[yt-users] Setting Units

[Kacper Kowalik]

On 09/26/2014 09:38 AM, John Regan wrote:
> HI Britton,
> 
> I've pretty much got everything working now as it should but there one
> thing that is throwing me. In the above script k7 was fairly straight
> forward but suppose I want to calculate the rates for something like:
> 
> ######################################################
> import yt
> from yt.utilities.physical_constants import kboltz
> import numpy as np
> 
> def _k17(field, data):
>     T = data["Temperature"]
>     print "T.shape = ", T.shape
>     k17rate = np.zeros(len(T))
You'd probably want something like:

  k17rate = np.zeros_like(T)

this will solve shape issues

>     i = 0
>     for t in T:
>         if t < 1e4:
>             k17rate[i] = 1.0e-8*pow(t, -0.4)
>         else:
>             k17rate[i] = 4.0e-4*pow(t, -1.4)*exp(-15100.0/t)
>         i = i + 1
>     return k17rate #cm^3 s^-1
> 
> 
> yt.add_field("k17rate", units="cm**3/s", function=_k17)
> Filename = "RD0000/RD0000"
> 
> ds = yt.load(Filename)
> sp = ds.sphere('max', (100, 'kpc'))
> print sp["k17rate"]
> ######################################################
> 
> This time the function is messy. There is probably a nice python way of
> doing the calculation
> without looping - maybe something similar to k17rate[T < 1e4] =
> 1.0e-8*np.power(T, -0.4) ?

That's ^^ exactly how you want to do that. You'll need same index in
power, i.e. T[T < 1e4].

Cheers,
Kacper

> 
> Either way this fails because the array that gets passed to k17 has a shape
> of (16, 16, 16) and so everything falls
> apart. The _k17 function actually gets called 5 times in total - firstly
> with the array of shape (16, 16, 16) and then
> with flat arrays but it fails on the first non-flat array anyway.
> 
> Just wondering if you know what's going on here (why the function gets
> called 5 times and why the first array in a 3D array).
> Any solutions would of course also be appreciated!
> 
> Cheers,
> John
> 
> 
> 
> 
> 
> 
> 
> On Fri, Sep 26, 2014 at 2:41 PM, John Regan <johnanthonyregan at gmail.com>
> wrote:
> 
>> Yip that works! Thanks Britton!
>>
>> On Fri, Sep 26, 2014 at 2:35 PM, Britton Smith <brittonsmith at gmail.com>
>> wrote:
>>
>>> Hi John,
>>>
>>> I think you should be able to wipe out the units being used in the
>>> function and add your own by doing:
>>>
>>> return data.ds.arr(krate.d, "cm**3/s")
>>>
>>> krate.d gives you just the data array without units.
>>>
>>> Britton
>>>
>>> On Fri, Sep 26, 2014 at 7:05 AM, John Regan <johnanthonyregan at gmail.com>
>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I'm having a little trouble with Units in YT-3.0.
>>>>
>>>> I want to calculate the rates for some collisional dissociations as used
>>>> in Enzo. The rates are fits so the dimensions are not going to be as
>>>> required and YT doesn't like that!
>>>>
>>>> An example script showing the problem is shown below:
>>>>
>>>> #####################################################
>>>> import yt
>>>> from yt.utilities.physical_constants import kboltz
>>>> import numpy as np
>>>>
>>>> def _k7(field, data): #H + e -> HM + gamma
>>>>     Tergs = data["Temperature"]*kboltz
>>>>     TeV = Tergs.convert_to_units('eV')
>>>>     krate = 6.77e-15*np.power(TeV, 0.8779)
>>>>     return krate #cm^3 s^-1
>>>>
>>>> yt.add_field(("gas", "k7rate"), units="cm**3/s", function=_k7)
>>>>
>>>> Filename = "....../RD0000/RD0000"
>>>>
>>>> ds = yt.load(Filename)
>>>> sp = ds.sphere('max', (100, 'kpc'))
>>>> print sp["k7rate"]
>>>> #######################################################
>>>>
>>>> The script fails with the error:
>>>> yt.utilities.exceptions.YTUnitConversionError: Unit dimensionalities do
>>>> not match. Tried to convert between eV**(8779/10000) (dim
>>>> (length)**(8779/5000)*(mass)**(8779/10000)/(time)**(8779/5000)) and cm**3/s
>>>> (dim (length)**3/(time)).
>>>>
>>>> which makes sense because the _k7() function is just a fit based on
>>>> temperature. Is there a way to "set" the units of k7 to be cm^3 s^-1?
>>>>
>>>> Cheers,
>>>> John
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>
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>>
> 
> 
> 
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