<div dir="ltr">I thinking that is almost well. I recieved the error message that you espected.<div><div>Do you know how i can fix it?</div><div><br></div><div>Thank you</div><div><br></div><div><br></div><div><br></div><div>
<div>yt : [WARNING ] 2014-04-15 12:53:57,895 RAMSES frontend assumes all simulations are cosmological!</div><div>yt : [INFO ] 2014-04-15 12:53:57,916 Parameters: current_time = -3.65552566796e+15</div><div>
yt : [INFO ] 2014-04-15 12:53:57,916 Parameters: domain_dimensions = [128 128 128]</div><div>yt : [INFO ] 2014-04-15 12:53:57,917 Parameters: domain_left_edge = [ 0. 0. 0.]</div><div>yt : [INFO ] 2014-04-15 12:53:57,917 Parameters: domain_right_edge = [ 1. 1. 1.]</div>
<div>yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: cosmological_simulation = 1</div><div>yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: current_redshift = 49.9999981951</div><div>yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: omega_lambda = 0.723999977112</div>
<div>yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: omega_matter = 0.275999993086</div><div>yt : [INFO ] 2014-04-15 12:53:57,918 Parameters: hubble_constant = 0.738000030518</div><div>yt : [INFO ] 2014-04-15 12:53:58,300 Loading field plugins.</div>
<div>yt : [INFO ] 2014-04-15 12:53:58,300 Loaded angular_momentum (8 new fields)</div><div>yt : [INFO ] 2014-04-15 12:53:58,302 Loaded astro (14 new fields)</div><div>yt : [INFO ] 2014-04-15 12:53:58,302 Loaded cosmology (20 new fields)</div>
<div>yt : [INFO ] 2014-04-15 12:53:58,302 Loaded fluid (56 new fields)</div><div>yt : [INFO ] 2014-04-15 12:53:58,303 Loaded fluid_vector (88 new fields)</div><div>yt : [INFO ] 2014-04-15 12:53:58,303 Loaded geometric (103 new fields)</div>
<div>yt : [INFO ] 2014-04-15 12:53:58,303 Loaded local (103 new fields)</div><div>yt : [INFO ] 2014-04-15 12:53:58,303 Loaded magnetic_field (109 new fields)</div><div>yt : [WARNING ] 2014-04-15 12:53:58,391 No particle_type, no creation_time, so not distinguishing.</div>
<div>---------------------------------------------------------------------------</div><div>YTFieldNotFound Traceback (most recent call last)</div><div>/home/marcelo/anaconda/lib/python2.7/site-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)</div>
<div> 202 else:</div><div> 203 filename = fname</div><div>--> 204 __builtin__.execfile(filename, *where)</div><div><br></div><div>/home/marcelo/Simulations/NBody/Ramses/branches/ramses_omp/run1/plot.py in <module>()</div>
<div> 12 </div><div> 13 ds = load(files[0])</div><div>---> 14 halos = HaloFinder(ds)</div><div> 15 #print ds.parameters</div><div> 16 #print "\n"</div><div><br></div><div>/home/marcelo/yt/yt/analysis_modules/halo_finding/halo_objects.pyc in __init__(self, pf, subvolume, threshold, dm_only, padding, total_mass)</div>
<div> 2387 select = self._get_dm_indices()</div><div> 2388 total_mass = \</div><div>-> 2389 self.comm.mpi_allreduce((self._data_source['all', "ParticleMassMsun"][select]).sum(dtype='float64'), op='sum')</div>
<div> 2390 else:</div><div> 2391 total_mass = self.comm.mpi_allreduce(self._data_source.quantities["TotalQuantity"]("ParticleMassMsun")[0], op='sum')</div><div><br>
</div><div>/home/marcelo/yt/yt/data_objects/data_containers.pyc in __getitem__(self, key)</div><div> 203 Returns a single field. Will add if necessary.</div><div> 204 """</div><div>--> 205 f = self._determine_fields([key])[0]</div>
<div> 206 if f not in self.field_data and key not in self.field_data:</div><div> 207 if f in self._container_fields:</div><div><br></div><div>/home/marcelo/yt/yt/data_objects/data_containers.pyc in _determine_fields(self, fields)</div>
<div> 451 raise YTFieldNotParseable(field)</div><div> 452 ftype, fname = field</div><div>--> 453 finfo = self.pf._get_field_info(ftype, fname)</div><div> 454 else:</div>
<div> 455 fname = field</div><div><br></div><div>/home/marcelo/yt/yt/data_objects/static_output.pyc in _get_field_info(self, ftype, fname)</div><div> 487 self._last_finfo = self.field_info[(ftype, fname)]</div>
<div> 488 return self._last_finfo</div><div>--> 489 raise YTFieldNotFound((ftype, fname), self)</div><div> 490 </div><div> 491 def _setup_classes(self):</div><div><br></div><div>
YTFieldNotFound: Could not find field '('all', 'ParticleMassMsun')' in info_00001.</div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 15 April 2014 10:24, Sam Geen <span dir="ltr"><<a href="mailto:samgeen@astro.ox.ac.uk" target="_blank">samgeen@astro.ox.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Marcelo,<br>
<br>
I believe a fix has been merged into the branch yt-3.0 of the yt
repository, i.e. call:<br>
<br>
hg pull && hg update yt-3.0<br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Sam<div><div class="h5"><br>
<br>
<div>On 14/04/2014 23:19, Sam Geen wrote:<br>
</div>
<blockquote type="cite">
<div>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.<br>
<br>
On 14/04/14 22:59, Marcelo Vargas dos Santos wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>yt module located at:</div>
<div> /home/marcelo/Downloads/yt-x86_64/src/yt-hg</div>
<div>The supplemental repositories are located at:</div>
<div> /home/marcelo/Downloads/yt-x86_64/src/yt-supplemental</div>
<div>aviso: ignorando pai desconhecido do diretório de
trabalho '794b2beb2c48'!</div>
<div><br>
</div>
<div>The current version of the code is:</div>
<div><br>
</div>
<div>---</div>
<div>000000000000</div>
<div>---</div>
<div> <br>
</div>
<div>This installation CAN be automatically updated.</div>
<div>yt dependencies were last updated on</div>
<div>Qui Abr 10 19:15:16 BRT 2014</div>
<div><br>
</div>
<div>To update all dependencies, run "yt update --all".</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 14 April 2014 17:57, Nathan
Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Marcelo,
<div><br>
</div>
<div>Can you tell us the output of 'yt instinfo' run
from the command line? That will give more precise
version information.</div>
<span><font color="#888888">
<div><br>
</div>
<div>-Nathan</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"> <br>
<br>
<div class="gmail_quote">On Mon, Apr 14, 2014 at
1:56 PM, Marcelo Vargas dos Santos <span dir="ltr"><<a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Sorry, i'm using the Bleeding
Edge version. There's no 4.0.0</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 14 April 2014
17:55, Marcelo Vargas dos Santos <span dir="ltr"><<a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">I'm using the yt-4.0.0.</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote"> On 14
April 2014 17:53, Sam Geen <span dir="ltr"><<a href="mailto:samgeen@astro.ox.ac.uk" target="_blank">samgeen@astro.ox.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.
<div>
<div><br>
<br>
On 14/04/14 22:17, Kim,
Ji-hoon wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Marcelo,<br>
<br>
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.<br>
<a href="https://bitbucket.org/mornkr/agora-analysis-script/src/655e46d0b3a06d2e6da222a0f50f79ca5da3b48f/script-Flagship-DM.py?at=default" target="_blank">https://bitbucket.org/mornkr/agora-analysis-script/src/655e46d0b3a06d2e6da222a0f50f79ca5da3b48f/script-Flagship-DM.py?at=default</a><br>
<br>
Thank you very much.<br>
<br>
Best wishes,<br>
Ji-hoon<br>
<br>
<br>
-------------------------------------------------------------------------<br>
Ji-hoon Kim<br>
Postdoctoral Scholar
in Astrophysics at
Caltech<br>
<a href="http://www.jihoonkim.org" target="_blank">www.jihoonkim.org</a><br>
<a href="mailto:me@jihoonkim.org" target="_blank">me@jihoonkim.org</a> / <a href="tel:1%28650%29714-2879" value="+16507142879" target="_blank">1(650)714-2879</a><br>
-------------------------------------------------------------------------<br>
<br>
<br>
<br>
<br>
On Apr 14, 2014, at
12:57 PM, Matthew Turk
<<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>>
wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Marcelo,<br>
<br>
Sorry to hear you're
having trouble. I
haven't done much
with RAMSES<br>
dark matter only
simulations, but I
think that Ji-hoon
Kim may have in<br>
support of the AGORA
project.
Additionally,
others here might
have<br>
some experience.<br>
<br>
In general, we are
happy to help get
things working and
running --<br>
this seems like a
genuine bug which we
will need to
address. Can you<br>
post the full
traceback?<br>
<br>
-Matt<br>
<br>
On Mon, Apr 14, 2014
at 3:45 PM, Marcelo
Vargas dos Santos<br>
<<a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I'm trying to use
HaloFinders on a
ramses simulation
without hydro. but
it's<br>
not working. Tha
error message is:<br>
<br>
No such file or
directory:<br>
'/home/marcelo/Simulations/NBody/Ramses/branches/ramses_omp/run1/output_00001/hydro_00001.out00001'<br>
<br>
someone know how
to fix it?<br>
<br>
Best.<br>
<br>
--<br>
Marcelo Vargas dos
Santos<br>
Professor e
Doutorando<br>
<br>
Sala A 318-05<br>
Tel.: <a href="tel:%2821%29%202562-7276" value="+12125627276" target="_blank">(21)
2562-7276</a><br>
E-mails: <a href="mailto:vargas@if.ufrj.br" target="_blank">vargas@if.ufrj.br</a>, <a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a><br>
Departamento de
Física Teórica -
Instituto de
Física<br>
Universidade
Federal do Rio de
Janeiro<br>
<br>
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-- <br>
<div dir="ltr">Marcelo Vargas
dos Santos<br>
Professor e Doutorando<br>
<br>
Sala A 318-05<br>
Tel.: <a href="tel:%2821%29%202562-7276" value="+12125627276" target="_blank">(21)
2562-7276</a><br>
E-mails: <a href="mailto:vargas@if.ufrj.br" target="_blank">vargas@if.ufrj.br</a>,
<a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a><br>
Departamento de Física Teórica
- Instituto de Física<br>
Universidade Federal do Rio de
Janeiro</div>
</div>
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</div>
</blockquote>
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<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">Marcelo Vargas dos Santos<br>
Professor e Doutorando<br>
<br>
Sala A 318-05<br>
Tel.: <a href="tel:%2821%29%202562-7276" value="+12125627276" target="_blank">(21)
2562-7276</a><br>
E-mails: <a href="mailto:vargas@if.ufrj.br" target="_blank">vargas@if.ufrj.br</a>,
<a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a><br>
Departamento de Física Teórica
- Instituto de Física<br>
Universidade Federal do Rio de Janeiro</div>
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-- <br>
<div dir="ltr">Marcelo Vargas dos Santos<br>
Professor e Doutorando<br>
<br>
Sala A 318-05<br>
Tel.: <a href="tel:%2821%29%202562-7276" value="+12125627276" target="_blank">(21) 2562-7276</a><br>
E-mails: <a href="mailto:vargas@if.ufrj.br" target="_blank">vargas@if.ufrj.br</a>,
<a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a><br>
Departamento de Física Teórica - Instituto de Física<br>
Universidade Federal do Rio de Janeiro</div>
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<br>
<fieldset></fieldset>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Marcelo Vargas dos Santos<br>Professor e Doutorando<br><br>Sala A 318-05<br>Tel.: (21) 2562-7276<br>E-mails: <a href="mailto:vargas@if.ufrj.br" target="_blank">vargas@if.ufrj.br</a>, <a href="mailto:marcelovsrj@gmail.com" target="_blank">marcelovsrj@gmail.com</a><br>
Departamento de Física Teórica - Instituto de Física<br>Universidade Federal do Rio de Janeiro</div>
</div>