lammps_wrappers.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 LAMMPS_WRAPPERS_H
#define LAMMPS_WRAPPERS_H
 
//System Headers
#include <string>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <mpi.h>
#include <vector>
#include <array>
#include <cmath>
 
//LAMMPS headers
#include "lammps.h"
#include "atom.h"
#include "molecule.h"
#include "library.h"
#include "input.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
 
//kMC Headers
#include "papreca_error.h"
#include "utilities.h"
 
 
namespace PAPRECA{
 
    //Initialize LAMMPS
    void initializeLMP( LAMMPS_NS::LAMMPS **lmp );
    void readLMPinput( const std::string &lmp_input , LAMMPS_NS::LAMMPS *lmp );
        
    //Execute LAMMPS
    void runLammps( LAMMPS_NS::LAMMPS *lmp , const int &timesteps_num );
    void MPIBcastAndExecuteCommand( LAMMPS_NS::LAMMPS *lmp , std::string &command ); //This function gets a line command (std::string), casts it to all other procs, and executes the command
    
    //Period Box Operations
    void remap3DArrayInPeriodicBox( LAMMPS_NS::LAMMPS *lmp , double *arr ); //Receives a 3D array and remaps it inside the existing periodic box.
    
    //kMC operations
    void deleteAtoms( LAMMPS_NS::LAMMPS *lmp , LAMMPS_NS::tagint *atom_ids , const int &num_atoms , const std::string &delete_bonds , const std::string &delete_molecule );
    void deleteAtoms( LAMMPS_NS::LAMMPS *lmp , std::vector< LAMMPS_NS::tagint > &atom_ids , const std::string &delete_bonds , const std::string &delete_molecule ); //Overloaded function of the deleteAtoms function to work with vectors
    void deleteAtomsInBoxRegion( LAMMPS_NS::LAMMPS *lmp , double &boxxlo , double &boxxhi , double &boxylo , double &boxyhi , double &boxzlo , double &boxzhi , const std::string &delete_bonds , const std::string &delete_molecule );
    void createAtom( LAMMPS_NS::LAMMPS *lmp , const double atom_pos[3] , const int &atom_type );
    void deleteBond( LAMMPS_NS::LAMMPS *lmp , const LAMMPS_NS::tagint &atom1id , const LAMMPS_NS::tagint &atom2id , const bool special );
    void formBond( LAMMPS_NS::LAMMPS *lmp , const LAMMPS_NS::tagint &atom1id , const LAMMPS_NS::tagint &atom2id , const int &bond_type );
    void resetMobileAtomsGroups( LAMMPS_NS::LAMMPS *lmp , const std::vector< int > &fluid_atomtypes );
    void insertMolecule( LAMMPS_NS::LAMMPS *lmp , const double site_pos[3] , const double rot_pos[3] , const double &rot_theta , const int &mol_id , const char *mol_name );
    void diffuseAtom( LAMMPS_NS::LAMMPS *lmp , const double vac_pos[3] , const LAMMPS_NS::tagint &parent_id , const int &parent_type , const int &is_displacive , const int &diffused_type );
    
    //Sigmas
    void initType2SigmaFromLammpsPairCoeffs( LAMMPS_NS::LAMMPS *lmp , INTPAIR2DOUBLE_MAP &type2sigma );
    
    //Neibs lists
    int getMaskedNeibIndex( int *neighbors , int &j );
    
    //Bond Lists
    void initAndGatherBondsList( LAMMPS_NS::LAMMPS *lmp , LAMMPS_NS::tagint **bonds_list , LAMMPS_NS::bigint &bonds_num );
    
    //Molecules
    static inline const int getMolIndexFromMolName( LAMMPS_NS::LAMMPS *lmp , std::string mol_name );
    void computeMolCenter( LAMMPS_NS::LAMMPS *lmp , std::string mol_name );
    
    //Files
    void dumpRestart( LAMMPS_NS::LAMMPS *lmp , const int &KMC_loopid , const int &dump_freq );
    
    //LAMMPS Maths wrappers
    double get3DSqrDistWithPBC( LAMMPS_NS::LAMMPS *lmp , const double *x1 , const double *x2 );
    
    
}//end of namespace PAPRECA
 
 
#endif