4392 lines
162 KiB
C++
4392 lines
162 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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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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------------------------------------------------------------------------- */
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#include "fix_bond_react.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "citeme.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "fix_bond_history.h"
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#include "force.h"
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#include "group.h"
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#include "input.h"
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#include "math_const.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "modify.h"
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#include "molecule.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "neighbor.h"
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#include "pair.h"
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#include "random_mars.h"
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#include "reset_mol_ids.h"
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#include "respa.h"
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#include "update.h"
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#include "variable.h"
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#include "superpose3d.h"
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#include <cctype>
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#include <cmath>
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#include <cstring>
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#include <algorithm>
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#include <random>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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using namespace MathConst;
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static const char cite_fix_bond_react[] =
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"fix bond/react: reacter.org\n\n"
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"@Article{Gissinger17,\n"
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" author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
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" title = {Modeling chemical reactions in classical molecular dynamics simulations},\n"
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" journal = {Polymer},\n"
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" year = 2017,\n"
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" volume = 128,\n"
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" pages = {211--217}\n"
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"}\n\n"
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"@Article{Gissinger20,\n"
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" author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
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" title = {REACTER: A Heuristic Method for Reactive Molecular Dynamics},\n"
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" journal = {Macromolecules},\n"
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" year = 2020,\n"
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" volume = 53,\n"
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" pages = {9953--9961}\n"
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"}\n\n";
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#define BIG 1.0e20
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#define DELTA 16
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#define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm
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#define MAXCONARGS 14 // max # of arguments for any type of constraint + rxnID
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#define NUMVARVALS 4 // max # of keyword values that have variables as input
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// various statuses of superimpose algorithm:
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// ACCEPT: site successfully matched to pre-reacted template
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// REJECT: site does not match pre-reacted template
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// PROCEED: normal execution (non-guessing mode)
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// CONTINUE: a neighbor has been assigned, skip to next neighbor
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// GUESSFAIL: a guess has failed (if no more restore points, status = 'REJECT')
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// RESTORE: restore mode, load most recent restore point
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enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
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// types of available reaction constraints
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enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD,CUSTOM};
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// ID type used by constraint
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enum{ATOM,FRAG};
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// keyword values that accept variables as input
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enum{NEVERY,RMIN,RMAX,PROB};
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// flag for one-proc vs shared reaction sites
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enum{LOCAL,GLOBAL};
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// values for molecule_keyword
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enum{OFF,INTER,INTRA};
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/* ---------------------------------------------------------------------- */
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FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (lmp->citeme) lmp->citeme->add(cite_fix_bond_react);
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fix1 = nullptr;
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fix2 = nullptr;
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fix3 = nullptr;
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reset_mol_ids = nullptr;
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if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: "
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"too few arguments");
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MPI_Comm_rank(world,&me);
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MPI_Comm_size(world,&nprocs);
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newton_bond = force->newton_bond;
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restart_global = 1;
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attempted_rxn = 0;
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force_reneighbor = 1;
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next_reneighbor = -1;
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vector_flag = 1;
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global_freq = 1;
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extvector = 0;
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rxnID = 0;
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maxnconstraints = 0;
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narrhenius = 0;
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status = PROCEED;
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// reaction functions used by 'custom' constraint
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nrxnfunction = 2;
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rxnfunclist.resize(nrxnfunction);
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rxnfunclist[0] = "rxnsum";
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rxnfunclist[1] = "rxnave";
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nvvec = 0;
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ncustomvars = 0;
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vvec = nullptr;
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nxspecial = nullptr;
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onemol_nxspecial = nullptr;
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twomol_nxspecial = nullptr;
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xspecial = nullptr;
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onemol_xspecial = nullptr;
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twomol_xspecial = nullptr;
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// these group names are reserved for use exclusively by bond/react
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master_group = (char *) "bond_react_MASTER_group";
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// by using fixed group names, only one instance of fix bond/react is allowed.
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if (modify->get_fix_by_style("^bond/react").size() != 0)
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error->all(FLERR,"Only one instance of fix bond/react allowed at a time");
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// let's find number of reactions specified
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nreacts = 0;
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for (int i = 3; i < narg; i++) {
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if (strcmp(arg[i],"react") == 0) {
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nreacts++;
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i = i + 6; // skip past mandatory arguments
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if (i > narg) error->all(FLERR,"Illegal fix bond/react command: "
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"'react' has too few arguments");
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}
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}
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if (nreacts == 0) error->all(FLERR,"Illegal fix bond/react command: "
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"missing mandatory 'react' argument");
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size_vector = nreacts;
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int iarg = 3;
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stabilization_flag = 0;
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reset_mol_ids_flag = 1;
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int num_common_keywords = 2;
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for (int m = 0; m < num_common_keywords; m++) {
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if (strcmp(arg[iarg],"stabilization") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
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"'stabilization' keyword has too few arguments");
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stabilization_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
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if (stabilization_flag) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command:"
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"'stabilization' keyword has too few arguments");
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exclude_group = utils::strdup(arg[iarg+2]);
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nve_limit_xmax = arg[iarg+3];
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iarg += 4;
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} else iarg += 2;
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} else if (strcmp(arg[iarg],"reset_mol_ids") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
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"'reset_mol_ids' keyword has too few arguments");
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reset_mol_ids_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg],"react") == 0) {
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break;
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} else error->all(FLERR,"Illegal fix bond/react command: unknown keyword");
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}
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if (reset_mol_ids_flag) {
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delete reset_mol_ids;
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reset_mol_ids = new ResetMolIDs(lmp);
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reset_mol_ids->create_computes(id,group->names[igroup]);
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}
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// set up common variables as vectors of length 'nreacts'
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// nevery, cutoff, onemol, twomol, superimpose file
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// this looks excessive
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// the price of vectorization (all reactions in one command)?
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memory->create(rxn_name,nreacts,MAXLINE,"bond/react:rxn_name");
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memory->create(nevery,nreacts,"bond/react:nevery");
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memory->create(cutsq,nreacts,2,"bond/react:cutsq");
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memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
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memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
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memory->create(fraction,nreacts,"bond/react:fraction");
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memory->create(max_rxn,nreacts,"bond/react:max_rxn");
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memory->create(nlocalskips,nreacts,"bond/react:nlocalskips");
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memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips");
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memory->create(seed,nreacts,"bond/react:seed");
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memory->create(limit_duration,nreacts,"bond/react:limit_duration");
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memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
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memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid");
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memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag");
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memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid");
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memory->create(overlapsq,nreacts,"bond/react:overlapsq");
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memory->create(molecule_keyword,nreacts,"bond/react:molecule_keyword");
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memory->create(nconstraints,nreacts,"bond/react:nconstraints");
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memory->create(constraintstr,nreacts,MAXLINE,"bond/react:constraintstr");
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memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag");
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memory->create(var_id,NUMVARVALS,nreacts,"bond/react:var_id");
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memory->create(iatomtype,nreacts,"bond/react:iatomtype");
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memory->create(jatomtype,nreacts,"bond/react:jatomtype");
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memory->create(ibonding,nreacts,"bond/react:ibonding");
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memory->create(jbonding,nreacts,"bond/react:jbonding");
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memory->create(closeneigh,nreacts,"bond/react:closeneigh");
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memory->create(groupbits,nreacts,"bond/react:groupbits");
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memory->create(reaction_count,nreacts,"bond/react:reaction_count");
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memory->create(local_rxn_count,nreacts,"bond/react:local_rxn_count");
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memory->create(ghostly_rxn_count,nreacts,"bond/react:ghostly_rxn_count");
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memory->create(reaction_count_total,nreacts,"bond/react:reaction_count_total");
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for (int i = 0; i < nreacts; i++) {
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fraction[i] = 1;
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seed[i] = 12345;
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max_rxn[i] = INT_MAX;
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stabilize_steps_flag[i] = 0;
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custom_charges_fragid[i] = -1;
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create_atoms_flag[i] = 0;
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modify_create_fragid[i] = -1;
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overlapsq[i] = 0;
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molecule_keyword[i] = OFF;
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nconstraints[i] = 0;
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// set default limit duration to 60 timesteps
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limit_duration[i] = 60;
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reaction_count[i] = 0;
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local_rxn_count[i] = 0;
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ghostly_rxn_count[i] = 0;
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reaction_count_total[i] = 0;
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for (int j = 0; j < NUMVARVALS; j++) {
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var_flag[j][i] = 0;
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var_id[j][i] = 0;
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}
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}
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char **files;
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files = new char*[nreacts];
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for (int rxn = 0; rxn < nreacts; rxn++) {
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if (strcmp(arg[iarg],"react") != 0) error->all(FLERR,"Illegal fix bond/react command: "
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"'react' or 'stabilization' has incorrect arguments");
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iarg++;
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int n = strlen(arg[iarg]) + 1;
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if (n > MAXLINE) error->all(FLERR,"Reaction name (react-ID) is too long (limit: 256 characters)");
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strcpy(rxn_name[rxn],arg[iarg++]);
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int groupid = group->find(arg[iarg++]);
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if (groupid == -1) error->all(FLERR,"Could not find fix group ID");
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groupbits[rxn] = group->bitmask[groupid];
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if (strncmp(arg[iarg],"v_",2) == 0) {
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char *str = utils::strdup(&arg[iarg][2]);
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var_id[NEVERY][rxn] = input->variable->find(str);
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if (var_id[NEVERY][rxn] < 0)
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error->all(FLERR,"Bond/react: Variable name does not exist");
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if (!input->variable->equalstyle(var_id[NEVERY][rxn]))
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error->all(FLERR,"Bond/react: Variable is not equal-style");
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var_flag[NEVERY][rxn] = 1;
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delete [] str;
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} else {
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nevery[rxn] = utils::inumeric(FLERR,arg[iarg],false,lmp);
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if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: "
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"'Nevery' must be a positive integer");
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}
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iarg++;
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if (strncmp(arg[iarg],"v_",2) == 0) {
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char *str = utils::strdup(&arg[iarg][2]);
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var_id[RMIN][rxn] = input->variable->find(str);
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if (var_id[RMIN][rxn] < 0)
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error->all(FLERR,"Bond/react: Variable name does not exist");
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if (!input->variable->equalstyle(var_id[RMIN][rxn]))
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error->all(FLERR,"Bond/react: Variable is not equal-style");
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double cutoff = input->variable->compute_equal(var_id[RMIN][rxn]);
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cutsq[rxn][0] = cutoff*cutoff;
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var_flag[RMIN][rxn] = 1;
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delete [] str;
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} else {
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double cutoff = utils::numeric(FLERR,arg[iarg],false,lmp);
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if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command: "
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"'Rmin' cannot be negative");
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cutsq[rxn][0] = cutoff*cutoff;
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}
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iarg++;
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if (strncmp(arg[iarg],"v_",2) == 0) {
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char *str = utils::strdup(&arg[iarg][2]);
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var_id[RMAX][rxn] = input->variable->find(str);
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if (var_id[RMAX][rxn] < 0)
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error->all(FLERR,"Bond/react: Variable name does not exist");
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if (!input->variable->equalstyle(var_id[RMAX][rxn]))
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error->all(FLERR,"Bond/react: Variable is not equal-style");
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double cutoff = input->variable->compute_equal(var_id[RMAX][rxn]);
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cutsq[rxn][1] = cutoff*cutoff;
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var_flag[RMAX][rxn] = 1;
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delete [] str;
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} else {
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double cutoff = utils::numeric(FLERR,arg[iarg],false,lmp);
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if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command:"
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"'Rmax' cannot be negative");
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cutsq[rxn][1] = cutoff*cutoff;
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}
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iarg++;
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unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
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if (unreacted_mol[rxn] == -1) error->all(FLERR,"Unreacted molecule template ID for "
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"fix bond/react does not exist");
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reacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
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if (reacted_mol[rxn] == -1) error->all(FLERR,"Reacted molecule template ID for "
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"fix bond/react does not exist");
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|
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//read superimpose file
|
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files[rxn] = utils::strdup(arg[iarg]);
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iarg++;
|
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|
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while (iarg < narg && strcmp(arg[iarg],"react") != 0) {
|
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if (strcmp(arg[iarg],"prob") == 0) {
|
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
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"'prob' keyword has too few arguments");
|
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// check if probability is a variable
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if (strncmp(arg[iarg+1],"v_",2) == 0) {
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char *str = utils::strdup(&arg[iarg+1][2]);
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var_id[PROB][rxn] = input->variable->find(str);
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if (var_id[PROB][rxn] < 0)
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error->all(FLERR,"Bond/react: Variable name does not exist");
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if (!input->variable->equalstyle(var_id[PROB][rxn]))
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error->all(FLERR,"Bond/react: Variable is not equal-style");
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fraction[rxn] = input->variable->compute_equal(var_id[PROB][rxn]);
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var_flag[PROB][rxn] = 1;
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delete [] str;
|
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} else {
|
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// otherwise probability should be a number
|
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fraction[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
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}
|
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seed[rxn] = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
|
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if (fraction[rxn] < 0.0 || fraction[rxn] > 1.0)
|
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error->all(FLERR,"Illegal fix bond/react command: "
|
||
"probability fraction must between 0 and 1, inclusive");
|
||
if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"probability seed must be positive");
|
||
iarg += 3;
|
||
} else if (strcmp(arg[iarg],"max_rxn") == 0) {
|
||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'max_rxn' has too few arguments");
|
||
max_rxn[rxn] = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||
if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'max_rxn' cannot be negative");
|
||
iarg += 2;
|
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} else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
|
||
if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "
|
||
"used without stabilization keyword");
|
||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'stabilize_steps' has too few arguments");
|
||
limit_duration[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||
stabilize_steps_flag[rxn] = 1;
|
||
iarg += 2;
|
||
} else if (strcmp(arg[iarg],"custom_charges") == 0) {
|
||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'custom_charges' has too few arguments");
|
||
if (strcmp(arg[iarg+1],"no") == 0) custom_charges_fragid[rxn] = -1; //default
|
||
else {
|
||
custom_charges_fragid[rxn] = atom->molecules[unreacted_mol[rxn]]->findfragment(arg[iarg+1]);
|
||
if (custom_charges_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for "
|
||
"'custom_charges' keyword does not exist");
|
||
}
|
||
iarg += 2;
|
||
} else if (strcmp(arg[iarg],"molecule") == 0) {
|
||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'molecule' has too few arguments");
|
||
if (strcmp(arg[iarg+1],"off") == 0) molecule_keyword[rxn] = OFF; //default
|
||
else if (strcmp(arg[iarg+1],"inter") == 0) molecule_keyword[rxn] = INTER;
|
||
else if (strcmp(arg[iarg+1],"intra") == 0) molecule_keyword[rxn] = INTRA;
|
||
else error->one(FLERR,"Bond/react: Illegal option for 'molecule' keyword");
|
||
iarg += 2;
|
||
} else if (strcmp(arg[iarg],"modify_create") == 0) {
|
||
if (iarg++ > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'modify_create' has too few arguments");
|
||
while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) {
|
||
if (strcmp(arg[iarg],"fit") == 0) {
|
||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'modify_create' has too few arguments");
|
||
if (strcmp(arg[iarg+1],"all") == 0) modify_create_fragid[rxn] = -1; //default
|
||
else {
|
||
modify_create_fragid[rxn] = atom->molecules[reacted_mol[rxn]]->findfragment(arg[iarg+1]);
|
||
if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for "
|
||
"'modify_create' keyword does not exist");
|
||
}
|
||
iarg += 2;
|
||
} else if (strcmp(arg[iarg],"overlap") == 0) {
|
||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'modify_create' has too few arguments");
|
||
overlapsq[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||
overlapsq[rxn] *= overlapsq[rxn];
|
||
iarg += 2;
|
||
} else break;
|
||
}
|
||
} else error->all(FLERR,"Illegal fix bond/react command: unknown keyword");
|
||
}
|
||
}
|
||
|
||
max_natoms = 0; // the number of atoms in largest molecule template
|
||
for (int myrxn = 0; myrxn < nreacts; myrxn++) {
|
||
twomol = atom->molecules[reacted_mol[myrxn]];
|
||
max_natoms = MAX(max_natoms,twomol->natoms);
|
||
}
|
||
|
||
memory->create(equivalences,max_natoms,2,nreacts,"bond/react:equivalences");
|
||
memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv");
|
||
memory->create(edge,max_natoms,nreacts,"bond/react:edge");
|
||
memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
|
||
memory->create(custom_charges,max_natoms,nreacts,"bond/react:custom_charges");
|
||
memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
|
||
memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms");
|
||
memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
|
||
|
||
for (int j = 0; j < nreacts; j++)
|
||
for (int i = 0; i < max_natoms; i++) {
|
||
edge[i][j] = 0;
|
||
custom_charges[i][j] = 1; // update all partial charges by default
|
||
delete_atoms[i][j] = 0;
|
||
create_atoms[i][j] = 0;
|
||
for (int k = 0; k < 6; k++) {
|
||
chiral_atoms[i][k][j] = 0;
|
||
}
|
||
// default equivalences to their own mol index
|
||
// all but created atoms will be updated
|
||
for (int m = 0; m < 2; m++) {
|
||
equivalences[i][m][j] = i+1;
|
||
}
|
||
}
|
||
|
||
// read all map files afterward
|
||
for (int i = 0; i < nreacts; i++) {
|
||
open(files[i]);
|
||
onemol = atom->molecules[unreacted_mol[i]];
|
||
twomol = atom->molecules[reacted_mol[i]];
|
||
onemol->check_attributes(0);
|
||
twomol->check_attributes(0);
|
||
get_molxspecials();
|
||
read(i);
|
||
fclose(fp);
|
||
if (ncreate == 0 && onemol->natoms != twomol->natoms)
|
||
error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
|
||
else if (ncreate > 0 && onemol->natoms + ncreate != twomol->natoms)
|
||
error->all(FLERR,"Bond/react: Incorrect number of created atoms");
|
||
iatomtype[i] = onemol->type[ibonding[i]-1];
|
||
jatomtype[i] = onemol->type[jbonding[i]-1];
|
||
find_landlocked_atoms(i);
|
||
if (custom_charges_fragid[i] >= 0) CustomCharges(custom_charges_fragid[i],i);
|
||
}
|
||
|
||
// get the names of per-atom variables needed by 'rxn' functions of custom constraint
|
||
customvarnames();
|
||
|
||
// initialize Marsaglia RNG with processor-unique seed (Arrhenius prob)
|
||
|
||
rrhandom = new RanMars*[narrhenius];
|
||
int tmp = 0;
|
||
for (int i = 0; i < nreacts; i++) {
|
||
for (int j = 0; j < nconstraints[i]; j++) {
|
||
if (constraints[j][i].type == ARRHENIUS) {
|
||
rrhandom[tmp++] = new RanMars(lmp,(int) constraints[j][i].par[4] + me);
|
||
}
|
||
}
|
||
}
|
||
|
||
for (int i = 0; i < nreacts; i++) {
|
||
delete [] files[i];
|
||
}
|
||
delete [] files;
|
||
|
||
if (atom->molecular != Atom::MOLECULAR)
|
||
error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems");
|
||
|
||
// check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
|
||
// if so, we don't need non-bonded neighbor list
|
||
for (int myrxn = 0; myrxn < nreacts; myrxn++) {
|
||
closeneigh[myrxn] = -1; // indicates will search non-bonded neighbors
|
||
onemol = atom->molecules[unreacted_mol[myrxn]];
|
||
get_molxspecials();
|
||
for (int k = 0; k < onemol_nxspecial[ibonding[myrxn]-1][2]; k++) {
|
||
if (onemol_xspecial[ibonding[myrxn]-1][k] == jbonding[myrxn]) {
|
||
closeneigh[myrxn] = 2; // index for 1-4 neighbor
|
||
if (k < onemol_nxspecial[ibonding[myrxn]-1][1])
|
||
closeneigh[myrxn] = 1; // index for 1-3 neighbor
|
||
if (k < onemol_nxspecial[ibonding[myrxn]-1][0])
|
||
closeneigh[myrxn] = 0; // index for 1-2 neighbor
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
|
||
// initialize Marsaglia RNG with processor-unique seed ('prob' keyword)
|
||
|
||
random = new RanMars*[nreacts];
|
||
for (int i = 0; i < nreacts; i++) {
|
||
random[i] = new RanMars(lmp,seed[i] + me);
|
||
}
|
||
|
||
// set comm sizes needed by this fix
|
||
// forward is big due to comm of broken bonds and 1-2 neighbors
|
||
|
||
comm_forward = MAX(2,2+atom->maxspecial);
|
||
comm_reverse = 2;
|
||
|
||
// allocate arrays local to this fix
|
||
nmax = 0;
|
||
partner = finalpartner = nullptr;
|
||
distsq = nullptr;
|
||
maxattempt = 0;
|
||
attempt = nullptr;
|
||
nattempt = nullptr;
|
||
allnattempt = 0;
|
||
local_num_mega = 0;
|
||
ghostly_num_mega = 0;
|
||
restore = nullptr;
|
||
|
||
// zero out stats
|
||
global_megasize = 0;
|
||
avail_guesses = 0;
|
||
glove_counter = 0;
|
||
guess_branch = new int[MAXGUESS]();
|
||
pioneer_count = new int[max_natoms];
|
||
local_mega_glove = nullptr;
|
||
ghostly_mega_glove = nullptr;
|
||
global_mega_glove = nullptr;
|
||
|
||
// these are merely loop indices that became important
|
||
pion = neigh = trace = 0;
|
||
|
||
id_fix1 = nullptr;
|
||
id_fix2 = nullptr;
|
||
id_fix3 = nullptr;
|
||
statted_id = nullptr;
|
||
custom_exclude_flag = 0;
|
||
|
||
// used to store restart info
|
||
set = new Set[nreacts];
|
||
memset(set,0,nreacts*sizeof(Set));
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
FixBondReact::~FixBondReact()
|
||
{
|
||
for (int i = 0; i < narrhenius; i++) {
|
||
delete rrhandom[i];
|
||
}
|
||
delete [] rrhandom;
|
||
|
||
for (int i = 0; i < nreacts; i++) {
|
||
delete random[i];
|
||
}
|
||
delete [] random;
|
||
|
||
delete reset_mol_ids;
|
||
|
||
memory->destroy(partner);
|
||
memory->destroy(finalpartner);
|
||
memory->destroy(nattempt);
|
||
memory->destroy(distsq);
|
||
memory->destroy(attempt);
|
||
memory->destroy(edge);
|
||
memory->destroy(equivalences);
|
||
memory->destroy(reverse_equiv);
|
||
memory->destroy(landlocked_atoms);
|
||
memory->destroy(custom_charges);
|
||
memory->destroy(delete_atoms);
|
||
memory->destroy(create_atoms);
|
||
memory->destroy(chiral_atoms);
|
||
if (vvec != nullptr) memory->destroy(vvec);
|
||
|
||
memory->destroy(rxn_name);
|
||
memory->destroy(nevery);
|
||
memory->destroy(cutsq);
|
||
memory->destroy(unreacted_mol);
|
||
memory->destroy(reacted_mol);
|
||
memory->destroy(fraction);
|
||
memory->destroy(seed);
|
||
memory->destroy(max_rxn);
|
||
memory->destroy(nlocalskips);
|
||
memory->destroy(nghostlyskips);
|
||
memory->destroy(limit_duration);
|
||
memory->destroy(var_flag);
|
||
memory->destroy(var_id);
|
||
memory->destroy(stabilize_steps_flag);
|
||
memory->destroy(custom_charges_fragid);
|
||
memory->destroy(molecule_keyword);
|
||
memory->destroy(nconstraints);
|
||
memory->destroy(constraintstr);
|
||
memory->destroy(create_atoms_flag);
|
||
memory->destroy(modify_create_fragid);
|
||
memory->destroy(overlapsq);
|
||
|
||
memory->destroy(iatomtype);
|
||
memory->destroy(jatomtype);
|
||
memory->destroy(ibonding);
|
||
memory->destroy(jbonding);
|
||
memory->destroy(closeneigh);
|
||
memory->destroy(groupbits);
|
||
memory->destroy(reaction_count);
|
||
memory->destroy(local_rxn_count);
|
||
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);
|
||
memory->destroy(glove);
|
||
memory->destroy(pioneers);
|
||
memory->destroy(local_mega_glove);
|
||
memory->destroy(ghostly_mega_glove);
|
||
}
|
||
|
||
memory->destroy(global_mega_glove);
|
||
|
||
if (stabilization_flag == 1) {
|
||
// check nfix in case all fixes have already been deleted
|
||
if (id_fix1 && modify->nfix) modify->delete_fix(id_fix1);
|
||
delete [] id_fix1;
|
||
|
||
if (id_fix3 && modify->nfix) modify->delete_fix(id_fix3);
|
||
delete [] id_fix3;
|
||
}
|
||
|
||
if (id_fix2 && modify->nfix) modify->delete_fix(id_fix2);
|
||
delete [] id_fix2;
|
||
|
||
delete [] statted_id;
|
||
delete [] guess_branch;
|
||
delete [] pioneer_count;
|
||
delete [] set;
|
||
|
||
if (group) {
|
||
group->assign(std::string(master_group) + " delete");
|
||
if (stabilization_flag == 1) {
|
||
group->assign(std::string(exclude_group) + " delete");
|
||
delete [] exclude_group;
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::setmask()
|
||
{
|
||
int mask = 0;
|
||
mask |= POST_INTEGRATE;
|
||
mask |= POST_INTEGRATE_RESPA;
|
||
return mask;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
let's add an internal nve/limit fix for relaxation of reaction sites
|
||
also let's add our per-atom property fix here!
|
||
this per-atom property will state the timestep an atom was 'limited'
|
||
it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group)
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::post_constructor()
|
||
{
|
||
// let's add the limit_tags per-atom property fix
|
||
id_fix2 = utils::strdup("bond_react_props_internal");
|
||
if (modify->find_fix(id_fix2) < 0)
|
||
modify->add_fix(std::string(id_fix2)+" all property/atom i_limit_tags i_react_tags ghost yes");
|
||
|
||
// create master_group if not already existing
|
||
// NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)
|
||
group->find_or_create(master_group);
|
||
std::string cmd = fmt::format("{} dynamic all property limit_tags",master_group);
|
||
group->assign(cmd);
|
||
|
||
if (stabilization_flag == 1) {
|
||
int groupid = group->find(exclude_group);
|
||
// create exclude_group if not already existing, or use as parent group if static
|
||
if (groupid == -1 || group->dynamic[groupid] == 0) {
|
||
|
||
// create stabilization per-atom property
|
||
id_fix3 = utils::strdup("bond_react_stabilization_internal");
|
||
if (modify->find_fix(id_fix3) < 0)
|
||
fix3 = modify->add_fix(std::string(id_fix3) + " all property/atom i_statted_tags ghost yes");
|
||
|
||
statted_id = utils::strdup("statted_tags");
|
||
|
||
// if static group exists, use as parent group
|
||
// also, rename dynamic exclude_group by appending '_REACT'
|
||
char *exclude_PARENT_group;
|
||
exclude_PARENT_group = utils::strdup(exclude_group);
|
||
delete [] exclude_group;
|
||
exclude_group = utils::strdup(std::string(exclude_PARENT_group)+"_REACT");
|
||
|
||
group->find_or_create(exclude_group);
|
||
if (groupid == -1)
|
||
cmd = fmt::format("{} dynamic all property statted_tags",exclude_group);
|
||
else
|
||
cmd = fmt::format("{} dynamic {} property statted_tags",exclude_group,exclude_PARENT_group);
|
||
group->assign(cmd);
|
||
delete [] exclude_PARENT_group;
|
||
|
||
// on to statted_tags (system-wide thermostat)
|
||
// initialize per-atom statted_flags to 1
|
||
// (only if not already initialized by restart)
|
||
if (fix3->restart_reset != 1) {
|
||
int flag,cols;
|
||
int index = atom->find_custom("statted_tags",flag,cols);
|
||
int *i_statted_tags = atom->ivector[index];
|
||
|
||
for (int i = 0; i < atom->nlocal; i++)
|
||
i_statted_tags[i] = 1;
|
||
}
|
||
} else {
|
||
// sleeping code, for future capabilities
|
||
custom_exclude_flag = 1;
|
||
// first we have to find correct fix group reference
|
||
int ifix = modify->find_fix(std::string("GROUP_")+exclude_group);
|
||
Fix *fix = modify->fix[ifix];
|
||
|
||
// this returns names of corresponding property
|
||
int unused;
|
||
char *idprop;
|
||
idprop = (char *) fix->extract("property",unused);
|
||
if (idprop == nullptr)
|
||
error->all(FLERR,"Exclude group must be a per-atom property group");
|
||
statted_id = utils::strdup(idprop);
|
||
|
||
// initialize per-atom statted_tags to 1
|
||
// need to correct for smooth restarts
|
||
//int flag,cols;
|
||
//int index = atom->find_custom(statted_id,flag,cols);
|
||
//int *i_statted_tags = atom->ivector[index];
|
||
//for (int i = 0; i < atom->nlocal; i++)
|
||
// i_statted_tags[i] = 1;
|
||
}
|
||
|
||
|
||
// let's create a new nve/limit fix to limit newly reacted atoms
|
||
id_fix1 = utils::strdup("bond_react_MASTER_nve_limit");
|
||
if (modify->find_fix(id_fix1) < 0)
|
||
fix1 = modify->add_fix(fmt::format("{} {} nve/limit {}",
|
||
id_fix1,master_group,nve_limit_xmax));
|
||
}
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::init()
|
||
{
|
||
|
||
if (utils::strmatch(update->integrate_style,"^respa"))
|
||
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]])
|
||
error->all(FLERR,"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);
|
||
|
||
lastcheck = -1;
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::init_list(int /*id*/, NeighList *ptr)
|
||
{
|
||
list = ptr;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Identify all pairs of potentially reactive atoms for this time step.
|
||
This function is modified from LAMMPS’ fix bond/create.
|
||
---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::post_integrate()
|
||
{
|
||
// check if any reactions could occur on this timestep
|
||
int nevery_check = 1;
|
||
for (int i = 0; i < nreacts; i++) {
|
||
if (var_flag[NEVERY][i])
|
||
nevery[i] = ceil(input->variable->compute_equal(var_id[NEVERY][i]));
|
||
if (nevery[i] <= 0)
|
||
error->all(FLERR,"Illegal fix bond/react command: "
|
||
"'Nevery' must be a positive integer");
|
||
if (!(update->ntimestep % nevery[i])) {
|
||
nevery_check = 0;
|
||
break;
|
||
}
|
||
}
|
||
|
||
for (int i = 0; i < nreacts; i++) {
|
||
reaction_count[i] = 0;
|
||
local_rxn_count[i] = 0;
|
||
ghostly_rxn_count[i] = 0;
|
||
nlocalskips[i] = 0;
|
||
nghostlyskips[i] = 0;
|
||
// update reaction probability
|
||
if (var_flag[PROB][i])
|
||
fraction[i] = input->variable->compute_equal(var_id[PROB][i]);
|
||
}
|
||
|
||
if (nevery_check) {
|
||
unlimit_bond();
|
||
return;
|
||
}
|
||
|
||
// acquire updated ghost atom positions
|
||
// necessary b/c are calling this after integrate, but before Verlet comm
|
||
|
||
comm->forward_comm();
|
||
|
||
// resize bond partner list and initialize it
|
||
// needs to be atom->nmax in length
|
||
|
||
if (atom->nmax > nmax) {
|
||
memory->destroy(partner);
|
||
memory->destroy(finalpartner);
|
||
memory->destroy(distsq);
|
||
memory->destroy(nattempt);
|
||
nmax = atom->nmax;
|
||
memory->create(partner,nmax,"bond/react:partner");
|
||
memory->create(finalpartner,nmax,"bond/react:finalpartner");
|
||
memory->create(distsq,nmax,2,"bond/react:distsq");
|
||
memory->create(nattempt,nreacts,"bond/react:nattempt");
|
||
}
|
||
|
||
// reset 'attempt' counts
|
||
for (int i = 0; i < nreacts; i++) {
|
||
nattempt[i] = 0;
|
||
}
|
||
|
||
int nlocal = atom->nlocal;
|
||
int nall = atom->nlocal + atom->nghost;
|
||
|
||
// loop over neighbors of my atoms
|
||
// each atom sets one closest eligible partner atom ID to bond with
|
||
|
||
tagint *tag = atom->tag;
|
||
int *type = atom->type;
|
||
|
||
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];
|
||
}
|
||
}
|
||
}
|
||
|
||
int j;
|
||
for (rxnID = 0; rxnID < nreacts; rxnID++) {
|
||
if ((update->ntimestep % nevery[rxnID]) ||
|
||
(max_rxn[rxnID] <= reaction_count_total[rxnID])) continue;
|
||
for (int ii = 0; ii < nall; ii++) {
|
||
partner[ii] = 0;
|
||
finalpartner[ii] = 0;
|
||
distsq[ii][0] = 0.0;
|
||
distsq[ii][1] = BIG;
|
||
}
|
||
|
||
// fork between far and close_partner here
|
||
if (closeneigh[rxnID] < 0) {
|
||
far_partner();
|
||
// reverse comm of distsq and partner
|
||
// not needed if newton_pair off since I,J pair was seen by both procs
|
||
commflag = 2;
|
||
if (force->newton_pair) comm->reverse_comm(this);
|
||
} else {
|
||
close_partner();
|
||
commflag = 2;
|
||
comm->reverse_comm(this);
|
||
}
|
||
|
||
// each atom now knows its winning partner
|
||
// forward comm of partner, so ghosts have it
|
||
|
||
commflag = 2;
|
||
comm->forward_comm(this,1);
|
||
|
||
// consider for reaction:
|
||
// only if both atoms list each other as winning bond partner
|
||
// if other atom is owned by another proc, it should do same thing
|
||
|
||
int temp_nattempt = 0;
|
||
for (int i = 0; i < nlocal; i++) {
|
||
if (partner[i] == 0) {
|
||
continue;
|
||
}
|
||
|
||
j = atom->map(partner[i]);
|
||
if (partner[j] != tag[i]) {
|
||
continue;
|
||
}
|
||
|
||
// store final bond partners and count the rxn possibility once
|
||
|
||
finalpartner[i] = tag[j];
|
||
finalpartner[j] = tag[i];
|
||
|
||
if (tag[i] < tag[j]) temp_nattempt++;
|
||
}
|
||
|
||
// cycle loop if no even eligible bonding atoms were found (on any proc)
|
||
int some_chance;
|
||
MPI_Allreduce(&temp_nattempt,&some_chance,1,MPI_INT,MPI_SUM,world);
|
||
if (!some_chance) continue;
|
||
|
||
// communicate final partner
|
||
|
||
commflag = 3;
|
||
comm->forward_comm(this);
|
||
|
||
// add instance to 'attempt' only if this processor
|
||
// owns the atoms with smaller global ID
|
||
// NOTE: we no longer care about ghost-ghost instances as bond/create did
|
||
// this is because we take care of updating topology later (and differently)
|
||
for (int i = 0; i < nlocal; i++) {
|
||
|
||
if (finalpartner[i] == 0) continue;
|
||
|
||
j = atom->map(finalpartner[i]);
|
||
if (tag[i] < tag[j]) {
|
||
if (nattempt[rxnID] > maxattempt-2) {
|
||
maxattempt += DELTA;
|
||
// third dim of 'attempt': bond/react integer ID
|
||
memory->grow(attempt,maxattempt,2,nreacts,"bond/react:attempt");
|
||
}
|
||
// to ensure types remain in same order
|
||
if (iatomtype[rxnID] == type[i]) {
|
||
attempt[nattempt[rxnID]][0][rxnID] = tag[i];
|
||
attempt[nattempt[rxnID]][1][rxnID] = finalpartner[i];
|
||
nattempt[rxnID]++;
|
||
// add another attempt if initiator atoms are same type
|
||
if (iatomtype[rxnID] == jatomtype[rxnID]) {
|
||
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
|
||
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
|
||
nattempt[rxnID]++;
|
||
}
|
||
} else {
|
||
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
|
||
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
|
||
nattempt[rxnID]++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// break loop if no even eligible bonding atoms were found (on any proc)
|
||
int some_chance;
|
||
|
||
allnattempt = 0;
|
||
for (int i = 0; i < nreacts; i++)
|
||
allnattempt += nattempt[i];
|
||
|
||
MPI_Allreduce(&allnattempt,&some_chance,1,MPI_INT,MPI_SUM,world);
|
||
if (!some_chance) {
|
||
unlimit_bond();
|
||
return;
|
||
}
|
||
|
||
// evaluate custom constraint variable values here and forward_comm
|
||
get_customvars();
|
||
commflag = 1;
|
||
comm->forward_comm(this,ncustomvars);
|
||
|
||
// run through the superimpose algorithm
|
||
// this checks if simulation topology matches unreacted mol template
|
||
superimpose_algorithm();
|
||
// free atoms that have been limited after reacting
|
||
unlimit_bond();
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Search non-bonded neighbor lists if bonding atoms are not in special list
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::far_partner()
|
||
{
|
||
int inum,jnum,itype,jtype,possible;
|
||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||
|
||
// loop over neighbors of my atoms
|
||
// each atom sets one closest eligible partner atom ID to bond with
|
||
|
||
double **x = atom->x;
|
||
tagint *tag = atom->tag;
|
||
int *mask = atom->mask;
|
||
int *type = atom->type;
|
||
|
||
inum = list->inum;
|
||
ilist = list->ilist;
|
||
numneigh = list->numneigh;
|
||
firstneigh = list->firstneigh;
|
||
|
||
// per-atom property indicating if in bond/react master group
|
||
int flag,cols;
|
||
int index1 = atom->find_custom("limit_tags",flag,cols);
|
||
int *i_limit_tags = atom->ivector[index1];
|
||
|
||
int i,j;
|
||
|
||
for (int ii = 0; ii < inum; ii++) {
|
||
i = ilist[ii];
|
||
if (!(mask[i] & groupbits[rxnID])) continue;
|
||
if (i_limit_tags[i] != 0) continue;
|
||
itype = type[i];
|
||
xtmp = x[i][0];
|
||
ytmp = x[i][1];
|
||
ztmp = x[i][2];
|
||
jlist = firstneigh[i];
|
||
jnum = numneigh[i];
|
||
|
||
for (int jj = 0; jj < jnum; jj++) {
|
||
j = jlist[jj];
|
||
j &= NEIGHMASK;
|
||
if (!(mask[j] & groupbits[rxnID])) {
|
||
continue;
|
||
}
|
||
|
||
if (i_limit_tags[j] != 0) {
|
||
continue;
|
||
}
|
||
|
||
if (molecule_keyword[rxnID] == INTER) {
|
||
if (atom->molecule[i] == atom->molecule[j]) continue;
|
||
} else if (molecule_keyword[rxnID] == INTRA) {
|
||
if (atom->molecule[i] != atom->molecule[j]) continue;
|
||
}
|
||
|
||
jtype = type[j];
|
||
possible = 0;
|
||
if (itype == iatomtype[rxnID] && jtype == jatomtype[rxnID]) {
|
||
possible = 1;
|
||
} else if (itype == jatomtype[rxnID] && jtype == iatomtype[rxnID]) {
|
||
possible = 1;
|
||
}
|
||
|
||
if (possible == 0) continue;
|
||
|
||
// do not allow bonding atoms within special list
|
||
for (int k = 0; k < nxspecial[i][2]; k++)
|
||
if (xspecial[i][k] == tag[j]) possible = 0;
|
||
if (!possible) continue;
|
||
|
||
delx = xtmp - x[j][0];
|
||
dely = ytmp - x[j][1];
|
||
delz = ztmp - x[j][2];
|
||
domain->minimum_image(delx,dely,delz); // ghost location fix
|
||
rsq = delx*delx + dely*dely + delz*delz;
|
||
|
||
if (var_flag[RMIN][rxnID]) {
|
||
double cutoff = input->variable->compute_equal(var_id[RMIN][rxnID]);
|
||
cutsq[rxnID][0] = cutoff*cutoff;
|
||
}
|
||
if (var_flag[RMAX][rxnID]) {
|
||
double cutoff = input->variable->compute_equal(var_id[RMAX][rxnID]);
|
||
cutsq[rxnID][1] = cutoff*cutoff;
|
||
}
|
||
if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) {
|
||
continue;
|
||
}
|
||
if (rsq < distsq[i][1]) {
|
||
partner[i] = tag[j];
|
||
distsq[i][1] = rsq;
|
||
}
|
||
if (rsq < distsq[j][1]) {
|
||
partner[j] = tag[i];
|
||
distsq[j][1] = rsq;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Slightly simpler to find bonding partner when a close neighbor
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::close_partner()
|
||
{
|
||
int n,i1,i2,itype,jtype;
|
||
double delx,dely,delz,rsq;
|
||
|
||
double **x = atom->x;
|
||
tagint *tag = atom->tag;
|
||
int *type = atom->type;
|
||
int *mask = atom->mask;
|
||
|
||
// per-atom property indicating if in bond/react master group
|
||
int flag,cols;
|
||
int index1 = atom->find_custom("limit_tags",flag,cols);
|
||
int *i_limit_tags = atom->ivector[index1];
|
||
|
||
// loop over special list
|
||
for (int ii = 0; ii < atom->nlocal; ii++) {
|
||
itype = type[ii];
|
||
n = 0;
|
||
if (closeneigh[rxnID] != 0)
|
||
n = nxspecial[ii][closeneigh[rxnID]-1];
|
||
for (; n < nxspecial[ii][closeneigh[rxnID]]; n++) {
|
||
i1 = ii;
|
||
i2 = atom->map(xspecial[ii][n]);
|
||
jtype = type[i2];
|
||
if (!(mask[i1] & groupbits[rxnID])) continue;
|
||
if (!(mask[i2] & groupbits[rxnID])) continue;
|
||
if (i_limit_tags[i1] != 0) continue;
|
||
if (i_limit_tags[i2] != 0) continue;
|
||
if (itype != iatomtype[rxnID] || jtype != jatomtype[rxnID]) continue;
|
||
|
||
if (molecule_keyword[rxnID] == INTER) {
|
||
if (atom->molecule[i1] == atom->molecule[i2]) continue;
|
||
} else if (molecule_keyword[rxnID] == INTRA) {
|
||
if (atom->molecule[i1] != atom->molecule[i2]) continue;
|
||
}
|
||
|
||
delx = x[i1][0] - x[i2][0];
|
||
dely = x[i1][1] - x[i2][1];
|
||
delz = x[i1][2] - x[i2][2];
|
||
domain->minimum_image(delx,dely,delz); // ghost location fix
|
||
rsq = delx*delx + dely*dely + delz*delz;
|
||
|
||
if (var_flag[RMIN][rxnID]) {
|
||
double cutoff = input->variable->compute_equal(var_id[RMIN][rxnID]);
|
||
cutsq[rxnID][0] = cutoff*cutoff;
|
||
}
|
||
if (var_flag[RMAX][rxnID]) {
|
||
double cutoff = input->variable->compute_equal(var_id[RMAX][rxnID]);
|
||
cutsq[rxnID][1] = cutoff*cutoff;
|
||
}
|
||
if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue;
|
||
|
||
if (closeneigh[rxnID] == 0) {
|
||
if (rsq > distsq[i1][0]) {
|
||
partner[i1] = tag[i2];
|
||
distsq[i1][0] = rsq;
|
||
}
|
||
if (rsq > distsq[i2][0]) {
|
||
partner[i2] = tag[i1];
|
||
distsq[i2][0] = rsq;
|
||
}
|
||
} else {
|
||
if (rsq < distsq[i1][1]) {
|
||
partner[i1] = tag[i2];
|
||
distsq[i1][1] = rsq;
|
||
}
|
||
if (rsq < distsq[i2][1]) {
|
||
partner[i2] = tag[i1];
|
||
distsq[i2][1] = rsq;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Set up global variables. Loop through all pairs; loop through Pioneers
|
||
until Superimpose Algorithm is completed for each pair.
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::superimpose_algorithm()
|
||
{
|
||
local_num_mega = 0;
|
||
ghostly_num_mega = 0;
|
||
|
||
// indicates local ghosts of other procs
|
||
int tmp;
|
||
localsendlist = (int *) comm->extract("localsendlist",tmp);
|
||
|
||
// quick description of important global indices you'll see floating about:
|
||
// 'pion' is the pioneer loop index
|
||
// 'neigh' in the first neighbor index
|
||
// 'trace' retraces the first nieghbors
|
||
// trace: once you choose a first neighbor, you then check for other nieghbors of same type
|
||
|
||
if (attempted_rxn == 1) {
|
||
memory->destroy(restore_pt);
|
||
memory->destroy(restore);
|
||
memory->destroy(glove);
|
||
memory->destroy(pioneers);
|
||
memory->destroy(local_mega_glove);
|
||
memory->destroy(ghostly_mega_glove);
|
||
}
|
||
|
||
memory->create(glove,max_natoms,2,"bond/react:glove");
|
||
memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt");
|
||
memory->create(pioneers,max_natoms,"bond/react:pioneers");
|
||
memory->create(restore,max_natoms,MAXGUESS*4,"bond/react:restore");
|
||
memory->create(local_mega_glove,max_natoms+1,allnattempt,"bond/react:local_mega_glove");
|
||
memory->create(ghostly_mega_glove,max_natoms+1,allnattempt,"bond/react:ghostly_mega_glove");
|
||
|
||
attempted_rxn = 1;
|
||
|
||
for (int i = 0; i < max_natoms+1; i++) {
|
||
for (int j = 0; j < allnattempt; j++) {
|
||
local_mega_glove[i][j] = 0;
|
||
ghostly_mega_glove[i][j] = 0;
|
||
}
|
||
}
|
||
|
||
// let's finally begin the superimpose loop
|
||
for (rxnID = 0; rxnID < nreacts; rxnID++) {
|
||
for (lcl_inst = 0; lcl_inst < nattempt[rxnID]; lcl_inst++) {
|
||
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
get_molxspecials();
|
||
|
||
status = PROCEED;
|
||
|
||
glove_counter = 0;
|
||
for (int i = 0; i < max_natoms; i++) {
|
||
for (int j = 0; j < 2; j++) {
|
||
glove[i][j] = 0;
|
||
}
|
||
}
|
||
|
||
for (int i = 0; i < MAXGUESS; i++) {
|
||
guess_branch[i] = 0;
|
||
}
|
||
|
||
int myibonding = ibonding[rxnID];
|
||
int myjbonding = jbonding[rxnID];
|
||
|
||
glove[myibonding-1][0] = myibonding;
|
||
glove[myibonding-1][1] = attempt[lcl_inst][0][rxnID];
|
||
glove_counter++;
|
||
glove[myjbonding-1][0] = myjbonding;
|
||
glove[myjbonding-1][1] = attempt[lcl_inst][1][rxnID];
|
||
glove_counter++;
|
||
|
||
// special case, only two atoms in reaction templates
|
||
// then: bonding onemol_nxspecials guaranteed to be equal, and either 0 or 1
|
||
if (glove_counter == onemol->natoms) {
|
||
tagint local_atom1 = atom->map(glove[myibonding-1][1]);
|
||
tagint local_atom2 = atom->map(glove[myjbonding-1][1]);
|
||
if ( (nxspecial[local_atom1][0] == onemol_nxspecial[myibonding-1][0] &&
|
||
nxspecial[local_atom2][0] == nxspecial[local_atom1][0]) &&
|
||
(nxspecial[local_atom1][0] == 0 ||
|
||
xspecial[local_atom1][0] == atom->tag[local_atom2]) &&
|
||
check_constraints()) {
|
||
if (fraction[rxnID] < 1.0 &&
|
||
random[rxnID]->uniform() >= fraction[rxnID]) {
|
||
status = REJECT;
|
||
} else {
|
||
status = ACCEPT;
|
||
glove_ghostcheck();
|
||
}
|
||
} else status = REJECT;
|
||
}
|
||
|
||
avail_guesses = 0;
|
||
|
||
for (int i = 0; i < max_natoms; i++)
|
||
pioneer_count[i] = 0;
|
||
|
||
for (int i = 0; i < onemol_nxspecial[myibonding-1][0]; i++)
|
||
pioneer_count[onemol_xspecial[myibonding-1][i]-1]++;
|
||
|
||
for (int i = 0; i < onemol_nxspecial[myjbonding-1][0]; i++)
|
||
pioneer_count[onemol_xspecial[myjbonding-1][i]-1]++;
|
||
|
||
|
||
int hang_catch = 0;
|
||
while (!(status == ACCEPT || status == REJECT)) {
|
||
|
||
for (int i = 0; i < max_natoms; i++) {
|
||
pioneers[i] = 0;
|
||
}
|
||
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
if (glove[i][0] !=0 && pioneer_count[i] < onemol_nxspecial[i][0] && edge[i][rxnID] == 0) {
|
||
pioneers[i] = 1;
|
||
}
|
||
}
|
||
|
||
// run through the pioneers
|
||
// due to use of restore points, 'pion' index can change in loop
|
||
for (pion = 0; pion < onemol->natoms; pion++) {
|
||
if (pioneers[pion] || status == GUESSFAIL) {
|
||
make_a_guess();
|
||
if (status == ACCEPT || status == REJECT) break;
|
||
}
|
||
}
|
||
|
||
// reaction site found successfully!
|
||
if (status == ACCEPT) {
|
||
if (fraction[rxnID] < 1.0 &&
|
||
random[rxnID]->uniform() >= fraction[rxnID]) status = REJECT;
|
||
else glove_ghostcheck();
|
||
}
|
||
hang_catch++;
|
||
// let's go ahead and catch the simplest of hangs
|
||
//if (hang_catch > onemol->natoms*4)
|
||
if (hang_catch > atom->nlocal*30) {
|
||
error->one(FLERR,"Bond/react: Excessive iteration of superimpose algorithm. "
|
||
"Please check that all pre-reaction template atoms are linked to an initiator atom, "
|
||
"via at least one path that does not involve edge atoms.");
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
global_megasize = 0;
|
||
|
||
ghost_glovecast(); // consolidate all mega_gloves to all processors
|
||
dedup_mega_gloves(LOCAL); // make sure atoms aren't added to more than one reaction
|
||
|
||
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
|
||
|
||
int rxnflag = 0;
|
||
if (me == 0)
|
||
for (int i = 0; i < nreacts; i++) {
|
||
reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i];
|
||
rxnflag += reaction_count[i] + ghostly_rxn_count[i];
|
||
}
|
||
|
||
MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
|
||
MPI_Bcast(&rxnflag, 1, MPI_INT, 0, world);
|
||
|
||
if (!rxnflag) return;
|
||
|
||
// C++11 and later compatible version of Park pRNG
|
||
std::random_device rnd;
|
||
std::minstd_rand park_rng(rnd());
|
||
|
||
// check if we overstepped our reaction limit
|
||
for (int i = 0; i < nreacts; i++) {
|
||
if (reaction_count_total[i] > max_rxn[i]) {
|
||
// let's randomly choose rxns to skip, unbiasedly from local and ghostly
|
||
int *local_rxncounts;
|
||
int *all_localskips;
|
||
memory->create(local_rxncounts,nprocs,"bond/react:local_rxncounts");
|
||
memory->create(all_localskips,nprocs,"bond/react:all_localskips");
|
||
MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
|
||
if (me == 0) {
|
||
int overstep = reaction_count_total[i] - max_rxn[i];
|
||
int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
|
||
int *rxn_by_proc;
|
||
memory->create(rxn_by_proc,delta_rxn,"bond/react:rxn_by_proc");
|
||
for (int j = 0; j < delta_rxn; j++)
|
||
rxn_by_proc[j] = -1; // corresponds to ghostly
|
||
int itemp = 0;
|
||
for (int j = 0; j < nprocs; j++)
|
||
for (int k = 0; k < local_rxncounts[j]; k++)
|
||
rxn_by_proc[itemp++] = j;
|
||
std::shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn], park_rng);
|
||
for (int j = 0; j < nprocs; j++)
|
||
all_localskips[j] = 0;
|
||
nghostlyskips[i] = 0;
|
||
for (int j = 0; j < overstep; j++) {
|
||
if (rxn_by_proc[j] == -1) nghostlyskips[i]++;
|
||
else all_localskips[rxn_by_proc[j]]++;
|
||
}
|
||
memory->destroy(rxn_by_proc);
|
||
}
|
||
reaction_count_total[i] = max_rxn[i];
|
||
MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world);
|
||
MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world);
|
||
memory->destroy(local_rxncounts);
|
||
memory->destroy(all_localskips);
|
||
}
|
||
}
|
||
|
||
// this updates topology next step
|
||
next_reneighbor = update->ntimestep;
|
||
|
||
// call limit_bond in 'global_mega_glove mode.' oh, and local mode
|
||
limit_bond(LOCAL); // add reacting atoms to nve/limit
|
||
limit_bond(GLOBAL);
|
||
update_everything(); // change topology
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Screen for obvious algorithm fails. This is the return point when a guess
|
||
has failed: check for available restore points.
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::make_a_guess()
|
||
{
|
||
int *type = atom->type;
|
||
int nfirst_neighs = onemol_nxspecial[pion][0];
|
||
|
||
// per-atom property indicating if in bond/react master group
|
||
int flag,cols;
|
||
int index1 = atom->find_custom("limit_tags",flag,cols);
|
||
int *i_limit_tags = atom->ivector[index1];
|
||
|
||
if (status == GUESSFAIL && avail_guesses == 0) {
|
||
status = REJECT;
|
||
return;
|
||
}
|
||
|
||
if (status == GUESSFAIL && avail_guesses > 0) {
|
||
// load restore point
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
glove[i][0] = restore[i][(avail_guesses*4)-4];
|
||
glove[i][1] = restore[i][(avail_guesses*4)-3];
|
||
pioneer_count[i] = restore[i][(avail_guesses*4)-2];
|
||
pioneers[i] = restore[i][(avail_guesses*4)-1];
|
||
}
|
||
pion = restore_pt[avail_guesses-1][0];
|
||
neigh = restore_pt[avail_guesses-1][1];
|
||
trace = restore_pt[avail_guesses-1][2];
|
||
glove_counter = restore_pt[avail_guesses-1][3];
|
||
status = RESTORE;
|
||
neighbor_loop();
|
||
if (status != PROCEED) return;
|
||
}
|
||
|
||
nfirst_neighs = onemol_nxspecial[pion][0];
|
||
|
||
// check if any of first neighbors are in bond_react_MASTER_group
|
||
// if so, this constitutes a fail
|
||
// because still undergoing a previous reaction!
|
||
// could technically fail unnecessarily during a wrong guess if near edge atoms
|
||
// we accept this temporary and infrequent decrease in reaction occurrences
|
||
|
||
for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) {
|
||
if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) {
|
||
error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues.
|
||
}
|
||
if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) {
|
||
status = GUESSFAIL;
|
||
return;
|
||
}
|
||
}
|
||
|
||
// check for same number of neighbors between unreacted mol and simulation
|
||
if (nfirst_neighs != nxspecial[atom->map(glove[pion][1])][0]) {
|
||
status = GUESSFAIL;
|
||
return;
|
||
}
|
||
|
||
// make sure all neighbors aren't already assigned
|
||
// an issue discovered for coarse-grained example
|
||
int assigned_count = 0;
|
||
for (int i = 0; i < nfirst_neighs; i++)
|
||
for (int j = 0; j < onemol->natoms; j++)
|
||
if (xspecial[atom->map(glove[pion][1])][i] == glove[j][1]) {
|
||
assigned_count++;
|
||
break;
|
||
}
|
||
|
||
if (assigned_count == nfirst_neighs) status = GUESSFAIL;
|
||
|
||
// check if all neigh atom types are the same between simulation and unreacted mol
|
||
int *mol_ntypes = new int[atom->ntypes];
|
||
int *lcl_ntypes = new int[atom->ntypes];
|
||
|
||
for (int i = 0; i < atom->ntypes; i++) {
|
||
mol_ntypes[i] = 0;
|
||
lcl_ntypes[i] = 0;
|
||
}
|
||
|
||
for (int i = 0; i < nfirst_neighs; i++) {
|
||
mol_ntypes[(int)onemol->type[(int)onemol_xspecial[pion][i]-1]-1]++;
|
||
lcl_ntypes[(int)type[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])]-1]++; //added -1
|
||
}
|
||
|
||
for (int i = 0; i < atom->ntypes; i++) {
|
||
if (mol_ntypes[i] != lcl_ntypes[i]) {
|
||
status = GUESSFAIL;
|
||
delete [] mol_ntypes;
|
||
delete [] lcl_ntypes;
|
||
return;
|
||
}
|
||
}
|
||
|
||
delete [] mol_ntypes;
|
||
delete [] lcl_ntypes;
|
||
|
||
// okay everything seems to be in order. let's assign some ID pairs!!!
|
||
neighbor_loop();
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Loop through all First Bonded Neighbors of the current Pioneer.
|
||
Prepare appropriately if we are in Restore Mode.
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::neighbor_loop()
|
||
{
|
||
int nfirst_neighs = onemol_nxspecial[pion][0];
|
||
|
||
if (status == RESTORE) {
|
||
check_a_neighbor();
|
||
return;
|
||
}
|
||
|
||
for (neigh = 0; neigh < nfirst_neighs; neigh++) {
|
||
if (glove[(int)onemol_xspecial[pion][neigh]-1][0] == 0) {
|
||
check_a_neighbor();
|
||
}
|
||
}
|
||
// status should still = PROCEED
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Check if we can assign this First Neighbor to pre-reacted template
|
||
without guessing. If so, do it! If not, call crosscheck_the_nieghbor().
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::check_a_neighbor()
|
||
{
|
||
int *type = atom->type;
|
||
int nfirst_neighs = onemol_nxspecial[pion][0];
|
||
|
||
if (status != RESTORE) {
|
||
// special consideration for hydrogen atoms (and all first neighbors bonded to no other atoms) (and aren't edge atoms)
|
||
if (onemol_nxspecial[(int)onemol_xspecial[pion][neigh]-1][0] == 1 && edge[(int)onemol_xspecial[pion][neigh]-1][rxnID] == 0) {
|
||
|
||
for (int i = 0; i < nfirst_neighs; i++) {
|
||
|
||
if (type[(int)atom->map(xspecial[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1] &&
|
||
nxspecial[(int)atom->map(xspecial[(int)atom->map(glove[pion][1])][i])][0] == 1) {
|
||
|
||
int already_assigned = 0;
|
||
for (int j = 0; j < onemol->natoms; j++) {
|
||
if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) {
|
||
already_assigned = 1;
|
||
break;
|
||
}
|
||
}
|
||
|
||
if (already_assigned == 0) {
|
||
glove[(int)onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh];
|
||
glove[(int)onemol_xspecial[pion][neigh]-1][1] = xspecial[(int)atom->map(glove[pion][1])][i];
|
||
|
||
//another check for ghost atoms. perhaps remove the one in make_a_guess
|
||
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
|
||
error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away");
|
||
}
|
||
|
||
for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) {
|
||
pioneer_count[onemol_xspecial[onemol_xspecial[pion][neigh]-1][j]-1]++;
|
||
}
|
||
|
||
glove_counter++;
|
||
if (glove_counter == onemol->natoms) {
|
||
if (ring_check() && check_constraints()) status = ACCEPT;
|
||
else status = GUESSFAIL;
|
||
return;
|
||
}
|
||
// status should still == PROCEED
|
||
return;
|
||
}
|
||
}
|
||
}
|
||
// we are here if no matching atom found
|
||
status = GUESSFAIL;
|
||
return;
|
||
}
|
||
}
|
||
|
||
crosscheck_the_neighbor();
|
||
if (status != PROCEED) {
|
||
if (status == CONTINUE)
|
||
status = PROCEED;
|
||
return;
|
||
}
|
||
|
||
// finally ready to match non-duplicate, non-edge atom IDs!!
|
||
|
||
for (int i = 0; i < nfirst_neighs; i++) {
|
||
|
||
if (type[atom->map((int)xspecial[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1]) {
|
||
int already_assigned = 0;
|
||
|
||
//check if a first neighbor of the pioneer is already assigned to pre-reacted template
|
||
for (int j = 0; j < onemol->natoms; j++) {
|
||
if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) {
|
||
already_assigned = 1;
|
||
break;
|
||
}
|
||
}
|
||
|
||
if (already_assigned == 0) {
|
||
glove[(int)onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh];
|
||
glove[(int)onemol_xspecial[pion][neigh]-1][1] = xspecial[(int)atom->map(glove[pion][1])][i];
|
||
|
||
//another check for ghost atoms. perhaps remove the one in make_a_guess
|
||
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
|
||
error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away");
|
||
}
|
||
|
||
for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) {
|
||
pioneer_count[onemol_xspecial[onemol_xspecial[pion][neigh]-1][ii]-1]++;
|
||
}
|
||
|
||
glove_counter++;
|
||
if (glove_counter == onemol->natoms) {
|
||
if (ring_check() && check_constraints()) status = ACCEPT;
|
||
else status = GUESSFAIL;
|
||
return;
|
||
// will never complete here when there are edge atoms
|
||
// ...actually that could be wrong if people get creative...shouldn't affect anything
|
||
}
|
||
// status should still = PROCEED
|
||
return;
|
||
}
|
||
}
|
||
}
|
||
// status is still 'PROCEED' if we are here!
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Check if there a viable guess to be made. If so, prepare to make a
|
||
guess by recording a restore point.
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::crosscheck_the_neighbor()
|
||
{
|
||
int nfirst_neighs = onemol_nxspecial[pion][0];
|
||
|
||
if (status == RESTORE) {
|
||
inner_crosscheck_loop();
|
||
return;
|
||
}
|
||
|
||
for (trace = 0; trace < nfirst_neighs; trace++) {
|
||
if (neigh!=trace && onemol->type[(int)onemol_xspecial[pion][neigh]-1] == onemol->type[(int)onemol_xspecial[pion][trace]-1] &&
|
||
glove[onemol_xspecial[pion][trace]-1][0] == 0) {
|
||
|
||
if (avail_guesses == MAXGUESS) {
|
||
error->warning(FLERR,"Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info");
|
||
status = GUESSFAIL;
|
||
return;
|
||
}
|
||
avail_guesses++;
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
restore[i][(avail_guesses*4)-4] = glove[i][0];
|
||
restore[i][(avail_guesses*4)-3] = glove[i][1];
|
||
restore[i][(avail_guesses*4)-2] = pioneer_count[i];
|
||
restore[i][(avail_guesses*4)-1] = pioneers[i];
|
||
restore_pt[avail_guesses-1][0] = pion;
|
||
restore_pt[avail_guesses-1][1] = neigh;
|
||
restore_pt[avail_guesses-1][2] = trace;
|
||
restore_pt[avail_guesses-1][3] = glove_counter;
|
||
}
|
||
|
||
inner_crosscheck_loop();
|
||
return;
|
||
}
|
||
}
|
||
// status is still 'PROCEED' if we are here!
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
We are ready to make a guess. If there are multiple possible choices
|
||
for this guess, keep track of these.
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::inner_crosscheck_loop()
|
||
{
|
||
int *type = atom->type;
|
||
// arbitrarily limited to 5 identical first neighbors
|
||
tagint tag_choices[5];
|
||
int nfirst_neighs = onemol_nxspecial[pion][0];
|
||
|
||
int num_choices = 0;
|
||
for (int i = 0; i < nfirst_neighs; i++) {
|
||
|
||
int already_assigned = 0;
|
||
for (int j = 0; j < onemol->natoms; j++) {
|
||
if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) {
|
||
already_assigned = 1;
|
||
break;
|
||
}
|
||
}
|
||
|
||
if (already_assigned == 0 &&
|
||
type[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1]) {
|
||
if (num_choices > 5) { // here failed because too many identical first neighbors. but really no limit if situation arises
|
||
status = GUESSFAIL;
|
||
return;
|
||
}
|
||
tag_choices[num_choices++] = xspecial[atom->map(glove[pion][1])][i];
|
||
}
|
||
}
|
||
|
||
// guess branch is for when multiple identical neighbors. then we guess each one in turn
|
||
// guess_branch must work even when avail_guesses = 0. so index accordingly!
|
||
// ...actually, avail_guesses should never be zero here anyway
|
||
if (guess_branch[avail_guesses-1] == 0) guess_branch[avail_guesses-1] = num_choices;
|
||
|
||
//std::size_t size = sizeof(tag_choices) / sizeof(tag_choices[0]);
|
||
std::sort(tag_choices, tag_choices + num_choices); //, std::greater<int>());
|
||
glove[onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh];
|
||
glove[onemol_xspecial[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1];
|
||
guess_branch[avail_guesses-1]--;
|
||
|
||
//another check for ghost atoms. perhaps remove the one in make_a_guess
|
||
if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
|
||
error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away");
|
||
}
|
||
|
||
if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
|
||
|
||
for (int i = 0; i < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; i++) {
|
||
pioneer_count[onemol_xspecial[onemol_xspecial[pion][neigh]-1][i]-1]++;
|
||
}
|
||
glove_counter++;
|
||
if (glove_counter == onemol->natoms) {
|
||
if (ring_check() && check_constraints()) status = ACCEPT;
|
||
else status = GUESSFAIL;
|
||
return;
|
||
}
|
||
status = CONTINUE;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Check that newly assigned atoms have correct bonds
|
||
Necessary for certain ringed structures
|
||
------------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::ring_check()
|
||
{
|
||
// ring_check can be made more efficient by re-introducing 'frozen' atoms
|
||
// 'frozen' atoms have been assigned and also are no longer pioneers
|
||
|
||
// double check the number of neighbors match for all non-edge atoms
|
||
// otherwise, atoms at 'end' of symmetric ring can behave like edge atoms
|
||
for (int i = 0; i < onemol->natoms; i++)
|
||
if (edge[i][rxnID] == 0 &&
|
||
onemol_nxspecial[i][0] != nxspecial[atom->map(glove[i][1])][0])
|
||
return 0;
|
||
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
for (int j = 0; j < onemol_nxspecial[i][0]; j++) {
|
||
int ring_fail = 1;
|
||
int ispecial = onemol_xspecial[i][j];
|
||
for (int k = 0; k < nxspecial[atom->map(glove[i][1])][0]; k++) {
|
||
if (xspecial[atom->map(glove[i][1])][k] == glove[ispecial-1][1]) {
|
||
ring_fail = 0;
|
||
break;
|
||
}
|
||
}
|
||
if (ring_fail == 1) return 0;
|
||
}
|
||
}
|
||
return 1;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
evaluate constraints: return 0 if any aren't satisfied
|
||
------------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::check_constraints()
|
||
{
|
||
double x1[3],x2[3],x3[3],x4[3];
|
||
double delx,dely,delz,rsq;
|
||
double delx1,dely1,delz1,delx2,dely2,delz2;
|
||
double rsq1,rsq2,r1,r2,c,t,prrhob;
|
||
// for computation of dihedrals
|
||
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,ra2inv,rb2inv,rabinv;
|
||
double s,phi;
|
||
int ANDgate;
|
||
|
||
tagint atom1,atom2;
|
||
double **x = atom->x;
|
||
|
||
int *satisfied;
|
||
memory->create(satisfied,nconstraints[rxnID],"bond/react:satisfied");
|
||
for (int i = 0; i < nconstraints[rxnID]; i++)
|
||
satisfied[i] = 1;
|
||
|
||
for (int i = 0; i < nconstraints[rxnID]; i++) {
|
||
if (constraints[i][rxnID].type == DISTANCE) {
|
||
get_IDcoords(constraints[i][rxnID].idtype[0], constraints[i][rxnID].id[0], x1);
|
||
get_IDcoords(constraints[i][rxnID].idtype[1], constraints[i][rxnID].id[1], x2);
|
||
delx = x1[0] - x2[0];
|
||
dely = x1[1] - x2[1];
|
||
delz = x1[2] - x2[2];
|
||
domain->minimum_image(delx,dely,delz); // ghost location fix
|
||
rsq = delx*delx + dely*dely + delz*delz;
|
||
if (rsq < constraints[i][rxnID].par[0] || rsq > constraints[i][rxnID].par[1]) satisfied[i] = 0;
|
||
} else if (constraints[i][rxnID].type == ANGLE) {
|
||
get_IDcoords(constraints[i][rxnID].idtype[0], constraints[i][rxnID].id[0], x1);
|
||
get_IDcoords(constraints[i][rxnID].idtype[1], constraints[i][rxnID].id[1], x2);
|
||
get_IDcoords(constraints[i][rxnID].idtype[2], constraints[i][rxnID].id[2], x3);
|
||
|
||
// 1st bond
|
||
delx1 = x1[0] - x2[0];
|
||
dely1 = x1[1] - x2[1];
|
||
delz1 = x1[2] - x2[2];
|
||
domain->minimum_image(delx1,dely1,delz1); // ghost location fix
|
||
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
|
||
r1 = sqrt(rsq1);
|
||
|
||
// 2nd bond
|
||
delx2 = x3[0] - x2[0];
|
||
dely2 = x3[1] - x2[1];
|
||
delz2 = x3[2] - x2[2];
|
||
domain->minimum_image(delx2,dely2,delz2); // ghost location fix
|
||
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
|
||
r2 = sqrt(rsq2);
|
||
|
||
// angle (cos and sin)
|
||
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||
c /= r1*r2;
|
||
if (c > 1.0) c = 1.0;
|
||
if (c < -1.0) c = -1.0;
|
||
if (acos(c) < constraints[i][rxnID].par[0] || acos(c) > constraints[i][rxnID].par[1]) satisfied[i] = 0;
|
||
} else if (constraints[i][rxnID].type == DIHEDRAL) {
|
||
// phi calculation from dihedral style harmonic
|
||
get_IDcoords(constraints[i][rxnID].idtype[0], constraints[i][rxnID].id[0], x1);
|
||
get_IDcoords(constraints[i][rxnID].idtype[1], constraints[i][rxnID].id[1], x2);
|
||
get_IDcoords(constraints[i][rxnID].idtype[2], constraints[i][rxnID].id[2], x3);
|
||
get_IDcoords(constraints[i][rxnID].idtype[3], constraints[i][rxnID].id[3], x4);
|
||
|
||
vb1x = x1[0] - x2[0];
|
||
vb1y = x1[1] - x2[1];
|
||
vb1z = x1[2] - x2[2];
|
||
domain->minimum_image(vb1x,vb1y,vb1z);
|
||
|
||
vb2x = x3[0] - x2[0];
|
||
vb2y = x3[1] - x2[1];
|
||
vb2z = x3[2] - x2[2];
|
||
domain->minimum_image(vb2x,vb2y,vb2z);
|
||
|
||
vb2xm = -vb2x;
|
||
vb2ym = -vb2y;
|
||
vb2zm = -vb2z;
|
||
domain->minimum_image(vb2xm,vb2ym,vb2zm);
|
||
|
||
vb3x = x4[0] - x3[0];
|
||
vb3y = x4[1] - x3[1];
|
||
vb3z = x4[2] - x3[2];
|
||
domain->minimum_image(vb3x,vb3y,vb3z);
|
||
|
||
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||
az = vb1x*vb2ym - vb1y*vb2xm;
|
||
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||
by = vb3z*vb2xm - vb3x*vb2zm;
|
||
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||
|
||
rasq = ax*ax + ay*ay + az*az;
|
||
rbsq = bx*bx + by*by + bz*bz;
|
||
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
|
||
rg = sqrt(rgsq);
|
||
|
||
ra2inv = rb2inv = 0.0;
|
||
if (rasq > 0) ra2inv = 1.0/rasq;
|
||
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||
rabinv = sqrt(ra2inv*rb2inv);
|
||
|
||
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
|
||
|
||
if (c > 1.0) c = 1.0;
|
||
if (c < -1.0) c = -1.0;
|
||
phi = atan2(s,c);
|
||
|
||
ANDgate = 0;
|
||
if (constraints[i][rxnID].par[0] < constraints[i][rxnID].par[1]) {
|
||
if (phi > constraints[i][rxnID].par[0] && phi < constraints[i][rxnID].par[1]) ANDgate = 1;
|
||
} else {
|
||
if (phi > constraints[i][rxnID].par[0] || phi < constraints[i][rxnID].par[1]) ANDgate = 1;
|
||
}
|
||
if (constraints[i][rxnID].par[2] < constraints[i][rxnID].par[3]) {
|
||
if (phi > constraints[i][rxnID].par[2] && phi < constraints[i][rxnID].par[3]) ANDgate = 1;
|
||
} else {
|
||
if (phi > constraints[i][rxnID].par[2] || phi < constraints[i][rxnID].par[3]) ANDgate = 1;
|
||
}
|
||
if (ANDgate != 1) satisfied[i] = 0;
|
||
} else if (constraints[i][rxnID].type == ARRHENIUS) {
|
||
t = get_temperature(glove,0,1);
|
||
prrhob = constraints[i][rxnID].par[1]*pow(t,constraints[i][rxnID].par[2])*
|
||
exp(-constraints[i][rxnID].par[3]/(force->boltz*t));
|
||
if (prrhob < rrhandom[(int) constraints[i][rxnID].par[0]]->uniform()) satisfied[i] = 0;
|
||
} else if (constraints[i][rxnID].type == RMSD) {
|
||
// call superpose
|
||
int iatom;
|
||
int iref = -1; // choose first atom as reference
|
||
int n2superpose = 0;
|
||
double **xfrozen; // coordinates for the "frozen" target molecule
|
||
double **xmobile; // coordinates for the "mobile" molecule
|
||
int ifragment = constraints[i][rxnID].id[0];
|
||
if (ifragment >= 0) {
|
||
for (int j = 0; j < onemol->natoms; j++)
|
||
if (onemol->fragmentmask[ifragment][j]) n2superpose++;
|
||
memory->create(xfrozen,n2superpose,3,"bond/react:xfrozen");
|
||
memory->create(xmobile,n2superpose,3,"bond/react:xmobile");
|
||
int myincr = 0;
|
||
for (int j = 0; j < onemol->natoms; j++) {
|
||
if (onemol->fragmentmask[ifragment][j]) {
|
||
iatom = atom->map(glove[j][1]);
|
||
if (iref == -1) iref = iatom;
|
||
iatom = domain->closest_image(iref,iatom);
|
||
for (int k = 0; k < 3; k++) {
|
||
xfrozen[myincr][k] = x[iatom][k];
|
||
xmobile[myincr][k] = onemol->x[j][k];
|
||
}
|
||
myincr++;
|
||
}
|
||
}
|
||
} else {
|
||
int iatom;
|
||
int iref = -1; // choose first atom as reference
|
||
n2superpose = onemol->natoms;
|
||
memory->create(xfrozen,n2superpose,3,"bond/react:xfrozen");
|
||
memory->create(xmobile,n2superpose,3,"bond/react:xmobile");
|
||
for (int j = 0; j < n2superpose; j++) {
|
||
iatom = atom->map(glove[j][1]);
|
||
if (iref == -1) iref = iatom;
|
||
iatom = domain->closest_image(iref,iatom);
|
||
for (int k = 0; k < 3; k++) {
|
||
xfrozen[j][k] = x[iatom][k];
|
||
xmobile[j][k] = onemol->x[j][k];
|
||
}
|
||
}
|
||
}
|
||
Superpose3D<double, double **> superposer(n2superpose);
|
||
double rmsd = superposer.Superpose(xfrozen, xmobile);
|
||
memory->destroy(xfrozen);
|
||
memory->destroy(xmobile);
|
||
if (rmsd > constraints[i][rxnID].par[0]) satisfied[i] = 0;
|
||
} else if (constraints[i][rxnID].type == CUSTOM) {
|
||
satisfied[i] = custom_constraint(constraints[i][rxnID].str);
|
||
}
|
||
}
|
||
|
||
if (nconstraints[rxnID] > 0) {
|
||
char evalstr[MAXLINE],*ptr;
|
||
strcpy(evalstr,constraintstr[rxnID]);
|
||
for (int i = 0; i < nconstraints[rxnID]; i++) {
|
||
ptr = strchr(evalstr,'C');
|
||
*ptr = satisfied[i] ? '1' : '0';
|
||
}
|
||
double verdict = input->variable->evaluate_boolean(evalstr);
|
||
if (verdict == 0.0) {
|
||
memory->destroy(satisfied);
|
||
return 0;
|
||
}
|
||
}
|
||
|
||
// let's also check chirality within 'check_constraint'
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
if (chiral_atoms[i][0][rxnID] == 1) {
|
||
double my4coords[12];
|
||
// already ensured, by transitive property, that chiral simulation atom has four neighs
|
||
for (int j = 0; j < 4; j++) {
|
||
atom1 = atom->map(glove[i][1]);
|
||
// loop over known types involved in chiral center
|
||
for (int jj = 0; jj < 4; jj++) {
|
||
if (atom->type[atom->map(xspecial[atom1][j])] == chiral_atoms[i][jj+2][rxnID]) {
|
||
atom2 = atom->map(xspecial[atom1][j]);
|
||
atom2 = domain->closest_image(atom1,atom2);
|
||
for (int k = 0; k < 3; k++) {
|
||
my4coords[3*jj+k] = x[atom2][k];
|
||
}
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
if (get_chirality(my4coords) != chiral_atoms[i][1][rxnID]) {
|
||
memory->destroy(satisfied);
|
||
return 0;
|
||
}
|
||
}
|
||
}
|
||
|
||
memory->destroy(satisfied);
|
||
return 1;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
return pre-reaction atom or fragment location
|
||
fragment: given pre-reacted molID (onemol) and fragID,
|
||
return geometric center (of mapped simulation atoms)
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::get_IDcoords(int mode, int myID, double *center)
|
||
{
|
||
double **x = atom->x;
|
||
if (mode == ATOM) {
|
||
int iatom = atom->map(glove[myID-1][1]);
|
||
for (int i = 0; i < 3; i++)
|
||
center[i] = x[iatom][i];
|
||
} else {
|
||
int iref = -1; // choose first atom as reference
|
||
int iatom;
|
||
int nfragatoms = 0;
|
||
for (int i = 0; i < 3; i++)
|
||
center[i] = 0;
|
||
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
if (onemol->fragmentmask[myID][i]) {
|
||
if (iref == -1)
|
||
iref = atom->map(glove[i][1]);
|
||
iatom = atom->map(glove[i][1]);
|
||
iatom = domain->closest_image(iref,iatom);
|
||
for (int j = 0; j < 3; j++)
|
||
center[j] += x[iatom][j];
|
||
nfragatoms++;
|
||
}
|
||
}
|
||
for (int i = 0; i < 3; i++)
|
||
center[i] /= nfragatoms;
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
compute local temperature: average over all atoms in reaction template
|
||
------------------------------------------------------------------------- */
|
||
|
||
double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col)
|
||
{
|
||
int i,ilocal;
|
||
double adof = domain->dimension;
|
||
|
||
double **v = atom->v;
|
||
double *mass = atom->mass;
|
||
double *rmass = atom->rmass;
|
||
int *type = atom->type;
|
||
|
||
double t = 0.0;
|
||
|
||
if (rmass) {
|
||
for (i = 0; i < onemol->natoms; i++) {
|
||
ilocal = atom->map(myglove[i+row_offset][col]);
|
||
t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
|
||
v[ilocal][2]*v[ilocal][2]) * rmass[ilocal];
|
||
}
|
||
} else {
|
||
for (i = 0; i < onemol->natoms; i++) {
|
||
ilocal = atom->map(myglove[i+row_offset][col]);
|
||
t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
|
||
v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]];
|
||
}
|
||
}
|
||
|
||
// final temperature
|
||
double dof = adof*onemol->natoms;
|
||
double tfactor = force->mvv2e / (dof * force->boltz);
|
||
t *= tfactor;
|
||
return t;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
get per-atom variable names used by custom constraint
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::customvarnames()
|
||
{
|
||
int pos,pos1,pos2,pos3,prev3;
|
||
std::string varstr,argstr,varid;
|
||
|
||
// search all constraints' varstr for special 'rxn' functions
|
||
// add variable names to customvarstrs
|
||
// add values to customvars
|
||
|
||
for (rxnID = 0; rxnID < nreacts; rxnID++) {
|
||
for (int i = 0; i < nconstraints[rxnID]; i++) {
|
||
if (constraints[i][rxnID].type == CUSTOM) {
|
||
varstr = constraints[i][rxnID].str;
|
||
prev3 = -1;
|
||
while (true) {
|
||
// find next reaction special function occurrence
|
||
pos1 = INT_MAX;
|
||
for (int i = 0; i < nrxnfunction; i++) {
|
||
pos = varstr.find(rxnfunclist[i],prev3+1);
|
||
if (pos == std::string::npos) continue;
|
||
if (pos < pos1) pos1 = pos;
|
||
}
|
||
if (pos1 == INT_MAX) break;
|
||
|
||
pos2 = varstr.find("(",pos1);
|
||
pos3 = varstr.find(")",pos2);
|
||
if (pos2 == std::string::npos || pos3 == std::string::npos)
|
||
error->all(FLERR,"Bond/react: Illegal rxn function syntax\n");
|
||
prev3 = pos3;
|
||
argstr = varstr.substr(pos2+1,pos3-pos2-1);
|
||
argstr.erase(remove_if(argstr.begin(), argstr.end(), isspace), argstr.end()); // remove whitespace
|
||
pos2 = argstr.find(",");
|
||
if (pos2 != std::string::npos) varid = argstr.substr(0,pos2);
|
||
else varid = argstr;
|
||
// check if we already know about this variable
|
||
int varidflag = 0;
|
||
for (int j = 0; j < ncustomvars; j++) {
|
||
if (customvarstrs[j] == varid) {
|
||
varidflag = 1;
|
||
break;
|
||
}
|
||
}
|
||
if (!varidflag) {
|
||
customvarstrs.resize(ncustomvars+1);
|
||
customvarstrs[ncustomvars++] = varid;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
evaluate per-atom variables needed for custom constraint
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::get_customvars()
|
||
{
|
||
double *tempvvec;
|
||
std::string varid;
|
||
int nall = atom->nlocal + atom->nghost;
|
||
|
||
memory->create(tempvvec,nall,"bond/react:tempvvec");
|
||
if (vvec == nullptr) {
|
||
memory->create(vvec,nall,ncustomvars,"bond/react:vvec");
|
||
nvvec = nall;
|
||
}
|
||
if (nvvec < nall) {
|
||
memory->grow(vvec,nall,ncustomvars,"bond/react:vvec");
|
||
nvvec = nall;
|
||
}
|
||
for (int i = 0; i < ncustomvars; i++) {
|
||
varid = customvarstrs[i];
|
||
if (varid.substr(0,2) != "v_") error->all(FLERR,"Bond/react: Reaction special function variable "
|
||
"name should begin with 'v_'");
|
||
varid = varid.substr(2);
|
||
int ivar = input->variable->find(varid.c_str());
|
||
if (ivar < 0)
|
||
error->all(FLERR,"Bond/react: Reaction special function variable "
|
||
"name does not exist");
|
||
if (!input->variable->atomstyle(ivar))
|
||
error->all(FLERR,"Bond/react: Reaction special function must "
|
||
"reference an atom-style variable");
|
||
|
||
input->variable->compute_atom(ivar,igroup,tempvvec,1,0);
|
||
for (int j = 0; j < nall; j++) vvec[j][i] = tempvvec[j];
|
||
}
|
||
memory->destroy(tempvvec);
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
evaulate expression for variable constraint
|
||
------------------------------------------------------------------------- */
|
||
|
||
double FixBondReact::custom_constraint(const std::string& varstr)
|
||
{
|
||
int pos,pos1,pos2,pos3,irxnfunc;
|
||
int prev3 = -1;
|
||
double val;
|
||
std::string argstr,varid,fragid,evlcat;
|
||
std::vector<std::string> evlstr;
|
||
|
||
// search varstr for special 'rxn' functions
|
||
while (true) {
|
||
// find next reaction special function occurrence
|
||
pos1 = INT_MAX;
|
||
for (int i = 0; i < nrxnfunction; i++) {
|
||
pos = varstr.find(rxnfunclist[i],prev3+1);
|
||
if (pos == std::string::npos) continue;
|
||
if (pos < pos1) {
|
||
pos1 = pos;
|
||
irxnfunc = i;
|
||
}
|
||
}
|
||
if (pos1 == INT_MAX) break;
|
||
|
||
fragid = "all"; // operate over entire reaction site by default
|
||
pos2 = varstr.find("(",pos1);
|
||
pos3 = varstr.find(")",pos2);
|
||
if (pos2 == std::string::npos || pos3 == std::string::npos)
|
||
error->one(FLERR,"Bond/react: Illegal rxn function syntax\n");
|
||
evlstr.push_back(varstr.substr(prev3+1,pos1-(prev3+1)));
|
||
prev3 = pos3;
|
||
argstr = varstr.substr(pos2+1,pos3-pos2-1);
|
||
argstr.erase(remove_if(argstr.begin(), argstr.end(), isspace), argstr.end()); // remove whitespace
|
||
pos2 = argstr.find(",");
|
||
if (pos2 != std::string::npos) {
|
||
varid = argstr.substr(0,pos2);
|
||
fragid = argstr.substr(pos2+1);
|
||
} else varid = argstr;
|
||
evlstr.push_back(std::to_string(rxnfunction(rxnfunclist[irxnfunc], varid, fragid)));
|
||
}
|
||
evlstr.push_back(varstr.substr(prev3+1));
|
||
|
||
for (auto & evl : evlstr) evlcat += evl;
|
||
|
||
char *cstr = utils::strdup(evlcat);
|
||
val = input->variable->compute_equal(cstr);
|
||
delete [] cstr;
|
||
return val;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
currently two 'rxn' functions: rxnsum and rxnave
|
||
------------------------------------------------------------------------- */
|
||
|
||
double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string& varid,
|
||
const std::string& fragid)
|
||
{
|
||
int ivar = -1;
|
||
for (int i = 0; i < ncustomvars; i++) {
|
||
if (varid == customvarstrs[i]) {
|
||
ivar = i;
|
||
break;
|
||
}
|
||
}
|
||
// variable name should always be found, at this point
|
||
// however, let's double check for completeness
|
||
if (ivar < 0)
|
||
error->one(FLERR,"Bond/react: Reaction special function variable "
|
||
"name does not exist");
|
||
|
||
int ifrag = -1;
|
||
if (fragid != "all") {
|
||
ifrag = onemol->findfragment(fragid.c_str());
|
||
if (ifrag < 0) error->one(FLERR,"Bond/react: Molecule fragment "
|
||
"in reaction special function does not exist");
|
||
}
|
||
|
||
int iatom;
|
||
int nsum = 0;
|
||
double sumvvec = 0;
|
||
if (rxnfunc == "rxnsum" || rxnfunc == "rxnave") {
|
||
if (fragid == "all") {
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
iatom = atom->map(glove[i][1]);
|
||
sumvvec += vvec[iatom][ivar];
|
||
}
|
||
nsum = onemol->natoms;
|
||
} else {
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
if (onemol->fragmentmask[ifrag][i]) {
|
||
iatom = atom->map(glove[i][1]);
|
||
sumvvec += vvec[iatom][ivar];
|
||
nsum++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
if (rxnfunc == "rxnsum") return sumvvec;
|
||
if (rxnfunc == "rxnave") return sumvvec/nsum;
|
||
return 0.0;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
return handedness (1 or -1) of a chiral center, given ordered set of coordinates
|
||
------------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::get_chirality(double four_coords[12])
|
||
{
|
||
// define oriented plane with first three coordinates
|
||
double vec1[3],vec2[3],vec3[3],vec4[3],mean3[3],dot;
|
||
|
||
for (int i = 0; i < 3; i++) {
|
||
vec1[i] = four_coords[i]-four_coords[i+3];
|
||
vec2[i] = four_coords[i+3]-four_coords[i+6];
|
||
}
|
||
|
||
MathExtra::cross3(vec1,vec2,vec3);
|
||
|
||
for (int i = 0; i < 3; i++) {
|
||
mean3[i] = (four_coords[i] + four_coords[i+3] +
|
||
four_coords[i+6])/3;
|
||
vec4[i] = four_coords[i+9] - mean3[i];
|
||
}
|
||
|
||
dot = MathExtra::dot3(vec3,vec4);
|
||
dot = dot/fabs(dot);
|
||
return (int) dot;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Get xspecials for current 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];
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
Determine which pre-reacted template atoms are at least three bonds
|
||
away from edge atoms.
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::find_landlocked_atoms(int myrxn)
|
||
{
|
||
// landlocked_atoms are atoms for which all topology is contained in reacted template
|
||
// if dihedrals/impropers exist: this means that edge atoms are not in their 1-3 neighbor list
|
||
// note: due to various usage/definitions of impropers, treated same as dihedrals
|
||
// if angles exist: this means edge atoms not in their 1-2 neighbors list
|
||
// if just bonds: this just means that edge atoms are not landlocked
|
||
// Note: landlocked defined in terms of reacted template
|
||
// if no edge atoms (small reacting molecule), all atoms are landlocked
|
||
// we can delete all current topology of landlocked atoms and replace
|
||
|
||
// always remove edge atoms from landlocked list
|
||
for (int i = 0; i < twomol->natoms; i++) {
|
||
if (create_atoms[i][myrxn] == 0 && edge[equivalences[i][1][myrxn]-1][myrxn] == 1)
|
||
landlocked_atoms[i][myrxn] = 0;
|
||
else landlocked_atoms[i][myrxn] = 1;
|
||
}
|
||
int nspecial_limit = -1;
|
||
if (force->angle && twomol->angleflag) nspecial_limit = 0;
|
||
|
||
if ((force->dihedral && twomol->dihedralflag) ||
|
||
(force->improper && twomol->improperflag)) nspecial_limit = 1;
|
||
|
||
if (nspecial_limit != -1) {
|
||
for (int i = 0; i < twomol->natoms; i++) {
|
||
for (int j = 0; j < twomol_nxspecial[i][nspecial_limit]; j++) {
|
||
for (int k = 0; k < onemol->natoms; k++) {
|
||
if (equivalences[twomol_xspecial[i][j]-1][1][myrxn] == k+1 && edge[k][myrxn] == 1) {
|
||
landlocked_atoms[i][myrxn] = 0;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// bad molecule templates check
|
||
// if atoms change types, but aren't landlocked, that's bad
|
||
for (int i = 0; i < twomol->natoms; i++) {
|
||
if (create_atoms[i][myrxn] == 0) {
|
||
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) {
|
||
char str[128];
|
||
snprintf(str,128,"Bond/react: Atom type affected by reaction %s too close to template edge",rxn_name[myrxn]);
|
||
error->all(FLERR,str);
|
||
}
|
||
}
|
||
}
|
||
|
||
// additionally, if a bond changes type, but neither involved atom is landlocked, bad
|
||
// would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
|
||
for (int i = 0; i < twomol->natoms; i++) {
|
||
if (create_atoms[i][myrxn] == 0) {
|
||
if (landlocked_atoms[i][myrxn] == 0) {
|
||
for (int j = 0; j < twomol->num_bond[i]; j++) {
|
||
int twomol_atomj = twomol->bond_atom[i][j];
|
||
if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
|
||
int onemol_atomi = equivalences[i][1][myrxn];
|
||
int onemol_batom;
|
||
for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
|
||
onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
|
||
if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
|
||
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
|
||
char str[128];
|
||
snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]);
|
||
error->all(FLERR,str);
|
||
}
|
||
}
|
||
}
|
||
if (newton_bond) {
|
||
int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
|
||
for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
|
||
onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
|
||
if (onemol_batom == equivalences[i][1][myrxn]) {
|
||
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
|
||
char str[128];
|
||
snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]);
|
||
error->all(FLERR,str);
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// additionally, if a deleted atom is bonded to an atom that is not deleted, bad
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
if (delete_atoms[i][myrxn] == 1) {
|
||
int ii = reverse_equiv[i][1][myrxn] - 1;
|
||
for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
|
||
if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
|
||
error->all(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
|
||
if (me == 0)
|
||
for (int i = 0; i < twomol->natoms; i++) {
|
||
if (create_atoms[i][myrxn] == 0) {
|
||
if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
|
||
char str[128];
|
||
snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
|
||
error->warning(FLERR,str);
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
|
||
// 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) {
|
||
error->one(FLERR,"Bond/react: Created atom too close to template edge");
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
let's dedup global_mega_glove
|
||
allows for same site undergoing different pathways, in parallel
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::dedup_mega_gloves(int dedup_mode)
|
||
{
|
||
// dedup_mode == LOCAL for local_dedup
|
||
// dedup_mode == GLOBAL for global_mega_glove
|
||
for (int i = 0; i < nreacts; i++) {
|
||
if (dedup_mode == LOCAL) local_rxn_count[i] = 0;
|
||
if (dedup_mode == GLOBAL) ghostly_rxn_count[i] = 0;
|
||
}
|
||
|
||
int dedup_size = 0;
|
||
if (dedup_mode == LOCAL) {
|
||
dedup_size = local_num_mega;
|
||
} else if (dedup_mode == GLOBAL) {
|
||
dedup_size = global_megasize;
|
||
}
|
||
|
||
tagint **dedup_glove;
|
||
memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove");
|
||
|
||
if (dedup_mode == LOCAL) {
|
||
for (int i = 0; i < dedup_size; i++) {
|
||
for (int j = 0; j < max_natoms+1; j++) {
|
||
dedup_glove[j][i] = local_mega_glove[j][i];
|
||
}
|
||
}
|
||
} else if (dedup_mode == GLOBAL) {
|
||
for (int i = 0; i < dedup_size; i++) {
|
||
for (int j = 0; j < max_natoms+1; j++) {
|
||
dedup_glove[j][i] = global_mega_glove[j][i];
|
||
}
|
||
}
|
||
}
|
||
|
||
// dedup_mask is size dedup_size and filters reactions that have been deleted
|
||
// a value of 1 means this reaction instance has been deleted
|
||
int *dedup_mask = new int[dedup_size];
|
||
int *dup_list = new int[dedup_size];
|
||
|
||
for (int i = 0; i < dedup_size; i++) {
|
||
dedup_mask[i] = 0;
|
||
dup_list[i] = 0;
|
||
}
|
||
|
||
// let's randomly mix up our reaction instances first
|
||
// then we can feel okay about ignoring ones we've already deleted (or accepted)
|
||
// based off std::shuffle
|
||
int *temp_rxn = new int[max_natoms+1];
|
||
for (int i = dedup_size-1; i > 0; --i) { //dedup_size
|
||
// choose random entry to swap current one with
|
||
int k = floor(random[0]->uniform()*(i+1));
|
||
|
||
// swap entries
|
||
for (int j = 0; j < max_natoms+1; j++)
|
||
temp_rxn[j] = dedup_glove[j][i];
|
||
|
||
for (int j = 0; j < max_natoms+1; j++) {
|
||
dedup_glove[j][i] = dedup_glove[j][k];
|
||
dedup_glove[j][k] = temp_rxn[j];
|
||
}
|
||
}
|
||
delete [] temp_rxn;
|
||
|
||
for (int i = 0; i < dedup_size; i++) {
|
||
if (dedup_mask[i] == 0) {
|
||
int num_dups = 0;
|
||
int myrxnid1 = dedup_glove[0][i];
|
||
onemol = atom->molecules[unreacted_mol[myrxnid1]];
|
||
for (int j = 0; j < onemol->natoms; j++) {
|
||
int check1 = dedup_glove[j+1][i];
|
||
for (int ii = i + 1; ii < dedup_size; ii++) {
|
||
int already_listed = 0;
|
||
for (int jj = 0; jj < num_dups; jj++) {
|
||
if (dup_list[jj] == ii) {
|
||
already_listed = 1;
|
||
break;
|
||
}
|
||
}
|
||
if (dedup_mask[ii] == 0 && already_listed == 0) {
|
||
int myrxnid2 = dedup_glove[0][ii];
|
||
twomol = atom->molecules[unreacted_mol[myrxnid2]];
|
||
for (int jj = 0; jj < twomol->natoms; jj++) {
|
||
int check2 = dedup_glove[jj+1][ii];
|
||
if (check2 == check1) {
|
||
// add this rxn instance as well
|
||
if (num_dups == 0) dup_list[num_dups++] = i;
|
||
dup_list[num_dups++] = ii;
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
// here we choose random number and therefore reaction instance
|
||
int myrand = 1;
|
||
if (num_dups > 0) {
|
||
myrand = floor(random[0]->uniform()*num_dups);
|
||
for (int iii = 0; iii < num_dups; iii++) {
|
||
if (iii != myrand) dedup_mask[dup_list[iii]] = 1;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// we must update local_mega_glove and local_megasize
|
||
// we can simply overwrite local_mega_glove column by column
|
||
if (dedup_mode == LOCAL) {
|
||
int new_local_megasize = 0;
|
||
for (int i = 0; i < local_num_mega; i++) {
|
||
if (dedup_mask[i] == 0) {
|
||
local_rxn_count[(int) dedup_glove[0][i]]++;
|
||
for (int j = 0; j < max_natoms+1; j++) {
|
||
local_mega_glove[j][new_local_megasize] = dedup_glove[j][i];
|
||
}
|
||
new_local_megasize++;
|
||
}
|
||
}
|
||
|
||
local_num_mega = new_local_megasize;
|
||
}
|
||
|
||
// we must update global_mega_glove and global_megasize
|
||
// we can simply overwrite global_mega_glove column by column
|
||
if (dedup_mode == GLOBAL) {
|
||
int new_global_megasize = 0;
|
||
for (int i = 0; i < global_megasize; i++) {
|
||
if (dedup_mask[i] == 0) {
|
||
ghostly_rxn_count[dedup_glove[0][i]]++;
|
||
for (int j = 0; j < max_natoms + 1; j++) {
|
||
global_mega_glove[j][new_global_megasize] = dedup_glove[j][i];
|
||
}
|
||
new_global_megasize++;
|
||
}
|
||
}
|
||
global_megasize = new_global_megasize;
|
||
}
|
||
|
||
memory->destroy(dedup_glove);
|
||
delete [] dedup_mask;
|
||
delete [] dup_list;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
let's limit movement of newly bonded atoms
|
||
and exclude them from other thermostats via exclude_group
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::limit_bond(int limit_bond_mode)
|
||
{
|
||
//two types of passes: 1) while superimpose algorithm is iterating (only local atoms)
|
||
// 2) once more for global_mega_glove [after de-duplicating rxn instances]
|
||
//in second case, only add local atoms to group
|
||
//as with update_everything, we can pre-prepare these arrays, then run generic limit_bond code
|
||
|
||
//create local, generic variables for onemol->natoms and glove
|
||
//to be filled differently on respective passes
|
||
|
||
int nlocal = atom->nlocal;
|
||
int temp_limit_num = 0;
|
||
tagint *temp_limit_glove;
|
||
if (limit_bond_mode == LOCAL) {
|
||
int max_temp = local_num_mega * (max_natoms + 1);
|
||
temp_limit_glove = new tagint[max_temp];
|
||
for (int j = 0; j < local_num_mega; j++) {
|
||
rxnID = local_mega_glove[0][j];
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
temp_limit_glove[temp_limit_num++] = local_mega_glove[i+1][j];
|
||
}
|
||
}
|
||
|
||
} else if (limit_bond_mode == GLOBAL) {
|
||
int max_temp = global_megasize * (max_natoms + 1);
|
||
temp_limit_glove = new tagint[max_temp];
|
||
for (int j = 0; j < global_megasize; j++) {
|
||
rxnID = global_mega_glove[0][j];
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
if (atom->map(global_mega_glove[i+1][j]) >= 0 &&
|
||
atom->map(global_mega_glove[i+1][j]) < nlocal)
|
||
temp_limit_glove[temp_limit_num++] = global_mega_glove[i+1][j];
|
||
}
|
||
}
|
||
}
|
||
|
||
if (temp_limit_num == 0) {
|
||
delete [] temp_limit_glove;
|
||
return;
|
||
}
|
||
|
||
// we must keep our own list of limited atoms
|
||
// this will be a new per-atom property!
|
||
|
||
int flag,cols;
|
||
int index1 = atom->find_custom("limit_tags",flag,cols);
|
||
int *i_limit_tags = atom->ivector[index1];
|
||
|
||
int *i_statted_tags;
|
||
if (stabilization_flag == 1) {
|
||
int index2 = atom->find_custom(statted_id,flag,cols);
|
||
i_statted_tags = atom->ivector[index2];
|
||
}
|
||
|
||
int index3 = atom->find_custom("react_tags",flag,cols);
|
||
int *i_react_tags = atom->ivector[index3];
|
||
|
||
for (int i = 0; i < temp_limit_num; i++) {
|
||
// update->ntimestep could be 0. so add 1 throughout
|
||
i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1;
|
||
if (stabilization_flag == 1) i_statted_tags[atom->map(temp_limit_glove[i])] = 0;
|
||
i_react_tags[atom->map(temp_limit_glove[i])] = rxnID;
|
||
}
|
||
|
||
delete [] temp_limit_glove;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
let's unlimit movement of newly bonded atoms after n timesteps.
|
||
we give them back to the system thermostat
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::unlimit_bond()
|
||
{
|
||
// let's now unlimit in terms of i_limit_tags
|
||
// we just run through all nlocal, looking for > limit_duration
|
||
// then we return i_limit_tag to 0 (which removes from dynamic group)
|
||
int flag, cols;
|
||
int index1 = atom->find_custom("limit_tags",flag,cols);
|
||
int *i_limit_tags = atom->ivector[index1];
|
||
|
||
int *i_statted_tags;
|
||
if (stabilization_flag == 1) {
|
||
int index2 = atom->find_custom(statted_id,flag,cols);
|
||
i_statted_tags = atom->ivector[index2];
|
||
}
|
||
|
||
int index3 = atom->find_custom("react_tags",flag,cols);
|
||
int *i_react_tags = atom->ivector[index3];
|
||
|
||
int unlimitflag = 0;
|
||
for (int i = 0; i < atom->nlocal; i++) {
|
||
// unlimit atoms for next step! this resolves # of procs disparity, mostly
|
||
// first '1': indexing offset, second '1': for next step
|
||
if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) {
|
||
unlimitflag = 1;
|
||
i_limit_tags[i] = 0;
|
||
if (stabilization_flag == 1) i_statted_tags[i] = 1;
|
||
i_react_tags[i] = 0;
|
||
}
|
||
}
|
||
|
||
// really should only communicate this per-atom property, not entire reneighboring
|
||
MPI_Allreduce(MPI_IN_PLACE,&unlimitflag,1,MPI_INT,MPI_MAX,world);
|
||
if (unlimitflag) next_reneighbor = update->ntimestep;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
check mega_glove for ghosts
|
||
if so, flag for broadcasting for perusal by all processors
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::glove_ghostcheck()
|
||
{
|
||
// here we add glove to either local_mega_glove or ghostly_mega_glove
|
||
// ghostly_mega_glove includes atoms that are ghosts, either of this proc or another
|
||
// 'ghosts of another' indication taken from comm->sendlist
|
||
|
||
int ghostly = 0;
|
||
#if !defined(MPI_STUBS)
|
||
if (comm->style == 0) {
|
||
if (create_atoms_flag[rxnID] == 1) {
|
||
ghostly = 1;
|
||
} else {
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
int ilocal = atom->map(glove[i][1]);
|
||
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
|
||
ghostly = 1;
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
} else {
|
||
ghostly = 1;
|
||
}
|
||
#endif
|
||
|
||
if (ghostly == 1) {
|
||
ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
|
||
ghostly_rxn_count[rxnID]++; //for debuginng
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
ghostly_mega_glove[i+1][ghostly_num_mega] = glove[i][1];
|
||
}
|
||
ghostly_num_mega++;
|
||
} else {
|
||
local_mega_glove[0][local_num_mega] = rxnID;
|
||
local_rxn_count[rxnID]++; //for debuginng
|
||
for (int i = 0; i < onemol->natoms; i++) {
|
||
local_mega_glove[i+1][local_num_mega] = glove[i][1];
|
||
}
|
||
local_num_mega++;
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
broadcast entries of mega_glove which contain nonlocal atoms for perusal by all processors
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::ghost_glovecast()
|
||
{
|
||
#if !defined(MPI_STUBS)
|
||
|
||
global_megasize = 0;
|
||
|
||
int *allncols = new int[nprocs];
|
||
for (int i = 0; i < nprocs; i++)
|
||
allncols[i] = 0;
|
||
MPI_Allgather(&ghostly_num_mega, 1, MPI_INT, allncols, 1, MPI_INT, world);
|
||
for (int i = 0; i < nprocs; i++)
|
||
global_megasize = global_megasize + allncols[i];
|
||
|
||
if (global_megasize == 0) {
|
||
delete [] allncols;
|
||
return;
|
||
}
|
||
|
||
int *allstarts = new int[nprocs];
|
||
|
||
int start = 0;
|
||
for (int i = 0; i < me; i++) {
|
||
start += allncols[i];
|
||
}
|
||
MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world);
|
||
MPI_Datatype columnunsized, column;
|
||
int sizes[2] = {max_natoms+1, global_megasize};
|
||
int subsizes[2] = {max_natoms+1, 1};
|
||
int starts[2] = {0,0};
|
||
MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C,
|
||
MPI_LMP_TAGINT, &columnunsized);
|
||
MPI_Type_create_resized (columnunsized, 0, sizeof(tagint), &column);
|
||
MPI_Type_commit(&column);
|
||
|
||
memory->destroy(global_mega_glove);
|
||
memory->create(global_mega_glove,max_natoms+1,global_megasize,"bond/react:global_mega_glove");
|
||
|
||
for (int i = 0; i < max_natoms+1; i++)
|
||
for (int j = 0; j < global_megasize; j++)
|
||
global_mega_glove[i][j] = 0;
|
||
|
||
if (ghostly_num_mega > 0) {
|
||
for (int i = 0; i < max_natoms+1; i++) {
|
||
for (int j = 0; j < ghostly_num_mega; j++) {
|
||
global_mega_glove[i][j+start] = ghostly_mega_glove[i][j];
|
||
}
|
||
}
|
||
}
|
||
// let's send to root, dedup, then broadcast
|
||
if (me == 0) {
|
||
MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE
|
||
&(global_mega_glove[0][0]), allncols, allstarts,
|
||
column, 0, world);
|
||
} else {
|
||
MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column,
|
||
&(global_mega_glove[0][0]), allncols, allstarts,
|
||
column, 0, world);
|
||
}
|
||
|
||
if (me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode
|
||
MPI_Bcast(&global_megasize,1,MPI_INT,0,world);
|
||
MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world);
|
||
|
||
delete [] allstarts;
|
||
delete [] allncols;
|
||
|
||
MPI_Type_free(&column);
|
||
MPI_Type_free(&columnunsized);
|
||
#endif
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
update molecule IDs, charges, types, special lists and all topology
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::update_everything()
|
||
{
|
||
int nlocal = atom->nlocal; // must be redefined after create atoms
|
||
int *type = atom->type;
|
||
int **nspecial = atom->nspecial;
|
||
tagint **special = atom->special;
|
||
|
||
int **bond_type = atom->bond_type;
|
||
tagint **bond_atom = atom->bond_atom;
|
||
int *num_bond = atom->num_bond;
|
||
|
||
// used when deleting atoms
|
||
int ndel,ndelone;
|
||
int *mark;
|
||
int nmark = nlocal;
|
||
memory->create(mark,nmark,"bond/react:mark");
|
||
for (int i = 0; i < nmark; i++) mark[i] = 0;
|
||
|
||
// flag used to delete special interactions
|
||
int *delflag;
|
||
memory->create(delflag,atom->maxspecial,"bond/react:delflag");
|
||
|
||
tagint *tag = atom->tag;
|
||
AtomVec *avec = atom->avec;
|
||
|
||
// used when creating atoms
|
||
int inserted_atoms_flag = 0;
|
||
|
||
// update atom->nbonds, etc.
|
||
// TODO: correctly tally with 'newton off'
|
||
int delta_bonds = 0;
|
||
int delta_angle = 0;
|
||
int delta_dihed = 0;
|
||
int delta_imprp = 0;
|
||
|
||
// pass through twice
|
||
// redefining 'update_num_mega' and 'update_mega_glove' each time
|
||
// first pass: when glove is all local atoms
|
||
// second pass: search for local atoms in global_mega_glove
|
||
// add check for local atoms as well
|
||
|
||
int update_num_mega;
|
||
tagint **update_mega_glove;
|
||
memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
|
||
|
||
for (int pass = 0; pass < 2; pass++) {
|
||
update_num_mega = 0;
|
||
int *iskip = new int[nreacts];
|
||
for (int i = 0; i < nreacts; i++) iskip[i] = 0;
|
||
if (pass == 0) {
|
||
for (int i = 0; i < local_num_mega; i++) {
|
||
rxnID = local_mega_glove[0][i];
|
||
// reactions already shuffled from dedup procedure, so can skip first N
|
||
if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
|
||
|
||
// atoms inserted here for serial MPI_STUBS build only
|
||
if (create_atoms_flag[rxnID] == 1) {
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
if (insert_atoms(local_mega_glove,i)) {
|
||
inserted_atoms_flag = 1;
|
||
} else { // create aborted
|
||
reaction_count_total[rxnID]--;
|
||
continue;
|
||
}
|
||
}
|
||
|
||
for (int j = 0; j < max_natoms+1; j++)
|
||
update_mega_glove[j][update_num_mega] = local_mega_glove[j][i];
|
||
update_num_mega++;
|
||
}
|
||
} else if (pass == 1) {
|
||
for (int i = 0; i < global_megasize; i++) {
|
||
rxnID = global_mega_glove[0][i];
|
||
// reactions already shuffled from dedup procedure, so can skip first N
|
||
if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
|
||
|
||
// we can insert atoms here, now that reactions are finalized
|
||
// can't do it any earlier, due to skipped reactions (max_rxn)
|
||
// for MPI build, reactions that create atoms are always treated as 'global'
|
||
if (create_atoms_flag[rxnID] == 1) {
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
if (insert_atoms(global_mega_glove,i)) {
|
||
inserted_atoms_flag = 1;
|
||
} else { // create aborted
|
||
reaction_count_total[rxnID]--;
|
||
continue;
|
||
}
|
||
}
|
||
|
||
for (int j = 0; j < max_natoms+1; j++)
|
||
update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
|
||
update_num_mega++;
|
||
}
|
||
}
|
||
delete [] iskip;
|
||
|
||
// if inserted atoms and global map exists, reset map now instead
|
||
// of waiting for comm since other pre-exchange fixes may use it
|
||
// invoke map_init() b/c atom count has grown
|
||
// do this once after all atom insertions
|
||
if (inserted_atoms_flag == 1 && atom->map_style != Atom::MAP_NONE) {
|
||
atom->map_init();
|
||
atom->map_set();
|
||
}
|
||
|
||
// mark to-delete atoms
|
||
nlocal = atom->nlocal;
|
||
if (nlocal > nmark) {
|
||
memory->grow(mark,nlocal,"bond/react:mark");
|
||
for (int i = nmark; i < nlocal; i++) mark[i] = 0;
|
||
nmark = nlocal;
|
||
}
|
||
for (int i = 0; i < update_num_mega; i++) {
|
||
rxnID = update_mega_glove[0][i];
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
for (int j = 0; j < onemol->natoms; j++) {
|
||
int iatom = atom->map(update_mega_glove[j+1][i]);
|
||
if (delete_atoms[j][rxnID] == 1 && iatom >= 0 && iatom < nlocal) {
|
||
mark[iatom] = 1;
|
||
}
|
||
}
|
||
}
|
||
|
||
// update charges and types of landlocked atoms
|
||
for (int i = 0; i < update_num_mega; i++) {
|
||
rxnID = update_mega_glove[0][i];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
for (int j = 0; j < twomol->natoms; j++) {
|
||
int jj = equivalences[j][1][rxnID]-1;
|
||
if (atom->map(update_mega_glove[jj+1][i]) >= 0 &&
|
||
atom->map(update_mega_glove[jj+1][i]) < nlocal) {
|
||
if (landlocked_atoms[j][rxnID] == 1)
|
||
type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j];
|
||
if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) {
|
||
double *q = atom->q;
|
||
q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j];
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
int insert_num;
|
||
// very nice and easy to completely overwrite special bond info for landlocked atoms
|
||
for (int i = 0; i < update_num_mega; i++) {
|
||
rxnID = update_mega_glove[0][i];
|
||
onemol = atom->molecules[unreacted_mol[rxnID]];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
for (int j = 0; j < twomol->natoms; j++) {
|
||
int jj = equivalences[j][1][rxnID]-1;
|
||
int ilocal = atom->map(update_mega_glove[jj+1][i]);
|
||
if (ilocal < nlocal && ilocal >= 0) {
|
||
if (landlocked_atoms[j][rxnID] == 1) {
|
||
for (int k = 0; k < 3; k++) {
|
||
nspecial[ilocal][k] = twomol->nspecial[j][k];
|
||
}
|
||
for (int p = 0; p < twomol->nspecial[j][2]; p++) {
|
||
special[ilocal][p] = update_mega_glove[equivalences[twomol->special[j][p]-1][1][rxnID]][i];
|
||
}
|
||
}
|
||
// now delete and replace landlocked atoms from non-landlocked atoms' special info
|
||
// delete 1-2, 1-3, 1-4 specials individually. only delete if special exists in pre-reaction template
|
||
if (landlocked_atoms[j][rxnID] == 0) {
|
||
int ispec, fspec, imolspec, fmolspec, nspecdel[3];
|
||
for (int k = 0; k < 3; k++) nspecdel[k] = 0;
|
||
for (int k = 0; k < atom->maxspecial; k++) delflag[k] = 0;
|
||
for (int specn = 0; specn < 3; specn++) {
|
||
if (specn == 0) {
|
||
imolspec = 0;
|
||
ispec = 0;
|
||
} else {
|
||
imolspec = onemol->nspecial[jj][specn-1];
|
||
ispec = nspecial[ilocal][specn-1];
|
||
}
|
||
fmolspec = onemol->nspecial[jj][specn];
|
||
fspec = nspecial[ilocal][specn];
|
||
for (int k = ispec; k < fspec; k++) {
|
||
for (int p = imolspec; p < fmolspec; p++) {
|
||
if (update_mega_glove[onemol->special[jj][p]][i] == special[ilocal][k]) {
|
||
delflag[k] = 1;
|
||
for (int m = 2; m >= specn; m--) nspecdel[m]++;
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
int incr = 0;
|
||
for (int k = 0; k < nspecial[ilocal][2]; k++)
|
||
if (delflag[k] == 0) special[ilocal][incr++] = special[ilocal][k];
|
||
for (int m = 0; m < 3; m++) nspecial[ilocal][m] -= nspecdel[m];
|
||
// now reassign from reacted template
|
||
for (int k = 0; k < twomol->nspecial[j][2]; k++) {
|
||
if (k > twomol->nspecial[j][1] - 1) {
|
||
insert_num = nspecial[ilocal][2]++;
|
||
} else if (k > twomol->nspecial[j][0] - 1) {
|
||
insert_num = nspecial[ilocal][1]++;
|
||
nspecial[ilocal][2]++;
|
||
} else {
|
||
insert_num = nspecial[ilocal][0]++;
|
||
nspecial[ilocal][1]++;
|
||
nspecial[ilocal][2]++;
|
||
}
|
||
if (nspecial[ilocal][2] > atom->maxspecial)
|
||
error->one(FLERR,"Bond/react special bond generation overflow");
|
||
for (int n = nspecial[ilocal][2]-1; n > insert_num; n--) {
|
||
special[ilocal][n] = special[ilocal][n-1];
|
||
}
|
||
special[ilocal][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// 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]];
|
||
// let's first delete all bond info about landlocked atoms
|
||
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) {
|
||
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++)
|
||
dynamic_cast<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++)
|
||
dynamic_cast<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) {
|
||
for (int p = num_bond[atom->map(update_mega_glove[jj+1][i])]-1; p > -1 ; p--) {
|
||
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)
|
||
dynamic_cast<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)
|
||
dynamic_cast<FixBondHistory *>(ihistory)->shift_history(atom->map(update_mega_glove[jj+1][i]),m,m+1);
|
||
}
|
||
if (n_histories > 0)
|
||
for (auto &ihistory: histories)
|
||
dynamic_cast<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--;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
// now let's add the new bond 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_bond[atom->map(update_mega_glove[jj+1][i])] = twomol->num_bond[j];
|
||
delta_bonds += twomol->num_bond[j];
|
||
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)
|
||
dynamic_cast<FixBondHistory *>(ihistory)->check_cache(atom->map(update_mega_glove[jj+1][i]), p);
|
||
}
|
||
}
|
||
if (landlocked_atoms[j][rxnID] == 0) {
|
||
for (int p = 0; p < twomol->num_bond[j]; p++) {
|
||
if (landlocked_atoms[twomol->bond_atom[j][p]-1][rxnID] == 1) {
|
||
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)
|
||
dynamic_cast<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");
|
||
delta_bonds++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
if (n_histories > 0)
|
||
for (auto &ihistory: histories)
|
||
dynamic_cast<FixBondHistory *>(ihistory)->clear_cache();
|
||
|
||
// Angles! First let's delete all angle info:
|
||
if (force->angle && twomol->angleflag) {
|
||
int *num_angle = atom->num_angle;
|
||
int **angle_type = atom->angle_type;
|
||
tagint **angle_atom1 = atom->angle_atom1;
|
||
tagint **angle_atom2 = atom->angle_atom2;
|
||
tagint **angle_atom3 = atom->angle_atom3;
|
||
|
||
for (int i = 0; i < update_num_mega; i++) {
|
||
rxnID = update_mega_glove[0][i];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
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) {
|
||
delta_angle -= num_angle[atom->map(update_mega_glove[jj+1][i])];
|
||
num_angle[atom->map(update_mega_glove[jj+1][i])] = 0;
|
||
}
|
||
if (landlocked_atoms[j][rxnID] == 0) {
|
||
for (int p = num_angle[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) {
|
||
for (int n = 0; n < twomol->natoms; n++) {
|
||
int nn = equivalences[n][1][rxnID]-1;
|
||
if (n!=j && landlocked_atoms[n][rxnID] == 1 &&
|
||
(angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
|
||
for (int m = p; m < num_angle[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
|
||
angle_type[atom->map(update_mega_glove[jj+1][i])][m] = angle_type[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
angle_atom1[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
angle_atom2[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
angle_atom3[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
}
|
||
num_angle[atom->map(update_mega_glove[jj+1][i])]--;
|
||
delta_angle--;
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
// 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 (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,"Bond/react topology/atom exceed system topology/atom");
|
||
delta_angle++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// Dihedrals! first let's delete all dihedral info for landlocked atoms
|
||
if (force->dihedral && twomol->dihedralflag) {
|
||
int *num_dihedral = atom->num_dihedral;
|
||
int **dihedral_type = atom->dihedral_type;
|
||
tagint **dihedral_atom1 = atom->dihedral_atom1;
|
||
tagint **dihedral_atom2 = atom->dihedral_atom2;
|
||
tagint **dihedral_atom3 = atom->dihedral_atom3;
|
||
tagint **dihedral_atom4 = atom->dihedral_atom4;
|
||
|
||
for (int i = 0; i < update_num_mega; i++) {
|
||
rxnID = update_mega_glove[0][i];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
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) {
|
||
delta_dihed -= num_dihedral[atom->map(update_mega_glove[jj+1][i])];
|
||
num_dihedral[atom->map(update_mega_glove[jj+1][i])] = 0;
|
||
}
|
||
if (landlocked_atoms[j][rxnID] == 0) {
|
||
for (int p = num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) {
|
||
for (int n = 0; n < twomol->natoms; n++) {
|
||
int nn = equivalences[n][1][rxnID]-1;
|
||
if (n!=j && landlocked_atoms[n][rxnID] == 1 &&
|
||
(dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
|
||
for (int m = p; m < num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
|
||
dihedral_type[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_type[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
}
|
||
num_dihedral[atom->map(update_mega_glove[jj+1][i])]--;
|
||
delta_dihed--;
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
// 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 (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,"Bond/react topology/atom exceed system topology/atom");
|
||
delta_dihed++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
// finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms
|
||
if (force->improper && twomol->improperflag) {
|
||
int *num_improper = atom->num_improper;
|
||
int **improper_type = atom->improper_type;
|
||
tagint **improper_atom1 = atom->improper_atom1;
|
||
tagint **improper_atom2 = atom->improper_atom2;
|
||
tagint **improper_atom3 = atom->improper_atom3;
|
||
tagint **improper_atom4 = atom->improper_atom4;
|
||
|
||
for (int i = 0; i < update_num_mega; i++) {
|
||
rxnID = update_mega_glove[0][i];
|
||
twomol = atom->molecules[reacted_mol[rxnID]];
|
||
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) {
|
||
delta_imprp -= num_improper[atom->map(update_mega_glove[jj+1][i])];
|
||
num_improper[atom->map(update_mega_glove[jj+1][i])] = 0;
|
||
}
|
||
if (landlocked_atoms[j][rxnID] == 0) {
|
||
for (int p = num_improper[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) {
|
||
for (int n = 0; n < twomol->natoms; n++) {
|
||
int nn = equivalences[n][1][rxnID]-1;
|
||
if (n!=j && landlocked_atoms[n][rxnID] == 1 &&
|
||
(improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
|
||
improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
|
||
for (int m = p; m < num_improper[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
|
||
improper_type[atom->map(update_mega_glove[jj+1][i])][m] = improper_type[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
improper_atom1[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
improper_atom2[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
improper_atom3[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
improper_atom4[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom4[atom->map(update_mega_glove[jj+1][i])][m+1];
|
||
}
|
||
num_improper[atom->map(update_mega_glove[jj+1][i])]--;
|
||
delta_imprp--;
|
||
break;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
// 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 (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,"Bond/react topology/atom exceed system topology/atom");
|
||
delta_imprp++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
}
|
||
|
||
memory->destroy(update_mega_glove);
|
||
|
||
// delete atoms. taken from fix_evaporate. but don't think it needs to be in pre_exchange
|
||
// loop in reverse order to avoid copying marked atoms
|
||
ndel = ndelone = 0;
|
||
for (int i = atom->nlocal-1; i >= 0; i--) {
|
||
if (mark[i] == 1) {
|
||
avec->copy(atom->nlocal-1,i,1);
|
||
atom->nlocal--;
|
||
ndelone++;
|
||
|
||
if (atom->avec->bonds_allow) {
|
||
if (force->newton_bond) delta_bonds += atom->num_bond[i];
|
||
else {
|
||
for (int j = 0; j < atom->num_bond[i]; j++) {
|
||
if (tag[i] < atom->bond_atom[i][j]) delta_bonds++;
|
||
}
|
||
}
|
||
}
|
||
if (atom->avec->angles_allow) {
|
||
if (force->newton_bond) delta_angle += atom->num_angle[i];
|
||
else {
|
||
for (int j = 0; j < atom->num_angle[i]; j++) {
|
||
int m = atom->map(atom->angle_atom2[i][j]);
|
||
if (m >= 0 && m < nlocal) delta_angle++;
|
||
}
|
||
}
|
||
}
|
||
if (atom->avec->dihedrals_allow) {
|
||
if (force->newton_bond) delta_dihed += atom->num_dihedral[i];
|
||
else {
|
||
for (int j = 0; j < atom->num_dihedral[i]; j++) {
|
||
int m = atom->map(atom->dihedral_atom2[i][j]);
|
||
if (m >= 0 && m < nlocal) delta_dihed++;
|
||
}
|
||
}
|
||
}
|
||
if (atom->avec->impropers_allow) {
|
||
if (force->newton_bond) delta_imprp += atom->num_improper[i];
|
||
else {
|
||
for (int j = 0; j < atom->num_improper[i]; j++) {
|
||
int m = atom->map(atom->improper_atom2[i][j]);
|
||
if (m >= 0 && m < nlocal) delta_imprp++;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
}
|
||
memory->destroy(mark);
|
||
memory->destroy(delflag);
|
||
|
||
MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world);
|
||
|
||
atom->natoms -= ndel;
|
||
// done deleting atoms
|
||
|
||
// reset mol ids
|
||
if (reset_mol_ids_flag) reset_mol_ids->reset();
|
||
|
||
// something to think about: this could done much more concisely if
|
||
// all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG
|
||
|
||
int Tdelta_bonds;
|
||
MPI_Allreduce(&delta_bonds,&Tdelta_bonds,1,MPI_INT,MPI_SUM,world);
|
||
atom->nbonds += Tdelta_bonds;
|
||
|
||
int Tdelta_angle;
|
||
MPI_Allreduce(&delta_angle,&Tdelta_angle,1,MPI_INT,MPI_SUM,world);
|
||
atom->nangles += Tdelta_angle;
|
||
|
||
int Tdelta_dihed;
|
||
MPI_Allreduce(&delta_dihed,&Tdelta_dihed,1,MPI_INT,MPI_SUM,world);
|
||
atom->ndihedrals += Tdelta_dihed;
|
||
|
||
int Tdelta_imprp;
|
||
MPI_Allreduce(&delta_imprp,&Tdelta_imprp,1,MPI_INT,MPI_SUM,world);
|
||
atom->nimpropers += Tdelta_imprp;
|
||
|
||
if (ndel && (atom->map_style != Atom::MAP_NONE)) {
|
||
atom->nghost = 0;
|
||
atom->map_init();
|
||
atom->map_set();
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
insert created atoms
|
||
------------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
|
||
{
|
||
// inserting atoms based off fix_deposit->pre_exchange
|
||
int flag;
|
||
imageint *imageflags;
|
||
double **coords,lamda[3],rotmat[3][3];
|
||
double *newcoord;
|
||
double **v = atom->v;
|
||
double t,delx,dely,delz,rsq;
|
||
|
||
memory->create(coords,twomol->natoms,3,"bond/react:coords");
|
||
memory->create(imageflags,twomol->natoms,"bond/react:imageflags");
|
||
|
||
double *sublo,*subhi;
|
||
if (domain->triclinic == 0) {
|
||
sublo = domain->sublo;
|
||
subhi = domain->subhi;
|
||
} else {
|
||
sublo = domain->sublo_lamda;
|
||
subhi = domain->subhi_lamda;
|
||
}
|
||
|
||
// find current max atom and molecule IDs
|
||
tagint *tag = atom->tag;
|
||
double **x = atom->x;
|
||
tagint *molecule = atom->molecule;
|
||
int nlocal = atom->nlocal;
|
||
|
||
tagint maxtag_all,maxmol_all;
|
||
tagint max = 0;
|
||
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
|
||
MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
|
||
|
||
max = 0;
|
||
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
|
||
MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
|
||
|
||
int dimension = domain->dimension;
|
||
|
||
// only proc that owns reacting atom (use ibonding),
|
||
// fits post-reaction template to reaction site, for creating atoms
|
||
int n2superpose = 0;
|
||
for (int j = 0; j < twomol->natoms; j++) {
|
||
if (modify_create_fragid[rxnID] >= 0)
|
||
if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
|
||
if (!create_atoms[j][rxnID] && !delete_atoms[equivalences[j][1][rxnID]][rxnID])
|
||
n2superpose++;
|
||
}
|
||
|
||
int ifit = atom->map(my_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc
|
||
Superpose3D<double, double **> superposer(n2superpose);
|
||
int fitroot = 0;
|
||
if (ifit >= 0 && ifit < atom->nlocal) {
|
||
fitroot = me;
|
||
|
||
// get 'temperatere' averaged over site, used for created atoms' vels
|
||
t = get_temperature(my_mega_glove,1,iupdate);
|
||
|
||
double **xfrozen; // coordinates for the "frozen" target molecule
|
||
double **xmobile; // coordinates for the "mobile" molecule
|
||
memory->create(xfrozen,n2superpose,3,"bond/react:xfrozen");
|
||
memory->create(xmobile,n2superpose,3,"bond/react:xmobile");
|
||
tagint iatom;
|
||
tagint iref = -1; // choose first atom as reference
|
||
int fit_incr = 0;
|
||
for (int j = 0; j < twomol->natoms; j++) {
|
||
if (modify_create_fragid[rxnID] >= 0)
|
||
if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
|
||
int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index
|
||
if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) {
|
||
if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) {
|
||
printf("WARNING: eligible atoms skipped for created-atoms fit on %d\n",me);
|
||
continue;
|
||
}
|
||
iatom = atom->map(my_mega_glove[ipre+1][iupdate]);
|
||
if (iref == -1) iref = iatom;
|
||
iatom = domain->closest_image(iref,iatom);
|
||
for (int k = 0; k < 3; k++) {
|
||
xfrozen[fit_incr][k] = x[iatom][k];
|
||
xmobile[fit_incr][k] = twomol->x[j][k];
|
||
}
|
||
fit_incr++;
|
||
}
|
||
}
|
||
superposer.Superpose(xfrozen, xmobile);
|
||
for (int i = 0; i < 3; i++)
|
||
for (int j = 0; j < 3; j++)
|
||
rotmat[i][j] = superposer.R[i][j];
|
||
memory->destroy(xfrozen);
|
||
memory->destroy(xmobile);
|
||
}
|
||
MPI_Allreduce(MPI_IN_PLACE,&fitroot,1,MPI_INT,MPI_SUM,world);
|
||
MPI_Bcast(&t,1,MPI_DOUBLE,fitroot,world);
|
||
|
||
// get coordinates and image flags
|
||
for (int m = 0; m < twomol->natoms; m++) {
|
||
if (create_atoms[m][rxnID] == 1) {
|
||
// apply optimal rotation/translation for created atom coords
|
||
// also map coords back into simulation box
|
||
if (fitroot == me) {
|
||
MathExtra::matvec(rotmat,twomol->x[m],coords[m]);
|
||
for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i];
|
||
imageflags[m] = atom->image[ifit];
|
||
domain->remap(coords[m],imageflags[m]);
|
||
}
|
||
MPI_Bcast(&imageflags[m],1,MPI_LMP_IMAGEINT,fitroot,world);
|
||
MPI_Bcast(coords[m],3,MPI_DOUBLE,fitroot,world);
|
||
}
|
||
}
|
||
|
||
// check distance between any existing atom and inserted atom
|
||
// if less than near, abort
|
||
if (overlapsq[rxnID] > 0) {
|
||
int abortflag = 0;
|
||
for (int m = 0; m < twomol->natoms; m++) {
|
||
if (create_atoms[m][rxnID] == 1) {
|
||
for (int i = 0; i < nlocal; i++) {
|
||
delx = coords[m][0] - x[i][0];
|
||
dely = coords[m][1] - x[i][1];
|
||
delz = coords[m][2] - x[i][2];
|
||
domain->minimum_image(delx,dely,delz);
|
||
rsq = delx*delx + dely*dely + delz*delz;
|
||
if (rsq < overlapsq[rxnID]) {
|
||
abortflag = 1;
|
||
break;
|
||
}
|
||
}
|
||
if (abortflag) break;
|
||
}
|
||
}
|
||
MPI_Allreduce(MPI_IN_PLACE,&abortflag,1,MPI_INT,MPI_MAX,world);
|
||
if (abortflag) {
|
||
memory->destroy(coords);
|
||
memory->destroy(imageflags);
|
||
return 0;
|
||
}
|
||
}
|
||
|
||
// clear ghost count and any ghost bonus data internal to AtomVec
|
||
// same logic as beginning of Comm::exchange()
|
||
// do it now b/c inserting atoms will overwrite ghost atoms
|
||
atom->nghost = 0;
|
||
atom->avec->clear_bonus();
|
||
|
||
// check if new atoms are in my sub-box or above it if I am highest proc
|
||
// if so, add atom to my list via create_atom()
|
||
// initialize additional info about the atoms
|
||
// set group mask to "all" plus fix group
|
||
int preID; // new equivalences index
|
||
int add_count = 0;
|
||
for (int m = 0; m < twomol->natoms; m++) {
|
||
if (create_atoms[m][rxnID] == 1) {
|
||
// increase atom count
|
||
add_count++;
|
||
preID = onemol->natoms+add_count;
|
||
|
||
if (domain->triclinic) {
|
||
domain->x2lamda(coords[m],lamda);
|
||
newcoord = lamda;
|
||
} else newcoord = coords[m];
|
||
|
||
flag = 0;
|
||
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
|
||
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
|
||
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
|
||
else if (dimension == 3 && newcoord[2] >= domain->boxhi[2]) {
|
||
if (comm->layout != Comm::LAYOUT_TILED) {
|
||
if (comm->myloc[2] == comm->procgrid[2]-1 &&
|
||
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
|
||
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
|
||
} else {
|
||
if (comm->mysplit[2][1] == 1.0 &&
|
||
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
|
||
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
|
||
}
|
||
} else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) {
|
||
if (comm->layout != Comm::LAYOUT_TILED) {
|
||
if (comm->myloc[1] == comm->procgrid[1]-1 &&
|
||
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
|
||
} else {
|
||
if (comm->mysplit[1][1] == 1.0 &&
|
||
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
|
||
}
|
||
}
|
||
|
||
int root = 0;
|
||
if (flag) {
|
||
root = me;
|
||
|
||
atom->avec->create_atom(twomol->type[m],coords[m]);
|
||
int n = atom->nlocal - 1;
|
||
atom->tag[n] = maxtag_all + add_count;
|
||
|
||
// locally update mega_glove
|
||
my_mega_glove[preID][iupdate] = atom->tag[n];
|
||
|
||
if (atom->molecule_flag) {
|
||
if (twomol->moleculeflag) {
|
||
atom->molecule[n] = maxmol_all + twomol->molecule[m];
|
||
} else {
|
||
atom->molecule[n] = maxmol_all + 1;
|
||
}
|
||
}
|
||
|
||
atom->mask[n] = 1 | groupbit;
|
||
atom->image[n] = imageflags[m];
|
||
|
||
// 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]]);
|
||
v[n][0] = random[rxnID]->uniform();
|
||
v[n][1] = random[rxnID]->uniform();
|
||
v[n][2] = random[rxnID]->uniform();
|
||
double vnorm = sqrt(v[n][0]*v[n][0] + v[n][1]*v[n][1] + v[n][2]*v[n][2]);
|
||
v[n][0] = v[n][0]/vnorm*vtnorm;
|
||
v[n][1] = v[n][1]/vnorm*vtnorm;
|
||
v[n][2] = v[n][2]/vnorm*vtnorm;
|
||
modify->create_attribute(n);
|
||
|
||
// initialize group statuses
|
||
// why aren't these more global...
|
||
int flag,cols;
|
||
int index1 = atom->find_custom("limit_tags",flag,cols);
|
||
int *i_limit_tags = atom->ivector[index1];
|
||
|
||
int *i_statted_tags;
|
||
if (stabilization_flag == 1) {
|
||
int index2 = atom->find_custom(statted_id,flag,cols);
|
||
i_statted_tags = atom->ivector[index2];
|
||
}
|
||
|
||
int index3 = atom->find_custom("react_tags",flag,cols);
|
||
int *i_react_tags = atom->ivector[index3];
|
||
|
||
i_limit_tags[n] = update->ntimestep + 1;
|
||
if (stabilization_flag == 1) i_statted_tags[n] = 0;
|
||
i_react_tags[n] = rxnID;
|
||
}
|
||
// globally update mega_glove and equivalences
|
||
MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world);
|
||
MPI_Bcast(&my_mega_glove[preID][iupdate],1,MPI_LMP_TAGINT,root,world);
|
||
equivalences[m][0][rxnID] = m+1;
|
||
equivalences[m][1][rxnID] = preID;
|
||
reverse_equiv[preID-1][0][rxnID] = preID;
|
||
reverse_equiv[preID-1][1][rxnID] = m+1;
|
||
}
|
||
}
|
||
|
||
// reset global natoms here
|
||
// reset atom map elsewhere, after all calls to 'insert_atoms'
|
||
atom->natoms += add_count;
|
||
if (atom->natoms < 0)
|
||
error->all(FLERR,"Too many total atoms");
|
||
maxtag_all += add_count;
|
||
if (maxtag_all >= MAXTAGINT)
|
||
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
|
||
// atom creation successful
|
||
memory->destroy(coords);
|
||
memory->destroy(imageflags);
|
||
return 1;
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
read superimpose file
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::read(int myrxn)
|
||
{
|
||
char line[MAXLINE],keyword[MAXLINE];
|
||
char *eof,*ptr;
|
||
|
||
// skip 1st line of file
|
||
eof = fgets(line,MAXLINE,fp);
|
||
if (eof == nullptr) error->one(FLERR,"Bond/react: Unexpected end of superimpose file");
|
||
|
||
// read header lines
|
||
// skip blank lines or lines that start with "#"
|
||
// stop when read an unrecognized line
|
||
|
||
ncreate = 0;
|
||
while (true) {
|
||
|
||
readline(line);
|
||
|
||
// trim anything from '#' onward
|
||
// if line is blank, continue
|
||
|
||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||
if (strspn(line," \t\n\r") == strlen(line)) continue;
|
||
|
||
if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
|
||
else if (strstr(line,"equivalences")) {
|
||
sscanf(line,"%d",&nequivalent);
|
||
if (nequivalent != onemol->natoms)
|
||
error->one(FLERR,"Bond/react: Number of equivalences in map file must "
|
||
"equal number of atoms in reaction templates");
|
||
}
|
||
else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
|
||
else if (strstr(line,"createIDs")) sscanf(line,"%d",&ncreate);
|
||
else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral);
|
||
else if (strstr(line,"constraints")) {
|
||
sscanf(line,"%d",&nconstraints[myrxn]);
|
||
if (maxnconstraints < nconstraints[myrxn]) maxnconstraints = nconstraints[myrxn];
|
||
constraints.resize(maxnconstraints, std::vector<Constraint>(nreacts));
|
||
} else break;
|
||
}
|
||
|
||
// grab keyword and skip next line
|
||
|
||
parse_keyword(0,line,keyword);
|
||
readline(line);
|
||
|
||
// loop over sections of superimpose file
|
||
|
||
int equivflag = 0, bondflag = 0;
|
||
while (strlen(keyword)) {
|
||
if (strcmp(keyword,"InitiatorIDs") == 0 || strcmp(keyword,"BondingIDs") == 0) {
|
||
if (strcmp(keyword,"BondingIDs") == 0)
|
||
if (me == 0) error->warning(FLERR,"Bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead.");
|
||
bondflag = 1;
|
||
readline(line);
|
||
sscanf(line,"%d",&ibonding[myrxn]);
|
||
if (ibonding[myrxn] > onemol->natoms)
|
||
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
readline(line);
|
||
sscanf(line,"%d",&jbonding[myrxn]);
|
||
if (jbonding[myrxn] > onemol->natoms)
|
||
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
} else if (strcmp(keyword,"EdgeIDs") == 0) {
|
||
EdgeIDs(line, myrxn);
|
||
} else if (strcmp(keyword,"Equivalences") == 0) {
|
||
equivflag = 1;
|
||
Equivalences(line, myrxn);
|
||
} else if (strcmp(keyword,"DeleteIDs") == 0) {
|
||
DeleteAtoms(line, myrxn);
|
||
} else if (strcmp(keyword,"CreateIDs") == 0) {
|
||
CreateAtoms(line, myrxn);
|
||
} else if (strcmp(keyword,"ChiralIDs") == 0) {
|
||
ChiralCenters(line, myrxn);
|
||
} else if (strcmp(keyword,"Constraints") == 0) {
|
||
ReadConstraints(line, myrxn);
|
||
} else error->one(FLERR,"Bond/react: Unknown section in map file");
|
||
|
||
parse_keyword(1,line,keyword);
|
||
|
||
}
|
||
|
||
// error check
|
||
if (bondflag == 0 || equivflag == 0)
|
||
error->all(FLERR,"Bond/react: Map file missing InitiatorIDs or Equivalences section\n");
|
||
}
|
||
|
||
void FixBondReact::EdgeIDs(char *line, int myrxn)
|
||
{
|
||
// puts a 1 at edge(edgeID)
|
||
|
||
int tmp;
|
||
for (int i = 0; i < nedge; i++) {
|
||
readline(line);
|
||
sscanf(line,"%d",&tmp);
|
||
if (tmp > onemol->natoms)
|
||
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
edge[tmp-1][myrxn] = 1;
|
||
}
|
||
}
|
||
|
||
void FixBondReact::Equivalences(char *line, int myrxn)
|
||
{
|
||
int tmp1;
|
||
int tmp2;
|
||
for (int i = 0; i < nequivalent; i++) {
|
||
readline(line);
|
||
sscanf(line,"%d %d",&tmp1,&tmp2);
|
||
if (tmp1 > onemol->natoms || tmp2 > twomol->natoms)
|
||
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
//equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted
|
||
equivalences[tmp2-1][0][myrxn] = tmp2;
|
||
equivalences[tmp2-1][1][myrxn] = tmp1;
|
||
//reverse_equiv is-> clmn 1: pre-reacted, clmn 2: post-reacted
|
||
reverse_equiv[tmp1-1][0][myrxn] = tmp1;
|
||
reverse_equiv[tmp1-1][1][myrxn] = tmp2;
|
||
}
|
||
}
|
||
|
||
void FixBondReact::DeleteAtoms(char *line, int myrxn)
|
||
{
|
||
int tmp;
|
||
for (int i = 0; i < ndelete; i++) {
|
||
readline(line);
|
||
sscanf(line,"%d",&tmp);
|
||
if (tmp > onemol->natoms)
|
||
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
delete_atoms[tmp-1][myrxn] = 1;
|
||
}
|
||
}
|
||
|
||
void FixBondReact::CreateAtoms(char *line, int myrxn)
|
||
{
|
||
create_atoms_flag[myrxn] = 1;
|
||
int tmp;
|
||
for (int i = 0; i < ncreate; i++) {
|
||
readline(line);
|
||
sscanf(line,"%d",&tmp);
|
||
create_atoms[tmp-1][myrxn] = 1;
|
||
}
|
||
}
|
||
|
||
void FixBondReact::CustomCharges(int ifragment, int myrxn)
|
||
{
|
||
for (int i = 0; i < onemol->natoms; i++)
|
||
if (onemol->fragmentmask[ifragment][i])
|
||
custom_charges[i][myrxn] = 1;
|
||
else
|
||
custom_charges[i][myrxn] = 0;
|
||
}
|
||
|
||
void FixBondReact::ChiralCenters(char *line, int myrxn)
|
||
{
|
||
int tmp;
|
||
for (int i = 0; i < nchiral; i++) {
|
||
readline(line);
|
||
sscanf(line,"%d",&tmp);
|
||
if (tmp > onemol->natoms)
|
||
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
chiral_atoms[tmp-1][0][myrxn] = 1;
|
||
if (onemol->xflag == 0)
|
||
error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
|
||
if ((int) onemol_nxspecial[tmp-1][0] != 4)
|
||
error->one(FLERR,"Bond/react: Chiral atoms must have exactly four first neighbors");
|
||
for (int j = 0; j < 4; j++) {
|
||
for (int k = j+1; k < 4; k++) {
|
||
if (onemol->type[onemol_xspecial[tmp-1][j]-1] ==
|
||
onemol->type[onemol_xspecial[tmp-1][k]-1])
|
||
error->one(FLERR,"Bond/react: First neighbors of chiral atoms must be of mutually different types");
|
||
}
|
||
}
|
||
// record order of atom types, and coords
|
||
double my4coords[12];
|
||
for (int j = 0; j < 4; j++) {
|
||
chiral_atoms[tmp-1][j+2][myrxn] = onemol->type[onemol_xspecial[tmp-1][j]-1];
|
||
for (int k = 0; k < 3; k++) {
|
||
my4coords[3*j+k] = onemol->x[onemol_xspecial[tmp-1][j]-1][k];
|
||
}
|
||
}
|
||
// get orientation
|
||
chiral_atoms[tmp-1][1][myrxn] = get_chirality(my4coords);
|
||
}
|
||
}
|
||
|
||
void FixBondReact::ReadConstraints(char *line, int myrxn)
|
||
{
|
||
double tmp[MAXCONARGS];
|
||
char **strargs,*ptr,*lptr;
|
||
memory->create(strargs,MAXCONARGS,MAXLINE,"bond/react:strargs");
|
||
auto constraint_type = new char[MAXLINE];
|
||
strcpy(constraintstr[myrxn],"("); // string for boolean constraint logic
|
||
for (int i = 0; i < nconstraints[myrxn]; i++) {
|
||
readline(line);
|
||
// find left parentheses, add to constraintstr, and update line
|
||
for (int j = 0; j < strlen(line); j++) {
|
||
if (line[j] == '(') strcat(constraintstr[myrxn],"(");
|
||
if (isalpha(line[j])) {
|
||
line = line + j;
|
||
break;
|
||
}
|
||
}
|
||
// 'C' indicates where to sub in next constraint
|
||
strcat(constraintstr[myrxn],"C");
|
||
// special consideration for 'custom' constraint
|
||
// find final double quote, or skip two words
|
||
lptr = line;
|
||
if ((ptr = strrchr(lptr,'\"'))) lptr = ptr+1;
|
||
else {
|
||
while (lptr[0] != ' ') lptr++; // skip first 'word'
|
||
while (lptr[0] == ' ' || lptr[0] == '\t') lptr++; // skip blanks
|
||
while (lptr[0] != ' ') lptr++; // skip second 'word'
|
||
}
|
||
// find right parentheses
|
||
for (int j = 0; j < strlen(lptr); j++)
|
||
if (lptr[j] == ')') strcat(constraintstr[myrxn],")");
|
||
// find logic symbols, and trim line via ptr
|
||
if ((ptr = strstr(lptr,"&&"))) {
|
||
strcat(constraintstr[myrxn],"&&");
|
||
*ptr = '\0';
|
||
} else if ((ptr = strstr(lptr,"||"))) {
|
||
strcat(constraintstr[myrxn],"||");
|
||
*ptr = '\0';
|
||
} else if (i+1 < nconstraints[myrxn]) {
|
||
strcat(constraintstr[myrxn],"&&");
|
||
}
|
||
if ((ptr = strchr(lptr,')')))
|
||
*ptr = '\0';
|
||
sscanf(line,"%s",constraint_type);
|
||
if (strcmp(constraint_type,"distance") == 0) {
|
||
constraints[i][myrxn].type = DISTANCE;
|
||
sscanf(line,"%*s %s %s %lg %lg",strargs[0],strargs[1],&tmp[0],&tmp[1]);
|
||
readID(strargs[0], i, myrxn, 0);
|
||
readID(strargs[1], i, myrxn, 1);
|
||
// cutoffs
|
||
constraints[i][myrxn].par[0] = tmp[0]*tmp[0]; // using square of distance
|
||
constraints[i][myrxn].par[1] = tmp[1]*tmp[1];
|
||
} else if (strcmp(constraint_type,"angle") == 0) {
|
||
constraints[i][myrxn].type = ANGLE;
|
||
sscanf(line,"%*s %s %s %s %lg %lg",strargs[0],strargs[1],strargs[2],&tmp[0],&tmp[1]);
|
||
readID(strargs[0], i, myrxn, 0);
|
||
readID(strargs[1], i, myrxn, 1);
|
||
readID(strargs[2], i, myrxn, 2);
|
||
constraints[i][myrxn].par[0] = tmp[0]/180.0 * MY_PI;
|
||
constraints[i][myrxn].par[1] = tmp[1]/180.0 * MY_PI;
|
||
} else if (strcmp(constraint_type,"dihedral") == 0) {
|
||
constraints[i][myrxn].type = DIHEDRAL;
|
||
tmp[2] = 181.0; // impossible range
|
||
tmp[3] = 182.0;
|
||
sscanf(line,"%*s %s %s %s %s %lg %lg %lg %lg",strargs[0],strargs[1],
|
||
strargs[2],strargs[3],&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
|
||
readID(strargs[0], i, myrxn, 0);
|
||
readID(strargs[1], i, myrxn, 1);
|
||
readID(strargs[2], i, myrxn, 2);
|
||
readID(strargs[3], i, myrxn, 3);
|
||
constraints[i][myrxn].par[0] = tmp[0]/180.0 * MY_PI;
|
||
constraints[i][myrxn].par[1] = tmp[1]/180.0 * MY_PI;
|
||
constraints[i][myrxn].par[2] = tmp[2]/180.0 * MY_PI;
|
||
constraints[i][myrxn].par[3] = tmp[3]/180.0 * MY_PI;
|
||
} else if (strcmp(constraint_type,"arrhenius") == 0) {
|
||
constraints[i][myrxn].type = ARRHENIUS;
|
||
constraints[i][myrxn].par[0] = narrhenius++;
|
||
sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
|
||
constraints[i][myrxn].par[1] = tmp[0];
|
||
constraints[i][myrxn].par[2] = tmp[1];
|
||
constraints[i][myrxn].par[3] = tmp[2];
|
||
constraints[i][myrxn].par[4] = tmp[3];
|
||
} else if (strcmp(constraint_type,"rmsd") == 0) {
|
||
constraints[i][myrxn].type = RMSD;
|
||
strcpy(strargs[0],"0");
|
||
sscanf(line,"%*s %lg %s",&tmp[0],strargs[0]);
|
||
constraints[i][myrxn].par[0] = tmp[0]; // RMSDmax
|
||
constraints[i][myrxn].id[0] = -1; // optional molecule fragment
|
||
if (isalpha(strargs[0][0])) {
|
||
int ifragment = onemol->findfragment(strargs[0]);
|
||
if (ifragment < 0) error->one(FLERR,"Bond/react: Molecule fragment does not exist");
|
||
else constraints[i][myrxn].id[0] = ifragment;
|
||
}
|
||
} else if (strcmp(constraint_type,"custom") == 0) {
|
||
constraints[i][myrxn].type = CUSTOM;
|
||
std::vector<std::string> args = utils::split_words(line);
|
||
constraints[i][myrxn].str = args[1];
|
||
} else error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
|
||
}
|
||
strcat(constraintstr[myrxn],")"); // close boolean constraint logic string
|
||
delete [] constraint_type;
|
||
memory->destroy(strargs);
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
if ID starts with character, assume it is a pre-reaction molecule fragment ID
|
||
otherwise, it is a pre-reaction atom ID
|
||
---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::readID(char *strarg, int iconstr, int myrxn, int i)
|
||
{
|
||
if (isalpha(strarg[0])) {
|
||
constraints[iconstr][myrxn].idtype[i] = FRAG; // fragment vs. atom ID flag
|
||
int ifragment = onemol->findfragment(strarg);
|
||
if (ifragment < 0) error->one(FLERR,"Bond/react: Molecule fragment does not exist");
|
||
constraints[iconstr][myrxn].id[i] = ifragment;
|
||
} else {
|
||
constraints[iconstr][myrxn].idtype[i] = ATOM; // fragment vs. atom ID flag
|
||
int iatom = atoi(strarg);
|
||
if (iatom > onemol->natoms) error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
|
||
constraints[iconstr][myrxn].id[i] = iatom;
|
||
}
|
||
}
|
||
|
||
void FixBondReact::open(char *file)
|
||
{
|
||
fp = fopen(file,"r");
|
||
if (fp == nullptr) {
|
||
char str[128];
|
||
snprintf(str,128,"Bond/react: Cannot open map file %s",file);
|
||
error->one(FLERR,str);
|
||
}
|
||
}
|
||
|
||
void FixBondReact::readline(char *line)
|
||
{
|
||
int n;
|
||
if (me == 0) {
|
||
if (fgets(line,MAXLINE,fp) == nullptr) n = 0;
|
||
else n = strlen(line) + 1;
|
||
}
|
||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||
if (n == 0) error->all(FLERR,"Bond/react: Unexpected end of map file");
|
||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||
}
|
||
|
||
void FixBondReact::parse_keyword(int flag, char *line, char *keyword)
|
||
{
|
||
if (flag) {
|
||
|
||
// read upto non-blank line plus 1 following line
|
||
// eof is set to 1 if any read hits end-of-file
|
||
|
||
int eof = 0;
|
||
if (me == 0) {
|
||
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
|
||
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
|
||
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
|
||
}
|
||
if (fgets(keyword,MAXLINE,fp) == nullptr) eof = 1;
|
||
}
|
||
|
||
// if eof, set keyword empty and return
|
||
|
||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||
if (eof) {
|
||
keyword[0] = '\0';
|
||
return;
|
||
}
|
||
|
||
// bcast keyword line to all procs
|
||
|
||
int n;
|
||
if (me == 0) n = strlen(line) + 1;
|
||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||
}
|
||
|
||
// copy non-whitespace portion of line into keyword
|
||
|
||
int start = strspn(line," \t\n\r");
|
||
int stop = strlen(line) - 1;
|
||
while (line[stop] == ' ' || line[stop] == '\t'
|
||
|| line[stop] == '\n' || line[stop] == '\r') stop--;
|
||
line[stop+1] = '\0';
|
||
strcpy(keyword,&line[start]);
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
double FixBondReact::compute_vector(int n)
|
||
{
|
||
// now we print just the totals for each reaction instance
|
||
return (double) reaction_count_total[n];
|
||
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::post_integrate_respa(int ilevel, int /*iloop*/)
|
||
{
|
||
if (ilevel == nlevels_respa-1) post_integrate();
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
|
||
int /*pbc_flag*/, int * /*pbc*/)
|
||
{
|
||
int i,j,k,m,ns;
|
||
|
||
m = 0;
|
||
|
||
if (commflag == 1) {
|
||
for (i = 0; i < n; i++) {
|
||
j = list[i];
|
||
for (k = 0; k < ncustomvars; k++)
|
||
buf[m++] = vvec[j][k];
|
||
}
|
||
return m;
|
||
}
|
||
|
||
if (commflag == 2) {
|
||
for (i = 0; i < n; i++) {
|
||
j = list[i];
|
||
buf[m++] = ubuf(partner[j]).d;
|
||
}
|
||
return m;
|
||
}
|
||
|
||
m = 0;
|
||
for (i = 0; i < n; i++) {
|
||
j = list[i];
|
||
buf[m++] = ubuf(finalpartner[j]).d;
|
||
ns = nxspecial[j][0];
|
||
buf[m++] = ubuf(ns).d;
|
||
for (k = 0; k < ns; k++)
|
||
buf[m++] = ubuf(xspecial[j][k]).d;
|
||
}
|
||
return m;
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::unpack_forward_comm(int n, int first, double *buf)
|
||
{
|
||
int i,j,k,m,ns,last;
|
||
|
||
m = 0;
|
||
last = first + n;
|
||
|
||
if (commflag == 1) {
|
||
for (i = first; i < last; i++)
|
||
for (k = 0; k < ncustomvars; k++)
|
||
vvec[i][k] = buf[m++];
|
||
} else if (commflag == 2) {
|
||
for (i = first; i < last; i++)
|
||
partner[i] = (tagint) ubuf(buf[m++]).i;
|
||
} else {
|
||
m = 0;
|
||
last = first + n;
|
||
for (i = first; i < last; i++) {
|
||
finalpartner[i] = (tagint) ubuf(buf[m++]).i;
|
||
ns = (int) ubuf(buf[m++]).i;
|
||
nxspecial[i][0] = ns;
|
||
for (j = 0; j < ns; j++)
|
||
xspecial[i][j] = (tagint) ubuf(buf[m++]).i;
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
int FixBondReact::pack_reverse_comm(int n, int first, double *buf)
|
||
{
|
||
int i,m,last;
|
||
|
||
m = 0;
|
||
last = first + n;
|
||
|
||
for (i = first; i < last; i++) {
|
||
buf[m++] = ubuf(partner[i]).d;
|
||
if (closeneigh[rxnID] != 0)
|
||
buf[m++] = distsq[i][1];
|
||
else
|
||
buf[m++] = distsq[i][0];
|
||
}
|
||
return m;
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
|
||
{
|
||
int i,j,m;
|
||
|
||
m = 0;
|
||
|
||
for (i = 0; i < n; i++) {
|
||
j = list[i];
|
||
if (closeneigh[rxnID] != 0) {
|
||
if (buf[m+1] < distsq[j][1]) {
|
||
partner[j] = (tagint) ubuf(buf[m++]).i;
|
||
distsq[j][1] = buf[m++];
|
||
} else m += 2;
|
||
} else {
|
||
if (buf[m+1] > distsq[j][0]) {
|
||
partner[j] = (tagint) ubuf(buf[m++]).i;
|
||
distsq[j][0] = buf[m++];
|
||
} else m += 2;
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
write Set data to restart file
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::write_restart(FILE *fp)
|
||
{
|
||
set[0].nreacts = nreacts;
|
||
for (int i = 0; i < nreacts; i++) {
|
||
set[i].reaction_count_total = reaction_count_total[i];
|
||
strncpy(set[i].rxn_name,rxn_name[i],MAXLINE);
|
||
set[i].rxn_name[MAXLINE-1] = '\0';
|
||
}
|
||
|
||
if (me == 0) {
|
||
int size = nreacts*sizeof(Set);
|
||
fwrite(&size,sizeof(int),1,fp);
|
||
fwrite(set,sizeof(Set),nreacts,fp);
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
use selected state info from restart file to restart the Fix
|
||
------------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::restart(char *buf)
|
||
{
|
||
Set *set_restart = (Set *) buf;
|
||
for (int i = 0; i < set_restart[0].nreacts; i++) {
|
||
for (int j = 0; j < nreacts; j++) {
|
||
if (strcmp(set_restart[i].rxn_name,rxn_name[j]) == 0) {
|
||
reaction_count_total[j] = set_restart[i].reaction_count_total;
|
||
}
|
||
}
|
||
}
|
||
}
|
||
|
||
/* ----------------------------------------------------------------------
|
||
memory usage of local atom-based arrays
|
||
------------------------------------------------------------------------- */
|
||
|
||
double FixBondReact::memory_usage()
|
||
{
|
||
int nmax = atom->nmax;
|
||
double bytes = (double)nmax * sizeof(int);
|
||
bytes = 2*nmax * sizeof(tagint);
|
||
bytes += (double)nmax * sizeof(double);
|
||
return bytes;
|
||
}
|
||
|
||
/* ---------------------------------------------------------------------- */
|
||
|
||
void FixBondReact::print_bb()
|
||
{
|
||
#if 0
|
||
//fix bond/create cargo code. eg nbonds needs to be added
|
||
|
||
for (int i = 0; i < atom->nlocal; i++) {
|
||
// printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
|
||
for (int j = 0; j < atom->num_bond[i]; j++) {
|
||
// printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]);
|
||
}
|
||
// printf("\n");
|
||
// printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
|
||
for (int j = 0; j < atom->num_angle[i]; j++) {
|
||
// printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
|
||
atom->angle_atom1[i][j], atom->angle_atom2[i][j],
|
||
atom->angle_atom3[i][j]);
|
||
}
|
||
// printf("\n");
|
||
// printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
|
||
for (int j = 0; j < atom->num_dihedral[i]; j++) {
|
||
// printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
|
||
TAGINT_FORMAT ",", atom->dihedral_atom1[i][j],
|
||
atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
|
||
atom->dihedral_atom4[i][j]);
|
||
}
|
||
// printf("\n");
|
||
// printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]);
|
||
for (int j = 0; j < atom->num_improper[i]; j++) {
|
||
// printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
|
||
TAGINT_FORMAT ",",atom->improper_atom1[i][j],
|
||
atom->improper_atom2[i][j],atom->improper_atom3[i][j],
|
||
atom->improper_atom4[i][j]);
|
||
}
|
||
// printf("\n");
|
||
// printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
|
||
atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
|
||
for (int j = 0; j < atom->nspecial[i][2]; j++) {
|
||
printf(" " TAGINT_FORMAT,atom->special[i][j]);
|
||
}
|
||
// printf("\n");
|
||
}
|
||
#endif
|
||
}
|