[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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