input_file.h File Reference

Declarations of functions related to the reading of the PAPRECA input file, and the initialization of the PAPRECA::PaprecaConfig object from the PAPRECA input file. More...

#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <unordered_set>
#include <mpi.h>
#include "lammps.h"
#include "random_mars.h"
#include "update.h"
#include "papreca_error.h"
#include "papreca_config.h"
#include "event_list.h"
#include "rates_calc.h"
#include "utilities.h"
#include "lammps_wrappers.h"

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Namespaces
	PAPRECA

Functions
void	PAPRECA::setTimeUnitsConversionConstant (LAMMPS_NS::LAMMPS *lmp, PaprecaConfig &papreca_config)
void	PAPRECA::checkForAcceptableKeywordsUsedMultipleTimes (std::vector< std::string > &commands, const std::string &keyword)
void	PAPRECA::check4AcceptableKeywords (std::vector< std::string > &commands, const int &start, std::unordered_set< std::string > &acceptable_keywords, const bool &accept_bool)
void	PAPRECA::processCatalyzedOption (std::vector< std::string > &commands, int &current_pos, std::vector< int > &catalyzing_types)
void	PAPRECA::processBondLimitOption (std::vector< std::string > &commands, int &current_pos, double &length_equil, double &length_perc)
void	PAPRECA::processSigmaMixOptions (std::vector< std::string > &commands, int &current_pos)
double	PAPRECA::getBinWidthFromElementalDistributions (std::vector< std::string > &commands, int &current_pos)
double	PAPRECA::getStickingCoeffFromDepositionEventOptions (std::vector< std::string > &commands, int &current_pos)
double	PAPRECA::getRateFromInputRateOptions (std::vector< std::string > &commands, int &current_pos)
void	PAPRECA::processCustomDiffEventOptions (std::vector< std::string > &commands, int &current_pos, std::string &custom_style, std::vector< int > &style_atomtypes)
void	PAPRECA::executeKMCstepsCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeKMCperMDCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeTimeEndCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeRandomSeedCommand (LAMMPS_NS::LAMMPS *lmp, std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeFluidAtomTypesCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeFrozenAtomTypesCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeDesorptionCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeHeightCalculationCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeSpeciesMaxBondsCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeSpeciesMaxBondTypesCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeMinimizePriorCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeMinimizeAfterCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeTrajectoryDurationCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeDepoheightsCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeRandomDepovecsCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeRandomDiffvecsCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeCreateBondBreakCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeCreateBondFormCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeCreateDiffusionHopCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeCreateDepositionCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeCreateMonoatomicDesorptionCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeExportHeightVtimeCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeExportSurfaceCoverageCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeExportElementalDistributionsCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeExportExecutionTimesCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeRestartFreqCommand (std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeSigmasOptionsCommand (LAMMPS_NS::LAMMPS *lmp, std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executeInitSigmaCommand (LAMMPS_NS::LAMMPS *lmp, std::vector< std::string > &commands, PaprecaConfig &papreca_config)
void	PAPRECA::executePaprecaCommand (LAMMPS_NS::LAMMPS *lmp, std::vector< std::string > &commands, PaprecaConfig &papreca_config)
std::vector< std::string >	PAPRECA::processLine (char *line)
void	PAPRECA::abortIllegalRun (const int &proc_id, PaprecaConfig &papreca_config)
void	PAPRECA::readInputAndInitPaprecaConfig (LAMMPS_NS::LAMMPS *lmp, const int &proc_id, const char *file_name, PaprecaConfig &papreca_config)

Detailed Description

Declarations of functions related to the reading of the PAPRECA input file, and the initialization of the PAPRECA::PaprecaConfig object from the PAPRECA input file.