[yt-users] Ramses without hydro

Nathan Goldbaum nathan12343 at gmail.com
Tue Apr 15 09:49:02 PDT 2014


Hi Marcelo,

You need to replace "ParticleMassMsun" with "particle_mass".

With yt 3.0 we've switched to a new field naming scheme that we think is
much nicer to work with and more rational. Basically, CamelCase field names
like ParticleMass are replaced with lower_case_underscore names like
particle_mass. With the new unit system we've also eliminated redundant
field names that are only different in units.  So, ParticleMassMsun gets
replaced with particle_mass.

We're working on the documentation for all of this - sorry it's a bit
confusing to use right now while it's still under active development.
 There will definitely be documentation to cover all of this when we do the
stable release for yt 3.0.

-Nathan


On Tue, Apr 15, 2014 at 8:56 AM, Marcelo Vargas dos Santos <
marcelovsrj at gmail.com> wrote:

> I thinking that is almost well. I recieved the error message that you
> espected.
> Do you know how i can fix it?
>
> Thank you
>
>
>
> yt : [WARNING  ] 2014-04-15 12:53:57,895 RAMSES frontend assumes all
> simulations are cosmological!
> yt : [INFO     ] 2014-04-15 12:53:57,916 Parameters: current_time
>      = -3.65552566796e+15
> yt : [INFO     ] 2014-04-15 12:53:57,916 Parameters: domain_dimensions
>     = [128 128 128]
> yt : [INFO     ] 2014-04-15 12:53:57,917 Parameters: domain_left_edge
>      = [ 0.  0.  0.]
> yt : [INFO     ] 2014-04-15 12:53:57,917 Parameters: domain_right_edge
>     = [ 1.  1.  1.]
> yt : [INFO     ] 2014-04-15 12:53:57,918 Parameters:
> cosmological_simulation   = 1
> yt : [INFO     ] 2014-04-15 12:53:57,918 Parameters: current_redshift
>      = 49.9999981951
> yt : [INFO     ] 2014-04-15 12:53:57,918 Parameters: omega_lambda
>      = 0.723999977112
> yt : [INFO     ] 2014-04-15 12:53:57,918 Parameters: omega_matter
>      = 0.275999993086
> yt : [INFO     ] 2014-04-15 12:53:57,918 Parameters: hubble_constant
>     = 0.738000030518
> yt : [INFO     ] 2014-04-15 12:53:58,300 Loading field plugins.
> yt : [INFO     ] 2014-04-15 12:53:58,300 Loaded angular_momentum (8 new
> fields)
> yt : [INFO     ] 2014-04-15 12:53:58,302 Loaded astro (14 new fields)
> yt : [INFO     ] 2014-04-15 12:53:58,302 Loaded cosmology (20 new fields)
> yt : [INFO     ] 2014-04-15 12:53:58,302 Loaded fluid (56 new fields)
> yt : [INFO     ] 2014-04-15 12:53:58,303 Loaded fluid_vector (88 new
> fields)
> yt : [INFO     ] 2014-04-15 12:53:58,303 Loaded geometric (103 new fields)
> yt : [INFO     ] 2014-04-15 12:53:58,303 Loaded local (103 new fields)
> yt : [INFO     ] 2014-04-15 12:53:58,303 Loaded magnetic_field (109 new
> fields)
> yt : [WARNING  ] 2014-04-15 12:53:58,391 No particle_type, no
> creation_time, so not distinguishing.
> ---------------------------------------------------------------------------
> YTFieldNotFound                           Traceback (most recent call last)
> /home/marcelo/anaconda/lib/python2.7/site-packages/IPython/utils/py3compat.pyc
> in execfile(fname, *where)
>     202             else:
>     203                 filename = fname
> --> 204             __builtin__.execfile(filename, *where)
>
> /home/marcelo/Simulations/NBody/Ramses/branches/ramses_omp/run1/plot.py in
> <module>()
>      12
>      13 ds = load(files[0])
> ---> 14 halos = HaloFinder(ds)
>      15 #print ds.parameters
>      16 #print "\n"
>
> /home/marcelo/yt/yt/analysis_modules/halo_finding/halo_objects.pyc in
> __init__(self, pf, subvolume, threshold, dm_only, padding, total_mass)
>    2387                 select = self._get_dm_indices()
>    2388                 total_mass = \
> -> 2389
> self.comm.mpi_allreduce((self._data_source['all',
> "ParticleMassMsun"][select]).sum(dtype='float64'), op='sum')
>    2390             else:
>    2391                 total_mass =
> self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("ParticleMassMsun")[0],
> op='sum')
>
> /home/marcelo/yt/yt/data_objects/data_containers.pyc in __getitem__(self,
> key)
>     203         Returns a single field.  Will add if necessary.
>     204         """
> --> 205         f = self._determine_fields([key])[0]
>     206         if f not in self.field_data and key not in self.field_data:
>     207             if f in self._container_fields:
>
> /home/marcelo/yt/yt/data_objects/data_containers.pyc in
> _determine_fields(self, fields)
>     451                     raise YTFieldNotParseable(field)
>     452                 ftype, fname = field
> --> 453                 finfo = self.pf._get_field_info(ftype, fname)
>     454             else:
>     455                 fname = field
>
> /home/marcelo/yt/yt/data_objects/static_output.pyc in
> _get_field_info(self, ftype, fname)
>     487                     self._last_finfo = self.field_info[(ftype,
> fname)]
>     488                     return self._last_finfo
> --> 489         raise YTFieldNotFound((ftype, fname), self)
>     490
>     491     def _setup_classes(self):
>
> YTFieldNotFound: Could not find field '('all', 'ParticleMassMsun')' in
> info_00001.
>
>
> On 15 April 2014 10:24, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>
>>  Hi Marcelo,
>>
>> I believe a fix has been merged into the branch yt-3.0 of the yt
>> repository, i.e. call:
>>
>> hg pull && hg update yt-3.0
>>
>> Let me know if this works for you or if it throws an exception again.
>> Note that I believe the particle field names have been updated recently
>> (e.g. particle_mass instead of ParticleMassMsun), so be careful with that.
>>
>> Cheers,
>>
>> Sam
>>
>>
>> On 14/04/2014 23:19, Sam Geen wrote:
>>
>> OK, my local version wasn't up to date, which is why I was confused
>> before. There seems to be a check for a hydro file (line 370 of
>> data_structures.py) but I don't think it'd work (it's a check against a
>> string, not against an os.path.exists call), and it'd only run if you're
>> checking for fields. I suspect it's a bug in the latest version of the
>> RAMSES frontend, and we should check that yt doesn't throw an error if you
>> try to feed it a particle-only dataset, i.e. do a check for a
>> "hydro_?????.out00001" file, and only read if it exists. If I get time
>> tomorrow I might try to take a look.
>>
>> On 14/04/14 22:59, Marcelo Vargas dos Santos wrote:
>>
>>  yt module located at:
>>     /home/marcelo/Downloads/yt-x86_64/src/yt-hg
>> The supplemental repositories are located at:
>>     /home/marcelo/Downloads/yt-x86_64/src/yt-supplemental
>> aviso: ignorando pai desconhecido do diretório de trabalho '794b2beb2c48'!
>>
>>  The current version of the code is:
>>
>>  ---
>> 000000000000
>> ---
>>
>>  This installation CAN be automatically updated.
>> yt dependencies were last updated on
>> Qui Abr 10 19:15:16 BRT 2014
>>
>>  To update all dependencies, run "yt update --all".
>>
>>
>>
>> On 14 April 2014 17:57, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>>
>>> Hi Marcelo,
>>>
>>>  Can you tell us the output of 'yt instinfo' run from the command line?
>>>  That will give more precise version information.
>>>
>>>  -Nathan
>>>
>>>
>>> On Mon, Apr 14, 2014 at 1:56 PM, Marcelo Vargas dos Santos <
>>> marcelovsrj at gmail.com> wrote:
>>>
>>>> Sorry, i'm using the Bleeding Edge version. There's no 4.0.0
>>>>
>>>>
>>>> On 14 April 2014 17:55, Marcelo Vargas dos Santos <
>>>> marcelovsrj at gmail.com> wrote:
>>>>
>>>>> I'm using the yt-4.0.0.
>>>>>
>>>>>
>>>>>  On 14 April 2014 17:53, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
>>>>>
>>>>>> Out of interest, Marcelo, what version are you using? I just looked
>>>>>> at the yt-3.0 code and it looks a little different, and doesn't seem to
>>>>>> rely on hydro files existing as your log suggests. If you're not using
>>>>>> yt-3.0 it's definitely worth trying it for the RAMSES module.
>>>>>>
>>>>>>
>>>>>> On 14/04/14 22:17, Kim, Ji-hoon wrote:
>>>>>>
>>>>>>> Dear Marcelo,
>>>>>>>
>>>>>>> As noted by Matt, you may want to take a look at the yt script that
>>>>>>> was developed and used by the AGORA collaboration, to analyze the dark
>>>>>>> matter-only simulations of various astrophysical codes including Ramses.
>>>>>>>
>>>>>>> https://bitbucket.org/mornkr/agora-analysis-script/src/655e46d0b3a06d2e6da222a0f50f79ca5da3b48f/script-Flagship-DM.py?at=default
>>>>>>>
>>>>>>> Thank you very much.
>>>>>>>
>>>>>>> Best wishes,
>>>>>>> Ji-hoon
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------------------------
>>>>>>> Ji-hoon Kim
>>>>>>> Postdoctoral Scholar in Astrophysics at Caltech
>>>>>>> www.jihoonkim.org
>>>>>>> me at jihoonkim.org / 1(650)714-2879
>>>>>>>
>>>>>>> -------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Apr 14, 2014, at 12:57 PM, Matthew Turk <matthewturk at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>  Hi Marcelo,
>>>>>>>>
>>>>>>>> Sorry to hear you're having trouble.  I haven't done much with
>>>>>>>> RAMSES
>>>>>>>> dark matter only simulations, but I think that Ji-hoon Kim may have
>>>>>>>> in
>>>>>>>> support of the AGORA project.  Additionally, others here might have
>>>>>>>> some experience.
>>>>>>>>
>>>>>>>> In general, we are happy to help get things working and running --
>>>>>>>> this seems like a genuine bug which we will need to address.  Can
>>>>>>>> you
>>>>>>>> post the full traceback?
>>>>>>>>
>>>>>>>> -Matt
>>>>>>>>
>>>>>>>> On Mon, Apr 14, 2014 at 3:45 PM, Marcelo Vargas dos Santos
>>>>>>>> <marcelovsrj at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> I'm trying to use HaloFinders on a ramses simulation without
>>>>>>>>> hydro. but it's
>>>>>>>>> not working. Tha error message is:
>>>>>>>>>
>>>>>>>>> No such file or directory:
>>>>>>>>>
>>>>>>>>> '/home/marcelo/Simulations/NBody/Ramses/branches/ramses_omp/run1/output_00001/hydro_00001.out00001'
>>>>>>>>>
>>>>>>>>> someone know how to fix it?
>>>>>>>>>
>>>>>>>>> Best.
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Marcelo Vargas dos Santos
>>>>>>>>> Professor e Doutorando
>>>>>>>>>
>>>>>>>>> Sala A 318-05
>>>>>>>>> Tel.: (21) 2562-7276 <%2821%29%202562-7276>
>>>>>>>>> E-mails: vargas at if.ufrj.br,  marcelovsrj at gmail.com
>>>>>>>>> Departamento de Física Teórica - Instituto de Física
>>>>>>>>> Universidade Federal do Rio de Janeiro
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> yt-users mailing list
>>>>>>>>> yt-users at lists.spacepope.org
>>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>>>>>
>>>>>>>>>  _______________________________________________
>>>>>>>> yt-users mailing list
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>>>>>>>
>>>>>>>
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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>  --
>>>>> Marcelo Vargas dos Santos
>>>>> Professor e Doutorando
>>>>>
>>>>> Sala A 318-05
>>>>> Tel.: (21) 2562-7276 <%2821%29%202562-7276>
>>>>> E-mails: vargas at if.ufrj.br,  marcelovsrj at gmail.com
>>>>> Departamento de Física Teórica - Instituto de Física
>>>>> Universidade Federal do Rio de Janeiro
>>>>>
>>>>
>>>>
>>>>
>>>>  --
>>>> Marcelo Vargas dos Santos
>>>> Professor e Doutorando
>>>>
>>>> Sala A 318-05
>>>> Tel.: (21) 2562-7276 <%2821%29%202562-7276>
>>>> E-mails: vargas at if.ufrj.br,  marcelovsrj at gmail.com
>>>> Departamento de Física Teórica - Instituto de Física
>>>> Universidade Federal do Rio de Janeiro
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
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>>
>>
>>  --
>> Marcelo Vargas dos Santos
>> Professor e Doutorando
>>
>> Sala A 318-05
>> Tel.: (21) 2562-7276
>> E-mails: vargas at if.ufrj.br,  marcelovsrj at gmail.com
>> Departamento de Física Teórica - Instituto de Física
>> Universidade Federal do Rio de Janeiro
>>
>>
>> _______________________________________________
>> yt-users mailing listyt-users at lists.spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>>
>>
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>>
>
>
> --
> Marcelo Vargas dos Santos
> Professor e Doutorando
>
> Sala A 318-05
> Tel.: (21) 2562-7276
> E-mails: vargas at if.ufrj.br,  marcelovsrj at gmail.com
> Departamento de Física Teórica - Instituto de Física
> Universidade Federal do Rio de Janeiro
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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