Mailman 3 July 2012 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins April 11, 2020

April 11, 2020

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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p.modify["point"]
by Elizabeth Tasker Oct. 5, 2012

Oct. 5, 2012

Hi, I'm trying to add text to a particular point in my slice. I've got: position = na.array([20.2, 13.8, 16.0]) pc = PlotCollection(pf, center=position) p = pc.add_projection("Density", 2) p.set_width(2, 'kpc') for c in range(len(t1clouds)): r = abs(t1clouds[c]['position']-position) if r[0] < 1.0 and r[1] < 1.0: p.modify["point"](t1clouds[c]['position'], str(t1clouds[c]['track'])) p.modify["marker"](t1clouds[c]['position'], marker='o') pc.save("%s_tracking" % (fn)) But python complains with: TypeError: text() argument after ** must be a mapping, not NoneType Did I call the modifier incorrectly? Elizabeth

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Crashing PDFs and Login screen after Yt installation
by Héctor Aceves Campos Aug. 6, 2012

Aug. 6, 2012

Dear all I have recently tried to install Yt, including Enzo, with the installation script provided in the Yt webpage; setting the Enzo flag=1 and installing as superuser in /usr/local all the files I had the following two problems: 1) the enzo clone was not installed... just before finishing the script said something like Python SSL not found or supported, and the enzo installation was aborted. 2) After all this, I was not able to (a) open any pdf file either with evince or xpdf (under linux; either ubuntu 10.04 and linux mint 13 - running gnome), (b) login .. my "welcome screen" was off, completely gone or black as in my laptop (a toshiba with linux mint). so I could not login! In the case of my desktop at work, I had to reinstall the operating system. Have any of the people of this forum seen this kind of problems? Any ideas what might have gone wrong or how to fix this? cheers, hector

3 5

error in light_ray periodic ray creation
by Joshua Eric Moloney Aug. 1, 2012

Aug. 1, 2012

Hi all, I've been trying to get a script (provided to me by Britton) working to create a bunch of light rays from an Enzo simulation. Depending on the initial seed value, it makes some of them correctly but eventually fails with the following error: Traceback (most recent call last): File "make_light_rays.py", line 32, in <module> get_los_velocity=True, get_nearest_galaxy=False) File "/home/student/jomo9722/Enzo/ yt-x86_64/src/yt-hg/yt/analysis_modules/light_ray/light_ray.py", line 275, in make_light_ray (sub_ray[field])]) File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 319, in __getitem__ self.get_data(key) File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 508, in get_data if field not in ("dts", "t") and self._generate_field(field): File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 349, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 316, in __call__ dd = self._function(self, data) File "/data/moloney/cosmology_test/test_new/ion_balance/SD93IonBalance.py", line 178, in _ion_number_density return solarAbundance[atom] * data[fractionField] * data['Metallicity'] * \ File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 319, in __getitem__ self.get_data(key) File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 508, in get_data if field not in ("dts", "t") and self._generate_field(field): File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 349, in _generate_field self[field] = self.pf.field_info[field](self) File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 316, in __call__ dd = self._function(self, data) File "/data/moloney/cosmology_test/test_new/ion_balance/SD93IonBalance.py", line 193, in _ion_fraction_field fraction = na.power(10, interp(data)) File "/home/student/jomo9722/Enzo/yt-x86_64/src/yt-hg/yt/utilities/linear_interpolators.py", line 44, in __call__ x_i = (na.digitize(x_vals, self.x_bins) - 1).astype('int32') ValueError: Both x and bins must have non-zero length Working through the debugger, I found that for the segment where it failed the periodic_ray function had produced the following list of segments. [[array([ 0.16103374, 0.78830872, 0.24846128]), array([ 0.14031834, 0.57367409, 1. ])], [array([ 0.14031834, 0.57367409, 1. ]), array([ 0.14031834, 0.57367409, 1. ])], [array([ 0.14031834, 0.57367409, 0. ]), array([ 0.13268221, 0.49455532, 0.2770327 ])]] The second segment here has identical start and end points, which is leading yt to try to interpolate a field with nothing in it (and therefore throwing the above error). It seems that what's happening is that due to rounding errors the first segment being produced actually has a value < 1 for the third dimension so that when it checks to see if the segment hit any of the box walls it thinks that it didn't. It then tries to start a new segment that's already at the boundary of the box, producing a ray segment containing 0 grid cells. Has anyone run into this problem before, and is there a fix for it floating around out there somewhere? If not I could probably work something up that checks to see if the distance from the segment endpoint to the wall is < SmallNumber and set it equal to the value at the wall if it is. Thanks.

3 6

YT dies after second attempt to run script
by Francia F. Riesco July 30, 2012

July 30, 2012

Dear Everybody, my name is Francia and I am new working with YT. I have Enzo data and I was able to run a basic example of YT. I succeeded to get result in my first attempt. However, the same command now gives me and error and I am unable to find the solution. I am wondering if somebody has gotten this same error. Mac OS X V 10.7.4 Python 2.7.2 (default, Jul 30 2012, 17:08:59) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)] on darwin This is the script I am running: ----- import sys from yt.mods import * # set up our namespace from pkg_resources import load_entry_point import yt.frontends.enzo.api yt.frontends.enzo.api.EnzoHierarchy._bn = "%s.grid.cpu%%04i" from yt.analysis_modules.halo_finding.api import * fn = "/Users/friesco/astro/redshift0058/redshift0058" pf = load(fn) # load data halos = HaloFinder(pf) halos.write_out("/Users/friesco/astro/halo_output.out") --- I got this results yt : [INFO ] 2012-07-26 17:45:45,860 Parameters: current_time = 636.417235913 yt : [INFO ] 2012-07-26 17:45:45,860 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2012-07-26 17:45:45,860 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-07-26 17:45:45,860 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2012-07-26 17:45:45,861 Parameters: cosmological_simulation = 1 yt : [INFO ] 2012-07-26 17:45:45,861 Parameters: current_redshift = -2.5139174098e-07 yt : [INFO ] 2012-07-26 17:45:45,861 Parameters: omega_lambda = 0.721 yt : [INFO ] 2012-07-26 17:45:45,861 Parameters: omega_matter = 0.279 yt : [INFO ] 2012-07-26 17:45:45,861 Parameters: hubble_constant = 0.7 yt : [INFO ] 2012-07-26 17:45:45,865 Getting creation_time using ParticleIO yt : [INFO ] 2012-07-26 17:49:00,341 Getting field creation_time from 29485 yt : [INFO ] 2012-07-26 17:50:35,384 Getting ParticleMassMsun using ParticleIO yt : [INFO ] 2012-07-26 17:53:29,555 Getting field ParticleMassMsun from 29485 yt : [INFO ] 2012-07-26 17:53:39,376 Initializing HOP yt : [INFO ] 2012-07-26 17:53:39,447 Getting particle_position_x using ParticleIO yt : [INFO ] 2012-07-26 17:57:03,605 Getting field particle_position_x from 29485 yt : [INFO ] 2012-07-26 17:59:50,822 Getting particle_position_y using ParticleIO yt : [INFO ] 2012-07-26 18:07:23,564 Getting field particle_position_y from 29485 yt : [INFO ] 2012-07-26 18:10:24,062 Getting particle_position_z using ParticleIO yt : [INFO ] 2012-07-26 18:13:54,161 Getting field particle_position_z from 29485 Copying arrays for 44247253 particles Calling hop... 44247253 1.600e+02 nSmooth = 65 kd->nActive = 44247253 Building Tree... Finding Densities... Finding Densest Neighbors... Grouping... Merging Groups... Writing Output... However, when I try to run this same script now I get this Yt : [INFO ] 2012-07-30 17:45:26,874 Parameters: current_time = 636.417235913 yt : [INFO ] 2012-07-30 17:45:26,874 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2012-07-30 17:45:26,874 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2012-07-30 17:45:26,874 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2012-07-30 17:45:26,875 Parameters: cosmological_simulation = 1 yt : [INFO ] 2012-07-30 17:45:26,875 Parameters: current_redshift = -2.5139174098e-07 yt : [INFO ] 2012-07-30 17:45:26,875 Parameters: omega_lambda = 0.721 yt : [INFO ] 2012-07-30 17:45:26,875 Parameters: omega_matter = 0.279 yt : [INFO ] 2012-07-30 17:45:26,875 Parameters: hubble_constant = 0.7 >>> >>> yt : [INFO ] 2012-07-30 17:45:26,880 Getting the binary hierarchy yt : [INFO ] 2012-07-30 17:45:27,141 Finished with binary hierarchy reading yt : [INFO ] 2012-07-30 17:45:27,919 Getting creation_time using ParticleIO Segmentation fault: 11 Does anybody have a suggestion? PS: very nice to meet you! ^_^ -- Francia F.R.

2 1

Having trouble running yt on kraken
by Yuan Li July 29, 2012

July 29, 2012

Hi all, I have been having trouble running yt on kraken. I am using the same script that I use on trestles (where it sort of works). The issue I have on kraken is that when I submit a non-interactive job, I get this error: + aprun -n 12 ./try1.py --parallel Traceback (most recent call last): File "/var/spool/alps/2310447/try1.py", line 3, in <module> slice(imin=12, imax=47, width=20) TypeError: slice() does not take keyword arguments If I run an interactive job (./try1.py --parallel), I get this error: yuan@krakenpf2:~/scratch/Thermal09> Assertion failed in file /ptmp/ulib/mpt/nightly/5.2/051011/mpich2/src/mpid/cray/src/adi/mpid_init.c at line 115: 0 aborting job: (null) I can run a non-parallel interactive job (./try1.py) without any problem. My script looks like this: #!/lustre/scratch/proj/sw/yt/dev/bin/python from profile import * slice(imin=41, imax=47, width=20) Thanks! Yuan

3 5

analyze flash data with uniform grid
by Ji Suoqing July 28, 2012

July 28, 2012

Hi all, Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file: >>> pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min' So, does YT provides a way to deal with the uniform grid? Thanks for your care and consideration. Best wishes, Suoqing

2 6

Counting number of cells
by Devan Conroy July 27, 2012

July 27, 2012

Hi all, My name is Devan Conroy and I am working at SLAC as a summer intern in the SULI program with Jeff Oishi. I am trying to figure out how to count the number of cells in the grid when loading in data. I tried using (len(DataIn)), but got the error: object of type 'AMRRegion' has no len(). Any suggestions? Thank you, Devan Conroy -- Devan Conroy Fairfield University 2013 Mathematics Major Computer Science/French Minor

2 2

Counting the number of cells
by Devan Conroy July 26, 2012

July 26, 2012

Hi all, My name is Devan Conroy and I am working at SLAC as a summer intern in the SULI program with Jeff Oishi. I am trying to figure out how to count the number of cells in the grid when loading in data. I tried using (len(DataIn)), but got the error: object of type 'AMRRegion' has no len(). Any suggestions? Thank you, Devan Conroy -- Devan Conroy Fairfield University 2013 Mathematics Major Computer Science/French Minor

4 3