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<div class="moz-cite-prefix">Yes, the user will always be able to
change the "fields" keyword in load() to override the defaults.<br>
<br>
A user-defined default field vector sounds like something that
needs careful thought, since it's common to run simulations with
and without metals, MHD, etc, in the same project, in which case
different field arrays are needed in rapid succession. Of course,
it's always possible for users to create modules for themselves
and add them to their $PYTHONPATH, so in this case, I think the
simplest solution would be to write a module with something like
the following:<br>
<br>
myfields = ["blah1","blah2",...]<br>
def myload(fileloc):<br>
from yt.mods import load<br>
return load(fileloc, fields=myfields)<br>
<br>
then import that module to get a personal default loading
interface.<br>
<br>
On 26/11/13 19:52, Romain Teyssier wrote:<br>
</div>
<blockquote
cite="mid:A3C58892-D443-4CAE-9D9F-AD6A7CA260D3@gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
I like Sam’s suggestion (option a).
<div>Based on how many variables we have in the file, we propose a
default variable name vector,</div>
<div>like the ones proposed by Sam, but the user should always
have the possibility to overwrite the default </div>
<div>because he is the only one to really know which variables he
used.</div>
<div><br>
</div>
<div>One cool option would be for the user to be able define a
default variable name vector himself.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Romain</div>
<div><br>
</div>
<div><br>
<div>
<div>On 26 Nov 2013, at 16:44, Sam Geen <<a
moz-do-not-send="true"
href="mailto:samgeen@astro.ox.ac.uk">samgeen@astro.ox.ac.uk</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Quick question for RAMSES
users - do you prefer:<br>
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<br>
b) YT assumes density,vx,vy,vz,pressure only *unless*
you do:<br>
load("mydata/info_blahblah.txt",metals=True)<br>
(with similar flags for mhd, etc?)<br>
<br>
In all cases if you set "fields" as a parameter (as
normal), YT will use that, of course.<br>
<br>
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.<br>
<br>
On 25/11/13 20:56, Nathan Goldbaum wrote:<br>
</div>
<blockquote
cite="mid:CAJXewOnr-_gsLrq+UMGanVqPzayO6hU1CX8HOcqZO1mJunNE7A@mail.gmail.com"
type="cite">
<div dir="ltr">Just for completeness, the yt developer
guide is here: <a moz-do-not-send="true"
href="http://yt-project.org/doc/developing/developing.html">http://yt-project.org/doc/developing/developing.html</a></div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Nov 25, 2013 at 11:38
AM, Matthew Turk <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:matthewturk@gmail.com"
target="_blank">matthewturk@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Yup, there is, but stop by IRC if you run into
trouble. It should be<br>
as easy as making sure your ~/.hgrc has your
name/email in [ui], for<br>
instance:<br>
<br>
[ui]<br>
username = Matthew Turk <<a
moz-do-not-send="true"
href="mailto:matthewturk@gmail.com">matthewturk@gmail.com</a>><br>
<br>
then:<br>
<br>
cd /path/to/yt/hg/repo<br>
<br>
-edit edit edit-<br>
hg commit<br>
<br>
On the BitBucket site you can fork our repository
(do not make a<br>
branch though!) here: <a moz-do-not-send="true"
href="https://bitbucket.org/yt_analysis/yt-3.0/fork"
target="_blank">https://bitbucket.org/yt_analysis/yt-3.0/fork</a><br>
<br>
and you can then just push to your repo:<br>
<br>
hg push -f <a moz-do-not-send="true"
href="http://bitbucket.org/SamsUserName/yt-3.0"
target="_blank">http://bitbucket.org/SamsUserName/yt-3.0</a><br>
<br>
Then pull request away!<br>
<br>
-Matt<br>
<div class="HOEnZb">
<div class="h5"><br>
On Mon, Nov 25, 2013 at 2:35 PM, Sam Geen <<a
moz-do-not-send="true"
href="mailto:samgeen@astro.ox.ac.uk">samgeen@astro.ox.ac.uk</a>>
wrote:<br>
> OK, will try to figure out all that
tomorrow. I guess there's a guide to<br>
> issuing pull requests on the yt site?<br>
><br>
><br>
> On 25/11/13 20:30, Matthew Turk wrote:<br>
>><br>
>> Hi Sam,<br>
>><br>
>> This looks great. Any chance you
could add this to the<br>
>> yt/frontends/ramses/definitions.py
file as a function, issue a pull<br>
>> request, and we'll get your name in
the commit log? I'll then modify<br>
>> it to fit in and we'll use it as
fallback when fields are specified.<br>
>><br>
>> -Matt<br>
>><br>
>> On Mon, Nov 25, 2013 at 1:39 PM, Sam
Geen <<a moz-do-not-send="true"
href="mailto:samgeen@astro.ox.ac.uk">samgeen@astro.ox.ac.uk</a>>
wrote:<br>
>>><br>
>>> I've hacked up a simple example
of what I mean (attached).<br>
>>><br>
>>><br>
>>> On 25/11/13 17:50, Nathan
Goldbaum wrote:<br>
>>><br>
>>> Matt's opened a PR for this here:<br>
>>><br>
>>><br>
>>> <a moz-do-not-send="true"
href="https://bitbucket.org/yt_analysis/yt-3.0/pull-request/140/adding-field_aliases-to-ramses-datasets/diff"
target="_blank">https://bitbucket.org/yt_analysis/yt-3.0/pull-request/140/adding-field_aliases-to-ramses-datasets/diff</a><br>
>>><br>
>>> Sam, if you could enumerate how
to map from the boolean flags you're<br>
>>> suggesting to a final field list,
I think that would help immensely.<br>
>>><br>
>>><br>
>>> On Mon, Nov 25, 2013 at 8:42 AM,
Sam Geen <<a moz-do-not-send="true"
href="mailto:samgeen@astro.ox.ac.uk">samgeen@astro.ox.ac.uk</a>>
wrote:<br>
>>>><br>
>>>> Yes and no. NVAR must be big
enough, but it can be bigger than necessary<br>
>>>> (I think); it's a Makefile
setting when compiling Ramses. You can<br>
>>>> guarantee<br>
>>>> that the first 4 variables
are the same, but after that I suspect the<br>
>>>> best<br>
>>>> approach is to use boolean
flags to specify whether the run contains<br>
>>>> MHD,<br>
>>>> RHD, metals, etc. Normally
it's a good guess that 5 is pressure and 6<br>
>>>> (if it<br>
>>>> exists) is metals, but as I
said it seems like MHD puts the B-field<br>
>>>> before<br>
>>>> pressure and metallicity.<br>
>>>><br>
>>>><br>
>>>> On 25/11/13 17:36, Nathan
Goldbaum wrote:<br>
>>>><br>
>>>> Does that mean that it should
be possible to infer the field list from<br>
>>>> NVAR alone?<br>
>>>><br>
>>>><br>
>>>> On Mon, Nov 25, 2013 at 8:29
AM, Sam Geen <<a moz-do-not-send="true"
href="mailto:samgeen@astro.ox.ac.uk">samgeen@astro.ox.ac.uk</a>><br>
>>>> wrote:<br>
>>>>><br>
>>>>> For MHD, the variables
stored are the B-field strengths on the faces
of<br>
>>>>> each cell - the fields in
order are: (1) density, (2-4) [x,y,z]<br>
>>>>> velocity,<br>
>>>>> (5-7) [x,y,z] B-field
left, (8-10) [x,y,z] B-field right, (11)
pressure<br>
>>>>> (thermal + MHD), then
(12+) any passive scalars (metals, etc) - see<br>
>>>>> mhd/output_hydro.f90.
Note that the MHD module adds 3 variables, so
the<br>
>>>>> number of variables will
be nvar+3.<br>
>>>>><br>
>>>>> For RHD (Joki Rosdahl's
M1 method implementation, at least - someone<br>
>>>>> else<br>
>>>>> will have to help with
the ATON version), there is a separate "rt_"<br>
>>>>> output<br>
>>>>> file for each CPU (like
the hydro/amr/particles), as well as a
separate<br>
>>>>> info<br>
>>>>> file (there is a
bitbucket link on the Ramses homepage if you
want to<br>
>>>>> see<br>
>>>>> what the latest version
of the code does in detail). The RHD module<br>
>>>>> divides<br>
>>>>> photons into "nGroups"
different flux bins; for each bin, it writes a<br>
>>>>> photon<br>
>>>>> density and then a flux
vector. nGroups is stored in the rt info file;<br>
>>>>> nrtvar is written to the
rt_ binary file, but this is (I think) a<br>
>>>>> Makefile<br>
>>>>> setting and not
guaranteed to be nGroups/(1+ndim) (the user
is, I<br>
>>>>> believe,<br>
>>>>> normally free to waste
memory by allocating more variables than they<br>
>>>>> need).<br>
>>>>> For details it might be
easiest to download the latest code and look
at<br>
>>>>> the<br>
>>>>> code in the folder rt/,
or ask Romain or Joki Rosdahl directly.<br>
>>>>><br>
>>>>> (Feel free to correct me
if any of this is wrong!)<br>
>>>>><br>
>>>>> I agree that setting the
default to the standard five (perhaps some<br>
>>>>> boolean variables for
common configurations such as metals, RHD,
MHD,<br>
>>>>> etc)<br>
>>>>> and then letting users
set or add their own fields by hand if they
need<br>
>>>>> to<br>
>>>>> is a good approach.<br>
>>>>><br>
>>>>><br>
>>>>> On 25/11/13 16:23,
Matthew Turk wrote:<br>
>>>>>><br>
>>>>>> Hi all, especially
RAMSES users,<br>
>>>>>><br>
>>>>>> I'm setting up
aliases to make it easier to load RAMSES
datasets that<br>
>>>>>> have different field
configurations.<br>
>>>>>><br>
>>>>>> Right now, to specify
a different set of fields, you have to do:<br>
>>>>>><br>
>>>>>> pf = load( ... ,
fields = [ "Density", "x-velocity", ...])<br>
>>>>>><br>
>>>>>> I am going to change
this to add on different field configurations<br>
>>>>>> that can be specified
with just a string. For instance:<br>
>>>>>><br>
>>>>>> pf = load(..., fields
= "standard_five")<br>
>>>>>><br>
>>>>>> I'm wondering what
the different configurations are. I have
these<br>
>>>>>> two:<br>
>>>>>><br>
>>>>>> standard_five:
Density, x-velocity, y-velocity, z-velocity,
Pressure<br>
>>>>>> standard_six:
Density, x-velocity, y-velocity, z-velocity,
Pressure,<br>
>>>>>> Metallicity<br>
>>>>>><br>
>>>>>> But for MHD and RHD,
what are the additional fields that should be<br>
>>>>>> added, and in what
order? And are there other common
configurations<br>
>>>>>> that should be
aliased?<br>
>>>>>><br>
>>>>>> If we can come up
with a set of aliases that match most use
cases,<br>
>>>>>> that'd work quite
well. I'm going to issue a PR for this
shortly, and<br>
>>>>>> hopefully it will
make everybody's life a bit easier.<br>
>>>>>><br>
>>>>>> -Matt<br>
>>>>>>
_______________________________________________<br>
>>>>>> yt-users mailing list<br>
>>>>>> <a
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href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
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target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>>>>><br>
>>>>><br>
>>>>>
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>>>>> yt-users mailing list<br>
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>>>><br>
>>>><br>
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>
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