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Merge pull request #3905 from jrgissing/bond_react_fixes_aug23

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Assorted bond/react fixes
This commit is contained in:
Axel Kohlmeyer
2024-01-18 14:41:01 -05:00
committed by GitHub
parent 3b3ab4207b f3c5002634
commit bf9b8606ef
10 changed files with 153 additions and 180 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
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@ -40,7 +40,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo_style custom step temp press density f_myrxns[*]
thermo 100

4
examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt
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@ -26,7 +26,7 @@ read_data large_nylon_melt.data.gz &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
extra/special/per/atom 25
velocity all create 800.0 4928459 dist gaussian
@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 800 800 100
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
thermo_style custom step temp press density f_myrxns[*] # cumulative reaction counts
# restart 100 restart1 restart2

5
examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized
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@ -20,7 +20,8 @@ improper_style class2
special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower
read_data tiny_epoxy.data
read_data tiny_epoxy.data &
extra/special/per/atom 25
velocity all create 300.0 4928459 dist gaussian
@ -44,7 +45,7 @@ fix rxns all bond/react stabilization yes statted_grp .03 &
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
thermo_style custom step temp f_rxns[*]
run 2000

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
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@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -54,7 +54,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
View File

@ -47,7 +47,7 @@ fix myrxns all bond/react stabilization no &
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized
View File

@ -51,7 +51,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
thermo_style custom step temp press density f_rxn1[*]
run 10000

3
src/REACTION/README
View File

@ -25,4 +25,5 @@ The REACTER methodology is detailed in:
https://doi.org/10.1021/acs.macromol.0c02012
This package was created by Jacob Gissinger
(jacob.r.gissinger@gmail.com) at the NASA Langley Research Center.
(jgissing@stevens.edu) while at the NASA Langley Research Center
and Stevens Institute of Technology.

307
src/REACTION/fix_bond_react.cpp
View File

@ -13,7 +13,7 @@ See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com)
Contributing Author: Jacob Gissinger (jgissing@stevens.edu)
------------------------------------------------------------------------- */
#include "fix_bond_react.h"
@ -670,15 +670,6 @@ FixBondReact::~FixBondReact()
memory->destroy(ghostly_rxn_count);
memory->destroy(reaction_count_total);
if (newton_bond == 0) {
memory->destroy(xspecial);
memory->destroy(nxspecial);
memory->destroy(onemol_xspecial);
memory->destroy(onemol_nxspecial);
memory->destroy(twomol_xspecial);
memory->destroy(twomol_nxspecial);
}
if (attempted_rxn == 1) {
memory->destroy(restore_pt);
memory->destroy(restore);
@ -827,11 +818,10 @@ void FixBondReact::init()
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
// check cutoff for iatomtype,jatomtype
for (int i = 0; i < nreacts; i++) {
if (!utils::strmatch(force->pair_style,"^hybrid"))
if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
if (!utils::strmatch(force->pair_style,"^hybrid"))
for (int i = 0; i < nreacts; i++)
if (force->pair == nullptr || (closeneigh[i] < 0 && cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]))
error->all(FLERR,"Fix bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
}
// need a half neighbor list, built every Nevery steps
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
@ -931,29 +921,10 @@ void FixBondReact::post_integrate()
neighbor->build_one(list,1);
// here we define a full special list, independent of Newton setting
if (newton_bond == 1) {
nxspecial = atom->nspecial;
xspecial = atom->special;
} else {
int nall = atom->nlocal + atom->nghost;
memory->destroy(nxspecial);
memory->destroy(xspecial);
memory->create(nxspecial,nall,3,"bond/react:nxspecial");
memory->create(xspecial,nall,atom->maxspecial,"bond/react:xspecial");
for (int i = 0; i < atom->nlocal; i++) {
nxspecial[i][0] = atom->num_bond[i];
for (int j = 0; j < nxspecial[i][0]; j++) {
xspecial[i][j] = atom->bond_atom[i][j];
}
nxspecial[i][1] = atom->nspecial[i][1];
nxspecial[i][2] = atom->nspecial[i][2];
int joffset = nxspecial[i][0] - atom->nspecial[i][0];
for (int j = nxspecial[i][0]; j < nxspecial[i][2]; j++) {
xspecial[i][j+joffset] = atom->special[i][j];
}
}
}
// here we define a full special list
// may need correction for unusual special bond settings
nxspecial = atom->nspecial;
xspecial = atom->special;
int j;
for (rxnID = 0; rxnID < nreacts; rxnID++) {
@ -2541,49 +2512,15 @@ int FixBondReact::get_chirality(double four_coords[12])
/* ----------------------------------------------------------------------
Get xspecials for current molecule templates
may need correction when specials defined explicitly in molecule templates
------------------------------------------------------------------------- */
void FixBondReact::get_molxspecials()
{
if (newton_bond == 1) {
onemol_nxspecial = onemol->nspecial;
onemol_xspecial = onemol->special;
twomol_nxspecial = twomol->nspecial;
twomol_xspecial = twomol->special;
} else {
memory->destroy(onemol_nxspecial);
memory->destroy(onemol_xspecial);
memory->create(onemol_nxspecial,onemol->natoms,3,"bond/react:onemol_nxspecial");
memory->create(onemol_xspecial,onemol->natoms,atom->maxspecial,"bond/react:onemol_xspecial");
for (int i = 0; i < onemol->natoms; i++) {
onemol_nxspecial[i][0] = onemol->num_bond[i];
for (int j = 0; j < onemol_nxspecial[i][0]; j++) {
onemol_xspecial[i][j] = onemol->bond_atom[i][j];
}
onemol_nxspecial[i][1] = onemol->nspecial[i][1];
onemol_nxspecial[i][2] = onemol->nspecial[i][2];
int joffset = onemol_nxspecial[i][0] - onemol->nspecial[i][0];
for (int j = onemol_nxspecial[i][0]; j < onemol_nxspecial[i][2]; j++) {
onemol_xspecial[i][j+joffset] = onemol->special[i][j];
}
}
memory->destroy(twomol_nxspecial);
memory->destroy(twomol_xspecial);
memory->create(twomol_nxspecial,twomol->natoms,3,"bond/react:twomol_nxspecial");
memory->create(twomol_xspecial,twomol->natoms,atom->maxspecial,"bond/react:twomol_xspecial");
for (int i = 0; i < twomol->natoms; i++) {
twomol_nxspecial[i][0] = twomol->num_bond[i];
for (int j = 0; j < twomol_nxspecial[i][0]; j++) {
twomol_xspecial[i][j] = twomol->bond_atom[i][j];
}
twomol_nxspecial[i][1] = twomol->nspecial[i][1];
twomol_nxspecial[i][2] = twomol->nspecial[i][2];
int joffset = twomol_nxspecial[i][0] - twomol->nspecial[i][0];
for (int j = twomol_nxspecial[i][0]; j < twomol_nxspecial[i][2]; j++) {
twomol_xspecial[i][j+joffset] = twomol->special[i][j];
}
}
}
onemol_nxspecial = onemol->nspecial;
onemol_xspecial = onemol->special;
twomol_nxspecial = twomol->nspecial;
twomol_xspecial = twomol->special;
}
/* ----------------------------------------------------------------------
@ -2682,16 +2619,43 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
}
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
int warnflag = 0;
if (comm->me == 0)
for (int i = 0; i < twomol->natoms; i++) {
if ((create_atoms[i][myrxn] == 0) &&
(twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) &&
(landlocked_atoms[i][myrxn] == 0))
error->warning(FLERR, "Fix bond/react: Atom affected by reaction {} is too close "
"to template edge",rxn_name[myrxn]);
break;
(landlocked_atoms[i][myrxn] == 0)) {
warnflag = 1;
break;
}
}
// also, if an atom changes any of its bonds, but is not landlocked, that could be bad
int thereflag;
if (comm->me == 0)
for (int i = 0; i < twomol->natoms; i++) {
if (landlocked_atoms[i][myrxn] == 1) continue;
for (int j = 0; j < twomol_nxspecial[i][0]; j++) {
int oneneighID = equivalences[twomol_xspecial[i][j]-1][1][myrxn];
int ii = equivalences[i][1][myrxn] - 1;
thereflag = 0;
for (int k = 0; k < onemol_nxspecial[ii][0]; k++) {
if (oneneighID == onemol_xspecial[ii][k]) {
thereflag = 1;
break;
}
}
if (thereflag == 0) {
warnflag = 1;
break;
}
}
if (warnflag == 1) break;
}
if (comm->me == 0 && warnflag == 1) error->warning(FLERR, "Fix bond/react: Atom affected "
"by reaction {} is too close to template edge",rxn_name[myrxn]);
// finally, if a created atom is not landlocked, bad!
for (int i = 0; i < twomol->natoms; i++) {
if (create_atoms[i][myrxn] == 1 && landlocked_atoms[i][myrxn] == 0) {
@ -3349,7 +3313,7 @@ void FixBondReact::update_everything()
dynamic_cast<FixBondHistory *>(ihistory)->clear_cache();
// Angles! First let's delete all angle info:
if (force->angle && twomol->angleflag) {
if (force->angle) {
int *num_angle = atom->num_angle;
int **angle_type = atom->angle_type;
tagint **angle_atom1 = atom->angle_atom1;
@ -3390,33 +3354,35 @@ void FixBondReact::update_everything()
}
}
// now let's add the new angle info.
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
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) {
num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j];
delta_angle += twomol->num_angle[j];
for (int p = 0; p < twomol->num_angle[j]; p++) {
angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p];
angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i];
angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
if (twomol->angleflag) {
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
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) {
num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j];
delta_angle += twomol->num_angle[j];
for (int p = 0; p < twomol->num_angle[j]; p++) {
angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p];
angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i];
angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
}
}
}
if (landlocked_atoms[j][rxnID] == 0) {
for (int p = 0; p < twomol->num_angle[j]; p++) {
if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) {
insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])];
angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p];
angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i];
angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
num_angle[atom->map(update_mega_glove[jj+1][i])]++;
if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom");
delta_angle++;
if (landlocked_atoms[j][rxnID] == 0) {
for (int p = 0; p < twomol->num_angle[j]; p++) {
if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) {
insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])];
angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p];
angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i];
angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
num_angle[atom->map(update_mega_glove[jj+1][i])]++;
if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom");
delta_angle++;
}
}
}
}
@ -3426,7 +3392,7 @@ void FixBondReact::update_everything()
}
// Dihedrals! first let's delete all dihedral info for landlocked atoms
if (force->dihedral && twomol->dihedralflag) {
if (force->dihedral) {
int *num_dihedral = atom->num_dihedral;
int **dihedral_type = atom->dihedral_type;
tagint **dihedral_atom1 = atom->dihedral_atom1;
@ -3470,36 +3436,38 @@ void FixBondReact::update_everything()
}
}
// now let's add new dihedral info
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
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) {
num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j];
delta_dihed += twomol->num_dihedral[j];
for (int p = 0; p < twomol->num_dihedral[j]; p++) {
dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p];
dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i];
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i];
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
if (twomol->dihedralflag) {
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
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) {
num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j];
delta_dihed += twomol->num_dihedral[j];
for (int p = 0; p < twomol->num_dihedral[j]; p++) {
dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p];
dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i];
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i];
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
}
}
}
if (landlocked_atoms[j][rxnID] == 0) {
for (int p = 0; p < twomol->num_dihedral[j]; p++) {
if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) {
insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])];
dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p];
dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i];
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i];
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom");
delta_dihed++;
if (landlocked_atoms[j][rxnID] == 0) {
for (int p = 0; p < twomol->num_dihedral[j]; p++) {
if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) {
insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])];
dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p];
dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i];
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i];
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom");
delta_dihed++;
}
}
}
}
@ -3509,7 +3477,7 @@ void FixBondReact::update_everything()
}
// finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms
if (force->improper && twomol->improperflag) {
if (force->improper) {
int *num_improper = atom->num_improper;
int **improper_type = atom->improper_type;
tagint **improper_atom1 = atom->improper_atom1;
@ -3553,36 +3521,38 @@ void FixBondReact::update_everything()
}
}
// now let's add new improper info
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
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) {
num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j];
delta_imprp += twomol->num_improper[j];
for (int p = 0; p < twomol->num_improper[j]; p++) {
improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p];
improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i];
improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i];
improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
if (twomol->improperflag) {
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
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) {
num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j];
delta_imprp += twomol->num_improper[j];
for (int p = 0; p < twomol->num_improper[j]; p++) {
improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p];
improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i];
improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i];
improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
}
}
}
if (landlocked_atoms[j][rxnID] == 0) {
for (int p = 0; p < twomol->num_improper[j]; p++) {
if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) {
insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])];
improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p];
improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i];
improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i];
improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
num_improper[atom->map(update_mega_glove[jj+1][i])]++;
if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom");
delta_imprp++;
if (landlocked_atoms[j][rxnID] == 0) {
for (int p = 0; p < twomol->num_improper[j]; p++) {
if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 ||
landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) {
insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])];
improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p];
improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i];
improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i];
improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
num_improper[atom->map(update_mega_glove[jj+1][i])]++;
if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom");
delta_imprp++;
}
}
}
}
@ -3895,7 +3865,8 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
// guess a somewhat reasonable initial velocity based on reaction site
// further control is possible using bond_react_MASTER_group
// compute |velocity| corresponding to a given temperature t, using specific atom's mass
double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / atom->mass[twomol->type[m]]);
double mymass = atom->rmass ? atom->rmass[n] : atom->mass[twomol->type[m]];
double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / mymass);
v[n][0] = random[rxnID]->uniform();
v[n][1] = random[rxnID]->uniform();
v[n][2] = random[rxnID]->uniform();

4
src/REACTION/fix_bond_react.h
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com)
Contributing Author: Jacob Gissinger (jgissing@stevens.edu)
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
@ -139,7 +139,7 @@ class FixBondReact : public Fix {
int avail_guesses; // num of restore points available
int *guess_branch; // used when there is more than two choices when guessing
int **restore_pt; // contains info about restore points
tagint **restore; // contaings info about restore points
tagint **restore; // contains info about restore points
int *pioneer_count; // counts pioneers
int **edge; // atoms in molecule templates with incorrect valences