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@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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