* arts-2-1-590

* src/m_abs_lookup.cc (abs_lookupCalc):

Increase spec index if a species is skipped (Zeeman / free_electrons).
Otherwise the following species are stored in the wrong place.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8363 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-1-591

	* Introduced a "particles" abs_species, that takes the absorption
	properties from scat_data_raw and "vmr"s prom pnd_field. Note that this
	approach completely ignores scattering - both in extinction as well as
	in source part! Allows to consistently use the cloud/dust optical
	property data and density fields from arts-xml-data in non-scattering
	calcs (and only there!).
	The only change required for "usual" ARTS setups is when applying DOIT,
	iyEmissionStandard in the iy_main_agenda needs to get passed an empty
	dummy pnd_field.
	TO DO: Adapt documentation in AUG. Adapt abs_mat_fieldCalc.

	* src/abs_species_tags.cc:
	Adapted constructor and tag name extraction for new species "particles".

	* src/species_data.cc, partition_function_data.cc, abs_species_tags.h:
	Introduced species "particles" and type PARTICLES.

	* src/m_abs.cc
	(propmat_clearskyAddParticles): Introduced this method. Provides the
	propmat_clearsky for abs_species "particles" from scat_data_raw and
	rtp_pnd (taken from pnd_field).
	(abs_xsec_agenda_checkedCalc, propmat_clearsky_agenda_checkedCalc):
	Adapted for new abs_species "particles" and its type PARTICLES.

	* src/workspace.cc: Added rtp_pnd.

	* src/agendas.cc: Added rtp_pnd as input to propmat_clearsky_agenda.

	* src/rte.[cc,h]
	(get_ppath_atmvars): Added ppath_pnd as output, pnd_field and cloudbox_on
	as input, and functionality to calc ppath_pnd (only in case cloudbox_on
	is false).
	(get_ppath_abs): Added ppath_pnd as input and pass to
	propmat_clearsky_agenda.

	* src/m_rte.cc (iyEmissionStandard): Added pnd_field as input allowing
	to use in clear-sky absorption calculations (for abs_species "particle).
	Adapted	all calls of get_ppath_atmvars and get_ppath_abs accordingly.

	* src/m_transmitter.cc, m_cloudradar.cc, m_fos.cc (iyRadioLink,
	iyTransmissionStandard, iyCloudRadar, iyFOS):
	Adapted calls of get_ppath_atmvars and get_ppath_abs.

	* src/montecarlo.cc, disort.cc, doit.cc:
	Adapted all calls of propmat_clearsky_agenda passing a dummy rtp_pnd.

	* src/m_abs_lookup.cc
	(abs_lookupCalc, abs_speciesSet): Adapted for use with abs_species
	"particles".
	(abs_mat_fieldCalc): Temporarily adapted call of propmat_clearsky_agenda
	passing a dummy rtp_pnd.

	* src/gas_abs_lookup.cc (GasAbsLookup::Extract):
	Adapted for new type PARTICLES (no extraction for this. in analogy to
	FREE_ELECTRONS).

	* src/m_atmosphere.cc (basics_checkedCalc):
	Added some pnd_field and "particles" abs_species related checks
	("particles" only allowed when cloudbox off; if cloudbox off &
	pnd_field set, then pnd_field needs to cover whole atmo AND "particles"
	need to be in abs_species).

	* src/m_cloudbox.cc
	(ParticleTypeAdd, ParticleTypeAddAll): Removed any usage of
	cloudbox_limits.
	(pnd_fieldCalc): Allow empty cloudbox_limits assuming then pnd_field has
	to cover complete atmosphere (this facilitates the non-cloudbox usage of
	pnd_field for "particles" abs_species).

	* src/cloudbox.[cc,h] (chk_pnd_data, chk_pnd_raw_data): Removed check
	for all non-zero pnd values to be inside the cloudbox. Makes
	ParticleTypeAdd independent of the cloudbox definition, i.e. allows to
	get the particle data before defining the cloudbox (useful e.g. for
	auto-cloudbox detection). Check	is then anyway done by pnd_fieldCalc
	using chk_pnd_field_raw_only_in_cloudbox.

	* src/m_doit.cc, m_doit2.cc
	(CloudboxGetIncoming): Moved if (!cloudbox_on) to the very beginning.
	We don't need to do anything here, if cloudbox is off - not even
	checking that certain other checks were done.
	(CloudboxGetIncoming1DAtm): As CloudboxGetIncoming. And added
	sensor_checked for consitency with CloudboxGetIncoming.
	(CloudboxGetIncoming2): Added sensor_checked for consitency with
	CloudboxGetIncoming.

	* src/methods.cc: Adapted to changes above.

	* controlfiles/general/agendas.arts,
	controlfiles/artscomponents/helpers/TestAgendaCopy.arts,
	controlfiles/artscomponents/faraday/TestFaradayRotation.arts:
	Adapted propmat_clearsky_agenda definitions to ignore rtp_pnd.

	* controlfiles/general/general.arts:
	Default set FlagOff( cloudbox_on ) and empty pnd_field.

	* controlfiles/artscomponents/doit/TestDOIT.arts,
	doitbatch/TestDOITBatch.arts:
	Pass empty dummy pnd_field into iyEmissionStandard (to avoid it trying
	to use the real, cloudbox-targeted pnd_field when called from
	CloudboxGetIncoming with a cloudbox_on=false flag)

	* controlfiles/artscomponents/montecarlo/TestMonteCarloDataPrepare.arts,
	TestMonteCarloGeneral.arts:
	Use named method parameters.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8364 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-592

* src/rational.{cc,h} (operator>>):

Implement input operator for quantum numbers.

* src/quantum.cc (operator<<): Prettier output with QN names.

* src/absorption.cc (LineRecord::ReadFromHitran2004Stream):

Parse upper/lower global quanta v1 value for O2.

* src/test_quantum.cc: More tests.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8365 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-593

* src/m_linemixing.cc (line_mixing_o2Read):

Implement reading of line mixing data and matching it to lines in
abs_lines_per_species. Needs more work in picking the right species.
Currently just looks for the first O2 tag.

* src/absorption.{cc,h} (find_matching_lines):

Use -1 as wildcard for species and isotopologue. Add docs.

* src/methods.cc, src/m_linemixing.cc (line_mixing_o2Init): Added.

* src/workspace.cc (line_mixing_o2_lut): Update docs.

* src/test_quantum.cc: Updated.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8366 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-594

* src/absorption.cc (LineRecord::ReadFromHitran2004Stream):

Fix parsing of v1 for O2. Add parsing of F'' for O2.

* src/quantum.{h,cc}: Add quantum number F.

* src/rational.cc (operator>>): Don't check for EINVAL.

* src/m_linemixing.cc (line_mixing_o2Read): Add out3 info for matches.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8367 aaf1aab0-4228-0410-ad68-8dceda47f409