export_files.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 EXPORT_FILES_H
#define EXPORT_FILES_H
 
//System Headers
#include <cstdio>
#include <chrono>
#include <cmath>
#include <fstream>
#include <iomanip>
#include <mpi.h>
 
//LAMMPS headers
#include "lammps.h"
#include "domain.h"
namespace PAPRECA{
 
    /* The classes below manage the result files exported by a run. New export files should be added here and a relevant implementation in the papreca_config.h and input_file.h headers should be included to read/manage/setup the files. */
 
    class File{
        
        
        friend class PaprecaConfig; //PaprecaConfig reads the protected/private variables of file classes so it is declared as a friend class.
        
        public:
            //Constructors/Destructors
            File( );
            File( const int &print_freq_in );
            virtual ~File( );
            
            //Functions
            virtual void close( );
            void setActive( );
            void setIncative( );
            const bool isActive( ) const;
            void setPrintFreq( const int &print_freq_in );
            const int getPrintFreq( ) const;
            
        protected:
            std::ofstream file;
            bool is_active = false;
            int print_freq = 0;
        
    };
 
 
    class Log : public File{
    
        
        friend class PaprecaConfig;
        
        public:
            //Constructors/Destructors
            Log( );
            ~Log( );
            
            //functions
            void init( );
            void appendDeposition( const int &KMC_loopid , const double &time , const double *site_pos , const double *rot_pos , const double &rot_theta , const double &insertion_vel , const char *mol_name );
            void appendBondForm( const int &KMC_loopid , const double &time , const LAMMPS_NS::tagint &atom1_id , const LAMMPS_NS::tagint &atom2_id , const int &bond_type);
            void appendBondBreak( const int &KMC_loopid , const double &time , const LAMMPS_NS::tagint &atom1_id , const LAMMPS_NS::tagint &atom2_id , const int &bond_type);
            void appendDiffusion( const int &KMC_loopid , const double &time , const double *vac_pos , const LAMMPS_NS::tagint &parent_id , const int &parent_type , const double &insertion_vel , const int &is_displacive , const int &diffused_type );
            void appendMonoatomicDesorption( const int &KMC_loopid , const double &time , const int &parent_id , const int &parent_type );
    };
    
    
    
    
    class HeightVtime : public File{
        
        
        friend class PaprecaConfig;
        
        public:
            //Constructors/Destructors
            HeightVtime( );
            HeightVtime( const int &print_freq_in );
            ~HeightVtime( );
            
            //functions
            void init( );
            void append( const double &time , const double &film_height );
    
    };
    
    class SurfaceCoverage : public File{
        
        
        friend class PaprecaConfig;
        
        public:
            //Constructors/Destructors
            SurfaceCoverage( );
            SurfaceCoverage( const int &print_freq_in );
            ~SurfaceCoverage( );
            
            //Functions
            void init( );
            void append( const double &time , const double &surface_coverage ); 
        
    };
    
    class ElementalDistribution : public File{
        
        
        friend class PaprecaConfig;
        
        public:
            //Constructors/Destructors
            ElementalDistribution( );
            ElementalDistribution( const int &print_freq_in );
            ~ElementalDistribution( );
            
            //functions
            void init( const int &KMC_loopid , const int &types_num );
            void append( LAMMPS_NS::LAMMPS *lmp , double **mass_profiles , const int &types_num , const int &bins_num , const double &bin_width , double *atom_mass );
            
    };
    
    
    class ExecTime : public File{
        
        
        friend class PaprecaConfig;
        
        public:
            //Constructors/Destructors
            ExecTime( );
            ExecTime( const int &print_freq_in );
            ~ExecTime( );
            
            //functions
            void init( );
            void append( const int &step_num , const int &atoms_num );
            void close( ) override;
            //Total Time Calculation
            void setHybridStartTimeStamp( );
            void calcHybridTime( const int &nprocs );
            void resetHybridTimeVariables( );
            //MD time calculation
            void setMDstartTimeStamp( );
            void calcMDtime( const int &nprocs );
            void resetMDtimeVariables( );   
            //KMC time calculation
            void calcKMCtime( const int &nprocs );
            void resetKMCtimeVariables( );
            //General functions
            void calcTimes( const int &nprocs );
            void resetTimeVariables( );
            
        
        protected:
            
            double t_hybrid = 0.0 , t1_hybrid = 0.0 , t2_hybrid = 0.0 , t_md = 0.0 , t1_md = 0.0 , t2_md = 0.0 , t_kmc = 0.0;
            double thybrid_min = 0.0 , thybrid_avg = 0.0 , thybrid_max = 0.0;
            double tkmc_min = 0.0 , tkmc_avg = 0.0 , tkmc_max = 0.0;
            double tmd_min = 0.0 , tmd_avg = 0.0 , tmd_max = 0.0;
            double thybrid_total = 0.0 , tkmc_total = 0.0 , tmd_total = 0.0;
            
        
    };
 
 
}//end of namespace Papreca
 
 
#endif