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
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.
Hi everyone,
I'm having a problem using fields that use ghost zones. The following
simple script:
http://paste.yt-project.org/show/2010/
gives this error:
http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/
I am working from the tip, but I get the same behavior from yt/2.3. In
yt/2.2, everything is working. I am working now to narrow that range down
a bit, but does anyone have an idea?
Britton
Hello everyone,
It looks like there is a bug with the csh environment setting. I am a Unix beginner so I might have done an error.
I had to make these modifications to the install script to set up yt in a csh shell OSX Lion machine :
* Disable the install of zlib. The HDF5 build failed because of some sort of version confusion.
* Force the use of gcc over the newer clang compiler by setting :
export CC=gcc
at the top of the install script. Matplotlib-1.1.0 fails to compile with the default Lion cc which is clang based.
Once installed, I had difficulties to run it. I tried to follow the Extremely Simple Data Inspection.
$ yt stats $YT_DEST/src/yt-hg/tests/DD0010/moving7_0010
BUT that is what happens :
yt : [ERROR ] 2012-03-23 11:17:08,651 Couldn't figure out output type for /Users/acoucke/yt-i386:/src/yt-hg/tests/DD0010/moving7_0010
Traceback (most recent call last):
File "/Users/acoucke/yt-i386/bin/yt", line 9, in <module>
load_entry_point('yt==2.3', 'console_scripts', 'yt')()
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 1610, in run_main
sys.exit(YT.main())
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 257, in main
return self.cmd(args)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd
retval = self.onecmd(argv)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd
return self._dispatch_cmd(handler, argv)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd
return handler(argv[0], opts, *args)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 256, in arg_iterate
func(self, subcmd, opts, arg)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 627, in do_stats
pf = _fix_pf(arg)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 44, in _fix_pf
raise IOError
IOError
Then if I type :
$ echo $YT_DEST
/Users/acoucke/yt-i386:
It seems that there is an unexpected colon here because :
$ ls /Users/acoucke/yt-i386:
ls: /Users/acoucke/yt-i386:: No such file or directory
I have to use :
setenv YT_DEST /Users/acoucke/yt-i386
to make that works.
Best,
Alice Coucke
Hi all,
I tried using macports to install yt and ran into a couple of issues.
First, there was a conflict because I had hdf5 installed to use flash and yt required hdf5-18. Secondly, after uninstalling hdf5 to see what would happen, I received these errors:
Error: Checksum (md5) mismatch for yt-2.2.tar.gz
Error: Checksum (sha1) mismatch for yt-2.2.tar.gz
Error: Checksum (rmd160) mismatch for yt-2.2.tar.gz
Error: Target org.macports.checksum returned: Unable to verify file checksums
Error: Status 1 encountered during processing.
Any ideas?
Thanks!
Erica
Hi everyone,
I get an error when executing the simple script below:
------------------------------------------------------------------------------
from yt.mods import *
output = 'DD0010/data0010'
pf = load(output)
region = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.0],[1.0,1.0,1.0])
------------------------------------------------------------------------------
I have pasted the output there:
http://paste.yt-project.org/show/awqlzVK7mAhtiIVihFfC/
I think the problem is that my simulation has only 2 particles (no gas)
and both particles are in subgrids so the root grid is empty:
------------------------------------------------------------------------------
[19:46:54] Obiwan:$ h5ls DD0010/data0010.cpu0000
Grid00000001 Group
Grid00000002 Group
Metadata Group
[19:47:09] Obiwan:$ h5ls DD0010/data0010.cpu0000/Grid00000001
[19:47:15] Obiwan:$ h5ls DD0010/data0010.cpu0000/Grid00000002
particle_index Dataset {2}
particle_mass Dataset {2}
particle_position_x Dataset {2}
particle_position_y Dataset {2}
particle_position_z Dataset {2}
particle_type Dataset {2}
particle_velocity_x Dataset {2}
particle_velocity_y Dataset {2}
particle_velocity_z Dataset {2}
------------------------------------------------------------------------------
I would really appreciate if someone could help me to fix this.
Thanks a lot,
JC
Hi everyone,
nothing dramatic but I get a warning when I start iyt:
---------------------------------------------------------------------------------------------------------------------
[19:25:12] lattice:$ iyt
/home/jcpassy/yt-x86_64/lib/python2.7/site-packages/matplotlib/__init__.py:908:
UserWarning: This call to matplotlib.use() has no effect
because the the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
if warn: warnings.warn(_use_error_msg)
Welcome to pylab, a matplotlib-based Python environment [backend: agg].
For more information, type 'help(pylab)'.
==================
| Welcome to yt! |
==================
---------------------------------------------------------------------------------------------------------------------
I did not get this problem before I updated to the most recent
changeset, and I reproduced the warning on two different Linux machines.
If anyone has an idea about how to get rid of it, please let me know.
Cheers,
JC
Hello,
I was trying to get the position and mass information for the dark matter
(and stellar) particles in an Enzo simulation. I have tried a couple of
different ways and I was curious about the units on the following method.
In this case I am presumably accessing the dark matter particles
(particle_type = 1)
*from yt.mods import **
*pf = load("DD0252/DD0252")*
*array = pf.h.find_particles_by_type(ptype=1, max_num=3)*
*print "(%.5f, %.5f, %.5f) = %f\n" %(array['particle_position_x'][0],
array['particle_position_y'][0], array['particle_position_z'][0],
array['particle_mass'][0])*
This returns *(0.01055, 0.01873, 0.00224) = 0.835448. *What are the mass
units on the *0.835448*? I don't think that they are cgs, and there
doesn't appear to be a conversion factor available via pf[' * ']. If I
continue and enter
*print pf.field_info['Density'].get_units()*
*print pf.field_info['particle_mass'].get_units()*
*
*
The 'Density' line returns *\rm{g}/\rm{cm}^3, *but the 'particle_mass'
line returns nothing. So I can't get the units from here. I can, however,
access the same particle (or at least a particle at the same location) by
using
*from yt.mods import **
*pf = load("DD0252/DD0252")*
*dd = pf.h.all_data()*
*print "(%f %f %f) = %f Msun, ptype= %i\n"%(dd["particle_position_x"][0],
dd["particle_pos ition_y"][0], dd["particle_position_z"][0],
dd["ParticleMassMsun"][0],dd["particle_type"][0])*
Which returns *(0.010554 0.018727 0.002239) = 82255596.670652 Msun, ptype=
1*
This seems to give reasonable values. Both methods should be equivalent
ways of to access the particle (both stellar and dark matter) data,
correct? So how do I get my units in solar masses when using *
pf.h.find_particles_by_type()*? Thanks for your time!
~ali
This is my first time using yt so bear with me please...
Every time I try to upload a file as FLASH, I get an error message saying that it couldn't figure out the output type. I even went back and tried using a sample file, still got the same error message.
Thanks,
Nick
Hi,
For iso-density surface I have a primitive question: how do I make certain contour level totally opaque?
I can do " tf.add_gaussian(-25.5, 0.05, [1.0, 0, 0, 1.0])"
but specifying alpha=1.0 in this example does not seem to make that level (red) totally opaque.
Thanks,
Renyue
