event_detect.h

Go to the documentation of this file.

/*----------------------------------------------------------------------------------------
PAPRECA hybrid off-lattice kinetic Monte Carlo/Molecular dynamics simulator.
Copyright (C) 2024 Stavros Ntioudis, James P. Ewen, Daniele Dini, and C. Heath Turner
 
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
 
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
----------------------------------------------------------------------------------------*/
 
 
#ifndef EVENT_DETECT_H
#define EVENT_DETECT_H
 
//System Headers
#include <vector>
#include <mpi.h>
 
 
//LAMMPS headers
#include "lammps.h"
#include "pointers.h"
 
//KMC headers
#include "event.h"
#include "event_list.h"
#include "bond.h"
#include "papreca_config.h"
#include "lammps_wrappers.h"
#include "geometry_calc.h"
#include "utilities.h"
 
namespace PAPRECA{
 
    //Diffusion events
    const bool feCandidateHas4PO4Neibs( PaprecaConfig &papreca_config , PredefinedDiffusionHop *diff_template , LAMMPS_NS::tagint *atom_ids , int *atom_types , int *neighbors , int &neighbors_num , ATOM2BONDS_MAP &atomID2bonds );
    void getDiffPointCandidateCoords( LAMMPS_NS::LAMMPS *lmp  , PaprecaConfig &papreca_config , double *iatom_xyz , double *candidate_xyz , PredefinedDiffusionHop *diff_template );
    const bool candidateDiffHasCollisions( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , int *neighbors , int &neighbors_num , double *candidate_xyz , const int &diffused_type , double *iatom_xyz , const int &iatom_type );
    void getDiffEventsFromAtom( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , const int &iatom , int *neighbors , int &neighbors_num , std::vector< Event* > &events_local , ATOM2BONDS_MAP &atomID2bonds );
    
    //Deposition events
    const bool atomIsInDepoScanRange( PaprecaConfig &papreca_config , double *iatom_xyz , double &film_height );
    void getDepoPointCandidateCoords( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , double *iatom_xyz ,  double *candidate_xyz , PredefinedDeposition *depo_template );
    const bool depoCandidateIsBelowRejectionHeight( PaprecaConfig &papreca_config , double *candidate_xyz , const double &film_height );
    void getMolCoords( LAMMPS_NS::LAMMPS *lmp , double **mol_xyz , double **mol_dx , const int &mol_natoms , double *candidate_center );
    void initMolCoordsArr( double ***mol_xyz , const int &mol_natoms );
    void deleteMolCoordsArr( double **mol_xyz , const int &mol_natoms );
    bool atomHasCollisionWithMolAtoms( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , double *atom_xyz , const int &atom_type , const int &mol_natoms , double **mol_xyz , int *mol_atomtype );
    bool candidateDepoHasCollisions( LAMMPS_NS::LAMMPS *lmp , const int &proc_id , const int &nprocs , PaprecaConfig &papreca_config , int *neighbors , int neighbors_num , double *candidate_center , double *iatom_xyz , const int &iatom_type , PredefinedDeposition *depo_template );
    void getDepoEventsFromAtom( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , const int &proc_id , const int &nprocs , const int &iatom , int *neighbors , int &neighbors_num , double &film_height , std::vector< Event* > &events_local );
    
    //Bond-Breaking and formation events
    const bool headAtomIsCatalyzed( PredefinedReaction *reaction_template , int *atom_types , int *neighbors , int &neighbors_num );
    void getBondBreakingEventsFromAtom( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , const int &iatom , int *neighbors , int &neighbors_num , std::vector<Event*> &events_local , ATOM2BONDS_MAP &atomID2bonds );
    const bool atomsBelong2TheSameMol( const LAMMPS_NS::tagint &iatom_mol , const LAMMPS_NS::tagint &jneib_mol );
    const bool atomHasMaxBonds( PaprecaConfig &papreca_config , ATOM2BONDS_MAP &atomID2bonds , const LAMMPS_NS::tagint &atom_id , const int atom_type );
    bool bondBetweenAtomsExists( ATOM2BONDS_MAP &atomID2bonds , const LAMMPS_NS::tagint &atom1_id , const LAMMPS_NS::tagint &atom2_id );
    const bool atomCandidatesAreLone( const LAMMPS_NS::tagint atom1_id , const LAMMPS_NS::tagint atom2_id , ATOM2BONDS_MAP &atomID2bonds );
    const bool atomHasMaxBondTypes( PaprecaConfig &papreca_config , ATOM2BONDS_MAP &atomID2bonds , const LAMMPS_NS::tagint &atom_id , const int &atom_type , const int &bond_type );
    void getBondFormEventsFromAtom( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , const int &iatom , int *neighbors , int &neighbors_num , std::vector<Event*> &events_local , ATOM2BONDS_MAP &atomID2bonds );
    
    //Monoatomic Desorption events
    void getMonoDesEventsFromAtom( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config , const int &iatom , std::vector< Event* > &events_local , ATOM2BONDS_MAP &atomID2bonds );
    
    //General Functions
    void loopAtomsAndIdentifyEvents( LAMMPS_NS::LAMMPS *lmp , const int &proc_id , int &nprocs , const int &KMC_loopid , PaprecaConfig &papreca_config , std::vector<Event*> &events_local , ATOM2BONDS_MAP &atomID2bonds , double &film_height );
        
 
}//end of PAPRECA namespace 
 
 
#endif