[yt-users] troubles with derived field: 1+1 is not equal to 2

[Andrew Myers]

Hi Antoine,

Actually, on closer inspection I think you may have found a bug in the
Chombo frontend. Thanks for bringing this to our attention. Would you mind
checking whether these
<https://bitbucket.org/yt_analysis/yt/pull-request/1137/a-patch-that-fixes-an-issue-uncovered-by>
changes fix the problem for you?

Thanks,
Andrew


On Thu, Aug 7, 2014 at 11:28 AM, Andrew Myers <atmyers2 at gmail.com> wrote:

> Hi Antoine,
>
> I'm having some trouble reproducing your issue. When I run the attached
> script on the TurbBoxLowRes dataset, I get the following png files, the
> last of which is different than yours. Could you tell us what version of yt
> you're running?
>
> Thanks,
> Andrew Myers
>
>
> On Thu, Aug 7, 2014 at 10:29 AM, Antoine Strugarek <
> strugarek at astro.umontreal.ca> wrote:
>
>> Hi Nathan,
>>
>> Many thanks for the fast answer. I just tried to reproduce my problem
>> with existing data (the ‘TurbBoxLowRes’ data from yt-project.org/data)
>> and I get the same issue.
>>
>> I just attached at the end of this email the small script I use to
>> generate my fields VRA, VRB and VVR, which is adapted to the TurbBoxLowRes
>> case. I also tried your suggestions of not adding my derived field as type
>> ‘chombo’, but it did not solve the problem.
>>
>> I also attached the same snapshots from the TurbBoxLowRes case, VVR
>> should be the sum of the two other and as you can see the blue negative
>> patch on the right should clearly not be there (the color scale is the same
>> in all the plots). It does not seem overall far off so I guess this is
>> really dumb on my side, thanks again for your help!
>>
>> Antoine
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Le 2014-08-07 à 13:07 , Nathan Goldbaum <nathan12343 at gmail.com> a écrit :
>>
>>  Hi Antoine,
>>
>> I'm not sure what's going wrong here.  I have a few ideas below.  If the
>> dataset is small enough it would probably help if you could share it using
>> e.g. dropbox or google drive along with your full analysis script.
>> Alternately, can you reproduce the issue using one of the public datasets
>> on yt-project.org/data?
>>
>>
>> On Thu, Aug 7, 2014 at 9:10 AM, Antoine Strugarek <
>> strugarek at astro.umontreal.ca> wrote:
>>
>>> Hello,
>>>
>>> I’m new to yt so this maybe solved easily, though it puzzled me for
>>> quite some time and I still don’t understand what is going on.
>>>
>>> I try to create derived fields to analyze a simulation using AMR, from
>>> an output from CHOMBO. I define the following derived fields:
>>>
>>> def _VRA(field,data):
>>>     return  data['Cylsin']*data['Vx2']
>>> def _VRB(field,data):
>>>     return  data['Cylcos']*data['Vx1']
>>> def _VVR(field,data):
>>>     return  data['VRA']+data['VRB']
>>>
>>
>> Are 'Cylsin' and 'Cylcos' on-disk fields or are they derived fields as
>> well?  If so, can you share their definitions?
>>
>>
>>>
>>> Then I add them to my yt object:
>>>
>>>     ds=yt.load(file)
>>>     ds.index
>>>     ds.add_field(('chombo','VRA'),function=_VRA,units='cm/s',take_log=
>>> False)
>>>     ds.add_field(('chombo','VRB'),function=_VRB,units='cm/s',take_log=
>>> False)
>>>     ds.add_field(('chombo','VVR'),function=_VVR,units='cm/s',take_log=
>>> False)
>>>
>>> and everything goes on smoothly (they are the only variables named this
>>> way). Now, If I try to slice VRA and VRB I obtain the (correct) attached
>>> plots. Both VRA and VRB are strictly positive. If I try to slice VVR which
>>> is the sum VRA+VRB, I obtained the third attached plot which does not
>>> correspond to the expected sum (there are even negative values)! I suspect
>>> something went odd in the slice function, but I used the exact same lines
>>> of code to generate the three plots.
>>>
>>
>> What happens if instead of passing in the field tuple ('chombo', 'VRA'),
>> you instead pass in 'VRA' or ('gas', 'VRA').  Saying the field type is
>> 'chombo' for a derived field doesn't really make much sense.  For a chombo
>> dataset, a 'chombo' field must be on-disk and is always in code units.  By
>> creating a derived field with explicit CGS units you might be confusing
>> yt's field system.
>>
>>
>>
>>>
>>> I must be missing something here but I really don’t get it. Many thanks
>>> in advance for your help!
>>>
>>> Antoine
>>>
>>>
>>>   Antoine STRUGAREK
>>> -------------------------------------------------------------------
>>> Webpage
>>> <https://googledrive.com/host/0BxBaqwiaesNkcDBWcUFCdmMxSUU/strugarek.html>
>>>
>>> Département de physique, Université de Montréal
>>> strugarek at astro.umontreal.ca
>>> (+1) 514 343 7077
>>> --------------------------------------------------------------------
>>> DSM/IRFU/SAp/LDEE CEA Saclay
>>> DSM/IRFM/SCCP CEA Cadarache
>>> antoine.strugarek at cea.fr
>>> --------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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