Mailman 3 June 2011 - yt-users

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, 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! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Clear memory?
by Elizabeth Tasker 01 Sep '11

01 Sep '11

Hi, 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. Elizabeth

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new fields in output
by Elizabeth Tasker 17 Jul '11

17 Jul '11

Hi, I've added PotentialField to the data that gets outputted. I'd like to read this into yt, but how does this work when yt won't be expecting PotentialField to be one of the data sets? Elizabeth

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Paraview and yt
by samskillman＠gmail.com 29 Jun '11

29 Jun '11

If you have trouble viewing or submitting this form, you can fill it out online: https://spreadsheets.google.com/spreadsheet/viewform?formkey=dHhhR0JOZjZFb2… 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 Nope 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 exploration 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 Other: If you are willing to brainstorm about this, what's your email address? (Leave empty for 'no') Any other comments or suggestions? Powered by Google Docs Report Abuse - Terms of Service - Additional Terms

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Santa Barbara Cluster Comparison
by Casey W. Stark 29 Jun '11

29 Jun '11

Hello yt. 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 = 0. 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?

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Problem with yt bootstrap_dev
by Sam Geen 28 Jun '11

28 Jun '11

Hi, 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: http://www-astro.physics.ox.ac.uk/~GeenS/bootstrap_devlog.txt 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. Thanks! Sam

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cannot access pressure field
by Jean-Claude Passy 27 Jun '11

27 Jun '11

Hi all, 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 http://paste.enzotools.org/show/7up5l2Q3Rc8nnLZA3VKu Has anyone ever encountered that ? Thanks a lot, JC PS: I really like the new home page of the yt website. Congrats !

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Particle Positions
by Brian Crosby 25 Jun '11

25 Jun '11

Hi everyone, 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. Thanks, Brian

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SFR analysis on 3200 cube data
by gso＠physics.ucsd.edu 24 Jun '11

24 Jun '11

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 behavior. 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 of fields 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 ParticleIO From G.S.

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Re: [yt-users] [Yt-svn] commit/yt: MatthewTurk: Fix issue with id_offset in amr_kdtree. This fixes issues with non-Enzo codes
by Sam Skillman 20 Jun '11

20 Jun '11

Hi all, 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! Sam On Mon, Jun 20, 2011 at 6:14 PM, Bitbucket <commits-noreply(a)bitbucket.org>wrote: > 1 new changeset in yt: > > http://bitbucket.org/yt_analysis/yt/changeset/e58ca7f8823a/ > 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 > -0400 > +++ b/yt/utilities/amr_kdtree/amr_kdtree.py Mon Jun 20 17:14:05 2011 > -0700 > @@ -259,6 +259,7 @@ > self.current_split_dim = 0 > > self.pf = pf > + self._id_offset = pf.h.grids[0]._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 @@ > None > > """ > - thisnode.grid = self.pf.hierarchy.grids[thisnode.grid - 1] > + thisnode.grid = self.pf.hierarchy.grids[thisnode.grid - > self._id_offset] > > 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 < > self.l_max: > # Get the children that are actually in the current > volume > - children = [child.id - 1 for child in > thisgrid.Children > + children = [child.id - self._id_offset for child > in thisgrid.Children > if na.all(child.LeftEdge < > current_node.r_corner) & > na.all(child.RightEdge > > current_node.l_corner)] > > 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. > _______________________________________________ > Yt-svn mailing list > Yt-svn(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-svn-spacepope.org >

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