bond.h

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/*----------------------------------------------------------------------------------------
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 BOND_H
#define BOND_H
 
//System Headers
#include <vector>
#include <unordered_map>
#include <cstdlib>
#include <cstdio>
 
 
//LAMMPS headers
#include "pointers.h"
 
//PAPRECA headers
#include "lammps_wrappers.h"
 
 
namespace PAPRECA{
 
    class Bond; //Forward definition of bond class
    typedef std::vector< Bond > BOND_VECTOR;
    typedef std::unordered_map< LAMMPS_NS::tagint , BOND_VECTOR > ATOM2BONDS_MAP; 
    
    class Bond{
        
        
 
        private:
            LAMMPS_NS::tagint bond_atom = -1;
            int bond_type = -1;
            bool head_parent_atom = false;
            
        public:
            //Constructors/Destructors
            Bond( ); //Default
            Bond( const LAMMPS_NS::tagint &bond_atom_in , const int &bond_type_in , const bool &head_parent_atom_in );  
            ~Bond( );
            
            //Member functions
            const LAMMPS_NS::tagint &getBondAtom( ) const;
            const int &getBondType( ) const;
            bool parentAtomIsHead( ) const; 
            void assignBondAtom( const LAMMPS_NS::tagint &bond_atom_in );
            void assignBondType( const int &bond_type_in );
            
            //Static functions
            static const bool atomIDIsMapped( LAMMPS_NS::tagint &parent_atomID , ATOM2BONDS_MAP &atomID2bonds );
            static void addBond2BondVector( int &bond_type , LAMMPS_NS::tagint &parent_atomID , LAMMPS_NS::tagint &bond_atomID , const bool &head_atom_parent , ATOM2BONDS_MAP &atomID2bonds );
            static void fillAtomID2BondsContainer( ATOM2BONDS_MAP &atomID2bonds , LAMMPS_NS::tagint *bonds_list , const LAMMPS_NS::bigint &bonds_num );
            static void initAtomID2BondsMap( LAMMPS_NS::LAMMPS *lmp , const int &proc_id , ATOM2BONDS_MAP &atomID2bonds );
            static bool atomHasBonds( const LAMMPS_NS::tagint &iatom_id , ATOM2BONDS_MAP &atomID2bonds );
            static void recursiveCollectBondedAtoms( LAMMPS_NS::tagint &atom_id , std::vector< LAMMPS_NS::tagint > &delids_local , TAGINT_SET &delids_set , ATOM2BONDS_MAP &atomID2bonds );
    };
    
} //End of PAPRECA namespace
 
#endif