[yt-users] gradient field in yt3

[Nathan Goldbaum]

So I *think* the parenthesis in the units are coming from this line:

https://bitbucket.org/yt_analysis/yt/src/603eab147248f1a165778c76208906201eb7baae/yt/fields/fluid_fields.py?at=yt#fluid_fields.py-218

And I think this is happening because no one has tried to create a gradient
field for a unitless field. This is something we should be able to do, but
it's definitely a corner case.

I don't have a script to run to test out any possible fixes, is there any
chance you could make a script that uses one of the public test datasets on
yt-project.org/data so I can reproduce your issue locally?

Please also feel free to try fixing this yourself in your local copy of yt
so you can make a PR.  I think all we need to do is modify the line I
linked to so if "field_units" is an empty string, we drop the parenthesis
and just make the gradient field units "1/cm".

On Thu, Aug 13, 2015 at 2:30 PM, Yuan Li <bear0980 at gmail.com> wrote:

> Traceback (most recent call last):
>   File "logP.py", line 11, in <module>
>     a=dd["gas","logP_gradient_y"]
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 253, in __getitem__
>     self.get_data(f)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 751, in get_data
>     self._generate_fields(fields_to_generate)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 771, in _generate_fields
>     fd = self._generate_field(field)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 290, in _generate_field
>     tr = self._generate_fluid_field(field)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 308, in _generate_fluid_field
>     rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
> line 318, in _generate_spatial_fluid
>     rv = self.ds.arr(np.empty(self.ires.size, dtype="float64"), units)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line
> 332, in __new__
>     units = Unit(input_units, registry=registry)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py",
> line 204, in __new__
>     unit_data = _get_unit_data_from_expr(unit_expr, registry.lut)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py",
> line 496, in _get_unit_data_from_expr
>     unit_data = _get_unit_data_from_expr(expr, unit_symbol_lut)
>   File
> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py",
> line 504, in _get_unit_data_from_expr
>     "objects." % str(unit_expr))
> yt.units.unit_object.UnitParseError: Cannot parse for unit data from '()'.
> Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
>
> On Thu, Aug 13, 2015 at 3:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan at astro.columbia.edu> wrote:
>>
>>> Hi all:
>>>
>>> I am having trouble creating a gradient field in yt3. What I want is the
>>> gradient of logP, where logP is defined as:
>>>
>>> @derived_field(name="logP",units="")
>>> def _logP(field,data):
>>>     return numpy.log(numpy.array(data["gas","pressure"]))
>>>
>>> Then I add the gradient field:
>>>
>>> pf.add_gradient_fields(("gas","logP"))
>>>
>>
>>> which seems to work and I can find it in pf.derived_field_list.
>>>
>>> But if I try to use it, I get this error message:
>>> yt.units.unit_object.UnitParseError: Cannot parse for unit data from
>>> '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
>>>
>>
>> Can you pastebin the full traceback?
>>
>>
>>>
>>> Is this because logP does not have a unit?
>>>
>>> Also, I had another unrelated question about the gradient fields:
>>> Can I add the gradient fields globally instead of to a specific dataset?
>>>
>>>
>> Not right now, no.
>>
>>
>>>
>>> Thanks!
>>> Yuan
>>>
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