* arts-2-3-34

	Make sure, SingleScatteringData and UseDOIT wiki parts are represented
	in AUG or built-in doc.

	* doc/uguide/clouds.tex: Checked for complete coverage of wiki's
	SingleScatteringData info. Some small issues updated along the way.
	FIXMEs raised on angular grid requirements.

	* doc/uguide/scattering.tex: removed DOIT theory part from here, i.e.
	the scattering doc in AUG. Checked for complete coverage of wiki's
	UseDOIT info. Some small issues updated along the way.

	* doc/uguide/doit.tex: Added. DOIT part for ATD, containing the method
	theory description formerly in AUG.

	* doc/uguide/montecarlo.tex, atmosphere.tex, ppath.tex, absorption.tex,
	integration.tex, concept.tex, arts_user.tex:
	References adapted to AUG/ATD separation of DOIT part.
	
	* doc/uguide/arts_theory.tex, CMakeLists.txt:
	Adapted to cover moved ATD DOIT chapter.

	* src/cloudbox.cc: spellfix.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8997 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-35

* src/xml_io_compound_types.cc (xml_read_from_stream):

Add runtime error check for ptype for SingleScatteringData version < 2.

* src/cloudbox.cc (chk_scat_data):

Change ptype check to assertion. Runtime error check is now done in
the reading routine.

Replace references to ptype 10,20,30 with strings.

* src/montecarlo.cc (opt_propExtract), src/rte.cc (emission_rtstep):

Replace references to ptype 30 with string.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8998 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-36

* src/absorption.{cc,h}:  Added support for several pressure levels
in line mixing.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8999 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-37

* src/absorption.{cc,h}:  Small optimization for several pressure levels
in line mixing.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9000 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-38

* src/absorption.cc (xsec_species_line_mixing_wrapper):

Vectorized pressure loop.

Use index array to select non-linemixing lines to improve performance.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9001 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-39

* src/absorption.cc (xsec_species_line_mixing_2nd_order,
xsec_species_line_mixing_LBLRTM, xsec_species_LBLRTM_O2NonResonant):

Slight performance improvements.

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

* src/m_zeeman.cc (propmat_clearskyAddZeeman):

Approx. 50% performance improvement for extensive test case.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9002 aaf1aab0-4228-0410-ad68-8dceda47f409
2014-10-14  Richard Larsson <ric.larsson@gmail.com>

* arts-2-3-40

* src/m_zeeman.cc:   Starting modularization of code.

* src/zeeman.{cc,h}: Modules for the Zeeman code added.  The goal is to 
make Zeeman more modular to make extensions of functionality easier.
Hope is for more speed improvements.  Work still in progress.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9004 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-41

* src/quantum.{cc,h} (QuantumNumbers):

Change QuantumContainer from std::map to Array. Speeds up the extensive
zeeman test case by 1.5x on Linux and 2x on Mac. Even though the array
now allocates space for all quantum numbers instead of just the ones
that actually exist, early test have shown that it does not use more
memory than the prior std::map implementation.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9005 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-42

* src/m_zeeman.cc:   Created two new functions to calculate Zeeman
effect a little bit different.  These new methods makes the Zeeman 
test cases 10 to 25% faster, but should offer much larger speed
improvements on higher p_grid:s.  

The old Zeeman code still works as before but will be slower for
magnetic fields that are exactly zero.  Documentation pending.

Use (ZeemanLineRecordPreCalc) after the linerecords are finalized
and change (propmat_clearskyAddZeeman) to
(propmat_clearskyAddZeemanFromPreCalc) in the agenda to use the
new method.

* src/zeeman.{cc,h}: Incorporated linerecord creation in this
file.

* src/workspace.cc:  Added zeeman_linerecord_precalc.

* {the rest}:  Controlfiles for test added; looks at the same
comparison with both Zeeman methods.  Agenda call added to agendas.arts.
Corresponding fixes in m_checked and methods.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9006 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-3-43

	Change of scattering meta data structure. Adaption of all methods that
	use scat_meta. Removed material tag fromscat_species.

	* src/optproperties.h (ScatteringMetaData): Revised format of class.

	* src/xml_io_compound_types.cc: Read/write support for new (version3)
	nScatteringMetaData class format. Removed version1 and 2 support.

	* src/m_cloudbox.cc
	(ScatteringParticlesSelect): Removed obsolote material tag based selection.

	(pnd_fieldSetup): Removed any use of material meta info.

	(dNdD_*): Renamed from dN_* to properly reflect output parameter.
	Removed density as input parameter.

	(particle_massesFromMetaDataSingleCategory): Use mass info from meta data.

	(particle_massesFromMetaDataAndScat_species): Renamed (from 
	particle_massesFromMetaDataAndScat_species). Use mass info from meta data.

	* src/cloudbox.cc/h:
	(chk_scat_species): Adapt for removed material tag.

	(pnd_fieldMH97, pnd_fieldH11, pnd_fieldH13, pnd_fieldH13Shape,
	pnd_fieldMP48, pnd_fieldH98):
	Adapted to new fromat of scattering meta data. Cleaned up a little.

	(IWCtopnd_MH97, IWCtopnd_H11, IWCtopnd_H13, IWCtopnd_H13Shape,
	area_ratioH13, LWCtopnd, PRtopnd_MP48):
	Removed density from method interfaces. More consistent naming of method
	parameters.

	(chk_pndsum): Replace method input volume and density by mass.

	(scale_H11, scale_H13, parse_part_material): Removed obsolete methods.

	* src/m_tmatrix.cc: Removed methods scat_metaAddTmatrix,
	scat_dataFromMeta, scat_metaAddTmatrixOldVersion. New meta data format
	does not support Tmatrix inpu anymore.

	* src/constants.cc: Density of water ice and liquid water added.

	* src/methods.cc, workspace.cc: Revised scat_meta_single and
	scat_species documentation. Revised documntation of methods using these.

	* controlfiles/artscomponents/doitbatch/TestDOITBatch.arts:
	Adapted to scat_meta and scat_species changes.

	* controlfiles/artscomponents/doitbatch/scatData/*.meta.xml.gz:
	Adapted test case meta data to new format.

	* controlfiles/artscomponents/doitbatch/ScatteringMetaFile_H2Oice.xml,
	ScatteringMetaFile_H2Oliquid.xml, SingleScatteringFile_H2Oice.xml,
	SingleScatteringFile_H2Oliquid.xml:
	Added. Scattering data and meta files for DoitBatch test case, separated
	by scattering species.

	* controlfiles/artscomponents/doitbatch/SingleScatteringFile.xml,
	ScatteringMetaFile.xml: Removed.

	* doc/uguide/scattering.tex: Bugfix.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9007 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-44

* src/cloudbox.cc (pnd_fieldMH97, pnd_fieldH11, pnd_fieldH13,
pnd_fieldH13Shape, pnd_fieldMP48, pnd_fieldH98):

Fix bug introduced in arts-2-3-31. The scat_meta elements were
used in unsorted order. Bug found by Jana.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9008 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-45

* src/array.h (TotalNumberOfElements, FlattenedIndex):

Add missing & to array argument.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9010 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-46

* controlfiles/*{zeeman,linemixing}*:  Fixed to reflect the changes.

* src/absorption.cc:  Cutoff was implemented poorly for phase, and 
the implementation does not work with line mixing at all.  Now, cutoff
must be turned off for line mixing and Zeeman calculations to work.

* src/rational.{h,cc}: Less Simplify() calls.

* src/*zeeman.{h,cc}:  Small speed improvements moving variables around.
Still a huge speed loss for copying inputs to speedy Zeeman case.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9012 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-3-47

	* src/cloudbox.cc(pnd_field*): Ensure that meta data required by
	specific size distribution method is available for each individual
	scattering element, else throw error.

	* src/methods.cc, m_cloudbox.cc(dNdD_MH97, dNdD_MP48),
	cloudbox.cc(pnd_fieldMH97, pnd_fieldMP48, IWCtopnd_MH97, PRtopnd_MP48):
	Change from using volume equivalent diameter to mass equivalent
	diameter, Dmass, in MH97 and melted equivalent diameter, Dmelt, in MP48.
	MH97 according to definition in MH97 paper. For MP48 literature is not
	very clear. MP48 itself only discussed rain drops, but MP48 is
	widely used for precipitating hydrometeors in general, e.g. in RTTOV
	(see doherty07:_ice_amsu_b_qjrms). Literature is not clear though, what
	diameter to be used in case of frozen hydrometeors. Considering the
	measurement technique used by MP48 is seems most plausible to assume
	melted diameter.

	* controlfiles/artscomponents/doitbatch/TestDOITBatch.ybatch.ref.xml:
	Adjusted. Using Dmass instead of Dvol in MH97 causes small changes in
	BT due to slightly different assumption of ice density.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9013 aaf1aab0-4228-0410-ad68-8dceda47f409
2014-10-22  Patrick Eriksson  <patrick.eriksson@chalmers.se>

	* controlfiles/CMakeLists.txt: TestTMatrixSSD.arts removed.

	* controlfiles/artscomponents/tmatrix/TestTMatrix.arts: Extended,
	now also testing scat_data_singleTmatrix,
	diameter_maxFromDiameter_volume_equ and
	diameter_volume_equFromDiameter_max. 

	* controlfiles/artscomponents/tmatrix/TestTMatrixSSD.arts: Removed.

	* src/m_tmatrix.cc (diameter_maxFromDiameter_volume_equ): New name
	of theis WSM. And now also returns maximum axial area.
	(diameter_volume_equFromDiameter_max): New name of this WSM.
	(scat_data_singleTmatrix): Now also setting single_meta_data.

	* src/methods.cc:
	* src/tmatrix.h:
	* src/tmatrix.cc:
	* src/m_tmatrix.cc: Changed "aspect ratio" to "axial ratio"
	throughout the code, to follow what seems to be the standard
	nomenclature. At least, this is the name used in
	Mishchenko&Travis, 1998.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9014 aaf1aab0-4228-0410-ad68-8dceda47f409
Now with version number in ChangeLog.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9015 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-49

* src/abs_species_tags.cc:  Turned off test forcing LM to run
alone without continua as another tag.  Hopefullt this will
reduce discrepancies found by Manfred.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9016 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-50

* src/parser.cc (ArtsParser::set_gin_to_default,
ArtsParser::parse_numvector_from_string):

Add support for "NaN" values in defaults for generic inputs (for
Numeric and Vector).
Note, it does not work yet to pass 'NaN' values to generic inputs in
the controlfile. E.g., this will not work: Test(ginput1=3., ginput2=NaN)

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9017 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-3-51

* controlfiles/artscomponents/doitbatch/ScatteringMetaFile_H2Oice.xml,
controlfiles/artscomponents/doitbatch/ScatteringMetaFile_H2Oliquid.xml:

Correct wrong xml version. Should be 1.0 not 3.0.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9018 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-3-52

	Renamed massdensity_field to scat_species_mass_density_field, added
	scat_species_mass_flux_field and scat_species_number_density_field (so
	far only placeholders) and changed some massdensity_field methods to
	support the new fields.

	* src/workspace.cc: Renamed massdensity_field to
	scat_species_mass_density_field. Added scat_species_mass_flux_field and
	scat_species_number_density_field. Adapted documentation.

	* src/methods.cc, m_cloudbox.cc, m_atmosphere.cc:
	Renamed all occurences of massdensity_field to scat_species_mass_density_field.

	* src/methods.cc,  m_cloudbox.cc (Massdensity_cleanup):
	Renamed method to scat_species_fieldCleanup and adapted to be applicable
	for all	scat_species_XX_fields, i.e. now taking/providing generic
	Tensor4	in/output.

	* src/cloudbox.cc, cloudbox.h (chk_massdensity_field):
	Renamed method to chk_scat_species_field and adapted to be applicable
	for all	scat_species_XX_fields

	* controlfiles/artscomponents/doitbatch/TestDOITBatch.arts:
	Adapt for change of Massdensity_cleanup to scat_species_fieldCleanup.

	* src/m_basic_types.cc: Spell fix.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@9021 aaf1aab0-4228-0410-ad68-8dceda47f409