<div dir="ltr"><div dir="ltr" class="gmail_msg">Hi again everyone. <div class="gmail_msg">Sorry for not getting back to you faster.</div><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">I've tried implementing what you said Britton, and it seems to work.</div><div class="gmail_msg">However I'm still doing something wrong.</div><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">I'm using this script to make the halo catalog: <a href="http://paste.yt-project.org/show/7077/">http://paste.yt-project.org/show/7077/</a><br></div><div class="gmail_msg">And this one to load the sim and the catalog, and making radial temperature profiles: <a href="http://paste.yt-project.org/show/7078/">http://paste.yt-project.org/show/7078/</a><br></div><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">I'm simply copying the example found here: <a href="http://yt-project.org/doc/cookbook/halo_analysis_example.html#Finding-Radial-Profiles">http://yt-project.org/doc/cookbook/halo_analysis_example.html#Finding-Radial-Profiles</a><br><br></div><div class="gmail_msg">In the example we calculate the virial radius instead of just using the one I already have in the catalog.</div><div class="gmail_msg">I'm not sure how to use the one I already have so any tips on that is also appreciated.</div><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">Still, it is extremely slow and returns the following:</div><div class="gmail_msg"><div class="gmail_msg">yt : [INFO     ] 2017-03-10 11:55:17,007 Calculating 1D profile for halo 1.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:23:13,269 Calculating virial quantities for halo 1.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:23:13,270 Calculating 1D profile for halo 1.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:23:13,270 Skipping halo 1 since data_object is None.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:23:13,272 Calculating 1D profile for halo 2.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:40:49,659 Calculating virial quantities for halo 2.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:40:49,660 Calculating 1D profile for halo 2.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:40:49,660 Skipping halo 2 since data_object is None.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:40:49,662 Calculating 1D profile for halo 3.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:46:30,547 Calculating virial quantities for halo 3.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:46:30,548 Calculating 1D profile for halo 3.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:46:30,548 Skipping halo 3 since data_object is None.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:46:30,550 Calculating 1D profile for halo 4.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:54:56,886 Calculating virial quantities for halo 4.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:54:56,888 Calculating 1D profile for halo 4.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:54:56,888 Skipping halo 4 since data_object is None.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 12:54:56,890 Calculating 1D profile for halo 5.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 13:01:48,086 Calculating virial quantities for halo 5.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 13:01:48,087 Calculating 1D profile for halo 5.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 13:01:48,087 Skipping halo 5 since data_object is None.</div><div class="gmail_msg">yt : [INFO     ] 2017-03-10 13:01:48,089 Calculating 1D profile for halo 6.</div></div><div class="gmail_msg"><br></div><div class="gmail_msg">I at this point I killed it.<br></div><div class="gmail_msg">Thank you for any insight you can provide on this.<br></div><div class="gmail_msg"><br></div><div class="gmail_msg">Best,<br></div><div class="gmail_msg">Andreas Ellewsen<br class="gmail_msg"></div></div><br class="gmail_msg"><div class="gmail_quote gmail_msg"><div dir="ltr" class="gmail_msg">On Fri, 3 Mar 2017 at 20:09 Britton Smith <<a href="mailto:brittonsmith@gmail.com" class="gmail_msg" target="_blank">brittonsmith@gmail.com</a>> wrote:<br class="gmail_msg"></div><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg">Hi Andreas,<div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">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.</div></div><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">Britton</div></div><div class="gmail_extra gmail_msg"><br class="gmail_msg"><div class="gmail_quote gmail_msg">On Fri, Mar 3, 2017 at 10:46 AM, Thor Andreas Seiff Ellewsen <span dir="ltr" class="gmail_msg"><<a href="mailto:tellewsen@gmail.com" class="gmail_msg" target="_blank">tellewsen@gmail.com</a>></span> wrote:<br class="gmail_msg"><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Hi again,<div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Thanks again for helping me Britton.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">That actually made a difference. Unfortunately I now get a RuntimeError from </div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">hc = HaloCatalog(data_ds=ds, halo_ds=ds_halo)</div><br class="gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">RuntimeError: HaloCatalog quantity must be a registered function or a field of a known type.<br class="gmail_msg"><br class="gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Best,<br class="gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Andreas Ellewsen<br class="gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="gmail_msg"><br class="gmail_msg"></div></div><div class="gmail_msg"><div class="m_3711938124692402432m_39738510565725595h5 gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">On Fri, 3 Mar 2017 at 19:16 Britton Smith <<a href="mailto:brittonsmith@gmail.com" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">brittonsmith@gmail.com</a>> wrote:<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><blockquote class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Hi Andreas,<div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I forgot about the constraints of the naming conventions for halo catalog files.  They need to be named in the following convention:</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><prefix>.<integer>.h5</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Let me know if that doesn't fix it.</div></div><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Britton</div></div><div class="gmail_extra m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">On Fri, Mar 3, 2017 at 6:28 AM, Thor Andreas Seiff Ellewsen <span dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><<a href="mailto:tellewsen@gmail.com" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">tellewsen@gmail.com</a>></span> wrote:<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><blockquote class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Hi again.</div><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Thank for helping me Britton!</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I think I've gotten the halo catalog saved to file now, but I'm having problems loading it using HaloCatalog.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I've used the code you provided, and everything seems to be going fine until I try loading the catalog.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">If I try this:</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">save_as_dataset(ds,'test.h5', data, field_types=ftypes, extra_attrs=extra_attrs)</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">ds_halo = load('test.h5')<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">hc = HaloCatalog(data_ds=ds, halos_ds=ds_halo)<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">This returns</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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)<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I tried using </div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">save_as_dataset(ds,'test.0.h5', data, field_types=ftypes, extra_attrs=extra_attrs)<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">ds_halo = load('test.0.h5')</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">hc = HaloCatalog(data_ds=ds, halos_ds=ds_halo)</div></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">instead, but then I get<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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)</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">It seems it's trying to open more than one file for some reason?</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Did I misunderstand something?</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I've uploaded the code again to <a href="http://paste.yt-project.org/show/7062/" class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">http://paste.yt-project.org/show/7062/</a></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Best,</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Andreas Ellewsen</div></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409h5 m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">On Thu, 2 Mar 2017 at 19:37 Britton Smith <<a href="mailto:brittonsmith@gmail.com" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">brittonsmith@gmail.com</a>> wrote:<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><blockquote class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Hi Andreas,<div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I think all this can be done very cleanly using yt's halo analysis toolkit.  I'd be happy to help you with this.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Documentation for the halo analysis, also called the HaloCatalog, is here:</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><a href="http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_catalogs.html#halo-catalog-analysis" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_catalogs.html#halo-catalog-analysis</a><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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:</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><a href="http://paste.yt-project.org/show/7061/" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">http://paste.yt-project.org/show/7061/</a><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">The code snippet there assumes some of the variables you've got in the script you posted.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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.</div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Britton</div></div><div class="gmail_extra m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div></div><div class="gmail_extra m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">On Wed, Mar 1, 2017 at 5:16 AM, Thor Andreas Seiff Ellewsen <span dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><<a href="mailto:tellewsen@gmail.com" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">tellewsen@gmail.com</a>></span> wrote:<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div></div><div class="gmail_extra m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><blockquote class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Hi everyone.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div>I'm currently working on making temperature and density profiles from some ramses simulations.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">I'd like to make these profiles the average radial profile of the halos in the simulation.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">To do this I need help with two things:<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">The first one is how to scale the radius of each profile to the corresponding virial radius.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">The other is how to actually average all these profiles.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Is this something that can be done?<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">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.<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">The code I'm currently using for this can be found at <br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><a href="http://paste.yt-project.org/show/7058/" class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" target="_blank">http://paste.yt-project.org/show/7058/</a><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Best,<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div><div class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">Andreas Ellewsen<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></div></div>
<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"></blockquote></div></div><div class="gmail_extra m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><div class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg"><blockquote class="gmail_quote m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">_______________________________________________<br class="m_3711938124692402432m_39738510565725595m_1637550399533872085m_4207535260054391558m_-3552537250508506409m_7109324586509489322gmail_msg m_3711938124692402432m_39738510565725595m_1637550399533872085gmail_msg gmail_msg">
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