Stuff related to the calculation of absorption coefficients. More...

#include <algorithm>
#include <cmath>
#include "absorption.h"
#include "array.h"
#include "arts.h"
#include "auto_md.h"
#include "check_input.h"
#include "legacy_continua.h"
#include "file.h"
#include "global_data.h"
#include "jacobian.h"
#include "m_xml.h"
#include "math_funcs.h"
#include "matpackI.h"
#include "messages.h"
#include "montecarlo.h"
#include "optproperties.h"
#include "parameters.h"
#include "physics_funcs.h"
#include "rte.h"
#include "xml_io.h"
#include <netcdf.h>
#include "nc_io.h"

Functions
void	AbsInputFromRteScalars (Vector &abs_p, Vector &abs_t, Matrix &abs_vmrs, const Numeric &rtp_pressure, const Numeric &rtp_temperature, const Vector &rtp_vmr, const Verbosity &)
	WORKSPACE METHOD: AbsInputFromRteScalars. More...

void	abs_lines_per_speciesCreateFromLines (ArrayOfArrayOfAbsorptionLines &abs_lines_per_species, const ArrayOfAbsorptionLines &abs_lines, const ArrayOfArrayOfSpeciesTag &tgs, const Verbosity &)
	WORKSPACE METHOD: abs_lines_per_speciesCreateFromLines. More...

void	abs_speciesDefineAllInScenario (ArrayOfArrayOfSpeciesTag &tgs, Index &propmat_clearsky_agenda_checked, Index &abs_xsec_agenda_checked, const String &basename, const Verbosity &verbosity)
	WORKSPACE METHOD: abs_speciesDefineAllInScenario. More...

void	abs_speciesDefineAll (ArrayOfArrayOfSpeciesTag &abs_species, Index &propmat_clearsky_agenda_checked, Index &abs_xsec_agenda_checked, const Verbosity &verbosity)
	WORKSPACE METHOD: abs_speciesDefineAll. More...

void	AbsInputFromAtmFields (Vector &abs_p, Vector &abs_t, Matrix &abs_vmrs, const Index &atmosphere_dim, const Vector &p_grid, const Tensor3 &t_field, const Tensor4 &vmr_field, const Verbosity &)
	WORKSPACE METHOD: AbsInputFromAtmFields. More...

void	abs_coefCalcFromXsec (Matrix &abs_coef, Matrix &src_coef, ArrayOfMatrix &dabs_coef_dx, ArrayOfMatrix &dsrc_coef_dx, ArrayOfMatrix &abs_coef_per_species, ArrayOfMatrix &src_coef_per_species, const ArrayOfMatrix &abs_xsec_per_species, const ArrayOfMatrix &src_xsec_per_species, const ArrayOfArrayOfMatrix &dabs_xsec_per_species_dx, const ArrayOfArrayOfMatrix &dsrc_xsec_per_species_dx, const ArrayOfArrayOfSpeciesTag &abs_species, const ArrayOfRetrievalQuantity &jacobian_quantities, const Matrix &abs_vmrs, const Vector &abs_p, const Vector &abs_t, const Verbosity &verbosity)
	WORKSPACE METHOD: abs_coefCalcFromXsec. More...

void	abs_xsec_per_speciesInit (ArrayOfMatrix &abs_xsec_per_species, ArrayOfMatrix &src_xsec_per_species, ArrayOfArrayOfMatrix &dabs_xsec_per_species_dx, ArrayOfArrayOfMatrix &dsrc_xsec_per_species_dx, const ArrayOfArrayOfSpeciesTag &tgs, const ArrayOfRetrievalQuantity &jacobian_quantities, const ArrayOfIndex &abs_species_active, const Vector &f_grid, const Vector &abs_p, const Index &abs_xsec_agenda_checked, const Index &nlte_do, const Verbosity &verbosity)
	WORKSPACE METHOD: abs_xsec_per_speciesInit. More...

void	abs_xsec_per_speciesAddConts (ArrayOfMatrix &abs_xsec_per_species, ArrayOfArrayOfMatrix &dabs_xsec_per_species_dx, const ArrayOfArrayOfSpeciesTag &tgs, const ArrayOfRetrievalQuantity &jacobian_quantities, const ArrayOfIndex &abs_species_active, const Vector &f_grid, const Vector &abs_p, const Vector &abs_t, const Matrix &abs_vmrs, const ArrayOfString &abs_cont_names, const ArrayOfVector &abs_cont_parameters, const ArrayOfString &abs_cont_models, const Verbosity &verbosity)
	WORKSPACE METHOD: abs_xsec_per_speciesAddConts. More...

void	abs_cont_descriptionInit (ArrayOfString &abs_cont_names, ArrayOfString &abs_cont_options, ArrayOfVector &abs_cont_parameters, const Verbosity &verbosity)
	WORKSPACE METHOD: abs_cont_descriptionInit. More...

void	abs_cont_descriptionAppend (ArrayOfString &abs_cont_names, ArrayOfString &abs_cont_models, ArrayOfVector &abs_cont_parameters, const String &tagname, const String &model, const Vector &userparameters, const Verbosity &)
	WORKSPACE METHOD: abs_cont_descriptionAppend. More...

void	nlte_sourceFromTemperatureAndSrcCoefPerSpecies (ArrayOfStokesVector &nlte_source, ArrayOfStokesVector &dnlte_dx_source, ArrayOfStokesVector &nlte_dsource_dx, const ArrayOfMatrix &src_coef_per_species, const ArrayOfMatrix &dsrc_coef_dx, const ArrayOfRetrievalQuantity &jacobian_quantities, const Vector &f_grid, const Numeric &rtp_temperature, const Verbosity &)
	WORKSPACE METHOD: nlte_sourceFromTemperatureAndSrcCoefPerSpecies. More...

void	propmat_clearskyAddFromAbsCoefPerSpecies (ArrayOfPropagationMatrix &propmat_clearsky, ArrayOfPropagationMatrix &dpropmat_clearsky_dx, const ArrayOfMatrix &abs_coef_per_species, const ArrayOfMatrix &dabs_coef_dx, const Verbosity &)
	WORKSPACE METHOD: propmat_clearskyAddFromAbsCoefPerSpecies. More...

void	propmat_clearskyInit (ArrayOfPropagationMatrix &propmat_clearsky, ArrayOfStokesVector &nlte_source, ArrayOfPropagationMatrix &dpropmat_clearsky_dx, ArrayOfStokesVector &dnlte_dx_source, ArrayOfStokesVector &nlte_dsource_dx, const ArrayOfArrayOfSpeciesTag &abs_species, const ArrayOfRetrievalQuantity &jacobian_quantities, const Vector &f_grid, const Index &stokes_dim, const Index &propmat_clearsky_agenda_checked, const Index &nlte_do, const Verbosity &)
	WORKSPACE METHOD: propmat_clearskyInit. More...

void	propmat_clearskyAddFaraday (ArrayOfPropagationMatrix &propmat_clearsky, ArrayOfPropagationMatrix &dpropmat_clearsky_dx, const Index &stokes_dim, const Index &atmosphere_dim, const Vector &f_grid, const ArrayOfArrayOfSpeciesTag &abs_species, const ArrayOfRetrievalQuantity &jacobian_quantities, const Vector &rtp_vmr, const Vector &rtp_los, const Vector &rtp_mag, const Verbosity &)
	WORKSPACE METHOD: propmat_clearskyAddFaraday. More...

void	propmat_clearskyAddParticles (ArrayOfPropagationMatrix &propmat_clearsky, ArrayOfPropagationMatrix &dpropmat_clearsky_dx, const Index &stokes_dim, const Index &atmosphere_dim, const Vector &f_grid, const ArrayOfArrayOfSpeciesTag &abs_species, const ArrayOfRetrievalQuantity &jacobian_quantities, const Vector &rtp_vmr, const Vector &rtp_los, const Numeric &rtp_temperature, const ArrayOfArrayOfSingleScatteringData &scat_data, const Index &scat_data_checked, const Index &use_abs_as_ext, const Verbosity &verbosity)
	WORKSPACE METHOD: propmat_clearskyAddParticles. More...

void	propmat_clearskyAddOnTheFly (Workspace &ws, ArrayOfPropagationMatrix &propmat_clearsky, ArrayOfStokesVector &nlte_source, ArrayOfPropagationMatrix &dpropmat_clearsky_dx, ArrayOfStokesVector &dnlte_dx_source, ArrayOfStokesVector &nlte_dsource_dx, const Vector &f_grid, const ArrayOfArrayOfSpeciesTag &abs_species, const ArrayOfRetrievalQuantity &jacobian_quantities, const Numeric &rtp_pressure, const Numeric &rtp_temperature, const EnergyLevelMap &rtp_nlte, const Vector &rtp_vmr, const Agenda &abs_xsec_agenda, const Verbosity &verbosity)
	WORKSPACE METHOD: propmat_clearskyAddOnTheFly. More...

void	propmat_clearskyZero (ArrayOfPropagationMatrix &propmat_clearsky, const Vector &f_grid, const Index &stokes_dim, const Verbosity &)
	WORKSPACE METHOD: propmat_clearskyZero. More...

void	propmat_clearskyForceNegativeToZero (ArrayOfPropagationMatrix &propmat_clearsky, const Verbosity &)
	WORKSPACE METHOD: propmat_clearskyForceNegativeToZero. More...

void	isotopologue_ratiosInitFromBuiltin (SpeciesAuxData &isotopologue_ratios, const Verbosity &)
	WORKSPACE METHOD: isotopologue_ratiosInitFromBuiltin. More...

void	partition_functionsInitFromBuiltin (SpeciesAuxData &partition_functions, const Verbosity &)
	WORKSPACE METHOD: partition_functionsInitFromBuiltin. More...

void	WriteMolTau (const Vector &f_grid, const Tensor3 &z_field, const Tensor7 &propmat_clearsky_field, const Index &atmosphere_dim, const String &filename, const Verbosity &)
	WORKSPACE METHOD: WriteMolTau. More...

void	abs_xsec_per_speciesAddLines (ArrayOfMatrix &abs_xsec_per_species, ArrayOfMatrix &src_xsec_per_species, ArrayOfArrayOfMatrix &dabs_xsec_per_species_dx, ArrayOfArrayOfMatrix &dsrc_xsec_per_species_dx, const ArrayOfArrayOfSpeciesTag &abs_species, const ArrayOfRetrievalQuantity &jacobian_quantities, const ArrayOfIndex &abs_species_active, const Vector &f_grid, const Vector &abs_p, const Vector &abs_t, const EnergyLevelMap &abs_nlte, const Matrix &abs_vmrs, const ArrayOfArrayOfAbsorptionLines &abs_lines_per_species, const SpeciesAuxData &isotopologue_ratios, const SpeciesAuxData &partition_functions, const Index &lbl_checked, const Verbosity &)
	WORKSPACE METHOD: abs_xsec_per_speciesAddLines. More...

Variables
const Numeric	ELECTRON_CHARGE

const Numeric	ELECTRON_MASS

const Numeric	PI

const Numeric	SPEED_OF_LIGHT

const Numeric	VACUUM_PERMITTIVITY

Detailed Description

Stuff related to the calculation of absorption coefficients.

Author: Stefan Buehler

Date: 2001-03-12

Definition in file m_abs.cc.

Function Documentation

◆ abs_coefCalcFromXsec()

void abs_coefCalcFromXsec	(	Matrix &	abs_coef,
		Matrix &	src_coef,
		ArrayOfMatrix &	dabs_coef_dx,
		ArrayOfMatrix &	dsrc_coef_dx,
		ArrayOfMatrix &	abs_coef_per_species,
		ArrayOfMatrix &	src_coef_per_species,
		const ArrayOfMatrix &	abs_xsec_per_species,
		const ArrayOfMatrix &	src_xsec_per_species,
		const ArrayOfArrayOfMatrix &	dabs_xsec_per_species_dx,
		const ArrayOfArrayOfMatrix &	dsrc_xsec_per_species_dx,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const Matrix &	abs_vmrs,
		const Vector &	abs_p,
		const Vector &	abs_t,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_coefCalcFromXsec.

Calculate absorption coefficients from cross sections.

This calculates both the total absorption and the absorption per species.

Cross sections are multiplied by n*VMR.

Author: Stefan Buehler; Axel von Engeln

Parameters

[out]	abs_coef	WS Output
[out]	src_coef	WS Output
[out]	dabs_coef_dx	WS Output
[out]	dsrc_coef_dx	WS Output
[out]	abs_coef_per_species	WS Output
[out]	src_coef_per_species	WS Output
[in]	abs_xsec_per_species	WS Input
[in]	src_xsec_per_species	WS Input
[in]	dabs_xsec_per_species_dx	WS Input
[in]	dsrc_xsec_per_species_dx	WS Input
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	abs_vmrs	WS Input
[in]	abs_p	WS Input
[in]	abs_t	WS Input

Definition at line 258 of file m_abs.cc.

References chk_size(), CREATE_OUT3, dnumber_density_dt(), equivalent_propmattype_indexes(), i, n, ConstMatrixView::ncols(), Array< base >::nelem(), NotPropagationMatrixType, ConstMatrixView::nrows(), number_density(), Matrix::resize(), and _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str().

Referenced by abs_coefCalcFromXsec_g(), and propmat_clearskyAddOnTheFly().

◆ abs_cont_descriptionAppend()

void abs_cont_descriptionAppend	(	ArrayOfString &	abs_cont_names,
		ArrayOfString &	abs_cont_models,
		ArrayOfVector &	abs_cont_parameters,
		const String &	tagname,
		const String &	model,
		const Vector &	userparam,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_cont_descriptionAppend.

Appends the description of a continuum model or a complete absorption model to abs_cont_names and abs_cont_parameters.

See online documentation for abs_cont_names for a list of allowed models and for information what parameters they require. See file includes/continua.arts for default parameters for the various models.

Author: Thomas Kuhn; Stefan Buehler

Parameters

[in,out]	abs_cont_names	WS Input/Output
[in,out]	abs_cont_models	WS Input/Output
[in,out]	abs_cont_parameters	WS Input/Output
[in]	tagname	Generic Input
[in]	model	Generic Input
[in]	userparam	Generic Input (Default: "[]")

Definition at line 839 of file m_abs.cc.

References check_continuum_model().

Referenced by abs_cont_descriptionAppend_g(), ARTS::Continua::addH2OPWR98(), and ARTS::Continua::addO2PWR98().

◆ abs_cont_descriptionInit()

void abs_cont_descriptionInit	(	ArrayOfString &	abs_cont_names,
		ArrayOfString &	abs_cont_models,
		ArrayOfVector &	abs_cont_parameters,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_cont_descriptionInit.

Initializes the two workspace variables for the continuum description, abs_cont_names* and abs_cont_parameters.

This method does not really do anything, except setting the two variables to empty Arrays. It is just necessary because the method abs_cont_descriptionAppend* wants to append to the variables.

Formally, the continuum description workspace variables are required by the absorption calculation methods (e.g., abs_coefCalcFromXsec). Therefore you always have to call at least abs_cont_descriptionInit, even if you do not want to use any continua.

Author: Thomas Kuhn; Stefan Buehler

Parameters

[out]	abs_cont_names	WS Output
[out]	abs_cont_models	WS Output
[out]	abs_cont_parameters	WS Output

Definition at line 823 of file m_abs.cc.

References CREATE_OUT2.

Referenced by abs_cont_descriptionInit_g(), and ARTS::Continua::init().

◆ abs_lines_per_speciesCreateFromLines()

void abs_lines_per_speciesCreateFromLines	(	ArrayOfArrayOfAbsorptionLines &	abs_lines_per_species,
		const ArrayOfAbsorptionLines &	abs_lines,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_lines_per_speciesCreateFromLines.

Split lines up into the different species.

The order of the splitting will match the outer layer of abs_species There will be no respect for the internal layer of abs_species

Author: Stefan Buehler

Parameters

[out]	abs_lines_per_species	WS Output
[in]	abs_lines	WS Input
[in]	abs_species	WS Input

Definition at line 90 of file m_abs.cc.

References Absorption::createEmptyCopy(), i, SpeciesRecord::Isotopologue(), max, Array< base >::nelem(), and SpeciesDataOfBand().

Referenced by abs_lines_per_speciesCreateFromLines_g(), and abs_linesWriteSpeciesSplitXML().

◆ abs_speciesDefineAll()

void abs_speciesDefineAll	(	ArrayOfArrayOfSpeciesTag &	abs_species,
		Index &	propmat_clearsky_agenda_checked,
		Index &	abs_xsec_agenda_checked,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_speciesDefineAll.

Sets abs_species[i][0] to all species in ARTS

Author: Richard Larsson

Parameters

[out]	abs_species	WS Output
[out]	propmat_clearsky_agenda_checked	WS Output
[out]	abs_xsec_agenda_checked	WS Output

Definition at line 214 of file m_abs.cc.

References abs_speciesSet(), and global_data::species_data.

Referenced by abs_speciesDefineAll_g().

◆ abs_speciesDefineAllInScenario()

void abs_speciesDefineAllInScenario	(	ArrayOfArrayOfSpeciesTag &	abs_species,
		Index &	propmat_clearsky_agenda_checked,
		Index &	abs_xsec_agenda_checked,
		const String &	basename,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_speciesDefineAllInScenario.

Define one tag group for each species known to ARTS and included in an atmospheric scenario.

You can use this as an alternative to abs_speciesSet if you want to make an absorption calculation that is as complete as possible. The method goes through all defined species and tries to open the VMR file. If this works the tag is included, otherwise it is skipped.

Author: Stefan Buehler

Parameters

[out]	abs_species	WS Output
[out]	propmat_clearsky_agenda_checked	WS Output
[out]	abs_xsec_agenda_checked	WS Output
[in]	basename	Generic Input

Definition at line 153 of file m_abs.cc.

References CREATE_OUT2, find_xml_file(), i, and global_data::species_data.

Referenced by abs_speciesDefineAllInScenario_g().

◆ abs_xsec_per_speciesAddConts()

void abs_xsec_per_speciesAddConts	(	ArrayOfMatrix &	abs_xsec_per_species,
		ArrayOfArrayOfMatrix &	dabs_xsec_per_species_dx,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const ArrayOfIndex &	abs_species_active,
		const Vector &	f_grid,
		const Vector &	abs_p,
		const Vector &	abs_t,
		const Matrix &	abs_vmrs,
		const ArrayOfString &	abs_cont_names,
		const ArrayOfVector &	abs_cont_parameters,
		const ArrayOfString &	abs_cont_models,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_xsec_per_speciesAddConts.

Calculate absorption cross sections per tag group for continua.

Author: Stefan Buehler

Parameters

[in,out]	abs_xsec_per_species	WS Input/Output
[in,out]	dabs_xsec_per_species_dx	WS Input/Output
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	abs_species_active	WS Input
[in]	f_grid	WS Input
[in]	abs_p	WS Input
[in]	abs_t	WS Input
[in]	abs_vmrs	WS Input
[in]	abs_cont_names	WS Input
[in]	abs_cont_parameters	WS Input
[in]	abs_cont_models	WS Input

Definition at line 531 of file m_abs.cc.

References CREATE_OUT3, do_frequency_jacobian(), do_temperature_jacobian(), equivalent_propmattype_indexes(), frequency_perturbation(), i, is_frequency_parameter(), joker, n, ConstMatrixView::ncols(), Array< base >::nelem(), ConstVectorView::nelem(), ConstMatrixView::nrows(), Vector::resize(), Matrix::resize(), set_vmr_from_first_species(), global_data::species_data, _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str(), supports_continuum(), Temperature, temperature_perturbation(), SpeciesTag::TYPE_PREDEF, and xsec_continuum_tag().

Referenced by ARTS::Agenda::abs_xsec_agenda_standard(), ARTS::Agenda::abs_xsec_agenda_standard_with_cia(), and abs_xsec_per_speciesAddConts_g().

◆ abs_xsec_per_speciesAddLines()

void abs_xsec_per_speciesAddLines	(	ArrayOfMatrix &	abs_xsec_per_species,
		ArrayOfMatrix &	src_xsec_per_species,
		ArrayOfArrayOfMatrix &	dabs_xsec_per_species_dx,
		ArrayOfArrayOfMatrix &	dsrc_xsec_per_species_dx,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const ArrayOfIndex &	abs_species_active,
		const Vector &	f_grid,
		const Vector &	abs_p,
		const Vector &	abs_t,
		const EnergyLevelMap &	abs_nlte,
		const Matrix &	abs_vmrs,
		const ArrayOfArrayOfAbsorptionLines &	abs_lines_per_species,
		const SpeciesAuxData &	isotopologue_ratios,
		const SpeciesAuxData &	partition_functions,
		const Index &	lbl_checked,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_xsec_per_speciesAddLines.

Calculates the line spectrum for both attenuation and phase for each tag group and adds it to abs_xsec_per_species.

Author: Richard Larsson

Parameters

[in,out]	abs_xsec_per_species	WS Input/Output
[in,out]	src_xsec_per_species	WS Input/Output
[in,out]	dabs_xsec_per_species_dx	WS Input/Output
[in,out]	dsrc_xsec_per_species_dx	WS Input/Output
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	abs_species_active	WS Input
[in]	f_grid	WS Input
[in]	abs_p	WS Input
[in]	abs_t	WS Input
[in]	abs_nlte	WS Input
[in]	abs_vmrs	WS Input
[in]	abs_lines_per_species	WS Input
[in]	isotopologue_ratios	WS Input
[in]	partition_functions	WS Input
[in]	lbl_checked	WS Input

Definition at line 1809 of file m_abs.cc.

References EnergyLevelMap::Data(), ConstTensor4View::empty(), equivalent_propmattype_indexes(), SpeciesAuxData::getIsotopologueRatio(), SpeciesAuxData::getParam(), SpeciesAuxData::getParamType(), i, is_zeeman(), min, Array< base >::nelem(), Absorption::nelem(), ConstMatrixView::nrows(), supports_propmat_clearsky(), and xsec_species().

Referenced by ARTS::Agenda::abs_xsec_agenda_standard(), ARTS::Agenda::abs_xsec_agenda_standard_with_cia(), and abs_xsec_per_speciesAddLines_g().

◆ abs_xsec_per_speciesInit()

void abs_xsec_per_speciesInit	(	ArrayOfMatrix &	abs_xsec_per_species,
		ArrayOfMatrix &	src_xsec_per_species,
		ArrayOfArrayOfMatrix &	dabs_xsec_per_species_dx,
		ArrayOfArrayOfMatrix &	dsrc_xsec_per_species_dx,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const ArrayOfIndex &	abs_species_active,
		const Vector &	f_grid,
		const Vector &	abs_p,
		const Index &	abs_xsec_agenda_checked,
		const Index &	nlte_do,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: abs_xsec_per_speciesInit.

Initialize abs_xsec_per_species.

The initialization is necessary, because methods abs_xsec_per_speciesAddLines and abs_xsec_per_speciesAddConts just add to abs_xsec_per_species. The size is determined from abs_species.

Author: Stefan Buehler

Parameters

[out]	abs_xsec_per_species	WS Output
[out]	src_xsec_per_species	WS Output
[out]	dabs_xsec_per_species_dx	WS Output
[out]	dsrc_xsec_per_species_dx	WS Output
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	abs_species_active	WS Input
[in]	f_grid	WS Input
[in]	abs_p	WS Input
[in]	abs_xsec_agenda_checked	WS Input
[in]	nlte_do	WS Input

Definition at line 443 of file m_abs.cc.

References CREATE_OUT3, equivalent_propmattype_indexes(), i, Array< base >::nelem(), ConstVectorView::nelem(), _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str(), and supports_propmat_clearsky().

Referenced by ARTS::Agenda::abs_xsec_agenda_standard(), ARTS::Agenda::abs_xsec_agenda_standard_with_cia(), and abs_xsec_per_speciesInit_g().

◆ AbsInputFromAtmFields()

void AbsInputFromAtmFields	(	Vector &	abs_p,
		Vector &	abs_t,
		Matrix &	abs_vmrs,
		const Index &	atmosphere_dim,
		const Vector &	p_grid,
		const Tensor3 &	t_field,
		const Tensor4 &	vmr_field,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: AbsInputFromAtmFields.

Initialises the WSVs abs_p, abs_t and abs_vmrs from p_grid, t_field and vmr_field.

This only works for a 1D atmosphere!

Author: Stefan Buehler

Parameters

[out]	abs_p	WS Output
[out]	abs_t	WS Output
[out]	abs_vmrs	WS Output
[in]	atmosphere_dim	WS Input
[in]	p_grid	WS Input
[in]	t_field	WS Input
[in]	vmr_field	WS Input

Definition at line 234 of file m_abs.cc.

References joker, and _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str().

Referenced by AbsInputFromAtmFields_g().

◆ AbsInputFromRteScalars()

void AbsInputFromRteScalars	(	Vector &	abs_p,
		Vector &	abs_t,
		Matrix &	abs_vmrs,
		const Numeric &	rtp_pressure,
		const Numeric &	rtp_temperature,
		const Vector &	rtp_vmr,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: AbsInputFromRteScalars.

Initialize absorption input WSVs from local atmospheric conditions.

The purpose of this method is to allow an explicit line-by-line calculation, e.g., by abs_coefCalcFromXsec, to be put inside the propmat_clearsky_agenda*. What the method does is to prepare absorption input parameters (pressure, temperature, VMRs), from the input parameters to propmat_clearsky_agenda.

Author: Stefan Buehler

Parameters

[out]	abs_p	WS Output
[out]	abs_t	WS Output
[out]	abs_vmrs	WS Output
[in]	rtp_pressure	WS Input
[in]	rtp_temperature	WS Input
[in]	rtp_vmr	WS Input

Definition at line 67 of file m_abs.cc.

References ConstVectorView::nelem(), Vector::resize(), and Matrix::resize().

Referenced by AbsInputFromRteScalars_g(), and propmat_clearskyAddOnTheFly().

◆ isotopologue_ratiosInitFromBuiltin()

void isotopologue_ratiosInitFromBuiltin	(	SpeciesAuxData &	isotopologue_ratios,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: isotopologue_ratiosInitFromBuiltin.

Initialize isotopologue ratios with default values from built-in species data.

Author: Oliver Lemke

Parameters

[out] isotopologue_ratios WS Output

Definition at line 1625 of file m_abs.cc.

References fillSpeciesAuxDataWithIsotopologueRatiosFromSpeciesData().

Referenced by isotopologue_ratiosInitFromBuiltin_g(), and main().

◆ nlte_sourceFromTemperatureAndSrcCoefPerSpecies()

void nlte_sourceFromTemperatureAndSrcCoefPerSpecies	(	ArrayOfStokesVector &	nlte_source,
		ArrayOfStokesVector &	dnlte_dx_source,
		ArrayOfStokesVector &	nlte_dsource_dx,
		const ArrayOfMatrix &	src_coef_per_species,
		const ArrayOfMatrix &	dsrc_coef_dx,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const Vector &	f_grid,
		const Numeric &	rtp_temperature,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: nlte_sourceFromTemperatureAndSrcCoefPerSpecies.

Turn NLTE absorption per species into the source function by multiplying NLTE absorption per species with the LTE Planck source function.

Author: Richard Larsson

Parameters

[out]	nlte_source	WS Output
[out]	dnlte_dx_source	WS Output
[out]	nlte_dsource_dx	WS Output
[in]	src_coef_per_species	WS Input
[in]	dsrc_coef_dx	WS Input
[in]	jacobian_quantities	WS Input
[in]	f_grid	WS Input
[in]	rtp_temperature	WS Input

Definition at line 862 of file m_abs.cc.

References dplanck_df(), dplanck_dt(), equivalent_propmattype_indexes(), is_frequency_parameter(), joker, PropagationMatrix::Kjj(), Array< base >::nelem(), NotPropagationMatrixType, planck(), _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str(), and Temperature.

Referenced by nlte_sourceFromTemperatureAndSrcCoefPerSpecies_g(), and propmat_clearskyAddOnTheFly().

◆ partition_functionsInitFromBuiltin()

void partition_functionsInitFromBuiltin	(	SpeciesAuxData &	partition_functions,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: partition_functionsInitFromBuiltin.

Initialize partition functions with default values from built-in species data.

Author: Oliver Lemke

Parameters

[out] partition_functions WS Output

Definition at line 1631 of file m_abs.cc.

References fillSpeciesAuxDataWithPartitionFunctionsFromSpeciesData().

Referenced by main(), partition_functionsInitFromBuiltin_g(), and test_hitran2017().

◆ propmat_clearskyAddFaraday()

void propmat_clearskyAddFaraday	(	ArrayOfPropagationMatrix &	propmat_clearsky,
		ArrayOfPropagationMatrix &	dpropmat_clearsky_dx,
		const Index &	stokes_dim,
		const Index &	atmosphere_dim,
		const Vector &	f_grid,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const Vector &	rtp_vmr,
		const Vector &	rtp_los,
		const Vector &	rtp_mag,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyAddFaraday.

Calculates absorption matrix describing Faraday rotation.

Faraday rotation is a change of polarization state of an electromagnetic wave propagating through charged matter by interaction with a magnetic field. Hence, this method requires abs_species* to contain 'free_electrons' and electron content field (as part of vmr_field) as well as magnetic field (mag_u_field, mag_v_field*, mag_w_field) to be specified.

Faraday rotation affects Stokes parameters 2 and 3 (but not intensity!). Therefore, this method requires stokes_dim>2.

Like all 'propmat_clearskyAdd*' methods, the method is additive, i.e., does not overwrite the propagation matrix propmat_clearsky, but adds further contributions.

Author: Patrick Eriksson

Parameters

[in,out]	propmat_clearsky	WS Input/Output
[in,out]	dpropmat_clearsky_dx	WS Input/Output
[in]	stokes_dim	WS Input
[in]	atmosphere_dim	WS Input
[in]	f_grid	WS Input
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	rtp_vmr	WS Input
[in]	rtp_los	WS Input
[in]	rtp_mag	WS Input

Definition at line 1074 of file m_abs.cc.

References abs, do_magnetic_jacobian(), dotprod_with_los(), ELECTRON_CHARGE, ELECTRON_MASS, Electrons, equivalent_propmattype_indexes(), is_frequency_parameter(), magnetic_field_perturbation(), MagneticU, MagneticV, MagneticW, Array< base >::nelem(), ConstVectorView::nelem(), PI, r, SPEED_OF_LIGHT, _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str(), supports_faraday(), SpeciesTag::TYPE_FREE_ELECTRONS, and VACUUM_PERMITTIVITY.

Referenced by propmat_clearskyAddFaraday_g().

◆ propmat_clearskyAddFromAbsCoefPerSpecies()

void propmat_clearskyAddFromAbsCoefPerSpecies	(	ArrayOfPropagationMatrix &	propmat_clearsky,
		ArrayOfPropagationMatrix &	dpropmat_clearsky_dx,
		const ArrayOfMatrix &	abs_coef_per_species,
		const ArrayOfMatrix &	dabs_coef_dx,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyAddFromAbsCoefPerSpecies.

Copy propmat_clearsky from abs_coef_per_species. This is handy for putting an explicit line-by-line calculation into the propmat_clearsky_agenda*. This method is also used internally by. propmat_clearskyAddOnTheFly*. Like all other propmat_clearsky methods, this method does not overwrite prior content of propmat_clearsky, but adds to it.

Author: Stefan Buehler

Parameters

[in,out]	propmat_clearsky	WS Input/Output
[out]	dpropmat_clearsky_dx	WS Output
[in]	abs_coef_per_species	WS Input
[in]	dabs_coef_dx	WS Input

Definition at line 968 of file m_abs.cc.

References joker, Array< base >::nelem(), and _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str().

Referenced by propmat_clearskyAddFromAbsCoefPerSpecies_g(), and propmat_clearskyAddOnTheFly().

◆ propmat_clearskyAddOnTheFly()

void propmat_clearskyAddOnTheFly	(	Workspace &	ws,
		ArrayOfPropagationMatrix &	propmat_clearsky,
		ArrayOfStokesVector &	nlte_source,
		ArrayOfPropagationMatrix &	dpropmat_clearsky_dx,
		ArrayOfStokesVector &	dnlte_dx_source,
		ArrayOfStokesVector &	nlte_dsource_dx,
		const Vector &	f_grid,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const Numeric &	rtp_pressure,
		const Numeric &	rtp_temperature,
		const EnergyLevelMap &	rtp_nlte,
		const Vector &	rtp_vmr,
		const Agenda &	abs_xsec_agenda,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyAddOnTheFly.

Calculates gas absorption coefficients line-by-line.

This method can be used inside propmat_clearsky_agenda just like propmat_clearskyAddFromLookup*. It is a shortcut for putting in some other methods explicitly, namely:

1. AbsInputFromRteScalars 2. Execute abs_xsec_agenda 3. abs_coefCalcFromXsec 4. propmat_clearskyAddFromAbsCoefPerSpecies

The calculation is for one specific atmospheric condition, i.e., a set of pressure, temperature, and VMR values.

Author: Stefan Buehler, Richard Larsson

Parameters

[in,out]	ws	Workspace
[in,out]	propmat_clearsky	WS Input/Output
[in,out]	nlte_source	WS Input/Output
[in,out]	dpropmat_clearsky_dx	WS Input/Output
[in,out]	dnlte_dx_source	WS Input/Output
[in,out]	nlte_dsource_dx	WS Input/Output
[in]	f_grid	WS Input
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	rtp_pressure	WS Input
[in]	rtp_temperature	WS Input
[in]	rtp_nlte	WS Input
[in]	rtp_vmr	WS Input
[in]	abs_xsec_agenda	WS Input

Definition at line 1504 of file m_abs.cc.

References abs_coefCalcFromXsec(), abs_xsec_agendaExecute(), AbsInputFromRteScalars(), i, Array< base >::nelem(), nlte_sourceFromTemperatureAndSrcCoefPerSpecies(), and propmat_clearskyAddFromAbsCoefPerSpecies().

Referenced by calc_lookup_error(), ARTS::Agenda::propmat_clearsky_agenda_on_the_fly(), ARTS::Agenda::propmat_clearsky_agenda_on_the_fly_zeeman(), and propmat_clearskyAddOnTheFly_g().

◆ propmat_clearskyAddParticles()

void propmat_clearskyAddParticles	(	ArrayOfPropagationMatrix &	propmat_clearsky,
		ArrayOfPropagationMatrix &	dpropmat_clearsky_dx,
		const Index &	stokes_dim,
		const Index &	atmosphere_dim,
		const Vector &	f_grid,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const Vector &	rtp_vmr,
		const Vector &	rtp_los,
		const Numeric &	rtp_temperature,
		const ArrayOfArrayOfSingleScatteringData &	scat_data,
		const Index &	scat_data_checked,
		const Index &	use_abs_as_ext,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyAddParticles.

Calculates absorption coefficients of particles to be used in clearsky (non-cloudbox) calculations.

This is a method to include particles (neglecting possible scattering components) in a clearsky calculation, i.e. without applying the cloudbox and scattering solvers. Particles are handled as absorbing species with one instance of 'particles' per scattering element considered added to abs_species. Particle absorption cross- sections at current atmospheric conditions are extracted from the single scattering data stored in scat_data, i.e., one array element per 'particles' instance in abs_species is required. Number densities are stored in vmr_field_raw or vmr_field as for all abs_species*, but can be taken from (raw) pnd_field type data.

Note that the absorption coefficient is applied both in the extinction term (neglecting scattering out of the line of sight) and the emission term (neglecting the scattering source term, i.e. scattering into the line of sight).

Optionally, particle extinction (sum of absorption and scattering coefficient) can be used instead of absorption only. To choose this case, set the use_abs_as_ext flag to 0. However, be aware that this creates some unphysical emission term, hence is only suitable, where the source term is negligible anyways, e.g. for occultation simulations.

A line-of-sight direction rtp_los is required as particles can exhibit directional dependent absorption properties, which is taken into account by this method. ScatElementsToabs_speciesAdd* can be used to add all required settings/data for individual scattering elements at once, i.e. a 'particles' tag to abs_species, a set of single scattering data to scat_data* and a number density field to vmr_field_raw (vmr_field is derived applying AtmFieldsCalc once VMRs for all abs_species* have been added) is appended for each scattering element.

Like all 'propmat_clearskyAdd*' methods, the method is additive, i.e., does not overwrite the propagation matrix propmat_clearsky, but adds further contributions.

Author: Jana Mendrok

Parameters

[in,out]	propmat_clearsky	WS Input/Output
[in,out]	dpropmat_clearsky_dx	WS Input/Output
[in]	stokes_dim	WS Input
[in]	atmosphere_dim	WS Input
[in]	f_grid	WS Input
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	rtp_vmr	WS Input
[in]	rtp_los	WS Input
[in]	rtp_temperature	WS Input
[in]	scat_data	WS Input
[in]	scat_data_checked	WS Input
[in]	use_abs_as_ext	Generic Input (Default: "1")

Definition at line 1202 of file m_abs.cc.

References CREATE_OUT1, do_frequency_jacobian(), do_temperature_jacobian(), equivalent_propmattype_indexes(), joker, mirror_los(), Array< base >::nelem(), ConstVectorView::nelem(), ns, opt_prop_NScatElems(), Particulates, Vector::resize(), _CS_basic_sstream_base< _CS_cT, _CS_Tr, _CS_Al >::str(), supports_particles(), Temperature, temperature_perturbation(), TotalNumberOfElements(), and SpeciesTag::TYPE_PARTICLES.

Referenced by propmat_clearskyAddParticles_g().

◆ propmat_clearskyForceNegativeToZero()

void propmat_clearskyForceNegativeToZero	(	ArrayOfPropagationMatrix &	propmat_clearsky,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyForceNegativeToZero.

Sets propmat_clearsky to match zero attenuation if negative value. Useful for line mixing in some cases.

Use this method just if you know what you are doing!

Author: Richard Larsson

Parameters

[in,out] propmat_clearsky WS Input/Output

Definition at line 1617 of file m_abs.cc.

References i, and pm.

Referenced by propmat_clearskyForceNegativeToZero_g().

◆ propmat_clearskyInit()

void propmat_clearskyInit	(	ArrayOfPropagationMatrix &	propmat_clearsky,
		ArrayOfStokesVector &	nlte_source,
		ArrayOfPropagationMatrix &	dpropmat_clearsky_dx,
		ArrayOfStokesVector &	dnlte_dx_source,
		ArrayOfStokesVector &	nlte_dsource_dx,
		const ArrayOfArrayOfSpeciesTag &	abs_species,
		const ArrayOfRetrievalQuantity &	jacobian_quantities,
		const Vector &	f_grid,
		const Index &	stokes_dim,
		const Index &	propmat_clearsky_agenda_checked,
		const Index &	nlte_do,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyInit.

Initialize propmat_clearsky and nlte_source.

This method must be used inside propmat_clearsky_agenda and then be called first.

Author: Oliver Lemke, Richard Larsson

Parameters

[out]	propmat_clearsky	WS Output
[out]	nlte_source	WS Output
[out]	dpropmat_clearsky_dx	WS Output
[out]	dnlte_dx_source	WS Output
[out]	nlte_dsource_dx	WS Output
[in]	abs_species	WS Input
[in]	jacobian_quantities	WS Input
[in]	f_grid	WS Input
[in]	stokes_dim	WS Input
[in]	propmat_clearsky_agenda_checked	WS Input
[in]	nlte_do	WS Input

Definition at line 1028 of file m_abs.cc.

References equivalent_propmattype_indexes(), Array< base >::nelem(), and ConstVectorView::nelem().

Referenced by calc_lookup_error(), ARTS::Agenda::propmat_clearsky_agenda_on_the_fly(), ARTS::Agenda::propmat_clearsky_agenda_on_the_fly_zeeman(), and propmat_clearskyInit_g().

◆ propmat_clearskyZero()

void propmat_clearskyZero	(	ArrayOfPropagationMatrix &	propmat_clearsky,
		const Vector &	f_grid,
		const Index &	stokes_dim,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: propmat_clearskyZero.

Sets propmat_clearsky to match zero attenuation.

Use this method just if you know what you are doing!

If you want to make a calculation with no clear-sky attenuation at all, fill propmat_clearsky_agenda with this method and required Ignore statements (don't include propmat_clearskyInit).

Author: Patrick Eriksson

Parameters

[out]	propmat_clearsky	WS Output
[in]	f_grid	WS Input
[in]	stokes_dim	WS Input

Definition at line 1607 of file m_abs.cc.

References ConstVectorView::nelem().

Referenced by propmat_clearskyZero_g().

◆ WriteMolTau()

void WriteMolTau	(	const Vector &	f_grid,
		const Tensor3 &	z_field,
		const Tensor7 &	propmat_clearsky_field,
		const Index &	atmosphere_dim,
		const String &	filename,
		const Verbosity &	verbosity
	)

WORKSPACE METHOD: WriteMolTau.

Writes a 'molecular_tau_file' as required for libRadtran.

The libRadtran (www.libradtran.org) radiative transfer package is a comprehensive package for various applications, it can be used to compute radiances, irradiances, actinic fluxes, ... for the solar and the thermal spectral ranges. Absorption is usually treated using k-distributions or other parameterizations. For calculations with high spectral resolution it requires absorption coefficients from an external line-by-line model. Using this method, arts generates a file that can be used by libRadtran (option molecular_tau_file).

Author: Claudia Emde

Parameters

[in]	f_grid	WS Input
[in]	z_field	WS Input
[in]	propmat_clearsky_field	WS Input
[in]	atmosphere_dim	WS Input
[in]	filename	Generic Input

Definition at line 1639 of file m_abs.cc.

References ConstTensor7View::nbooks(), nca_error(), ConstVectorView::nelem(), ConstTensor3View::npages(), and SPEED_OF_LIGHT.

Referenced by WriteMolTau_g().

Variable Documentation

◆ ELECTRON_CHARGE

const Numeric ELECTRON_CHARGE

Referenced by propmat_clearskyAddFaraday().

◆ ELECTRON_MASS

const Numeric ELECTRON_MASS

Referenced by propmat_clearskyAddFaraday().

◆ PI

const Numeric PI

Referenced by propmat_clearskyAddFaraday().

◆ SPEED_OF_LIGHT

const Numeric SPEED_OF_LIGHT

Referenced by propmat_clearskyAddFaraday(), and WriteMolTau().

◆ VACUUM_PERMITTIVITY

const Numeric VACUUM_PERMITTIVITY

Referenced by propmat_clearskyAddFaraday().

Functions

Variables

Detailed Description

Function Documentation

◆ abs_coefCalcFromXsec()

◆ abs_cont_descriptionAppend()

◆ abs_cont_descriptionInit()

◆ abs_lines_per_speciesCreateFromLines()

◆ abs_speciesDefineAll()

◆ abs_speciesDefineAllInScenario()

◆ abs_xsec_per_speciesAddConts()

◆ abs_xsec_per_speciesAddLines()

◆ abs_xsec_per_speciesInit()

◆ AbsInputFromAtmFields()

◆ AbsInputFromRteScalars()

◆ isotopologue_ratiosInitFromBuiltin()

◆ nlte_sourceFromTemperatureAndSrcCoefPerSpecies()

◆ partition_functionsInitFromBuiltin()

◆ propmat_clearskyAddFaraday()

◆ propmat_clearskyAddFromAbsCoefPerSpecies()

◆ propmat_clearskyAddOnTheFly()

◆ propmat_clearskyAddParticles()

◆ propmat_clearskyForceNegativeToZero()

◆ propmat_clearskyInit()

◆ propmat_clearskyZero()

◆ WriteMolTau()

Variable Documentation

◆ ELECTRON_CHARGE

◆ ELECTRON_MASS

◆ PI

◆ SPEED_OF_LIGHT

◆ VACUUM_PERMITTIVITY