[yt-users] Stacked temperature profiles

[Britton Smith]

Hi Andreas,

Ah, I think I see the problem.  It wants the halos_ds to have halo ids and
masses.  If it's possible, could you add fields to your save_as_dataset
script called "particle_identifier" for halo ids and "particle_mass" for
masses.  If you don't have those fields specifically, you can probably just
make up values.  When I fix the other issues, I'll make sure to make this a
little smarter as well.

Britton

On Fri, Mar 3, 2017 at 10:46 AM, Thor Andreas Seiff Ellewsen <
tellewsen at gmail.com> wrote:

> Hi again,
>
> Thanks again for helping me Britton.
> That actually made a difference. Unfortunately I now get a RuntimeError
> from
> hc = HaloCatalog(data_ds=ds, halo_ds=ds_halo)
>
> RuntimeError: HaloCatalog quantity must be a registered function or a
> field of a known type.
>
> Best,
> Andreas Ellewsen
>
>
> On Fri, 3 Mar 2017 at 19:16 Britton Smith <brittonsmith at gmail.com> wrote:
>
> Hi Andreas,
>
> I forgot about the constraints of the naming conventions for halo catalog
> files.  They need to be named in the following convention:
> <prefix>.<integer>.h5
> where the integer should start at 0.  That integer is in case your catalog
> is split over multiple files.  In examining the code, I can see that it
> counts the number of files by basically doing glob(<prefix>*h5), so if
> you've got a file named test.h5 and test.0.h5 in the same directory, it
> will fool the code into thinking there should be test.0.h5 and test.1.h5.
> This is clearly a bit of a silly shortcoming of this approach, and I will
> submit a pull request to make this more intelligent.  In the mean time, I
> think you can fix this by making sure that there is only one file,
> test.0.h5 in the directory.
>
> Let me know if that doesn't fix it.
>
> Britton
>
> On Fri, Mar 3, 2017 at 6:28 AM, Thor Andreas Seiff Ellewsen <
> tellewsen at gmail.com> wrote:
>
> Hi again.
>
> Thank for helping me Britton!
>
> I think I've gotten the halo catalog saved to file now, but I'm having
> problems loading it using HaloCatalog.
> I've used the code you provided, and everything seems to be going fine
> until I try loading the catalog.
>
> If I try this:
> save_as_dataset(ds,'test.h5', data, field_types=ftypes,
> extra_attrs=extra_attrs)
> ds_halo = load('test.h5')
> hc = HaloCatalog(data_ds=ds, halos_ds=ds_halo)
>
> This returns
> IOError: Unable to open file (Unable to open file: name = '.0.h5', errno =
> 2, error message = 'no such file or directory', flags = 0, o_flags = 0)
>
> I tried using
> save_as_dataset(ds,'test.0.h5', data, field_types=ftypes,
> extra_attrs=extra_attrs)
> ds_halo = load('test.0.h5')
> hc = HaloCatalog(data_ds=ds, halos_ds=ds_halo)
> instead, but then I get
>
> IOError: Unable to open file (Unable to open file: name = 'test.1.h5',
> errno = 2, error message = 'no such file or directory', flags = 0, o_flags
> = 0)
>
> It seems it's trying to open more than one file for some reason?
> Did I misunderstand something?
>
> I've uploaded the code again to http://paste.yt-project.org/show/7062/
>
> Best,
> Andreas Ellewsen
>
> On Thu, 2 Mar 2017 at 19:37 Britton Smith <brittonsmith at gmail.com> wrote:
>
> Hi Andreas,
>
> I think all this can be done very cleanly using yt's halo analysis
> toolkit.  I'd be happy to help you with this.
>
> Documentation for the halo analysis, also called the HaloCatalog, is here:
> http://yt-project.org/docs/dev/analyzing/analysis_
> modules/halo_catalogs.html#halo-catalog-analysis
>
> The HaloCatalog works with the simulation snapshot and the halo finder
> output in tandem to run a pipeline of analysis that you define.  yt comes
> with a number of functions out of the box for doing profiling, etc,
> including scaling of profiles to r_vir.
>
> Before that, you will need to convert your halo finder output into a form
> that yt can read in using yt.load.  This should be relatively
> straightforward.  I've sketched out how to do this here:
> http://paste.yt-project.org/show/7061/
> The code snippet there assumes some of the variables you've got in the
> script you posted.
>
> There may be some hiccups still, but I'm happy to work with you to get it
> going.  Once that works, you should be able to use the HaloCatalog as
> documented to do the rest, but feel free to ask any other questions you
> might have.
>
> Britton
>
> On Wed, Mar 1, 2017 at 5:16 AM, Thor Andreas Seiff Ellewsen <
> tellewsen at gmail.com> wrote:
>
> Hi everyone.
>
> I'm currently working on making temperature and density profiles from some
> ramses simulations.
> I'd like to make these profiles the average radial profile of the halos in
> the simulation.
>
> I think the included rockstar in yt supports this in some form, but my
> halo catalog is made using AHF and then imported from an ascii file.
>
> To do this I need help with two things:
> The first one is how to scale the radius of each profile to the
> corresponding virial radius.
> The other is how to actually average all these profiles.
>
> Is this something that can be done?
>
> I will be trying to compare the resulting profile with the same for
> different simulations in the end, but I don't expect to have any big
> problems with that.
>
> The code I'm currently using for this can be found at
> http://paste.yt-project.org/show/7058/
>
> Best,
> Andreas Ellewsen
>
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