Physical absorption routines. More...

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

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

void	define_species_map ()
	Define the species data map. 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	find_broad_spec_locations (ArrayOfIndex &broad_spec_locations, const ArrayOfArrayOfSpeciesTag &abs_species, const Index this_species)
	Find the location of all broadening species in abs_species. More...

void	calc_gamma_and_deltaf_artscat4 (Numeric &gamma, Numeric &deltaf, const Numeric p, const Numeric t, ConstVectorView vmrs, const Index this_species, const ArrayOfIndex &broad_spec_locations, const LineRecord &l_l, const Verbosity &verbosity)
	Calculate line width and pressure shift for artscat4. 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...

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)

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

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...

Variables
std::map< String, Index >	SpeciesMap
	The map associated with species_data. 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

◆ calc_gamma_and_deltaf_artscat4()

void calc_gamma_and_deltaf_artscat4	(	Numeric &	gamma,
		Numeric &	deltaf,
		const Numeric	p,
		const Numeric	t,
		ConstVectorView	vmrs,
		const Index	this_species,
		const ArrayOfIndex &	broad_spec_locations,
		const LineRecord &	l_l,
		const Verbosity &	verbosity
	)

Calculate line width and pressure shift for artscat4.

Return values

gamma	Line width [Hz].
deltaf	Pressure shift [Hz].

Parameters

p	Pressure [Pa].
t	Temperature [K].
vmrs	Vector of VMRs for different species [dimensionless].
this_species	Index of current species in vmrs.
broad_spec_locations	Has length of number of allowed broadening species (6 in artscat-4). Gives for each species the position in vmrs, or negative if it should be ignored. See function find_broad_spec_locations for details.
l_l	Spectral line data record (a single line).
verbosity	Verbosity flag.

Author: Stefan Buehler

Date: 2012-09-05

Definition at line 432 of file absorption.cc.

References abs, LineRecord::BroadSpecName(), CREATE_OUT2, LineRecord::Delta_foreign(), LineRecord::Gamma_foreign(), LineRecord::N_foreign(), LineRecord::NBroadSpec(), Array< base >::nelem(), LineRecord::Nself(), LineRecord::Sgam(), and LineRecord::Ti0().

Referenced by xsec_species().

◆ checkIsotopologueRatios()

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

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

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 SpeciesAuxData::initParams(), SpeciesAuxData::setParam(), and global_data::species_data.

Referenced by isotopologue_ratiosInitFromBuiltin().

◆ find_broad_spec_locations()

void find_broad_spec_locations	(	ArrayOfIndex &	broad_spec_locations,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Index	this_species
	)

Find the location of all broadening species in abs_species.

Set to -1 if not found. The length of array broad_spec_locations is the number of allowed broadening species (in ARTSCAT-4 N2, O2, H2O, CO2, H2, H2). The value means:

-1 = not in abs_species

-2 = in abs_species, but should be ignored because it is identical to Self

N = species is number N in abs_species

The catalogue contains also broadening parameters for "Self", but we ignore this here, since we know the position of species "Self" anyway.

Return values

broad_spec_locations See above.

Parameters

abs_species	List of absorption species
this_species	Index of the current species in abs_species

Author: Stefan Buehler

Date: 2012-09-04

Definition at line 372 of file absorption.cc.

References LineRecord::BroadSpecSpecIndex(), find_first_species_tg(), LineRecord::NBroadSpec(), and Array< base >::nelem().

Referenced by xsec_species().

◆ 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 SpeciesAuxData &	sad
	)

Output operator for SpeciesAuxData.

Author: Oliver Lemke

Definition at line 343 of file absorption.cc.

References SpeciesAuxData::getParams().

◆ operator<<() [3/3]

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(), and SpeciesRecord::Name().

◆ 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_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 SpeciesRecord::Name(), and 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(), 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().

Variable Documentation

◆ SpeciesMap

std::map<String, Index> SpeciesMap

The map associated with species_data.

Definition at line 50 of file absorption.cc.

Referenced by define_species_map(), and species_index_from_species_name().

Functions

Variables

Detailed Description

Function Documentation

◆ calc_gamma_and_deltaf_artscat4()

◆ checkIsotopologueRatios()

◆ convHitranIERF()

◆ convHitranIERSH()

◆ convMytranIER()

◆ define_species_map()

◆ fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData()

◆ find_broad_spec_locations()

◆ 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()

Variable Documentation

◆ SpeciesMap