[yt-users] Plotting SFRs

Nathan Goldbaum nathan12343 at gmail.com
Wed Sep 13 08:44:41 PDT 2017 

On Wed, Sep 13, 2017 at 7:58 AM, Ashley Jarvis <ajarvis at star.sr.bham.ac.uk>
wrote:

> Thanks for your help. I have submitted a new issue about the documentation
> problem as you suggested.
>
> I have used the other example to produce a plot, but I’m not sure if the
> particles are being filtered correctly. I am using Enzo simulation data. I
> think I want to select all particles that are stars, and then only keep
> those that have a creation time greater than 0; I am unsure how to do this.
> Is it possible to combine two conditions within the filter definition?
>

Yup, you can combine boolean arrays using boolean operators in Numpy. For
your problem it would look like this:

    def formed_star(pfilter, data):
        # identify stars (particle_type 2) that have creation times after
the beginning
        # of the simulation
        filter = (data["all", "creation_time"] > 0) & (data['all',
'particle_type'] == 2)
        return filter

-Nathan


> Many thanks,
> Ashley
>
>
>
> On 12 Sep 2017, at 21:57, nathan12343 at gmail.com wrote:
>
> 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/a
>>> nalyzing/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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