[yt-users] Stacked temperature profiles

Britton Smith brittonsmith at gmail.com
Tue Mar 14 14:03:27 PDT 2017 

Hi Andreas,

My guess is that there is an issue with the units of the spheres' radii. If
you have yt installed from source, then you can stick a python debugger
around line 89 of
yt/analysis_modules/halo_analysis/halo_callbacks.py

Just add the following:
import pdb ; pdb.set_trace()

If that's not possible, then you might just try creating a single sphere
object from the first object in your halo list.  The reason I suspect this
is because if yt tries to create a sphere that does not contain any
elements, the YTSphereTooSmall exception will be raised.  This exception is
caught by the sphere halo callback, causing it to set the sphere object to
None, as per the error message you're seeing.  If this is the problem, it
will just be a matter of making sure that your radius field has the correct
units on it.  Let us know if you need any help looking into this.

Britton

On Tue, Mar 14, 2017 at 9:38 AM, Thor Andreas Seiff Ellewsen <
tellewsen at gmail.com> wrote:

> 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
>>
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