biomodule2.cpp File Reference

#include <Population.h>
#include <Node.h>
#include <Vessel.h>
#include <Benthos.h>
#include <options.h>
#include <readdata.h>
#include <helpers.h>
#include <fisheriesmanagmt.h>
#include <storage/sqliteoutputstorage.h>
#include "storage/tables/poptable.h"
#include "storage/tables/funcgroupstable.h"
#include <ipc.h>
#include <profiler.h>
#include <thread>
#include <condition_variable>
#include <errno.h>
#include <unistd.h>

Macros
#define	GetCurrentDir   getcwd

Functions
bool	applyBiologicalModule2 (int tstep, int a_month_i, const string &namesimu, const string &namefolderinput, const string &namefolderoutput, const string &pathoutput, ofstream &popstats, ofstream &popdyn_N, ofstream &popdyn_F, ofstream &popdyn_SSB, ofstream &popdyn_annual_indic, ofstream &popnodes_inc, ofstream &popnodes_impact, ofstream &popnodes_cumulcatches_per_pop, ofstream &nodes_envt, ofstream &popnodes_cumftime, ofstream &popnodes_cumsweptarea, ofstream &popnodes_cumcatches, ofstream &popnodes_cumcatches_with_threshold, ofstream &popnodes_cumdiscards, ofstream &popnodes_cumdiscardsratio, ofstream &popnodes_nbchoked, ofstream &popnodes_tariffs, ofstream &export_individual_tacs, ofstream &popnodes_end, ofstream &benthosbiomassnodes, ofstream &benthosnumbernodes, int nbbenthospops, bool use_gui, const string &popstats_filename, const string &popdyn_N_filename, const string &popdyn_F_filename, const string &popdyn_SSB_filename, const string &popnodes_inc_filename, const string &popnodes_end_filename, const string &popnodes_impact_filename, const string &popnodes_cumulcatches_per_pop_filename, const string &nodes_envt_filename, const string &popnodes_cumftime_filename, const string &popnodes_cumsweptarea_filename, const string &popnodes_cumcatches_filename, const string &popnodes_cumcatches_with_threshold_filename, const string &popnodes_cumdiscards_filename, const string &popnodes_cumdiscardsratio_filename, const string &popnodes_nbchoked_filename, const string &popnodes_tariffs_filename, const string &popnodes_benthos_biomass_filename, const string &popnodes_benthos_number_filename, const vector< int > &tsteps_quarters, const vector< int > &tsteps_semesters, const vector< int > &tsteps_years, const vector< int > &tsteps_months, const vector< int > &implicit_pops, const vector< double > &calib_oth_landings, vector< vector< double > > &selectivity_per_stock_ogives_for_oth_land, bool is_tacs, int export_vmslike, int freq_do_growth, const multimap< int, double > &init_weight_per_szgroup, const vector< vector< double > > &species_interactions_mortality_proportion_matrix, vector< Population * > &populations, vector< Node * > &nodes, vector< Vessel * > &vessels, vector< Benthos * > &benthoss, const PopSceOptions &dyn_pop_sce, const DynAllocOptions &dyn_alloc_sce, vector< vector< double > > &Ws_at_szgroup, vector< vector< vector< vector< double > > > > &predKernel, vector< vector< double > > &searchVolMat, vector< vector< double > > &juveniles_diet_preference, vector< vector< double > > &adults_diet_preference, vector< int > &mat_cats)

Variables
std::mutex	glob_mutex
bool	enable_sqlite_out
std::shared_ptr< SQLiteOutputStorage >	outSqlite

Macro Definition Documentation

GetCurrentDir

#define GetCurrentDir   getcwd

Function Documentation

applyBiologicalModule2()

bool applyBiologicalModule2	(	int	tstep,
		int	a_month_i,
		const string &	namesimu,
		const string &	namefolderinput,
		const string &	namefolderoutput,
		const string &	pathoutput,
		ofstream &	popstats,
		ofstream &	popdyn_N,
		ofstream &	popdyn_F,
		ofstream &	popdyn_SSB,
		ofstream &	popdyn_annual_indic,
		ofstream &	popnodes_inc,
		ofstream &	popnodes_impact,
		ofstream &	popnodes_cumulcatches_per_pop,
		ofstream &	nodes_envt,
		ofstream &	popnodes_cumftime,
		ofstream &	popnodes_cumsweptarea,
		ofstream &	popnodes_cumcatches,
		ofstream &	popnodes_cumcatches_with_threshold,
		ofstream &	popnodes_cumdiscards,
		ofstream &	popnodes_cumdiscardsratio,
		ofstream &	popnodes_nbchoked,
		ofstream &	popnodes_tariffs,
		ofstream &	export_individual_tacs,
		ofstream &	popnodes_end,
		ofstream &	benthosbiomassnodes,
		ofstream &	benthosnumbernodes,
		int	nbbenthospops,
		bool	use_gui,
		const string &	popstats_filename,
		const string &	popdyn_N_filename,
		const string &	popdyn_F_filename,
		const string &	popdyn_SSB_filename,
		const string &	popnodes_inc_filename,
		const string &	popnodes_end_filename,
		const string &	popnodes_impact_filename,
		const string &	popnodes_cumulcatches_per_pop_filename,
		const string &	nodes_envt_filename,
		const string &	popnodes_cumftime_filename,
		const string &	popnodes_cumsweptarea_filename,
		const string &	popnodes_cumcatches_filename,
		const string &	popnodes_cumcatches_with_threshold_filename,
		const string &	popnodes_cumdiscards_filename,
		const string &	popnodes_cumdiscardsratio_filename,
		const string &	popnodes_nbchoked_filename,
		const string &	popnodes_tariffs_filename,
		const string &	popnodes_benthos_biomass_filename,
		const string &	popnodes_benthos_number_filename,
		const vector< int > &	tsteps_quarters,
		const vector< int > &	tsteps_semesters,
		const vector< int > &	tsteps_years,
		const vector< int > &	tsteps_months,
		const vector< int > &	implicit_pops,
		const vector< double > &	calib_oth_landings,
		vector< vector< double > > &	selectivity_per_stock_ogives_for_oth_land,
		bool	is_tacs,
		int	export_vmslike,
		int	freq_do_growth,
		const multimap< int, double > &	init_weight_per_szgroup,
		const vector< vector< double > > &	species_interactions_mortality_proportion_matrix,
		vector< Population * > &	populations,
		vector< Node * > &	nodes,
		vector< Vessel * > &	vessels,
		vector< Benthos * > &	benthoss,
		const PopSceOptions &	dyn_pop_sce,
		const DynAllocOptions &	dyn_alloc_sce,
		vector< vector< double > > &	Ws_at_szgroup,
		vector< vector< vector< vector< double > > > > &	predKernel,
		vector< vector< double > > &	searchVolMat,
		vector< vector< double > > &	juveniles_diet_preference,
		vector< vector< double > > &	adults_diet_preference,
		vector< int > &	mat_cats
	)

!!!!!!!!!!!!// !!!!!!!!!!!!// !!TSTEP 0!!!// !!!!!!!!!!!!// !!!!!!!!!!!!//

!!!!!!!!!!!!!!!!!!!!!!!!// !!!!!!!!!!!!!!!!!!!!!!!!// !!TSTEPS START MONTHS!!!// !!!!!!!!!!!!!!!!!!!!!!!!// !!!!!!!!!!!!!!!!!!!!!!!!//

Variable Documentation

enable_sqlite_out

bool enable_sqlite_out

glob_mutex

std::mutex glob_mutex

outSqlite

std::shared_ptr<SQLiteOutputStorage> outSqlite