[yt-users] Custom units.

Tue Nov 1 12:50:48 PDT 2016

On Tue, Nov 1, 2016 at 2:40 PM, Kuo-Chuan Pan <pankuoch at msu.edu> wrote:

> Dear Nathan,
>
> Thanks very much for your email and suggestions.
> I followed your suggested code but it is not working.
> yt gives an error message:
> yt : [ERROR ] 2016-11-01 15:25:27,650 YTFieldUnitParseError: The field
> '('gas', 'Entropy')' has unparseable units 'kB’.
>

Did you use ds.add_field as I showed in my previous e-mail or yt.add_field
as you originally had in your last e-mail? You need to use ds.add_field as
I showed in my code snippet for my workaround to work properly.

If you *did* use ds.add_field, can you pastebin the full script, along with
any error messages and tracebacks you received upon running the script?

We have paste.yt-project.org set up for this purpose.

-Nathan

>
> The vales of my “entr” field is already in “kB/baryon” (specific entropy)
> but the unit is incorrect.
> Following your suggestions, I want to create two new units called “kB” and
> “baryon” (1.674e-24 g)
> and override the “entr” and “Entropy” units to “kB/baryon” (from
> dimensionless).
> Is it possible to do that?
>
> Many thanks,
> Kuo-Chuan
>
>
> On Nov 1, 2016, at 2:52 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
> One could argue that it would be useful for save_annotated to optionally
> take a fully user-specified colorbar label. That's not the case now but it
> would be a relatively easy modification.
>
> Your 'entr' field isn't being recognized by yt with units because it's not
> a field that is "known" by yt in the FLASH frontend:
>
> https://bitbucket.org/yt_analysis/yt/src/334cceb2c6e197acf1a8c7f273ee9d
> d0bd592f58/yt/frontends/flash/fields.py?at=yt&fileviewer=
> file-view-default#fields.py-43
>
> Specifically, it does not appear in the known_other_fields tuple in the
> flash fields.py file. If entr is not specific to your version of FLASH it
> may be worthwhile to add an entry there so that the entr field is read in
> with the correct units.
>
> Similarly, kB isn't a unit that the yt unit system understands out of the
> box (although I think one could make a case that it's worth including).
> There is a way to add new units to the unit system though:
>
>     from yt.units import kb
>     from yt.units.dimensions import energy, temperature
>
>     # load your dataset
>     ds = yt.load(...)
>
>     ds.unit_registry.add('kB', 1.3806488e-16,
> dimensions=energy/temperature, tex_repr='k_{B}')
>
>     def _entrdens(field,data):
>          """
>          create a new derived field to show both entropy and density
>          """
>          dens = data["dens"]
>          entr = data["entr"]
>          entrdens = entr*(np.exp(-(dens.in_cgs()/P
> NS_DENSITY)**5))+PNS_ENTR
>          return kb*entrdens
>     ds.add_field("Entropy",function=_entrdens, units="kB",
> display_name="Entropy per Baryon")
>
> And then make your volume rendering as you were doing before. It should
> show up in the label as "Entropy per baryon" and with units of "kB".
>
> Please feel free to open issues or pull requests about any of the things I
> raised above.
>
> -Nathan
>
>
> On Tue, Nov 1, 2016 at 1:25 PM, Kuo-Chuan Pan <pankuoch at msu.edu> wrote:
>
>> Dear Nathan,
>>
>> Thanks very much for your help.
>> entropy is a filed in my FLASH dataset. The unit of entropy is kB/baryon
>> in the code but it is recognised as dimensionless in yt.
>>
>> The field “entr" is the entropy in my dataset. The derived field
>> “Entropy” is the one I want to visualise.
>> PNS_DENSITY and PNS_ENTR are just constants.
>>
>> Many thanks,
>> Kuo-Chuan
>>
>>   11 def _entrdens(field,data):
>>   12     """
>>   13     create a new derived field to show both entropy and density
>>   14     """
>>   15     dens = data["dens"]
>>   16     entr = data["entr"]
>>   17     entrdens = entr*(np.exp(-(dens.in_cgs()/P
>> NS_DENSITY)**5))+PNS_ENTR
>>   18     return entrdens
>>   19 yt.add_field("Entropy",function=_entrdens,units="dimensionless")
>>
>>
>> On Nov 1, 2016, at 2:20 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>> Hi Kuo-Chuan,
>>
>> Can you show us how you've defined your derived field?
>>
>> Is entropy a derived field as well or is it a field that's included in
>> your dataset? This is the entropy per baryon, right?
>>
>> -Nathan
>>
>> On Tue, Nov 1, 2016 at 1:09 PM, Kuo-Chuan Pan <pankuoch at msu.edu> wrote:
>>
>>> Dear all,
>>>
>>> I have a custom new derived field based on density (g/cm^3) and entropy
>>> (kB/baryon but it is recognised as dimensionless).
>>> Currently, this new derived field is set to dimensionless (it should be
>>> kB/baryon).
>>>
>>> Could anyone teach me how to set this new derived filed to its correct
>>> unit (which should be kB/baryon)?
>>> Or is it possible to simply override the field label in my volume
>>> rendering plot before using save_annotated()?
>>>
>>> Many thanks,
>>> Kuo-Chuan
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>
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