[yt-users] yt errors

Nathan Goldbaum nathan12343 at gmail.com
Mon Feb 8 20:44:15 PST 2016 

On Mon, Feb 8, 2016 at 10:42 PM, tazkera haque <h.tazkera at gmail.com> wrote:

> Hi Nathan ,
>
> Thanks, I need one last correction from you. my final goal is to get the
> Ejected_Mass. How can I get rid of this error?
>
> Thanks in advance
>
> import yt
> import numpy as np
>
> from yt import derived_field
>
>
> @derived_field(name = "__mass_ejects")
> def shock(field,data):
>     dm = data['cell_mass']
>     xv = data['velx']
>     yv = data['vely']
>     zv = data['velz']
>     grav_pot= data['gpot']
> #define total energy
>     E_total=0.5*dm*(xv**2+yv**2+zv**2)+grav_pot*dm
>
>     return np.greater(E_total, 0)
>
>
> ds = yt.load('~/super3d_hdf5_plt_cnt_0118')
>
> ds.index
> print ds.field_info["gas", "cell_mass"].get_source()
> print ds.field_info["gas", "__mass_ejects"].get_source()
>

You need something like data = ds.all_data() here.


>
> Ejected = data['cell_mass']*data['__mass_ejected']
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>     def _cell_mass(field, data):
>         return data[ftype, "density"] * data["index", "cell_volume"]
>
> @derived_field(name = "__mass_ejects")
> def shock(field,data):
>     dm = data['cell_mass']
>     xv = data['velx']
>     yv = data['vely']
>     zv = data['velz']
>     grav_pot= data['gpot']
> #define total energy
>     E_total=0.5*dm*(xv**2+yv**2+zv**2)+grav_pot*dm
>
>     return np.greater(E_total, 0)
>
>
> ---------------------------------------------------------------------------NameError                                 Traceback (most recent call last)<ipython-input-5-bbb0b768fd76> in <module>()     24 print ds.field_info["gas", "__mass_ejects"].get_source()     25 ---> 26 Ejected = data['cell_mass']*data['__mass_ejected']
> NameError: name 'data' is not defined
>
>
>
>
> On Mon, Feb 8, 2016 at 11:18 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Hi Tazkera,
>>
>> It works if I do this:
>>
>> http://paste.yt-project.org/show/6233/
>>
>> The issue with your example is that your derived field definition either
>> returns 1 or 0, when instead it should return an array with the same shape
>> as E_total.
>>
>> -Nathan
>>
>>
>> On Mon, Feb 8, 2016 at 9:49 PM, tazkera haque <h.tazkera at gmail.com>
>> wrote:
>>
>>> I am trying to derive a new field here and will test it with one of the
>>> scripts first. but I am getting  error when I am checking if that field has
>>> been added already. please take a look at the errors for me.
>>>
>>> import yt
>>>
>>> from yt import derived_field
>>>
>>>
>>> @derived_field(name = "__mass_ejects")
>>> def shock(field,data):
>>>     dm = data['cell_mass']
>>>     xv = data['velx']
>>>     yv = data['vely']
>>>     zv = data['velz']
>>>     grav_pot= data['gpot']
>>> #define total energy
>>>     E_total=0.5*dm*(xv**2+yv**2+zv**2)+grav_pot*dm
>>>
>>>
>>>     if E_total >0:
>>>         return 0
>>>     else :
>>>         return 1
>>> ds.index
>>> print ds.field_info["gas", "cell_mass"].get_source()
>>> print ds.field_info["gas", "__mass_ejects"].get_source()
>>>
>>>
>>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>
>>>  def _cell_mass(field, data):
>>>         return data[ftype, "density"] * data["index", "cell_volume"]
>>>
>>>
>>> ---------------------------------------------------------------------------KeyError                                  Traceback (most recent call last)<ipython-input-29-bfb3007289ba> in <module>()      1 ds.index      2 print ds.field_info["gas", "cell_mass"].get_source()----> 3 print ds.field_info["gas", "__mass_ejects"].get_source()
>>> /home/trina/anaconda2/lib/python2.7/site-packages/yt/fields/field_info_container.pyc in __missing__(self, key)    285     def __missing__(self, key):    286         if self.fallback is None:--> 287             raise KeyError("No field named %s" % (key,))    288         return self.fallback[key]    289
>>> KeyError: "No field named ('gas', '__mass_ejects')"
>>>
>>>
>>>
>>>
>>> On Mon, Feb 8, 2016 at 11:18 AM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> This error happens when yt can't find a field for a given dataset. In
>>>> this case it's looking for a field named 'absReynoldsStress'. It reports it
>>>> with the funny spelling "('all', 'absReynoldsStrss')" because it's guessing
>>>> that it's a particle field.
>>>>
>>>> Since that isn't a field in your FLASH dataset (unless you've modified
>>>> FLASH to output such a field), and it's not defined as a derived field in
>>>> that script or in yt itself, yt isn't able to generate it.
>>>>
>>>> Do you have an 'absReynoldsStress' derived field defined somewhere else?
>>>>
>>>> -Nathan
>>>>
>>>> On Sun, Feb 7, 2016 at 9:53 PM, tazkera haque <h.tazkera at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi, can anyone please check my script and the corresponding error?
>>>>>
>>>>> On Sun, Feb 7, 2016 at 1:29 PM, tazkera haque <h.tazkera at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> thanks very much everyone. solves my problem.
>>>>>>
>>>>>> On Sun, Feb 7, 2016 at 11:15 AM, Kacper Kowalik <
>>>>>> xarthisius.kk at gmail.com> wrote:
>>>>>>
>>>>>>> On 02/06/2016 09:03 PM, tazkera haque wrote:
>>>>>>>
>>>>>>>> Hi , thanks very much for the helps. but I happen to get the errors
>>>>>>>> still
>>>>>>>> though I did the exact same things as suggested. I am attaching the
>>>>>>>> summary
>>>>>>>> and error.
>>>>>>>>
>>>>>>>
>>>>>>> Hi Tazkera,
>>>>>>>
>>>>>>> clean.sh unfortunately doesn't remove cythonized modules (.c files).
>>>>>>> You can either manually remove the offending file
>>>>>>> (yt/geometry/grid_container.c) or use hg purge. In order to do the latter
>>>>>>> you'll need to add the following to $HOME/.hgrc:
>>>>>>>
>>>>>>> [extensions]
>>>>>>> hgext.purge =
>>>>>>>
>>>>>>> Then try:
>>>>>>>
>>>>>>> $ cd /work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/
>>>>>>> $ hg purge --all
>>>>>>> $ python setup.py build_ext -i  # (or python setup.py develop)
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Kacper
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Feb 6, 2016 at 9:05 PM, Nathan Goldbaum <
>>>>>>>> nathan12343 at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> It looks like yt's C extensions need to be recompiled. Can you
>>>>>>>>> activate
>>>>>>>>> the yt environment and do the following:
>>>>>>>>>
>>>>>>>>> $ cd /work/03858/thaque56/sw/yt-3.1/yt-x86_64/src/yt-hg/
>>>>>>>>> $ bash ./clean.sh
>>>>>>>>> $ hg pull
>>>>>>>>> $ hg update
>>>>>>>>> $ python setup.py develop
>>>>>>>>>
>>>>>>>>> If that doesn't work, can you reply with the output of "hg
>>>>>>>>> summary", as
>>>>>>>>> well as the error that you see?
>>>>>>>>>
>>>>>>>>> Hope that helps,
>>>>>>>>>
>>>>>>>>> Nathan
>>>>>>>>>
>>>>>>>>> On Sat, Feb 6, 2016 at 7:25 PM, tazkera haque <h.tazkera at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Hi , I am trying to run a python file with yt packages on
>>>>>>>>>> STAMPEDE. and
>>>>>>>>>> getting some errors each time. I think the error is due to some
>>>>>>>>>> installation error of yt at first place. can you please look at
>>>>>>>>>> both my
>>>>>>>>>> code and error and send me the solutions to solve the problem.
>>>>>>>>>> both the
>>>>>>>>>> files are attached for your convenience.
>>>>>>>>>>
>>>>>>>>>> regards
>>>>>>>>>> Tazkera
>>>>>>>>>>
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>>>>>>>>>>
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>>>>>>>>
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