[yt-users] yt errors

tazkera haque h.tazkera at gmail.com
Thu Feb 11 23:10:20 PST 2016 

Can anyone please explain me what is going on in the name of memory error
in my codes? I tried using only one hdf5_chk_file and it worked fine. my
code and error is attached. Thanks in advance.



On Mon, Feb 8, 2016 at 11:44 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> 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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