yt-users December 2013

yt-users@python.org

32 participants
40 discussions

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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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! 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. Thanks, d. -- Sent from my computer.

6 8

Notebook server question
by Andrew Myers 19 Apr '14

19 Apr '14

Hello yt users, I have a (perhaps naive) ssh question related to the yt notebook. I would like to run a yt notebook server on machine A. However, machine A cannot be directly accessed via ssh from the wider internet. Instead, I must first ssh into machine B, and then ssh from B to A. Machine B cannot run the notebook server itself. Does anyone know how I can configure things - perhaps by using a more complicated ssh tunnel command - so I that access a notebook server running on machine A through machine B? Thanks, Andrew

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Light Cone Projection
by Pengfei Chen 01 Mar '14

01 Mar '14

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

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YT parallel error
by John Regan 02 Jan '14

02 Jan '14

Hi All, I've started to see a strange error in a simple enough parallel computation. I can reproduce it with the script below but with some other scripts where the code is embedded it runs fine so it may be a race condition. from yt.mods import * pf = load("/wrk/regan/H2/Ctrl/DD0035/Data0035") v, c = pf.h.find_max("Density") print v, c Thanks in advance for any help! Cheers, John Error: Traceback (most recent call last): P001 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> P003 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) File "ptest.py", line 5, in <module> Traceback (most recent call last): File "ptest.py", line 5, in <module> P002 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): P004 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> P005 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> P006 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at 0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid EnzoGrid_1214 at level 18 (3, 3, 2) Traceback (most recent call last): File "ptest.py", line 5, in <module> Traceback (most recent call last): File "ptest.py", line 5, in <module> Traceback (most recent call last): File "ptest.py", line 5, in <module> File "ptest.py", line 5, in <module> v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") v, c = pf.h.find_max("Density") File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 51, in find_max mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 66, in find_max_cell_location mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels) File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 66, in find_max_cell_location File "/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py", line 66, in find_max_cell_location mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)

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TotalQuantity vs. summing manually
by Geoffrey So 23 Dec '13

23 Dec '13

Hi all, I found that using a Enzo dataset I was getting slightly different numbers when 1) using the list of dark matter particles selected by creation_time < 0.0 In [97]: sph_dm = sph['creation_time'] < 0.0 In [98]: print "%12.12e" % (sph['ParticleMassMsun'][sph_dm]).sum() 1.211311468567e+11 2) compared to summing the dark matter particles inside a 3D container with TotalQuantity In [101]: print "%12.12e" % (sph.quantities['TotalQuantity']('Dark_Matter_Density')[0]*vol/Msun) 1.188937185993e+11 I'm wondering if the field and particles are handled differently when being counted as inside or outside the 3D container? From G.S.

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Re: [yt-users] [enzo-users] Visualizing Tracer Particles
by John ZuHone 22 Dec '13

22 Dec '13

Hi Brandon, Sorry for the delayed reply! I'm cross-posting this over to the yt-users list since at this point it is really a yt problem. > Ideally, the type of plot I would like to end up with would be to use the grid/data from an Enzo data dump then overplot the tracer particles. For example: > > pf = ("TP0000/TPDD0000.h5", "r") > pf2 = load("DD0000/data0000) > > slc = SlicePlot(pf2, "z", "Density") > slc.annotate_particles(from_pf) > > Is there a function that would allow that? At the moment, we don't have an _easy_ way to do this (unless I am mistaken). But we should, frankly. There's a somewhat convoluted way to do this, and I can try to have a script that shows how to do that to you by tomorrow. Best, John

1 0

RAMSES field autodetection
by Matthew Turk 20 Dec '13

20 Dec '13

Hi all, I just pulled in Sam Geen's fix to make RAMSES fields be autodetected. If you are manually specifying fields you should not have to change anything, but it might work now if you don't try specifying them. -Matt

2 1

radmc3d exporter
by Mike Butler 19 Dec '13

19 Dec '13

Hi all, I've been trying to export some of my Enzo data to radmc3d input files and have run into an issue with the amr grid writer - it writes the amr_grid.inp file in units of kpc, rather than cgs like radmc3d wants. Is there a way to fix this short of modifying the .inp file manually afterward? Thanks a lot, Mike

2 1

Radial velocity Projections
by John Regan 19 Dec '13

19 Dec '13

Hi All, I was trying to make an OffAxis radial projection. Naively using proj = OffAxisProjectionPlot(pf, L, "RadialVelocityKMS", center='max', width=(width, 'pc'), depth=depth) fails with a message of type yt.data_objects.field_info_container.NeedsParameter: (['center']) The RadialVelocity probably isn't the field to use here and requires some manipulation to be a quantity suitable for plotting. Any suggestions on the best way forward would be much appreciated. Cheers, John

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yt-users December 2013