2013-03-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-553

            * controlfiles/testdata/tropical.expanded.t.xml:
            * controlfiles/testdata/tropical.expanded.z.xml: Grids still
            lacked name. 



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8301 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-03-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-554

            * doc/uguide/atmosphere.tex:
            * doc/uguide/absorption.tex
            * doc/uguide/concept.tex: As below, but inside AUG.

            * src/m_abs_lookup.cc:
            * src/mc_interp.h:
            * src/m_optproperties.cc:
            * src/mc_interp.cc:
            * controlfiles/general/agendas.arts:
            * src/m_refraction.cc:
            * src/refraction.cc:
            * src/doit.cc :
            * src/m_abs_o2_models.cc:
            * src/m_zeeman.cc:
            * src/montecarlo.cc:
            * src/mc_NotUsed.cc:
            * src/disort.cc:
            * src/montecarlo.h:
            * src/methods.cc: Changed all rte_temperature, rte_pressure,
            * rte_mag
            * src/agendas.cc: rte_doppler and rtp_abs_species, to new rtp-
            * src/m_abs.cc: correspondance.

            * src/workspace.cc: Renamed rtp_abs_species to rtp_vmr.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8303 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-555

* src/abs_species_tags.cc (SpeciesTag::SpeciesTag):

Get the species index before handling the free_electrons tag.

(SpeciesTag::Name): Use name from species_data for free_electrons.

* src/species_data.cc (define_basic_species_data):

Add tag 'free_electrons'.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8304 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-03-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-556

            * controlfiles/artscomponents/faraday/TestFaradayRotation.arts:
            Updated. Faraday rotation handled by the changes below. Perfect
            match to old reference data.

            * src/m_transmitter.cc (iyRadioLink, iyTransmissionStandard): The
            auxiliary Faraday quantities now filled by data taken from
            propmat_clearsky.

            * src/m_abs.cc (propmat_clearskyAddFaraday): Included input checks
            and physics. Completed.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8305 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-03-21  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-557

            * Big cleaning, to finish the transition to new way for handling
            Faraday and storing free electrons.

            * doc/uguide/faraday.tex: Updated to new approach for Faraday
            rotation.

            * doc/uguide/rte_basics.tex:
            * doc/uguide/atmosphere.tex: Removed refences to unknown WSVs.

            *
              controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Venus.arts:
              *
              controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Jupiter.arts:
              *
              controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Mars.arts:
              *
              controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Earth.arts:
              Added
                Tensor3Create( edensity_field )
                to keep the cfiles OK.

                * controlfiles/artscomponents/faraday/TestFaradayRotation.arts:
                * controlfiles/artscomponents/radiolink/TestRadioLink.arts:
                * controlfiles/artscomponents/radiolink/TestRadioOccultation.arts:
                * controlfiles/general/agendas.arts:
                * controlfiles/general/general.arts: Removed everything around
                edensity.

                * src/m_refraction.cc (refr_indexFreeElectrons): Now using
                  rtp_vmr
                  instead of rtp_edensity.

                  * src/montecarlo.h:
                  * src/montecarlo.cc (mcPathTraceGeneral):
                  * src/m_montecarlo.cc (MCGeneral):
                  * src/m_rte.cc:
                  * src/refraction.cc:
                  * src/m_atmosphere.cc (basics_checkedCalc):
                  * src/ppath.cc:
                  * src/m_doit.cc:
                  * src/rte.cc:
                  * src/m_cloudradar.cc:
                  * src/doit.h:
                  * src/doit.cc: Removed everything around edensity_field.

                  * src/m_transmitter.cc (iyTransmissionStandard, iyRadioLink):
                  * src/m_rte.cc (iyEmissionStandard):
                  * src/m_cloudradar.cc (iyCloudRadar): Adopted to changes in
                  * rte.cc.

                  * src/rte.cc (get_ppath_atmvars): Removed part around
                    ppath_ne.

                    (get_ppath_trans, get_ppath_trans2): Removed everything
                    around
                    Faraday rotation.

                    * src/agendas.cc: Removed rtp_edensity as input for
                      refr_index_agenda.
                      And edensity_field from both ppath agendas.

                      * src/workspace.cc (define_wsv_data): Removed
                      rtp_edensity. This
                      is now part of rtp_vmr. And removed edensity_field. Now
                      part of
                      vmr_field.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8306 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-558

* WARNING! This version requires you to adapt your controlfiles:

Replace SpeciesSet with abs_speciesSet!

Insert abs_xsec_agenda_checkedCalc and
propmat_clearsky_agenda_checkedCalc where needed.

I recommend to always call abs_speciesSet, abs_speciesAdd and
abs_speciesDefineAllInScenario by keyword:

Use abs_speciesSet( species=["CO2"] ) instead of
abs_speciesSet( abs_species, ["CO2"] ).

Same for abs_speciesAdd and DefineAllScenarios:

abs_speciesAdd( species=["H2O"] )
abs_speciesDefineAllInScenario( basename="testdata/tropical" )

* src/methods.cc, src/m_abs.cc, src/m_abs_lookup.cc:

(abs_xsec_agenda_checkedCalc, propmat_clearsky_agenda_checkedCalc):

Two new checks that have to be called before abs_xsec_agenda or
propmat_clearsky_agenda are used. They ensure that the two agendas
contain the required methods to satisfy calculation of all tags set in
abs_species.

(abs_speciesDefineAllInScenario, abs_speciesAdd, abs_speciesAdd2):

Add propmat_clearsky_agenda_checked and abs_xsec_agenda_checked as
output.

(propmat_clearskyInit): Add propmat_clearsky_agenda_checked as input.

(abs_xsec_per_speciesInit): Add abs_xsec_agenda_checked as input.

(abs_speciesSet):
Change abs_species output type from generic to specific and rename the
function accordingly.
In almost all cases this method is called with abs_species. By
changing it to a specific output, it can be left out in the call. The
rare case of setting abs_nls directly can be easily done by calling:

abs_speciesSet( abs_species=abs_nls, species=["H2O-PWR98"] )

* src/agenda_class.{cc,h} (Agenda::has_method): Added.

* src/workspace.cc:

Add abs_xsec_agenda_checked and propmat_clearsky_agenda_checked.

* src/abs_species_tags.cc (get_tagindex_for_Strings): Removed.

* doc/uguide/absorption.tex: SpeciesSet -> abs_speciesSet.

* controlfiles/*/*/*.arts:

Use keywords in SpeciesSet, abs_speciesAdd and
abs_speciesDefineAllInScenario.

Insert abs_xsec_agenda_checkedCalc,
propmat_clearsky_agenda_checkedCalc where needed.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8307 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-559

* src/m_doit.cc (DoitInit):

Throw runtime_error if scat_za_grid is not increasing. Fixes assertion
in doit_scat_fieldCalcLimb reported by Jana.

Fix typo in the scat_aa_grid runtime error (s/za/aa/).

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8308 aaf1aab0-4228-0410-ad68-8dceda47f409