Module that defines the runtime behaviour of the model. More...

Data Types
type	output_arrays_step_def
	This data structure keeps the output values for each time step. It should normally be instantiated as an allocatable array of the size equal to the total number of time steps in the model run. More...

type	output_stats_total_def
	Overall output statistics that are output from the model. More...

Functions/Subroutines
pure integer(long) function	total_timesteps (hours)
	Calculate the total number of time steps in the model from the number of hours. This in fact converts hours to seconds. More...

impure subroutine	output_arrays_init (time_steps)
	Allocate model output arrays output_arrays. More...

impure subroutine	output_arrays_update_step (this_fish, time_step, temperature)
	Update model output arrays output_arrays. More...

impure subroutine	output_arrays_add_ingested (is_given, is_eaten, time_step, add_eaten)
	Update the cumulative count of food items ingested. This cannot normally be done in output_arrays_update_step() and requires an input argument. More...

impure subroutine	output_arrays_save_csv (file_name, is_gui_dialog, is_write_error)
	Save the model output arrays to a CSV data file. More...

impure subroutine	output_arrays_save_rate_data_csv (file_name, is_gui_dialog, is_write_error)
	Save the rate data arrays to a CSV data file. More...

impure subroutine	csv_file_error_report (csv_handle, is_gui_dialog)
	Report CSV file write error. More...

impure subroutine	stomach_transport_save_csv (csv_file)
	Save the stomach transport data pattern for a single food item. More...

impure subroutine	appetite_function_save_csv (csv_file)
	Save the appetite function the_fish::appetite_func() pattern for plotting, testing or analysis. More...

pure character(len=:) function, allocatable	model_output_stats_txt ()
	Produce a text string containing general model output statistics. More...

character(len=:) function, allocatable	model_output_stats_row_csv (show_header)
	Produce a text string containing general model output statistics. More...

impure subroutine	test_run ()
	The procedure below is TEMPORARY, for testing and debugging. More...

impure subroutine	init_provisioning (time_steps)
	Initialise the food provisioning schedule / pattern. More...

impure integer function, dimension(:), allocatable	get_food_schedule_display ()
	Determine the food schedule array for separate display and analysis The primary role of this function is to plan (produce and display) the food provisioning pattern before simulation in GUI. More...

real(srp) function, dimension(:), allocatable	get_ingestion_ratio_waste (rate_unit)
	calculate the array of the consumption ratio, i.e. eaten/provided, so it is also easy to calculate the waste rate More...

Variables
logical, parameter	is_extended_logging_debug_test = .FALSE.
	Flag for extended/detailed debug logging. More...

logical, parameter, private	is_urinal_branchial_kj_day = .TRUE.
	Flag that defines how urinal and branchial energy loss (UE+ZE) is calculated for model output arrays. If TRUE, UE+ZE is computed in kJ per kg per day (default), otherwise, in O2 equivalent unit: mg O2 / kg/hour. More...

integer, public	gui_idx_progress
	Progress bar widget ID for the GUI mode, needed to update at runtime. More...

type(output_arrays_step_def), dimension(:), allocatable, public	output_arrays
	output_arrays instantiates the global data structure that keeps the model output arrays. More...

type(output_stats_total_def)	output_stats
	output_stats instantiates non-array global data structure that keeps total model output statistics, that are not arrays by time step. More...

Detailed Description

Module that defines the runtime behaviour of the model.

Function/Subroutine Documentation

◆ total_timesteps()

pure integer(long) function simulate::total_timesteps ( integer, intent(in), optional hours )

Calculate the total number of time steps in the model from the number of hours. This in fact converts hours to seconds.

Parameters

[in] hours Optional hours to be converted to seconds. If absent, the default value is obtained from the global parameter commondata::global_run_model_hours.

Definition at line 115 of file m_simulate.f90.

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◆ output_arrays_init()

impure subroutine simulate::output_arrays_init ( integer(long), intent(in), optional time_steps )

Allocate model output arrays output_arrays.

Parameters

[in] time_steps Optional overall number of time steps of the model

Note: Note that this argument has the integer type of the kind commondata::long. This might taint default integer values.; This procedure cannot be pure because it allocates a global module-scope array.

Definition at line 131 of file m_simulate.f90.

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◆ output_arrays_update_step()

impure subroutine simulate::output_arrays_update_step	(	class(fish), intent(in)	this_fish,
		integer(long), intent(in), optional	time_step,
		real(srp), intent(in), optional	temperature
	)

Update model output arrays output_arrays.

Parameters

[in]	this_fish	The fish that is participating in the simulation run.
[in]	time_step	Optional time step, which coincides with the index of the model output arrays. The default value used if the argument is not given is defined by the global time step commondata::global_time_step.
[in]	temperature	Optional temperature

Update oxygen uptake, convert to mg O2 per kg of body mass per hour

Update baseline meabolic rate, mg O2 per kg per hour

Update Active metabolic rate, mg O2 per kg per hour

Update SDA, mg O2 per hour per kg

Update urinal and branchial energy in kJ/kg per day

Alternatively, urinal and branchial energy is output as equivalent mg O2 per kg per hour

Warning: This makes sense only if UE+ZE is defined as factor of SMR rather than fixed rate (see commondata::global_is_ue_ze_fixed_rate)

Definition at line 181 of file m_simulate.f90.

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◆ output_arrays_add_ingested()

impure subroutine simulate::output_arrays_add_ingested	(	logical, intent(in)	is_given,
		logical, intent(in)	is_eaten,
		integer(long), intent(in), optional	time_step,
		integer, intent(in), optional	add_eaten
	)

Update the cumulative count of food items ingested. This cannot normally be done in output_arrays_update_step() and requires an input argument.

Parameters

[in]	is_given	Logical indicator whether a fod item is ingested at the current time step (TRUE) or not (FALSE). The cumulative number of food items consumed is updated (added) only if this parameter is TRUE.
[in]	is_eaten	Logical indicator whether a fod item is ingested at the current time step (TRUE) or not (FALSE). The cumulative number of food items consumed is updated (added) only if this parameter is TRUE.
[in]	time_step	Optional time step, which coincides with the index of the model output arrays. The default value used if the argument is not given is defined by the global time step commondata::global_time_step.
[in]	add_eaten	Optional number of food items ingested, default value is 1.

Implementation notes

To update the cumulative count of food items ingested, the number of items ingested at this time step is added to the value at the previous time step. At the first step the counter is set to zero.

To update the cumulative count of food items not ingested, the number of items not ingested at this time step is added to the value at the previous time step. At the first step the counter is set to zero.

Definition at line 293 of file m_simulate.f90.

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◆ output_arrays_save_csv()

impure subroutine simulate::output_arrays_save_csv	(	character(len=*), intent(in)	file_name,
		logical, intent(in), optional	is_gui_dialog,
		logical, intent(out), optional	is_write_error
	)

Save the model output arrays to a CSV data file.

Parameters

[in]	file_name	The name of the CSV file to save the data into.
[in]	is_gui_dialog	Optional indicator that error should report to GUI.
[out]	is_write_error	Optional file error indicator flag, if TRUE, reports error

handle_csv is the CSV file handle object defining the file name, Fortran unit and error descriptor, see HEDTOOLS manual for details.
csv_record is the temporary character string that keeps the whole record of the file, i.e. the whole row of the spreadsheet table.
COLUMNS is a parameter array that keeps all column headers; its size is equal to the total number of variables (columns) in the data spreadsheet file.

Definition at line 374 of file m_simulate.f90.

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◆ output_arrays_save_rate_data_csv()

impure subroutine simulate::output_arrays_save_rate_data_csv	(	character(len=*), intent(in)	file_name,
		logical, intent(in), optional	is_gui_dialog,
		logical, intent(out), optional	is_write_error
	)

Save the rate data arrays to a CSV data file.

Parameters

[in]	file_name	The name of the CSV file to save the data into.
[in]	is_gui_dialog	Optional indicator that error should report to GUI.
[out]	is_write_error	Optional file error indicator flag, if TRUE, reports error

handle_csv is the CSV file handle object defining the file name, Fortran unit and error descriptor, see HEDTOOLS manual for details.
csv_record is the temporary character string that keeps the whole record of the file, i.e. the whole row of the spreadsheet table.

Definition at line 506 of file m_simulate.f90.

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◆ csv_file_error_report()

impure subroutine simulate::csv_file_error_report	(	type(csv_file), intent(inout)	csv_handle,
		logical, intent(in), optional	is_gui_dialog
	)

Report CSV file write error.

Parameters

[in] is_gui_dialog Optional indicator that error should report to GUI.

Definition at line 626 of file m_simulate.f90.

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◆ stomach_transport_save_csv()

impure subroutine simulate::stomach_transport_save_csv ( character(len=*), intent(in) csv_file )

Save the stomach transport data pattern for a single food item.

Parameters

[in] csv_file The name of the CSV file is given as the argument.

Definition at line 638 of file m_simulate.f90.

◆ appetite_function_save_csv()

impure subroutine simulate::appetite_function_save_csv ( character(len=*), intent(in) csv_file )

Save the appetite function the_fish::appetite_func() pattern for plotting, testing or analysis.

Parameters

[in] csv_file The name of the CSV file is given as the argument.

Definition at line 661 of file m_simulate.f90.

◆ model_output_stats_txt()

pure character(len=:) function, allocatable simulate::model_output_stats_txt

Produce a text string containing general model output statistics.

Note: Note that this procedure outputs table formatted data string for terminal output and visual inspection.

Definition at line 690 of file m_simulate.f90.

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◆ model_output_stats_row_csv()

character(len=:) function, allocatable simulate::model_output_stats_row_csv ( logical, intent(in), optional show_header )

Produce a text string containing general model output statistics.

Note: Note that this procedure outputs CSV-formatted data string for saving in CSV output file. It does not write the csv output file.

Parameters

[in] show_header Optional flag indicating that variable names header is included as the first line of the string

Definition at line 768 of file m_simulate.f90.

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◆ test_run()

impure subroutine simulate::test_run

The procedure below is TEMPORARY, for testing and debugging.

Maximum number of food items to show, this should never be greater than commondata::max_food_items_index.

Provide and schedule a food item
- The fish decides to eat the food item scheduled
Update one time step of the fish stomach and mid-gut
Update the output arrays, use output_arrays_update_step().
Update the total count of food items eaten and not eaten

Definition at line 934 of file m_simulate.f90.

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◆ init_provisioning()

impure subroutine simulate::init_provisioning ( integer(long), intent(in), optional time_steps )

Initialise the food provisioning schedule / pattern.

Parameters

[in] time_steps Optional overall number of time steps of the model

Note: Note that this argument has the integer type of the kind commondata::long. This might taint default integer values.; This procedure cannot be pure because it allocates a global module-scope array.

Definition at line 1251 of file m_simulate.f90.

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◆ get_food_schedule_display()

impure integer function, dimension(:), allocatable simulate::get_food_schedule_display

Determine the food schedule array for separate display and analysis The primary role of this function is to plan (produce and display) the food provisioning pattern before simulation in GUI.

Definition at line 1299 of file m_simulate.f90.

◆ get_ingestion_ratio_waste()

real(srp) function, dimension(:), allocatable simulate::get_ingestion_ratio_waste ( integer, intent(in), optional rate_unit )

calculate the array of the consumption ratio, i.e. eaten/provided, so it is also easy to calculate the waste rate

Parameters

[in] rate_unit Optional rate parameter, the rate is calculated per this number of seconds, the default is per minute

Definition at line 1324 of file m_simulate.f90.

Variable Documentation

◆ is_extended_logging_debug_test

logical, parameter simulate::is_extended_logging_debug_test = .FALSE.

Flag for extended/detailed debug logging.

Definition at line 26 of file m_simulate.f90.

◆ is_urinal_branchial_kj_day

logical, parameter, private simulate::is_urinal_branchial_kj_day = .TRUE.

private

Flag that defines how urinal and branchial energy loss (UE+ZE) is calculated for model output arrays. If TRUE, UE+ZE is computed in kJ per kg per day (default), otherwise, in O2 equivalent unit: mg O2 / kg/hour.

Definition at line 32 of file m_simulate.f90.

◆ gui_idx_progress

integer, public simulate::gui_idx_progress

Progress bar widget ID for the GUI mode, needed to update at runtime.

Definition at line 35 of file m_simulate.f90.

◆ output_arrays

type(output_arrays_step_def), dimension(:), allocatable, public simulate::output_arrays

output_arrays instantiates the global data structure that keeps the model output arrays.

Definition at line 96 of file m_simulate.f90.

◆ output_stats

type(output_stats_total_def) simulate::output_stats

output_stats instantiates non-array global data structure that keeps total model output statistics, that are not arrays by time step.

Definition at line 109 of file m_simulate.f90.

Data Types

Functions/Subroutines

Variables

Detailed Description

Function/Subroutine Documentation

◆ total_timesteps()

◆ output_arrays_init()

◆ output_arrays_update_step()

◆ output_arrays_add_ingested()

Implementation notes

◆ output_arrays_save_csv()

◆ output_arrays_save_rate_data_csv()

◆ csv_file_error_report()

◆ stomach_transport_save_csv()

◆ appetite_function_save_csv()

◆ model_output_stats_txt()

◆ model_output_stats_row_csv()

◆ test_run()

◆ init_provisioning()

◆ get_food_schedule_display()

◆ get_ingestion_ratio_waste()

Variable Documentation

◆ is_extended_logging_debug_test

◆ is_urinal_branchial_kj_day

◆ gui_idx_progress

◆ output_arrays

◆ output_stats