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@ -13,7 +13,7 @@ See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing Author: Jacob Gissinger (jacob.r.gissinger@gmail.com)
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Contributing Author: Jacob Gissinger (jgissing@stevens.edu)
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------------------------------------------------------------------------- */
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#include "fix_bond_react.h"
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@ -670,15 +670,6 @@ FixBondReact::~FixBondReact()
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memory->destroy(ghostly_rxn_count);
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memory->destroy(reaction_count_total);
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if (newton_bond == 0) {
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memory->destroy(xspecial);
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memory->destroy(nxspecial);
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memory->destroy(onemol_xspecial);
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memory->destroy(onemol_nxspecial);
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memory->destroy(twomol_xspecial);
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memory->destroy(twomol_nxspecial);
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}
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if (attempted_rxn == 1) {
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memory->destroy(restore_pt);
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memory->destroy(restore);
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@ -827,11 +818,10 @@ void FixBondReact::init()
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nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
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// check cutoff for iatomtype,jatomtype
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for (int i = 0; i < nreacts; i++) {
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if (!utils::strmatch(force->pair_style,"^hybrid"))
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if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
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for (int i = 0; i < nreacts; i++)
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if (force->pair == nullptr || (closeneigh[i] < 0 && cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]))
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error->all(FLERR,"Fix bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
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}
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// need a half neighbor list, built every Nevery steps
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neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
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@ -931,29 +921,10 @@ void FixBondReact::post_integrate()
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neighbor->build_one(list,1);
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// here we define a full special list, independent of Newton setting
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if (newton_bond == 1) {
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// here we define a full special list
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// may need correction for unusual special bond settings
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nxspecial = atom->nspecial;
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xspecial = atom->special;
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} else {
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int nall = atom->nlocal + atom->nghost;
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memory->destroy(nxspecial);
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memory->destroy(xspecial);
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memory->create(nxspecial,nall,3,"bond/react:nxspecial");
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memory->create(xspecial,nall,atom->maxspecial,"bond/react:xspecial");
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for (int i = 0; i < atom->nlocal; i++) {
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nxspecial[i][0] = atom->num_bond[i];
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for (int j = 0; j < nxspecial[i][0]; j++) {
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xspecial[i][j] = atom->bond_atom[i][j];
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}
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nxspecial[i][1] = atom->nspecial[i][1];
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nxspecial[i][2] = atom->nspecial[i][2];
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int joffset = nxspecial[i][0] - atom->nspecial[i][0];
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for (int j = nxspecial[i][0]; j < nxspecial[i][2]; j++) {
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xspecial[i][j+joffset] = atom->special[i][j];
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}
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}
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}
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int j;
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for (rxnID = 0; rxnID < nreacts; rxnID++) {
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@ -2541,49 +2512,15 @@ int FixBondReact::get_chirality(double four_coords[12])
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/* ----------------------------------------------------------------------
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Get xspecials for current molecule templates
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may need correction when specials defined explicitly in molecule templates
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------------------------------------------------------------------------- */
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void FixBondReact::get_molxspecials()
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{
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if (newton_bond == 1) {
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onemol_nxspecial = onemol->nspecial;
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onemol_xspecial = onemol->special;
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twomol_nxspecial = twomol->nspecial;
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twomol_xspecial = twomol->special;
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} else {
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memory->destroy(onemol_nxspecial);
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memory->destroy(onemol_xspecial);
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memory->create(onemol_nxspecial,onemol->natoms,3,"bond/react:onemol_nxspecial");
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memory->create(onemol_xspecial,onemol->natoms,atom->maxspecial,"bond/react:onemol_xspecial");
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for (int i = 0; i < onemol->natoms; i++) {
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onemol_nxspecial[i][0] = onemol->num_bond[i];
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for (int j = 0; j < onemol_nxspecial[i][0]; j++) {
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onemol_xspecial[i][j] = onemol->bond_atom[i][j];
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}
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onemol_nxspecial[i][1] = onemol->nspecial[i][1];
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onemol_nxspecial[i][2] = onemol->nspecial[i][2];
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int joffset = onemol_nxspecial[i][0] - onemol->nspecial[i][0];
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for (int j = onemol_nxspecial[i][0]; j < onemol_nxspecial[i][2]; j++) {
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onemol_xspecial[i][j+joffset] = onemol->special[i][j];
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}
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}
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memory->destroy(twomol_nxspecial);
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memory->destroy(twomol_xspecial);
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memory->create(twomol_nxspecial,twomol->natoms,3,"bond/react:twomol_nxspecial");
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memory->create(twomol_xspecial,twomol->natoms,atom->maxspecial,"bond/react:twomol_xspecial");
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for (int i = 0; i < twomol->natoms; i++) {
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twomol_nxspecial[i][0] = twomol->num_bond[i];
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for (int j = 0; j < twomol_nxspecial[i][0]; j++) {
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twomol_xspecial[i][j] = twomol->bond_atom[i][j];
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}
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twomol_nxspecial[i][1] = twomol->nspecial[i][1];
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twomol_nxspecial[i][2] = twomol->nspecial[i][2];
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int joffset = twomol_nxspecial[i][0] - twomol->nspecial[i][0];
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for (int j = twomol_nxspecial[i][0]; j < twomol_nxspecial[i][2]; j++) {
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twomol_xspecial[i][j+joffset] = twomol->special[i][j];
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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@ -2682,15 +2619,42 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
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}
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// also, if atoms change number of bonds, but aren't landlocked, that could be bad
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int warnflag = 0;
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if (comm->me == 0)
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for (int i = 0; i < twomol->natoms; i++) {
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if ((create_atoms[i][myrxn] == 0) &&
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(twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) &&
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(landlocked_atoms[i][myrxn] == 0))
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error->warning(FLERR, "Fix bond/react: Atom affected by reaction {} is too close "
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"to template edge",rxn_name[myrxn]);
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(landlocked_atoms[i][myrxn] == 0)) {
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warnflag = 1;
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break;
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}
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}
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// also, if an atom changes any of its bonds, but is not landlocked, that could be bad
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int thereflag;
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if (comm->me == 0)
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for (int i = 0; i < twomol->natoms; i++) {
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if (landlocked_atoms[i][myrxn] == 1) continue;
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for (int j = 0; j < twomol_nxspecial[i][0]; j++) {
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int oneneighID = equivalences[twomol_xspecial[i][j]-1][1][myrxn];
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int ii = equivalences[i][1][myrxn] - 1;
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thereflag = 0;
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for (int k = 0; k < onemol_nxspecial[ii][0]; k++) {
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if (oneneighID == onemol_xspecial[ii][k]) {
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thereflag = 1;
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break;
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}
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}
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if (thereflag == 0) {
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warnflag = 1;
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break;
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}
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}
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if (warnflag == 1) break;
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}
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if (comm->me == 0 && warnflag == 1) error->warning(FLERR, "Fix bond/react: Atom affected "
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"by reaction {} is too close to template edge",rxn_name[myrxn]);
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// finally, if a created atom is not landlocked, bad!
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for (int i = 0; i < twomol->natoms; i++) {
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@ -3349,7 +3313,7 @@ void FixBondReact::update_everything()
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dynamic_cast<FixBondHistory *>(ihistory)->clear_cache();
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// Angles! First let's delete all angle info:
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if (force->angle && twomol->angleflag) {
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if (force->angle) {
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int *num_angle = atom->num_angle;
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int **angle_type = atom->angle_type;
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tagint **angle_atom1 = atom->angle_atom1;
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@ -3390,6 +3354,7 @@ void FixBondReact::update_everything()
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}
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}
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// now let's add the new angle info.
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if (twomol->angleflag) {
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for (int j = 0; j < twomol->natoms; j++) {
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int jj = equivalences[j][1][rxnID]-1;
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if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
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@ -3424,9 +3389,10 @@ void FixBondReact::update_everything()
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}
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}
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}
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}
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// Dihedrals! first let's delete all dihedral info for landlocked atoms
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if (force->dihedral && twomol->dihedralflag) {
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if (force->dihedral) {
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_type = atom->dihedral_type;
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tagint **dihedral_atom1 = atom->dihedral_atom1;
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@ -3470,6 +3436,7 @@ void FixBondReact::update_everything()
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}
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}
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// now let's add new dihedral info
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if (twomol->dihedralflag) {
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for (int j = 0; j < twomol->natoms; j++) {
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int jj = equivalences[j][1][rxnID]-1;
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if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
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@ -3507,9 +3474,10 @@ void FixBondReact::update_everything()
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}
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}
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}
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}
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// finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms
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if (force->improper && twomol->improperflag) {
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if (force->improper) {
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int *num_improper = atom->num_improper;
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int **improper_type = atom->improper_type;
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tagint **improper_atom1 = atom->improper_atom1;
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@ -3553,6 +3521,7 @@ void FixBondReact::update_everything()
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}
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}
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// now let's add new improper info
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if (twomol->improperflag) {
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for (int j = 0; j < twomol->natoms; j++) {
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int jj = equivalences[j][1][rxnID]-1;
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if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
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@ -3590,6 +3559,7 @@ void FixBondReact::update_everything()
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}
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}
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}
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}
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}
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@ -3895,7 +3865,8 @@ int FixBondReact::insert_atoms(tagint **my_update_mega_glove, int iupdate)
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// guess a somewhat reasonable initial velocity based on reaction site
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// further control is possible using bond_react_MASTER_group
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// compute |velocity| corresponding to a given temperature t, using specific atom's mass
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double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / atom->mass[twomol->type[m]]);
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double mymass = atom->rmass ? atom->rmass[n] : atom->mass[twomol->type[m]];
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double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / mymass);
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v[n][0] = random[rxnID]->uniform();
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v[n][1] = random[rxnID]->uniform();
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v[n][2] = random[rxnID]->uniform();
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Axel Kohlmeyer