Dear Pengwang,
Yeah, you have to copy abs_species to abs_species active. I forgot about
that. The Copy( out, in ) function does that so add
Copy( abs_species active, abs_species)
before you call the xsec agenda.
To explain the reasoning for the active tag: Not all species can be
handled by the xsec calculations. So some must be inactive. For your
calculations --- that is to emulate how the old abs_coefCalc worked as I
understand it --- this is not a problem.
//Richard
2016-02-16 13:44 GMT+01:00 Pengwang Zhai <pwz...@umbc.edu>:
> Thanks, Richard. I tried your suggestion. Unfortunately, it does not
> work. The error message is:
>
> arts TestAbsCoeff.arts
>
> Version: arts-2.2.57 (compiled Fri Feb 12 21:05:27 2016)
> Executing Arts
> {…
> …
> …
> }
> This run took 11.10s (11.07s CPU time)
> Run-time error in controlfile: TestAbsCoeff.arts
> Run-time error in method: AgendaExecute
> Run-time error in method: abs_xsec_per_speciesInit
> Method abs_xsec_per_speciesInit needs input variable: abs_species_active
> Stopping ARTS execution.
> Goodbye.
>
> Here is the script:
>
>
> ____________________________
>
> #DEFINITIONS: -*-sh-*-
> #
> # An example ARTS controlfile that calculates absorption
> # coefficients.
> # SAB 16.06.2000
>
> Arts2 {
>
> INCLUDE "general/general.arts"
> INCLUDE "general/continua.arts"
> INCLUDE "general/agendas.arts"
> INCLUDE "general/planet_earth.arts"
>
> # Agenda for scalar gas absorption calculation
> Copy(abs_xsec_agenda, abs_xsec_agenda__noCIA)
> # on-the-fly absorption
> Copy( propmat_clearsky_agenda, propmat_clearsky_agenda__OnTheFly )
>
> abs_linesReadFromHitran( abs_lines,
> "/RT/HITRAN/HITRAN2012.par",
> 3.880627143214052e+14,
> 3.961610390054004e+14 )
>
> abs_speciesSet( species=[ "H2O-PWR98",
> "O2-PWR93" ] )
>
> # This separates the lines into the different tag groups and creates
> # the workspace variable `abs_lines_per_species':
> abs_lines_per_speciesCreateFromLines
>
> # Dimensionality of the atmosphere
> AtmosphereSet1D
>
> VectorNLogSpace( p_grid, 200, 100000, 10 )
>
> # Atmospheric profiles
> AtmRawRead( t_field_raw, z_field_raw, vmr_field_raw, abs_species,
> "testdata/tropical" )
>
> # Now interpolate all the raw atmospheric input onto the pressure
> # grid and create the atmospheric variables `t_field', `z_field',
> `vmr_field'
> AtmFieldsCalc
>
> # Initialize the input variables of abs_coefCalc from the Atm fields:
> AbsInputFromAtmFields
>
> # Create the frequency grid `f_grid':
> VectorNLinSpace( f_grid, 25000,3.880627143214052e+14,
> 3.961610390054004e+14 )
>
> IndexSet(stokes_dim, 1)
>
> # Calculate absorption coefficients, both total (`abs_coef') and
> # separately for each tag group (`abs_coef_per_species'):
>
> atmfields_checkedCalc
> abs_xsec_agenda_checkedCalc
> AgendaExecute(abs_xsec_agenda)
> abs_coefCalcFromXsec
>
> # Optionally write these to files:
> WriteXML( output_file_format,abs_coef_per_species)
> }
>
> ____________________________
>
> > On Feb 16, 2016, at 3:15 AM, Richard Larsson <ric.lars...@gmail.com>
> wrote:
> >
> > Dear Pengwang Zhai,
> >
> > I think we still have what you are looking for in ARTS.
> >
> > The variable you are actually interested in is not abs_coef, but
> abs_coef_per_species.
> >
> > The way to create this is to first run abs_xsec_agenda and then
> abs_coefCalcFromXsec.
> >
> > I think your code should only change from:
> >
> > abs_coefCalc
> >
> > to
> >
> > abs_xsec_agendaExecute
> > abs_coefCalcFromXsec
> >
> > Now abs_coef_per_species is an array of matrices. The array-size is the
> species and the matrices are the size of f_grid and p_grid. Save this and
> do what you want with it.
> >
> > This said, there is potentially a few other changes depending on what
> version you are using and what species you are interested in. You will
> want to run jacobianOff, for instance, if you are using the dev-branch.
> >
> > Cheers,
> > //Richard
> >
> > 2016-02-15 22:11 GMT+01:00 Pengwang Zhai <pwz...@umbc.edu>:
> > Thanks, Jana.
> >
> > > Note that for deriving abs_coef for this, you need to sum up over all
> species (i.e. over the 0th dimension of propmat_clearsky_field.
> >
> > This is exactly what I wanted to do within arts to get “abs_coef”. If
> it is not possible with arts, I will use matlab to do this.
> >
> > The three dimensions are: [species, f_grid, p_grid]
> >
> > Cheers,
> >
> > PZ
> >
> >
> > > On Feb 15, 2016, at 3:47 PM, Jana Mendrok <jana.mend...@gmail.com>
> wrote:
> > >
> > > Hi,
> > >
> > > what do you intend to do with abs_coeff_user?
> > > Do you really process this further within ARTS itself? only then it
> makes sense to process propmat_clearsky_field into a Tensor3*, i think.
> > > Else, I strongly recommend to do any re-shaping / reduction outside of
> ARTS; other programming languages are much better suited for this kind of
> task (e.g. you can use the matlab-interface atmlab to have easy access to
> ARTS output. or the python interface typhon).
> > >
> > > abs_coef was a Matrix of dimension [f_grid, abs_p] (and
> abs_coef_per_species an Array holding one abs_coef matrix per defined
> abs_species).
> > > propmat_clearsky_field is a Tensor7 of dimension [species, f_grid,
> stokes_dim, stokes_dim, p_grid, lat_grid, lon_grid].
> > >
> > > That is, for reducing propmat_clearsky_field to what was
> abs_coef_per_species before would be
> > > propmat_clearsky_field[:, :, 0, 0, :, lat_index, lon_index] (in case
> of 0-indexed varibales; in case of a 1D calculation furthermore
> lat_index=lon_index=0). As far as I know, that's not possible (at least not
> easily possible) within ARTS itself.
> > >
> > > Note that for deriving abs_coef for this, you need to sum up over all
> species (i.e. over the 0th dimension of propmat_clearsky_field.
> > >
> > > Best wishes,
> > > Jana
> > >
> > >
> > > ps.
> > > *by the way, what are the 3 dimensions? neither abs_coeff nor
> abs_coef_per_species is (or has been for a long time) a Tensor3. That is,
> you must have post-processed abs_coef(_per_species) anyways?
> > >
> > > On Mon, Feb 15, 2016 at 6:09 PM, Pengwang Zhai <pwz...@umbc.edu>
> wrote:
> > > Thanks, Jana. Too bad that the only arts feature that I am using is
> now obsolete.
> > >
> > > Now given propmat_clearsky_field, can I somehow obtain abs_coeff from
> it?
> > >
> > > I used the following commands to create abs_coeff_user, which is the
> absorption coefficients per specie,
> > >
> > > Tensor3Create(abs_coeff_user)
> > > Reduce(abs_coeff_user,propmat_clearsky_field)
> > >
> > > can I add the coefficients per specie abs_coeff_user together to
> create abs_coeff within arts?
> > >
> > > I could do this with other tools but wish to know how to do in arts,
> which is more convenient.
> > >
> > > Thanks,
> > >
> > > Pengwang
> > >
> > >
> > > > On Feb 15, 2016, at 12:00 PM, Jana Mendrok <jana.mend...@gmail.com>
> wrote:
> > > >
> > > > Dear Pengwang,
> > > >
> > > > please take a look at the workspace variable propmat_clearsky_field
> (and the workspace method propmat_clearsky_fieldCalc, that calculates this
> variables). Could they probably provide the output you need?
> > > >
> > > > abs_coef and its *Calc method are obsolete and not supported anymore.
> > > >
> > > > Best wishes,
> > > > Jana
> > > >
> > > >
> > > > On Mon, Feb 15, 2016 at 4:30 PM, Pengwang Zhai <pwz...@umbc.edu>
> wrote:
> > > > Hi,
> > > >
> > > > I used earlier version of ARTS to calculate the total absorption
> coefficients with:
> > > >
> > > > abs_coefCalc
> > > >
> > > > and found it is very useful. Now with the new version, this does
> not work any more. After reading the change log I found that it is replaced
> with
> > > >
> > > > abs_coefCalcFromXsec
> > > >
> > > > However, after numerous attemps I could not make this method working
> for me. Would you please provide a template arts file on the usage of this
> method?
> > > >
> > > > Thanks very much and hope all the best,
> > > >
> > > > Yours
> > > >
> > > > _______________________________________________
> > > > arts_users.mi mailing list
> > > > arts_users.mi@lists.uni-hamburg.de
> > > > https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
> > > >
> > > >
> > > >
> > > > --
> > > > =====================================================================
> > > > Jana Mendrok, Ph.D. (Project Assistent)
> > > > Chalmers University of Technology
> > > > Earth and Space Sciences
> > > > SE-412 96 Gothenburg, Sweden
> > > >
> > > > Phone : +46 (0)31 772 1883
> > > > =====================================================================
> > >
> > >
> > >
> > >
> > > --
> > > =====================================================================
> > > Jana Mendrok, Ph.D. (Project Assistent)
> > > Chalmers University of Technology
> > > Earth and Space Sciences
> > > SE-412 96 Gothenburg, Sweden
> > >
> > > Phone : +46 (0)31 772 1883
> > > =====================================================================
> >
> > _______________________________________________
> > arts_users.mi mailing list
> > arts_users.mi@lists.uni-hamburg.de
> > https://mailman.rrz.uni-hamburg.de/mailman/listinfo/arts_users.mi
> >
>
>
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