yt-users October 2013

yt-users@python.org

31 participants
37 discussions

by Pengfei Chen

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

6 years, 1 month

Running Rockstar Halo Finder to create a merger tree

by Hilary Egan

Hi all, I'm quite confused on a number of points related to running the rockstar halo finder, so I hope its alright that I put all these questions into this one email! 1. I can't seem to run the rockstar halo finder at all without getting this error followed by a segmentation fault and crash. [Warning] Network IO Failure (PID XXXXXX): Connection reset by peer [Network] Packet receive retry count at: 1 It sort of seems like this issue ( http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2012-November/002…) but I couldn't really figure out what the resolution was from the thread. Im attempting to run this on kraken and it doesn't matter if I use a single compute node or multiple, I get the same error. (I hope this isn't the infiniband issue the docs warned about, I couldn't figure out if that is how kraken is connected and I got an error that the suggested flag doesn't exist so I didn't press the issue.) 2. Whenever I finally do get the halo finder to work, I need the results to be in a form that the merger tree can use. It seems as though the MergerTree needs the results in the same form as the other halo finders give, so would getting the halo list and then dumping it as usual be the appropriate strategy? Ie: rh.run() halo_list = rh.halo_list() halo_list.dump('MergerHalos') 2.5. The docs sort of give mixed messages on whether or not I could just be calling MergerTree with the argument halo_finder_function = RockstarHaloFinder. At this point I've pretty thoroughly convinced myself that I can't, but it would be nice if that was clarified. (Just a thoroughly overwhelmed new user's perspective!) 3. I'm a little confused as to whether or not I have to use a TimeSeriesData object rather than the usual single time output when instantiating the halo finder. Under "Rockstar Halo Finding" it uses TimeSeriesData, unlike the rest of the examples, but under the subheading "Output Analysis" it just uses pf. The "Output Analysis" example also doesn't call the run() method, which leads me to believe something else entirely is going on, but its not quite clear. Thanks! -Hilary

6 years, 3 months

Athena units

by Stephanie Tonnesen

Hi Again, Everyone! So I would also like my figures to be in physical units, instead of in my code units. I *think* the Athena frontend doesn't read in what the unit conversions are (and I am not sure how it would do that). Can I just do something simple like: DensityUnits = 3. density_physunits = grid['density'] * DensityUnits Then, of course, I don't know how I would do a SlicePlot, ProjectionPlot or phaseplot in physical units... Any help/advice/direction is appreciated! Thanks, Stephanie

6 years, 4 months

chombo/orion2 projection issue

by William Gray

Hello yt-users, I am having an issue in creating off axis projection plots with short depths in yt. I am looking for disks around particles which necessitates using the off axis projection functionality. What I want to do is create a projection where the depth is the same as or similar to the width of the plot. However, I am finding that unless the depth is orders of magnitude larger than the width I will always create a blank plot (for example, the width is ~100 au, the depth to get a plot has to be ~1000xwidth, I want a plot where the width and depth are ~100 au). I have tried using both off_axis_projection and the OffAxisProjection methods with similar (bad) results. As a comparison, I ran a low resolution FLASH simulation that did not seem to have this problem. I also know that such a plot was possible with ORION2 data in the recent past (spring of this year) since a colleague was able produce such a plot. That same script now also fails. Does anyone know of a way around this problem? Has there been any recent changes that broke volume rendering for chombo/orion2 data? Thanks, William Gray

6 years, 5 months

Loading RAMSES Data into yt.

by k.grisdale＠surrey.ac.uk

Hi, I have been trying to load RAMSES data into yt 2.5. Orginaly it was loading in but the graphs I was able to produce didn’t make sense. So I tried to change to yt3 using the commands cd $YT_DEST/src/yt-hg/ hg pull http://bitbucket.org/yt_analysis/yt-3.0 hg up -C yt-3.0 python2.7 setup.py build_ext -i -f The commands appear to have worked. But when I try to use yt to load in RAMSES data I now get this error: Traceback (most recent call last): File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/gui/reason/basic_repl.py", line 81, in execute exec code in self.locals File "", line 1, in File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 76, in load if c._is_valid(*args, **kwargs): candidates.append(n) File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/art/data_structures.py", line 427, in _is_valid amr_header_vals = read_attrs(fh, amr_header_struct, '>') File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py", line 62, in read_attrs vals = list(struct.unpack(net_format, f.read(size))) error: unpack requires a string argument of length 892 Any idea what I need to do? Thanks Kearn

6 years, 5 months

Re: [yt-users] Scipy installation failure

by Yong Zheng

Dear yt-developers: I am trying to install scipy by using the install script, but it keeps failing all the time. Could you help me to check what's wrong with it? Thank you very much for your help! Here are the last few lines in the log file. Installed /home/yzheng/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg Processing dependencies for distribute==0.6.32 Finished processing dependencies for distribute==0.6.32 After install bootstrap. /home/yzheng/yt-x86_64/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info already exists Searching for pip Best match: pip 1.4.1 Processing pip-1.4.1-py2.7.egg pip 1.4.1 is already the active version in easy-install.pth Installing pip script to /home/yzheng/yt-x86_64/bin Installing pip-2.7 script to /home/yzheng/yt-x86_64/bin Using /home/yzheng/yt-x86_64/lib/python2.7/site-packages/pip-1.4.1-py2.7.egg Processing dependencies for pip Finished processing dependencies for pip Running from scipy source directory. blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/home/yzheng/yt-x86_64/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/home/yzheng/yt-x86_64/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/home/yzheng/yt-x86_64/lib', '/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu'] NOT AVAILABLE /home/yzheng/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/system_info.py:1494: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) Best, - Yong

6 years, 5 months

merger tree crash

by Latif

Hi all, I am running merger tree on Enzo simulations following the recipe given in YT documentation. YT crashes by producing the following error. I am using yt version "b118390aa42c". Any ideas what is going on here? FOF CPU TIME: 2.408634 secs ========== Cycle 00009 (z=9.999997) ========== Parent halo = 0 --> Most massive progenitor == Halo -1 ========== Cycle 00008 (z=14.999989) ========== ========== Cycle 00007 (z=19.999992) ========== ========== Cycle 00006 (z=29.999961) ========== Traceback (most recent call last): File "enzo.py", line 33, in <module> mt.save_halo_evolution('halos.h5') File "/home/uni05/mlatif/ytnew/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_merger_tree/enzofof_merger_tree.py", line 507, in save_halo_evolution halo_id = self.levels[cycle_fin][0].halo_id IndexError: list index out of range Thanks in advance, Cheers Latif

6 years, 5 months

Flux through spherical surfaces

by Morgan MacLeod

Dear all, I am hoping to calculate the flux of mass ("mdot") and angular momentum ("Ldot") through a series of concentric spherical surfaces in a simulation snapshot (centered around an absorbing "sink" within the grid). So far, I've attempted this along these lines: pf = load(fn) # load data rad = 0.1 sp = pf.h.sphere([0,0,0],1.1*rad) surf = pf.h.surface(sp,"Radius",rad) flux = surf.calculate_flux("x-velocity","y-velocity","z-velocity","Density") where flux gets assigned to the mass accretion rate in this case. I believe I could do the angular momentum by calculating the flux of a derived variable that is defined as data["SpecificAngularMomentumZ"] * data["Density"] such that the resulting units are angular momentum per volume. I was wondering if there is a better way to go about this calculation, it seems that others must have tried to look at similar questions. In particular, defining an "isoradius" surface seems to accomplish what I was hoping to do, but there must be a cleaner way. Thanks so much for your advice, Morgan

6 years, 5 months

How to use if, elif, else statements in creating a derived field

by Reju Sam John

Dear all, I would like to create a derived field which should return a value according to specified conditions. My definition of new field is shown below.. But it is giving error. @derived_field(name = "MyField") def my_new_field(field, data): if data.pf["MachNumber"] < 2 : return (.5* (data["MachNumber"])**2) - 1 elif data.pf["MachNumber"] < 100 : return (.5* (data["MachNumber"])**4) + (.5* (data["MachNumber"])**3) else: return 5.446361E-01 Please suggest me how to implement if, elif, else statements in creating a derived field. Thank You Reju Sam John

6 years, 5 months

running out of memory in a loop

by Stephanie Tonnesen

Hi everyone, Okay, so I am trying to make a SlicePlot, a ProjectionPlot, and a phase_object for a bunch of different outputs. My code keeps using up all my memory and dying after the first loop. I am not using variables, I think, so how do I free up my memory at the end of each loop? See code below. Thanks, Stephanie import matplotlib.pylab as pl from mpl_toolkits.mplot3d import Axes3D from yt.mods import * def _xkpc(field,data): return(data["x"]*26.) def _ykpc(field,data): return(data["y"]*26.) def _zkpc(field,data): return(data["z"]*26.) def _CellMassSolar(field,data): return(data["CellMass"]/1.99e33) add_field("xkpc",function=_xkpc,units="kpc") add_field("ykpc",function=_ykpc,units="kpc") add_field("zkpc",function=_zkpc,units="kpc") add_field("CellMassSolar",function=_CellMassSolar,units=r'M$_{\odot}$') outstring = ['0020','0030','0040','0050','0060','0070','0080','0090','0100','0110','0120','0130'] i = 0 while i < len(outstring): pf = load("id0/rps."+outstring[i]+".vtk",parameters={"TimeUnits":3.086e14,"LengthUnits":8.0236e22,"DensityUnits":9.999e-30,"VelocityUnits":2.6e8}) p = SlicePlot(pf,"x","Density") p.set_log("Density", True) p.save() p2 = ProjectionPlot(pf,"x","Density") p2.set_log("Density", True) p2.save() alld = pf.h.all_data() pc = PlotCollection(pf) tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25", "grid['z'] > 0.04"]) tp25extrema = tracerp25.quantities["Extrema"]("Density") pc.add_phase_object(tracerp25,["zkpc","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds = [-1e8,1.5e8],x_log=False,y_log=False) pc.set_zlim(10000,1e10) pc.save() i = i+1

6 years, 5 months

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yt-users October 2013