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This commit is contained in:
Axel Kohlmeyer
2024-01-19 00:03:13 -05:00
parent 4015d1bb39
commit e28f93dca4
7 changed files with 73 additions and 100 deletions
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52
src/REACTION/fix_bond_react.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -58,26 +57,26 @@ using namespace FixConst;
using namespace MathConst;
static const char cite_fix_bond_react[] =
"fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012\n\n"
"@Article{Gissinger17,\n"
" author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},\n"
" title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},\n"
" journal = {Polymer},\n"
" year = 2017,\n"
" volume = 128,\n"
" pages = {211--217}\n"
"}\n\n"
"@Article{Gissinger20,\n"
" author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
" title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},\n"
" journal = {Macromolecules},\n"
" year = 2020,\n"
" volume = 53,\n"
" number = 22,\n"
" pages = {9953--9961}\n"
"}\n\n";
"fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, "
"doi:10.1021/acs.macromol.0c02012\n\n"
"@Article{Gissinger17,\n"
" author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},\n"
" title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},\n"
" journal = {Polymer},\n"
" year = 2017,\n"
" volume = 128,\n"
" pages = {211--217}\n"
"}\n\n"
"@Article{Gissinger20,\n"
" author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
" title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},\n"
" journal = {Macromolecules},\n"
" year = 2020,\n"
" volume = 53,\n"
" number = 22,\n"
" pages = {9953--9961}\n"
"}\n\n";
static constexpr double BIG = 1.0e20;
static constexpr int DELTA = 16;
static constexpr int MAXGUESS = 20; // max # of guesses allowed by superimpose algorithm
@ -91,24 +90,25 @@ static constexpr int NUMVARVALS = 5; // max # of keyword values that have va
// CONTINUE: a neighbor has been assigned, skip to next neighbor
// GUESSFAIL: a guess has failed (if no more restore points, status = 'REJECT')
// RESTORE: restore mode, load most recent restore point
enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
enum { ACCEPT, REJECT, PROCEED, CONTINUE, GUESSFAIL, RESTORE };
// types of available reaction constraints
enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD,CUSTOM};
enum { DISTANCE, ANGLE, DIHEDRAL, ARRHENIUS, RMSD, CUSTOM };
// ID type used by constraint
enum{ATOM,FRAG};
enum { ATOM, FRAG };
// keyword values that accept variables as input
enum{NEVERY,RMIN,RMAX,PROB,NRATE};
enum { NEVERY, RMIN, RMAX, PROB, NRATE };
// flag for one-proc vs shared reaction sites
enum{LOCAL,GLOBAL};
enum { LOCAL, GLOBAL };
// values for molecule_keyword
enum{OFF,INTER,INTRA};
enum { OFF, INTER, INTRA };
/* ---------------------------------------------------------------------- */
// clang-format off
FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)