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Revamping public methods for history, adding support for bond react

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This commit is contained in:
Joel Thomas Clemmer
2021-12-13 17:35:53 -07:00
parent 668d7805d6
commit 744e615dbb
8 changed files with 157 additions and 25 deletions
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36
src/REACTION/fix_bond_react.cpp
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@ -24,6 +24,7 @@ Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com)
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_bond_history.h"
#include "force.h"
#include "group.h"
#include "input.h"
@ -3091,6 +3092,10 @@ void FixBondReact::update_everything()
// next let's update bond info
// cool thing is, newton_bond issues are already taken care of in templates
// same with class2 improper issues, which is why this fix started in the first place
// also need to find any instances of bond history to update histories
auto histories = modify->get_fix_by_style("BOND_HISTORY");
int n_histories = histories.size();
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
twomol = atom->molecules[reacted_mol[rxnID]];
@ -3100,6 +3105,14 @@ void FixBondReact::update_everything()
if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
if (landlocked_atoms[j][rxnID] == 1) {
delta_bonds -= num_bond[atom->map(update_mega_glove[jj+1][i])];
// If deleting all bonds, first cache then remove all histories
if (n_histories > 0)
for (auto &ihistory: histories) {
for (int n = 0; n < num_bond[atom->map(update_mega_glove[jj+1][i])]; n++)
((FixBondHistory *) ihistory)->cache_history(atom->map(update_mega_glove[jj+1][i]), n);
for (int n = 0; n < num_bond[atom->map(update_mega_glove[jj+1][i])]; n++)
((FixBondHistory *) ihistory)->delete_history(atom->map(update_mega_glove[jj+1][i]), 0);
}
num_bond[atom->map(update_mega_glove[jj+1][i])] = 0;
}
if (landlocked_atoms[j][rxnID] == 0) {
@ -3107,10 +3120,21 @@ void FixBondReact::update_everything()
for (int n = 0; n < twomol->natoms; n++) {
int nn = equivalences[n][1][rxnID]-1;
if (n!=j && bond_atom[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] && landlocked_atoms[n][rxnID] == 1) {
// Cache history information, shift history, then delete final element
if (n_histories > 0)
for (auto &ihistory: histories)
((FixBondHistory *) ihistory)->cache_history(atom->map(update_mega_glove[jj+1][i]), p);
for (int m = p; m < num_bond[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
bond_type[atom->map(update_mega_glove[jj+1][i])][m] = bond_type[atom->map(update_mega_glove[jj+1][i])][m+1];
bond_atom[atom->map(update_mega_glove[jj+1][i])][m] = bond_atom[atom->map(update_mega_glove[jj+1][i])][m+1];
if (n_histories > 0)
for (auto &ihistory: histories)
((FixBondHistory *) ihistory)->shift_history(atom->map(update_mega_glove[jj+1][i]),m,m+1);
}
if (n_histories > 0)
for (auto &ihistory: histories)
((FixBondHistory *) ihistory)->delete_history(atom->map(update_mega_glove[jj+1][i]),
num_bond[atom->map(update_mega_glove[jj+1][i])]-1);
num_bond[atom->map(update_mega_glove[jj+1][i])]--;
delta_bonds--;
}
@ -3129,6 +3153,10 @@ void FixBondReact::update_everything()
for (int p = 0; p < twomol->num_bond[j]; p++) {
bond_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->bond_type[j][p];
bond_atom[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
// Check cached history data to see if bond regenerated
if (n_histories > 0)
for (auto &ihistory: histories)
((FixBondHistory *) ihistory)->check_cache(atom->map(update_mega_glove[jj+1][i]), p);
}
}
if (landlocked_atoms[j][rxnID] == 0) {
@ -3137,6 +3165,10 @@ void FixBondReact::update_everything()
insert_num = num_bond[atom->map(update_mega_glove[jj+1][i])];
bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p];
bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
// Check cached history data to see if bond regenerated
if (n_histories > 0)
for (auto &ihistory: histories)
((FixBondHistory *) ihistory)->check_cache(atom->map(update_mega_glove[jj+1][i]), insert_num);
num_bond[atom->map(update_mega_glove[jj+1][i])]++;
if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom)
error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
@ -3148,6 +3180,10 @@ void FixBondReact::update_everything()
}
}
if (n_histories > 0)
for (auto &ihistory: histories)
((FixBondHistory *) ihistory)->clear_cache();
// Angles! First let's delete all angle info:
if (force->angle && twomol->angleflag) {
int *num_angle = atom->num_angle;