[yt-users] yt errors

tazkera haque h.tazkera at gmail.com
Mon Feb 8 20:42:56 PST 2016


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()

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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