/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ #ifdef FIX_CLASS FixStyle(bond/react,FixBondReact) #else #ifndef LMP_FIX_BOND_REACT_H #define LMP_FIX_BOND_REACT_H #include "fix.h" namespace LAMMPS_NS { class FixBondReact : public Fix { public: FixBondReact(class LAMMPS *, int, char **); ~FixBondReact(); int setmask(); void post_constructor(); void init(); void init_list(int, class NeighList *); void post_integrate(); void post_integrate_respa(int, int); int pack_forward_comm(int, int *, double *, int, int *); void unpack_forward_comm(int, int, double *); int pack_reverse_comm(int, int, double *); void unpack_reverse_comm(int, int *, double *); double compute_vector(int); double memory_usage(); private: int me,nprocs; int newton_bond; int nreacts; int *nevery; FILE *fp; int *iatomtype,*jatomtype; int *seed; double **cutsq,*fraction; tagint lastcheck; int stabilization_flag; int custom_exclude_flag; int *stabilize_steps_flag; int *update_edges_flag; int *max_rxn_flag,*max_rxn; int *var_fraction_flag, *var_fraction_id; int status; int *groupbits; int rxnID; // integer ID for identifying current bond/react int *reaction_count; int *reaction_count_total; int nmax; // max num local atoms int max_natoms; // max natoms in a molecule template tagint *partner,*finalpartner; double **distsq,*probability; int *ncreate; int maxcreate; int allncreate; tagint ***created; class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template Fix *fix1; // nve/limit used to relax reaction sites Fix *fix2; // properties/atom used to indicate 1) relaxing atoms // 2) to which 'react' atom belongs Fix *fix3; // property/atom used for system-wide thermostat class RanMars **random; class NeighList *list; int *reacted_mol,*unreacted_mol; int *limit_duration; // indicates how long to relax char *nve_limit_xmax; // indicates max distance allowed to move when relaxing char *id_fix1; // id of internally created fix nve/limit char *id_fix2; // id of internally created fix per-atom properties char *id_fix3; // id of internally created 'stabilization group' per-atom property fix char *statted_id; // name of 'stabilization group' per-atom property char *master_group; // group containing relaxing atoms from all fix rxns char *exclude_group; // group for system-wide thermostat int countflag,commflag; int nlevels_respa; void superimpose_algorithm(); // main function of the superimpose algorithm int *ibonding,*jbonding; int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file int attempted_rxn; // there was an attempt! int *local_rxn_count; int *ghostly_rxn_count; int avail_guesses; // num of restore points available int *guess_branch; // used when there is more than two choices when guessing int **restore_pt; // contains info about restore points tagint **restore; // contaings info about restore points int *pioneer_count; // counts pioneers int **edge; // atoms in molecule templates with incorrect valences int ***equivalences; // relation between pre- and post-reacted templates int ***reverse_equiv; // re-ordered equivalences int **landlocked_atoms; // all atoms at least three bonds away from edge atoms int **custom_edges; // atoms in molecule templates with incorrect valences int **delete_atoms; // atoms in pre-reacted templates to delete int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list int pion,neigh,trace; // important indices for various loops. required for restore points int lcl_inst; // reaction instance tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs // for all mega_gloves and global_mega_glove: first row is the ID of bond/react tagint **local_mega_glove; // consolidation local of reaction instances tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms int *localsendlist; // indicates ghosts of other procs int local_num_mega; // num of local reaction instances int ghostly_num_mega; // num of ghostly reaction instances int global_megasize; // num of reaction instances in global_mega_glove int *pioneers; // during Superimpose Algorithm, atoms which have been assigned, but whose first neighbors haven't int glove_counter; // used to determine when to terminate Superimpose Algorithm void read(int); void EdgeIDs(char *,int); void Equivalences(char *,int); void CustomEdges(char *,int); void DeleteAtoms(char *,int); void make_a_guess (); void neighbor_loop(); void check_a_neighbor(); void crosscheck_the_neighbor(); void inner_crosscheck_loop(); void ring_check(); void open(char *); void readline(char *); void parse_keyword(int, char *, char *); void skip_lines(int, char *); int parse(char *, char **, int); void far_partner(); void close_partner(); void get_molxspecials(); void find_landlocked_atoms(int); void glove_ghostcheck(); void ghost_glovecast(); void update_everything(); void unlimit_bond(); void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove // DEBUG void print_bb(); }; } #endif #endif /* ERROR/WARNING messages: E: Illegal ... command Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. E: Invalid exclude group name Exclude group name should not previously be defined. E: Cannot use fix bond/react with non-molecular systems Only systems with bonds that can be changed can be used. Atom_style template does not qualify. E: Fix bond/react cutoff is longer than pairwise cutoff This is not allowed because bond creation is done using the pairwise neighbor list. E: Molecule template ID for fix bond/react does not exist A valid molecule template must have been created with the molecule command. E: Superimpose file errors: Please ensure superimpose file is properly formatted. E: Atom affected by reaction too close to template edge This means an atom which changes type during the reaction is too close to an 'edge' atom defined in the superimpose file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. E: Fix bond/react needs ghost atoms from farther away This is because a processor needs to superimpose the entire unreacted molecule template onto simulation atoms it can 'see.' The comm_modify cutoff command can be used to extend the communication range. E: Excessive iteration of superimpose algorithm You may have discovered a bug! But first, please double check that your molecule template atom types, bond types, etc. are consistent with your simulation, and that all atoms affected by a reaction are sufficently separated from edge atoms. If this issue persists, please contact the developer. */