[yt-users] Custom units.

Nathan Goldbaum nathan12343 at gmail.com
Tue Nov 1 13:03:33 PDT 2016 

At the top of your script, you have:

from yt.units import kb

but later you have:

return kB*entrdens

It should be:

return kb*entrdens

On Tue, Nov 1, 2016 at 3:00 PM, Kuo-Chuan Pan <pankuoch at msu.edu> wrote:

> Dear Nathan,
>
> Thank you very much for your help.
> I was using ds.add_field()
>
> I have pasted my script and error message here:
> http://paste.yt-project.org/show/wToLggLnTYVpMxeqJtln/
>
> Many thanks,
> Kuo-Chuan
>
>
> On Nov 1, 2016, at 3:50 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>
>
> 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/334cceb2c6e197acf1a
>> 8c7f273ee9dd0bd592f58/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
>>>> _______________________________________________
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>>>>
>>>
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