Re: [yt-users] cannot find some particle fields

24 Apr 2013

      Hi Matt,

don't feel bad, it worked!
I will try to remember to remove that file before emailing the list. I think that this trick solved about half of the problems I have had... ;-)

Cheers,

JC

On Apr 24, 2013, at 1:05 PM, Matthew Turk  wrote:
...
Hi JC,
THis looks like another failure of the field detection algorithm.
We're working on improving it, but it's set up this way because there
is no canonical list of Enzo fields, and there's no way to check every
grid without slowing thigns down considerably.  I know this is
terrible to suggest, and I feel bad for doing so, but you might be
able to get something if you remove the .yt and try again.  :-(
-Matt
On Wed, Apr 24, 2013 at 11:39 AM, Jean-Claude Passy  wrote:
...
Hi Matt,
thanks for your quick reply.
It only gives me the gas fields:
-----------------------------
In [5]: pf.h.field_list
Out[5]: ['z-velocity', 'y-velocity', 'x-velocity', 'TotalEnergy', 'Density']
-----------------------------
Btw, I am using the latest dev version of yt (changeset 7439:34b95297062b).
Cheers,
JC
On Apr 24, 2013, at 7:52 AM, Matthew Turk  wrote:
Hi JC,
What's the output of:
pf.h.field_list
?
-Matt
On Wed, Apr 24, 2013 at 12:35 AM, Jean-Claude Passy 
wrote:
Hi all,
sorry, I have a pretty dumb question.
I have a non-cosmological simulation with only 1 particle. I can get the
particle_mass field, but yt throws the following error when I try to grab
particle_index:
---------------------------------------------------------------------------------------------------------------------------------
In [1]: pf = load('CE0001')
yt : [INFO     ] 2013-04-24 00:32:02,190 Parameters: current_time
= 0.00149998503444
yt : [INFO     ] 2013-04-24 00:32:02,190 Parameters: domain_dimensions
= [32 32 32]
yt : [INFO     ] 2013-04-24 00:32:02,190 Parameters: domain_left_edge
= [ 0.  0.  0.]
yt : [INFO     ] 2013-04-24 00:32:02,190 Parameters: domain_right_edge
= [ 1.  1.  1.]
yt : [INFO     ] 2013-04-24 00:32:02,191 Parameters: cosmological_simulation
= 0.0
In [2]: region = pf.h.region([0.5, 0.5, 0.5], [0.0, 0.0, 0.0], [1.0, 1.0,
1.0])
yt : [INFO     ] 2013-04-24 00:32:05,802 Getting the binary hierarchy
yt : [INFO     ] 2013-04-24 00:32:05,805 Finished with binary hierarchy
reading
In [3]: region['particle_mass']
yt : [INFO     ] 2013-04-24 00:32:12,685 Getting particle_mass using
ParticleIO
Out[3]: array([ 6585896.1408])
In [4]: region['particle_index']
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/scripts/iyt in <module>()
----> 1 region['particle_index']
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
in __getitem__(self, key)
  328             if key not in self.fields:
  329                 self.fields.append(key)
--> 330             self.get_data(key)
  331         return self.field_data[key]
  332
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
in get_data(self, fields, in_grids, force_particle_read)
 2614                     pass
 2615             if field not in self.hierarchy.field_list and not
in_grids:
-> 2616                 if self._generate_field(field):
 2617                     continue # True means we already assigned it
 2618             mylog.info("Getting field %s from %s", field,
len(self._grids))
/Users/jcpassy/Work/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc
in _generate_field(self, field)
  361                 return True
  362         else: # Can't find the field, try as it might
--> 363             raise KeyError(field)
  364
  365     def _generate_field_in_grids(self, field, num_ghost_zones=0):
KeyError: 'particle_index'
---------------------------------------------------------------------------------------------------------------------------------
However, the field is there:
---------------------------------------------------------------------------------------------------------------------------------
[ 0:30:13] Obiwan:$ h5ls CE0001.cpu0000/Grid00000004
Dark_Matter_Density      Dataset {52, 52, 52}
Density                  Dataset {52, 52, 52}
TotalEnergy              Dataset {52, 52, 52}
particle_index           Dataset {1}
particle_mass            Dataset {1}
particle_position_x      Dataset {1}
particle_position_y      Dataset {1}
particle_position_z      Dataset {1}
particle_type            Dataset {1}
particle_velocity_x      Dataset {1}
particle_velocity_y      Dataset {1}
particle_velocity_z      Dataset {1}
x-velocity               Dataset {52, 52, 52}
y-velocity               Dataset {52, 52, 52}
z-velocity               Dataset {52, 52, 52}
[ 0:30:13] Obiwan:$ h5ls -d CE0001.cpu0000/Grid00000004/particle_index
particle_index           Dataset {1}
  Data:
      (0) 0
---------------------------------------------------------------------------------------------------------------------------------
Am I missing something obvious?
Thanks a lot for you help,
JC
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