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'm working on a project where I'm comparing different RAMSES simulations.
However I'm running into a problem with memory.
It seems that yt loads the whole simulation into memory even though I'm
only interested in a number of dark matter halos which I have the
It also seems like it doesn't drop the first simulation out of memory when
I'm done making the figures I want for that one.
This quickly fills up the memory.
You can find the relevant parts of my code at the pastebin at
I'm running yt version 3.3.2
What am I doing wrong?
Also, is there a way to change the axis names?
I'm making some dark matter density profiles using the
('deposit','io_density') field and this gives IO Density on the y axis, but
I just want it to say Dark matter density so my readers actually understand
what I'm talking about.
Thanks for helping
I have been running zoom simulations with with two scalar fields,
Therefore I run ramses compiled with NVAR=8.
when I load the dataset with YT, I see “metallicity”,“var6” and “var7”
var6 and 7 are for Rpgas and zoom sim (as ramses treats zoom sim itself as
a scalar variable).
When I turned on the delayed cooling, which is yet another scalar field in
I compiled and run the code with NVAR=9. However, YT still sees two
variables and I don’t
see any “var8” in the field_list. In other words I have three scalar fields
but YT is not detecting them.
Is there a way around this?
Thank you very much,
Mohammadtaher Safarzadeh, Ph.D.
We are pleased to announce the official release of Trident, a universal,
Python-based, open-source tool for post-processing hydrodynamics
simulations to produce synthetic absorption spectra and related data.
Trident's features include:
--Creates absorption-line spectra for any trajectory through a simulated
--Reproduces the spectral characteristics of common spectrographs like COS
--Operates across the ultraviolet, optical and infrared using customizable
absorption line lists
--Traces simulated physical structures directly to spectral features
--Approximates the presence of ion species absent from the simulation
--Generates column density maps for any ion
--Provides support for all major astrophysical hydrodynamical codes.
--Fully parallelizable using MPI and MPI4PY
--Built as an extension of the yt analysis code <http://yt-project.org>
For more information about its features, including a video demonstrating
its use, and links to its documentation and source code, please see our
website: http://trident-project.org .
There is an accompanying method paper that was released today on the arXiv
available at: https://arxiv.org/abs/1612.03935
Please spread word of this announcement to others who might be interested.
The Trident Developer Team--
NSF Postdoctoral Fellow
Department of Astronomy
California Institute of Technology
I am trying to do volume rendering for my data and create a time lapse
Is there a way to extract and put lower and upper bound while volume
render? This is to maintain a consistency between frames.
My code is below
Thanks in advance
import numpy as np
import matplotlib.pylab as pl
from yt.visualization.api import Streamlines
from yt.units import km
from mpl_toolkits.mplot3d import Axes3D
ms = 52728000
dims = (260,260,260)
x = x.reshape((17576000, 3), order="F")
field1 = x[:,2].reshape(dims, order="F")
field2 = x[:,1].reshape(dims, order="F")
field3 = x[:,0].reshape(dims, order="F")
data = dict(field_z = field1,
field_y = field2,
field_x = field3)
bbox = np.array([[-130, 129], [-130, 129], [-130, 129]])
pf = yt.load_uniform_grid(data, dims, km, bbox=bbox, nprocs=1)
im, sc =
sc.camera.width = (150, 'km')
# Save the zoomed in rendering
On Mon, Dec 12, 2016 at 12:54 PM, <yt-users-request(a)lists.spacepope.org>
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> Today's Topics:
> 1. ANN: yt 3.3.3 release (Cameron Hummels)
> Message: 1
> Date: Mon, 12 Dec 2016 10:34:53 -0800
> From: Cameron Hummels <chummels(a)gmail.com>
> To: "yt-dev(a)lists.spacepope.org" <yt-dev(a)lists.spacepope.org>,
> Discussion of the yt analysis package <
> Subject: [yt-users] ANN: yt 3.3.3 release
> Content-Type: text/plain; charset="utf-8"
> We are proud to announce the release of yt 3.3.3!
> Version 3.3.3 is a regularly scheduled bugfix release including fixes for a
> number of issues reported since the release of yt 3.3.2. We urge all users
> to update to the latest version.
> If your python installation is managed via conda, update following:
> $ conda update -c conda-forge yt
> If your python installation is managed via pip, update following:
> $ pip install -U yt
> Finally, if you manage your yt installation by running out of a clone of
> the yt mercurial repository, update following:
> $ yt update
> We would like to thank the following people for their contributions to this
> Nathan Goldbaum
> Cameron Hummels
> Ben Keller
> Kacper Kowalik
> Jonah Miller
> Andrew Myers
> Hsi-Yu Schive
> Britton Smith
> Matthew Turk
> John Wise
> John ZuHone
> A summary of changes in this release, along with the number of the pull
> request implementing the change follows below:
> Additional docstrings for unstructured mesh data. See PR 2403
> Speedup in clump finding. See PR 2426
> Speedup in tests. See PR 2427
> Bugfixes and docs for Tipsy data. PR 2430
> , PR 2431
> Bugfix in Ramses time calculation. PR 2433
> Bugfix in octree indexing. PR 2434
> Fixing behavior of ProfilePlots and Profiles PR 2437
> , PR 2448
> Bugfix for EPSWritter handing dicts in PlotsWindow instances. PR 2440
> Ensuring ion fields utilize dataset's metal-specific fields PR 2442
> Assure no orphaned mercurial processes PR 2449
> Adding checks for bad values in AbsorptionSpectrum PR 2450
> Bugfix in geographic handler PR 2452
> Bringing gadget data more inline with other SPH datasets PR 2456
> , PR 2436
> Bugfix when OpenMP unavailable PR 2458
> Enable light_ray_solution saved to actual LightRay class PR 2460
> Assure path uses dataset's own unit system. PR 2462
> Cameron Hummels,
> On behalf of the yt development team
> Cameron Hummels
> NSF Postdoctoral Fellow
> Department of Astronomy
> California Institute of Technology
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> End of yt-users Digest, Vol 106, Issue 7
*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
I am trying to compute vorticity for a fire snapshot. I've put down a
sphere (sp), and can access some other derived fields, but for some reason
things like vorticity give me the following error. Does anyone have
suggestions as to what I'm doing wrong?
YTArray([ 53724618.56288539, 48756921.3449135 , 46197475.78549621, ...,
53664392.60568497, 46881343.68564206, 50050673.058614 ]) cm/s
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
data_objects/data_containers.py", line 281, in __getitem__
data_objects/data_containers.py", line 1295, in get_data
data_objects/data_containers.py", line 1315, in _generate_fields
fd = self._generate_field(field)
data_objects/data_containers.py", line 318, in _generate_field
tr = self._generate_fluid_field(field)
data_objects/data_containers.py", line 336, in _generate_fluid_field
rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
data_objects/data_containers.py", line 359, in _generate_spatial_fluid
for i, chunk in enumerate(chunks):
geometry/particle_geometry_handler.py", line 179, in _chunk_spatial
g = og.retrieve_ghost_zones(ngz, , smoothed=True)
AttributeError: 'ParticleOctreeSubset' object has no attribute
This a quick (and final) reminder that the deadline for applications to
Python in Astronomy 2017 is this *Friday 9th December*. The conference
will be held on 8th - 12th May 2017 at the Lorentz Center in Leiden, the
Netherlands. Please fill out this form
The Python in Astronomy conferences aim to bring together a wide variety
of people who currently use, develop or teach people about Python
packages in the context of all forms of Astronomy. Participant selection
will be made with the goal of growing the Python in Astronomy community
and we particularly encourage requests to attend from junior astronomers
and people who are new to contributing to open source software. This
conference is neither intended to be an introduction to Python bootcamp
nor only for expert-level Python developers, but we do expect all
participants to have at least a basic familiarity with Python.
Please fill out the application and indicate the level of financial
support you will likely require in order to attend. Once the
participants have been selected, we’ll get back in touch with everyone
about their specific financial support requirements.
See http://openastronomy.org/pyastro/2017/ for more information.
Stuart Mumford, SOC Chair
I have been trying to overplot contour of [Fe/H] on top of a projected
but I get strange errors (apparently due to unit mismatch). I was wondering
if there is a way
to do this. All I need is to divide projected metal density by projected
density, save it, and plot its contour. How do you do this with YT?
Thank you very much!
Mohammadtaher Safarzadeh, Ph.D.