input_file.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 INPUT_FILE_H
#define INPUT_FILE_H
 
//System Headers
#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <unordered_set>
#include <mpi.h>
 
//LAMMPS Headers
#include "lammps.h"
#include "random_mars.h"
#include "update.h"
 
//kMC Headers
#include "papreca_error.h"
#include "papreca_config.h"
#include "event_list.h"
#include "rates_calc.h"
#include "utilities.h"
#include "lammps_wrappers.h"
 
namespace PAPRECA{
    
    //SUPPLEMENTARY SETTER FUNCTIONS FOR APRECAT CONFIG
    void setTimeUnitsConversionConstant( LAMMPS_NS::LAMMPS *lmp , PaprecaConfig &papreca_config );
    
    //ACCEPTABLE OPTIONAL COMMAND KEYWORDS and KEYWORD IDENTIFICATION FUNCTIONS.
    void checkForAcceptableKeywordsUsedMultipleTimes( std::vector< std::string > &commands , const std::string &keyword );
    void check4AcceptableKeywords( std::vector< std::string > &commands , const int &start , std::unordered_set< std::string > &acceptable_keywords , const bool &accept_bool );
    void processCatalyzedOption( std::vector< std::string > &commands , int &current_pos , std::vector< int > &catalyzing_types );
    void processBondLimitOption( std::vector< std::string > &commands , int &current_pos , double &length_equil , double &length_perc );
    void processSigmaMixOptions( std::vector< std::string > &commands , int &current_pos );
    double getBinWidthFromElementalDistributions( std::vector< std::string > &commands , int &current_pos );
    double getStickingCoeffFromDepositionEventOptions( std::vector< std::string > &commands , int &current_pos );
    double getRateFromInputRateOptions( std::vector< std::string > &commands , int &current_pos );
    void processCustomDiffEventOptions( std::vector< std::string > &commands , int &current_pos , std::string &custom_style , std::vector< int > &style_atomtypes );
    
    //ACCEPTABLE COMMANDS
    void executeKMCstepsCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeKMCperMDCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeTimeEndCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeRandomSeedCommand( LAMMPS_NS::LAMMPS *lmp , std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeFluidAtomTypesCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeFrozenAtomTypesCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeDesorptionCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeHeightCalculationCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeSpeciesMaxBondsCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeSpeciesMaxBondTypesCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeMinimizePriorCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeMinimizeAfterCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeTrajectoryDurationCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeDepoheightsCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeRandomDepovecsCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeRandomDiffvecsCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeCreateBondBreakCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeCreateBondFormCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeCreateDiffusionHopCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeCreateDepositionCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeCreateMonoatomicDesorptionCommand( std::vector< std:: string > &commands , PaprecaConfig &papreca_config );
    void executeExportHeightVtimeCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeExportSurfaceCoverageCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeExportElementalDistributionsCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeExportExecutionTimesCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeRestartFreqCommand( std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeSigmasOptionsCommand( LAMMPS_NS::LAMMPS *lmp , std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    void executeInitSigmaCommand( LAMMPS_NS::LAMMPS *lmp , std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    
    //General command execution functions
    void executePaprecaCommand( LAMMPS_NS::LAMMPS *lmp , std::vector< std::string > &commands , PaprecaConfig &papreca_config );
    std::vector< std::string > processLine( char *line );
    void abortIllegalRun( const int &proc_id , PaprecaConfig &papreca_config );
    void readInputAndInitPaprecaConfig( LAMMPS_NS::LAMMPS *lmp , const int &proc_id , const char *file_name , PaprecaConfig &papreca_config ); //Main function reading the input file and passing information (i.e., commands) to the execute commands function
 
    
}//end of namespace PAPRECA
 
#endif