Declarations required for the calculation of absorption coefficients. More...

#include <stdexcept>
#include <cmath>
#include "matpackI.h"
#include "array.h"
#include "mystring.h"
#include "make_array.h"
#include "messages.h"
#include "abs_species_tags.h"
#include "linerecord.h"
#include "linemixingrecord.h"

Include dependency graph for absorption.h:

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Go to the source code of this file.

Classes
class	LineshapeRecord
	Lineshape related information. More...

class	LineshapeNormRecord
	Lineshape related normalization function information. More...

class	LineshapeSpec
	Lineshape related specification like which lineshape to use, the normalizationfactor, and the cutoff. More...

class	IsotopologueRecord
	Contains the lookup data for one isotopologue. More...

class	SpeciesRecord
	Contains the lookup data for one species. More...

class	SpeciesAuxData
	Auxiliary data for isotopologues. More...

class	SpecIsoMap

Typedefs
typedef void(*	lsf_type) (Vector &, Vector &, Vector &, const Numeric, const Numeric, const Numeric, ConstVectorView)
	The type that is used to store pointers to lineshape functions. More...

typedef void(*	lsnf_type) (Vector &, const Numeric, ConstVectorView, const Numeric)
	The type that is used to store pointers to lineshape normalization functions. More...

typedef Array< LineshapeSpec >	ArrayOfLineshapeSpec
	Holds a list of lineshape specifications: function, normalization, cutoff. More...

Functions
ostream &	operator<< (ostream &os, const LineshapeSpec &lsspec)

void	checkIsotopologueRatios (const ArrayOfArrayOfSpeciesTag &abs_species, const SpeciesAuxData &sad)
	Check that isotopologue ratios for the given species are correctly defined. More...

void	fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData (SpeciesAuxData &sad)
	Fill SpeciesAuxData with default isotopologue ratios from species data. More...

ostream &	operator<< (ostream &os, const SpeciesRecord &sr)
	Output operator for SpeciesRecord. More...

ostream &	operator<< (ostream &os, const SpeciesAuxData &sad)
	Output operator for SpeciesAuxData. More...

void	define_species_map ()
	Define the species data map. More...

void	xsec_species (MatrixView xsec_attenuation, MatrixView xsec_phase, ConstVectorView f_grid, ConstVectorView abs_p, ConstVectorView abs_t, ConstMatrixView all_vmrs, const ArrayOfArrayOfSpeciesTag &abs_species, const Index this_species, const ArrayOfLineRecord &abs_lines, const Index ind_ls, const Index ind_lsn, const Numeric cutoff, const SpeciesAuxData &isotopologue_ratios, const Verbosity &verbosity)
	Calculate line absorption cross sections for one tag group. More...

void	xsec_species_line_mixing_wrapper (MatrixView xsec_attenuation, MatrixView xsec_phase, const ArrayOfArrayOfLineMixingRecord &line_mixing_data, const ArrayOfArrayOfIndex &line_mixing_data_lut, ConstVectorView f_grid, ConstVectorView abs_p, ConstVectorView abs_t, ConstMatrixView all_vmrs, const ArrayOfArrayOfSpeciesTag &abs_species, const Index this_species, const ArrayOfLineRecord &abs_lines, const Index ind_ls, const Index ind_lsn, const Numeric cutoff, const SpeciesAuxData &isotopologue_ratios, const Verbosity &verbosity)
	This will work as a wrapper for linemixing when abs_species contain relevant data. More...

void	xsec_species_line_mixing_2nd_order (MatrixView xsec_attenuation, MatrixView xsec_phase, const ArrayOfArrayOfLineMixingRecord &line_mixing_data, const ArrayOfArrayOfIndex &line_mixing_data_lut, ConstVectorView f_grid, ConstVectorView abs_p, ConstVectorView abs_t, ConstMatrixView all_vmrs, const ArrayOfArrayOfSpeciesTag &abs_species, const Index this_species, const ArrayOfLineRecord &abs_lines, const Index ind_ls, const Index ind_lsn, const Numeric cutoff, const SpeciesAuxData &isotopologue_ratios, const Verbosity &verbosity)
	This is the second order line mixing correction as presented by: Makarov, D.S, M.Yu. More...

Numeric	wavenumber_to_joule (Numeric e)
	A little helper function to convert energy from units of wavenumber (cm^-1) to Joule (J). More...

Index	species_index_from_species_name (String name)
	Return species index for given species name. More...

String	species_name_from_species_index (const Index spec_ind)
	Return species name for given species index. More...

void	convHitranIERF (Numeric &mdf, const Index &df)

void	convHitranIERSH (Numeric &mdh, const Index &dh)

void	convMytranIER (Numeric &mdh, const Index &dh)

void	abs_n2Set (Vector &abs_n2, const ArrayOfArrayOfSpeciesTag &abs_species, const Matrix &abs_vmrs, const Verbosity &)
	abs_n2Set. More...

void	abs_h2oSet (Vector &abs_h2o, const ArrayOfArrayOfSpeciesTag &abs_species, const Matrix &abs_vmrs, const Verbosity &)
	abs_h2oSet. More...

Detailed Description

Declarations required for the calculation of absorption coefficients.

This is the file from arts-1-0, back-ported to arts-1-1.

Author: Stefan Buehler, Axel von Engeln

Definition in file absorption.h.

Typedef Documentation

◆ ArrayOfLineshapeSpec

typedef Array<LineshapeSpec> ArrayOfLineshapeSpec

Holds a list of lineshape specifications: function, normalization, cutoff.

Author: Axel von Engeln

Definition at line 185 of file absorption.h.

◆ lsf_type

typedef void(* lsf_type) (Vector &, Vector &, Vector &, const Numeric, const Numeric, const Numeric, ConstVectorView)

The type that is used to store pointers to lineshape functions.

Definition at line 45 of file absorption.h.

◆ lsnf_type

typedef void(* lsnf_type) (Vector &, const Numeric, ConstVectorView, const Numeric)

The type that is used to store pointers to lineshape normalization functions.

Definition at line 96 of file absorption.h.

Function Documentation

◆ abs_h2oSet()

void abs_h2oSet	(	Vector &	abs_h2o,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Matrix &	abs_vmrs,
		const Verbosity &
	)

abs_h2oSet.

Sets abs_h2o to the profile of the first tag group containing water.

This is necessary, because for example abs_coefCalc requires abs_h2o to contain the water vapour profile(the reason for this is the calculation of oxygen line broadening requires water vapour profile). Then this function can be used to copy the profile of the first tag group of water.

Author: Stefan Buehler

Parameters

[out]	abs_h2o	WS Output
[in]	abs_species	WS Input
[in]	abs_vmrs	WS Input

Definition at line 1287 of file m_abs.cc.

References find_first_species_tg(), joker, ConstMatrixView::ncols(), Vector::resize(), and species_index_from_species_name().

Referenced by abs_xsec_per_speciesAddConts().

◆ abs_n2Set()

void abs_n2Set	(	Vector &	abs_n2,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Matrix &	abs_vmrs,
		const Verbosity &
	)

abs_n2Set.

Sets abs_n2 to the profile of the first tag group containing molecular nitrogen. See abs_h2oSet for more details.

Author: Stefan Buehler

Parameters

[out]	abs_n2	WS Output
[in]	abs_species	WS Input
[in]	abs_vmrs	WS Input

Definition at line 1315 of file m_abs.cc.

References find_first_species_tg(), joker, ConstMatrixView::ncols(), Vector::resize(), and species_index_from_species_name().

Referenced by abs_xsec_per_speciesAddConts().

◆ checkIsotopologueRatios()

void checkIsotopologueRatios	(	const ArrayOfArrayOfSpeciesTag &	abs_species,
		const SpeciesAuxData &	sad
	)

Check that isotopologue ratios for the given species are correctly defined.

Definition at line 245 of file absorption.cc.

References SpeciesAuxData::getParam(), SpeciesAuxData::getParams(), iso(), SpeciesRecord::Isotopologue(), SpeciesRecord::Name(), Array< base >::nelem(), and global_data::species_data.

Referenced by abs_xsec_per_speciesAddLines(), and propmat_clearskyAddZeeman().

◆ convHitranIERF()

void convHitranIERF	(	Numeric &	mdf,
		const Index &	df
	)

Definition at line 1327 of file absorption.cc.

Referenced by LineRecord::ReadFromHitran2001Stream(), and LineRecord::ReadFromHitran2004Stream().

◆ convHitranIERSH()

void convHitranIERSH	(	Numeric &	mdh,
		const Index &	dh
	)

Definition at line 1374 of file absorption.cc.

Referenced by LineRecord::ReadFromHitran2001Stream(), and LineRecord::ReadFromHitran2004Stream().

◆ convMytranIER()

void convMytranIER	(	Numeric &	mdh,
		const Index &	dh
	)

Definition at line 1433 of file absorption.cc.

Referenced by LineRecord::ReadFromMytran2Stream().

◆ define_species_map()

void define_species_map ( )

Define the species data map.

Author: Stefan Buehler

Define the species data map.

Author: Stefan Buehler

Definition at line 322 of file absorption.cc.

References global_data::species_data, and SpeciesMap.

Referenced by main().

◆ fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData()

void fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData ( SpeciesAuxData & sad )

Fill SpeciesAuxData with default isotopologue ratios from species data.

Definition at line 305 of file absorption.cc.

References IsotopologueRecord::Abundance(), SpeciesAuxData::initParams(), SpeciesAuxData::setParam(), and global_data::species_data.

Referenced by isotopologue_ratiosInitFromBuiltin().

◆ operator<<() [1/3]

ostream& operator<<	(	ostream &	os,
		const LineshapeSpec &	lsspec
	)

Definition at line 1494 of file absorption.cc.

References LineshapeSpec::Cutoff(), LineshapeSpec::Ind_ls(), and LineshapeSpec::Ind_lsn().

◆ operator<<() [2/3]

ostream& operator<<	(	ostream &	os,
		const SpeciesRecord &	sr
	)

Output operator for SpeciesRecord.

Incomplete version: only writes SpeciesName.

Author: Jana Mendrok

Definition at line 333 of file absorption.cc.

References SpeciesRecord::Isotopologue(), SpeciesRecord::Name(), and Array< base >::nelem().

◆ operator<<() [3/3]

ostream& operator<<	(	ostream &	os,
		const SpeciesAuxData &	sad
	)

Output operator for SpeciesAuxData.

Author: Oliver Lemke

Definition at line 343 of file absorption.cc.

References SpeciesAuxData::getParams().

◆ species_index_from_species_name()

Index species_index_from_species_name ( String name )

Return species index for given species name.

This is useful in connection with other functions that need a species index.

See also: find_first_species_tg.

Parameters

name	Species name.

Returns: Species index, -1 means not found.

Author: Stefan Buehler

Date: 2003-01-13

Definition at line 1260 of file absorption.cc.

References SpeciesMap, and my_basic_string< charT >::trim().

Referenced by abs_h2oSet(), abs_lookupCalc(), abs_lookupSetup(), abs_lookupSetupBatch(), abs_lookupSetupWide(), abs_lookupTestAccMC(), abs_lookupTestAccuracy(), abs_n2Set(), abs_o2Set(), LineRecord::BroadSpecSpecIndex(), choose_abs_nls(), GasAbsLookup::Extract(), find_nonlinear_continua(), refr_index_airMWgeneral(), refr_index_airThayer(), CIARecord::SetMoleculeName(), SpeciesTag::SpeciesTag(), xml_read_from_stream(), and z_fieldFromHSE().

◆ species_name_from_species_index()

String species_name_from_species_index ( const Index spec_ind )

Return species name for given species index.

This is useful in connection with other functions that use a species index.

Does an assertion that the index really corresponds to a species.

Parameters

spec_ind Species index.

Returns: Species name

Author: Stefan Buehler

Date: 2013-01-04

Definition at line 1301 of file absorption.cc.

References global_data::species_data.

Referenced by abs_cia_dataReadFromCIA(), abs_cia_dataReadFromXML(), get_species_name(), CIARecord::MoleculeName(), SpeciesTag::Name(), and xml_write_to_stream().

◆ wavenumber_to_joule()

Numeric wavenumber_to_joule ( Numeric e )

A little helper function to convert energy from units of wavenumber (cm^-1) to Joule (J).

This is used when reading HITRAN or JPL catalogue files, which have the lower state energy in cm^-1.

Returns: Energy in J.

Parameters

e	Energy in cm^-1.

Author: Stefan Buehler

Date: 2001-06-26

Definition at line 1227 of file absorption.cc.

References PLANCK_CONST, and SPEED_OF_LIGHT.

Referenced by LineRecord::ReadFromHitran2001Stream(), LineRecord::ReadFromHitran2004Stream(), LineRecord::ReadFromJplStream(), and LineRecord::ReadFromMytran2Stream().

◆ xsec_species()

void xsec_species	(	MatrixView	xsec_attenuation,
		MatrixView	xsec_phase,
		ConstVectorView	f_grid,
		ConstVectorView	abs_p,
		ConstVectorView	abs_t,
		ConstMatrixView	all_vmrs,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Index	this_species,
		const ArrayOfLineRecord &	abs_lines,
		const Index	ind_ls,
		const Index	ind_lsn,
		const Numeric	cutoff,
		const SpeciesAuxData &	isotopologue_ratios,
		const Verbosity &	verbosity
	)

Calculate line absorption cross sections for one tag group.

All lines in the line list must belong to the same species. This must be ensured by abs_lines_per_speciesCreateFromLines, so it is only verified with assert. Also, the input vectors abs_p, and abs_t must all have the same dimension.

This is mainly a copy of abs_species which is removed now, with the difference that the vmrs are removed from the absorption coefficient calculation. (the vmr is still used for the self broadening)

Continua are not handled by this function, you have to call xsec_continuum_tag for those.

Return values

xsec	Cross section of one tag group. This is now the true absorption cross section in units of m^2.

Parameters

f_grid	Frequency grid.
abs_p	Pressure grid.
abs_t	Temperatures associated with abs_p.
all_vmrs	Gas volume mixing ratios [nspecies, np].
abs_species	Species tags for all species.
this_species	Index of the current species in abs_species.
abs_lines	The spectroscopic line list.
ind_ls	Index to lineshape function.
ind_lsn	Index to lineshape norm.
cutoff	Lineshape cutoff.
isotopologue_ratios	Isotopologue ratios.

Author: Stefan Buehler and Axel von Engeln

Date: 2001-01-11

Changed from pseudo cross sections to true cross sections

Author: Stefan Buehler

Date: 2007-08-08

Adapted to new Perrin line parameters, treating broadening by different gases explicitly

Author: Stefan Buehler

Date: 2012-09-03

Definition at line 594 of file absorption.cc.

References LineRecord::Agam(), arts_omp_get_max_threads(), arts_omp_get_thread_num(), arts_omp_in_parallel(), AVOGADROS_NUMB, BOLTZMAN_CONST, calc_gamma_and_deltaf_artscat4(), IsotopologueRecord::CalculatePartitionFctRatio(), LineRecord::Elow(), LineRecord::F(), fac(), find_broad_spec_locations(), SpeciesAuxData::getParam(), LineRecord::I0(), is_sorted(), LineRecord::Isotopologue(), LineRecord::IsotopologueData(), joker, global_data::lineshape_data, global_data::lineshape_norm_data, IsotopologueRecord::Mass(), LineRecord::Nair(), IsotopologueRecord::Name(), ConstMatrixView::ncols(), Array< base >::nelem(), ConstVectorView::nelem(), ConstMatrixView::nrows(), LineRecord::Nself(), PLANCK_CONST, LineRecord::Psf(), LineRecord::Sgam(), LineRecord::Species(), SPEED_OF_LIGHT, LineRecord::Tgam(), LineRecord::Ti0(), and LineRecord::Version().

Referenced by abs_xsec_per_speciesAddLines(), xsec_species_line_mixing_2nd_order(), and xsec_species_line_mixing_wrapper().

◆ xsec_species_line_mixing_2nd_order()

void xsec_species_line_mixing_2nd_order	(	MatrixView	xsec_attenuation,
		MatrixView	xsec_phase,
		const ArrayOfArrayOfLineMixingRecord &	line_mixing_data,
		const ArrayOfArrayOfIndex &	line_mixing_data_lut,
		ConstVectorView	f_grid,
		ConstVectorView	abs_p,
		ConstVectorView	abs_t,
		ConstMatrixView	all_vmrs,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Index	this_species,
		const ArrayOfLineRecord &	abs_lines,
		const Index	ind_ls,
		const Index	ind_lsn,
		const Numeric	cutoff,
		const SpeciesAuxData &	isotopologue_ratios,
		const Verbosity &	verbosity
	)

This is the second order line mixing correction as presented by: Makarov, D.S, M.Yu.

Tretyakov and P.W. Rosenkranz, 2011, 60-GHz oxygen band: Precise experimental profiles and extended absorption modeling in a wide temperature range, JQSRT 112, 1420-1428.

Return values

xsec_attenuation	Cross section of one tag group. This is now the true attenuation cross section in units of m^2.
xsec_phase	Cross section of one tag group. This is now the true phase cross section in units of m^2.

Parameters

line_mixing_data	Line mixing data for specific type of line mixing.
line_mixing_data_lut	Line mixing data lookup table.
f_grid	Frequency grid.
abs_p	Pressure grid.
abs_t	Temperatures associated with abs_p.
all_vmrs	Gas volume mixing ratios [nspecies, np].
abs_species	Species tags for all species.
this_species	Index of the current species in abs_species.
abs_lines	The spectroscopic line list.
ind_ls	Index to lineshape function.
ind_lsn	Index to lineshape norm.
cutoff	Lineshape cutoff.
isotopologue_ratios	Isotopologue ratios.

Author: Richard Larsson

Date: 2013-04-24

Definition at line 1598 of file absorption.cc.

References joker, global_data::lineshape_data, ll, Array< base >::nelem(), ConstVectorView::nelem(), ConstMatrixView::nrows(), and xsec_species().

Referenced by xsec_species_line_mixing_wrapper().

◆ xsec_species_line_mixing_wrapper()

void xsec_species_line_mixing_wrapper	(	MatrixView	xsec_attenuation,
		MatrixView	xsec_phase,
		const ArrayOfArrayOfLineMixingRecord &	line_mixing_data,
		const ArrayOfArrayOfIndex &	line_mixing_data_lut,
		ConstVectorView	f_grid,
		ConstVectorView	abs_p,
		ConstVectorView	abs_t,
		ConstMatrixView	all_vmrs,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Index	this_species,
		const ArrayOfLineRecord &	abs_lines,
		const Index	ind_ls,
		const Index	ind_lsn,
		const Numeric	cutoff,
		const SpeciesAuxData &	isotopologue_ratios,
		const Verbosity &	verbosity
	)

This will work as a wrapper for linemixing when abs_species contain relevant data.

The funciton will only pass on arguments to xsec_species if there is no linemixing.

Return values

xsec_attenuation	Cross section of one tag group. This is now the true attenuation cross section in units of m^2.
xsec_phase	Cross section of one tag group. This is now the true phase cross section in units of m^2.

Parameters

line_mixing_data	Line mixing data for specific type of line mixing.
line_mixing_data_lut	Line mixing data lookup table.
f_grid	Frequency grid.
abs_p	Pressure grid.
abs_t	Temperatures associated with abs_p.
all_vmrs	Gas volume mixing ratios [nspecies, np].
abs_species	Species tags for all species.
this_species	Index of the current species in abs_species.
abs_lines	The spectroscopic line list.
ind_ls	Index to lineshape function.
ind_lsn	Index to lineshape norm.
cutoff	Lineshape cutoff.
isotopologue_ratios	Isotopologue ratios.

Author: Richard Larsson

Date: 2013-04-24

Definition at line 1530 of file absorption.cc.

References SpeciesTag::LINE_MIXING_TYPE_2NDORDER, SpeciesTag::LINE_MIXING_TYPE_NONE, xsec_species(), and xsec_species_line_mixing_2nd_order().

Referenced by abs_xsec_per_speciesAddLines(), and xsec_species_line_mixing_wrapper_with_zeeman().

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ ArrayOfLineshapeSpec

◆ lsf_type

◆ lsnf_type

Function Documentation

◆ abs_h2oSet()

◆ abs_n2Set()

◆ checkIsotopologueRatios()

◆ convHitranIERF()

◆ convHitranIERSH()

◆ convMytranIER()

◆ define_species_map()

◆ fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData()

◆ operator<<() [1/3]

◆ operator<<() [2/3]

◆ operator<<() [3/3]

◆ species_index_from_species_name()

◆ species_name_from_species_index()

◆ wavenumber_to_joule()

◆ xsec_species()

◆ xsec_species_line_mixing_2nd_order()

◆ xsec_species_line_mixing_wrapper()