Hi Eric, Thanks for figuring it out. Then how do I load "lagos" under iyt? Or I'll have to go with a script? You mentioned raven as well, but then what is its relationship with lagos? I am a bit confused... Thanks, Kai PS. sorry, but I only know very little YT (and nothing about python)... Quoting Eric Hallman <Eric.Hallman@colorado.edu>:
Ok, I am not 100% sure what is going on, I've only tried this a few times with dm_only, but I have noticed not too many other people are around, so I will tell you what I know.
There are some quirky things with dm_only, for instance:
if you start with from yt.mods import * pf = EnzoStaticOutput("datasetname",data_style="enzo_packed_3d")
(or pf = load(...)) the behavior of creating plot collections, reading field lists is different than if you use
from yt.lagos import * pf = EnzoStaticOutput("datasetname",data_style="enzo_packed_3d")
In the first case, if you type
print pf.h.field_list
it fails
in the second case, it works. Unclear why.
You can project quantities, or take slices, but not for all the particle quantities as they are (as near as I can tell). Some of the derived quantites (e.g. particle_density_pyx) can be projected without a problem, once you import raven. Though I am not the expert on the particle quantities, I seem to remember that you can only take slices/ projections with grid quantities.
Anyway, I would start with loading up the data by importing lagos first, loading the dataset, then check your field list and derived field list for what you want to make slices of. There is some more documentation on the enzotools site on how to manage particle data etc.
Hopefully someone else can help with the real answers here at some point.
Sorry I couldn't help more.
On Dec 22, 2009, at 12:52 PM, kcai@pa.uky.edu wrote:
Hi Eric,
Quoting Eric Hallman <Eric.Hallman@colorado.edu>:
Kai, I am getting a completely different error than you are, but I also fail at the same step. Which version of yt are you using?
I think it is yt-1.5, but I'm not 100% sure. I used the installation script.
I will see if I can get this figured out.
Thank you for this! Kai
On Dec 22, 2009, at 11:58 AM, kcai@pa.uky.edu wrote:
Eric, No, 'Dark_Matter_Density' does not work, either... -> similar error:
In [5]: pc.add_slice('Dark_Matter_Density', 0) Exception AttributeError: "EnzoHierarchy instance has no attribute '_data_file'" in <bound method EnzoHierarchy.__del__ of <yt.lagos.HierarchyType.EnzoHierarchy instance at 0x2aa1cfbcf8>> ignored --------------------------------------------------------------------------- KeyError Traceback (most recent call last)
/share/home/kca223/src/yt-1.5/scripts/iyt in <module>() ----> 1 2 3 4 5
/share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in add_slice(self, *args, **kwargs) 180 *fig_size* in (height_inches, width_inches) 181 """ --> 182 return self.__add_slice(PlotTypes.SlicePlot, *args, **kwargs) 183 184 def add_slice_interpolated(self, *args, **kwargs):
/share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in __add_slice(self, ptype, field, axis, coord, center, use_colorbar, figure, axes, fig_size, periodic, data_source, **kwargs) 204 coord = center[axis] 205 if data_source is None: --> 206 data_source = self.pf.hierarchy.slice(axis, coord, field, center, **kwargs) 207 p = self._add_plot(ptype(data_source, field, use_colorbar=use_colorbar, 208 axes=axes, figure=figure,
/share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in _get_hierarchy(self) 144 if self._hierarchy_class == None: 145 raise RuntimeError("You should not instantiate StaticOutput.") --> 146 self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) 147 return self.__hierarchy 148
/share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in __init__(self, pf, data_style) 689 break 690 self.__guess_data_style(pf["TopGridRank"], testGrid, testGridID) --> 691 self._setup_data_queue() 692 # For some reason, r8 seems to want Float64 693 if pf.has_key("CompilerPrecision") \
/share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in _setup_data_queue(self) 137 138 def _setup_data_queue(self): --> 139 self.queue = _data_style_funcs[self.data_style][5]() 140 141 def _setup_grid_corners(self):
KeyError: 'enzo_packed_3d'
I think it is I did not set the "data_style" right...
Thanks, Kai
Quoting Eric Hallman <Eric.Hallman@colorado.edu>:
, I think the solution is that dark matter only runs do not have the field "Density", but only dark matter density is defined as a field. Density is a baryon field.
On Dec 22, 2009, at 9:18 AM, kcai@pa.uky.edu wrote:
Sorry - forgot to change the subject of last email...
Quoting kcai@pa.uky.edu:
> Hi Matt, > Last night I was browsing the archives of the yt-users list, and > came across this thread of emails: > > [yt-users] corrupt enzo restart file? > Matthew Turk matthewturk at gmail.com > Thu Nov 12 09:30:36 PST 2009 > > Hi Stephen, > > A problem with the way yt opens up dark matter only simulations is > that the data_style has to be specified. This would be, for running > on trunk, done with the parameter: > > data_style="enzo_packed_3d" > > to the StaticOutput initialization. Britton Smith has done some work > recently on improving this, so he might be able to chime in with more > info. > > -Matt > > On Thu, Nov 12, 2009 at 9:27 AM, Stephen Skory <stephenskory at > yahoo.com> wrote: >> Hi all, >> >> I am getting this error <http://paste.enzotools.org/show/257/ >> > when I attempt to instantiate the grid hierarchy. > ...... > > > I am encountering the same "TypeError" when I tried to analyze > a DM- only run. > But I use iyt (the interactive yt) - how do I add the > data_style then? I tried > with > > pf = load("RD0000/RD0000", data_style="enzo_packed_3d") > and then > In [3]: pc = PlotCollection(pf, center=[0.5,0.5,0.5]) > yt INFO 2009-12-22 00:01:13,536 Created plot collection > with default plot-center = [0.5, 0.5, 0.5] > > But when I tried to plot a slice, I got: > In [4]: pc.add_slice("Density", 0) > --------------------------------------------------------------------------- > KeyError Traceback (most > recent call last) > > /share/home/kca223/src/yt-1.5/scripts/iyt in <module>() > ----> 1 > 2 > 3 > 4 > 5 > > /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in > add_slice(self, *args, **kwargs) > 180 *fig_size* in (height_inches, width_inches) > 181 """ > --> 182 return self.__add_slice(PlotTypes.SlicePlot, > *args, **kwargs) > 183 > 184 def add_slice_interpolated(self, *args, **kwargs): > > /share/home/kca223/src/yt-1.5/yt/raven/PlotCollection.pyc in > __add_slice(self, ptype, field, axis, coord, center, use_colorbar, > figure, axes, fig_size, periodic, data_source, **kwargs) > 204 coord = center[axis] > 205 if data_source is None: > --> 206 data_source = > self.pf.hierarchy.slice(axis, coord, > field, center, **kwargs) > 207 p = self._add_plot(ptype(data_source, field, > use_colorbar=use_colorbar, > 208 axes=axes, figure=figure, > > /share/home/kca223/src/yt-1.5/yt/lagos/OutputTypes.pyc in > _get_hierarchy(self) > 144 if self._hierarchy_class == None: > 145 raise RuntimeError("You should not instantiate > StaticOutput.") > --> 146 self.__hierarchy = self._hierarchy_class(self, > data_style=self.data_style) > 147 return self.__hierarchy > 148 > > /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in > __init__(self, pf, data_style) > 689 break > 690 self.__guess_data_style(pf["TopGridRank"], testGrid, > testGridID) > --> 691 self._setup_data_queue() > 692 # For some reason, r8 seems to want Float64 > 693 if pf.has_key("CompilerPrecision") \ > > /share/home/kca223/src/yt-1.5/yt/lagos/HierarchyType.pyc in > _setup_data_queue(self) > 137 > 138 def _setup_data_queue(self): > --> 139 self.queue = _data_style_funcs[self.data_style] [5] () > 140 > 141 def _setup_grid_corners(self): > > KeyError: 'enzo_packed_3d' > > Thanks a lot! > Kai >
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