2013-08-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-742

            * Work in progress, no active changes yet.

            * Start on revision of checked WSVs and WSMs. Following the lines
            of Jana's changes, but instead using more WSVs. And trying to
            better distinguish between atmospheric and absorption parts. For
            example, basics_checkedCalc requires f_grid to be set, while
            f_grid is not always used, such as when calling ppathCalc.
            Now planning to have these flag WSVs:
              abs_checked
          atmfields_checked
          atmgeom_checked
          cloudbox_checked
          sensor_checked

          For abs_checked to be true, both abs_xsec_agenda_checked and
        propmat_clearsky_agenda_checked must be true, and some additional
        tests done. So it is a "super flag" for the absorption part.

        * src/m_checked.cc: New file and placed all WSM returning
        checked-variables here. The idea is by putting them side-by-side
        it should be easier to make sure that the checks are complete and
        there is a good logic between the methods.

        (atmfields_checkedCalc, atmgeom_checkedCalc, abs_checkedCalc): New
        methods, not yet active.

        * Corrected date for commit below.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8613 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-743

* Warning! WSM and WSV renaming in this commit!!!

* controlfiles/artscomponents/disort/TestDISORT.arts,
controlfiles/artscomponents/doit/TestDOIT.arts,
controlfiles/artscomponents/doitbatch/TestDOITBatch.arts,
controlfiles/artscomponents/montecarlo/TestMonteCarloDataPrepare.arts,
controlfiles/artscomponents/montecarlo/TestMonteCarloGeneral.arts,
controlfiles/artscomponents/montecarlo/TestMonteCarloGeneralGaussian.arts,
controlfiles/artscomponents/montecarlo/TestRteCalcMC.arts,
controlfiles/artscomponents/tmatrix/TestTMatrixSSD.arts,
doc/uguide/absorption.tex, doc/uguide/clouds.tex,
doc/uguide/rte_basics.tex, doc/uguide/scattering.tex,
src/cloudbox.cc, src/cloudbox.h, src/disort.cc, src/disort.h,
src/m_abs.cc, src/m_batch.cc, src/m_checked.cc, src/m_cloudbox.cc,
src/m_cloudradar.cc, src/m_disort.cc, src/m_doit.cc, src/m_fos.cc,
src/m_montecarlo.cc, src/m_optproperties.cc, src/m_rte.cc,
src/m_tmatrix.cc, src/m_transmitter.cc, src/mc_NotUsed.cc,
src/methods.cc, src/montecarlo.cc, src/montecarlo.h,
src/partition_function_data.cc, src/rte.cc, src/rte.h,
src/workspace.cc:

single_scattering_data -> scat_data
scat_data_raw          -> scat_data_array
scat_data_mono         -> scat_data_array_mono
scat_data_nelem        -> scat_data_array_nelem
scat_data_meta         -> scat_meta
scat_data_meta_array   -> scat_meta_array

Resulting WSM renames:

scat_data_meta_arrayAddTmatrix -> scat_meta_arrayAddTmatrix
scat_data_meta_arrayInit       -> scat_meta_arrayInit
scat_data_monoCalc             -> scat_data_array_monoCalc
scat_data_rawCheck             -> scat_data_arrayCheck
scat_data_rawFromMeta          -> scat_data_arrayFromMeta

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8614 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-744

* One more WSV rename. This concludes the renaming of the scattering
WSVs / WSM.

* controlfiles/artscomponents/doitbatch/TestDOITBatch.arts,
src/m_cloudbox.cc, src/methods.cc, src/workspace.cc:

scat_data_array_nelem -> part_species_nout

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8616 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-1-745

	* controlfiles/artscomponents/arts-xml-data/TestSurf_Mars.y.xml:
	Added. Reference file for test case TestSurf_Mars.arts (missed in
	arts-2-1-738).

	* doc/uguide/absorption.tex: Spellfix.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8617 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-08-20  Johan Strandgren  <johsat-9@student.ltu.se>

	* arts-2-1-746

	* src/workspace.cc:

	(scat_meta, scat_meta_array): updated online doc.

	* src/methods.cc:

	(scat_meta_arrayAddTmatrix, scat_data_arrayFromMeta):
	updated online doc.


git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8618 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-08-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-747

            * src/methods.cc (particle_massesFromMetaDataSingleCategory):
            Extended doc text, for hopefully better clarity.

            * src/geodetic.cc (cart2poslos): Removed assrt of 
            abs( abs(za) - RAD2DEG*acos(dr) ) < 1e-4

            Added this assert as a double check that correct angle was
            resolved and there is no real loopholes in the code. Ole Martin
            now got a case with a difference of 1.018e-4. This is a numerical
            issue. No point in just relaxing the assert, the assert has
            fulfilled its purpose.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8619 aaf1aab0-4228-0410-ad68-8dceda47f409
2013-08-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

	* arts-2-1-748

	* Warning! New WSVs and WSMs introduced. You need to change your
	2.1 cfiles. Basically all cfiles should be affected.

	* Revision of the variables and method of check-type now
	activated. More WSVs of checked-type, for better modularity and
	making the variables easier to use in WSMs.

	Note that the checked-variables only are used in methods normally
	called directly in the control file, but not used in methods
	normally placed in agendas, for efficiency reasons. So, yCalc,
	ppathCalc etc. uses the variables, but I have removed old checks
	in e.g. iyMC and CloudboxGetIncoming to be consistent with this
	rule.

	That is, if you make direct calls of methods like iyMC,
	iyEmissionStandard and CloudboxGetIncoming its on your own risk.
	If you use bad input for such calls, you can obtain an assert
	instead of an error, or even worse, incorrect result. However, you can
	of course call e.g. atmfields_checkedCalc anyhow before calling
	e.g. iyMC. That will decrease the risk of bad surprises later on.

	For a claculation with yCalc you now need these calls
           propmat_clearsky_agenda_checkedCalc
           abs_checkedCalc
	   atmfields_checkedCalc
           atmgeom_checkedCalc
           cloudbox_checkedCalc
           sensor_checkedCalc

	* controlfiles/instruments/odinsmr/TestOdinSMR_1D.arts:
	* controlfiles/instruments/odinsmr/TestOdinSMR.arts:
	* controlfiles/instruments/mhs/TestMHS_generic.arts:
	* controlfiles/instruments/hirs/TestHIRS.arts:
	* controlfiles/instruments/avhrr/TestAVHRR.arts:
	* controlfiles/instruments/amsu/TestAMSU_generic.arts:
	* controlfiles/artscomponents/arts-xml-data/TestPlanetIsoRatios.arts:
	* controlfiles/artscomponents/arts-xml-data/TestSurf_Venus.arts:
	* controlfiles/artscomponents/arts-xml-data/TestSurf_Mars.arts:
	* controlfiles/artscomponents/arts-xml-data/TestSurf_Earth.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScen_Venus.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScen_Mars.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScen_Jupiter.arts:
	* controlfiles/artscomponents/cia/TestRTwithCIA.arts:
	* controlfiles/artscomponents/disort/TestDISORT.arts:
	* controlfiles/artscomponents/groundbased/TestFgrid.arts:
	* controlfiles/artscomponents/montecarlo/TestMonteCarloGeneralGaussian.arts:
	* controlfiles/artscomponents/montecarlo/TestMonteCarloGeneral.arts:
	* controlfiles/artscomponents/montecarlo/TestRteCalcMC.arts:
	* controlfiles/artscomponents/ppath/TestRefractPlanets.arts:
	* controlfiles/artscomponents/wfuns/TestWfuns.arts:
	* controlfiles/artscomponents/zeeman/TestZeeman.arts:
	* controlfiles/artscomponents/doitbatch/TestDOITBatch.arts:
	* controlfiles/artscomponents/doit/TestDOIT.arts:
	* controlfiles/artscomponents/faraday/TestFaradayRotation.arts:
	* controlfiles/artscomponents/radiolink/TestRadioOccultation.arts:
	* controlfiles/artscomponents/radiolink/TestRadioLink2.arts:
	* controlfiles/artscomponents/radiolink/TestRadioLink.arts:
	* controlfiles/artscomponents/transmission/TestTransmission.arts:
	* controlfiles/artscomponents/clearsky/TestClearSky2.arts:
	* controlfiles/artscomponents/clearsky/TestClearSky.arts:
	* controlfiles/artscomponents/pencilbeam/TestPencilBeam.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Venus.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Earth.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Jupiter.arts:
	* controlfiles/artscomponents/arts-xml-data/TestAtmScenSup_Mars.arts:
	* controlfiles/artscomponents/absorption/TestIsoRatios.arts:
	* controlfiles/artscomponents/absorption/TestCompareArtscat3And4.arts:
	* controlfiles/artscomponents/absorption/TestAbsDoppler.arts:
	* controlfiles/artscomponents/groundbased/TestWinds.arts:
	* controlfiles/artscomponents/groundbased/TestGbased.arts:
	* controlfiles/artscomponents/ppath/TestPpath3D.arts:
	* controlfiles/artscomponents/ppath/TestPpath2D.arts:
	* controlfiles/artscomponents/ppath/TestPpath1D.arts:
	* controlfiles/artscomponents/helpers/TestHSE.arts: Adopted to
	changes below.

	* src/m_doit2.cc (CloudboxGetIncoming2, iyInterpCloudboxField2):
	Removed these from methods.cc. Unfinished work. Do not even
	remember that I had started this!

	* src/m_rte.cc (iyMC):
	* src/m_doit.cc (CloudboxGetIncoming1DAtm):
	* src/m_doit.cc (CloudboxGetIncoming):
	* src/m_ppath.cc (ppathFromRtePos2): Now not using any of the
	check variables, see comment at top.

	* src/m_abs_lookup.cc (propmat_clearsky_fieldCalc): Now using
	abs_checked and atmfields_checked, instead of basics_checked.

	* src/m_rte.cc (iy_auxFillParticleVariables):
	* src/m_atmosphere.cc (z_fieldFromHSE): Now using atmfields_checked,
	instead of basics_checked.

	* src/m_ppath.cc (ppathCalc): Now using atmgeom_checked, instead
	of basics_checked.

	* src/m_montecarlo.cc (MCGeneral):
	* src/m_rte.cc (iyCalc):
	* src/m_cloudradar.cc (yCloudRadar):
	* src/m_rte.cc (yCalc): Now using abs_checked, atmgeom_checked,
	atmfields_checked, instead of basics_checked.

	* src/m_checked.cc (basics_checkedCalc, basics_checkedCalcNoGeo):
	Removed these WSMs and related internal functions. Code already
	reused in atmfields_checkedCalc, atmgeom_checkedCalc.

	(propmat_clearsky_agenda_checkedCalc): Commented out
	needs_free_electrons, variable not used.

	* src/workspace.cc: Removed basics_checked, and added:
	   abs_checked
	   atmfields_checked
	   atmgeom_checked



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8620 aaf1aab0-4228-0410-ad68-8dceda47f409