Mailman 3 June 2014 - yt-users

Generic UniGrid Data
by Junhwan Choi (최준환) 16 Jun '14

16 Jun '14

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

4 8

Temperature Slice Issues with Gasoline data
by ALEXANDER WOODFINDEN 16 Jun '14

16 Jun '14

Hi everyone, I'm new to yt and am using the latest version (3.0), with support for TIPSY output. I'm having issues creating temperature slices. The data I am using is a periodic box, not equal length in all dimensions. My script goes like this: pf = load(fn, parameter_file=paramfile) pf.field_list slc = SlicePlot(pf,'z','temperature',width=(1,'kpc'),center=[0,0,0]) When I try to create the slice, I receive the following error: In [9]: slc = SlicePlot(pf,'z','temperature',width=(1,'kpc'),center=[0,0,0]) yt : [INFO ] 2014-06-16 11:14:40,033 xlim = -0.500000 0.500000 yt : [INFO ] 2014-06-16 11:14:40,033 ylim = -0.500000 0.500000 yt : [INFO ] 2014-06-16 11:14:40,033 Making a fixed resolution buffer of (('gas', 'temperature')) 800 by 800 yt : [INFO ] 2014-06-16 11:14:40,076 Making a fixed resolution buffer of (('deposit', 'Gas_smoothed_temperature')) 800 by 800 yt : [INFO ] 2014-06-16 11:14:40,096 xlim = -0.500000 0.500000 yt : [INFO ] 2014-06-16 11:14:40,096 ylim = -0.500000 0.500000 yt : [INFO ] 2014-06-16 11:14:40,097 Making a fixed resolution buffer of (('gas', 'temperature')) 800 by 800 yt : [INFO ] 2014-06-16 11:14:40,117 Making a fixed resolution buffer of (('deposit', 'Gas_smoothed_temperature')) 800 by 800 yt : [INFO ] 2014-06-16 11:14:40,138 Making a fixed resolution buffer of (('gas', 'temperature')) 800 by 800 yt : [INFO ] 2014-06-16 11:14:40,159 Making a fixed resolution buffer of (('deposit', 'Gas_smoothed_temperature')) 800 by 800 yt : [INFO ] 2014-06-16 11:14:40,183 Making a fixed resolution buffer of (('all', 'temperature')) 800 by 800 --------------------------------------------------------------------------- error Traceback (most recent call last) <ipython-input-9-4dae35760081> in <module>() ----> 1 slc = SlicePlot(pf,'z','temperature',width=(1,'kpc'),center=[0,0,0]) /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/visualization/plot_window.pyc in SlicePlot(pf, normal, fields, axis, *args, **kwargs) 1779 del kwargs['north_vector'] 1780 -> 1781 return AxisAlignedSlicePlot(pf, normal, fields, *args, **kwargs) /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/visualization/plot_window.pyc in __init__(self, pf, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters) 1006 if axes_unit is None: 1007 axes_unit = get_axes_unit(width, pf) -> 1008 self.set_axes_unit(axes_unit) 1009 1010 class ProjectionPlot(PWViewerMPL): /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/visualization/plot_container.pyc in newfunc(*args, **kwargs) 53 rv = f(*args, **kwargs) 54 args[0]._plot_valid = False ---> 55 args[0]._setup_plots() 56 return rv 57 return newfunc /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/visualization/plot_window.pyc in _setup_plots(self) 745 zlim = (None, None) 746 --> 747 image = self._frb[f] 748 749 if image.max() == image.min(): /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/visualization/fixed_resolution.pyc in __getitem__(self, item) 123 buff = self.pf.coordinates.pixelize(self.data_source.axis, 124 self.data_source, item, bounds, self.buff_size, --> 125 int(self.antialias)) 126 # Need to add _period and self.periodic 127 # self._period, int(self.periodic) /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/geometry/cartesian_coordinates.pyc in pixelize(self, dimension, data_source, field, bounds, size, antialias, periodic) 52 if dimension < 3: 53 return self._ortho_pixelize(data_source, field, bounds, size, ---> 54 antialias, dimension, periodic) 55 else: 56 return self._oblique_pixelize(data_source, field, bounds, size, /net/imp/3/home/woodfiaj/python/yt-3.0/yt/yt/geometry/cartesian_coordinates.pyc in _ortho_pixelize(self, data_source, field, bounds, size, antialias, dim, periodic) 69 data_source[field], size[0], size[1], 70 bounds, int(antialias), ---> 71 period, int(periodic)).transpose() 72 return buff 73 error: data is of incorrect type (wanted 1D float) I have no idea what could be causing this, any ideas on how to solve this error? Alex

2 2

yt installation Fedora 20
by Varadarajan Parthasarathy 16 Jun '14

16 Jun '14

Greetings, I am having an installation problem with yt in Fedora 20. I used pip install yt Downloading/unpacking yt Downloading yt-2.6.2.tar.gz (2.4MB): 2.4MB downloaded Running setup.py egg_info for package yt /bin/sh: svnversion: command not found non-existing path in 'yt/utilities/spatial': 'tests' It seems that include prefix is different from lib prefix Please use either env variable or cfg to set proper path Reading PNG location from png.cfg failed. Please place the base directory of your PNG install in png.cfg and restart. (ex: "echo '/usr/local/' > png.cfg" ) You can locate the path by looking for png.h Complete output from command python setup.py egg_info: /bin/sh: svnversion: command not found non-existing path in 'yt/utilities/spatial': 'tests' It seems that include prefix is different from lib prefix Please use either env variable or cfg to set proper path Reading PNG location from png.cfg failed. Please place the base directory of your PNG install in png.cfg and restart. (ex: "echo '/usr/local/' > png.cfg" ) You can locate the path by looking for png.h I tried doing echo /usr/local/ > png.cfg and even tried with /usr/ > png.cfg, but it did not help. Did any other Fedora 20 user face the same issue ? Regards, Varadarajan

3 2

length of octree and smoothed arrays
by Desika Narayanan 12 Jun '14

12 Jun '14

Hi All, First, I'm on an updated yt 3.0 updated about 5 minutes ago. (hg id: ea182fc68fae (yt-3.0) tip) This might be related to Matt's update on octree on June 8th (in response to the CIC stuff) that I don't quite understand, but I've run into the following issue highlighted in the example code: http://paste.yt-project.org/show/4781/ Here, I create a fake data set (motivated by Nathan's shared notebook earlier this week), construct the octree, and then smooth the density onto a grid with: >density = ad["deposit","all_density"] What I find is that the number of elements in the density array is not the same as the number of 0's (i.e Falses) in the generated octree (revealed by >saved["octree"] in the above script). Nominally, I thought the smoothing happened onto the same octree mesh that I generate with ds.index.oct_handler.save_octree(). Is this not the case? Or, is there a way to make it the case in the order that I call things? Thanks, desika

2 6

cloud in cell mesh construction for particle data
by Brendan Griffen 11 Jun '14

11 Jun '14

Hi, I was wondering if there were any Cython routines within yt which takes particle data and converts it into a cloud-in-cell based mesh which can be written to a file of my choosing. I heard a while ago there was some such functionality but it could be too far down the yt rabbit hole to be used as a standalone? Is this true? I have my own Python code for doing it but it just isn't fast enough and thought I'd ask the yt community if there were any wrapper tools available to boost the speed. Thanks. Brendan

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What is code units? How to convert it into kps or mps
by Reju Sam John 11 Jun '14

11 Jun '14

Dear all, >>> vr = halo[i].virial_radius(virial_overdensity=200.0, bins=100) will return the virial radius of the halo in code units. What is code units? How to convert it into kps or mps? -- Reju Sam John

2 2

(no subject)
by Francia Riesco 10 Jun '14

10 Jun '14

Hello Everybody, I hope you are fine I am writing you to see if anybody has this problem installing yt on pycharm Error occurred when installing packages. The following command was executed: packaging_tool.py install --build-dir /private/var/folders/nf/12x9821x4mq51y56wj9cr1600000gp/T/pycharm-packaging3493387491340383194.tmp --user yt The error output of the command: Downloading/unpacking yt Running setup.py egg_info for package yt Traceback (most recent call last): File "<string>", line 16, in <module> File "/private/var/folders/nf/12x9821x4mq51y56wj9cr1600000gp/T/pycharm-packaging3493387491340383194.tmp/yt/setup.py", line 11, in <module> if StrictVersion(setuptools.__version__) < StrictVersion('0.7.0'): File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/version.py", line 40, in __init__ self.parse(vstring) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/version.py", line 107, in parse raise ValueError, "invalid version number '%s'" % vstring ValueError: invalid version number '0.6c12' Complete output from command python setup.py egg_info: Traceback (most recent call last): File "<string>", line 16, in <module> File "/private/var/folders/nf/12x9821x4mq51y56wj9cr1600000gp/T/pycharm-packaging3493387491340383194.tmp/yt/setup.py", line 11, in <module> if StrictVersion(setuptools.__version__) < StrictVersion('0.7.0'): File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/version.py", line 40, in __init__ self.parse(vstring) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/version.py", line 107, in parse raise ValueError, "invalid version number '%s'" % vstring ValueError: invalid version number '0.6c12' ---------------------------------------- Cleaning up... Command python setup.py egg_info failed with error code 1 in /private/var/folders/nf/12x9821x4mq51y56wj9cr1600000gp/T/pycharm-packaging3493387491340383194.tmp/yt Storing complete log in /Users/friesco/Library/Logs/pip.log This is the latest pycharm in maverick ios. Let me know if you have any idea or suggestion how to solve it Thank you in advance

2 1

extracting data of PhasePlot
by Alexander A. Kaurov 08 Jun '14

08 Jun '14

Hi All, Is there an easy way to extract numpy array with 2d histogram from PhasePlot? Same question for other types of plots. Thanks! - Alexander

2 2

rockstar build failure
by Desika Narayanan 07 Jun '14

07 Jun '14

Hi All, I just installed two identical versions of yt bleeding edge: one with rockstar=0 in the install_script, and one with it =1. I'm on Mac OS X Mavericks. Rockstar=0 built with no problem at all, but when I set =1, I get the following build error: http://paste.yt-project.org/show/4741/ any hints? Would it be safest to try one of the more stable yt's as a separate build if I want to use the rockstar functionality? thanks -desika

5 9

definition (source code) of virial_mass(virial_overdensity=200.0, bins=300)
by Reju Sam John 07 Jun '14

07 Jun '14

Where can I find the definition (source code) of the following function ? virial_mass(virial_overdensity=200.0, bins=300) Like this function I have to create a new function for my derived field. -- Reju Sam John

1 0