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

Nathan Goldbaum nathan12343 at gmail.com
Fri Aug 8 10:22:47 PDT 2014


On Fri, Aug 8, 2014 at 4:31 AM, Antoine Strugarek <
strugarek at astro.umontreal.ca> wrote:

> Hi Nathan and Andrew,
>
> Many thanks for your help, the fix from Andrew indeed fixed my problem!
>

Excellent!  Glad to hear things are working now.  Hopefully we will have
Andrew's fix merged in soon.


> Nathan, originally I wanted to use the geometrical field that were
> automatically computed by yt, but in my case the cylindrical coordinates
> are not correct. They do not use the shifted version of the original axes,
> meaning that it seems they supposed the origin (0,0,0) was at the bottom
> left of the simulation box. I’m not sure if this is the expected behaviour
> when reading my data set, but I had to recompute them anyway to derive my
> fields.
>

By default yt uses coordinate system the simulation was run with. Is it not
doing that in this case?

You should be able to supply parameters to the coordinate system using a
field parameter:
http://yt-project.org/docs/3.0/analyzing/fields.html#field-parameters

In yt 3.0 both SlicePlot and ProjectionPlot take field parameters as
keyword arguments.  You can also create a custom data object (e.g.
ds.slice, ds.proj), set your field parameters, and then use the to_pw
method to get back a SlicePlot or ProjectionPlot created using your custom
data source.


>
> Best regards,
>
> Antoine
>
>
> Le 2014-08-07 à 19:16 , Andrew Myers <atmyers2 at gmail.com> a écrit :
>
> 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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