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
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