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add sticker-bond support to fix bond/swap

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This commit is contained in:
Steve Plimpton
2021-07-02 11:46:25 -06:00
parent 105c86399b
commit 2a21c4b29f
2 changed files with 39 additions and 22 deletions
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21
doc/src/fix_bond_swap.rst
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@ -65,14 +65,19 @@ monomers for this timestep. Choosing a small *fraction* value can
reduce the likelihood of a reverse swap occurring soon after an
initial swap.
For each monomer A1, its neighbors are examined to find a possible B1
monomer. Both A1 and B1 must be in the fix group, their separation
must be less than the specified *cutoff*\ , and the molecule IDs of A1
and B1 must be the same (see below). If a suitable partner is found,
the energy change due to swapping the 2 bonds is computed. This
includes changes in pairwise, bond, and angle energies due to the
altered connectivity of the 2 chains. Dihedral and improper
interactions are not allowed to be defined when this fix is used.
NOTE: is cutoff applied to all new bonds?
For each monomer A1, its neighbors are looped over as B1 monomers.
All bond partners of both A1 and B1 are also looped over. For a pair
of A1-A2 and B1-B2 bonds to be eligible for swapping, these criteria
must be met. All 4 monomers must be in the fix group. The separation
between A1 and B1 must be less than the specified *cutoff*\ . And the
molecule IDs of A1 and B1 must be the same (see below). If an
eligible B1 partner is found, the energy change due to swapping the 2
bonds is computed. This includes changes in pairwise, bond, and angle
energies due to the altered connectivity of the 2 chains. Dihedral
and improper interactions are not allowed to be defined when this fix
is used.
If the energy decreases due to the swap operation, the bond swap is
accepted. If the energy increases it is accepted with probability

40
src/MC/fix_bond_swap.cpp
View File

@ -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:
// if user defines mol IDs appropriately for linear chains,
// this will mean they are same distance from (either) chain end
// use case 2:
// if user defines a unique mol ID for desired bond sites (on any chain)
// and defines the fix group for these sites,
// this will mean they are eligible bond sites
int ntest = static_cast<int> (fraction * neligible);
int accept = 0;
@ -277,23 +284,28 @@ 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
// for use case 1 (above): this insures chain length is preserved
// for use 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 +318,7 @@ 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