A class to hold and interpolate time series data read from a NetCDF file. More...

#include <REMORA_NCTimeSeries.H>

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Public Member Functions
	NCTimeSeries (const amrex::Vector< std::string > &a_file_names, const std::string a_field_name, const std::string a_time_name, const amrex::Box &a_domain, amrex::MultiFab *a_mf_var, bool a_is2d, bool a_save_interpolated, double a_time_ref)
	Constructor.

void	Initialize ()
	Read in time array from file and allocate data arrays.

void	update_interpolated_to_time (double time, int lev, amrex::MultiFab *mf_lev, const amrex::Vector< amrex::Geometry > &geom, const amrex::Vector< amrex::IntVect > &ref_ratio)
	Calculate interpolated values at time, in seconds on the model clock, and fill data for level lev.

const amrex::MultiFab *	get_interpolated_mf (int lev) const
	Access interpolated data saved for a specific level.

Private Member Functions
void	read_in_at_time (amrex::MultiFab *mf, int itime)
	Read in data from file at time index itime and fill into mf.

amrex::IntVect	cumulative_ref_ratio (int lev, const amrex::Vector< amrex::IntVect > &ref_ratio) const
	Build cumulative refinement ratio from level 0 to lev.

Private Attributes
amrex::Vector< std::string >	file_names
	File names to read from.

amrex::Vector< int >	file_is_spatially_uniform
	Whether each file stores this field as one value per time record.

std::string	field_name
	Field name in netcdf file.

std::string	time_name
	Field name for time series in netcdf file.

amrex::Box	domain
	Domain.

bool	is2d
	Whether the field we're reading in is 2d.

bool	save_interpolated

double	time_ref

amrex::Vector< double >	ocean_times

amrex::Vector< int >	file_for_time
	File index to access a particular time.

amrex::Vector< int >	file_itime_offset
	Offset to access a particular time within its file.

int	i_time_before
	Time index immediately before the last time interpolated to.

double	time_before
	Time in ocean_times immediately before the last time interpolated to.

double	time_after
	Time in ocean_times immediately after the last time interpolated to.

bool	is_cycle
	Whether the time series is a cycle.

double	cycle_length
	If a cycle, what is the cycle length?

amrex::MultiFab *	mf_before
	Multifab to store data at time_before.

amrex::MultiFab *	mf_after
	Multifab to store data at time_after.

amrex::MultiFab *	mf_interp_lev0
	Multifab storing temporally interpolated data on level 0.

amrex::Vector< std::unique_ptr< amrex::MultiFab > >	mf_interpolated_lev
	Interpolated data on each requested AMR level if save_interpolated=true.

int	last_updated_lev = -1

amrex::MultiFab *	mf_var

Detailed Description

A class to hold and interpolate time series data read from a NetCDF file.

The class only ever holds the two time steps necessary to interpoplate to the current simulation time.

Definition at line 16 of file REMORA_NCTimeSeries.H.

Constructor & Destructor Documentation

◆ NCTimeSeries()

NCTimeSeries::NCTimeSeries	(	const amrex::Vector< std::string > &	a_file_names,
		const std::string	a_field_name,
		const std::string	a_time_name,
		const amrex::Box &	a_domain,
		amrex::MultiFab *	a_mf_var,
		bool	a_is2d,
		bool	a_save_interpolated,
		double	a_time_ref
	)

Constructor.

Parameters

[in]	a_file_names	vector of file name(s) to read from
[in]	a_field_name	name of field to read in
[in]	a_time_name	name of time variable in NetCDF file
[in]	a_domain	simulation domain
[in,out]	a_mf_var	MultiFab of data to either store into or reference for dimensions
[in]	a_is2d	Whether the variable we're working with is 2D
[in]	a_save_interpolated	Whether the interpolated value should be saved internally
[in]	a_time_ref	remora.time_ref, the reference date of the model clock

Definition at line 25 of file REMORA_NCTimeSeries.cpp.

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Member Function Documentation

◆ cumulative_ref_ratio()

amrex::IntVect NCTimeSeries::cumulative_ref_ratio	(	int	lev,
		const amrex::Vector< amrex::IntVect > &	ref_ratio
	)		const

private

Build cumulative refinement ratio from level 0 to lev.

Definition at line 326 of file REMORA_NCTimeSeries.cpp.

Referenced by update_interpolated_to_time().

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◆ get_interpolated_mf()

const amrex::MultiFab * NCTimeSeries::get_interpolated_mf ( int lev ) const

Access interpolated data saved for a specific level.

Definition at line 338 of file REMORA_NCTimeSeries.cpp.

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◆ Initialize()

void NCTimeSeries::Initialize ( )

Read in time array from file and allocate data arrays.

Definition at line 40 of file REMORA_NCTimeSeries.cpp.

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◆ read_in_at_time()

void NCTimeSeries::read_in_at_time	(	amrex::MultiFab *	mf,
		int	itime
	)

private

Read in data from file at time index itime and fill into mf.

Parameters

[in,out]	mf	multifab to store time step data into
[in]	itime	index of time step to read from file

Definition at line 355 of file REMORA_NCTimeSeries.cpp.

Referenced by update_interpolated_to_time().

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◆ update_interpolated_to_time()

void NCTimeSeries::update_interpolated_to_time	(	double	time,
		int	lev,
		amrex::MultiFab *	mf_lev,
		const amrex::Vector< amrex::Geometry > &	geom,
		const amrex::Vector< amrex::IntVect > &	ref_ratio
	)

Calculate interpolated values at time, in seconds on the model clock, and fill data for level lev.

Parameters

time	time to interpolate to

Definition at line 201 of file REMORA_NCTimeSeries.cpp.

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Member Data Documentation

◆ cycle_length

double NCTimeSeries::cycle_length

private

If a cycle, what is the cycle length?

Definition at line 85 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ domain

amrex::Box NCTimeSeries::domain

private

Domain.

Definition at line 57 of file REMORA_NCTimeSeries.H.

Referenced by NCTimeSeries(), and read_in_at_time().

◆ field_name

std::string NCTimeSeries::field_name

private

Field name in netcdf file.

Definition at line 53 of file REMORA_NCTimeSeries.H.

Referenced by get_interpolated_mf(), Initialize(), NCTimeSeries(), read_in_at_time(), and update_interpolated_to_time().

◆ file_for_time

amrex::Vector<int> NCTimeSeries::file_for_time

private

File index to access a particular time.

Definition at line 73 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and read_in_at_time().

◆ file_is_spatially_uniform

amrex::Vector<int> NCTimeSeries::file_is_spatially_uniform

private

Whether each file stores this field as one value per time record.

Definition at line 51 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and read_in_at_time().

◆ file_itime_offset

amrex::Vector<int> NCTimeSeries::file_itime_offset

private

Offset to access a particular time within its file.

Definition at line 75 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and read_in_at_time().

◆ file_names

amrex::Vector<std::string> NCTimeSeries::file_names

private

File names to read from.

Definition at line 49 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), NCTimeSeries(), and read_in_at_time().

◆ i_time_before

int NCTimeSeries::i_time_before

private

Time index immediately before the last time interpolated to.

Definition at line 77 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ is2d

bool NCTimeSeries::is2d

private

Whether the field we're reading in is 2d.

Definition at line 60 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), NCTimeSeries(), and read_in_at_time().

◆ is_cycle

bool NCTimeSeries::is_cycle

private

Whether the time series is a cycle.

Definition at line 83 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ last_updated_lev

int NCTimeSeries::last_updated_lev = -1

private

Level of the most recent update. One series serves every level, and under subcycling the levels ask for different times, so a saved buffer is only current for the level that last updated it. Callers update immediately before reading; this records enough to catch a caller that stops doing so.

Definition at line 100 of file REMORA_NCTimeSeries.H.

Referenced by get_interpolated_mf(), and update_interpolated_to_time().

◆ mf_after

amrex::MultiFab* NCTimeSeries::mf_after

private

Multifab to store data at time_after.

Definition at line 90 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ mf_before

amrex::MultiFab* NCTimeSeries::mf_before

private

Multifab to store data at time_before.

Definition at line 88 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ mf_interp_lev0

amrex::MultiFab* NCTimeSeries::mf_interp_lev0

private

Multifab storing temporally interpolated data on level 0.

Definition at line 92 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ mf_interpolated_lev

amrex::Vector<std::unique_ptr<amrex::MultiFab> > NCTimeSeries::mf_interpolated_lev

private

Interpolated data on each requested AMR level if save_interpolated=true.

Definition at line 94 of file REMORA_NCTimeSeries.H.

Referenced by get_interpolated_mf(), and update_interpolated_to_time().

◆ mf_var

amrex::MultiFab* NCTimeSeries::mf_var

private

Pointer to REMORA data that corresponds to the variable being interpolated. Filled by update_interpolated_to_time if save_interpolated==false. Otherwise, just used for getting box array, nodality, and distribution mapping

Definition at line 104 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and NCTimeSeries().

◆ ocean_times

amrex::Vector<double> NCTimeSeries::ocean_times

private

Time points in netcdf file, in seconds on the model clock. Double, like every time on the model clock: see REMORA::t_new.

Definition at line 71 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and update_interpolated_to_time().

◆ save_interpolated

bool NCTimeSeries::save_interpolated

private

Whether to save interpolated results in mf_interpolated. If false, data will be calculated to mf_var

Definition at line 63 of file REMORA_NCTimeSeries.H.

Referenced by get_interpolated_mf(), NCTimeSeries(), and update_interpolated_to_time().

◆ time_after

double NCTimeSeries::time_after

private

Time in ocean_times immediately after the last time interpolated to.

Definition at line 81 of file REMORA_NCTimeSeries.H.

Referenced by update_interpolated_to_time().

◆ time_before

double NCTimeSeries::time_before

private

Time in ocean_times immediately before the last time interpolated to.

Definition at line 79 of file REMORA_NCTimeSeries.H.

Referenced by update_interpolated_to_time().

◆ time_name

std::string NCTimeSeries::time_name

private

Field name for time series in netcdf file.

Definition at line 55 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and NCTimeSeries().

◆ time_ref

double NCTimeSeries::time_ref

private

remora.time_ref: the reference date the model clock counts from. The file's times are placed on that clock from the reference date in their units attribute. Double, like every reference date.

Definition at line 67 of file REMORA_NCTimeSeries.H.

Referenced by Initialize(), and NCTimeSeries().

The documentation for this class was generated from the following files:

/home/runner/work/REMORA/REMORA/Source/IO/REMORA_NCTimeSeries.H
/home/runner/work/REMORA/REMORA/Source/IO/REMORA_NCTimeSeries.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NCTimeSeries()

Member Function Documentation

◆ cumulative_ref_ratio()

◆ get_interpolated_mf()

◆ Initialize()

◆ read_in_at_time()

◆ update_interpolated_to_time()

Member Data Documentation

◆ cycle_length

◆ domain

◆ field_name

◆ file_for_time

◆ file_is_spatially_uniform

◆ file_itime_offset

◆ file_names

◆ i_time_before

◆ is2d

◆ is_cycle

◆ last_updated_lev

◆ mf_after

◆ mf_before

◆ mf_interp_lev0

◆ mf_interpolated_lev

◆ mf_var

◆ ocean_times

◆ save_interpolated

◆ time_after

◆ time_before

◆ time_name

◆ time_ref