[yt-users] Stacked temperature profiles
Thor Andreas Seiff Ellewsen
tellewsen at gmail.com
Tue Mar 14 09:38:07 PDT 2017
Hi again folks
I think I'm close to getting this to work now.
Hopefully you can tell me what I'm doing wrong.
I figured out why it was so slow.
Calculating the mean inside the overdensity field is not a good idea..
At this point I have the same code as before to convert from AHF to
something yt understands.
And the code for making the profiles is
http://paste.yt-project.org/show/7085/
When running that code, the ouput you get is the following:
yt : [INFO ] 2017-03-14 17:26:17,543 Calculating 1D profile for halo 1.
yt : [INFO ] 2017-03-14 17:26:20,124 Calculating virial quantities for
halo 1.
yt : [INFO ] 2017-03-14 17:26:20,125 Calculating 1D profile for halo 1.
yt : [INFO ] 2017-03-14 17:26:20,125 Skipping halo 1 since data_object
is None.
yt : [INFO ] 2017-03-14 17:26:20,125 Calculating 1D profile for halo 1.
yt : [INFO ] 2017-03-14 17:26:20,125 Skipping halo 1 since data_object
is None.
yt : [INFO ] 2017-03-14 17:26:20,128 Calculating 1D profile for halo 2.
yt : [INFO ] 2017-03-14 17:26:21,869 Calculating virial quantities for
halo 2.
yt : [INFO ] 2017-03-14 17:26:21,869 Calculating 1D profile for halo 2.
yt : [INFO ] 2017-03-14 17:26:21,869 Skipping halo 2 since data_object
is None.
yt : [INFO ] 2017-03-14 17:26:21,870 Calculating 1D profile for halo 2.
yt : [INFO ] 2017-03-14 17:26:21,870 Skipping halo 2 since data_object
is None.
So for some reason it's skipping the halos.
I don't see why it would do that.
Any ideas?
Thanks for the great help!
Best,
Andreas Ellewsen
On Fri, 10 Mar 2017 at 13:30 Thor Andreas Seiff Ellewsen <
tellewsen at gmail.com> wrote:
> Hi again everyone.
> Sorry for not getting back to you faster.
>
> I've tried implementing what you said Britton, and it seems to work.
> However I'm still doing something wrong.
>
> I'm using this script to make the halo catalog:
> http://paste.yt-project.org/show/7077/
> And this one to load the sim and the catalog, and making radial
> temperature profiles: http://paste.yt-project.org/show/7078/
>
> I'm simply copying the example found here:
> http://yt-project.org/doc/cookbook/halo_analysis_example.html#Finding-Radial-Profiles
>
> In the example we calculate the virial radius instead of just using the
> one I already have in the catalog.
> I'm not sure how to use the one I already have so any tips on that is also
> appreciated.
>
> Still, it is extremely slow and returns the following:
> yt : [INFO ] 2017-03-10 11:55:17,007 Calculating 1D profile for halo 1.
> yt : [INFO ] 2017-03-10 12:23:13,269 Calculating virial quantities for
> halo 1.
> yt : [INFO ] 2017-03-10 12:23:13,270 Calculating 1D profile for halo 1.
> yt : [INFO ] 2017-03-10 12:23:13,270 Skipping halo 1 since data_object
> is None.
> yt : [INFO ] 2017-03-10 12:23:13,272 Calculating 1D profile for halo 2.
> yt : [INFO ] 2017-03-10 12:40:49,659 Calculating virial quantities for
> halo 2.
> yt : [INFO ] 2017-03-10 12:40:49,660 Calculating 1D profile for halo 2.
> yt : [INFO ] 2017-03-10 12:40:49,660 Skipping halo 2 since data_object
> is None.
> yt : [INFO ] 2017-03-10 12:40:49,662 Calculating 1D profile for halo 3.
> yt : [INFO ] 2017-03-10 12:46:30,547 Calculating virial quantities for
> halo 3.
> yt : [INFO ] 2017-03-10 12:46:30,548 Calculating 1D profile for halo 3.
> yt : [INFO ] 2017-03-10 12:46:30,548 Skipping halo 3 since data_object
> is None.
> yt : [INFO ] 2017-03-10 12:46:30,550 Calculating 1D profile for halo 4.
> yt : [INFO ] 2017-03-10 12:54:56,886 Calculating virial quantities for
> halo 4.
> yt : [INFO ] 2017-03-10 12:54:56,888 Calculating 1D profile for halo 4.
> yt : [INFO ] 2017-03-10 12:54:56,888 Skipping halo 4 since data_object
> is None.
> yt : [INFO ] 2017-03-10 12:54:56,890 Calculating 1D profile for halo 5.
> yt : [INFO ] 2017-03-10 13:01:48,086 Calculating virial quantities for
> halo 5.
> yt : [INFO ] 2017-03-10 13:01:48,087 Calculating 1D profile for halo 5.
> yt : [INFO ] 2017-03-10 13:01:48,087 Skipping halo 5 since data_object
> is None.
> yt : [INFO ] 2017-03-10 13:01:48,089 Calculating 1D profile for halo 6.
>
> I at this point I killed it.
> Thank you for any insight you can provide on this.
>
> Best,
> Andreas Ellewsen
>
> On Fri, 3 Mar 2017 at 20:09 Britton Smith <brittonsmith at gmail.com> wrote:
>
> 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
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20170314/f0234570/attachment.html>
More information about the yt-users
mailing list