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

Sam Geen samgeen at astro.ox.ac.uk
Tue Nov 26 07:44:33 PST 2013


Quick question for RAMSES users - do you prefer:
a) YT figures out what variables are in the file from NVAR, e.g. NVAR=5 
gives density,vx,vy,vz,pressure, NVAR=6 adds metallicity, NVAR=10/11 
assumes MHD
b) YT assumes density,vx,vy,vz,pressure only *unless* you do:
load("mydata/info_blahblah.txt",metals=True)
(with similar flags for mhd, etc?)

In all cases if you set "fields" as a parameter (as normal), YT will use 
that, of course.

For RT YT just has to find a info_rt_blahblah.txt file, so no user input 
is needed. If anyone can give info on how RAMSES-ATON outputs work, it 
would be appreciated.

On 25/11/13 20:56, Nathan Goldbaum wrote:
> Just for completeness, the yt developer guide is here: 
> http://yt-project.org/doc/developing/developing.html
>
>
> On Mon, Nov 25, 2013 at 11:38 AM, Matthew Turk <matthewturk at gmail.com 
> <mailto:matthewturk at gmail.com>> wrote:
>
>     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
>     <mailto: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
>     <mailto: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 <mailto: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 <mailto: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 <mailto: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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