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.
Sent from my computer.
I've recently been trying to use yt's inline analysis functionality with
Enzo and am having some difficultly getting it to work in parallel. I am
using the development tip of yt. In serial, everything works fine, but in
parallel, I get the following error:
It seems that the issue is that yt is not correctly identifying which grids
are available on a given processory for the EnzoDatasetInMemory object.
Does anyone have an idea of how to fix this? Has anyone else seen this?
For reference, my user_script is just this:
from yt.frontends.enzo.api import EnzoDatasetInMemory
ds = EnzoDatasetInMemory()
ad = ds.all_data()
Thanks for any help,
I'm looking to convert particle based quantities into a uniform grid based
quantity (arepo data is input). So say I have a collection of gas elements
with some density rho and x,y,z positions. I want to construct an 256^3
mesh representing the cells in a mesh.
x,y,z,rho --> cic mesh where the values at i,j,k is the smoothed density
are created by the cic algorithm
Now, generalising this more, can I have rho to be any quantity? So now say
I have star particles which similarly have x,y,z but I want to distribute
their luminosity. Again, I want to do it for say the gas velocity field as
well. Is there any general functionality for converting particle quantities
to mesh quantites in yt with the deposit all_cic functionality? I have a
basic code for just x,y,z particle data and distributing that based on
density to a cic (see below)
ad = pf.all_data()
level = int(math.log(ndim,2))
cg = pf.covering_grid(level=level, left_edge=[0,0,0],dims=[ndim,ndim,ndim])
arr = cg['deposit', 'all_cic'],
but I'm not sure what to do for the other variables. Any help is
appreciated in advance.
Does anyone know how to specify the tickmark locations on the colorbar
axis? I am able to do this on the plot axes without issue, but have not
been able to successfully do the same with the colorbar.
Attached is a pic of one of my plots using default colorbar axis ticks. I
have tried to use the following code (and many variants of it I have found
in the python/matplotlib documentation) to specify the location of the
tickmarks, but they don't place the ticks accurately. My data is
temperature plotted over the range of 300K to 5500K and I want to have
tickmarks at 300K, 800K, 3500K, and 4500K. Also attached is pic of my plot
showing an attempted custom colorbar axis.
I'm not sure if it makes a difference, but I made the colormap in
colorbar_axes = p.plots[string].cax
colorbar_axes.yaxis.set_ticks([0, 0.1, 0.8])
Thanks for the help!
Hi Michael, John, Nathan,
My strealines script can be see here:
Modifying the periodicity manually via
ds.periodicity = (True, True, True)
causes the script to appear to execute for a very long time. I have never
seen it run to completion, even for a single streamline. Perhaps I am just
If I do not directly modify the periodicity, the output I have pasted here:
Any help is appreciated.
I have a few plotting questions:
In the above plot, Colorbar range is approximately Mass=10^5-10^9. When
making a plot using ParticlePlot or ParticleProjectionPlot, can I manually
force the range on the colorbar?
2. The label on the colorbar says "Particle Mass". Instead, shouldn't it be
saying something like mass_per_pixel, since the plot is showing the total
number of particles projected along the z-axis? How can we rename the
3. Can contours of mass be added to the above plot, using annotate?
I'm trying to plot 3D streamlines from a FLASH (v.4) dataset. I've based my
streamlines script off the version presented on the yt-project.org website.
I consistently get an error about going up the ghost cells in my volume.
The error message is:
RuntimeError: Error: yt attempted to read outside the boundaries of a
> non-periodic domain along dimension 0.
> Region left edge = -3e+18 code_length, Region right edge = 4.5e+18
> Dataset left edge = 0.0 code_length, Dataset right edge = 1.2e+19
> This commonly happens when trying to compute ghost cells up to the domain
> boundary. Two possible solutions are to load a smaller region that does not
> border the edge or override the periodicity for this dataset.
My FLASH datasets have x/y/zmin = 0.0 and x/y/zmax 1.2e19 cm.
I seems like yt is trying to read outside my domain, or is bumping up
against the guardcells and I have no idea how to prevent it from doing
this. I have tried inspecting the code for an obvious solution. A very
similar error shows up when I try to make 1D profiles of the entire dataset
(dd = ds.all_data()).
is it possible that yt doesn't support volumes where the (0,0,0) coordinate
is a corner of the volume? Any easy solution to the above issue?
I have just learned about yt and I'd like to try it out. I tried to install it using the shell script but i got the following error:I am using Ubuntu 14.04 64 bit.
Installing pip******************************************** FAILURE REPORT:********************************************
bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmp4MGuKb/pip.zip/pip/__init__.py", line 15, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/wheel.py", line 35, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmp4MGuKb/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module>ImportError: cannot import name HTTPSHandler
I have also attached the last lines from the log file.
Does anyone knows how can this error be fixed?
I’ve run into an error whenever I try to execute any yt command (see yt_run_error.txt, attached because I can’t use “yt pastebin”). I’ve tried following the steps on the help page, including re-installing yt, and I still get this same error. I just installed the latest stable yt version (I can’t execute the command to give you specific numbers) on Mac OS X 10.10.4.
Does anyone know where I should start to fix this?
Astrophysics | Lyman Briggs College
Women’s & Gender Studies | College of Arts & Letters
LGBTQ and Sexuality Studies Specialization
Women in Science, President
Undergraduate Teaching Assistant
Undergraduate Research Assistant
Department of Physics and Astronomy
Michigan State University