[yt-users] different hydrogen densities from different versions of yt

Fri Mar 3 15:04:55 PST 2017

Yeah, I added the H_p0_number_density field to alias H_number_density
field, to make it consistent with the other fields (e.g.
H_p1_number_density), but H_number_density has always referred to the
neutral species number density.

Hope this solves Lauren's confusion.

Cameron

On Fri, Mar 3, 2017 at 2:23 PM, Britton Smith <brittonsmith at gmail.com>
wrote:

> I'll take the blame for that naming convention.  I think my thought
> process was that "nuclei" replaces "number" conceptually.
>
> On Fri, Mar 3, 2017 at 2:16 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Fri, Mar 3, 2017 at 4:10 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Ah, I see, this is covered in YTEP-0003:
>>>
>>> http://ytep.readthedocs.io/en/latest/YTEPs/YTEP-0003.html#mo
>>> lecular-and-atomic-species-names
>>>
>>> And what Lauren wants to use in yt-3 is the "H_nuclei_number_density"
>>> field. Except now that I check, we don't have that field at all, we only
>>> have 'H_nuclei_density'. I'll submit a pull request that adds the number
>>> density field automatically, but for now Lauren is going to need to define
>>> her own nuclei number density field.
>>>
>>
>> And it looks like ('gas', 'H_nuclei_density') *is* a number density after
>> all:
>>
>> In [3]: ds.fields.gas.H_nuclei_density
>> Out[3]: Derived Field (gas, H_nuclei_density): (units: cm**(-3))
>>
>> This is a tad annoying because the naming scheme here is inconsistent
>> with the naming scheme of the other species fields.
>>
>> So that's the field you want to use Lauren. Hope my flailing around here
>> over the course of this thread wasn't too confusing :)
>>
>>
>>> Apologies for the noise about bugs!
>>>
>>> -Nathan
>>>
>>> On Fri, Mar 3, 2017 at 4:06 PM, Britton Smith <brittonsmith at gmail.com>
>>> wrote:
>>>
>>>> Hi Nathan,
>>>>
>>>> This is not a bug.  I will dig up the reference when I can, but at some
>>>> point it was decided that X_density should alias to X_p0_density, for
>>>> whatever X is.  Actually, I believe that this may go all the way back to
>>>> when this naming convention was decided upon, and it was actually the other
>>>> way around.  X_density was originally designated to be the neutral density
>>>> of element X, and sometime later X_p0 was added as an alias of this.  I'll
>>>> look to see if I can find the exact references for when this happened.
>>>>
>>>> britton
>>>>
>>>> On Fri, Mar 3, 2017 at 2:01 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Lauren,
>>>>>
>>>>> Thanks for the detailed report. It was very straightforward to
>>>>> reproduce what you're seeing using one of the test cosmological datasets on
>>>>> yt-project.org/data.
>>>>>
>>>>> I'm pretty sure you've stumbled across a bug in the way species fields
>>>>> are set up for Enzo.
>>>>>
>>>>> Here's what's happening:
>>>>>
>>>>> In yt-2, the field "H_NumberDensity" corresponds to the number density
>>>>> of all hydrogen ion species (i.e. HI + HII number density).
>>>>>
>>>>> In yt-3, for some reason, ('gas', 'H_number_density') represents the
>>>>> number density of just HI ions. To get what you had before, you'd need to
>>>>> defined a new field which sums ('gas', 'H_number_density') and ('gas',
>>>>> 'H_p1_number_density').
>>>>>
>>>>> The following IPython session illustrates the issue:
>>>>>
>>>>> In [10]: ds.fields.gas.H_density
>>>>> Out[10]: Alias Field for "('enzo', 'HI_Density')" (gas, H_density):
>>>>> (units: g/cm**3)
>>>>>
>>>>> In [11]: ds.fields.gas.H_p0_density
>>>>> Out[11]: Alias Field for "('gas', 'H_density')" (gas, H_p0_density):
>>>>> (units: g/cm**3)
>>>>>
>>>>> In [12]: ds.fields.gas.H_p1_density
>>>>> Out[12]: Alias Field for "('enzo', 'HII_Density')" (gas,
>>>>> H_p1_density): (units: g/cm**3)
>>>>>
>>>>> Right now ('gas', 'H_density') is an alias to ('enzo', 'HI_Density'),
>>>>> and ('gas', 'H_p0_density') is an alias to ('gas', 'H_density'). I'm pretty
>>>>> sure that's wrong, ('gas', 'H_p0_density') should be an alias to ('enzo',
>>>>> 'HI_Density') and ('gas', 'H_density') should be a derived field formed by
>>>>> summing HI_density and HII_density.
>>>>>
>>>>> Now, I'm pretty sure this is a bug, but I also don't normally with
>>>>> with Enzo multispecies data, so I'd like some confirmation about this from
>>>>> others who are more experienced with cosmological enzo data before I make a
>>>>> pull request.
>>>>>
>>>>> -Nathan
>>>>>
>>>>> On Fri, Mar 3, 2017 at 2:44 PM, Lauren Corlies <laurennc009 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I've been a yt user for a while now but have recently noticed
>>>>>> something concerning. A few months ago, I made the switch to yt3 and am
>>>>>> currently using the new yt 3.3.4
>>>>>>
>>>>>> I've been working with recently generated, cosmological zoom in
>>>>>> simulations and I've generated a basic yt ray object.  When I plot the
>>>>>> hydrogen number density along the ray, the values that it's generating are
>>>>>> un-physically low (seen here <http://i.imgur.com/1C1oAVr.png>).
>>>>>>
>>>>>> It's especially concerning because when I use the old yt2
>>>>>> installation:
>>>>>> Version = 2.7-dev
>>>>>> Changeset = 1f9ca06815d0
>>>>>>
>>>>>> and generate a yt ray object with the exact same trajectory, the
>>>>>> hydrogen number density values are much more sensible (seen here
>>>>>> <http://i.imgur.com/tcDcNd8.png>). The rays in both yt versions have
>>>>>> mostly the same shape but there are some strong features in the yt2 version
>>>>>> than in the yt3 one.
>>>>>>
>>>>>> The discrepancy is specifically with this field and not other
>>>>>> intrinsic fields like temperature or regular density (also attached).
>>>>>>
>>>>>> Am I accessing the field incorrectly and there's a better way to get
>>>>>> these values with the new version of yt? Or is there something deeper
>>>>>> happening? The hydrogen number density is particularly important for the
>>>>>> ion densities and emission that I've been interested in.
>>>>>>
>>>>>> All of the plots and the script
>>>>>> <http://paste.yt-project.org/show/7066/> to generate them are
>>>>>> attached and posted online as described on the docs page, tagged with my
>>>>>> last name with links included as an attachment.
>>>>>>
>>>>>> Thanks for the help,
>>>>>> Lauren Corlies
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
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-- 
Cameron Hummels
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
http://chummels.org
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