[yt-users] Plotting SFRs

Thu Oct 5 07:13:16 PDT 2017

Hi Nathan,

I managed to implement the filter definition that you provided, but I have
come across another problem. When I try to generate the SFR plots for the
simulation at different time steps, there is always a sharp decline in the
rate around 25Myr before the output time of the data dump (see attached
plots).

Is this happening because of something in the simulation itself, e.g.
there is a delay between the region reaching a given density limit and the
star particle actually being created (to represent the formation time of
the stars), or is it being caused by something in the yt plotting process?

Many thanks,
Ashley

https://i.imgur.com/mjCQvZy.png
https://i.imgur.com/Cv5D1HK.png
https://i.imgur.com/6ZA2xgq.png

> 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 Iâ€™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,
>>>>
>>>> Iâ€™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:
>>>>
>>>> â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”
>>>>
>>>> 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.
>>>>
>>>> â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”â€”
>>>>
>>>> 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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