Physical absorption routines. More...

#include "absorption.h"
#include <algorithm>
#include <cfloat>
#include <cmath>
#include <cstdlib>
#include <map>
#include "arts.h"
#include "auto_md.h"
#include "file.h"
#include "interpolation_poly.h"
#include "linescaling.h"
#include "logic.h"
#include "math_funcs.h"
#include "messages.h"
#include "global_data.h"
#include "linefunctions.h"

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

void	checkPartitionFunctions (const ArrayOfArrayOfSpeciesTag &abs_species, const SpeciesAuxData &partfun)
	Check that partition functions for the given species are correctly defined. More...

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

void	fillSpeciesAuxDataWithPartitionFunctionsFromSpeciesData (SpeciesAuxData &sad)
	Fill SpeciesAuxData with default partition functions 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...

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	set_vmr_from_first_species (Vector &vmr, const String &species_name, const ArrayOfArrayOfSpeciesTag &abs_species, const Matrix &abs_vmrs)
	set_abs_from_first_species. More...

const SpeciesRecord &	SpeciesDataOfBand (const AbsorptionLines &band)
	Returns the species data. More...

void	xsec_species (Matrix &xsec, Matrix &source, Matrix &phase, ArrayOfMatrix &dxsec_dx, ArrayOfMatrix &dsource_dx, ArrayOfMatrix &dphase_dx, const ArrayOfRetrievalQuantity &jacobian_quantities, const ArrayOfIndex &jacobian_propmat_positions, const Vector &f_grid, const Vector &abs_p, const Vector &abs_t, const EnergyLevelMap &abs_nlte, const Matrix &abs_vmrs, const ArrayOfArrayOfSpeciesTag &abs_species, const AbsorptionLines &band, const Numeric &isot_ratio, const SpeciesAuxData::AuxType &partfun_type, const ArrayOfGriddedField1 &partfun_data)
	Cross-section algorithm. More...

Detailed Description

Physical absorption routines.

The absorption workspace methods are in file m_abs.cc

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

Author: Stefan Buehler and Axel von Engeln

Definition in file absorption.cc.

Function Documentation

◆ checkIsotopologueRatios()

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

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

Definition at line 301 of file absorption.cc.

References SpeciesAuxData::getParam(), i, iso(), SpeciesRecord::Isotopologue(), SpeciesRecord::Name(), Array< base >::nelem(), SpeciesAuxData::nisotopologues(), SpeciesAuxData::nspecies(), global_data::species_data, and _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str().

Referenced by lbl_checkedCalc().

◆ checkPartitionFunctions()

void checkPartitionFunctions	(	const ArrayOfArrayOfSpeciesTag &	abs_species,
		const SpeciesAuxData &	partfun
	)

Check that partition functions for the given species are correctly defined.

Definition at line 356 of file absorption.cc.

References i, SpeciesRecord::Isotopologue(), SpeciesRecord::Name(), Array< base >::nelem(), SpeciesAuxData::nisotopologues(), SpeciesAuxData::nspecies(), global_data::species_data, and _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str().

Referenced by lbl_checkedCalc().

◆ fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData()

void fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData ( SpeciesAuxData & sad )

Fill SpeciesAuxData with default isotopologue ratios from species data.

Definition at line 394 of file absorption.cc.

References SpeciesAuxData::AT_ISOTOPOLOGUE_RATIO, SpeciesAuxData::InitFromSpeciesData(), SpeciesAuxData::setParam(), and global_data::species_data.

Referenced by isotopologue_ratiosInitFromBuiltin().

◆ fillSpeciesAuxDataWithPartitionFunctionsFromSpeciesData()

void fillSpeciesAuxDataWithPartitionFunctionsFromSpeciesData ( SpeciesAuxData & sad )

Fill SpeciesAuxData with default partition functions from species data.

Definition at line 417 of file absorption.cc.

References SpeciesAuxData::AT_PARTITIONFUNCTION_COEFF, SpeciesAuxData::InitFromSpeciesData(), ConstVectorView::nelem(), nlinspace(), SpeciesAuxData::setParam(), and global_data::species_data.

Referenced by partition_functionsInitFromBuiltin().

◆ operator<<() [1/2]

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

Output operator for SpeciesRecord.

Incomplete version: only writes SpeciesName.

Author: Jana Mendrok

Definition at line 467 of file absorption.cc.

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

◆ operator<<() [2/2]

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

Output operator for SpeciesAuxData.

Author: Oliver Lemke

Definition at line 474 of file absorption.cc.

References SpeciesAuxData::getParam(), SpeciesAuxData::getTypeString(), iso(), Array< base >::nelem(), SpeciesAuxData::nisotopologues(), SpeciesAuxData::nspecies(), global_data::species_data, and species_name_from_species_index().

◆ set_vmr_from_first_species()

void set_vmr_from_first_species	(	Vector &	vmr,
		const String &	species_name,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Matrix &	abs_vmrs
	)

set_abs_from_first_species.

Returns vmr for the profile of the first tag group containing the given species.

Author: Oliver Lemke

Parameters

[out]	vmr	Volume mixing ratio
[in]	species_name	Species Name
[in]	abs_species	WS Input
[in]	abs_vmrs	WS Input

Definition at line 597 of file absorption.cc.

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

Referenced by abs_xsec_per_speciesAddConts().

◆ 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

[in] name Species name.

Returns: Species index, -1 means not found.

Author: Stefan Buehler

Date: 2003-01-13

Definition at line 531 of file absorption.cc.

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

Referenced by abs_lookupCalc(), abs_lookupSetup(), abs_lookupSetupBatch(), abs_lookupTestAccMC(), abs_lookupTestAccuracy(), choose_abs_nls(), GasAbsLookup::Extract(), find_nonlinear_continua(), get_lande_spin_constant(), SpeciesTag::IsIsotopologue(), SpeciesTag::IsSpecies(), parse_a1_sym_hitran(), parse_a1_x_hitran(), postprocess_group1_hitran(), postprocess_group5_hitran(), postprocess_group6_hitran(), postprocess_group6oh_hitran(), refr_index_airMicrowavesEarth(), set_vmr_from_first_species(), QuantumParserHITRAN2004::SetClassGroup(), CIARecord::SetMoleculeName(), SpeciesTag::SpeciesTag(), test_K1_and_K2(), test_partitionfunction(), 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

[in] spec_ind Species index.

Returns: Species name

Author: Stefan Buehler

Date: 2013-01-04

Definition at line 569 of file absorption.cc.

References global_data::species_data.

Referenced by abs_cia_dataReadFromCIA(), abs_cia_dataReadFromXML(), get_species_name(), CIARecord::MoleculeName(), SpeciesTag::Name(), operator<<(), XsecRecord::SpeciesName(), QuantumIdentifier::SpeciesName(), and SpeciesTag::SpeciesNameMain().

◆ SpeciesDataOfBand()

const SpeciesRecord& SpeciesDataOfBand ( const AbsorptionLines & band )

Returns the species data.

Parameters

band	An absorption band

Returns: const ref to the species record

Definition at line 611 of file absorption.cc.

References Absorption::Lines::Species(), and global_data::species_data.

Referenced by abs_lines_per_speciesCreateFromLines().

◆ 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

[in] e Energy in cm^-1.

Author: Stefan Buehler

Date: 2001-06-26

Definition at line 500 of file absorption.cc.

◆ xsec_species()

void xsec_species	(	Matrix &	xsec,
		Matrix &	source,
		Matrix &	phase,
		ArrayOfMatrix &	dxsec_dx,
		ArrayOfMatrix &	dsource_dx,
		ArrayOfMatrix &	dphase_dx,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const ArrayOfIndex &	jacobian_propmat_positions,
		const Vector &	f_grid,
		const Vector &	abs_p,
		const Vector &	abs_t,
		const EnergyLevelMap &	abs_nlte,
		const Matrix &	abs_vmrs,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const AbsorptionLines &	band,
		const Numeric &	isot_ratio,
		const SpeciesAuxData::AuxType &	partfun_type,
		const ArrayOfGriddedField1 &	partfun_data
	)

Cross-section algorithm.

Parameters

[in,out]	xsec	Cross section of one tag group. This is now the true attenuation cross section in units of m^2.
[in,out]	sourceCross	section of one tag group. This is now the true source cross section in units of m^2.
[in,out]	phase	Cross section of one tag group. This is now the true phase cross section in units of m^2.
[in,out]	dxsec	Partial derivatives of xsec.
[in,out]	dsource	Partial derivatives of source.
[in,out]	dphase	Partial derivatives of phase.
[in]	jacobian_quantities	As WSV
[in]	jacobian_propmat_positions	Positions in jacobian_quantities affected by propmat calculations
[in]	f_grid	As WSV
[in]	abs_p	As WSV
[in]	abs_t	As WSV
[in]	abs_nlte	As WSV
[in]	abs_vmrs	As WSV
[in]	abs_species	As WSV
[in]	band	A single absorption band
[in]	isot_ratio	Isotopologue ratio of this species
[in]	partfun_type	Partition function type for this species
[in]	partfun_data	Partition function model data for this species

Author: Richard Larsson

Date: 2019-10-10

Definition at line 616 of file absorption.cc.

References Absorption::Lines::BroadeningSpeciesVMR(), Linefunctions::dDopplerConstant_dT(), Linefunctions::InternalData::dF, Linefunctions::InternalData::dN, Linefunctions::DopplerConstant(), dsingle_partition_function_dT(), ConstMatrixView::empty(), Linefunctions::InternalData::F, joker, MapToEigen(), Linefunctions::InternalData::N, Array< base >::nelem(), ConstVectorView::nelem(), ConstMatrixView::nrows(), Absorption::Lines::NumLines(), Linefunctions::set_cross_section_of_band(), single_partition_function(), Absorption::Lines::SpeciesMass(), Absorption::Lines::T0(), and temperature_perturbation().

Referenced by abs_xsec_per_speciesAddLines().