Category Archives: codes

Finding codes and Russian nesting dolls

As those familiar with the ASCL know, those working on it take an active approach to sharing astrophysical source code, ferreting out codes, looking for their download sites, and creating entries for them in the ASCL. We welcome and indeed (enthusiastically!) encourage code authors to create entries for their codes, but most of the indexing of codes is currently done by ASCL associate editor Kim DuPrie and me.

I regularly read through pre-prints looking for mention of codes not yet indexed by the ASCL; Advisory Committee Chairman Peter Teuben does the same. He has access to publications I cannot get to, such as MNRAS, and looks there for codes as well. A paper may yield a code new to the ASCL, and sometimes, a paper will reveal what Peter and I refer to as Russian dolls: the deeper we get into a paper, the more codes it reveals. One paper he sent to me recently revealed 37 (!) codes, only 5 of which the ASCL had indexed. Thirty-two new codes to try to find!

Other times, a paper will mention two or three or more codes which lead us to other papers which mention yet more codes, which lead us to papers which mention even more codes… and though the ASCL indexes over 600 codes, there are still hundreds, probably thousands, out there it hasn’t indexed, so some of these more more MORE codes that we come across also need to be found. Like Russian nesting dolls, the codes go on and on and on.

It’s times like that — finding 32 new codes in just one paper! peeling back layers and layers of new codes! — I wish I could work on the ASCL full-time. Well, also the times I look at the list we’d already compiled (a list I stopped adding to over a year ago) of ~ 200 codes to find. Also the times I look at the list of things still to be done for/on/about the ASCL beyond indexing new codes.

So many codes, so little time to spend on them, alas!

Where do they come from? ASCL pageviews by country

Idly browsing through Google Analytics statistics on the ASCL, I pulled out pageviews by country, these just of the ASCL forum on Asterisk for this month so far. Of the 4,843 pageviews, 1,939 (40%) are from the US, which means of course that 60% are not. People from eighty-three countries have accessed the code entries forum; I’ve tagged the pie slices below of the ten countries with at least 2% of the total pageviews. Click on the pie to see the chart at full size.

March pageviews by country, as of 3/25/2013

March pageviews by Country, as of 3/25/2013

 

Updated codes

Gyula Józsa has been updating TiRiFiC and fixing minor bugs, and has added features and made the code standalone software, no longer requiring GIPSY; instead, input files are in FITS format now. You can be alerted to updates by subscribing to the TiRiFiC thread on the ASCL.

Peter Teuben reported on the ASCL that an updated version of ZEUS-MP (V1.5) has been made public by the U.Maryland group. Please find the updated version here: http://www.netpurgatory.com/zeusmp.html

He also provided an additional download site for new code GRID-core.

If you would like to receive an email whenever a new post is made on the ASCL forum which houses the code entries, instructions for subscribing to the forum are available.

February 2013 additions to the ASCL

Seventeen codes were added to the ASCL in February:

ACS: ALMA Common Software
DisPerSE: Discrete Persistent Structures Extractor
EPICS: Experimental Physics and Industrial Control System
ESO-MIDAS: General tools for image processing and data reduction
FASTPHOT: A simple and quick IDL PSF-fitting routine

GALA: Stellar atmospheric parameters and chemical abundances
GRID-core: Gravitational Potential Identification of Cores
IAS Stacking Library in IDL
ICORE: Image Co-addition with Optional Resolution Enhancement
ISIS: Interactive Spectral Interpretation System for High Resolution X-Ray Spectroscopy

MARX: Model of AXAF Response to X-rays
ME(SSY)**2: Monte Carlo Code for Star Cluster Simulations
Minerva: Cylindrical coordinate extension for Athena
NIFTY: A versatile Python library for signal inference
pNbody: A python parallelized N-body reduction toolbox

SYNMAG Photometry: Catalog-level Matched Colors of Extended Sources
XDQSO: Photometic quasar probabilities and redshifts

We also added CSCview: A Graphical User Interface to the Chandra Source Catalog to our web tools page, and pyro: hydro by example — A simple python-based tutorial on computational methods for hydrodynamics to our list of online resources. As of February 28, there were 585 codes in the ASCL.

Omar Laurino joins panel for AAS splinter meeting “Astrophysics Code Sharing?”

Omar Laurino (Harvard-Smithsonian Center for Astrophysics) has joined the panel for the ASCL-sponsored splinter meeting “Astrophysics Code Sharing?” at the upcoming AAS meeting in Long Beach. The topic of his short presentation is What do we want to accomplish?

Session date/time/location:
Wednesday, January 9
2:00 PM – 3:00 PM
Regency Ballroom D (Downtown Hyatt Long Beach)

Peter Teuben (Astronomy Department, UMD) will discuss the results of sessions on code release and discoverability from earlier conferences; he will also moderate the discussion. Robert Hanisch (STScI/VAO) will talk on Integrity in the publication process and Bruce Berriman (IPAC, Caltech) will cover Code repositories in other disciplines. ASCL editor Alice Allen will share a little information about (surprise!) the ASCL. The floor will be open for discussion and sharing after the five-minute presentations. And we’ll have glow-in-the-dark pencils to give away, too!

A preferred reference method seems to be evolving

Looking recently at references to code entries, I see most are in the format:

    author, year, in Astrophysics Source Code Library, record ascl ID

For example: Barnes, J. E., 2011, Astrophysics Source Code Library, record ascl:1102.027

Using the entire ascl ID (ascl:xxxx.xxx) in the reference enables ADS to more easily pick up the citation. It may be helpful to the reader to include the name of the code as well:

    Barnes, J. E., 2011, ZENO, Astrophysics Source Code Library, record ascl:1102.027

The ascl ID number can be used to provide a link to a particular entry. For the example above, typing ascl.net/1102.027 into your browser brings up the entry for the code ZENO.

ADS BibTeX records for citing ASCL entries

ADS is currently generating incorrect BibTeX records for citations to code entries in the ASCL. This will be fixed, but in the meantime, here’s an example of what is being generated and how to fix it, courtesy of Mark Taylor and Alberto Accomazzi.

Hitting the “Bibtex entry for this abstract” button on the ADS page for the ASCL Sherpa entry gives:

@ARTICLE{2011ascl.soft07005F,
author = {{Freeman}, P. and {Nguyen}, D. and {Doe}, S. and {Siemiginowska}, A.
},
title = “{Sherpa: CIAO Modeling and Fitting Package}”,
journal = {Astrophysics Source Code Library},
year = 2011,
month = jul,
pages = {7005},
adsurl = {http://adsabs.harvard.edu/abs/2011ascl.soft07005F},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

The identifier that should be in “pages” is “1107.005” as ASCL IDs are all of the form yymm.nnn. However, a better Bibtex entry format is:

@ARTICLE{2011ascl.soft07005F,
author = {{Freeman}, P. and {Nguyen}, D. and {Doe}, S. and {Siemiginowska}, A.
},
title = “{Sherpa: CIAO Modeling and Fitting Package}”,
journal = {Astrophysics Source Code Library},
year = 2011,
month = jul,
eprint = {ascl:1107.005},
adsurl = {http://adsabs.harvard.edu/abs/2011ascl.soft07005F},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

Note the removal of “page” and the addition of the “eprint” field.

After running LaTeX and BibTeX on it, it should generate an entry in the .bbl file that looks like this:

bibitem[{{Freeman et al.}(2011)]{2011ascl.soft07005F}
{Freeman}, P., {Nguyen}, D., {Doe}, S., and {Siemiginowska}, A. 2011
Astrophysics Source Code Library, eprint{ascl:1107.005}

My thanks to Dr. Accomazzi and Dr. Taylor for their work on this!

October 2012 additions

Thirty-one codes were added to the ASCL in October; on October 31, there were 546 codes in the library.

BOOTTRAN: Error Bars for Keplerian Orbital Parameters
CALCLENS: Curved-sky grAvitational Lensing for Cosmological Light conE simulatioNS
Consistent Trees: Gravitationally Consistent Halo Catalogs and Merger Trees for Precision Cosmology
ConvPhot: A profile-matching algorithm for precision photometry
EZ: A Tool For Automatic Redshift Measurement

FLUKA: Fully integrated particle physics Monte Carlo simulation package
GASGANO: Data File Organizer
GOSSIP: SED fitting code
GP2PCF: Brute-force computation of 2-point correlation functions
HAM2D: 2D Shearing Box Model

inf_solv: Kerr inflow solver
McPHAC: McGill Planar Hydrogen Atmosphere Code
ORBADV: ORBital ADVection by interpolation
PAHFIT: Properties of PAH Emission
pPXF: Penalized Pixel-Fitting stellar kinematics extraction

PVS-GRMHD: Conservative GRMHD Primitive Variable Solvers
PyCosmic: Detecting cosmics in CALIFA and other fiber-fed integral-field spectroscopy datasets
QFitsView: FITS file viewer
QYMSYM: A GPU-accelerated hybrid symplectic integrator
Rockstar: Phase-space halo finder

RVLIN: Fitting Keplerian curves to radial velocity data
Sapporo: N-body simulation library for GPUs
SearchCal: The JMMC Evolutive Search Calibrator Tool
SGNAPS: Software for Graphical Navigation, Analysis and Plotting of Spectra
SMART: Spectroscopic Modeling Analysis and Reduction Tool

Specview: 1-D spectral visualization and analysis of astronomical spectrograms
Systemic Console: Advanced analysis of exoplanetary data
TA-DA: A Tool for Astrophysical Data Analysis
Tempo2: Pulsar Timing Package
TRIP: General computer algebra system for celestial mechanics

TwoDSSM: Self-gravitating 2D shearing sheet