* arts-2-1-516

* src/make_auto_md_cc.cc:

Bug fix: Workspace method parameters that are defined to be
exclusively used as output are initialized to a specific values in
debug mode. Due to the bug, always the default variable was
initialized, not the variable that was actually passed to the WSM,
e.g.:

IndexCreate(i)
AtmosphereSet1D(i, lat_grid, lon_grid)
Print(i)
Print(atmosphere_dim)

This code should throw an error in the 2nd Print statement that
atmosphere_dim is uninitialized. Instead, although i was initialized
correctly to 1, also atmosphere_dim was set to -1.

Added initialization code for Tensor4-7.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8226 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-02-21  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-517

            * Treatment of Doppler shifts streamlined. Now possible to include
            sensor movement (but so far only on iyCalc level), and prepared
            for frequency dependent shift.

            * controlfiles/artscomponents/radiolink/TestRadioLink.arts:
            * controlfiles/artscomponents/radiolink/TestRadioOccultation.arts:
            Adopted call of iyRadioLink.

            * src/make_array.h: Had to add define MakeArray for 37 arguments.
            (iyRadioLink appearently has this record for input arguments).

            * src/m_transmitter.cc (iyTransmissionStandard, iyRadioLink):
            * src/m_rte.cc (iyEmissionStandard):
            * src/m_cloudradar.cc (iyCloudRadar): Adopted to changes below.
            And now also taking rte_alonglos_v as input (passed on to
            get_ppath_doppler).

            * src/rte.cc (get_ppath_xxxx): Now winds and mag-field stored as
            vectors even for ppath_wind and ppath_mag.
            (get_ppath_doppler): New. Returns frequency dependent Doppler
            shift.
            (calc_doppler): Removed (replaced by function above).
            (get_ppath_abs): Now using ppath_doppler.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8227 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-1-518

        * src/methods.cc (SpeciesPartitionLookupOnthefly): Added.

        * src/m_abs_lookup.cc (SpeciesPartitionLookupOnthefly): Added.

        * src/agendas.cc
	(abs_xsec_agenda): Renamed from abs_xsec_per_species_agenda.

        * src/workspace.cc
	(abs_species_active): Added.
	(abs_species_lookup): Added.
	(abs_species_onthefly): Added.
	(abs_xsec_agenda): Renamed from abs_xsec_per_species_agenda.

        * controlfiles/general/agendas.arts
	(abs_xsec_agenda): Renamed from abs_xsec_per_species_agenda.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8229 aaf1aab0-4228-0410-ad68-8dceda47f409
Updated documentation and fixed test file.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8230 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-02-24  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-520

            * Doppler shift now also included in call of
            blackbody_radiation_agenda, as well as when calculating particle
            extinction. However, for efficiency reasons, for particles only
            the mean shift along the path is considered. This as it is time
            consuming to extract the data from scat_data_raw. So this is done
            assuming a constant shift along the path. This allows to at least
            include big shifts caused by e.g. satellite velocity. The smaller
            shifts are here of less importance as the particle extinction is
            quite smooth with frequency.

            * doc/uguide/winds.tex: Chapter revised.

            * doc/uguide/atmosphere.tex (section{Wind and magnetic vector
              fields}):
              * doc/uguide/rte.tex (section{Dispersion}): Some smaller changes
              related to revision of the Doppler chapter.

              * controlfiles/artscomponents/wfuns/TestWfuns.arts:
              * controlfiles/artscomponents/groundbased/TestGbased.arts:
              * Removed
              some obselete stuff related to jacobians.

              * doc/uguide/matrix_vector.tex: Added that the mean function is
              defined for vector and matrix. Also added a small note that min.
              max and mean for matrices is for the complete matrix.

              * controlfiles/artscomponents/absorption/TestIsoRatios.arts:
              Changed rte_ to rtp_, where necessary.

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

              * src/rte.cc (get_ppath_f): get_ppath_doppler renamed, as now
              shifted f_grid is returned, and not only the shift.

              (get_ppath_abs): Temporary solution for rtp_doppler, until
              settled how to handle frequency shifts for abslookup.

              (get_ppath_blackrad,get_ppath_ext): Now takes ppath_f as input.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8232 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-521

* New controlfile feature: Named arguments!

Besides calling a workspace method with positional arguments, it is now
possible to use named arguments. Omitted arguments will be set to
their defaults. For specific inputs/outputs the default WSV will be
used and for generic in/out the default value.

For example, calling a method with all the default arguments and only
pass in two custom values for the generic input required this code
before:

doit_i_fieldUpdateSeq1D(
	  doit_i_field, doit_scat_field, cloudbox_limits,
	  abs_mat_per_species_agenda, vmr_field, spt_calc_agenda,
	  scat_za_grid, scat_aa_grid, pnd_field, opt_prop_part_agenda,
	  ppath_step_agenda, ppath_lraytrace, p_grid, z_field,
	  refellipsoid, t_field, edensity_field, f_grid, f_index,
	  surface_rtprop_agenda, doit_za_interp,
	  1, 0.05 )

now one can simply write:

doit_i_fieldUpdateSeq1D( normalize=1,
			 norm_error_threshold=0.05 )

* src/parser.{h,cc}: Add named argument support.

* src/sourcetext.h (SourceText):

Add new member functions LineRaw, ColumnRaw and SetPosition.

* src/methods.cc:

Make generic input/output variables names more consistent. Generic
output in ...Set... WSMs is called 'out', generic input that is usually
given as a literal is called 'value' (e.g. in VectorSet or
MatrixSetConstant), otherwise 'in'.

Add docs for FieldFromGriddedField.

Set default value for userparam to [] in abs_cont_descriptionAppend.

* controlfiles/general/continua.arts,
controlfiles/general/general.arts,
controlfiles/artscomponents/doit/TestDOIT.arts:

Updated to use named arguments.

* doc/uguide/concept.tex: Add paragraph about named arguments.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8235 aaf1aab0-4228-0410-ad68-8dceda47f409