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

Jared Coughlin Jared.W.Coughlin.29 at nd.edu
Tue Aug 25 15:27:16 PDT 2015 

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


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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