yt volume render/AMRKDtree help
by Renyue Cen
Hi,
I did some simple volume rendering with the following script:
volume2 = AMRKDTree(pf, fields=["Dark_Matter_Density"],
no_ghost=False, tree_type="domain",
le=c-0.5*WW, re=c+0.5*WW)
cam = pf.h.camera(c, L, W, N, tf, volume=volume2, no_ghost=False,
north_vector=L, steady_north=True)
cam.snapshot(fn="%s_iso-DMdensity-%3.3d.png" % (filenameTHIS, j))
I got rather strange results in that the pictures look symmetric, which I am pretty
sure can not be true.
I attach the obtained plot.
Note that I am using KD tree and using 32 cores.
Your help at your earliest convenience is appreciated.
Best,
Renyue
5 years, 4 months
eps_writer question
by Jun-Hwan Choi
Hi yt user,
This question mostly goes to John Wise (maybe not).
I try to use eps_writer module in the yt to generate a high-quality .eps
figure.
I attempt to make four phase plot (rho-T) from four different times (i.e.
four different data output)
But, I got the following error message:
File "Phase_eps.py", line 39, in <module>
ep = eps.multiplot_yt(2,2,pc)
File
"/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/visualization/eps_writer.py",
line 1010, in multiplot_yt
"x ncol(%d)." % (len(plot_col.plots), nrow, ncol)
TypeError: not all arguments converted during string formatting
It look that there is a problem when I over write PlotCollection object for
four different data output (or maybe not).
How can I solve the issue?
I paste my script at http://paste.yt-project.org/show/3112/ .
In addition, I would like to get more information/document about eps_writer.
For example, I would like to write the time of four phase respectively.
Where can I get the information about it?
Thank you in advance,
Junhwan
--
--------------------------------------------------------------
Jun-Hwan Choi, Ph.D.
Department of Physics and Astronomy, University of Kentucky
Tel: (859) 897-6737 Fax: (859) 323-2846
Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi
--------------------------------------------------------------
5 years, 11 months
errno.h
by Mark Kremenetsky
Guys,
I am using a script recommended on ENZO boot-camp page
$ bash install_script.sh
in order to set up all libraries needed for enzo compilation.
Everything is going good and well until I got a following error:
gcc -fPIC -c bzip2.c
In file included from /usr/include/errno.h:36,
from bzip2.c:55:
/usr/include/bits/errno.h:25:26: error: linux/errno.h: No such file or directory
make: *** [bzip2.o] Error 1
I checked and certainly I don't have such thing as /usr/include/linux/errno.h
Any advice ?
Thanks,
Mark
5 years, 11 months
Improved support for isolated boundary conditions
by Nathan Goldbaum
Hi all,
As you may know, yt was originally written to handle outputs from cosmological simulations produced by the Enzo code. Due to this pedigree, yt assumes internally in a number of places that the simulation box has periodic boundary conditions.
In the last couple of years, we've been working on improving support for both non-cosmological simulations and datasets produced by codes besides Enzo. This effort has come a long way, but until recently the nature of the boundary conditions has received relatively little development attention. However, as yt becomes commonly used by people outside of the enzo community, the lack of proper support for general periodic or non-periodic boundary conditions is starting to be felt. A particularly nasty case is the radius field, which in the current codebase assumes periodic boundary conditions, producing incorrect results when someone tries to profile a field versus radius in a simulation that assumed some sort of isolated boundary conditions.
Recently, Matt Turk came up with a summary of our strategy for improving support general boundary conditions, summarized in YTEP-0006: https://bitbucket.org/yt_analysis/ytep/src/tip/source/YTEPs/YTEP-0006.rst
The main take-away points are that each of the code frontends will need to define a periodicity attribute that hangs off of each of the StaticOutput class. This way, one can check the periodicity of a parameter file by doing something like:
>>> pf = load(filename)
>>> print pf.periodicity
(True, True, True)
Here, pf.periodicity is a tuple, from which one can read off that the simulation is periodic along all three directions. We intend to fully support simulations that have arbitrary mixed periodic and isolated boundary conditions. We will then use the new periodicity attribute to modify the places in the code where we need to worry about boundary conditions.
I've gone ahead and added the periodicity attribute for most of the code frontends. I've also enhanced the Radius and ParticleRadius fields to properly handle the periodicity. These modifications are included in Pull Request #410: https://bitbucket.org/yt_analysis/yt/pull-request/410/first-pass-at-ytep-...
At this point, the PR is more or less ready to go. However, since this is a somewhat invasive change that might temporarily break code frontends if there is a bug somewhere, it would be great if some of you would check to make sure that everything works correctly for your datasets. In particular, I need help figuring out how to set the periodicity for the orion, chombo (i.e. pluto and orion2), maestro, and nyx frontends. It would also be great to hear from users who commonly work with 1D or 2D data, as these sorts of datasets have caused trouble in the past.
I'll also note that if you're interested in helping out with yt development, finishing up YTEP-0006 would be an excellent starter project. If you run into trouble, please send a message to the yt-users or yt-dev mailing lists or, if you're looking for low-latency discussion, stop by on our IRC channel (#yt on freenode, or use the web chat interface: http://yt-project.org/irc.html).
Cheers,
Nathan Goldbaum
5 years, 11 months
yt + x11 on a mac
by Mark Krumholz
Hi yt Users,
I'm trying to figure out how to get yt working using an x11-based backend on my mac, so that I can forward python windows. For my non-yt python install, which is handled via macports, the trick (gleaned from http://www.astrobetter.com/remote-display-in-python-ask-astrobetter/) was to use macports to recompile the tk package so that it uses x11 rather than quartz, via the command
sudo port upgrade --enforce-variants tk -quartz +x11
This works fine. However, it is not clear to me how to force a similar change in the sandbox python install used by yt. Nor have I been able to get any other x11-based backend to work with yt's python install on my mac. The packages required for the gtk or wx backends refuse to install via pip install, and the Qt backend fails to load with the cryptic error "no module named sip".
I'd appreciate any suggestions.
--
Mark Krumholz
5 years, 11 months
need to plot a box with borders
by henry wasker
Hello,
I am new to yt and I am interesting in plotting a volume rendering with
output file from enzo cosmology simulation.
For the time being, I get to plot a box ; here's the result :
http://imgur.com/dPwSQEh
I would like now to plot borders of this box too like on this image :
http://imgur.com/bJ25I0l
Here's the yt script I use :
------------------------------------------------------------------------------------------------------------
from yt.mods import *
from yt.utilities.amr_kdtree.api import AMRKDTree
from time import time
import matplotlib.colorbar as cb
# Load up your dataset
num='70'
pf = load('RD00'+num+'/RedshiftOutput00'+num)
c = [0.5]*3 # Center
L = [1.0,1.0,1.0] # Viewpoint
W = na.sqrt(3) # Width
N = 768 # Pixels (512^2)
up = [0.,0.,1.]
# Get density min, max
# These might take a long time, so I'd suggest hand-coding mi, ma so
# that you don't have to find the maxima and minima each time you
# test. Note that mi, ma, should be a log value since we are
# rendering the log of density.
mi, ma = pf.h.all_data().quantities['Extrema']('Density')[0]
mi, ma = na.log10(mi), na.log10(ma)
print mi, ma
#mi, ma = -31.0, -26.0
# Construct transfer function, pad the TF space by a bit so that
# gaussians sampling the data range don't hit the edge.
tf = ColorTransferFunction((mi-10, ma+10), nbins=1024)
# Sample transfer function with 20 gaussians. Use col_bounds keyword
# to restrict color mapping to true data range.
tf.add_layers(20, w=0.001,
col_bounds=(mi,ma),colormap='jet')
# Create the camera object
cam = pf.h.camera(c, L, W, (N,N), transfer_function=tf, north_vector=up,
no_ghost=True)
cam.snapshot("volume_rendered%s.png" % num, clip_ratio=8.0)
------------------------------------------------------------------------------------------------------------
Is there an option for 'camera" or "snapshot" which allows to add the
borders for this box ?
Any help would be really appreciated.
5 years, 12 months
Define a field of spacial derivatives for FLASH4 2D cylindrical uniform grid
by Ji Suoqing
Hi,
I would like to compute some spacial derivatives for FLASH4 2D cylindrical uniform grid datafile with YT.
For simplicity, I tried the example given in YT docs, although I know the derivative form is only valid for Cartesian, and this is just for code test purposes. My script are:
@derived_field(name='DivV') # I do not use ValidateSpatial… ghost_zone… because the ghost cells are not stored in FLSAH check point file
def DivV(field, data):
sl_left = slice(None,-2)
sl_right = slice(2,None)
div_fac = 2.0
ds = div_fac * data['dx'].flat[0]
f = data["velx"][sl_right,1:-1]/ds
f -= data["vely"][sl_left ,1:-1]/ds
ds = div_fac * data['dy'].flat[0]
f += data["velx"][1:-1,sl_right]/ds
f -= data["vely"][1:-1,sl_left]/ds
new_field = na.zeros(data["velx"].shape, dtype='float64')
new_field[1:-1,1:-1] = f
return new_field
Then, if I add:
pf = load('relax_hdf5_chk_0001')
pf.h.find_max('DivV')
The script works, but if I use:
dd = pf.h.all_data()
print dd['DivV'].sum()
and it will give error:
yt : [INFO ] 2013-01-23 21:17:01,551 Getting field dx from 256
yt : [INFO ] 2013-01-23 21:17:01,625 Getting field velx from 256
Traceback (most recent call last):
File "test.py", line 28, in <module>
print dd['DivV'].sum()
File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 330, in __getitem__
self.get_data(key)
File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 2607, in get_data
if self._generate_field(field):
File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/data_containers.py", line 360, in _generate_field
self[field] = self.pf.field_info[field](self)
File "/usr/local/yt-i386/src/yt-hg/yt/data_objects/field_info_container.py", line 378, in __call__
dd = self._function(self, data)
File "test.py", line 11, in DivV
f = data["velx"][sl_right,1:-1]/ds
IndexError: too many indices
Nor can I make slice plot for this field.
I would appreciate your suggestions for this issue.
Best wishes,
Suoqing
5 years, 12 months
ProjectionTransferFunction()
by Michael Kuhlen
Hi all
I'm not having any success with off-axis projections using the
pf.h.camera() with AMRKDTree and ProjectionTransferFunction().
cam.snapshot() returns an all-zeros array, even in situations where
ColorTransferFunction() produces great images.
This script (based on the first part of amrkdtree_downsampling.py)
demonstrates the problem: http://paste.yt-project.org/show/3072/
Any ideas what's going wrong? Maybe something to do with preventing the
log'ing of the field, which I attempted to do with
"pf.field_info['Density'].take_log=False"?
Thanks for you help!
Mike
--
*********************************************************************
* *
* Dr. Michael Kuhlen Theoretical Astrophysics Center *
* email: mqk(a)astro.berkeley.edu UC Berkeley *
* cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 *
* skype username: mikekuhlen Berkeley, CA 94720 *
* *
*********************************************************************
5 years, 12 months
new yt feature: yt update --all
by Britton Smith
Greetings everyone,
I would like to announce a new feature that has been added to the
development version of yt. For some time now, one could update their yt
installation by issuing the command "yt update". However, updating yt's
dependencies has required one to rerun the install script manually. Now
you can simply do:
yt update --all
and yt will rerun the install script for you with the proper installation
path.
Additionally, when you type "yt instinfo", yt will print the last time the
dependencies were updated.
In order to have this feature, you will need to be using the development
version of yt, and will have to first run "yt update" once.
Note: only use this if you originally used the install script for your
installation. Custom installations, such as those using the system python,
should still be updated manually.
We hope this will simplify the process of keeping one's installation up to
date. As always, please let us know if you encounter any unexpected
behavior with this.
Team yt
5 years, 12 months
yt.utilities.amr_utils
by Renyue Cen
Hi,
I am trying to compute gridded density of some subset of particles.
So I tried to import some modules first in the python script as follows:
from yt.data_objects.field_info_container import \
FieldInfoContainer, \
NullFunc, \
TranslationFunc, \
FieldInfo, \
ValidateParameter, \
ValidateDataField, \
ValidateProperty, \
ValidateSpatial, \
ValidateGridType
import yt.data_objects.universal_fields
from yt.utilities.physical_constants import mh
from yt.funcs import *
import yt.utilities.amr_utils as amr_utils
But I got this error message:
Traceback (most recent call last):
File "SFR.py", line 28, in <module>
import yt.utilities.amr_utils as amr_utils
ImportError: No module named amr_utils
Am I doing something wrong?
Thanks,
Renyue
5 years, 12 months
