Mailman 3 August 2014 - yt-users

Cutting region confusion
by Stephanie Tonnesen Aug. 4, 2014

Aug. 4, 2014

Hi all, I am trying to get the total mass in a disk region of my simulation. I am using athena data and yt 2.7-dev. I thought I was defining the region in the same way using two methods: alld = pf.h.all_data() tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.25","grid['z'] < 0.1925","grid['z'] > -0.1925","grid['cyl_Rcode'] < 1.2"]) disk = pf.h.disk([0.0,0.0,0.0],[0.0,0.0,1.0],1.2,0.385) tdp25 = disk.cut_region(["grid['specific_scalar[0]'] > 0.25"]) but when I print the total mass I get answers that differ by 10% print tracerp25.quantities["TotalQuantity"]("CellMassMsun") print tdp25.quantities["TotalQuantity"]("CellMassMsun") >>[8019047231.5192223] >>[8886968784.4710732] Can someone point out where my difference is? Thanks! Stephanie

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updated to latest change set - now can't load gadget data
by Brendan Griffen Aug. 4, 2014

Aug. 4, 2014

Hi, I just did: loadyt; cd $YT_DEST/src/yt-hg; hg pull http://bitbucket.org/MatthewTurk/yt-3.0; hg up; python2.7 setup.py build_ext -i I then did the following (which worked previously): pf = load(basepath+ext+'.0.hdf5') yt : [INFO ] 2014-08-04 14:11:07,101 Calculating time from 2.128e-02 to be 1.671e+15 seconds yt : [INFO ] 2014-08-04 14:11:07,102 Assuming length units are in Mpc/h (comoving) yt : [INFO ] 2014-08-04 14:11:07,102 Parameters: current_time = 1.67110631651e+15 yt : [INFO ] 2014-08-04 14:11:07,102 Parameters: domain_dimensions = [2 2 2] yt : [INFO ] 2014-08-04 14:11:07,103 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-08-04 14:11:07,103 Parameters: domain_right_edge = [ 100. 100. 100.] yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: cosmological_simulation = 1 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: current_redshift = 45.999999479 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: omega_lambda = 0.6825 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: omega_matter = 0.3175 yt : [INFO ] 2014-08-04 14:11:07,104 Parameters: hubble_constant = 0.6711 yt : [INFO ] 2014-08-04 14:11:07,285 Allocating for 1.074e+09 particles yt : [INFO ] 2014-08-04 14:14:25,748 Identified 6.401e+07 octs yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Coordinates') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'ParticleIDs') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Potential') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Velocities') to list of fields yt : [INFO ] 2014-08-04 14:14:25,994 Adding unknown field ('PartType1', 'Masses') to list of fields yt : [INFO ] 2014-08-04 14:14:26,095 Adding unknown field ('all', 'Potential') to list of fields --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /nfs/blank/h4231/bgriffen/data/lib/yt-x86_64/lib/python2.7/site-packages/IPython/utils/py3compat.pyc in execfile(fname, *where) 202 else: 203 filename = fname --> 204 __builtin__.execfile(filename, *where) /nfs/blank/h4231/bgriffen/work/projects/caterpillar/c2ray/code/submitcic/ytcic.py in <module>() ---> 59 rho_crit_0 = pf.cosmology.critical_density(0.) AttributeError: 'GadgetHDF5StaticOutput' object has no attribute 'cosmology' It seems the data has no attributes now? Brendan

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ANN: yt-3.0 released!
by Matthew Turk Aug. 4, 2014

Aug. 4, 2014

The yt community is proud to announce the release of yt 3.0. yt (http://yt-project.org) is an open source, community-developed toolkit for analysis and visualization of volumetric data of all types, with a particular emphasis on astrophysical simulations and nuclear engineering simulations. This release of yt features an entirely rewritten infrastructure for data ingestion, indexing, and representation. While past versions of yt were focused on analysis and visualization of data structured as regular grids, this release features full support for particle (discrete point) data such as N-body and SPH data, irregular hexahedral mesh data, and data organized via octrees. This infrastructure will be extended in future versions for high-fidelity representation of unstructured mesh datasets. Highlighted changes in yt 3.0: * Units now permeate the code base, enabling self-consistent unit transformations of all arrays and quantities returned by yt. * Particle data is now supported using a lightweight octree. SPH data can be smoothed onto an adaptively-defined mesh using standard SPH smoothing * Support for octree AMR codes * Preliminary Support for non-Cartesian data, such as cylindrical, spherical, and geographical * Revamped analysis framework for halos and halo catalogs, including direct ingestion and analysis of halo catalogs of several different formats * Support for multi-fluid datasets and datasets containing multiple particle types * Flexible support for dynamically defining new particle types using filters on existing particle types or by combining different particle types. * Vastly improved support for loading generic grid, AMR, hexahedral mesh, and particle without hand-coding a frontend for a particular data format. * New frontends for ART, ARTIO, Boxlib, Chombo, FITS, GDF, Subfind, Rockstar, Pluto, RAMSES, SDF, Gadget, OWLS, PyNE, Tipsy, as well as rewritten frontends for Enzo, FLASH, Athena, and generic data. * First release to support installation of yt on Windows * Extended capabilities for construction of simulated observations, and new facilities for analyzing and visualizing FITS images and cube data * Many performance improvements This release is the first of several; while most functionality from the previous generation of yt has been updated to work with yt 3.0, it does not yet have feature parity in all respects. While the core of yt is stable, we suggest the support for analysis modules and volume rendering be viewed as a late-stage beta, with a series of additional releases (3.1, 3.2, etc) appearing over the course of the next year to improve support in these areas. For more information, including installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt-3.0 at http://yt-project.org/docs/3.0 yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. yt 3.0 features contributions from over 60 individuals, constituting almost 5000 commits. For many contributors, this is the first release featuring their work. Please forward this announcement on to any interested parties, and look for information soon about upcoming workshops focused on yt and applying it to your data. Thank you,

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units error in cloud-in-cell construction in yt
by Brendan Griffen Aug. 4, 2014

Aug. 4, 2014

Hi, I've been trying to construct a CiC mesh but couldn't get an answer comparable with theory for the mean density of the mesh yt gave me. I've put all the relevant code and output in a pastebin here: http://pastebin.com/hbVM0rYN I've spoken with Britton Smith and he thinks the physical size of the mesh might be wrong by a factor of (1+z) which translates to the densities all being off by (1+z)^3. There also seems to be a missing h**3 somewhere which brings everything in "rough" alignment. I've run it for two redshifts z = 46 and z = 0 and put the output in the above pastebin. I've added a correction where I forcefully put /(1+z)^3 term at the end and it gives reasonable results. I've also added another two values including the missing /h**3 term. Can this be corrected or can someone tell me where I went wrong in what I'm doing? Thanks! Brendan

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critical density calculation from yt
by Brendan Griffen Aug. 2, 2014

Aug. 2, 2014

Hi, I'm using the cosmology.critical_density(z) calculation from yt and I was wondering what is the exact type of critical density? Is it baryon critical density? That is what I need. Thanks. Brendan

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