Mailman 3 January 2017 - yt-users

problem with slice after upgrade
by Slavin, Jonathan 25 Jan '17

25 Jan '17

Hi all, After upgrading yt to 3.3.3 I'm having trouble with slices. Specifically I'm doing: ds = yt.load(file) slc = ds.slice(2,0.) dx = slc['dr'].min() This is for FLASH data from a run in cylindrical (r,z) symmetry. What I get is: ValueError Traceback (most recent call last) /export/slavin/FLASH/mmsnr/plot_image.py in <module>() 101 slc = ds.slice(2,0.) 102 if first: --> 103 dx = slc['dr'].min() 104 xgl = ds.index.grids[0].LeftEdge[0] 105 xgr = ds.index.grids[-1].RightEdge[0] /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in __getitem__(self, key) 270 return self.field_data[f] 271 else: --> 272 self.get_data(f) 273 # fi.units is the unit expression string. We depend on the registry 274 # hanging off the dataset to define this unit object. /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in get_data(self, fields) 1119 def get_data(self, fields=None): 1120 if self._current_chunk is None: -> 1121 self.index._identify_base_chunk(self) 1122 if fields is None: return 1123 nfields = [] /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in _identify_base_chunk(self, dobj) 302 # fast_index = self._get_grid_tree() 303 if getattr(dobj, "size", None) is None: --> 304 dobj.size = self._count_selection(dobj, fast_index = fast_index) 305 if getattr(dobj, "shape", None) is None: 306 dobj.shape = (dobj.size,) /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in _count_selection(self, dobj, grids, fast_index) 312 return fast_index.count(dobj.selector) 313 if grids is None: grids = dobj._chunk_info --> 314 count = sum((g.count(dobj.selector) for g in grids)) 315 return count 316 /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/grid_geometry_handler.pyc in <genexpr>((g,)) 312 return fast_index.count(dobj.selector) 313 if grids is None: grids = dobj._chunk_info --> 314 count = sum((g.count(dobj.selector) for g in grids)) 315 return count 316 /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.pyc in count(self, selector) 381 382 def count(self, selector): --> 383 mask = self._get_selector_mask(selector) 384 if mask is None: return 0 385 return self._last_count /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.pyc in _get_selector_mask(self, selector) 363 mask = self._last_mask 364 else: --> 365 mask = selector.fill_mask(self) 366 if self._cache_mask: 367 self._last_mask = mask /export/slavin/python/anaconda/lib/python2.7/site-packages/yt/geometry/selection_routines.pyx in yt.geometry.selection_routines.SliceSelector.fill_mask (yt/geometry/selection_routines.c:21029)() 1235 if i == self.axis: 1236 ind[i][0] = \ -> 1237 <int> ((self.coord - (gobj.LeftEdge[i]).to_ndarray()) / 1238 gobj.dds[i]) 1239 ind[i][1] = ind[i][0] + 1 ValueError: cannot convert float NaN to integer Anyone have any ideas on why this is happening? Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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Question with annotate_velocity
by Lu, Yinghe 19 Jan '17

19 Jan '17

Hi, I have a question regarding how the function annotate_velocity is performed. From one of the datasets I am analyzing ( I use FLASH4 data), at regions around simulation coordinates r=0 with the default setting (no scaling, no normalization), yt seems to plot velocity vectors pointing to random directions which is inconsistent with the field values of "velocity_magnitude" in that region that my simulation set it to. I wonder if anyone else has encountered this kind of problem before, and if there's a easy way to double check on the data. Thanks!

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ANN: ytree 1.1 released
by Britton Smith 13 Jan '17

13 Jan '17

Hello everyone, I am pleased to announce the release of ytree version 1.1. ytree is a merger-tree code with yt-like syntax for loading data and accessing fields. ytree can: * return tree and halo data fields with symbolic units like in yt * create merger-trees for Gadget FoF/Subfind catalogs * load merger-trees from Rockstar halo catalogs and consistent-trees outputs * save individual and collections of merger-trees into a reloadable format As of ytree version 1.1, field access is even more yt-like. >>> import ytree >>> a = ytree.load("tree_0_0_0.dat") # consistent-trees >>> # masses for roots of all trees >>> print (a["mvir"].to("Msun")) [ 1.65035971e+13, 1.43309353e+13, 5.18129496e+14, ... 3.47482014e+12, 1.30273381e+12, 3.47482014e+12] Msun >>> # mass for the root of the first tree >>> print (a[0]["mvir"]) 11470000000000.0 Msun/h >>> # most massive progenitors for first tree >>> print (a[0]["line", "mvir"]) [ 1.14700000e+13, 1.20700000e+13, 1.23700000e+13, ... 3.32000000e+12, 1.20700000e+12, 2.71600000e+12] Msun/h ytree is compatible with both Python 2 and 3 and can be installed with pip as: pip install ytree For more information, please visit: http://ytree.readthedocs.io/ ytree is an open-source project. If you're interested in contributing, please do! Thanks! Britton

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Scheduled maintenance
by Kacper Kowalik 07 Jan '17

07 Jan '17

Hi all, our cloud provider "will have a brief network outage starting at 10AM (CST/UTC-6) on Friday, January 13th in order to upgrade its network hardware. The upgrade will install new hardware and software and will double the bandwidth. Before the outage the new hardware will already be configured and connected to the network so the interruption should be brief, hopefully about 5 minutes." This affects: hub (only running notebooks), jenkins, blog, pastebin, slackbots (yt-fido, irc bridge). In theory it should go unnoticed. On the other hand, what could possibly go wrong on Friday 13th...? Cheers, Kacper

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variance versus standard deviation
by Andrew Cunningham 04 Jan '17

04 Jan '17

In the following cookbook example: http://yt-project.org/doc/cookbook/simple_plots.html#profiles-with-variance… the variance along the profile is extracted: variance = prof.variance['gas', 'velocity_magnitude'].value but is then labelled as the standard deviation when the plot is created: plt.loglog(radius, variance, label='Standard Deviation') So, does "prof.variance" return the standard deviation and not the variance? Or, is the plot mislabelled? Should the plot instead be: plt.loglog(radius, np.sqrt(variance), label='Standard Deviation')

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How the field ('gas', 'temperature') was derived?
by hudan_bazhaoyu 03 Jan '17

03 Jan '17

Dear yt: I have one simple question, but it bothers me these days. I used the yt to analysis the "hdf5" files, which generated by Gadget-2. These files have basic fields, like: ("PartType0", "*"), ("PartType1", "*") and ("all", "*"). Then I want to plot the density map and temperature map, it seems need some derived fields, like: ("gas", "density") and ("gas", "temperature"). I'm curious about how the ("gas","temperature") was derived, so I browsed a lots of documents on the Web, but found nothing. Please see http://yt-project.org/doc/reference/field_list.html?highlight=field%20list About the field of ('gas','temperature'), there is "No source available" in "Field Source"! In my data, the field ("PartType0","InternalEnergy") is provided by me, and I think the temperature should calculated by Internal Energy "E" with the function: k*T = (Gamma -1)*µ*mp*E, where k = 1.38E-16 erg/K is Boltzmann constant, Gamma = 5/3 for adiabat particles, μ = 0.6 is the corresponding mean molecular weight, and mp = 1.67E-24 g is proton mass. But this result is about half of the value of ("gas","temperature"). So what you may know is why, which one is right? I need your help! Thank you a lot, and happy new year! Regard, Dan -- Dan Hu ======================================= Department of Physics, Shanghai Jiao Tong University 800 Dongchuan Road, Minhang, Shanghai 200240, PRC E-mail : hudan_bazhaoyu(a)163.com <mailto:hudan_bazhaoyu@163.com> hudan_bazhaoyu(a)sjtu.edu.cn <mailto:hudan_bazhaoyu@sjtu.edu.cn> =======================================

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RAMSES multiple sims memory issue
by Thor Andreas Seiff Ellewsen 02 Jan '17

02 Jan '17

Hi all, I'm working on a project where I'm comparing different RAMSES simulations. However I'm running into a problem with memory. It seems that yt loads the whole simulation into memory even though I'm only interested in a number of dark matter halos which I have the coordinates for. It also seems like it doesn't drop the first simulation out of memory when I'm done making the figures I want for that one. This quickly fills up the memory. You can find the relevant parts of my code at the pastebin at http://paste.yt/p4946.html I'm running yt version 3.3.2 What am I doing wrong? Also, is there a way to change the axis names? I'm making some dark matter density profiles using the ('deposit','io_density') field and this gives IO Density on the y axis, but I just want it to say Dark matter density so my readers actually understand what I'm talking about. Thanks for helping Best, Andreas Ellewsen

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