Mailman 3 May 2014 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman Aug. 15, 2022

Aug. 15, 2022

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

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 April 11, 2020

April 11, 2020

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.

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Generic UniGrid Data
by Junhwan Choi (최준환) June 16, 2014

June 16, 2014

Dear yt user, I try to use Generic UnicGrid Data (256^3 gas density cube + position of particle that is subset of a huge simulation). It is preliminary work, but I still have some questions. 1. In order to set density unit as cgs, I made following script: ...... data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ..... Then, I got the following error message: Traceback (most recent call last): File "cutout2.py", line 62, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 461, in load_uniform_grid psize = get_psize(np.array(data[key].shape), nprocs) AttributeError: 'tuple' object has no attribute 'shape' Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = dict(density = map)" and it work. If this is the case, how can I define the density unit and show it when I make Slice/Projection? In addition, I would like to know how I can set the unit in Generic UnicGrid Data in general? The length unit can be provide to script in load_uniform_grid(... 3.086e24 ....) but I do not know how to set other units. 2. When I add particle information as follow: ..... npart = 100000 # number of particles data = dict(density = map, number_of_particles = npart, particle_position_x = posx, particle_position_y = posy, particle_position_z = posz) bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) ... I got the following error message: Traceback (most recent call last): File "cutout.py", line 107, in <module> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 519, in load_uniform_grid assign_particle_data(spf, pdata) File "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", line 371, in assign_particle_data pdata.pop("number_of_particles") KeyError: 'number_of_particles' So, I change "number_of_particles = npart," --> "number_of_particles = 100000," and it works. How could it happen? 3. Can I do halo finder (hop/fof) using the above particle data? Or, what information do I need to provide to do grouping? In this case, how can I set the units and linking length? 4. Can I make particle distribution to particle data like data['Dark_Matter_position_x']? This process will allow me additional analysis such as profile and obtaining total value. I may ask too many for new tool, but it will help a lot to use yt for general data set. Thank you, Junhwan

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PerspectiveCamera question
by Michael Zingale June 4, 2014

June 4, 2014

I'd like to try using the PerspectiveCamera instead of the normal orthographic Camera. My script renders fine with Camera(), but I thought that I should be able to just change Camera() to PerspectiveCamera() and it should render with the perspective. Instead, I get an empty rendering -- is there something else one needs to do to use the PerspectiveCamera rather than just changing the class name but otherwise keeping the argument list the same? Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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projection of max level along line of sight?
by Brian O'Shea May 30, 2014

May 30, 2014

Hi folks, I'm trying to make a projection of an Enzo dataset using yt-3, showing the maximum level along the line of sight. This command: ProjectionPlot(pf,"x","grid_level",weight_field=None,data_source=reg,width=(0.25,'unitary')).save() definitely seems to make projections of grid levels, but I'm not convinced that it is the maximum level along the LOS. Is there a better way to do this? Thanks! --Brian

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Plot Background
by Andrew James Emerick May 30, 2014

May 30, 2014

Is there a way to set the background color for projection plots? I'd like to set it to be black instead of white, which I assume is the default. Thanks, Andrew E. -- Graduate Student Columbia University Department of Astronomy

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Re: [yt-users] Generic UniGrid Data
by John ZuHone May 28, 2014

May 28, 2014

Hi Junhwan, I'm having trouble finding anything wrong with your script, actually. I would recommend changing this: ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4) to this: ds = load_uniform_grid(data, data['density'][0].shape, length_unit=(1.0,"Mpc"), bbox=bbox, nprocs=4) but I doubt that would make much of a difference. Have you inspected what data["density"][0] is in your script, and what npart is? I set up an example on my own with random particle data, and I set the number_of_particles dictionary key to a variable npart that was set previously, and saw no issues there. If it's possible to post the file that this script works with somewhere, that would enable me to reproduce the buggy behavior. Best, John Z On May 22, 2014, at 6:19 PM, John ZuHone <jzuhone(a)gmail.com> wrote: > Hi Junhwan, > > Sorry, I kind of got lost in some other things--I'll have a look at your script tonight and get back to you. > > Best, > > > On May 22, 2014, at 6:17 PM, Junhwan Choi (최준환) <choi.junhwan(a)gmail.com> wrote: > >> Hi, >> >> I have read more about the "generic array data" from the document in yt webpage. >> I found that the the how to set data dict and call "load_uniform_grid" >> by yt-2.6 and yt-3.0 are quite different, and it looks that yt-3.0 >> supports better unit treatment. >> >> However, my yt-3.0 looks use old formate for load_uniform_grid as follow: >> ..... >> def load_uniform_grid(data, domain_dimensions, sim_unit_to_cm, bbox=None, >> nprocs=1, sim_time=0.0, periodicity=(True, True, True)): >> .... >> >> This load_uniform_grid arguments are different with those presented in >> yt-3.0 document. >> I think this is part of the reason that I have a difficulty. >> >> How can I use that load_uniform_grid for the version shown in yt-3.0 document? >> >> Thank you, >> Junhwan >> >> On Fri, May 16, 2014 at 11:28 AM, Junhwan Choi (최준환) >> <choi.junhwan(a)gmail.com> wrote: >>> Here, I post my script in http://paste.yt-project.org/show/4641 >>> >>> Thank you, >>> Junhwan >>> >>> On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone(a)gmail.com> wrote: >>>> Junhwan, >>>> >>>> Can you post your script somewhere? It might be easier to debug it that way. >>>> >>>> Best, >>>> >>>> John Z >>>> >>>> On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan(a)gmail.com> wrote: >>>> >>>> Hi Nathan, >>>> >>>> I think that I am using the yt 3.0 unless there is stabke yt 3.0 version. >>>> >>>> Junhwan >>>> >>>> >>>> >>>> On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: >>>> >>>> Hi Junhwan, >>>> >>>> Just to clarify (since the answers you receive will be different depending >>>> on your response) is this for the in-development yt 3.0 release or the >>>> current stable release? >>>> >>>> Nathan >>>> >>>> On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan(a)gmail.com> wrote: >>>>> >>>>> Dear yt user, >>>>> >>>>> I try to use Generic UnicGrid Data (256^3 gas density cube + position >>>>> of particle that is subset of a huge simulation). >>>>> It is preliminary work, but I still have some questions. >>>>> >>>>> 1. In order to set density unit as cgs, I made following script: >>>>> ...... >>>>> data = dict(density = (map, "g/cm**3")) #map is 256^3 density data array >>>>> bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) >>>>> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, >>>>> bbox=bbox, nprocs=4) >>>>> ..... >>>>> >>>>> Then, I got the following error message: >>>>> Traceback (most recent call last): >>>>> File "cutout2.py", line 62, in <module> >>>>> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, >>>>> bbox=bbox, nprocs=4) >>>>> File >>>>> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", >>>>> line 461, in load_uniform_grid >>>>> psize = get_psize(np.array(data[key].shape), nprocs) >>>>> AttributeError: 'tuple' object has no attribute 'shape' >>>>> >>>>> Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data = >>>>> dict(density = map)" and it work. >>>>> If this is the case, how can I define the density unit and show it >>>>> when I make Slice/Projection? >>>>> In addition, I would like to know how I can set the unit in Generic >>>>> UnicGrid Data in general? >>>>> The length unit can be provide to script in load_uniform_grid(... >>>>> 3.086e24 ....) but I do not know how to set other units. >>>>> >>>>> 2. When I add particle information as follow: >>>>> ..... >>>>> npart = 100000 # number of particles >>>>> data = dict(density = map, >>>>> number_of_particles = npart, >>>>> particle_position_x = posx, >>>>> particle_position_y = posy, >>>>> particle_position_z = posz) >>>>> bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]]) >>>>> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, >>>>> bbox=bbox, nprocs=4) >>>>> ... >>>>> >>>>> I got the following error message: >>>>> Traceback (most recent call last): >>>>> File "cutout.py", line 107, in <module> >>>>> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, >>>>> bbox=bbox, nprocs=4) >>>>> File >>>>> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", >>>>> line 519, in load_uniform_grid >>>>> assign_particle_data(spf, pdata) >>>>> File >>>>> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py", >>>>> line 371, in assign_particle_data >>>>> pdata.pop("number_of_particles") >>>>> KeyError: 'number_of_particles' >>>>> >>>>> So, I change "number_of_particles = npart," --> "number_of_particles = >>>>> 100000," and it works. >>>>> How could it happen? >>>>> >>>>> 3. Can I do halo finder (hop/fof) using the above particle data? >>>>> Or, what information do I need to provide to do grouping? >>>>> In this case, how can I set the units and linking length? >>>>> >>>>> 4. Can I make particle distribution to particle data like >>>>> data['Dark_Matter_position_x']? >>>>> This process will allow me additional analysis such as profile and >>>>> obtaining total value. >>>>> >>>>> I may ask too many for new tool, but it will help a lot to use yt for >>>>> general data set. >>>>> >>>>> Thank you, >>>>> Junhwan >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users(a)lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >

2 3

how to find virial radius from enzo output
by Reju Sam John May 27, 2014

May 27, 2014

Dear All, How to find virial radius from enzo output. From the following page http://yt-project.org/docs/2.6/reference/api/generated/yt.analysis_modules.… I came to know that there is a function called virial_radius(). But how to use it? In the provided example >>> vr = halos[0].virial_radius() what is ' halos[0] ' ? Thank You -- Reju Sam John

2 2

camera question
by Stephanie Tonnesen May 24, 2014

May 24, 2014

Hi all, I am trying to make a nice volume rendering, and am having some trouble. My camera commands are: tf = ColorTransferFunction((-29,-24)) tf.add_layers(8,w=0.1,colormap="Hue Sat Value 2") tf.sample_colormap(-26.5,w=0.02,colormap="Hue Sat Value 2") cam = pf.h.camera([0.0,2.,1.8],[0.0,-1.0,-0.2],4.0,512,tf) cam.show() I will attach the image, also (v11). First, when I use add_layers, can I get yt to print out WHERE the layers are? Second, but related, when I just use add_layers I only see the higher density gas. I have to add sample_colormap to see lower density gas (the blue stuff). Compare v11 to v6 to see what I am talking about. Thanks! Stephanie

3 4

question about transfer function colorbar
by Michael Zingale May 23, 2014

May 23, 2014

I'm trying to show the transfer function on a volume render. Plotting a velocity component, I set the transfer function with 4 Gaussians all with the same width. The range of the transfer function is -1.e7 to 1.e7, but for some reason, when output, the upper label in the colorbar is not 1.e7 but a bit lower (9.92e6). I am not sure where the code is that draws this, and I am confused why it is not setting the tick at 1.e7. It gets the bottom tick right. Here's an image: http://bender.astro.sunysb.edu/random/test_0000.png and the script: http://bender.astro.sunysb.edu/random/vol_rotate.py any pointers are appreciated. Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

3 7

physical quantities
by Desika Narayanan May 22, 2014

May 22, 2014

Hi yt, I have a pretty simple question that I ought to know the answer to - how do I extract the actual values in the field_list or derived_field_list of a ds? For example, I have a field: ('PartType0', 'Coordinates'), but printing something like pf[('PartType0','Coordinates')] doesn't return the list of particle type 0 coordinates (or anything for that matter). Do I have to access this through a pf.all_data() command somehow? Thanks -desika

3 2

Plot of domain subset
by Juan Camilo Ibanez Mejia May 22, 2014

May 22, 2014

Hi yt users, I wanted to know if it is possible somehow to make plots (projections and slices) of a subregion of the domain, e.g. I define a sphere like : sph= pf.h.sphere(center=[0,0,0], radius=(100,'pc’)) Now I want to plot the projection of the density of that region in the x axis: slc = SlicePlot(sph, 'x', 'dens') But then I get the following error: AttributeError: 'AMRSphere' object has no attribute 'domain_width' thanks for your help, Juan _____________________________ Juan Camilo Ibañez Mejia Department of Astrophysics American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> _____________________________

2 1

Completely baffled by camera
by Stephanie Tonnesen May 22, 2014

May 22, 2014

Hi all, I am totally baffled by the camera right now. I have a galaxy that is being stripped by an oncoming wind, and I would like to be able to see both the disk and the tail. I am attaching three different ways (out of what think has been a million permutations) I have tried to get a nice volume rendering, and none do a good job. In particular, when I try to choose specific values for tf layers, by adding a single layer I get a TOTALLY different rendering! (v1 and v2). Can anyone explain why I no longer see the disk when I add that extra layer? Also, when I choose to use tf.add_layers, can I get yt to print out where it has put the layers? Thank you! Stephanie

1 0

ARTIO and find_field_value_at_point
by Alexander A. Kaurov May 21, 2014

May 21, 2014

Hi all, I'm trying to access field value in a given point in ARTIO file (sample data file: sizmbhloz-clref04SNth-rs9_a0.9011 ). The function ' find_field_value_at_point ' seems to be not working. May be I'm using it wrong? Here is the code: from yt.mods import * pf=load('test-data/sizmbhloz-clref04SNth-rs9_a0.9011/sizmbhloz-clref04SNth-rs9_a0.9011.art') pf.h. find_field_value_at_point(('artio', 'HVAR_GAS_DENSITY'),[0.1,0.1,0.1]) And the error: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/kaurov/anaconda/lib/python2.7/site-packages/yt-3.0dev-py2.7-linux-x86_64.egg/yt/data_objects/static_output.py", line 84, in __getattr__ raise AttributeError AttributeError Thanks! Sasha

4 8

Memory overloading on time series
by Sam Geen May 20, 2014

May 20, 2014

Hi, The memory usage in yt is filling up the machine for a time series with ~100 outputs. It seems like the data from previous datasets isn't being cleared from memory, despite calling "del pf" and "gc.collect()". I've tried various suggestions made previously in the mailing list to no effect. I'm using the Ramses frontend with the script attached. Any ideas? Thanks, Sam

3 6

log scale image for zero dynamic range
by Chang-Goo Kim May 19, 2014

May 19, 2014

Hi all, When initial condition is uniform, it has zero dynamic range. Although it has no dynamic range, sometimes I need to plot it with log scale colorbar to make a movie with the same colorbar for later times. But, yt forced switch to linear colorbar. How can I make yt not to do that. Thanks, Chang-Goo

2 7

volume rendering in cylindrical coordinates
by j s oishi May 16, 2014

May 16, 2014

Hi all, I just wanted to introduce Yanfei Jiang, a postdoc at the CfA who using Athena to do global radiation MHD simulations of black hole accretion disks. He's really keen to start using yt, but he wants to know what the status of doing volume rendering in cylindrical coordinates. Sam, I know you've been thinking about this. I'm also quite interested in doing volume rendering of cylindrical coordinates! thanks, Jeff

3 4

yt install error on Mac
by Junhwan Choi (최준환) May 15, 2014

May 15, 2014

Hi yt users, Recently, I try to install the yt on my mac desktop that uses OS X 10.8.4. While installing yt, I face on strange error and fail to insall. ........ self._load() File "/Users/junhwan2/common/lib/python2.7/site-packages/mercurial/demandimport.py", line 74, in _load mod = _hgextimport(_import, head, globals, locals, None, level) File "/Users/junhwan2/common/lib/python2.7/site-packages/mercurial/demandimport.py", line 43, in _hgextimport return importfunc(name, globals, *args) ImportError: dlopen(/Users/junhwan2/common/lib/python2.7/site-packages/mercurial/osutil.so, 2): Symbol not found: __cg_png_create_info_struct Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Users/junhwan2/common/lib/libPng.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO /Users/junhwan2/common/bin/python2.7: can't open file '/Users/junhwan2/common/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory As far as I know, yt script needs to make src/yt-hg directory and cp distribute_setup.py. Hence, I can not understand what this error for. Can anyone tell me how it happens and how I can fix it? FYI, I set DEST_DIR="/Users/junhwan2/common" in the script to install yt in my home dir. Thank you in advance, Junhwan Choi

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particle smoothing bug in latest version of yt
by Desika Narayanan May 15, 2014

May 15, 2014

Hi YT, I have a function that loads a pf from a Gadget data set, and then smooths a few physical quantities (gas metallicity; mass; density) onto an octree, and then returns them: http://paste.yt-project.org/show/4624/ in an older version of yt (3.0) that I'm using: 7cf523a36d10 (yt-3.0) this works, no problem. if I run yt-update, to get to: 4d1488b8fa47 this gives the following traceback copied below. Has something important changed that should affect the way I use smoothing functions? -desika File "/Users/desika/Dropbox/powderday/particle_smooth_yt.py", line 41, in yt_smooth saved["metallicity"] = ad["gas", "metallicity"] File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 214, in __getitem__ self.get_data(f) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 623, in get_data self._generate_fields(fields_to_generate) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 640, in _generate_fields fd = self._generate_field(field) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 251, in _generate_field tr = self._generate_fluid_field(field) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 271, in _generate_fluid_field rv = finfo(gen_obj) File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/derived_field.py", line 178, in __call__ dd = self._function(self, data) File "/Users/desika/yt-x86_64/src/yt-hg/yt/fields/fluid_fields.py", line 153, in _metallicity tr = data[ftype, "metal_density"] / data[ftype, "density"] File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 207, in __getitem__ f = self._determine_fields([key])[0] File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 455, in _determine_fields finfo = self.pf._get_field_info(ftype, fname) File "/Users/desika/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 487, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('gas', 'metal_density')' in snapshot_006.

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Spherical coordinates
by Joseph Smidt May 15, 2014

May 15, 2014

Hey everyone, This blog post [1] makes it look like if you have the latest hg tip of yt you might be able to do slices of data in spherical coordinates. Could someone explain how with a simple example since I don't see any documentation? Thanks. [1] http://blog.yt-project.org/post/WhatsUpWith30.html -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931

2 3

yt installation issues
by Kaylea Nelson May 14, 2014

May 14, 2014

Hi, I'm trying to install the latest stable yt version via the install_script.sh on a Red Hat 6 based HPC. I'm getting a very confusing error during the final steps of the installation, which can be seen here: http://paste.yt-project.org/show/4612/ Basically, during the step where yt updates from the repo and then attempts to install, it looks in a very odd place for the distribute python package. I can't simply update that version, because I'm on an HPC, but I think the problem is deeper than that. Its looking for it in a version of python that I don't even have loaded in my environment, in a directory that isn't in my PYTHONPATH. I've tried wiping out my python path prior to install as well, but with the same results. From my understanding, yt shouldn't even be trying to use the system version of python any way? Any help would be much appreciated! Kaylea

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RAMSES units bug in yt-3.0
by Sam Geen May 13, 2014

May 13, 2014

Hi, Just to say that in the latest version of yt-3.0 (i.e. since various fields were renamed or re-implemented), I've found a bug in the implementation of "cell_mass", which is giving results that are too low in my runs; I believe the issue is that it's missing a factor of pf["boxlen"]**3 (which is of course only a problem if boxlen is not 1). The previous "CellMass_Msun" worked fine. If I get time I might take a look and issue a pull request, but otherwise I'm just flagging this in case someone else runs into problems; you can just manually multiply the result by pf["boxlen"]**3 until it's fixed. Cheers, Sam

3 13

set_zlim in phase plot
by Chang-Goo Kim May 12, 2014

May 12, 2014

Hi all, set_zlim didn't readjust colormap scale. Here's my simple code and resulting figure. Note that I have tried to reset color scale with set_zlim, but the range remains the same. What did I miss? dd=pf.all_data() ph=PhasePlot(dd,'nH','pok',['cell_mass'],weight_field=None,x_bins=64,y_bins=64,fractional=True) ph.set_zlim('cell_mass',1.e-5,1) ph.show() ph.save('phaseplot.png') http://i.imgur.com/aZ2v7XJ.png BTW, thanks for recent update for fractional keyword. Now, the fractional keyword gives exactly what I want. Chang-Goo

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cylindrical coordinates
by Τρίτσης Άρης- Ευάγγελος May 12, 2014

May 12, 2014

Hi yt users! I am new to yt and would like to ask if anyone has come across issues similar to mine. Is it possible to make slice,projection and 1D-profle plots in cylindrical coordinates in a Flash output file in any orientation and if not does anyone know when such a feature will be implemented to yt? Secondly, when I try to update all dependencies I get the following error: /home/*/yt-x86_64/bin/python2.7: can't open file '/distribute_setup.py': [Errno 2] No such file or directory I would appreciate any help :) Aris

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