p.modify["point"]
by Elizabeth Tasker
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
6 years, 5 months
Crashing PDFs and Login screen after Yt installation
by Héctor Aceves Campos
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
6 years, 7 months
error in light_ray periodic ray creation
by Joshua Eric Moloney
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.
6 years, 7 months
YT dies after second attempt to run script
by Francia F. Riesco
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.
6 years, 7 months
Having trouble running yt on kraken
by Yuan Li
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
6 years, 8 months
analyze flash data with uniform grid
by Ji Suoqing
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
6 years, 8 months
Counting number of cells
by Devan Conroy
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
6 years, 8 months
Counting the number of cells
by Devan Conroy
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
6 years, 8 months
Plot collections on non-square slices
by Mark Krumholz
Hi YT Users,
I have a computational domain that is not cubical, and I want to plot
a slice through it that is rectangular rather than square. I can make
a slice with PlotCollection, but when I write the image to a file
using save, I find that it has been padded with whitesapce on the left
and right to make it square. I would like the image to have the same
aspect ratio as the data, not be white-padded. Is there a way to do
this with PlotCollection, or should I just give up and use
FixedResolutionBuffer to extract the data and construct the image
myself?
Thanks.
--
Mark Krumholz
krumholz(a)ucolick.org
6 years, 8 months
Slices from Flash data
by Alice Coucke
Good morning,
I am currently working on visualization from Flash Data. I am using Slices of the internal energy along the x-axis. I have a weird line at the top of the slice (see attachment). That looks like a periodic boundary conditions problem.
The thing is, I don't know whether it is a problem in my code or that I am using yt wrong. I feel like is a plot problem, I looked at the data with another visualization tool (Visit) and it doesn't seem to have this line ...
Thank you for your help and have a great day,
Alice
[cid:AC8237E3-8ABE-47F3-9F64-9E5B7F633DCC@internal.amnh.org]
6 years, 8 months
