[yt-users] Absorption Spectrum from Gadget snapshot problem

Cameron Hummels chummels at gmail.com
Thu Aug 20 11:03:08 PDT 2015


Hi Jared,

Yes, the setup functions are what you should use to postprocess the dataset
prior to using the make_spectrum() call.  Essentially, just create whatever
derived field you choose (in this case H_number_density) using the setup
function and then make_spectrum() should work ok.

Cameron

On Thu, Aug 20, 2015 at 8:43 AM, Jared Coughlin <Jared.W.Coughlin.29 at nd.edu>
wrote:

> I do not write the hydrogen number density to the snapshot. I was planning
> on adding it post-processing. I read about the setup functions, but I don't
> really understand how they work. I already have a routine in place that
> gets n_HI from the density and temperature in the snapshot. Are set up
> functions the tool I should be using?
> -Jared
> Hi Jared,
>
>
>>
>> I have two questions. First: When calling make_light_ray and passing it
>> fields, do I need to pass it H_number_density? Second: Does yt read in
>> those fields from the gadget snapshot, or does it calculate them from the
>> data in the snapshot (for example, a standard gadget snapshot does not
>> write the temperature, but rather the internal energy)?  Thanks!
>>
>
>
> When you run sp.add_line(), you're trying to add a line associated with a
> field, in this case, you're associating it with the "H_number_density"
> field.  AbsorptionSpectrum expects that field to be present in the light
> ray (in this case lr.h5) when you run make_spectrum().  The
> "H_number_density" field is a grid-celled neutral hydrogen number density,
> which is present in some simulation outputs, however, I do not know if it
> is automatically populated for the custom gadget dataset on which you're
> running.  Do you trace the neutral hydrogen in your gadget simulation?  If
> so, does it spit out to a particle field that you can then deposit into a
> grid-based field?  Or were you looking to approximate the HI number density
> in yt  by making some assumptions based on the density, temperature,
> radiation field, etc.?
>
> Cameron
> --
> Cameron Hummels
> NSF Postdoctoral Fellow
> Department of Astronomy
> California Institute of Technology
> http://chummels.org
>
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-- 
Cameron Hummels
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
http://chummels.org
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