<div dir="ltr">Hi Marcelo,<div><br></div><div>You need to replace "ParticleMassMsun" with "particle_mass".</div><div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 15, 2014 at 8:56 AM, 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 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="HOEnZb"><div class="h5"><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><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>
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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>
<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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<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>
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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.: <a href="tel:%2821%29%202562-7276" value="+12125627276" target="_blank">(21) 2562-7276</a><br>
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