Mailman 3 February 2012 - 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

8 14

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

problem with fields that use ghost zones
by Britton Smith 30 May '12

30 May '12

Hi everyone, I'm having a problem using fields that use ghost zones. The following simple script: http://paste.yt-project.org/show/2010/ gives this error: http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/ I am working from the tip, but I get the same behavior from yt/2.3. In yt/2.2, everything is working. I am working now to narrow that range down a bit, but does anyone have an idea? Britton

8 19

shine through images
by Elizabeth Tasker 13 Mar '12

13 Mar '12

Hi, Is there a way to create an image that, rather than being a projection, shows the maximum or minimum point of a field? Elizabeth

3 6

Kraken yt/dev import error
by Britton Smith 01 Mar '12

01 Mar '12

Hi, The yt/dev and yt/dev-local modules on Kraken are giving errors when trying to do 'from yt.mods import *'. Just doing that give the following error: http://paste.yt-project.org/show/5A6G4lAjr7UE2y1wsLNQ I get the exact same thing with both of those two modules. Thanks! Britton

3 4

Velocity dispersion profile
by Jun-Hwan Choi 29 Feb '12

29 Feb '12

Hi YT users, I would like to make a (spherical and/or cylindrical) profile of the velocity dispersion. In order to do so, I need to compute the mean velocity (BulkVelocity) for a given shell (or ring), and pass this value to newly defined velocity dispersion field, and then make a profile for the velocity dispersion field. Is there a particular way in yt to handle this? Junhwan P.S.: A few weeks ago I posted a similar question and Matt gave me a following hint. @derived_field(name = "deltaLocalCircularVelocity") def delta_LocalCircularVelocity(fi eld, data): fn, x, cv = data.get_field_parameter("local_circular_velocity") cv0 = na.interp(data[fn].ravel(), x, cv) cv0 = cv0.reshape(data[fn].shape) delta_cv = cv0 - data["LocalCircularVelocity"] return delta_cv You'll need to do something like this on the data object from which you are getting your data: sp.set_field_parameter("local_circular_velocity", (fn, prof[fn], prof["LocalCircularVelocity"])) However, it does not work for me and it is also complicate to understand and modify it. -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

6 8

Velocity dispersion profile
by Jun-Hwan Choi 29 Feb '12

29 Feb '12

Hi YT users, I would like to make a (spherical and/or cylindrical) profile of the velocity dispersion. In order to do so, I need to compute the mean velocity (BulkVelocity) for a given shell (or ring), and pass this value to newly defined velocity dispersion field, and then make a profile for the velocity dispersion field. Is there a particular way in yt to handle this? Junhwan P.S.: A few weeks ago I posted a similar question and Matt gave me a following hint. @derived_field(name = "deltaLocalCircularVelocity") def delta_LocalCircularVelocity(field, data): fn, x, cv = data.get_field_parameter("local_circular_velocity") cv0 = na.interp(data[fn].ravel(), x, cv) cv0 = cv0.reshape(data[fn].shape) delta_cv = cv0 - data["LocalCircularVelocity"] return delta_cv You'll need to do something like this on the data object from which you are getting your data: sp.set_field_parameter("local_circular_velocity", (fn, prof[fn], prof["LocalCircularVelocity"])) However, it does not work for me and it is also complicate to understand and modify it. -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

1 0

yt error on kraken
by Yuan Li 29 Feb '12

29 Feb '12

Hi all, I am trying to make a simple density projection of my data using yt on kraken. I have done this successfully many times before both on kraken and other machines, but lately I have been getting errors on kraken. I tried to run it interactively and it worked, but when I submit it as a job, I get this error: P000 yt : [INFO ] 2012-02-24 03:40:43,722 Created plot collection with default plot-center = [0.50027465 8203125, 0.500335693359375, 0.499969482421875] Traceback (most recent call last): File "/var/spool/alps/8952326/try1.py", line 8, in <module> profile("Feb2012/cluster_64/",imax=20) File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile File "/lustre/scratch/yuan/enzo_yt/cluster256_nog/yuan.py", line 23, in profile pc.add_projection("Density", 0) File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visua lization/plot_collection.py", line 758, in add_projection P000 yt : [INFO ] 2012-02-24 03:40:43,919 Starting 'Projecting level 0 / 8 ' **field_parameters) **field_parameters) File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64. egg/yt/data_objects/data_containers.py", line 1648, in __init__ File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/data_ objects/data_containers.py", line 309, in _refresh_data ....... File "/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/funcs .py", line 104, in get_memory_usage return float(os.popen('ps -o rss= -p %d' % pid).read()) / 1024 ValueError: could not convert string to float: PID Uid VmSize Stat Command 1 root 584 S init 2 root SW [migration/0] 3 root SWN [ksoftirqd/0] 4 root SW [migration/1] 5 roo It seems that something went wrong at "get_memory_usage", but I had never had this error before and an interactive job does not get this error either. Sorry the error message is quite messy... Yuan

3 4

volume rendering brightness
by Geoffrey So 28 Feb '12

28 Feb '12

Hi volume rendering experts, I was playing around with a density volume render of a tiny cube on my laptop, everything went smoothly, however, I notice a change in "overall" brightness between images when I did a rotation. I'm not sure how to explain this, but it seems that from images of different angles, sometimes the average brightness is consistent, but sometimes it suddenly drops and the image would look about half as bright, and after a couple frames it would light back up. I'm guessing this is after each image is ray casted, it gets normalized to a certain value, and that value changes depending on the angle? Is there a way to pin the brightness between images so if I make a movie it won't dim and light up as I rotate? Also I was wondering if I'm the only person to notice this? (the only other post I found about volume render brightness is about AMR cell contributions) From G.S.

3 3

Bad grid edges in particle fields
by Casey W. Stark 28 Feb '12

28 Feb '12

Hi all. This is a projection of the Dark_Matter_Density field from the initial output of a standard enzo cosmological run with just 2 cores. It looks like something is going wrong on the grid boundaries. This occurs for projections and slices, but only for gridded particle data. The gas density looks fine. It seems to occur at every grid boundary, which I tested by increasing the number of cores (so the same number of grids). I can't tell if this is an enzo or yt issue, but I figured I should ask here first in case I missed something on the yt side. Has anyone seen this before? Best, Casey P.S. What is the status of the yt image server? Should we attach or imgur images in the future?

2 3

Enzo cic_particle_* error
by Casey W. Stark 27 Feb '12

27 Feb '12

Hi all. I'm trying to make a covering grid of the full domain of an enzo (cosmological) simulation, getting the dark matter density and velocity fields. This works fine with the gas: In [1]: cg = pf.h.covering_grid(0, [0,0,0], [256,256,256], fields=["Density", "x-velocity", "y-velocity", "z-velocity"]) But then I try the DM fields: In [2]: cg = pf.h.covering_grid(0, [0,0,0], [256,256,256], fields=["Dark_Matter_Density", "cic_particle_velocity_x", "cic_particle_velocity_y", "cic_particle_velocity_z"]) ... ipython cruft ... /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, level, left_edge, dims, fields, pf, num_ghost_zones, use_pbar, **kwargs) 3342 self.domain_width = na.rint((self.pf.domain_right_edge - 3343 self.pf.domain_left_edge)/self.dds).astype('int64') -> 3344 self._refresh_data() 3345 3346 def _get_list_of_grids(self, buffer = 0.0): /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 3359 3360 def _refresh_data(self): -> 3361 AMR3DData._refresh_data(self) 3362 self['dx'] = self.dds[0] * na.ones(self.ActiveDimensions, dtype='float64') 3363 self['dy'] = self.dds[1] * na.ones(self.ActiveDimensions, dtype='float64') /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/data_objects/data_containers.pyc in _refresh_data(self) 307 """ 308 self.clear_data() --> 309 self.get_data() 310 311 def keys(self): /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 3377 try: 3378 #print "Generating", field -> 3379 self._generate_field(field) 3380 continue 3381 except NeedsOriginalGrid, ngt_exception: /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field) 3404 # First we check the validator; this might even raise! 3405 self.pf.field_info[field].check_available(self) -> 3406 self[field] = self.pf.field_info[field](self) 3407 else: # Can't find the field, try as it might 3408 raise KeyError(field) /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/data_objects/field_info_container.pyc in __call__(self, data) 314 ii = self.check_available(data) 315 original_fields = data.keys() # Copy --> 316 dd = self._function(self, data) 317 dd *= self._convert_function(data) 318 for field_name in data.keys(): /project/projectdirs/nyx/yt-installs/yt-hopper/src/yt-hg/yt/frontends/enzo/fields.pyc in _cic_particle_field(field, data) 332 particle_field = field.name[4:] 333 top = na.zeros(data.ActiveDimensions, dtype='float32') --> 334 if data.NumberOfParticles == 0: return top 335 particle_field_data = data[particle_field] * data['particle_mass'] 336 amr_utils.CICDeposit_3(data["particle_position_x"].astype(na.float64), AttributeError: 'AMRCoveringGrid' object has no attribute 'NumberOfParticles' Are you not supposed to use a covering grid with these fields or am I creating the covering grid incorrectly? I get reasonable looking plots if I slice/project cic_particle_velocity_x, so I believe it's working otherwise. Best, Casey

2 5

Hop in parallel?
by Michael Kuhlen 25 Feb '12

25 Feb '12

Is running Hop in parallel currently broken? I get way fewer halos in my catalog when I run Hop with 8 processors than with 1. Am I doing something wrong? This is my script: $ cat find_halos.py from yt.mods import * pf = load('RD0004/RedshiftOutput0004') halo_list = HaloFinder(pf, padding=0.02) halo_list.write_out('RD0004/RedshiftOutput0004_Hop.out') When I run 'python find_halos.py' I get 3716 halos, but when I run it with 'mpiexec -np 8 python find_halos.py --parallel' I only get 244. This is independent of the value of padding used. Note that the parallel catalog is a subset of the serial one. The problem occurs within HaloFinder, not during the write_out stage, since len(halo_list) = 242 on all 8 processors. Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

5 12

memory usage of HOP halo finder
by Michael Kuhlen 24 Feb '12

24 Feb '12

I have a question about memory usage of yt's HOP HaloFinder. I have a N=256^3 DM only Enzo simulation that I ran with a 512^3 root grid and fairly aggressive DM refinement with MaximumRefinementLevel=7. Although the run only has 256^3 particles, the AMR has resulted in 163,951 grids and more than 1.5e9 grid cells. Running HOP like so halo_list = HaloFinder(pf) I'm finding that yt is using around 14GB of memory during the particle reading (prior to actually starting the HOP process), which is way out of proportion to the relatively small number of particles. It seems that the memory usage is being driven by the huge number of grids rather than the number of particles. I've traced the memory increase to the calculation of the total mass, specifically to this line: total_mass = self.comm.mpi_allreduce(self._data_source["ParticleMassMsun"].sum(dtype='float64'), op='sum') and again further down: sub_mass = self._data_source["ParticleMassMsun"].sum(dtype='float64') When I specify the total mass as a keyword and comment out the sub_mass calculation (forcing sub_mass = total_mass), then the memory usage remains small. So there's something about the summing up that is leaking memory. Can anyone here shed any light on this puzzling memory hunger? Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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yt installation problem in fedora 14
by Prakash Sarkar 24 Feb '12

24 Feb '12

While Installing yt through installation script it fails while installing numpy-1.6.1 in fedora 14. the output of the script is shown below [root@shashank yt]# bash install_script.sh ======================================================================== Hi there! This is the YT installation script. We're going to download some stuff and install it to create a self-contained, isolated environment for YT to run within. Inside the installation script you can set a few variables. Here's what they're currently set to -- you can hit Ctrl-C and edit the values in the script if you aren't such a fan. INST_ZLIB = 1 so I will be installing zlib INST_BZLIB = 1 so I will be installing bzlib INST_PNG = 1 so I will be installing libpng INST_FTYPE = 1 so I will be installing freetype2 INST_SQLITE3 = 1 so I will be installing SQLite3 INST_FORTHON = 1 so I will be installing Forthon (for Halo Finding, etc) INST_HG = 1 so I will be installing Mercurial INST_ENZO = 1 so I will be checking out Enzo HDF5_DIR is not set, so I will be installing HDF5 Installation will be to /usr/local/yt/yt-x86_64 and I'll be logging the installation in /usr/local/yt/yt-x86_64/yt_install.log I think that about wraps it up. If you want to continue, hit enter. If you'd rather stop, maybe think things over, even grab a sandwich, hit Ctrl-C. ======================================================================== [hit enter] Awesome! Here we go. Using wget Downloading HDF5 Downloading hdf5-1.8.7.tar.gz from yt-project.org Downloading zlib-1.2.3.tar.bz2 from yt-project.org Downloading bzip2-1.0.5.tar.gz from yt-project.org Downloading libpng-1.2.43.tar.gz from yt-project.org Downloading freetype-2.4.4.tar.gz from yt-project.org Downloading sqlite-autoconf-3070500.tar.gz from yt-project.org Downloading Python-2.7.2.tgz from yt-project.org Downloading numpy-1.6.1.tar.gz from yt-project.org Downloading matplotlib-1.1.0.tar.gz from yt-project.org Downloading mercurial-2.0.tar.gz from yt-project.org Downloading ipython-0.10.tar.gz from yt-project.org Downloading h5py-2.0.1.tar.gz from yt-project.org Downloading Cython-0.15.1.tar.gz from yt-project.org Downloading Forthon-0.8.5.tar.gz from yt-project.org Downloading ext-3.3.2.zip from yt-project.org Downloading ext-slate-110328.zip from yt-project.org Downloading PhiloGL-1.4.2.zip from yt-project.org Installing Mercurial. Setting YT_DIR=/usr/local/yt/yt-x86_64/src/yt-hg/ Installing distribute Installing pip Installing numpy-1.6.1 (arguments: 'numpy-1.6.1') Failure. Check /usr/local/yt/yt-x86_64/yt_install.log. [root@shashank yt]# I have attached the yt_install.log file Please help thanks in advance Prakash

2 5

question about parameter file
by Ali Snedden 23 Feb '12

23 Feb '12

Hello, If load in a parameter file ( *pf = load("~/data/Enzo/DD0252/DD0252")*) and access the dictionary via *pf['Density'] *it returns a value of 2.49711e-30. I realize that if I enter *pf['mpc'] *it returns the conversion factor to go from system units to physical units. If yt keeps everything in cgs, then what conversion factor (if any) does *pf['Density'] *return? Thanks! ~ali

2 1

yt on kraken
by Nathan Goldbaum 23 Feb '12

23 Feb '12

Hi all, I'm trying to run yt on a login node on kraken. All I'm doing is invoking python from the command line and importing yt. However, python hangs on 'from yt.mods import *'. The python interpreter also takes a very long time (~ a minute or so) to start from the command line. This happens using both the yt/dev and yt/2.3 module. Anyone have any ideas? Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

8 15

pf.h.region error
by Elizabeth Tasker 22 Feb '12

22 Feb '12

Occasionally, when I try and create a region, I get this error; ValueError Traceback (most recent call last) /work/taskere/orca/yt-2-orca/src/yt-hg/scripts/iyt in <module>() 20 pc = PlotCollection(pf, center=center) 21 ---> 22 reg = pf.h.region(center, [center[0]-0.5*width, center[1]-0.5*width, center[2]-0.5*depth], [center[0]+0.5*width, center[1]+0.5*width, center[2]+0.5*dept h]) 23 24 p = pc.add_projection('Density', 2, data_source=reg) /work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/static_output.pyc in hierarchy(self) 167 raise RuntimeError("You should not instantiate StaticOutput.") 168 self._instantiated_hierarchy = self._hierarchy_class( --> 169 self, data_style=self.data_style) 170 return self._instantiated_hierarchy 171 h = hierarchy # alias /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style) 160 self.float_type = 'float64' 161 --> 162 AMRHierarchy.__init__(self, pf, data_style) 163 # sync it back 164 self.parameter_file.data_style = self.data_style /work/taskere/orca/yt-2-orca/src/yt-hg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.") /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self) 226 return line.split()[2:] 227 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 228 if self._parse_binary_hierarchy(): return 229 t1 = time.time() 230 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next|This)Level = (\d*)\s+$" /work/taskere/orca/yt-2-orca/src/yt-hg/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self) 300 except h5py.h5.H5Error: 301 return False --> 302 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 303 self.grid_left_edge[:] = f["/LeftEdges"][:] 304 self.grid_right_edge[:] = f["/RightEdges"][:] ValueError: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file: <image_object.py> What I don't understand is that it'll happen on one data set, but then the next one (or the one before) in the simulation will be totally fine. My dtdump steps are small too, so I'm confused as to why this would occur. Both "width" and "depth" are neither very small or very large compared to "centre". (In kpc, centre = 16, 22, 16 and width = 4 and depth = 1.) Elizabeth

3 4

width of projection
by Elizabeth Tasker 21 Feb '12

21 Feb '12

Hi, Is there a way to control how deep the projection is with add_projection? I'd like to project along only 1kpc of my disk, if that were possible? Elizabeth

3 3

Call for homepage viz
by Matthew Turk 15 Feb '12

15 Feb '12

Hi all, I'd like to update the viz on the yt-project.org home page. If you have some yt-created visualization you're particularly proud of, please drop me a line off-list with a reasonably sized image and appropriate credit, and if it fits the feel of the site, I'll put it up in the main rotation. A few of the existing images will get rotated out, too. Thanks, Matt

1 0

Enzo installation problem
by Khan Muhammad 15 Feb '12

15 Feb '12

Hi all, I have been trying to install enzo for a cosmological simulation project. I used the instructions given in: http://code.google.com/p/enzo/wiki/EnzoBootCamp install_script.sh ran just fine, I also got a message pointing towards the enzo path /home/md/enzo/yt-x86_64/src/enzo-hg-stable But when I actually check I see that there is no directory named "enzo-hg-stable" in the "src" directory. It would be great if someone could help me in this regard. :) Regards, Khan Muhammad Bin Asad University of Goettingen, Germany

2 3

EPS figures in matplotlib (*slightly* off topic)
by John ZuHone 12 Feb '12

12 Feb '12

Hi all, Firstly, I recognize I should probably send this to a matplotlib list so I will do that also. However, I figure this is not a bad place to ask. I'm using matplotlib to write EPS figures, just simply using fig.savefig("test.eps"). However, I'm getting banding effects in the colorbar that I'm not seeing with other formats. I've attached an example. Any suggestions? Best, John Z

4 3

FLASH hydro parameters?
by Nathan Goldbaum 12 Feb '12

12 Feb '12

Hi all, I just noticed that hydro parameters like Gamma and EOSType are not defined for flash parameter files. This makes it impossible to compute the sound speed using the definition in universal_fields.py. I've already modified the FLASH reader to ignore EOSType but I can't figure out how to gracefully figure out what Gamma is. It looks like enzo somehow automatically detects the existence of the Gamma parameter, but I don't see how the enzo reader does this. Can someone point me to the correct place? Thanks, Nathan

2 1

error extracting 2d phase info with user defined field
by Christine Simpson 10 Feb '12

10 Feb '12

Hi all, I'm having trouble with the script pasted here: http://paste.yt-project.org/show/2159/ I am trying to extract a 2d phase profile with a user defined field. I can make the phase plot in a plot collection with this field by using add_phase_sphere, but I want to write the data to a file and I am getting an error with BinnedProfile2D. The error is pasted with the script. It seems that yt accesses all the fields needed to compute the field, but the field is empty somehow? I'm kind of confused; doesn't add_phase_sphere use BinnedProfile2D to do what it does? Christine

2 2

readline and ncurses
by Elizabeth Tasker 08 Feb '12

08 Feb '12

Hi, I'm trying to install readline to work with iyt via: yt/bin/pip install readline But gcc can't find the libncurses library: gcc -pthread -shared -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ -L/home/taskere/yt/lib/ -L/home/taskere/yt/lib64/ build/temp.linux-x86_64-2.7/Modules/2.x/readline.o readline/libreadline.a readline/libhistory.a -lncurses -o build/lib.linux-x86_64-2.7/readline.so /usr/bin/ld: cannot find -lncurses which is totally on this machine: [taskere@iqaluk ~]$ locate libncurses /lib64/libncurses.so.5 /lib64/libncurses.so.5.7 /lib64/libncursesw.so.5 /lib64/libncursesw.so.5.7 /lib64 is in my LD_LIBRARY_PATH, but it looks like gcc doesn't check that. Any ideas? Elizabeth

2 4

Obtaining projection data value
by Jun-Hwan Choi 08 Feb '12

08 Feb '12

Hi all, I wonder whether that I can obtain the value that generate projection plot. I can make a projection image for my disk using add_projection in the plot_collation. I am interested in to get the projected density value and its position (and its pixel size) to perform the FFT analysis in order to find the non-axisymmertic feature such as disk-bar. Is there way to get this values using yt? Thank you in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

5 7

YT analysis questions: cylindrical profile and RMS velocity
by Jun-Hwan Choi 06 Feb '12

06 Feb '12

Hi YT users, I have two questions on the YT analysis: First, I would like to make profiles (mass, angular momentum) in the cylindrical coordinate. In other world, the profiles depend on r_xy (x-y is the cylinder plane). I define disk object and compute Profile as follow: > disk = pf.h.disk(center, [0, 0, -1], (100., 'pc'), (1., 'pc')) > profile = BinnedProfile1D(disk, 50, 'Radius', smallest_bin, largest_bin, lazy_reader=True) ,but I find that Radius is for x,y, and z distance. Can I get the cylindrical profile, if I simply make derived field for RadiusXY and replace Radius? And does there any RadiusXY kind of field exist? Second, I would like to compute the RMS velocity in my disk. However, I would like to compute RMS velocity according to local mean velocity (e.g. mean velocity inside 0.1 pc sphere center on a given position), instead of compute according to global mean velocity. Is there a routine (or way) to compute the local mean velocity in YT and compute RMS of it? I found that some papers with Enzo simulation compute the RMS velocity (such as Kitsuk et al 2007 and Wise et al 2008 although I am not sure whether they use YT or not). Thank you in advance, Junhwan Choi -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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Install yt on Eureka.alcf.anl.gov
by Min Long 06 Feb '12

06 Feb '12

Dear yter, Is there anyone who once successfully installed "stable" version of yt on Eureka.alcf.anl.gov? I've tried: $ wget http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh but it got stuck during the installation of Mercurial: Downloading HDF5 Downloading hdf5-1.8.7.tar.gz from yt-project.org Downloading zlib-1.2.3.tar.bz2 from yt-project.org Downloading bzip2-1.0.5.tar.gz from yt-project.org Downloading libpng-1.2.43.tar.gz from yt-project.org Downloading freetype-2.4.4.tar.gz from yt-project.org Downloading sqlite-autoconf-3070500.tar.gz from yt-project.org Downloading Python-2.7.2.tgz from yt-project.org Downloading numpy-1.6.1.tar.gz from yt-project.org Downloading matplotlib-1.1.0.tar.gz from yt-project.org Downloading mercurial-2.0.tar.gz from yt-project.org Downloading ipython-0.10.tar.gz from yt-project.org Downloading h5py-2.0.1.tar.gz from yt-project.org Downloading Cython-0.15.1.tar.gz from yt-project.org Downloading Forthon-0.8.5.tar.gz from yt-project.org Downloading ext-3.3.2.zip from yt-project.org Downloading ext-slate-110328.zip from yt-project.org Downloading PhiloGL-1.4.2.zip from yt-project.org Installing Mercurial. Installing mercurial-2.0 (arguments: 'mercurial-2.0') Failure. Check /home/long/yt/yt-x86_64/yt_install.log. Below I attached the "yt_install.log" and will very appreciate if you have any suggestions. Thanks, Min -- Min Long Flash Center for Computational Science Dept of Astronomy and Astrophysics University of Chicago 5747 S Ellis Ave. Jo 322 Chicago, IL 60637

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Installing on an IBM Power6
by Andrew Davis 02 Feb '12

02 Feb '12

Hi folks, I'm working on installing yt and enzo on a new (to me) cluster, which is an IBM Power6 running AIX. It's having major issues with installing stuff, from basic things like the tar command not having a -z option, to significant issues actually compiling things. I'm still workign through things, but figured I'd ask if anyone has compiled yt and enzo on an AIX machine before? If not, I'll try to submit the final install script that works, along with details of how I've had to modify various makefiles. Thanks, Andrew ************************************************************* ** Dr. Andrew J. Davis adavis(a)mpe.mpg.de ** ** TMoX Research Group ** ** MPE, Garching www.astro.yale.edu/adavis ** *************************************************************

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modify['marker']
by Elizabeth Tasker 01 Feb '12

01 Feb '12

Hi, Would it be possible to add in the option to specify a colour for the 'marker' plot modification mechanism, like that for 'particles'? Currently, yt colours all the markers differently, but if you have a lot of the same type, it would be great to keep them the same. Elizabeth

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yt workshop 2012: A success!
by Matthew Turk 01 Feb '12

01 Feb '12

Hi all, The yt workshop last week in Chicago ( http://yt-project.org/workshop2012/ ) was an enormous success. On behalf of the organizing and technical committees, I'd like to specifically thank the FLASH Center, particularly Don Lamb, Mila Kuntu, Carrie Eder, for their hospitality; the venue was outstanding and their hospitality touching. Additionally, we're very grateful to the Adler Planetarium's Doug Roberts and Mark SubbaRao for hosting us on Wednesday evening -- seeing the planetarium show as well as volume renderings made by yt users up on the dome was so much fun. The yt workshop was supported by NSF Grant 1214147. Thanks to everyone who attended -- your energy and excitement helped make it a success. Thanks also to the organizing and technical committees: Britton Smith, John ZuHone, Brian O'Shea, Jeff Oishi, Stephen Skory, Sam Skillman, and Cameron Hummels. All talks have been recorded, and you can clone a unified repository of talk slides and worked examples: hg clone https://bitbucket.org/yt_analysis/workshop2012/ A few photos have been put up online, too: http://goo.gl/g02uP As I am able to edit and upload talks, they'll appear on the yt youtube channel as well as on the yt homepage: http://www.youtube.com/ytanalysis Thanks again, and wow, what a week! Matt

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Videos of the 2012 yt workshop have been posted
by Matthew Turk 01 Feb '12

01 Feb '12

Hi all, All of the videos and slides from the yt workshop last week at the FLASH center in Chicago have been posted (in HD, no less!) These talks cover everything from starting to use yt, understanding how it views data, up to visualizing and volume rendering data, and ending with an overview of how the yt development process works and how to contribute. The list of talks with slides and links to source code repositories has been updated with links to individual talk recordings: http://yt-project.org/workshop2012/ There's also the playlist mode on the ytanalysis YouTube channel: http://www.youtube.com/playlist?list=PL65CE3A08841CA10B The unified repository (as well as all of the individual repositories) contains all of the source code for all of the examples during the week. The final two talks, including the conference wrap-up, were unfortunately recorded without audio, so they have not been posted. Thanks to everyone who participated or spoke! If you have any feedback or comments about the videos or the workshop, please feel free to contact me directly. -Matt

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