[yt-users] RFC: RAMSES field aliases in yt-3.0

Matthew Turk matthewturk at gmail.com
Mon Nov 25 11:38:10 PST 2013 

Yup, there is, but stop by IRC if you run into trouble.  It should be
as easy as making sure your ~/.hgrc has your name/email in [ui], for
instance:

[ui]
username = Matthew Turk <matthewturk at gmail.com>

then:

cd /path/to/yt/hg/repo

-edit edit edit-
hg commit

On the BitBucket site you can fork our repository (do not make a
branch though!) here: https://bitbucket.org/yt_analysis/yt-3.0/fork

and you can then just push to your repo:

hg push -f http://bitbucket.org/SamsUserName/yt-3.0

Then pull request away!

-Matt

On Mon, Nov 25, 2013 at 2:35 PM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
> OK, will try to figure out all that tomorrow. I guess there's a guide to
> issuing pull requests on the yt site?
>
>
> On 25/11/13 20:30, Matthew Turk wrote:
>>
>> Hi Sam,
>>
>> This looks great.  Any chance you could add this to the
>> yt/frontends/ramses/definitions.py file as a function, issue a pull
>> request, and we'll get your name in the commit log?  I'll then modify
>> it to fit in and we'll use it as fallback when fields are specified.
>>
>> -Matt
>>
>> On Mon, Nov 25, 2013 at 1:39 PM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>>>
>>> I've hacked up a simple example of what I mean (attached).
>>>
>>>
>>> On 25/11/13 17:50, Nathan Goldbaum wrote:
>>>
>>> Matt's opened a PR for this here:
>>>
>>>
>>> https://bitbucket.org/yt_analysis/yt-3.0/pull-request/140/adding-field_aliases-to-ramses-datasets/diff
>>>
>>> Sam, if you could enumerate how to map from the boolean flags you're
>>> suggesting to a final field list, I think that would help immensely.
>>>
>>>
>>> On Mon, Nov 25, 2013 at 8:42 AM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>>>>
>>>> Yes and no. NVAR must be big enough, but it can be bigger than necessary
>>>> (I think); it's a Makefile setting when compiling Ramses. You can
>>>> guarantee
>>>> that the first 4 variables are the same, but after that I suspect the
>>>> best
>>>> approach is to use boolean flags to specify whether the run contains
>>>> MHD,
>>>> RHD, metals, etc. Normally it's a good guess that 5 is pressure and 6
>>>> (if it
>>>> exists) is metals, but as I said it seems like MHD puts the B-field
>>>> before
>>>> pressure and metallicity.
>>>>
>>>>
>>>> On 25/11/13 17:36, Nathan Goldbaum wrote:
>>>>
>>>> Does that mean that it should be possible to infer the field list from
>>>> NVAR alone?
>>>>
>>>>
>>>> On Mon, Nov 25, 2013 at 8:29 AM, Sam Geen <samgeen at astro.ox.ac.uk>
>>>> wrote:
>>>>>
>>>>> For MHD, the variables stored are the B-field strengths on the faces of
>>>>> each cell - the fields in order are: (1) density, (2-4) [x,y,z]
>>>>> velocity,
>>>>> (5-7) [x,y,z] B-field left, (8-10) [x,y,z] B-field right, (11) pressure
>>>>> (thermal + MHD), then (12+) any passive scalars (metals, etc) - see
>>>>> mhd/output_hydro.f90. Note that the MHD module adds 3 variables, so the
>>>>> number of variables will be nvar+3.
>>>>>
>>>>> For RHD (Joki Rosdahl's M1 method implementation, at least - someone
>>>>> else
>>>>> will have to help with the ATON version), there is a separate "rt_"
>>>>> output
>>>>> file for each CPU (like the hydro/amr/particles), as well as a separate
>>>>> info
>>>>> file (there is a bitbucket link on the Ramses homepage if you want to
>>>>> see
>>>>> what the latest version of the code does in detail). The RHD module
>>>>> divides
>>>>> photons into "nGroups" different flux bins; for each bin, it writes a
>>>>> photon
>>>>> density and then a flux vector. nGroups is stored in the rt info file;
>>>>> nrtvar is written to the rt_ binary file, but this is (I think) a
>>>>> Makefile
>>>>> setting and not guaranteed to be nGroups/(1+ndim) (the user is, I
>>>>> believe,
>>>>> normally free to waste memory by allocating more variables than they
>>>>> need).
>>>>> For details it might be easiest to download the latest code and look at
>>>>> the
>>>>> code in the folder rt/, or ask Romain or Joki Rosdahl directly.
>>>>>
>>>>> (Feel free to correct me if any of this is wrong!)
>>>>>
>>>>> I agree that setting the default to the standard five (perhaps some
>>>>> boolean variables for common configurations such as metals, RHD, MHD,
>>>>> etc)
>>>>> and then letting users set or add their own fields by hand if they need
>>>>> to
>>>>> is a good approach.
>>>>>
>>>>>
>>>>> On 25/11/13 16:23, Matthew Turk wrote:
>>>>>>
>>>>>> Hi all, especially RAMSES users,
>>>>>>
>>>>>> I'm setting up aliases to make it easier to load RAMSES datasets that
>>>>>> have different field configurations.
>>>>>>
>>>>>> Right now, to specify a different set of fields, you have to do:
>>>>>>
>>>>>> pf = load( ... , fields = [ "Density", "x-velocity", ...])
>>>>>>
>>>>>> I am going to change this to add on different field configurations
>>>>>> that can be specified with just a string.  For instance:
>>>>>>
>>>>>> pf = load(..., fields = "standard_five")
>>>>>>
>>>>>> I'm wondering what the different configurations are.  I have these
>>>>>> two:
>>>>>>
>>>>>> standard_five: Density, x-velocity, y-velocity, z-velocity, Pressure
>>>>>> standard_six: Density, x-velocity, y-velocity, z-velocity, Pressure,
>>>>>> Metallicity
>>>>>>
>>>>>> But for MHD and RHD, what are the additional fields that should be
>>>>>> added, and in what order?  And are there other common configurations
>>>>>> that should be aliased?
>>>>>>
>>>>>> If we can come up with a set of aliases that match most use cases,
>>>>>> that'd work quite well.  I'm going to issue a PR for this shortly, and
>>>>>> hopefully it will make everybody's life a bit easier.
>>>>>>
>>>>>> -Matt
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