[yt-users] Generic UniGrid Data

Tue May 27 18:47:07 PDT 2014

Hi John,

I found that my yt was a bit old version, although it was still 3.0.
Hence, I install bleeding edge version of yt from the scratch, and it
is working.
Thank you.

Now, I would like to know that is it possible to perform advanced
analysis from generic unigrid data such as making and/or adding
additional fields (temp, velocity etc), galaxy group finding (hop and
fof), and generating profiles.
All of these analysis are provided in yt, but I can not find document
that explains how to do with generic unigrid data.
Is it simply possible through adding required information (such as
thermal energy field) when I define data dictionary?

Thank you,
Junhwan

On Fri, May 23, 2014 at 4:19 PM, John ZuHone <jzuhone at gmail.com> wrote:
> Hi Junhwan,
>
> I'm having trouble finding anything wrong with your script, actually.
>
> I would recommend changing this:
>
> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox,
> nprocs=4)
>
>
> to this:
>
> ds = load_uniform_grid(data, data['density'][0].shape,
> length_unit=(1.0,"Mpc"), bbox=bbox, nprocs=4)
>
>
> but I doubt that would make much of a difference.
>
> Have you inspected what data["density"][0] is in your script, and what npart
> is? I set up an example on my own with random particle data, and I set the
> number_of_particles dictionary key to a variable npart that was set
> previously, and saw no issues there.
>
> If it's possible to post the file that this script works with somewhere,
> that would enable me to reproduce the buggy behavior.
>
> Best,
>
> John Z
>
> On May 22, 2014, at 6:19 PM, John ZuHone <jzuhone at gmail.com> wrote:
>
> Hi Junhwan,
>
> Sorry, I kind of got lost in some other things--I'll have a look at your
> script tonight and get back to you.
>
> Best,
>
>
> On May 22, 2014, at 6:17 PM, Junhwan Choi (최준환) <choi.junhwan at gmail.com>
> wrote:
>
> Hi,
>
> I have read more about the "generic array data" from the document in yt
> webpage.
> I found that the the how to set data dict and call "load_uniform_grid"
> by yt-2.6 and yt-3.0 are quite different, and it looks that yt-3.0
> supports better unit treatment.
>
> However, my yt-3.0 looks use old formate for load_uniform_grid as follow:
> .....
> def load_uniform_grid(data, domain_dimensions, sim_unit_to_cm, bbox=None,
>                      nprocs=1, sim_time=0.0, periodicity=(True, True,
> True)):
> ....
>
> This load_uniform_grid arguments are different with those presented in
> yt-3.0 document.
> I think this is part of the reason that I have a difficulty.
>
> How can I use that load_uniform_grid for the version shown in yt-3.0
> document?
>
> Thank you,
> Junhwan
>
> On Fri, May 16, 2014 at 11:28 AM, Junhwan Choi (최준환)
> <choi.junhwan at gmail.com> wrote:
>
> Here, I post my script in http://paste.yt-project.org/show/4641
>
> Thank you,
> Junhwan
>
> On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone at gmail.com> wrote:
>
> Junhwan,
>
> Can you post your script somewhere? It might be easier to debug it that way.
>
> Best,
>
> John Z
>
> On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan at gmail.com> wrote:
>
> Hi Nathan,
>
> I think that I am using the yt 3.0 unless there is stabke yt 3.0 version.
>
> Junhwan
>
>
>
> On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
> Hi Junhwan,
>
> Just to clarify (since the answers you receive will be different depending
> on your response) is this for the in-development yt 3.0 release or the
> current stable release?
>
> Nathan
>
> On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan at gmail.com> wrote:
>
>
> Dear yt user,
>
> I try to use Generic UnicGrid Data (256^3 gas density cube + position
> of particle that is subset of a huge simulation).
> It is preliminary work, but I still have some questions.
>
> 1. In order to set density unit as cgs, I made following script:
> ......
> data = dict(density = (map, "g/cm**3"))  #map is 256^3 density data array
> bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]])
> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> bbox=bbox, nprocs=4)
> .....
>
> Then, I got the following error message:
> Traceback (most recent call last):
>  File "cutout2.py", line 62, in <module>
>    ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> bbox=bbox, nprocs=4)
>  File
> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
> line 461, in load_uniform_grid
>    psize = get_psize(np.array(data[key].shape), nprocs)
> AttributeError: 'tuple' object has no attribute 'shape'
>
> Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data =
> dict(density = map)" and it work.
> If this is the case, how can I define the density unit and show it
> when I make Slice/Projection?
> In addition, I would like to know how I can set the unit in Generic
> UnicGrid Data in general?
> The length unit can be provide to script in load_uniform_grid(...
> 3.086e24 ....) but I do not know how to set other units.
>
> 2. When I add particle information as follow:
> .....
> npart = 100000  # number of particles
> data = dict(density = map,
>            number_of_particles = npart,
>            particle_position_x = posx,
>            particle_position_y = posy,
>            particle_position_z = posz)
> bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]])
> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> bbox=bbox, nprocs=4)
> ...
>
> I got the following error message:
> Traceback (most recent call last):
>  File "cutout.py", line 107, in <module>
>    ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> bbox=bbox, nprocs=4)
>  File
> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
> line 519, in load_uniform_grid
>    assign_particle_data(spf, pdata)
>  File
> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
> line 371, in assign_particle_data
>    pdata.pop("number_of_particles")
> KeyError: 'number_of_particles'
>
> So, I change "number_of_particles = npart," --> "number_of_particles =
> 100000," and it works.
> How could it happen?
>
> 3. Can I do halo finder (hop/fof) using the above particle data?
> Or, what information do I need to provide to do grouping?
> In this case, how can I set the units and linking length?
>
> 4. Can I make particle distribution to particle data like
> data['Dark_Matter_position_x']?
> This process will allow me additional analysis such as profile and
> obtaining total value.
>
> I may ask too many for new tool, but it will help a lot to use yt for
> general data set.
>
> Thank you,
> Junhwan
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