* arts-2-1-877

* src/m_abs.cc (abs_xsec_per_speciesInit):

Add check to ensure that the species indexes in abs_species_active
are smaller than the number of species. Fixes assertion reported by
Theresa.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8857 aaf1aab0-4228-0410-ad68-8dceda47f409
	* arts-2-1-878

	* src/m_abs.cc
	(abs_lines_per_speciesAddMirrorLinesOld): Removed this function,
	since it is obsolete.
	(abs_lines_per_speciesAddMirrorLines): Added const qualifier to
	Index n definition.

	* src/methods.cc (abs_lines_per_speciesAddMirrorLinesOld): Removed.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8858 aaf1aab0-4228-0410-ad68-8dceda47f409
2014-05-19  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-879

            * src/m_rte.cc (yCalcAppend): Start on new WSM. So far just y
            itself that is handled.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8859 aaf1aab0-4228-0410-ad68-8dceda47f409
2014-05-20  Patrick Eriksson  <patrick.eriksson@chalmers.se>

	* arts-2-1-880

	* src/m_rte.cc (yCalcAppend): Completed.

	* controlfiles/CMakeLists.txt: Added the test below as a fast one.

	* controlfiles/artscomponents/ycalcappend/TestYCalcAppend.arts:
	New folder and file.

	* src/m_jacobian.cc (jacobianClose): Removed jacobian as output.
	It wa sjust sized and set to zero, which anyhow is (and should be)
	done) in yCalc.

	* src/workspace.cc: Removed old non-active variables.

	* src/m_rte.cc (iyEmissionStandard): Only first element of iy_aux
	was set for "Radiative background".



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8861 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-881

* src/m_cloudbox.cc, src/methods.cc (ScatteringDoitMergeParticles1D):

New experimental method to speed up DOIT calculations.

This method pre-calculates a weighted sum of all particles per pressure
level before the actual DOIT calculation is taking place in
*ScatteringDoit*. It should be called directly after pnd_fieldSetup
(but after cloudbox_checkedCalc).

*pnd_field* is resized to [np, np, 1, 1]. Where np is the number
of pressure levels inside the cloudbox. The diagonal elements of
the new *pnd_field* are set to 1, all others to 0. Accordingly,
*scat_data_array* is resized to np. Each particle is the weighted sum
of all particles at this presssure level. This is an experimental
method currently only working for very specific cases. All particles
must be of the same type and all particles must share the same f_grid
and za_grid. And pha_mat_data, ext_mat_data and abs_vec_data must be
all the same size. This method can only be used with a 1D atmosphere.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8862 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-882

* src/methods.cc (ScatteringDoitMergeParticles1D):

Put alphabetically in the correct place.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8863 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-883

* src/m_cloudbox.cc, src/m_optproperties.cc
(ScatteringDoitMergeParticles1D):

Moved to m_optproperties.cc.

Ignore particles with density <= PND_LIMIT.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8866 aaf1aab0-4228-0410-ad68-8dceda47f409
2014-05-22  Patrick Eriksson  <patrick.eriksson@chalmers.se>

            * arts-2-1-884

            * src/m_rte.cc (yCalcAppend): Removed a cout statement, that was
            just added for test purposes.



git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8867 aaf1aab0-4228-0410-ad68-8dceda47f409
* arts-2-1-885

* src/m_optproperties.cc (ScatteringDoitMergeParticles1D):

Don't force particles to have same temperature grid.

Don't calculate top-most pressure levels, it's 0 anyway in pnd_field.

Bug fix: Only set lower-most pnd_field to 0 if cloudbox does not touch
the surface.

* src/methods.cc (ScatteringDoitMergeParticles1D):

Add z_field and z_surface as inputs.

git-svn-id: https://www.sat.ltu.se/svn/rt/arts/trunk@8870 aaf1aab0-4228-0410-ad68-8dceda47f409