[yt-users] Plotting SFRs

[Nathan Goldbaum]

Hi Ashley,

Unfortunately Stephanie's suggestion won't work, since units like Mpccm,
which depend on details of the dataset, aren't available in yt.units. In
particular the conversion from comoving megaparsecs to physical units
depends on redshift and assumed cosmology.

I think what's happening here is that you are dealing with a
non-cosmological simulation which does not have Mpccm defined.

It looks like yt's StarFormationRate class that you're trying to use
assumes that it's being passed an output from a cosmological simulation and
is failing in a less than graceful fashion when you try pass a
non-cosmological output. We should probably emphasize more in the
documentation that StarFormationRate only accepts a cosmological output (or
improve it so that it *can* work with non-cosmological outputs) and improve
the error message you saw. If you'd like to file an issue about this
documentation problem (at https://github.com/yt-project/yt/issues/new) that
will help us to avoid losing track of this deficiency.

Rather than using the StarFormationRate class, I'd suggest looking at this
example in the cookbook section of the docs:

http://yt-project.org/doc/cookbook/calculating_information.html#using-
particle-filters-to-calculate-star-formation-rates

To adapt that example for your data, you're going to need to figure out how
to select the star particles in your simulation and then either adapt the
particle filter definition in the example for your data, or if you are
using a frontend like Gadget where the output format defines a star
particle type, just use that instead of the particle filter. The rest of
the cookbook recipe just uses numpy to bin the star particle ages according
to the formation time of the particle, and then backs out the star
formation rate history.

Hope that helps,

Nathan

On Tue, Sep 12, 2017 at 3:23 PM Stephanie Tonnesen <stonnes at gmail.com>
wrote:

> I am not sure, but the first thing I would do would be to add
>
> from yt.units import Mpccm
>
> At the top and see what happens next.
>
> Best,
> Stephanie
>
> On Tue, Sep 12, 2017 at 11:36 AM Ashley Jarvis <ajarvis at star.sr.bham.ac.uk>
> wrote:
>
>> Hi all,
>>
>> I’m attempting to adapt the example script for plotting star formation
>> rates (found at http://yt-project.org/doc/analyzing/analysis_modules/star
>> _analysis.html#star-formation-rate) to work with output data from a
>> simulation run using Enzo. However, when I attempt to run the script, I get
>> the following error:
>>
>> ———————————————————
>>
>> File "PlotSFR.py", line 26, in <module>
>>     sfr = StarFormationRate(data, star_mass=mass_old,
>> star_creation_time=ct_old, volume=sp.volume())
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/analysis
>> _modules/star_analysis/sfr_spectrum.py", line 115, in __init__
>>     self._ds.quan(1.0, 'Mpccm**3').units
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py",
>> line 1355, in __new__
>>     dtype=dtype, bypass_validation=bypass_validation)
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/yt_array.py",
>> line 430, in __new__
>>     units = Unit(input_units, registry=registry)
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py",
>> line 257, in __new__
>>     unit_data = _get_unit_data_from_expr(unit_expr, registry.lut)
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py",
>> line 572, in _get_unit_data_from_expr
>>     unit_data = _get_unit_data_from_expr(unit_expr.args[0],
>> unit_symbol_lut)
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py",
>> line 566, in _get_unit_data_from_expr
>>     return _lookup_unit_symbol(str(unit_expr), unit_symbol_lut)
>>   File "/usr/local/anaconda/lib/python2.7/site-packages/yt/units/unit_object.py",
>> line 657, in _lookup_unit_symbol
>>     "symbols." % symbol_str)
>> yt.units.unit_registry.UnitParseError: Could not find unit symbol
>> 'Mpccm' in the provided symbols.
>>
>> ———————————————————
>>
>> I am using version 3.3.5 of yt.
>>
>> Does anyone know how I can resolve this? Any suggestions would be greatly
>> appreciated.
>>
>> Thanks,
>> Ashley
>>
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
> --
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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