I’m trying to compute the two point halo correlation function for RAMSES data using the code found at http://yt-project.org/docs/2.6/analyzing/analysis_modules/two_point_functio… (I’ve already run HOP and written to HopAnalysis.out). I get an error saying ‘add_tree’ is not defined, but yt.utilities.kdtree is imported and build properly. Is this feature working in version 3.0?
I realize this is rather a question for the HDF group, but I was wondering if anyone had an explanation for what I am seeing.
I would like to restart an Enzo simulation with different BCs on the root grid. Therefore, I created a new data.boundary.hdf with this very simple script:
Aside from the different values in BoundaryDimensionType.X, the two files look completely identical to me (same datasets, attributes, types, sizes,…). However, I don't understand why the new file is about twice as big as the original one:
[15:42:09] Obiwan:$ du -sh CE0010.boundary*hdf
This is probably something simple, but I could not figure it out.
Any suggestion would be much appreciated! Script is attached and the hdf files can be found there:
Thanks a lot,
I'm running a simulation of the Large Magellanic Clouds and would
like to produce projections of the system as would be seen from the solar
neighborhood (i.e., actual observations!).
I'm thus looking to create projections in spherical coordinates
from a point that happens to lie a factor of unity beyond my simulation
box. I believe the camera objects can help me out here and I've messed
around with all_sky plots. But the PerspectiveCamera class
looks particularly useful. Unfortunately I could find any documentation for
this class. Anyone have some advice on how to use this?
Munier A. Salem // 845.489.6450
hi, helpful folks
I am once again very confused, and would appreciate any help. I am still
trying to make a plot which contains frb's created from datafiles at
different time steps. This is what I have that I think should work, and
from yt.mods import *
import matplotlib.pyplot as plt
import matplotlib.colorbar as cb
from matplotlib.colors import LogNorm
import numpy as np
ts = TimeSeriesData.from_filenames("Strat_Box_hdf5_plt_cnt_01*")
print len(ts) #just checking
num = len(ts)
for index, val in enumerate(ts):
print "%s = %s" % (index, val) #again, just checking that this does
what I think
orient = 'vertical'
fig, axes, colorbars = get_multi_plot( num, 1, colorbar=orient, bw = 6)
plots = 
for i, fn in enumerate(ts):
pf = load(fn) # load data
sl = pf.h.slice(0, pf.domain_center,fields=["Density","Temperature"]
frb = sl.to_frb( (1.0, 'kpc'), (4096,1024),height=(4.0, 'kpc'))
dens_axes = [axes[i]]
for ax in dens_axes:
plots = [dens_axes.imshow(frb["Density"], origin='lower',
These are the errors that I get;
TypeError Traceback (most recent call
last)<ipython-input-6-cd09eb0aaf88> in <module>() 1 for i, fn in
enumerate(ts):----> 2 pf = load(fn) # load data 3 sl =
pf.h.slice(0, pf.domain_center,fields=["Density","Temperature"] )
4 frb = sl.to_frb( (1.0, 'kpc'), (4096,1024),height=(4.0,
'kpc')) 5 dens_axes = [axes[i]]
/Users/kde/yt-x86_64/src/yt-hg/yt/convenience.pyc in load(*args,
**kwargs) 65 try: 66 from
yt.data_objects.time_series import TimeSeriesData---> 67
ts = TimeSeriesData.from_filenames(*args, **kwargs) 68
return ts 69 except YTOutputNotIdentified:
from_filenames(cls, filenames, parallel, **kwargs) 263
filenames = glob.glob(filenames) 264
filenames.sort()--> 265 obj = cls(filenames[:], parallel =
parallel, **kwargs) 266 return obj 267
__getitem__(self, key) 146 for d in [self.units,
self.time_units, self.parameters, \ 147
self.conversion_factors]:--> 148 if key in d: return
d[key] 149 raise KeyError(key) 150
TypeError: unhashable type
Kathy DeGioia Eastwood, Ph.D.
Professor of Physics and Astronomy
Northern Arizona University
Flagstaff, AZ 86011-6010
Ph: 928-523-7159 FX: 928-523-1371
deliveries: 602 S. Humphreys St., Bldg 19 Rm 209
Many thanks for your help, just pulled your changes and the issue is now resolved. The last remaining call to _grids shouldn’t be a problem for me right now.
Thanks for the speedy response!
I’m having some issues following the yt halo mass function example here: http://yt-project.org/docs/2.5/analysis_modules/hmf_howto.html for RAMSES data. The halo finder works, but I get the following error when trying to run the profiler: AttributeError: 'RAMSESGeometryHandler' object has no attribute ‘grids. I searched through the users archive but didn’t find anything. Appreciate any help (I’m using yt 3.0).
I recently used conda to install yt, but when I try to import
AbsorptionSpectrum, I get this error:
I'm not familiar with particle_trajectories, but is this something
that is actually needed by AbsorptionSpectrum? If not, should it even
being trying to import that? Any thoughts/help are, as always,
Devin W. Silvia
Department of Physics and Astronomy
Michigan State University
I am trying to install yt with SciPy on Michigan State University's HPCC
system and am running into errors that I cannot resolve by following the
instructions in the install script. I have tried uncommenting each of the
NUMPY_ARGS statements and had no success. I have attached the log file from
my most recent installation attempt as the error message is long. My guess
is that it has to do with the "recompile with -fPIC" message in lines 75202
and 75205 but I cannot figure out what that means.
Can anybody explain what this error message means and how to resolve it.
While trying to run the attached script from "yt-cookbook" to get halo mass function, I am getting NameError: global name 'fKD' is not defined.
It looks like I am tied up already, since I can't do "yt update" on the top of my manual installation. If I am not wrong, it looks to me that I have to build fKDpy.so, may you help me on how to do that. Thank you in advance for your kindest help.
yt : [INFO ] 2014-01-24 15:32:41,413 Building kd tree for 2097152 particles...
Traceback (most recent call last):
File "mass_function.py", line 15, in <module>
hp = amods.halo_profiler.HaloProfiler("/home/remudin/gas_plus_dm_uni_adia_simulation/RD0003/RedshiftOutput0003")
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 305, in __init__
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 983, in _load_halo_data
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_profiler/multi_halo_profiler.py", line 1140, in _run_hop
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 2305, in __init__
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1670, in __init__
HaloList.__init__(self, data_source, dm_only)
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1059, in __init__
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1698, in _run_finder
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 63, in __init__
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 1526, in _chain_hop
File "/usr/local/lib/python2.7/dist-packages/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py", line 341, in _init_kd_tree
fKD.dens = np.zeros(self.size, dtype='float64', order='F')
NameError: global name 'fKD' is not defined
Remudin Reshid; MEKURIA,
School of Physics, Wits University,
1 Jan Smuts Ave, Braamfontein, WITS 2050
Johannesburg, South Africa
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