I was trying to run the halo finder in parallel this morning after
updating YT and the particle IO stopped working. It was working last
friday with YT version 1578. I have since reverted back to 1578 and made
sure that it works. So the update made sometime in between caused this
error. Can someone else please confirm the error?
From
G.S.
We're proud to announce the release of yt version 1.6, a point release
of the analysis and visualization toolkit for Adaptive Mesh Refinement
data. This release contains many small improvements to the codebase,
as well as several large improvements. Most prominently, it features a
completely redesigned, massively parallel implementation of the halo
finding algorithm HOP, as well as attendant improvements to particle
data IO and parallel communication. Additionally, the underlying data
structures for hierarchical datasets have been rewritten for speed and
clarity, enabling the future addition of new multi-resolution data
formats to be easily added.
yt features native support for Enzo
(http://lca.ucsd.edu/projects/enzo) data, providing a natural and
intuitive way to address physical regions in space as well as
processed data.
Some of the changes since yt-1.5 (released on November 3, 2009) include:
* (New) Parallel HOP ( http://arxiv.org/abs/1001.3411 )
* (Beta!) Software ray casting and volume rendering (Sam Skillman has
a gallery here:
http://casa.colorado.edu/~skillman/simulation_gallery/simulation_gallery.ht…
)
* Rewritten, faster and better contouring engine for clump identification
* Spectral Energy Distribution calculation for stellar populations
* Optimized data structures such as the hierarchy
* Star particle analysis routines
* Halo mass function routines
* Completely rewritten, massively faster and more memory efficient Particle IO
* Fixes for plots, including normalized phase plots
* Better collective communication in parallel routines
* Consolidation of optimized C routines into amr_utils
* Many bug fixes and minor optimizations
* Installation instructions, documentation, recipes, mailing list
info and assorted other items can be found at the website,
http://yt.enzotools.org/ along with an annotated changelog at
http://yt.enzotools.org/doc/changelog.html .
yt is a Free and Open Source project, and we invite you to get
involved. For more information, join the yt-dev mailing list, or see
the hacking guidelines on the Wiki:
http://yt.enzotools.org/wiki/HackingGuidelines .
Sincerely,
The yt development team:
Matthew Turk
Stephen Skory
Britton Smith
Jeff Oishi
Sam Skillman
Devin Silvia
John Wise
David Collins
Hi Libby,
I've attached a quick shot at what you wanted. Please read through it and let me know if it does what you want and if I did something wrong (likely!), or if you don't understand why I did something.
There is one subtlety that I should point out. It is statistically improper to consider a pair of points farther apart that 1/2 the shortest dimension of the box. Consider your starting point at the center of the box. If you look epsilon less than 1/2 of the shorted dimension of the box away towards the closest face, you're looking at a point near the periodic edge of the box. If you then look epsilon more than 1/2 the box edge past that previous point, you've reflected around the periodic boundary, and your *actual* distance is epsilon less than 1/2 because of the period. So, any distances greater than 1/2 the minimum box edge are statistically improper.
I've also attached a plot which looks encouraging, I think! It would look smoother with more random points (bigger 'loopsize')
I hope this helps! If it does, please let me know and I'll make it prettier and such and stick it into the yt codebase with documentation.
_______________________________________________________
sskory(a)physics.ucsd.edu o__ Stephen Skory
http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
________________________________(_)_\(_)_______________
Dear fellow YT-users,
I would like to analyse turbulence in ENZO by comparing velocity difference
at different scales. To do this I would like to calculate the velocity
difference between each cell and cells a set distance bracket away, square,
sum over all cells, and square root to get a turbulent velocity at that
length scale. I would the like to do that for many different length scales
to form a graph of turbulent velocity against length scale.
Has anyone ever done anything like this with YT or have a suggestion for the
easiest way to go about doing this? (with either SH = 1 or 0)
Many thanks,
Libby
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Astrophysics, UofT
www.astro.utoronto.ca/~h-clark
h-clark(a)cita.utoronto.ca
AIM: edphc1
MSN: edphc1(a)hotmail.com
Skype: eharperclark
Office phone: 416-978-5759
Hi guys,
I want to use the nparticles rather than the particles callback so that I
only plot PARTICLE_TYPE_MUST_REFINE (4). I am trying (full script at end of
email):
p.modify["nparticles"](1.0,p_
size=4.0, col='g', ptype='4')
I tried with and without ' around the 4 but both times I get:
Traceback (most recent call last):
File "Density_movie.py", line 29, in <module>
p.modify["nparticles"](1.0,p_size=4.0, col='g', ptype='4')
File
"/scratch/YT-x86_64/lib/python2.5/site-packages/yt-1.6dev-py2.5-linux-x86_64.egg/yt/raven/PlotTypes.py",
line 52, in __getitem__
raise KeyError(item)
KeyError: 'nparticles'
Any idea what I am doing wrong?
Many thanks,
Libby
Density_movie.py:
from yt.mods import *
import pylab
import sys
import cmath
import matplotlib.ticker
#
# Code to make the frames for a movie showing density projection
#
rho_min = 1.e-22
rho_max = 1.e-32
frame_template = "aaWoC/%s/densityframe_%01i_%04i"
for n in range(12,200): # make density projection with particles on
#pf = lagos.EnzoStaticOutput("WOCbin/%s/DD%04i/data%04i" %
(sys.argv[-1],n, n))
pf = lagos.EnzoStaticOutput("WOCbin2/%s/DD%04i/data%04i" %
(sys.argv[-1],n, n))
#print pf.h.field_list
pc = raven.PlotCollection(pf, center=(0.5,0.5,0.5))
time = pf["InitialTime"]*pf["years"]
for ax in range(1):
p = pc.add_projection("Density", ax, weight_field="Density")
#pc.set_zlim(rho_min, rho_max)
p.set_cmap('hot')
sp = pf.h.all_data()
colours = sp["ParticleMassMsun"]
if sp["ParticleMassMsun"].size > 0:
p.modify["nparticles"](1.0,p_size=4.0, col='g', ptype='4')
p.modify["text"]((0.1,0.9),"time = %i years" %
(pf["InitialTime"]*pf["years"]), text_args = {'color':'w'})
#p.set_width(0.1, 'pc')
pc.save(frame_template % (sys.argv[-1],ax,n), override=True)
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Astrophysics, UofT
www.astro.utoronto.ca/~h-clark
h-clark(a)cita.utoronto.ca
AIM: edphc1
MSN: edphc1(a)hotmail.com
Skype: eharperclark
Office phone: 416-978-5759
