[yt-users] Problem with Units in a Derived Field

Jared Coughlin Jared.W.Coughlin.29 at nd.edu
Wed Aug 26 08:17:56 PDT 2015 

Sorry about that! Here's the script:

http://paste.yt-project.org/show/5842/

And the traceback:

http://paste.yt-project.org/show/5843/

Thanks!
-Jared

On Tue, Aug 25, 2015 at 7:41 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Tuesday, August 25, 2015, Jared Coughlin <Jared.W.Coughlin.29 at nd.edu>
> wrote:
>
>> Hello! I'm really sorry for the barrage of questions; hopefully this will
>> be the last one!
>> I now get the error:  operands could not be broadcast together with
>> shapes (2072685,) (2153824,)
>> on line: fHI = (recomb * ne) / (gamma_HI + (gamma_c * ne))
>>
>> I printed the shapes of all of those arrays, and this is what I get:
>> nH.shape
>> (16, 16, 16)
>> ne.shape
>> (16, 16, 16)
>> gamma_c.shape
>> (1,)
>> recomb.shape
>> (1,)
>> nH.shape
>> (2153824,)
>> ne.shape
>> (2153824,)
>> gamma_c.shape
>> (2072685,)
>> recomb.shape
>> (2072685,)
>>
>> Firstly, I'm a little confused as to why their dimensions change, but
>> what really matters are the bottom ones.  I know how many gas particles are
>> in my gadget simulation: 2072685.  All of the arrays were created from
>> either data["Gas", "InternalEnergy"] or data["gas", "density"], which
>> should, I would imagine, have the same dimensions: the number of gas
>> particles.  I was just wondering if anyone had seen something like this
>> before? The function in question was posted to a pastebin in an earlier
>> email on this thread, and I have since made all of the arrays YTArrays, as
>> suggested above. Thanks!
>> -Jared
>>
>>
> Hey Jared,
>
> I looked above but can't seem to find the correct link for the script
> you're using. Can you pastebin your updated script and the full error
> tracrback you're seeing now?
>
> Nathan
>
>
>
>>
>> On Tue, Aug 25, 2015 at 5:58 PM, Jared Coughlin <
>> Jared.W.Coughlin.29 at nd.edu> wrote:
>>
>>> Thanks, I'll try that!
>>> -Jared
>>>
>>> On Tue, Aug 25, 2015 at 5:55 PM, Andrew Myers <atmyers2 at gmail.com>
>>> wrote:
>>>
>>>> Hi Jared,
>>>>
>>>> You probably don't want to loop over the entire array in pure python;
>>>> that could be very slow for large datasets. One thing you can do is use
>>>> slicing to select the elements of the array that meet your criterion:
>>>>
>>>> indices = data['gas','InternalEnergy'] <= 1e4
>>>> data['gas', 'InternalEnergy'][indices] = *something*
>>>>
>>>> that would set all the elements where the InternalEnergy field is less
>>>> than or equal to 1e4 to *something*. Usually you can express most
>>>> operations you'd want to do this way without explicitly looping over the
>>>> elements.
>>>>
>>>> -Andrew
>>>>
>>>> On Tue, Aug 25, 2015 at 2:44 PM, Jared Coughlin <
>>>> Jared.W.Coughlin.29 at nd.edu> wrote:
>>>>
>>>>> That seemed to have worked, thanks!
>>>>>
>>>>> I just have another quick question, if you wouldn't mind? In my
>>>>> function to generate my new field, there's an if statement that looks at
>>>>> the value of the temperature: if data['gas','InternalEnergy'] <= 1e4:
>>>>> However, I get the error: "The truth value of an array with more than
>>>>> one element is ambiguous. Use a.any() or a.all()." I wasn't sure how to
>>>>> loop over the elements of the array to access a specific element, or if
>>>>> that's even possible? Using a.any() or a.all() don't seem to fit the bill
>>>>> for this particular problem, either. Thanks!
>>>>> -Jared
>>>>>
>>>>> On Tue, Aug 25, 2015 at 3:19 PM, Nathan Goldbaum <
>>>>> nathan12343 at gmail.com> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Aug 25, 2015 at 2:17 PM, Jared Coughlin <
>>>>>> Jared.W.Coughlin.29 at nd.edu> wrote:
>>>>>>
>>>>>>> Great, thanks! I tried that, and it gave me the error: "YTQuantity
>>>>>>> instances must be scalars." I'm not sure what to do about that, since all
>>>>>>> of these quantities depend on either temperature or density, both of which
>>>>>>> are arrays. I tried looking at the doc page for YTQuantity, but I didn't
>>>>>>> see anything that looked like it could solve this problem, though it's
>>>>>>> possible I missed it.
>>>>>>>
>>>>>>
>>>>>> You need to use YTArray instead. YTQuantity is a subclass of YTArray
>>>>>> that only holds scalars. YTArray can hold arrays of data with units.
>>>>>>
>>>>>>
>>>>>>> -Jared
>>>>>>>
>>>>>>> On Mon, Aug 24, 2015 at 8:13 PM, Nathan Goldbaum <
>>>>>>> nathan12343 at gmail.com> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Monday, August 24, 2015, Cameron Hummels <chummels at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Jared,
>>>>>>>>>
>>>>>>>>> The problem is one of units.  In order to make common arithmetic
>>>>>>>>> work like addition, yt requires both arguments going into the addition
>>>>>>>>> operator to have the same units.
>>>>>>>>>
>>>>>>>>> In your line,
>>>>>>>>>
>>>>>>>>> fHI = (recomb * ne) / (gamma_HI + (gamma_c *ne))
>>>>>>>>>
>>>>>>>>> you're adding two things (gamma_HI) and (gamma_c*ne) that have
>>>>>>>>> different units--in this case, something with (code_mass/code_length**3)
>>>>>>>>> units and something with no units defined as (1).
>>>>>>>>>
>>>>>>>>
>>>>>>>> Just a quick clarification: they need not have the same units, just
>>>>>>>> the same dimensions.  You can add two quantities with units of grams and
>>>>>>>> solar masses (for example) but not grams and liters.
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> In order to fix this, you can re-assign the appropriate units to
>>>>>>>>> different arrays or quantities with the YTArray and YTQuantity classes.  In
>>>>>>>>> this case, make sure that the two arguments going into the addition have
>>>>>>>>> the same units.  If you want to recast "ne" to have number density units,
>>>>>>>>> you can do this:  from yt.units.yt_array import YTQuantity; ne =
>>>>>>>>> YTQuantity(ne, 'cm**-3').  For more info on units, check out
>>>>>>>>> http://yt-project.org/docs/dev/analyzing/units/index.html
>>>>>>>>>
>>>>>>>>> I hope this helps!
>>>>>>>>>
>>>>>>>>> Cameron
>>>>>>>>>
>>>>>>>>> On Mon, Aug 24, 2015 at 4:12 PM, Jared Coughlin <
>>>>>>>>> Jared.W.Coughlin.29 at nd.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hello! I have a gadget snapshot for which the standard internal
>>>>>>>>>> energy block has been replaced by one containing the temperature.  I'm
>>>>>>>>>> trying to calculate a derived field for the neutral hydrogen number
>>>>>>>>>> density,  but I'm getting an error when I try to do ds.add_field():
>>>>>>>>>>
>>>>>>>>>> http://paste.yt-project.org/show/5833/
>>>>>>>>>>
>>>>>>>>>> However, I get an error about being unable to add quantities with
>>>>>>>>>> differing units:
>>>>>>>>>>
>>>>>>>>>> http://paste.yt-project.org/show/5834/
>>>>>>>>>>
>>>>>>>>>> The docs say not to do any unit conversion because that is
>>>>>>>>>> apparently taken care of behind the scenes, so I didn't.  I was just
>>>>>>>>>> wondering if there was a way around this? Thanks!
>>>>>>>>>> -Jared
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> yt-users mailing list
>>>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Cameron Hummels
>>>>>>>>> NSF Postdoctoral Fellow
>>>>>>>>> Department of Astronomy
>>>>>>>>> California Institute of Technology
>>>>>>>>> http://chummels.org
>>>>>>>>>
>>>>>>>>
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