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Today's Topics:
1. Re: yt3.3dev MPI puzzle (Stuart Levy)
2. smoothed particle velocities onto unigrid (Desika Narayanan)
3. covering_grid with RAMSES dataset (Enrico Garaldi)
4. Re: covering_grid with RAMSES dataset (Nathan Goldbaum)
5. Re: covering_grid with RAMSES dataset (Enrico Garaldi)
----------------------------------------------------------------------
Message: 1
Date: Tue, 22 Mar 2016 12:54:49 -0500
From: Stuart Levy <salevy@illinois.edu>
To: Discussion of the yt analysis package
<yt-users@lists.spacepope.org>
Subject: Re: [yt-users] yt3.3dev MPI puzzle
Message-ID: <56F186E9.2010506@illinois.edu>
Content-Type: text/plain; charset="windows-1252"
Ooh, slick! Thank you again!
On 3/22/16 12:44 PM, Kacper Kowalik wrote:
> cd $HOME
> hg clone https://bitbucket.org/MatthewTurk/hgbb
>
> create or edit your $HOME/.hgrc to contain:
>
> [extensions]
> hgbb = $HOME/hgbb/hgbb.py
>
> Then you'll be able to do the following in your local clone of yt repo:
>
> hg bbpr # will give you list of PRs
> hg bbpr -p 2066 # would download incoming changes and suggest rev
> # to update to
>
> Cheers,
> Kacper
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Message: 2
Date: Wed, 23 Mar 2016 11:04:28 -0400
From: Desika Narayanan <desika.narayanan@gmail.com>
To: yt-users <yt-users@lists.spacepope.org>
Subject: [yt-users] smoothed particle velocities onto unigrid
Message-ID:
<CAMMxB+MCMtJgT_YLg0iwQQHZC2E5Bhg-vBr9D7u7uKDuWjBZMQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hey All,
I'm having some trouble smoothing particle velocities onto a uniform
(arbitrary_grid) grid. The basic idea is that I create an arbitrary grid,
then want to access the particle quantities smoothed onto that grid. Some
are relatively easy, like:
mass = obj[('deposit','PartType0_mass')].in_units('Msun')
and for others, where deposited fields don't already exist, I can create
those fields and it all works well:
ds.add_deposited_particle_field(('PartType0', 'Temperature'),'sum')
temp = obj[('deposit', 'PartType0_sum_Temperature')]
but when either trying to access a deposited particle field, or creating
one with the velocities, errors are abound. I'm sure I'm just doing
something foolish, but could use a little nudge in the right direction. I
created a self-contained script using the gadget zoom data set on the yt
datsets to show the problem, with two different error messages pastebinned
(links in the script) here:
http://paste.yt-project.org/show/6352/
any help would be greatly appreciated!
thanks,
desika
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Message: 3
Date: Wed, 23 Mar 2016 17:36:34 +0100
From: "Enrico Garaldi" <egaraldi@uni-bonn.de>
To: yt-users@lists.spacepope.org
Subject: [yt-users] covering_grid with RAMSES dataset
Message-ID: <ximss-98622@be4.uni-bonn.de>
Content-Type: text/plain; charset="utf-8"; format="flowed"
Hi,
I am having troubles using the smoothed_covering_grid and covering_grid with
RAMSES dataset.
I have yt-project version 3.2.3 and I am using the "output_00080" dataset
from the yt sample datasets.
smoothed_covering_grid fails (raising a RuntimeError because tot != 0, line
880 of construction_data_containers.pyc), while covering_grid seems to leave
unfilled the refined regions. What I mean is that if a cell is refined
beyond the maximum allowed level for the grid, it is left unfilled (contrary
to what happens with ENZO datasets).
I am using this code:
import yt
import matplotlib.pyplot as plt
ds = yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt')
cgrid = ds.covering_grid(0, left_edge=ds.domain_left_edge,
dims=ds.domain_dimensions)
density_field = cgrid["density"]
print (density_field == 0.0).any() #should be False but it is True
plt.imshow(density_field[:,:,48].v, interpolation='none')
plt.show() ? #holes with zero-density corresponding to refined regions
Am I doing something wrong?
Thanks in advance,
Enrico
-------------------------------------
Enrico Garaldi - Ph.D. student
Argelander-Institut f?r Astronomie
Address: Auf dem H?gel 71, 53121 Bonn, Germany
Room: 1.024
Phone: +49 (0) 228 73 3433
egaraldi[at]uni-bonn[dot]de
------------------------------
Message: 4
Date: Wed, 23 Mar 2016 09:47:16 -0700
From: Nathan Goldbaum <nathan12343@gmail.com>
To: Discussion of the yt analysis package
<yt-users@lists.spacepope.org>
Subject: Re: [yt-users] covering_grid with RAMSES dataset
Message-ID:
<CAJXewOn3N_fJWBNQpXNVUtGg2s8tN_71wjmS3aL9yzqpNXVZ4A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Enrico,
I don't think you're doing anything wrong - this is a bug, likely a generic
issue with the way covering grids get filled out for octree data.
This issue with smoothed_covering_grid is likely another, different but
related bug.
Can you create an issue to track this?
https://bitbucket.org/yt_analysis/yt/issues/new
-Nathan
On Wed, Mar 23, 2016 at 9:36 AM, Enrico Garaldi <egaraldi@uni-bonn.de>
wrote:
> Hi,
> I am having troubles using the smoothed_covering_grid and covering_grid
> with RAMSES dataset.
> I have yt-project version 3.2.3 and I am using the "output_00080" dataset
> from the yt sample datasets.
>
> smoothed_covering_grid fails (raising a RuntimeError because tot != 0,
> line 880 of construction_data_containers.pyc), while covering_grid seems to
> leave unfilled the refined regions. What I mean is that if a cell is
> refined beyond the maximum allowed level for the grid, it is left unfilled
> (contrary to what happens with ENZO datasets).
>
> I am using this code:
>
> import yt
> import matplotlib.pyplot as plt
>
> ds = yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt')
>
> cgrid = ds.covering_grid(0, left_edge=ds.domain_left_edge,
> dims=ds.domain_dimensions)
>
> density_field = cgrid["density"]
>
> print (density_field == 0.0).any() #should be False but it is True
>
> plt.imshow(density_field[:,:,48].v, interpolation='none')
> plt.show() #holes with zero-density corresponding to refined regions
>
> Am I doing something wrong?
>
> Thanks in advance,
> Enrico
>
> -------------------------------------
> Enrico Garaldi - Ph.D. student
> Argelander-Institut f?r Astronomie
> Address: Auf dem H?gel 71, 53121 Bonn, Germany
> Room: 1.024
> Phone: +49 (0) 228 73 3433
> egaraldi[at]uni-bonn[dot]de
> _______________________________________________
> yt-users mailing list
> yt-users@lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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Message: 5
Date: Wed, 23 Mar 2016 18:24:07 +0100
From: "Enrico Garaldi" <egaraldi@uni-bonn.de>
To: "Discussion of the yt analysis package"
<yt-users@lists.spacepope.org>
Subject: Re: [yt-users] covering_grid with RAMSES dataset
Message-ID: <ximss-99088@be4.uni-bonn.de>
Content-Type: text/plain; charset="utf-8"; format="flowed"
Hi Nathan,
thanks for the feedback. I will create the issue right away.
Enrico
On Wed, 23 Mar 2016 09:47:16 -0700
Nathan Goldbaum <nathan12343@gmail.com> wrote:
> Hi Enrico,
>
> I don't think you're doing anything wrong - this is a
>bug, likely a generic
> issue with the way covering grids get filled out for
>octree data.
>
> This issue with smoothed_covering_grid is likely
>another, different but
> related bug.
>
> Can you create an issue to track this?
>
> https://bitbucket.org/yt_analysis/yt/issues/new
>
> -Nathan
>
> On Wed, Mar 23, 2016 at 9:36 AM, Enrico Garaldi
><egaraldi@uni-bonn.de>
> wrote:
>
>> Hi,
>> I am having troubles using the smoothed_covering_grid
>>and covering_grid
>> with RAMSES dataset.
>> I have yt-project version 3.2.3 and I am using the
>>"output_00080" dataset
>> from the yt sample datasets.
>>
>> smoothed_covering_grid fails (raising a RuntimeError
>>because tot != 0,
>> line 880 of construction_data_containers.pyc), while
>>covering_grid seems to
>> leave unfilled the refined regions. What I mean is that
>>if a cell is
>> refined beyond the maximum allowed level for the grid,
>>it is left unfilled
>> (contrary to what happens with ENZO datasets).
>>
>> I am using this code:
>>
>> import yt
>> import matplotlib.pyplot as plt
>>
>> ds =
>>yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt')
>>
>> cgrid = ds.covering_grid(0,
>>left_edge=ds.domain_left_edge,
>> dims=ds.domain_dimensions)
>>
>> density_field = cgrid["density"]
>>
>> print (density_field == 0.0).any() #should be False but
>>it is True
>>
>> plt.imshow(density_field[:,:,48].v,
>>interpolation='none')
>> plt.show() #holes with zero-density corresponding to
>>refined regions
>>
>> Am I doing something wrong?
>>
>> Thanks in advance,
>> Enrico
>>
>> -------------------------------------
>> Enrico Garaldi - Ph.D. student
>> Argelander-Institut f?r Astronomie
>> Address: Auf dem H?gel 71, 53121 Bonn, Germany
>> Room: 1.024
>> Phone: +49 (0) 228 73 3433
>> egaraldi[at]uni-bonn[dot]de
>> _______________________________________________
>> yt-users mailing list
>> yt-users@lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
-------------------------------------
Enrico Garaldi - Ph.D. student
Argelander-Institut f?r Astronomie
Address: Auf dem H?gel 71, 53121 Bonn, Germany
Room: 1.024
Phone: +49 (0) 228 73 3433
egaraldi[at]uni-bonn[dot]de
------------------------------
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