[j]; jbond++) {
jnext = atom->map(bond_atom[j][jbond]);
if (jnext >= nlocal || jnext < 0) continue;
if ((mask[jnext] & groupbit) == 0) continue;
jbondtype = bond_type[j][jbond];
if (molecule[inext] != molecule[jnext]) continue;
@ -306,7 +319,7 @@ void FixBondSwap::post_integrate()
// if angles are enabled:
// find other atoms i,inext,j,jnext are in angles with
// and angletypes: i/j angletype, i/j nextangletype
// use num_angle for this, not special list, so also find angletypes
// use num_angle for this, not special list, so also have angletypes
// 4 atoms consecutively along 1st chain: iprev,i,inext,ilast
// 4 atoms consecutively along 2nd chain: jprev,j,jnext,jlast
// prev or last atom can be non-existent at end of chain
@ -428,7 +441,7 @@ void FixBondSwap::post_integrate()
done:
// trigger immediate reneighboring if any swaps occurred
// trigger immediate reneighboring if swaps occurred on one or more procs
int accept_any;
MPI_Allreduce(&accept,&accept_any,1,MPI_INT,MPI_SUM,world);