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!
Elizabeth Harper-Clark MA MSci
PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT
Sciences and Engineering Coordinator, Teaching Assistants' Training Program,
Astronomy office phone: +1-416-978-5759
Is there any way in yt to get a script to delete (or ignore) all the .yt
and .harray files and clear its memory? I run into errors when I'm
re-doing a plot or I've re-run the simulation and over-written the last
data set I looked at with yt. I have to exit yt, delete the above files
by hand and restart, which is a bit of a pain.
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Paraview and yt
ParaView ( http://paraview.org/ ) is a visualization and analysis package
for large-scale data, designed to operate in parallel. Over the past few
months, an effort has been underway to build a plugin to enable cross-talk
between ParaView and yt -- providing interaction and in situ visualization
to yt, and cosmology and AMR analysis to ParaView. ( http://post.ly/2Cxhb ;
http://goo.gl/1rJmh ) A plugin has been built that enables any dataset
ParaView can recognize to be processed by yt, and vice versa. We're looking
at venues in which this can be useful, and would appreciate your thoughts
on this. Letting us know a lack of interest in something is as useful as
letting us know an interest in something.
Have you heard of ParaView?
Yes, and I have used it
Yes, but I have never used it
Which of these, if any, would be interesting for you?
yt-style volume rendering with ParaView user interface
Interactive exploration in ParaView guided by yt commands
Apply yt style derived fields to datasets in ParaView
Apply astrophysics analysis to datasets in ParaView
Use ParaView as an environment for running yt-style visualization
Visualization of running simulations with both yt scripting and ParaView
Web-based user interface for both yt scripting and ParaView exploration
Advanced ParaView analysis feeding into yt
Use yt analysis capabilities for ParaView supported datasets
If you are willing to brainstorm about this, what's your email address?
(Leave empty for 'no')
Any other comments or suggestions?
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I'm trying to generate plots like the ones in Frenk 1999, the Santa Barbara
Cluster Comparison Project. I would like to reproduce the plots of
projections of the dark matter density, gas density, and temperature at z =
The first step is pretty easy - just make a plotcollection and add a
projection. The part I'm not sure about is the smoothing. I need to apply
Gaussian smoothing to this 256^3 data. I figure I do something like what is
in AMRSmoothedCoveringGridBase, but I'm really not sure.
Has anyone done anything similar with yt?
I've been trying to run the "yt bootstrap_dev" command to start fiddling
with the yt code, and have run across a problem installing lxml. I have
the same error message when trying to install lxml manually, even with
the libxml2 and libxstl packages installed. The log of what happens when
I run the command is here:
Any ideas? I've e-mailed the administrator of our compute cluster to see
if he can figure out anything on our end that's causing it.
Alternatively, if there's a good way around it that doesn't require the
bootstrap_dev command then it would be good to know.
I must be doing something silly because I get a weird error when trying
to access the 'Pressure' field of a region:
TypeError: unsupported operand type(s) for *=: 'NoneType' and 'float'
It works fine with 'Density', 'x-velocity', 'x', ... I have pasted the
complete output error here
Has anyone ever encountered that ?
Thanks a lot,
PS: I really like the new home page of the yt website. Congrats !
I'm trying to find the initial (DD0000) locations of a collection particles that form a halo at a later time. I have a list of particle IDs from that halo that I want to find the x, y, and z positions for, but I can't seem to figure out how to do for just these particles and not all the particles in the simulation. Does anyone have a suggestion on how to do this? I've been trying to use pf.h.all_data() but am stuck on getting it to only return data for this certain list of particles.
Hi everyone, I recently got a hold of some 3200 cube data and was planning
on plotting the Star Formation Rate, but the job always ends suddenly
without any error messages, and I'm wondering if anyone else have seen
This is YT devel running on Lens, The current version of the code is:
749ce1a696de (yt) tip
using 1 node I requested all 16 cores but is running this in serial to
give all the node's memory to that core (64GB).
This is data at a high redshift with only 230595 particles. But I don't
know how much extra data YT reads in to calculate the SFR (I thought it's
only the particle's ages and mass), so this may be due to an memory issue,
but usually there will be OOM messages if I hit a memory limit.
The printout from YT ends with:
yt : [INFO ] 2011-06-15 15:01:39,700 Adding Gravitating_Mass_Field to
list of fields
yt : [INFO ] 2011-06-15 15:01:39,700 Adding kphHeI to list of fields
yt : [INFO ] 2011-06-15 15:01:39,701 Adding Particle_Density to list
yt : [INFO ] 2011-06-15 15:01:39,701 Adding PhotoGamma to list of fields
yt : [INFO ] 2011-06-15 15:01:39,701 Adding kphHeII to list of fields
yt : [INFO ] 2011-06-15 15:01:39,701 Adding kphHI to list of fields
yt : [INFO ] 2011-06-15 15:01:39,701 Adding Gravitational_Potential to
list of fields
Warning: invalid value encountered in sqrt
Warning: invalid value encountered in sqrt
yt : [INFO ] 2011-06-15 15:01:39,939 Getting creation_time using
This bug that Matt squashed should fix some problems with the volume
rendering for non-Enzo codes such as FLASH, Orion, and Castro. It had to do
with the AMR kd-tree build process and grid id offsets. Anyways, if you had
been having trouble with volume rendering, you may have better luck now.
Good catch Matt!
On Mon, Jun 20, 2011 at 6:14 PM, Bitbucket <commits-noreply(a)bitbucket.org>wrote:
> 1 new changeset in yt:
> changeset: e58ca7f8823a
> branch: yt
> user: MatthewTurk
> date: 2011-06-21 02:14:05
> summary: Fix issue with id_offset in amr_kdtree. This fixes issues
> with non-Enzo codes
> finding incorrect data sizes.
> affected #: 1 file (79 bytes)
> --- a/yt/utilities/amr_kdtree/amr_kdtree.py Mon Jun 20 16:29:49 2011
> +++ b/yt/utilities/amr_kdtree/amr_kdtree.py Mon Jun 20 17:14:05 2011
> @@ -259,6 +259,7 @@
> self.current_split_dim = 0
> self.pf = pf
> + self._id_offset = pf.h.grids._id_offset
> if nprocs > len(pf.h.grids):
> print('Parallel rendering requires that the number of \n \
> grids in the dataset is greater or equal to the number of \n \
> @@ -568,7 +569,7 @@
> - thisnode.grid = self.pf.hierarchy.grids[thisnode.grid - 1]
> + thisnode.grid = self.pf.hierarchy.grids[thisnode.grid -
> dds = thisnode.grid.dds
> gle = thisnode.grid.LeftEdge
> @@ -844,7 +845,7 @@
> # Check if we have children and have not exceeded l_max
> if len(thisgrid.Children) > 0 and thisgrid.Level <
> # Get the children that are actually in the current
> - children = [child.id - 1 for child in
> + children = [child.id - self._id_offset for child
> in thisgrid.Children
> if na.all(child.LeftEdge <
> current_node.r_corner) &
> na.all(child.RightEdge >
> Repository URL: https://bitbucket.org/yt_analysis/yt/
> This is a commit notification from bitbucket.org. You are receiving
> this because you have the service enabled, addressing the recipient of
> this email.
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