[ascl:1204.014]
WOMBAT: sWift Objects for Mhd BAsed on Tvd

WOMBAT (sWift Objects for Mhd BAsed on Tvd) is an astrophysical fluid code that is an implementation of a non-relativistic MHD TVD scheme; an extension for relativistic MHD has been added. The code operates on 1, 2, and 3D Eulerian meshes (cartesian and cylindrical coordinates) with magnetic field divergence restriction controlled by a constrained transport (CT) scheme. The user can tune code performance to a given processor based on chip cache sizes. Proper settings yield significant speed-ups due to efficient cache reuse.

[ascl:1204.015]
PROFIT: Emission-line PROfile FITting routine

The PROFIT is an IDL routine to do automated fitting of emission-line profiles by Gaussian curves or Gauss-Hermite series optimized for use in Integral Field and Fabry-Perot data cubes. As output PROFIT gives two-dimensional FITS files for the emission-line flux distribution, centroid velocity, velocity dispersion and higher order Gauss-Hermite moments (h3 and h4).

[ascl:1204.016]
ASCfit: Automatic Stellar Coordinate Fitting Package

A modular software package for automatically fitting astrometric world coordinates (WCS) onto raw optical or infrared FITS images. Image stars are identified with stars in a reference catalog (USNO-A2 or 2MASS), and coordinates derived as a simple linear transformation from (X,Y) pixels to (RA,DEC) to the accuracy level of the reference catalog used. The package works with both optical and infrared images, at sidereal and non-sidereal tracking rates.

[ascl:1204.017]
epsnoise: Pixel noise in ellipticity and shear measurements

epsnoise simulates pixel noise in weak-lensing ellipticity and shear measurements. This open-source python code can efficiently create an intrinsic ellipticity distribution, shear it, and add noise, thereby mimicking a "perfect" measurement that is not affected by shape-measurement biases. For theoretical studies, we provide the Marsaglia distribution, which describes the ratio of normal variables in the general case of non-zero mean and correlation. We also added a convenience method that evaluates the Marsaglia distribution for the ratio of moments of a Gaussian-shaped brightness distribution, which gives a very good approximation of the measured ellipticity distribution also for galaxies with different radial profiles. We provide four shear estimators, two based on the ε ellipticity measure, two on χ. While three of them are essentially plain averages, we introduce a new estimator which requires a functional minimization.

[ascl:1203.001]
AE: ACIS Extract

ACIS Extract (AE), written in the IDL language, provides innovative and automated solutions to the varied challenges found in the analysis of X-ray data taken by the ACIS instrument on NASA's Chandra observatory. AE addresses complications found in many Chandra projects: large numbers of point sources (hundreds to several thousand), faint point sources, misaligned multiple observations of an astronomical field, point source crowding, and scientifically relevant diffuse emission. AE can perform virtually all the data processing and analysis tasks that lie between Level 2 ACIS data and publishable LaTeX tables of point-like and diffuse source properties and spectral models.

[ascl:1203.002]
GALAPAGOS: Galaxy Analysis over Large Areas: Parameter Assessment by GALFITting Objects from SExtractor

GALAPAGOS, Galaxy Analysis over Large Areas: Parameter Assessment by GALFITting Objects from SExtractor (ascl:1010.064), automates source detection, two-dimensional light-profile Sersic modelling and catalogue compilation in large survey applications. Based on a single setup, GALAPAGOS can process a complete set of survey images. It detects sources in the data, estimates a local sky background, cuts postage stamp images for all sources, prepares object masks, performs Sersic fitting including neighbours and compiles all objects in a final output catalogue. For the initial source detection GALAPAGOS applies SExtractor, while GALFIT (ascl:1104.010) is incorporated for modelling Sersic profiles. It measures the background sky involved in the Sersic fitting by means of a flux growth curve. GALAPAGOS determines postage stamp sizes based on SExtractor shape parameters. In order to obtain precise model parameters GALAPAGOS incorporates a complex sorting mechanism and makes use of multiplexing capabilities. It combines SExtractor and GALFIT data in a single output table. When incorporating information from overlapping tiles, GALAPAGOS automatically removes multiple entries from identical sources. GALAPAGOS is programmed in the Interactive Data Language, IDL. A C implementation of the software, GALAPAGOS-C (ascl:1408.011), is available.

[ascl:1203.003]
spec2d: DEEP2 DEIMOS Spectral Pipeline

The DEEP2 DEIMOS Data Reduction Pipeline ("spec2d") is an IDL-based, automated software package designed to reduce Keck/DEIMOS multi-slit spectroscopic observations, collected as part of the DEEP2 Galaxy Redshift Survey. The pipeline is best suited for handling data taken with the 1200 line/mm grating tilted towards the red (lambda_c ~ 7800Å). The spec2d reduction package takes the raw DEIMOS data as its input and produces a variety of outputs including 2-d slit spectra and 1-d object spectra.

[ascl:1203.004]
FERENGI: Full and Efficient Redshifting of Ensembles of Nearby Galaxy Images

Bandpass shifting and the (1+z)5 surface brightness dimming (for a fixed width filter) make standard tools for the extraction of structural parameters of galaxies wavelength dependent. If only few (or one) observed high-res bands exist, this dependence has to be corrected to make unbiased statements on the evolution of structural parameters or on galaxy subsamples defined by morphology. FERENGI artificially redshifts low-redshift galaxy images to different redshifts by applying the correct cosmological corrections for size, surface brightness and bandpass shifting. A set of artificially redshifted galaxies in the range 0.1<z<1.1 using a set of ~100 SDSS low-redshift (v<7000 km s-1) images as input has been created to use as a training set of realistic images of galaxies of diverse morphologies and a large range of redshifts for the GEMS and COSMOS galaxy evolution projects. This training set allows other studies to investigate and quantify the effects of cosmological redshift on the determination of galaxy morphologies, distortions, and other galaxy properties that are potentially sensitive to resolution, surface brightness, and bandpass issues. The data sets are also available for download from the FERENGI website.

[ascl:1203.005]
Gyoto: General relativitY Orbit Tracer of Observatoire de Paris

GYOTO, a general relativistic ray-tracing code, aims at computing images of astronomical bodies in the vicinity of compact objects, as well as trajectories of massive bodies in relativistic environments. This code is capable of integrating the null and timelike geodesic equations not only in the Kerr metric, but also in any metric computed numerically within the 3+1 formalism of general relativity. Simulated images and spectra have been computed for a variety of astronomical targets, such as a moving star or a toroidal accretion structure. The underlying code is open source and freely available. It is user-friendly, quickly handled and very modular so that extensions are easy to integrate. Custom analytical metrics and astronomical targets can be implemented in C++ plug-in extensions independent from the main code.

[ascl:1203.006]
EMACSS: Evolve Me A Cluster of StarS

The star cluster evolution code Evolve Me A Cluster of StarS (EMACSS) is a simple yet physically motivated computational model that describes the evolution of some fundamental properties of star clusters in static tidal fields. The prescription is based upon the flow of energy within the cluster, which is a constant fraction of the total energy per half-mass relaxation time. According to Henon's predictions, this flow is independent of the precise mechanisms for energy production within the core, and therefore does not require a complete description of the many-body interactions therein. Dynamical theory and analytic descriptions of escape mechanisms is used to construct a series of coupled differential equations expressing the time evolution of cluster mass and radius for a cluster of equal-mass stars. These equations are numerically solved using a fourth-order Runge-Kutta integration kernel; the results were benchmarked against a data base of direct N-body simulations. EMACSS is publicly available and reproduces the N-body results to within ~10 per cent accuracy for the entire post-collapse evolution of star clusters.

[ascl:1203.007]
EBTEL: Enthalpy-Based Thermal Evolution of Loops

Observational and theoretical evidence suggests that coronal heating is impulsive and occurs on very small cross-field spatial scales. A single coronal loop could contain a hundred or more individual strands that are heated quasi-independently by nanoflares. It is therefore an enormous undertaking to model an entire active region or the global corona. Three-dimensional MHD codes have inadequate spatial resolution, and 1D hydro codes are too slow to simulate the many thousands of elemental strands that must be treated in a reasonable representation. Fortunately, thermal conduction and flows tend to smooth out plasma gradients along the magnetic field, so "0D models" are an acceptable alternative. We have developed a highly efficient model called Enthalpy-Based Thermal Evolution of Loops (EBTEL) that accurately describes the evolution of the average temperature, pressure, and density along a coronal strand. It improves significantly upon earlier models of this type--in accuracy, flexibility, and capability. It treats both slowly varying and highly impulsive coronal heating; it provides the differential emission measure distribution, DEM(T), at the transition region footpoints; and there are options for heat flux saturation and nonthermal electron beam heating. EBTEL gives excellent agreement with far more sophisticated 1D hydro simulations despite using four orders of magnitude less computing time. It promises to be a powerful new tool for solar and stellar studies.

[ascl:1203.008]
MegaLUT: Correcting ellipticity measurements of galaxies

MegaLUT is a simple and fast method to correct ellipticity measurements of galaxies from the distortion by the instrumental and atmospheric point spread function (PSF), in view of weak lensing shear measurements. The method performs a classification of galaxies and associated PSFs according to measured shape parameters, and builds a lookup table of ellipticity corrections by supervised learning. This new method has been applied to the GREAT10 image analysis challenge, and demonstrates a refined solution that obtains the highly competitive quality factor of Q = 142, without any power spectrum denoising or training. Of particular interest is the efficiency of the method, with a processing time below 3 ms per galaxy on an ordinary CPU.

[ascl:1203.009]
MYRIAD: N-body code for simulations of star clusters

MYRIAD is a C++ code for collisional N-body simulations of star clusters. The code uses the Hermite fourth-order scheme with block time steps, for advancing the particles in time, while the forces and neighboring particles are computed using the GRAPE-6 board. Special treatment is used for close encounters, binary and multiple sub-systems that either form dynamically or exist in the initial configuration. The structure of the code is modular and allows the appropriate treatment of more physical phenomena, such as stellar and binary evolution, stellar collisions and evolution of close black-hole binaries. Moreover, it can be easily modified so that the part of the code that uses GRAPE-6 could be replaced by another module that uses other accelerating-hardware like the Graphics Processing Units (GPUs). Appropriate choice of the free parameters give a good accuracy and speed for simulations of star clusters up to and beyond core collapse. The code accuracy becomes comparable and even better than the accuracy of existing codes when a number of close binary systems is dynamically created in a simulation; this is due to the high accuracy of the method that is used for close binary and multiple sub-systems. The code can be used for evolving star clusters containing equal-mass stars or star clusters with an initial mass function (IMF) containing an intermediate mass black hole (IMBH) at the center and/or a fraction of primordial binaries, which are systems of particular astrophysical interest.

[ascl:1203.010]
Youpi: YOUr processing PIpeline

Youpi is a portable, easy to use web application providing high level functionalities to perform data reduction on scientific FITS images. Built on top of various open source reduction tools released to the community by TERAPIX (http://terapix.iap.fr), Youpi can help organize data, manage processing jobs on a computer cluster in real time (using Condor) and facilitate teamwork by allowing fine-grain sharing of results and data. Youpi is modular and comes with plugins which perform, from within a browser, various processing tasks such as evaluating the quality of incoming images (using the QualityFITS software package), computing astrometric and photometric solutions (using SCAMP), resampling and co-adding FITS images (using SWarp) and extracting sources and building source catalogues from astronomical images (using SExtractor). Youpi is useful for small to medium-sized data reduction projects; it is free and is published under the GNU General Public License.

[ascl:1203.011]
SALT2: Spectral Adaptive Lightcurve Template

SALT (Spectral Adaptive Lightcurve Template) is a package for Type Ia Supernovae light curve fitting. Its main purpose is to provide a distance estimator but it can also be used for photometric redshifts, and spectroscopic + photometric identification. This code is also known by the name snfit.

[ascl:1203.012]
Astrometrica: Astrometric data reduction of CCD images

Astrometrica is an interactive software tool for scientific grade astrometric data reduction of CCD images. The current version of the software is for the Windows 32bit operating system family. Astrometrica reads FITS (8, 16 and 32 bit integer files) and SBIG image files. The size of the images is limited only by available memory. It also offers automatic image calibration (Dark Frame and Flat Field correction), automatic reference star identification, automatic moving object detection and identification, and access to new-generation star catalogs (PPMXL, UCAC 3 and CMC-14), in addition to online help and other features. Astrometrica is shareware, available for use for a limited period of time (100 days) for free; special arrangements can be made for educational projects.

[ascl:1203.013]
Figaro: Data Reduction Software

Figaro is a data reduction system that originated at Caltech and whose development continued at the Anglo-Australian Observatory. Although it is intended to be able to deal with any sort of data, almost all its applications to date are geared towards processing optical and infrared data. Figaro uses hierarchical data structures to provide flexibility in its data file formats. Figaro was originally written to run under DEC's VMS operating system, but is now available both for VMS and for various flavours of UNIX.

[ascl:1202.001]
CISM_DX: Visualization and analysis tool

CISM_DX is a community-developed suite of integrated data, models, and data and model explorers, for research and education. The data and model explorers are based on code written for OpenDX and Octave; OpenDX provides the visualization infrastructures as well as the process for creating user interfaces to the model and data, and Octave allows for extensive data manipulation and reduction operations. The CISM-DX package extends the capabilities of the core software programs to meet the needs of space physics researchers.

[ascl:1202.002]
ZODIPIC: Zodiacal Cloud Image Synthesis

ZODIPIC synthesizes images of exozodiacal clouds. As a default, ZODIPIC creates an image of the solar zodiacal cloud as seen from 10 pc, but it contains many parameters that are tweakable from the command line, making it a handy general-purpose model for optically-thin debris disks that yields both accurate images and photometric information simultaneously. Written in IDL, ZODIPIC includes dust with real optical constants, user-specified dust maps and can compute images as seen through a linear polarizer.

[ascl:1202.003]
NOVAS: Naval Observatory Vector Astrometry Software

Kaplan, George; Bartlett, Jennifer Lynn; Monet, Alice; Bangert, John; Puatua, Wendy; Harris, William; Fredericks, Amy; Barron, Eric G.; Barrett, Paul

NOVAS is an integrated package of subroutines and functions for computing various commonly needed quantities in positional astronomy. The package can provide, in one or two subroutine or function calls, the instantaneous coordinates of any star or planet in a variety of coordinate systems. At a lower level, NOVAS also supplies astrometric utility transformations, such as those for precession, nutation, aberration, parallax, and the gravitational deflection of light. The computations are accurate to better than one milliarcsecond. The NOVAS package is an easy-to-use facility that can be incorporated into data reduction programs, telescope control systems, and simulations. The U.S. parts of The Astronomical Almanac are prepared using NOVAS. Three editions of NOVAS are available: Fortran, C, and Python.

[ascl:1202.004]
TALYS: Nuclear Reaction Simulator

TALYS simulates nuclear reactions which involve neutrons, gamma-rays, protons, deuterons, tritons, helions and alpha-particles, in the 1 keV-200MeV energy range. A suite of nuclear reaction models has been implemented into a single code system, enabling one to evaluate basically all nuclear reactions beyond the resonance range. In particular, TALYS estimates the Maxwellian-averaged reaction rates that are of astrophysical relevance. This enables reaction rates to be calculated with increased accuracy and reliability and the approximations of previous codes to be investigated. The TALYS predictions for the thermonuclear rates of relevance to astrophysics are detailed and compared with those derived by widely-used codes for the same nuclear ingredients. TALYS predictions may differ significantly from those of previous codes, in particular for nuclei for which no or little nuclear data is available. The pre-equilibrium process is shown to influence the astrophysics rates of exotic neutron-rich nuclei significantly. The TALYS code provides a tool to estimate all nuclear reaction rates of relevance to astrophysics with improved accuracy and reliability.

[ascl:1202.005]
Mangle: Angular Mask Software

Mangle deals accurately and efficiently with complex angular masks, such as occur typically in galaxy surveys. Mangle performs the following tasks: converts masks between many handy formats (including HEALPix); rapidly finds the polygons containing a given point on the sphere; rapidly decomposes a set of polygons into disjoint parts; expands masks in spherical harmonics; generates random points with weights given by the mask; and implements computations for correlation function analysis. To mangle, a mask is an arbitrary union of arbitrarily weighted angular regions bounded by arbitrary numbers of edges. The restrictions on the mask are only (1) that each edge must be part of some circle on the sphere (but not necessarily a great circle), and (2) that the weight within each subregion of the mask must be constant. Mangle is complementary to and integrated with the HEALPix package (ascl:1107.018); mangle works with vector graphics whereas HEALPix works with pixels.

[ascl:1202.006]
CORSIKA: An Air Shower Simulation Program

CORSIKA (COsmic Ray Simulations for KAscade) is a program for detailed simulation of extensive air showers initiated by high energy cosmic ray particles. Protons, light nuclei up to iron, photons, and many other particles may be treated as primaries. The particles are tracked through the atmosphere until they undergo reactions with the air nuclei or, in the case of unstable secondaries, decay. The hadronic interactions at high energies may be described by several reaction models. Hadronic interactions at lower energies are described, and in particle decays all decay branches down to the 1% level are taken into account. Options for the generation of Cherenkov radiation and neutrinos exist. CORSIKA may be used up to and beyond the highest energies of 100 EeV.

[ascl:1202.007]
CRUNCH3D: Three-dimensional compressible MHD code

CRUNCH3D is a massively parallel, viscoresistive, three-dimensional compressible MHD code. The code employs a Fourier collocation spatial discretization, and uses a second-order Runge-Kutta temporal discretization. CRUNCH3D can be applied to MHD turbulence and magnetic fluxtube reconnection research.

[ascl:1202.008]
Chombo: Adaptive Solutions of Partial Differential Equations

Chombo provides a set of tools for implementing finite difference methods for the solution of partial differential equations on block-structured adaptively refined rectangular grids. Both elliptic and time-dependent modules are included. Chombo supports calculations in complex geometries with both embedded boundaries and mapped grids, and also supports particle methods. Most parallel platforms are supported, and cross-platform self-describing file formats are included.

The Chombo package is a product of the community of Collaborators working with the Applied Numerical Algorithms Group (ANAG), part of the Computational Research Division at LBNL.

[ascl:1202.009]
MOOG: LTE line analysis and spectrum synthesis

MOOG performs a variety of LTE line analysis and spectrum synthesis tasks. The typical use of MOOG is to assist in the determination of the chemical composition of a star. The basic equations of LTE stellar line analysis are followed. The coding is in various subroutines that are called from a few driver routines; these routines are written in standard FORTRAN. The standard MOOG version has been developed on unix, linux and macintosh computers.

One of the chief assets of MOOG is its ability to do on-line graphics. The plotting commands are given within the FORTRAN code. MOOG uses the graphics package SM, chosen for its ease of implementation in FORTRAN codes. Plotting calls are concentrated in just a few routines, and it should be possible for users of other graphics packages to substitute other appropriate FORTRAN commands.

[ascl:1202.010]
SPECTRE: Manipulation of single-order spectra

SPECTRE's chief purpose is the manipulation of single-order spectra, and it performs many of the tasks contained in such IRAF routines as "splot" and "rv". It is not meant to replace the much more general capabilities of IRAF, but does some functions in a manner that some might find useful. A brief list of SPECTRE tasks are: spectrum smoothing; equivalent width calculation; continuum rectification; noise spike excision; and spectrum comparison. SPECTRE was written to manipulate coude spectra, and thus is probably most useful for working on high dispersion spectra. Echelle spectra can be gathered from various observatories, reduced to singly-dimensioned spectra using IRAF, then written out as FITS files, thus becoming accessible to SPECTRE. Three different spectra may be manipulated and displayed simultaneously. SPECTRE, written in standard FORTRAN77, can be used only with the SM graphics package.

[ascl:1202.011]
Lattimer-Swesty Equation of State Code

The Lattimer-Swesty Equation of State code is rapid enough to use directly in hydrodynamical simulations such as stellar collapse calculations. It contains an adjustable nuclear force that accurately models both potential and mean-field interactions and allows for the input of various nuclear parameters, including the bulk incompressibility parameter, the bulk and surface symmetry energies, the symmetric matter surface tension, and the nucleon effective masses. This permits parametric studies of the equation of state in astrophysical situations. The equation of state is modeled after the Lattimer, Lamb, Pethick, and Ravenhall (LLPR) compressible liquid drop model for nuclei, and includes the effects of interactions and degeneracy of the nucleon outside nuclei.

[ascl:1202.012]
CoCoNuT: General relativistic hydrodynamics code with dynamical space-time evolution

CoCoNuT is a general relativistic hydrodynamics code with dynamical space-time evolution. The main aim of this numerical code is the study of several astrophysical scenarios in which general relativity can play an important role, namely the collapse of rapidly rotating stellar cores and the evolution of isolated neutron stars. The code has two flavors: CoCoA, the axisymmetric (2D) magnetized version, and CoCoNuT, the 3D non-magnetized version.

[ascl:1202.013]
SME: Spectroscopy Made Easy

Spectroscopy Made Easy (SME) is IDL software and a compiled external library that fits an observed high-resolution stellar spectrum with a synthetic spectrum to determine stellar parameters. The SME external library is available for Mac, Linux, and Windows systems. Atomic and molecular line data formatted for SME may be obtained from VALD. SME can solve for empirical log(gf) and damping parameters, using an observed spectrum of a star (usually the Sun) as a constraint.

[ascl:1202.014]
FISA: Fast Integrated Spectra Analyzer

FISA (Fast Integrated Spectra Analyzer) permits fast and reasonably accurate age and reddening determinations for small angular diameter open clusters by using their integrated spectra in the (3600-7400) AA range and currently available template spectrum libraries. This algorithm and its implementation help to achieve astrophysical results in shorter times than from other methods. FISA has successfully been applied to integrated spectroscopy of open clusters, both in the Galaxy and in the Magellanic Clouds, to determine ages and reddenings.

[ascl:1202.015]
RADMC-3D: A multi-purpose radiative transfer tool

Dullemond, C. P.; Juhasz, A.; Pohl, A.; Sereshti, F.; Shetty, R.; Peters, T.; Commercon, B.; Flock, M.

RADMC-3D is a software package for astrophysical radiative transfer calculations in arbitrary 1-D, 2-D or 3-D geometries. It is mainly written for continuum radiative transfer in dusty media, but also includes modules for gas line transfer and gas continuum transfer. RADMC-3D is a new incarnation of the older software package RADMC (ascl:1108.016).

[ascl:1201.001]
McScatter: Three-Body Scattering with Stellar Evolution

McScatter illustrates a method of combining stellar dynamics with stellar evolution. The method is intended for elaborate applications, especially the dynamical evolution of rich star clusters. The dynamics is based on binary scattering in a multi-mass field of stars with uniform density and velocity dispersion, using the scattering cross section of Giersz (MNRAS, 2001, 324, 218-30).

[ascl:1201.002]
Roche: Visualization and analysis tool for Roche-lobe geometry of evolving binaries

Roche is a visualization and analysis tool for drawing the Roche-lobe geometry of evolving binaries. Roche can be used as a standalone program reading data from the command line or from a file generated by SeBa (ascl:1201.003). Eventually Roche will be able to read data from any other binary evolution program. Roche requires Starlab (ascl:1010.076) version 4.1.1 or later and the pgplot (ascl:1103.002) libraries. Roche creates a series of images, based on the SeBa output file SeBa.data, displaying the evolutionary state of a binary.

[ascl:1201.003]
SeBa: Stellar and binary evolution

The stellar and binary evolution package SeBa is fully integrated into the kira integrator, although it can also be used as a stand-alone module for non-dynamical applications. Due to the interaction between stellar evolution and stellar dynamics, it is difficult to solve for the evolution of both systems in a completely self-consistent way. The trajectories of stars are computed using a block timestep scheme, as described earlier. Stellar and binary evolution is updated at fixed intervals (every 1/64 of a crossing time, typically a few thousand years). Any feedback between the two systems may thus experience a delay of at most one timestep. Internal evolution time steps may differ for each star and binary, and depend on binary period, perturbations due to neighbors, and the evolutionary state of the star. Time steps in this treatment vary from several milliseconds up to (at most) a million years.

[ascl:1201.004]
emGain: Determination of EM gain of CCD

The determination of the EM gain of the CCD is best done by fitting the histogram of many low-light frames. Typically, the dark+CIC noise of a 30ms frame itself is a sufficient amount of signal to determine accurately the EM gain with about 200 512x512 frames. The IDL code emGain takes as an input a cube of frames and fit the histogram of all the pixels with the EM stage output probability function. The function returns the EM gain of the frames as well as the read-out noise and the mean signal level of the frames.

[ascl:1201.005]
2LPTIC: 2nd-order Lagrangian Perturbation Theory Initial Conditions

Setting initial conditions in numerical simulations using the standard procedure based on the Zel'dovich approximation (ZA) generates incorrect second and higher-order growth and therefore excites long-lived transients in the evolution of the statistical properties of density and velocity fields. Using more accurate initial conditions based on second-order Lagrangian perturbation theory (2LPT) reduces transients significantly; initial conditions based on 2LPT are thus much more appropriate for numerical simulations devoted to precision cosmology. The 2LPTIC code provides initial conditions for running cosmological simulations based on second-order Lagrangian Perturbation Theory (2LPT), rather than first-order (Zel'dovich approximation).

[ascl:1201.006]
VIM: Visual Integration and Mining

VIM (Virtual Observatory Integration and Mining) is a data retrieval and exploration application that assumes an astronomer has a list of 'sources' (positions in the sky), and wants to explore archival catalogs, images, and spectra of the sources, in order to identify, select, and mine the list. VIM does this either through web forms, building a custom 'data matrix,' or locally through downloadable Python code. Any VO-registered catalog service can be used by VIM, as well as co-registered image cutouts from VO-image services, and spectra from VO-spectrum services. The user could, for example, show together: proper motions from GSC2, name and spectral type from NED, magnitudes and colors from 2MASS, and cutouts and spectra from SDSS. VIM can compute columns across surveys and sort on these (eg. 2MASS J magnitude minus SDSS g). For larger sets of sources, VIM utilizes the asynchronous Nesssi services from NVO, that can run thousands of cone and image services overnight.

[ascl:1201.007]
Fisher4Cast: Fisher Matrix Toolbox

The Fisher4Cast suite, which requires MatLab, provides a standard, tested tool set for general Fisher Information matrix prediction and forecasting for use in both research and education. The toolbox design is robust and modular, allowing for easy additions and adaptation while keeping the user interface intuitive and easy to use. Fisher4Cast is completely general but the default is coded for cosmology. It provides parameter error forecasts for cosmological surveys providing distance, Hubble expansion and growth measurements in a general, curved FLRW background.

[ascl:1201.008]
Mercury: A software package for orbital dynamics

Mercury is a new general-purpose software package for carrying out orbital integrations for problems in solar-system dynamics. Suitable applications include studying the long-term stability of the planetary system, investigating the orbital evolution of comets, asteroids or meteoroids, and simulating planetary accretion. Mercury is designed to be versatile and easy to use, accepting initial conditions in either Cartesian coordinates or Keplerian elements in "cometary" or "asteroidal" format, with different epochs of osculation for different objects. Output from an integration consists of osculating elements, written in a machine-independent compressed format, which allows the results of a calculation performed on one platform to be transferred (e.g. via FTP) and decoded on another.

During an integration, Mercury monitors and records details of close encounters, sungrazing events, ejections and collisions between objects. The effects of non-gravitational forces on comets can also be modeled. The package supports integrations using a mixed-variable symplectic routine, the Bulirsch-Stoer method, and a hybrid code for planetary accretion calculations.

[ascl:1201.009]
ExoFit: Orbital parameters of extra-solar planets from radial velocity

ExoFit is a freely available software package for estimating orbital parameters of extra-solar planets. ExoFit can search for either one or two planets and employs a Bayesian Markov Chain Monte Carlo (MCMC) method to fit a Keplerian radial velocity curve onto the radial velocity data.

[ascl:1201.010]
HNBody: Hierarchical N-Body Symplectic Integration Package

HNBody is a new set of software utilities geared to the integration of hierarchical (nearly-Keplerian) N-body systems. Our focus is on symplectic methods, and we have included explicit support for three classes of particles (heavy, light, and massless), second and fourth order methods, post-Newtonian corrections, and the use of a symplectic corrector (among other things). For testing purposes, we also provide support for more general integration schemes (Bulirsch-Stoer & Runge-Kutta). Configuration files employing an intuitive syntax allow for easy problem setup, and many simple simulations can be done without the user compiling any code. Low-level interfaces are also available, enabling extensive customization.

[ascl:1201.011]
Duchamp: A 3D source finder for spectral-line data

Duchamp is software designed to find and describe sources in 3-dimensional, spectral-line data cubes. Duchamp has been developed with HI (neutral hydrogen) observations in mind, but is widely applicable to many types of astronomical images. It features efficient source detection and handling methods, noise suppression via smoothing or multi-resolution wavelet reconstruction, and a range of graphical and text-based outputs to allow the user to understand the detections.

[ascl:1201.012]
CLUMPY: A code for gamma-ray signals from dark matter structures

CLUMPY is a public code for semi-analytical calculation of the gamma-ray flux astrophysical J-factor from dark matter annihilation/decay in the Galaxy, including dark matter substructures. The core of the code is the calculation of the line of sight integral of the dark matter density squared (for annihilations) or density (for decaying dark matter). The code can be used in three modes: i) to draw skymaps from the Galactic smooth component and/or the substructure contributions, ii) to calculate the flux from a specific halo (that is not the Galactic halo, e.g. dwarf spheroidal galaxies) or iii) to perform simple statistical operations from a list of allowed DM profiles for a given object. Extragalactic contributions and other tracers of DM annihilation (e.g. positrons, antiprotons) will be included in a second release.

[ascl:1201.013]
SPS: SPIRE Photometer Simulator

The SPS software simulates the operation of the Spectral and Photometric Imaging Receiver on-board the ESA’s Herschel Space Observatory. It is coded using the Interactive Data Language (IDL), and produces simulated data at the level-0 stage (non-calibrated data in digitised units). The primary uses for the simulator are to:

- optimize and characterize the photometer observing functions
- aid in the development, validation, and characterization of the SPIRE data pipeline
- provide a realistic example of SPIRE data, and thus to facilitate the development of specific analysis tools for specific science cases.

[ascl:1201.014]
Hammurabi: Simulating polarized Galactic synchrotron emission

The Hammurabi code is a publicly available C++ code for generating mock polarized observations of Galactic synchrotron emission with telescopes such as LOFAR, SKA, Planck, and WMAP, based on model inputs for the Galactic magnetic field (GMF), the cosmic-ray density distribution, and the thermal electron density. The Hammurabi code allows one to perform simulations of several different data sets simultaneously, providing a more reliable constraint of the magnetized ISM.

[ascl:1201.015]
FFTW: Fastest Fourier Transform in the West

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

Benchmarks performed on a variety of platforms show that FFTW's performance is typically superior to that of other publicly available FFT software, and is even competitive with vendor-tuned codes. In contrast to vendor-tuned codes, however, FFTW's performance is portable: the same program will perform well on most architectures without modification.

The FFTW library is required by other codes such as StarCrash and Hammurabi.

[ascl:1201.016]
LumFunc: Luminosity Function Modeling

LumFunc is a numerical code to model the Luminosity Function based on central galaxy luminosity-halo mass and total galaxy luminosity-halo mass relations. The code can handle rest b_J-band (2dFGRS), r'-band (SDSS), and K-band luminosities, and any redshift with redshift dependences specified by the user. It separates the luminosity function (LF) to conditional luminosity functions, LF as a function of halo mass, and also to galaxy types. By specifying a narrow mass range, the code will return the conditional luminosity functions. The code returns luminosity functions for galaxy types as well (broadly divided to early-type and late-type). The code also models the cluster luminosity function, either mass averaged or for individual clusters.

[ascl:1201.017]
Inflation: Monte-Carlo Code for Slow-Roll Inflation

Inflation is a numerical code to generate power spectra and other observables through numerical solutions to flow equations. The code generates tensor and scalar power spectra as a function of wavenumber and various other parameters at specific wavenumbers of interest (such as for CMB, scalar perturbations at smaller scales, gravitational wave detection at direct detection frequencies). The output can be easily ported to publicly available Markov Chain codes to constrain cosmological parameters with data.

[ascl:1112.001]
Eclipse: ESO C Library for an Image Processing Software Environment

Written in ANSI C, eclipse is a library offering numerous services related to astronomical image processing: FITS data access, various image and cube loading methods, binary image handling and filtering (including convolution and morphological filters), 2-D cross-correlation, connected components, cube and image arithmetic, dead pixel detection and correction, object detection, data extraction, flat-fielding with robust fit, image generation, statistics, photometry, image-space resampling, image combination, and cube stacking. It also contains support for mathematical tools like random number generation, FFT, curve fitting, matrices, fast median computation, and point-pattern matching. The main feature of this library is its ability to handle large amounts of input data (up to 2GB in the current version) regardless of the amount of memory and swap available on the local machine. Another feature is the very high speed allowed by optimized C, making it an ideal base tool for programming efficient number-crunching applications, e.g., on parallel (Beowulf) systems.

[ascl:1112.002]
Funtools: FITS Users Need Tools

Funtools is a "minimal buy-in" FITS library and utility package developed at the the High Energy Astrophysics Division of SAO. The Funtools library provides simplified access to a wide array of file types: standard astronomical FITS images and binary tables, raw arrays and binary event lists, and even tables of ASCII column data. A sophisticated region filtering library (compatible with ds9) filters images and tables using boolean operations between geometric shapes, support world coordinates, etc. Funtools also supports advanced capabilities such as optimized data searching using index files.

Because Funtools consists of a library and a set of user programs, it is most appropriately built from source. Funtools has been ported to Solaris, Linux, LinuxPPC, SGI, Alpha OSF1, Mac OSX (darwin) and Windows 98/NT/2000/XP. Once the source code tar file is retrieved, Funtools can be built and installed easily using standard commands.

[ascl:1112.003]
THERMINATOR 2: THERMal heavy IoN generATOR 2

THERMINATOR is a Monte Carlo event generator dedicated to studies of the statistical production of particles in relativistic heavy-ion collisions. The increased functionality of the code contains the following features: The input of any shape of the freeze-out hypersurface and the expansion velocity field, including the 3+1 dimensional profiles, in particular those generated externally with various hydrodynamic codes. The hypersufraces may have variable thermal parameters, which allows for studies departing significantly from the mid-rapidity region, where the baryon chemical potential becomes large. We include a library of standard sets of hypersurfaces and velocity profiles describing the RHIC Au+Au data at sqrt(s_(NN)) = 200 GeV for various centralities, as well as those anticipated for the LHC Pb+Pb collisions at sqrt(s_(NN)) = 5.5 TeV. A separate code, FEMTO-THERMINATOR, is provided to carry out the analysis of femtoscopic correlations which are an important source of information concerning the size and expansion of the system. We also include several useful scripts that carry out auxiliary tasks, such as obtaining an estimate of the number of elastic collisions after the freeze-out, counting of particles flowing back into the fireball and violating causality (typically very few), or visualizing various results: the particle p_T-spectra, the elliptic flow coefficients, and the HBT correlation radii. We also investigate the problem of the back-flow of particles into the hydrodynamic region, as well as estimate the elastic rescattering in terms of trajectory crossings. The package is written in C++ and uses the CERN ROOT environment.

[ascl:1112.004]
PHOX: X-ray Photon Simulator

PHOX is a novel, virtual X-ray observatory designed to obtain synthetic observations from hydro-numerical simulations. The code is a photon simulator and can be apply to simulate galaxy clusters. In fact, X-ray observations of clusters of galaxies continue to provide us with an increasingly detailed picture of their structure and of the underlying physical phenomena governing the gaseous component, which dominates their baryonic content. Therefore, it is fundamental to find the most direct and faithful way to compare such observational data with hydrodynamical simulations of cluster-like objects, which can currently include various complex physical processes. Here, we present and analyse synthetic Suzaku observations of two cluster-size haloes obtained by processing with PHOX the hydrodynamical simulation of the large-scale, filament-like region in which they reside. Taking advantage of the simulated data, we test the results inferred from the X-ray analysis of the mock observations against the underlying, known solution. Remarkably, we are able to recover the theoretical temperature distribution of the two haloes by means of the multi-temperature fitting of the synthetic spectra. Moreover, the shapes of the reconstructed distributions allow us to trace the different thermal structure that distinguishes the dynamical state of the two haloes.

[ascl:1112.005]
GIDGET: Gravitational Instability-Dominated Galaxy Evolution Tool

Observations of disk galaxies at z~2 have demonstrated that turbulence driven by gravitational instability can dominate the energetics of the disk. GIDGET is a 1D simulation code, which we have made publicly available, that economically evolves these galaxies from z~2 to z~0 on a single CPU in a matter of minutes, tracking column density, metallicity, and velocity dispersions of gaseous and multiple stellar components. We include an H$_2$ regulated star formation law and the effects of stellar heating by transient spiral structure. We use this code to demonstrate a possible explanation for the existence of a thin and thick disk stellar population and the age-velocity dispersion correlation of stars in the solar neighborhood: the high velocity dispersion of gas in disks at z~2 decreases along with the cosmological accretion rate, while at lower redshift, the dynamically colder gas forms the low velocity dispersion stars of the thin disk.

[ascl:1112.006]
PhAst: Display and Analysis of FITS Images

PhAst (Photometry-Astrometry) is an IDL astronomical image viewer based on the existing application ATV which displays and analyzes FITS images. It can calibrate raw images, provide astrometric solutions, and do circular aperture photometry. PhAst allows the user to load, process, and blink any number of images. Analysis packages include image calibration, photometry, and astrometry (provided through an interface with SExtractor, SCAMP, and missFITS). PhAst has been designed to generate reports for Minor Planet Center reporting.

[ascl:1112.007]
FLAGCAL: FLAGging and CALlibration Pipeline for GMRT Data

FLAGging and CALlibration (FLAGCAL) is a software pipeline developed for automatic flagging and calibration of the GMRT data. This pipeline can be used for preprocessing (before importing the data in AIPS) any other interferromteric data also (given that the data file is in FITS format and contains multiple channels & scans).There are also a few GUI based tools which can be used for quick visualization of the data.

[ascl:1112.008]
GGobi: A data visualization system

GGobi is an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification.

[ascl:1112.009]
LISACode: A scientific simulator of LISA

LISACode is a simulator of the LISA mission. Its ambition is to achieve a new degree of sophistication allowing to map, as closely as possible, the impact of the different subsystems on the measurements. Its also a useful tool for generating realistic data including several kind of sources (Massive Black Hole binaries, EMRIs, cosmic string cusp, stochastic background, etc) and for preparing their analysis. It’s fully integrated to the Mock LISA Data Challenge. LISACode is not a detailed simulator at the engineering level but rather a tool whose purpose is to bridge the gap between the basic principles of LISA and a future, sophisticated end-to-end simulator.

[ascl:1112.010]
MRS3D: 3D Spherical Wavelet Transform on the Sphere

Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D Spherical Fourier-Bessel (SFB) analysis is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. We present a new fast Discrete Spherical Fourier-Bessel Transform (DSFBT) based on both a discrete Bessel Transform and the HEALPIX angular pixelisation scheme. We tested the 3D wavelet transform and as a toy-application, applied a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and found we can successfully remove noise without much loss to the large scale structure. The new spherical 3D isotropic wavelet transform, called MRS3D, is ideally suited to analysing and denoising future 3D spherical cosmological surveys; it uses a novel discrete spherical Fourier-Bessel Transform. MRS3D is based on two packages, IDL and Healpix and can be used only if these two packages have been installed.

[ascl:1112.011]
CMBview: A Mac OS X program for viewing HEALPix-format sky map data on a sphere

CMBview is a viewer for FITS files containing HEALPix sky maps. Sky maps are projected onto a 3d sphere which can be rotated and zoomed interactively with the mouse. Features include:

- rendering of the field of Stokes vectors

- ray-tracing mode in which each screen pixel is projected onto the sphere for high quality rendering

- control over sphere lighting

- export an arbitrarily large rendered texture

- variety of preset colormaps

[ascl:1112.012]
CORA: Emission Line Fitting with Maximum Likelihood

CORA analyzes emission line spectra with low count numbers and fits them to a line using the maximum likelihood technique. CORA uses a rigorous application of Poisson statistics. From the assumption of Poissonian noise, the software derives the probability for a model of the emission line spectrum to represent the measured spectrum. The likelihood function is used as a criterion for optimizing the parameters of the theoretical spectrum and a fixed point equation is derived allowing an efficient way to obtain line fluxes. CORA has been applied to an X-ray spectrum with the Low Energy Transmission Grating Spectrometer (LETGS) on board the Chandra observatory.

[ascl:1112.013]
XEphem: Interactive Astronomical Ephemeris

XEphem is a scientific-grade interactive astronomical ephemeris package for UNIX-like systems. Written in C, X11 and Motif, it is easily ported to systems. XEphem computes heliocentric, geocentric and topocentric information for all objects and has built-in support for all planets, the moons of Mars, Jupiter, Saturn, Uranus and Earth, central meridian longitude of Mars and Jupiter, Saturn's rings, and Jupiter's Great Red Spot. It allows user-defined objects including stars, deepsky objects, asteroids, comets and Earth satellites, provides special efficient handling of large catalogs including Tycho, Hipparcos, GSC, displays data in configurable tabular formats in conjunction with several interactive graphical views, and displays a night-at-a-glance 24 hour graphic showing when any selected objects are up. It also displays 3-D stereo Solar System views that are particularly well suited for visualizing comet trajectories, quickly finds all close pairs of objects in the sky, and sorts and prints all catalogs with very flexible criteria for creating custom observing lists. Its capabilities are listed more fully in the user manual introduction.

[ascl:1112.014]
PyEphem: Astronomical Ephemeris for Python

PyEphem provides scientific-grade astronomical computations for the Python programming language. Given a date and location on the Earth’s surface, it can compute the positions of the Sun and Moon, of the planets and their moons, and of any asteroids, comets, or earth satellites whose orbital elements the user can provide. Additional functions are provided to compute the angular separation between two objects in the sky, to determine the constellation in which an object lies, and to find the times at which an object rises, transits, and sets on a particular day.

The numerical routines that lie behind PyEphem are those from the wonderful XEphem astronomy application, whose author, Elwood Downey, generously gave permission for us to use them as the basis for PyEphem.

[ascl:1112.015]
Dexter: Data Extractor for scanned graphs

The NASA Astrophysics Data System (ADS) now holds 1.3 million scanned pages, containing numerous plots and figures for which the original data sets are lost or inaccessible. The availability of scans of the figures can significantly ease the regeneration of the data sets. For this purpose, the ADS has developed Dexter, a Java applet that supports the user in this process. Dexter's basic functionality is to let the user manually digitize a plot by marking points and defining the coordinate transformation from the logical to the physical coordinate system. Advanced features include automatic identification of axes, tracing lines and finding points matching a template.

[ascl:1112.016]
PREDICT: Satellite tracking and orbital prediction

PREDICT is an open-source, multi-user satellite tracking and orbital prediction program written under the Linux operating system. PREDICT provides real-time satellite tracking and orbital prediction information to users and client applications through:

- the system console
- the command line
- a network socket
- the generation of audio speech

[ascl:1112.017]
ASpec: Astronomical Spectrum Analysis Package

ASpec is a spectrum and line analysis package developed at STScI. ASpec is designed as an add-on package for IRAF and incorporates a variety of analysis techniques for astronomical spectra. ASpec operates on spectra from a wide variety of ground-based and space-based instruments and allows simultaneous handling of spectra from different wavelength regimes. The package accommodates non-linear dispersion relations and provides a variety of functions, individually or in combination, with which to fit spectral features and the continuum. It also permits the masking of known bad data. ASpec provides a powerful, intuitive graphical user interface implemented using the IRAF Object Manager and customized to handle: data input/output (I/O); on-line help; selection of relevant features for analysis; plotting and graphical interaction; and data base management.

[ascl:1112.018]
SwiftVis: Data Analysis & Visualization For Planetary Science

SwiftVis is a tool originally developed as part of a rewrite of Swift to be used for analysis and plotting of simulations performed with Swift and Swifter. The extensibility built into the design has allowed us to make SwiftVis a general purpose analysis and plotting package customized to be usable by the planetary science community at large. SwiftVis is written in Java and has been tested on Windows, Linux, and Mac platforms. Its graphical interface allows users to do complex analysis and plotting without having to write custom code.

[ascl:1112.019]
Aladin: Interactive Sky Atlas

Aladin is an interactive software sky atlas allowing the user to visualize digitized astronomical images, superimpose entries from astronomical catalogues or databases, and interactively access related data and information from the Simbad database, the VizieR service and other archives for all known sources in the field.

Created in 1999, Aladin has become a widely-used VO tool capable of addressing challenges such as locating data of interest, accessing and exploring distributed datasets, visualizing multi-wavelength data. Compliance with existing or emerging VO standards, interconnection with other visualisation or analysis tools, ability to easily compare heterogeneous data are key topics allowing Aladin to be a powerful data exploration and integration tool as well as a science enabler.

[ascl:1111.001]
HIPE: Herschel Interactive Processing Environment

The Herschel Space Observatory is the fourth cornerstone mission in the ESA science programme and performs photometry and spectroscopy in the 55 - 672 micron range. The development of the Herschel Data Processing System started in 2002 to support the data analysis for Instrument Level Tests. The Herschel Data Processing System was used for the pre-flight characterisation of the instruments, and during various ground segment test campaigns. Following the successful launch of Herschel 14th of May 2009 the Herschel Data Processing System demonstrated its maturity when the first PACS preview observation of M51 was processed within 30 minutes of reception of the first science data after launch. Also the first HIFI observations on DR21 were successfully reduced to high quality spectra, followed by SPIRE observations on M66 and M74. A fast turn-around cycle between data retrieval and the production of science-ready products was demonstrated during the Herschel Science Demonstration Phase Initial Results Workshop held 7 months after launch, which is a clear proof that the system has reached a good level of maturity.

[ascl:1111.002]
CRBLASTER: A Parallel-Processing Computational Framework for Embarrassingly-Parallel Image-Analysis Algorithms

The development of parallel-processing image-analysis codes is generally a challenging task that requires complicated choreography of interprocessor communications. If, however, the image-analysis algorithm is embarrassingly parallel, then the development of a parallel-processing implementation of that algorithm can be a much easier task to accomplish because, by definition, there is little need for communication between the compute processes. I describe the design, implementation, and performance of a parallel-processing image-analysis application, called CRBLASTER, which does cosmic-ray rejection of CCD (charge-coupled device) images using the embarrassingly-parallel L.A.COSMIC algorithm. CRBLASTER is written in C using the high-performance computing industry standard Message Passing Interface (MPI) library. The code has been designed to be used by research scientists who are familiar with C as a parallel-processing computational framework that enables the easy development of parallel-processing image-analysis programs based on embarrassingly-parallel algorithms. The CRBLASTER source code is freely available at the official application website at the National Optical Astronomy Observatory. Removing cosmic rays from a single 800x800 pixel Hubble Space Telescope WFPC2 image takes 44 seconds with the IRAF script lacos_im.cl running on a single core of an Apple Mac Pro computer with two 2.8-GHz quad-core Intel Xeon processors. CRBLASTER is 7.4 times faster processing the same image on a single core on the same machine. Processing the same image with CRBLASTER simultaneously on all 8 cores of the same machine takes 0.875 seconds -- which is a speedup factor of 50.3 times faster than the IRAF script. A detailed analysis is presented of the performance of CRBLASTER using between 1 and 57 processors on a low-power Tilera 700-MHz 64-core TILE64 processor.

[ascl:1111.003]
Saada: A Generator of Astronomical Database

Saada transforms a set of heterogeneous FITS files or VOtables of various categories (images, tables, spectra, etc.) in a powerful database deployed on the Web. Databases are located on your host and stay independent of any external server. This job doesn’t require writing code. Saada can mix data of various categories in multiple collections. Data collections can be linked each to others making relevant browsing paths and allowing data-mining oriented queries. Saada supports 4 VO services (Spectra, images, sources and TAP) . Data collections can be published immediately after the deployment of the Web interface.

[ascl:1111.004]
CIGALE: Code Investigating GALaxy Emission

The CIGALE code has been developed to study the evolution of galaxies by comparing modelled galaxy spectral energy distributions (SEDs) to observed ones from the far ultraviolet to the far infrared. It extends the SED fitting algorithm written by Burgarella et al. (2005, MNRAS 360, 1411). While the previous code was designed to fit SEDs in the optical and near infrared, CIGALE is able to fit SEDs up to the far infrared using Dale & Helou (2002, ApJ 576, 159). CIGALE Bayesian and CIGALE Monte Carlo Markov Chain are available.

[ascl:1111.005]
SPECTCOL: Spectroscopic and Collisional Data Retrieval

Studies of astrophysical non-LTE media require the combination of atomic and molecular spectroscopic and collisional data often described differently in various databases. SPECTCOL is a tool that implements VAMDC standards, retrieve relevant information from different databases such as CDMS, HITRAN, BASECOL, and can upload local files. All transfer of data between the client and the databases use the VAMDC-XSAMS schema. The spectroscopic and collisional information is combined and useful outputs (ascii or xsams) are provided for the study of the interstellar medium.

[ascl:1111.006]
MOPEX: MOsaicker and Point source EXtractor

MOPEX (MOsaicker and Point source EXtractor) is a package for reducing and analyzing imaging data, as well as MIPS SED data. MOPEX includes the point source extraction package, APEX.

MOPEX is designed to allow the user to:

- perform sophisticated background matching of individual data frames
- mosaic the individual frames downloaded from the Spitzer archive
- perform both temporal and spatial outlier rejection during mosaicking
- apply offline pointing refinement for MIPS data (refinement is already applied to IRAC data)
- perform source detection on the mosaics using APEX
- compute aperture photometry or PRF-fitting photometry for point sources
- perform interpolation, coaddition, and spectrum extraction of MIPS SED images.

[ascl:1111.007]
CUBISM: CUbe Builder for IRS Spectra Maps

Sings Irs Team; Smith, J. D.; Armus, Lee; Bot, Caroline; Buckalew, Brent; Dale, Danny; Helou, George; Jarrett, Tom; Roussel, Helene; Sheth, Kartik

CUBISM, written in IDL, constructs spectral cubes, maps, and arbitrary aperture 1D spectral extractions from sets of mapping mode spectra taken with Spitzer's IRS spectrograph. CUBISM is optimized for non-sparse maps of extended objects, e.g. the nearby galaxy sample of SINGS, but can be used with data from any spectral mapping AOR (primarily validated for maps which are designed as suggested by the mapping HOWTO).

[ascl:1111.008]
SITools2: A Framework for Archival Systems

SITools2 is a CNES generic tool performed by a joint effort between CNES and scientific laboratories. SITools provides a self-manageable data access layer deployed on already existing scientific laboratory databases. This new version of SITools is a JAVA-based framework, under open source license, that provides a portable archive system, highly configurable, easy to use by laboratories, with a plugin mechanism so developers can add their own applications.

[ascl:1111.009]
MESS: Multi-purpose Exoplanet Simulation System

Bonavita, M.; Chauvin, G.; Desidera, S.; Gratton, R.; Janson, M.; Beuzit, J. L.; Kasper, M.; Mordasini, C.

MESS is a Monte Carlo simulation IDL code which uses either the results of the statistical analysis of the properties of discovered planets, or the results of the planet formation theories, to build synthetic planet populations fully described in terms of frequency, orbital elements and physical properties. They can then be used to either test the consistency of their properties with the observed population of planets given different detection techniques or to actually predict the expected number of planets for future surveys. It can be used to probe the physical and orbital properties of a putative companion within the circumstellar disk of a given star and to test constrain the orbital distribution properties of a potential planet population around the members of the TW Hydrae association. Finally, using in its predictive mode, the synergy of future space and ground-based telescopes instrumentation has been investigated to identify the mass-period parameter space that will be probed in future surveys for giant and rocky planets.

[ascl:1111.010]
Starbase Data Tables: An ASCII Relational Database for Unix

Database management is an increasingly important part of astronomical data analysis. Astronomers need easy and convenient ways of storing, editing, filtering, and retrieving data about data. Commercial databases do not provide good solutions for many of the everyday and informal types of database access astronomers need. The Starbase database system with simple data file formatting rules and command line data operators has been created to answer this need. The system includes a complete set of relational and set operators, fast search/index and sorting operators, and many formatting and I/O operators. Special features are included to enhance the usefulness of the database when manipulating astronomical data. The software runs under UNIX, MSDOS and IRAF.

[ascl:1111.011]
3DEX: Fast Fourier-Bessel Decomposition of Spherical 3D Surveys

High precision cosmology requires analysis of large scale surveys in 3D spherical coordinates, i.e. Fourier-Bessel decomposition. Current methods are insufficient for future data-sets from wide-field cosmology surveys. 3DEX (3D EXpansions) is a public code for fast Fourier-Bessel decomposition of 3D all-sky surveys which takes advantage of HEALPix for the calculation of tangential modes. For surveys with millions of galaxies, computation time is reduced by a factor 4-12 depending on the desired scales and accuracy. The formulation is also suitable for pre-calculations and external storage of the spherical harmonics, which allows for further speed improvements. The 3DEX code can accommodate data with masked regions of missing data. It can be applied not only to cosmological data, but also to 3D data in spherical coordinates in other scientific fields.

[ascl:1111.012]
VAPOR: Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers

VAPOR is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that runs on most UNIX and Windows systems equipped with modern 3D graphics cards. VAPOR provides:

- A visual data discovery environment tailored towards the specialized needs of the astro and geosciences CFD community
- A desktop solution capable of handling terascale size data sets
- Advanced interactive 3D visualization tightly coupled with quantitative data analysis
- Support for multi-variate, time-varying data
- Close coupling with RSI's powerful interpretive data language, IDL
- Support for 3D visualization of WRF-ARW datasets

[ascl:1111.013]
FIBRE-pac: FMOS Image-based Reduction Package

Iwamuro, F.; Moritani, Y.; Yabe, K.; Sumiyoshi, M.; Kawate, K.; Tamura, N.; Akiyama, M.; Kimura, M.; Takato, N.; Tait, P.; Ohta, K.; Totani, T.; Suzuki, Y.; Tonegawa, M.

The FIBRE-pac (FMOS image-based reduction package) is an IRAF-based reduction tool for the fiber multiple-object spectrograph (FMOS) of the Subaru telescope. To reduce FMOS images, a number of special techniques are necessary because each image contains about 200 separate spectra with airglow emission lines variable in spatial and time domains, and with complicated throughput patterns for the airglow masks. In spite of these features, almost all of the reduction processes except for a few steps are carried out automatically by scripts in text format making it easy to check the commands step by step. Wavelength- and flux-calibrated images together with their noise maps are obtained using this reduction package.

[ascl:1111.014]
FITSH: Software Package for Image Processing

FITSH provides a standalone environment for analysis of data acquired by imaging astronomical detectors. The package provides utilities both for the full pipeline of subsequent related data processing steps (including image calibration, astrometry, source identification, photometry, differential analysis, low-level arithmetic operations, multiple image combinations, spatial transformations and interpolations, etc.) and for aiding the interpretation of the (mainly photometric and/or astrometric) results. The package also features a consistent implementation of photometry based on image subtraction, point spread function fitting and aperture photometry and provides easy-to-use interfaces for comparisons and for picking the most suitable method for a particular problem. The utilities in the package are built on the top of the commonly used UNIX/POSIX shells (hence the name of the package), therefore both frequently used and well-documented tools for such environments can be exploited and managing massive amount of data is rather convenient.

[ascl:1111.015]
TIPSY: Code for Display and Analysis of N-body Simulations

The development of TIPSY was motivated by the need to quickly display and analyze the results of N-body simulations. Most data visualization packages are designed for the display of gridded data, and hence are unsuitable for use with particle data. Therefore, a special package was built that could easily perform the following functions:

1.) Display particle positions (as points), and velocities (as line segments) from an arbitrary viewpoint;

2.) Zoom in to a chosen position. Due to their extremely clustered nature, structure of interest in an N-body simulation is often so small that it cannot be seen when looking at the simulation as a whole;

3.) Color particles to display scalar fields. Examples of such fields are potential energy, or for SPH particles, density and temperature;

4.) Selection of a subset of the particles for display and analysis. Regions of interest are generally small subsets of the simulation;

5.) Following selected particles from one timestep to another; and,

6.) Finding cumulative properties of a collection of particles. This usually involves just a sum over the particles.

The basic data structure is an array of particle structures. Since TIPSY was built for use with cosmological N-body simulations, there are actually three separate arrays for each of the types of particle used in such simulations: collisionless particles, SPH particles, and star particles. A single timestep is read into these arrays from a disk file. Display is done by finding the x and y coordinates of the particles in the rotated coordinate system, and storing them in arrays. Screen coordinates are calculated from these arrays according to the current zoom factor. Also, a software Z-buffer is maintained to save time if many particles project to the same screen pixel. There are several types of display. An "all plot" displays all particles colored according to their type. A "radial plot" will color particles according to the projection of the velocity along the line-of-sight. A "gas plot" will color gas according to SPH quantities such as density, temperature, neutral hydrogen fraction, etc. Subsets of particles are maintained using boxes." A box structure contains a bounding box, and an array of pointers to particles within the box. All display and analysis functions are performed on the "active box." By default all particles are loaded into box 0, which becomes the active box. If a new timestep is read from disk, all boxes are destroyed. A selection of particles can be followed between timesteps via a "mark" array. Marked particles are displayed in a different color, and the analysis functions can be told to only operate on the marked particles.

[ascl:1110.001]
analytic_infall: A Molecular Line Infall Fitting Program

This code contains several simple radiative transfer models used for fitting the blue-asymmetric spectral line signature often found in infalling molecular cloud cores. It attempts to provide a direct measure of several physical parameters of the infalling core, including infall velocity, excitation temperature, and line of site optical depth. The code includes 6 radiative transfer models, however the conclusion of the associated paper is that the 5 parameter "hill" model (hill5) is most likely the best match to the physical excitation conditions of real infalling Bonnor-Ebert type clouds.

[ascl:1110.002]
DarkSUSY: Supersymmetric Dark Matter Calculations

Gondolo, Paolo; Edsjö, Joakim; Bergström, Lars; Ullio, Piero; Schelke, Mia; Baltz, Ted; Bringmann, Torsten; Duda, Gintaras

DarkSUSY, written in Fortran, is a publicly-available advanced numerical package for neutralino dark matter calculations. In DarkSUSY one can compute the neutralino density in the Universe today using precision methods which include resonances, pair production thresholds and coannihilations. Masses and mixings of supersymmetric particles can be computed within DarkSUSY or with the help of external programs such as FeynHiggs, ISASUGRA and SUSPECT. Accelerator bounds can be checked to identify viable dark matter candidates. DarkSUSY also computes a large variety of astrophysical signals from neutralino dark matter, such as direct detection in low-background counting experiments and indirect detection through antiprotons, antideuterons, gamma-rays and positrons from the Galactic halo or high-energy neutrinos from the center of the Earth or of the Sun.

[ascl:1110.003]
iGalFit: An Interactive Tool for GalFit

We present a suite of IDL routines to interactively run GALFIT whereby the various surface brightness profiles (and their associated parameters) are represented by regions, which the User is expected to place. The regions may be saved and/or loaded from the ASCII format used by ds9 or in the Hierarchical Data Format (version 5). The software has been tested to run stably on Mac OS X and Linux with IDL 7.0.4. In addition to its primary purpose of modeling galaxy images with GALFIT, this package has several ancillary uses, including a flexible image display routines, several basic photometry functions, and qualitatively assessing Source Extractor. We distribute the package freely and without any implicit or explicit warranties, guarantees, or assurance of any kind. We kindly ask users to report any bugs, errors, or suggestions to us directly (as opposed to fixing them themselves) to ensure version control and uniformity.

[ascl:1110.004]
SHTOOLS: Tools for Working with Spherical Harmonics

SHTOOLS is an archive of fortran 95 based software that can be used to perform (among others) spherical harmonic transforms and reconstructions, rotations of spherical harmonic coefficients, and multitaper spectral analyses on the sphere. The package accommodates any standard normalization of the spherical harmonic functions ("geodesy" 4π normalized, Schmidt semi-normalized, orthonormalized, and unnormalized), and either real or complex spherical harmonics can be employed. Spherical harmonic transforms are calculated by exact quadrature rules using either (1) the sampling theorem of Driscoll and Healy (1994) where data are equally sampled (or spaced) in latitude and longitude, or (2) Gauss-Legendre quadrature. A least squares inversion routine for irregularly sampled data is included as well. The Condon-Shortley phase factor of (-1)m can be used or excluded with the associated Legendre functions. The spherical harmonic transforms are accurate to approximately degree 2800, corresponding to a spatial resolution of better than 4 arc minutes. Routines are included for performing localized multitaper spectral analyses and standard gravity calculations, such as computation of the geoid, and the determination of the potential associated with finite-amplitude topography. The routines are fast. Spherical harmonic transforms and reconstructions take on the order of 1 second for bandwidths less than 600 and about 3 minutes for bandwidths close to 2800.

[ascl:1110.005]
ZEBRA: Zurich Extragalactic Bayesian Redshift Analyzer

The current version of the Zurich Extragalactic Bayesian Redshift Analyzer (ZEBRA) combines and extends several of the classical approaches to produce accurate photometric redshifts down to faint magnitudes. In particular, ZEBRA uses the template-fitting approach to produce Maximum Likelihood and Bayesian redshift estimates based on: (1.) An automatic iterative technique to correct the original set of galaxy templates to best represent the SEDs of real galaxies at different redshifts; (2.) A training set of spectroscopic redshifts for a small fraction of the photometric sample; and (3.) An iterative technique for Bayesian redshift estimates, which extracts the full two-dimensional redshift and template probability function for each galaxy.

[ascl:1110.006]
STIFF: Converting Scientific FITS Images to TIFF

STIFF is a program that converts scientific FITS1 images to the more popular TIFF2 format for illustration purposes. Most FITS readers and converters do not do a proper job at converting FITS image data to 8 bits. 8-bit images stored in JPEG, PNG or TIFF files have the intensities implicitely stored in a non-linear way. Most current FITS image viewers and converters provide the user an incorrect translation of the FITS image content by simply rescaling linearly input pixel values. A first consequence is that the people working on astronomical images usually have to apply narrow intensity cuts or square-root or logarithmic intensity transformations to actually see something on their deep-sky images. A less obvious consequence is that colors obtained by combining images processed this way are not consistent across such a large range of surface brightnesses. Though with other software the user is generally afforded a choice of nonlinear transformations to apply in order to make the faint stuff stand out more clearly in the images, with the limited selection of choices provides, colors will not be accurately rendered, and some manual tweaking will be necessary. The purpose of STIFF is to produce beautiful pictures in an automatic and consistent way.

[ascl:1110.007]
GammaLib: Toolbox for High-level Analysis of Astronomical Gamma-ray Data

The GammaLib is a versatile toolbox for the high-level analysis of astronomical gamma-ray data. It is implemented as a C++ library that is fully scriptable in the Python scripting language. The library provides core functionalities such as data input and output, interfaces for parameter specifications, and a reporting and logging interface. It implements instruments specific functionalities such as instrument response functions and data formats. Instrument specific functionalities share a common interface to allow for extension of the GammaLib to include new gamma-ray instruments. The GammaLib provides an abstract data analysis framework that enables simultaneous multi-mission analysis.

[ascl:1110.008]
Glnemo2: Interactive Visualization 3D Program

Glnemo2 is an interactive 3D visualization program developed in C++ using the OpenGL library and Nokia QT 4.X API. It displays in 3D the particles positions of the different components of an nbody snapshot. It quickly gives a lot of information about the data (shape, density area, formation of structures such as spirals, bars, or peanuts). It allows for in/out zooms, rotations, changes of scale, translations, selection of different groups of particles and plots in different blending colors. It can color particles according to their density or temperature, play with the density threshold, trace orbits, display different time steps, take automatic screenshots to make movies, select particles using the mouse, and fly over a simulation using a given camera path. All these features are accessible from a very intuitive graphic user interface.

Glnemo2 supports a wide range of input file formats (Nemo, Gadget 1 and 2, phiGrape, Ramses, list of files, realtime gyrfalcON simulation) which are automatically detected at loading time without user intervention. Glnemo2 uses a plugin mechanism to load the data, so that it is easy to add a new file reader. It's powered by a 3D engine which uses the latest OpenGL technology, such as shaders (glsl), vertex buffer object, frame buffer object, and takes in account the power of the graphic card used in order to accelerate the rendering. With a fast GPU, millions of particles can be rendered in real time. Glnemo2 runs on Linux, Windows (using minGW compiler), and MaxOSX, thanks to the QT4API.

[ascl:1110.009]
AAOGlimpse: Three-dimensional Data Viewer

AAOGlimpse is an experimental display program that uses OpenGL to display FITS data (and even JPEG images) as 3D surfaces that can be rotated and viewed from different angles, all in real-time. It is WCS-compliant and designed to handle three-dimensional data. Each plane in a data cube is surfaced in the same way, and the program allows the user to travel through a cube by 'peeling off' successive planes, or to look into a cube by suppressing the display of data below a given cutoff value. It can blink images and can superimpose images and contour maps from different sources using their world coordinate data. A limited socket interface allows communication with other programs.

[ascl:1110.010]
MOCASSIN: MOnte CArlo SimulationS of Ionized Nebulae

MOCASSIN is a fully 3D or 2D photoionisation and dust radiative transfer code which employs a Monte Carlo approach to the transfer of radiation through media of arbitrary geometry and density distribution. Written in Fortran, it was originally developed for the modelling of photoionised regions like HII regions and planetary nebulae and has since expanded and been applied to a variety of astrophysical problems, including modelling clumpy dusty supernova envelopes, star forming galaxies, protoplanetary disks and inner shell fluorence emission in the photospheres of stars and disk atmospheres. The code can deal with arbitrary Cartesian grids of variable resolution, it has successfully been used to model complex density fields from SPH calculations and can deal with ionising radiation extending from Lyman edge to the X-ray. The dust and gas microphysics is fully coupled both in the radiation transfer and in the thermal balance.

[ascl:1110.011]
Pacerman: Polarisation Angle CorrEcting Rotation Measure ANalysis

Pacerman, written in IDL, is a new method to calculate Faraday rotation measure maps from multi-frequency polarisation angle data. In order to solve the so called n-pi-ambiguity problem which arises from the observationally ambiguity of the polarisation angle which is only determined up to additions of n times pi, where n is an integer, we suggest using a global scheme. Instead of solving the n-pi-ambiguity for each data point independently, our algorithm, which we chose to call Pacerman solves the n-pi-ambiguity for a high signal-to-noise region "democratically" and uses this information to assist computations in adjacent low signal-to-noise areas.

[ascl:1110.012]
Starlink: Multi-purpose Astronomy Software

Starlink has many applications within it to meet a variety of needs; it includes:

- a general astronomical image viewer;
- data reduction tools, including programs for reducing CCD-like data;
- general-purpose data-analysis and visualisation tools;
- image processing, data visualisation, and manipulating NDF components;
- a flexible and powerful library for handling World Coordinate Systems (partly based on the SLALIB library);
- a library of routines intended to make accurate and reliable positional-astronomy applications easier to write; and
- and a Hierarchical Data System that is portable and flexible for storing and retrieving data.

[ascl:1110.013]
S2HAT: Scalable Spherical Harmonic Transform Library

Many problems in astronomy and astrophysics require a computation of the spherical harmonic transforms. This is in particular the case whenever data to be analyzed are distributed over the sphere or a set of corresponding mock data sets has to be generated. In many of those contexts, rapidly improving resolutions of both the data and simulations puts increasingly bigger emphasis on our ability to calculate the transforms quickly and reliably.

The scalable spherical harmonic transform library S2HAT consists of a set of flexible, massively parallel, and scalable routines for calculating diverse (scalar, spin-weighted, etc) spherical harmonic transforms for a class of isolatitude sky grids or pixelizations. The library routines implement the standard algorithm with the complexity of O(n^3/2), where n is a number of pixels/grid points on the sphere, however, owing to their efficient parallelization and advanced numerical implementation, they achieve very competitive performance and near perfect scalability. S2HAT is written in Fortran 90 with a C interface. This software is a derivative of the spherical harmonic transforms included in the HEALPix package and is based on both serial and MPI routines of its version 2.01, however, since version 2.5 this software is fully autonomous of HEALPix and can be compiled and run without the HEALPix library.

[ascl:1110.014]
pureS2HAT: S 2HAT-based Pure E/B Harmonic Transforms

The pS2HAT routines allow efficient, parallel calculation of the so-called 'pure' polarized multipoles. The computed multipole coefficients are equal to the standard pseudo-multipoles calculated for the apodized sky maps of the Stokes parameters Q and U subsequently corrected by so-called counterterms. If the applied apodizations fullfill certain boundary conditions, these multipoles correspond to the pure multipoles. Pure multipoles of one type, i.e., either E or B, are ensured not to contain contributions from the other one, at least to within numerical artifacts. They can be therefore further used in the estimation of the sky power spectra via the pseudo power spectrum technique, which has to however correctly account for the applied apodization on the one hand, and the presence of the counterterms, on the other.

In addition, the package contains the routines permitting calculation of the spin-weighted apodizations, given an input scalar, i.e., spin-0 window. The former are needed to compute the counterterms. It also provides routines for maps and window manipulations. The routines are written in C and based on the S2HAT library, which is used to perform all required spherical harmonic transforms as well as all inter-processor communication. They are therefore parallelized using MPI and follow the distributed-memory computational model. The data distribution patterns, pixelization choices, conventions etc are all as those assumed/allowed by the S2HAT library.

[ascl:1110.015]
atlant: Advanced Three Level Approximation for Numerical Treatment of Cosmological Recombination

atlant is a public numerical code for fast calculations of cosmological recombination of primordial hydrogen-helium plasma is presented. This code is based on the three-level approximation (TLA) model of recombination and allows us to take into account some "fine'' physical effects of cosmological recombination simultaneously with using fudge factors.

[ascl:1110.016]
REBOUND: Multi-purpose N-body code for collisional dynamics

REBOUND is a multi-purpose N-body code which is freely available under an open-source license. It was designed for collisional dynamics such as planetary rings but can also solve the classical N-body problem. It is highly modular and can be customized easily to work on a wide variety of different problems in astrophysics and beyond.

REBOUND comes with three symplectic integrators: leap-frog, the symplectic epicycle integrator (SEI) and a Wisdom-Holman mapping (WH). It supports open, periodic and shearing-sheet boundary conditions. REBOUND can use a Barnes-Hut tree to calculate both self-gravity and collisions. These modules are fully parallelized with MPI as well as OpenMP. The former makes use of a static domain decomposition and a distributed essential tree. Two new collision detection modules based on a plane-sweep algorithm are also implemented. The performance of the plane-sweep algorithm is superior to a tree code for simulations in which one dimension is much longer than the other two and in simulations which are quasi-two dimensional with less than one million particles.

[ascl:1110.017]
POWMES: Measuring the Power Spectrum in an N-body Simulation

POWMES is a F90 program to measure very accurately the power spectrum in a N-body simulation, using Taylor expansion of some order on the cosine and sine transforms. It can read GADGET format and requires FFTW2 to be installed.

[ascl:1110.018]
MADmap: Fast Parallel Maximum Likelihood CMB Map Making Code

MADmap produces maximum-likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by Cosmic Microwave Background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum-likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap has the ability to address problems typically encountered in the analysis of realistic CMB data sets. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analyzing the largest data sets now being collected on computing resources currently available.

[ascl:1110.019]
CosmoNest: Cosmological Nested Sampling

CosmoNest is an algorithm for cosmological model selection. Given a model, defined by a set of parameters to be varied and their prior ranges, and data, the algorithm computes the evidence (the marginalized likelihood of the model in light of the data). The Bayes factor, which is proportional to the relative evidence of two models, can then be used for model comparison, i.e. to decide whether a model is an adequate description of data, or whether the data require a more complex model.

For convenience, CosmoNest, programmed in Fortran, is presented here as an optional add-on to CosmoMC, which is widely used by the cosmological community to perform parameter fitting within a model using a Markov-Chain Monte-Carlo (MCMC) engine. For this reason it can be run very easily by anyone who is able to compile and run CosmoMC. CosmoNest implements a different sampling strategy, geared for computing the evidence very accurately and efficiently. It also provides posteriors for parameter fitting as a by-product.

[ascl:1110.020]
CROSS_CMBFAST: ISW-correlation Code

This code is an extension of CMBFAST4.5.1 to compute the ISW-correlation power spectrum and the 2-point angular ISW-correlation function for a given galaxy window function. It includes dark energy models specified by a constant equation of state (w) or a linear parameterization in the scale factor (w0,wa) and a constant sound speed (c2de). The ISW computation is limited to flat geometry. Differently from the original CMBFAST4.5 version dark energy perturbations are implemented for a general dark energy fluid specified by w(z) and c2de in synchronous gauge. For time varying dark energy models it is suggested not to cross the w=-1 line, as Dr. Wenkman says: "never cross the streams", bad things can happen.

[ascl:1110.021]
Univiewer: Visualisation Program for HEALPix Maps

Univiewer is a visualisation program for HEALPix maps. It is written in C++ and uses OpenGL and the wxWidgets library for cross-platform portability. Using it you can:

- Rotate and zoom maps on the sphere in 3D;
- Create high-resolution views of square patches of the map;
- Change maximum and minimum values of the colourmap interactively;
- Calculate the power spectrum of the full-sky map or a patch;
- Display any column of a HEALPix map FITS file on the sphere.

In the 3D view, a HEALPix map is projected onto a ECP pixelation to create a texture which is wrapped around the sphere. In calculating the power spectrum, the spherical harmonic transforms are computed using the same ECP pixelation. This inevitably leads to some discrepancies at small scales due to repixelation effects, but they are reasonably small.

[ascl:1110.022]
simple_cosfitter: Supernova-centric Cosmological Fitter

This is an implementation of a fairly simple-minded luminosity distance fitter, intended for use with supernova data. The calculational technique is based on evaluating the $chi^2$ of the model fit on a grid and marginalization over various nuisance parameters. Of course, the nature of these things is that this code has gotten steadily more complex, so perhaps the simple moniker is no longer justified.

[ascl:1110.023]
SiFTO: An Empirical Method for Fitting SN Ia Light Curves

SiFTO is an empirical method for modeling Type Ia supernova (SN Ia) light curves by manipulating a spectral template. We make use of high-redshift SN data when training the model, allowing us to extend it bluer than rest-frame U. This increases the utility of our high-redshift SN observations by allowing us to use more of the available data. We find that when the shape of the light curve is described using a stretch prescription, applying the same stretch at all wavelengths is not an adequate description. SiFTO therefore uses a generalization of stretch which applies different stretch factors as a function of both the wavelength of the observed filter and the stretch in the rest-frame B band. SiFTO has been compared to other published light-curve models by applying them to the same set of SN photometry, and it's been demonstrated that SiFTO and SALT2 perform better than the alternatives when judged by the scatter around the best-fit luminosity distance relationship. When SiFTO and SALT2 are trained on the same data set the cosmological results agree.

[ascl:1110.024]
CosmoMC SNLS: CosmoMC Plug-in to Analyze SNLS3 SN Data

This module is a plug-in for CosmoMC and requires that software. Though programmed to analyze SNLS3 SN data, it can also be used for other SN data provided the inputs are put in the right form. In fact, this is probably a good idea, since the default treatment that comes with CosmoMC is flawed. Note that this requires fitting two additional SN nuisance parameters (alpha and beta), but this is significantly faster than attempting to marginalize over them internally.

[ascl:1110.025]
MIS: A Miriad Interferometry Singledish Toolkit

MIS is a pipeline toolkit using the package MIRIAD to combine Interferometric and Single Dish data. This was prompted by our observations made with the Combined Array For Research in Millimeter-wave Astronomy (CARMA) interferometer of the star-forming region NGC 1333, a large survey highlighting the new 23-element and singledish observing modes. The project consists of 20 CARMA datasets each containing interferometric as well as simultaneously obtained single dish data, for 3 molecular spectral lines and continuum, in 527 different pointings, covering an area of about 8 by 11 arcminutes. A small group of collaborators then shared this toolkit and their parameters via CVS, and scripts were developed to ensure uniform data reduction across the group. The pipeline was run end-to-end each night that new observations were obtained, producing maps that contained all the data to date. This approach could serve as a model for repeated calibration and mapping of large mixed-mode correlation datasets from ALMA.

[ascl:1109.001]
PySpecKit: Python Spectroscopic Toolkit

PySpecKit is a Python spectroscopic analysis and reduction toolkit meant to be generally applicable to optical, infrared, and radio spectra. It is capable of reading FITS-standard and many non-standard file types including CLASS spectra. It contains procedures for line fitting including gaussian and voigt profile fitters, and baseline-subtraction routines. It is capable of more advanced line fitting using arbitrary model grids. Fitting can be done both in batch mode and interactively. PySpecKit also produces publication-quality plots with TeX axis labels and annotations. It is designed to be extensible, allowing user-written reader, writer, and fitting routines to be "plugged in." It is actively under development and currently in the 'alpha' phase, with plans for a beta release.

[ascl:1109.002]
ADIPLS: Aarhus Adiabatic Oscillation Package (ADIPACK)

The goal of the development of the Aarhus Adiabatic Oscillation Package was to have a simple and efficient tool for the computation of adiabatic oscillation frequencies and eigenfunctions for general stellar models, emphasizing also the accuracy of the results. The Fortran code offers considerable flexibility in the choice of integration method as well as ability to determine all frequencies of a given model, in a given range of degree and frequency. Development of the Aarhus adiabatic pulsation code started around 1978. Although the main features have been stable for more than a decade, development of the code is continuing, concerning numerical properties and output. The code has been provided as a generally available package and has seen substantial use at a number of installations. Further development of the package, including bringing the documentation closer to being up to date, is planned as part of the HELAS Coordination Action.

[ascl:1109.003]
SKIRT: Stellar Kinematics Including Radiative Transfer

SKIRT is a radiative transfer code based on the Monte Carlo technique. The name SKIRT, acronym for Stellar Kinematics Including Radiative Transfer, reflects the original motivation for its creation: it has been developed to study the effects of dust absorption and scattering on the observed kinematics of dusty galaxies. In a second stage, the SKIRT code was extended with a module to self-consistently calculate the dust emission spectrum under the assumption of local thermal equilibrium. This LTE version of SKIRT has been used to model the dust extinction and emission of various types of galaxies, as well as circumstellar discs and clumpy tori around active galactic nuclei. A new, extended version of SKIRT code can perform efficient 3D radiative transfer calculations including a self-consistent calculation of the dust temperature distribution and the associated FIR/submm emission with a full incorporation of the emission of transiently heated grains and PAH molecules.

[ascl:1109.004]
HAZEL: HAnle and ZEeman Light

A big challenge in solar and stellar physics in the coming years will be to decipher the magnetism of the solar outer atmosphere (chromosphere and corona) along with its dynamic coupling with the magnetic fields of the underlying photosphere. To this end, it is important to develop rigorous diagnostic tools for the physical interpretation of spectropolarimetric observations in suitably chosen spectral lines. HAZEL is a computer program for the synthesis and inversion of Stokes profiles caused by the joint action of atomic level polarization and the Hanle and Zeeman effects in some spectral lines of diagnostic interest, such as those of the He I 1083.0 nm and 587.6 nm (or D3) multiplets. It is based on the quantum theory of spectral line polarization, which takes into account in a rigorous way all the relevant physical mechanisms and ingredients (optical pumping, atomic level polarization, level crossings and repulsions, Zeeman, Paschen-Back and Hanle effects). The influence of radiative transfer on the emergent spectral line radiation is taken into account through a suitable slab model. The user can either calculate the emergent intensity and polarization for any given magnetic field vector or infer the dynamical and magnetic properties from the observed Stokes profiles via an efficient inversion algorithm based on global optimization methods.

[ascl:1109.005]
PolSpice: Spatially Inhomogeneous Correlation Estimator for Temperature and Polarisation

PolSpice (aka Spice) is a tool to statistically analyze Cosmic Microwave Background (CMB) data, as well as any other diffuse data pixelized on the sphere.

This Fortran90 program measures the 2 point auto (or cross-) correlation functions w(θ) and the angular auto- (or cross-) power spectra C(l) from one or (two) sky map(s) of Stokes parameters (intensity I and linear polarisation Q and U). It is based on the fast Spherical Harmonic Transforms allowed by isolatitude pixelisations such as Healpix [for Npix pixels over the whole sky, and a C(l) computed up to l=lmax, PolSpice complexity scales like Npix1/2 lmax2 instead of Npix lmax2]. It corrects for the effects of the masks and can deal with inhomogeneous weights given to the pixels of the map. In the case of polarised data, the mixing of the E and B modes due to the cut sky and pixel weights can be corrected for to provide an unbiased estimate of the "magnetic" (B) component of the polarisation power spectrum. Most of the code is parallelized for shared memory (SMP) architecture using OpenMP.

[ascl:1109.006]
MultiNest: Efficient and Robust Bayesian Inference

We present further development and the first public release of our multimodal nested sampling algorithm, called MultiNest. This Bayesian inference tool calculates the evidence, with an associated error estimate, and produces posterior samples from distributions that may contain multiple modes and pronounced (curving) degeneracies in high dimensions. The developments presented here lead to further substantial improvements in sampling efficiency and robustness, as compared to the original algorithm presented in Feroz & Hobson (2008), which itself significantly outperformed existing MCMC techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MultiNest algorithm is demonstrated by application to two toy problems and to a cosmological inference problem focusing on the extension of the vanilla $Lambda$CDM model to include spatial curvature and a varying equation of state for dark energy. The MultiNest software is fully parallelized using MPI and includes an interface to CosmoMC (ascl:1106.025). It will also be released as part of the SuperBayeS package (ascl:1109.007) for the analysis of supersymmetric theories of particle physics.

[ascl:1109.007]
SuperBayeS: Supersymmetry Parameters Extraction Routines for Bayesian Statistics

SuperBayeS is a package for fast and efficient sampling of supersymmetric theories. It uses Bayesian techniques to explore multidimensional SUSY parameter spaces and to compare SUSY predictions with observable quantities, including sparticle masses, collider observables, dark matter abundance, direct detection cross sections, indirect detection quantities etc. Scanning can be performed using Markov Chain Monte Carlo (MCMC) technology or even more efficiently by employing a new scanning technique called, MultiNest. which implements the nested sampling algorithm. Using MultiNest, a full 8-dimensional scan of the CMSSM takes about 12 hours on 10 2.4GHz CPUs. There is also an option for old-style fixed-grid scanning. A discussion forum for SuperBayeS is available.

The package combines SoftSusy, DarkSusy, FeynHiggs, Bdecay, MultiNest and MicrOMEGAs. Some of the routines and the plotting tools are based on CosmoMC.

SuperBayeS comes with SuperEGO, a MATLAB graphical user interface tool for interactive plotting of the results. SuperEGO has been developed by Rachid Lemrani and is based on CosmoloGUI by Sarah Bridle.

[ascl:1109.008]
Multipole Vectors: Decomposing Functions on a Sphere

We propose a novel representation of cosmic microwave anisotropy maps, where each multipole order l is represented by l unit vectors pointing in directions on the sky and an overall magnitude. These "multipole vectors and scalars" transform as vectors under rotations. Like the usual spherical harmonics, multipole vectors form an irreducible representation of the proper rotation group SO(3). However, they are related to the familiar spherical harmonic coefficients, alm, in a nonlinear way, and are therefore sensitive to different aspects of the CMB anisotropy. Nevertheless, it is straightforward to determine the multipole vectors for a given CMB map and we present an algorithm to compute them. Using the WMAP full-sky maps, we perform several tests of the hypothesis that the CMB anisotropy is statistically isotropic and Gaussian random. We find that the result from comparing the oriented area of planes defined by these vectors between multipole pairs 2<=l1!=l2<=8 is inconsistent with the isotropic Gaussian hypothesis at the 99.4% level for the ILC map and at 98.9% level for the cleaned map of Tegmark et al. A particular correlation is suggested between the l=3 and l=8 multipoles, as well as several other pairs. This effect is entirely different from the now familiar planarity and alignment of the quadrupole and octupole: while the aforementioned is fairly unlikely, the multipole vectors indicate correlations not expected in Gaussian random skies that make them unusually likely. The result persists after accounting for pixel noise and after assuming a residual 10% dust contamination in the cleaned WMAP map. While the definitive analysis of these results will require more work, we hope that multipole vectors will become a valuable tool for various cosmological tests, in particular those of cosmic isotropy.

[ascl:1109.009]
CMBquick: Spectrum and Bispectrum of Cosmic Microwave Background (CMB)

CMBquick is a package for Mathematica in which tools are provided to compute the spectrum and bispectrum of Cosmic Microwave Background (CMB). It is unavoidably slow, but the main goal is not to design a tool which can be used for systematic exploration of parameters in cosmology, but rather a toy CMB code which is transparent and easily modified. Considering this, the name chosen is nothing but a joke which refers to the widely spread and used softwares CMBFAST, CAMB or CMBeasy (ascl:1007.004), which should be used for serious and heavy first order CMB computations, and which are indeed very fast.

The package CMBquick is unavoidably slow when it comes to compute the multipoles Cls, and most of it is due to the access time for variables which in Mathematica is approximately ten times slower than in C or Fortran. CMBquick is thus approximately 10 times slower than CAMB and cannot be used for the same reasons. It uses the same method as CAMB for computing the CMB spectrum, which is based on the line of sight approach. However the integration is performed in a different gauge with different time steps and k-spacing. It benefits from the power of Mathematica on numerical resolution of stiff differential systems, and the transfer functions can be obtained with exquisite accuracy.

The purpose of CMBquick is thus twofold. First, CMBquick is a slow but precise and pedagogical, tool which can be used to explore and modify the physical content of the linear and non-linear dynamics. Second, it is a tool which can help developing templates for nonlinear computations, which could then be hard coded once their correctness is checked. The number of equations for non-linear dynamics is quite sizable and CMBquick makes it easy (but slow) to manipulate the non-linear equations, to solve them precisely, and to plot them.

[ascl:1109.010]
PyModelFit: Model-fitting Framework and GUI Tool

PyModelFit provides a pythonic, object-oriented framework that simplifies the task of designing numerical models to fit data. This is a very broad task, and hence the current functionality of PyModelFit focuses on the simpler tasks of 1D curve-fitting, including a GUI interface to simplify interactive work (using Enthought Traits). For more complicated modeling, PyModelFit also provides a wide range of classes and a framework to support more general model/data types (2D to Scalar, 3D to Scalar, 3D to 3D, and so on).

[ascl:1109.011]
GalactICS: Galaxy Model Building Package

GalactICS generates N-body realizations of axisymmetric galaxy models consisting of disk, bulge and halo. Some of the code is in Fortran 77, using lines longer than 72 characters in some cases. The -e flag in the makefile allow for this for a Solaris f77 compiler. Other programs are written in C. Again, the linking between these routines works on Solaris systems, but may need to be adjusted for other architectures. We have found that linking using f77 instead of ld will often automatically load the appropriate libraries.

The graphics output by some of the programs (dbh, plotforce, diskdf, plothalo) uses the PGPLOT library. Alternatively, remove all calls to routines with names starting with "PG", as well as the -lpgplot flag in the Makefile, and the programs should still run fine.

[ascl:1109.012]
EnBiD: Fast Multi-dimensional Density Estimation

We present a method to numerically estimate the densities of a discretely sampled data based on a binary space partitioning tree. We start with a root node containing all the particles and then recursively divide each node into two nodes each containing roughly equal number of particles, until each of the nodes contains only one particle. The volume of such a leaf node provides an estimate of the local density and its shape provides an estimate of the variance. We implement an entropy-based node splitting criterion that results in a significant improvement in the estimation of densities compared to earlier work. The method is completely metric free and can be applied to arbitrary number of dimensions. We use this method to determine the appropriate metric at each point in space and then use kernel-based methods for calculating the density. The kernel-smoothed estimates were found to be more accurate and have lower dispersion. We apply this method to determine the phase-space densities of dark matter haloes obtained from cosmological N-body simulations. We find that contrary to earlier studies, the volume distribution function v(f) of phase-space density f does not have a constant slope but rather a small hump at high phase-space densities. We demonstrate that a model in which a halo is made up by a superposition of Hernquist spheres is not capable in explaining the shape of v(f) versus f relation, whereas a model which takes into account the contribution of the main halo separately roughly reproduces the behaviour as seen in simulations. The use of the presented method is not limited to calculation of phase-space densities, but can be used as a general purpose data-mining tool and due to its speed and accuracy it is ideally suited for analysis of large multidimensional data sets.

[ascl:1109.013]
CULSP: Fast Calculation of the Lomb-Scargle Periodogram Using Graphics Processing Units

I introduce a new code for fast calculation of the Lomb-Scargle periodogram, that leverages the computing power of graphics processing units (GPUs). After establishing a background to the newly emergent field of GPU computing, I discuss the code design and narrate key parts of its source. Benchmarking calculations indicate no significant differences in accuracy compared to an equivalent CPU-based code. However, the differences in performance are pronounced; running on a low-end GPU, the code can match 8 CPU cores, and on a high-end GPU it is faster by a factor approaching thirty. Applications of the code include analysis of long photometric time series obtained by ongoing satellite missions and upcoming ground-based monitoring facilities; and Monte-Carlo simulation of periodogram statistical properties.

[ascl:1109.014]
Supernova Flux-averaging Likelihood Code

Flux-averaging justifies the use of the distance-redshift relation for a smooth universe in the analysis of type Ia supernova (SN Ia) data. Flux-averaging of SN Ia data is required to yield cosmological parameter constraints that are free of the bias induced by weak gravitational lensing. SN Ia data are converted into flux. For a given cosmological model, the distance dependence of the data is removed, then the data are binned in redshift, and placed at the average redshift in each redshift bin. The likelihood of the given cosmological model is then computed using "flux statistics''. These Fortran codes compute the likelihood of an arbitrary cosmological model [with given H(z)/H_0] using flux-averaged Type Ia supernova data.

[ascl:1109.015]
WCSTools: Image Astrometry Toolkit

WCSTools is a package of programs and a library of utility subroutines for setting and using the world coordinate systems (WCS) in the headers of the most common astronomical image formats, FITS and IRAF .imh, to relate image pixels to sky coordinates. In addition to dealing with image WCS information, WCSTools has extensive catalog search, image header manipulation, and coordinate and time conversion tasks. This software is all written in very portable C, so it should compile and run on any computer with a C compiler.

[ascl:1109.016]
aXe: Spectral Extraction and Visualization Software

aXe is a spectroscopic data extraction software package that was designed to handle large format spectroscopic slitless images such as those from the Wide Field Camera 3 (WFC3) and the Advanced Camera for Surveys (ACS) on HST. aXe is a PyRAF/IRAF package that consists of several tasks and is distributed as part of the Space Telescope Data Analysis System (STSDAS). The various aXe tasks perform specific parts of the extraction and calibration process and are successively used to produce extracted spectra.

[ascl:1109.017]
IRDR: InfraRed Data Reduction

We describe the InfraRed Data Reduction (IRDR) software package, a small ANSI C library of fast image processing routines for automated pipeline reduction of infrared (dithered) observations. We developed the software to satisfy certain design requirements not met in existing packages (e.g., full weight map handling) and to optimize the software for large data sets (non-interactive tasks that are CPU and disk efficient). The software includes stand-alone C programs for tasks such as running sky frame subtraction with object masking, image registration and coaddition with weight maps, dither offset measurement using cross-correlation, and object mask dilation. Although we currently use the software to process data taken with CIRSI (a near-IR mosaic imager), the software is modular and concise and should be easy to adapt/reuse for other work.

[ascl:1109.018]
GIPSY: Groningen Image Processing System

GIPSY is an acronym of Groningen Image Processing SYstem. It is a highly interactive software system for the reduction and display of astronomical data. It supports multi-tasking using a versatile user interface, it has an advanced data structure, a powerful script language and good display facilities based on the X Window system.

GIPSY consists of a number of components which can be divided into a number of classes:

- The user interfaces. Currently two user interfaces are available; one for interactive work and one for batch processing.
- The data structure.
- The display utilities.
- The application programs. These are the majority of programs.

[ascl:1109.019]
SkyCat: Visualization and Catalog and Data Access Tool

ESO's Data Management; Very Large Telescope (VLT) Project Divisions; Canadian Astronomical Data Center (CADC)

SkyCat is a tool that combines visualization of images and access to catalogs and archive data for astronomy. The tool, developed in Tcl/Tk, was originally conceived as a demo of the capabilities of the class library that was developed for the VLT. The Skycat sources currently consist of five packages:

- Tclutil - Generic Tcl and C++ utilities
- Astrotcl - Astronomical Tcl and C++ utilities
- RTD - Real-time Display classes and widgets
- Catlib - Catalog library and widgets
- Skycat - Skycat application and library package

[ascl:1109.020]
CMFGEN: Probing the Universe through Spectroscopy

A radiative transfer code designed to solve the radiative transfer and statistical equilibrium equations in spherical geometry. It has been designed for application to W-R stars, O stars, and Luminous Blue-Variables. CMFGEN allows fundamental parameters such as effective temperatures, stellar radii and stellar luminosities to be determined. It can provide constraints on mass-loss rates, and allow abundance determinations for a wide range of atomic species. Further it can provide accurate energy distributions, and hence ionizing fluxes, which can be used as input for codes which model the spectra of HII regions and ring nebular.

[ascl:1109.021]
TLUSTY: Stellar Atmospheres, Accretion Disks, and Spectroscopic Diagnostics

TLUSTY is a user-oriented package written in FORTRAN77 for modeling stellar atmospheres and accretion disks and wide range of spectroscopic diagnostics. In the program's maximum configuration, the user may start from scratch and calculate a model atmosphere of a chosen degree of complexity, and end with a synthetic spectrum in a wavelength region of interest for an arbitrary stellar rotation and an arbitrary instrumental profile. The user may also model the vertical structure of annuli of an accretion disk.

[ascl:1109.022]
Synspec: General Spectrum Synthesis Program

Synspec is a user-oriented package written in FORTRAN for modeling stellar atmospheres and for stellar spectroscopic diagnostics. It assumes an existing model atmosphere, calculated previously with Tlusty or taken from the literature (for instance, from the Kurucz grid of models). The opacity sources (continua, atomic and molecular lines) are fully specified by the user. An arbitrary stellar rotation and instrumental profile can be applied to the synthetic spectrum.

[ascl:1109.023]
MOKA: A New Tool for Strong Lensing Studies

MOKA simulates the gravitational lensing signal from cluster-sized haloes. This algorithm implements recent results from numerical simulations to create realistic lenses with properties independent of numerical resolution and can be used for studies of the strong lensing cross section in dependence of halo structure.

[ascl:1109.024]
Jupiter: Multidimensional Astrophysical Hydrocode

Jupiter is a multidimensional astrophysical hydrocode. It is based on a Godunov method, and it is parallelized with MPI. The mesh geometry can either be cartesian, cylindrical or spherical. It allows mesh refinement and includes special features adapted to the description of planets embedded in disks and nearly steady states.

[ascl:1108.001]
IMCAT: Image and Catalogue Manipulation Software

The IMCAT software was developed initially to do faint galaxy photometry for weak lensing studies, and provides a fairly complete set of tools for this kind of work. Unlike most packages for doing data analysis, the tools are standalone unix commands which you can invoke from the shell, via shell scripts or from perl scripts. The tools are arranges in a tree of directories. One main branch is the ’imtools’. These deal only with fits files. The most important imtool is the ’image calculator’ ’ic’ which allows one to do rather general operations on fits images. A second branch is the ’catools’ which operate only on catalogues. The key cattool is ’lc’; this effectively defines the format of IMCAT catalogues, and allows one to do very general operations on and filtering of such catalogues. A third branch is the ’imcattools’. These tend to be much more specialised than the cattools and imcattools and are focussed on faint galaxy photometry.

[ascl:1108.002]
SHERA: SHEar Reconvolution Analysis

Current and upcoming wide-field, ground-based, broad-band imaging surveys promise to address a wide range of outstanding problems in galaxy formation and cosmology. Several such uses of ground-based data, especially weak gravitational lensing, require highly precise measurements of galaxy image statistics with careful correction for the effects of the point-spread function (PSF). The SHERA (SHEar Reconvolution Analysis) software simulates ground-based imaging data with realistic galaxy morphologies and observing conditions, starting from space-based data (from COSMOS, the Cosmological Evolution Survey) and accounting for the effects of the space-based PSF. This code simulates ground-based data, optionally with a weak lensing shear applied, in a model-independent way using a general Fourier space formalism. The utility of this pipeline is that it allows for a precise, realistic assessment of systematic errors due to the method of data processing, for example in extracting weak lensing galaxy shape measurements or galaxy radial profiles, given user-supplied observational conditions and real galaxy morphologies. Moreover, the simulations allow for the empirical test of error estimates and determination of parameter degeneracies, via generation of many noise maps. The public release of this software, along with a large sample of cleaned COSMOS galaxy images (corrected for charge transfer inefficiency), should enable upcoming ground-based imaging surveys to achieve their potential in the areas of precision weak lensing analysis, galaxy profile measurement, and other applications involving detailed image analysis.

This code is no longer maintained and has been superseded by GalSim (ascl:1402.009).

[ascl:1108.003]
WCSLIB and PGSBOX

WCSLIB is a C library, supplied with a full set of Fortran wrappers, that implements the "World Coordinate System" (WCS) standard in FITS (Flexible Image Transport System). It also includes a PGPLOT-based routine, PGSBOX, for drawing general curvilinear coordinate graticules and a number of utility programs.

[ascl:1108.004]
Galacticus: A Semi-Analytic Model of Galaxy Formation

Galacticus is designed to solve the physics involved in the formation of galaxies within the current standard cosmological framework. It is of a type of model known as “semi-analytic” in which the numerous complex non-linear physics involved are solved using a combination of analytic approximations and empirical calibrations from more detailed, numerical solutions. Models of this type aim to begin with the initial state of the Universe (specified shortly after the Big Bang) and apply physical principles to determine the properties of galaxies in the Universe at later times, including the present day. Typical properties computed include the mass of stars and gas in each galaxy, broad structural properties (e.g. radii, rotation speeds, geometrical shape etc.), dark matter and black hole contents, and observable quantities such as luminosities, chemical composition etc.

[ascl:1108.005]
Gaepsi: Gadget Visualization Toolkit

Feng, Yu; Croft, Rupert A. C.; Di Matteo, Tiziana; Khandai, Nishikanta; Sargent, Randy; Nourbakhsh, Illah; Dille, Paul; Bartley, Chris; Springel, Volker; Jana, Anirban; Gardner, Jeffrey

Gaepsi is a PYTHON extension for visualizing cosmology simulations produced by Gadget. Visualization is the most important facet of Gaepsi, but it also allows data analysis on GADGET simulations with its growing number of physics related subroutines and constants. Unlike mesh based scheme, SPH simulations are directly visible in the sense that a splatting process is required to produce raster images from the simulations. Gaepsi produces images of 2-dimensional line-of-sight projections of the simulation. Scalar fields and vector fields are both supported.

Besides the traditional way of slicing a simulation, Gaepsi also has built-in support of 'Survey-like' domain transformation proposed by Carlson & White. An improved implementation is used in Gaepsi. Gaepsi both implements an interactive shell for plotting and exposes its API for batch processing. When complied with OpenMP, Gaepsi automatically takes the advantage of the multi-core computers. In interactive mode, Gaepsi is capable of producing images of size up to 32000 x 32000 pixels. The user can zoom, pan and rotate the field with a command in on the finger tip. The interactive mode takes full advantages of matplotlib's rich annotating, labeling and image composition facilities. There are also built-in commands to add objects that are commonly used in cosmology simulations to the figures.

[ascl:1108.006]
STARLIGHT: Spectral Synthesis Code

The study of stellar populations in galaxies is entering a new era with the availability of large and high quality databases of both observed galactic spectra and state-of-the-art evolutionary synthesis models. The power of spectral synthesis can be investigated as a mean to estimate physical properties of galaxies. Spectral synthesis is nothing more than the decomposition of an observed spectrum in terms of a superposition of a base of simple stellar populations of various ages and metallicities, producing astrophysically interesting output such as the star-formation and chemical enrichment histories of a galaxy, its extinction and velocity dispersion. This is what the STARLIGHT spectral synthesis code does.

[ascl:1108.007]
PÉGASE: Metallicity-consistent Spectral Evolution Model of Galaxies

PÉGASE (Projet d'Étude des GAlaxies par Synthèse Évolutive) is a code to compute the spectral evolution of galaxies. The evolution of the stars, gas and metals is followed for a law of star formation and a stellar initial mass function. The stellar evolutionary tracks extend from the main sequence to the white dwarf stage. The emission of the gas in HII regions is also taken into account. The main improvement in version 2 is the use of evolutionary tracks of different metallicities (from 10-4 to 5×solar). The effect of extinction by dust is also modelled using a radiative transfer code. PÉGASE.2 uses the BaSeL library of stellar spectra and can therefore synthesize low-resolution (R~200) ultraviolet to near-infrared spectra of Hubble sequence galaxies as well as of starbursts.

[ascl:1108.008]
PÉGASE-HR: Stellar Population Synthesis at High Resolution Spectra

Le Borgne, Damien; Fioc, Michel; Lançon, Ariane; Rocca-Volmerange, Brigitte; Prugniel, Philippe; Soubiran, Caroline

PÉGASE-HR is a code aimed at computing synthetic evolutive optical spectra of galaxies with a very high resolution (R=10 000, or dlambda=0.55) in the range Lambda=[4000, 6800] Angstroms. PÉGASE-HR is the result of combining the code PÉGASE.2 with the high-resolution stellar library ÉLODIE. This code can also be used at low resolution (R=200) over the range covered by the BaSeL library (from far UV to the near IR), and then produces the same results as PÉGASE.2. In PEGASE-HR, the BaSeL library is replaced by a grid of spectra interpolated from the high-resolution ÉLODIE library of stellar spectra. The ÉLODIE library is a stellar database of 1959 spectra for 1503 stars, observed with the echelle spectrograph ÉLODIE on the 193 cm telescope at the Observatoire de Haute Provence.

[ascl:1108.009]
LePHARE: Photometric Analysis for Redshift Estimate

LePHARE is a set of Fortran commands to compute photometric redshifts and to perform SED fitting. The latest version includes new features with FIR fitting and a more complete treatment of physical parameters and uncertainties based on PÉGASE and Bruzual & Charlot population synthesis models. The program is based on a simple chi2 fitting method between the theoretical and observed photometric catalogue. A simulation program is also available in order to generate realistic multi-colour catalogues taking into account observational effects.

[ascl:1108.010]
Hyperz: Photometric Redshift Code

From a photometric catalogue, hyperz finds the redshift of each object by means of a standard SED fitting procedure, i.e. comparing the observed magnitudes with the expected ones, computed from template Spectral Energy Distributions. The set of templates used in the minimization procedure (age, metallicity, reddening, absorption in the Lyman forest, ...) is studied in detail, through both real and simulated data. The expected accuracy of photometric redshifts, as well as the fraction of catastrophic identifications and wrong detections, is given as a function of the redshift range, the set of filters considered, and the photometric accuracy. Special attention is paid to the results expected from real data.

[ascl:1108.011]
BPZ: Bayesian Photometric Redshift Code

Photometric redshift estimation is becoming an increasingly important technique, although the currently existing methods present several shortcomings which hinder their application. Most of those drawbacks are efficiently eliminated when Bayesian probability is consistently applied to this problem. The use of prior probabilities and Bayesian marginalization allows the inclusion of valuable information, e.g. the redshift distributions or the galaxy type mix, which is often ignored by other methods. In those cases when the a priori information is insufficient, it is shown how to `calibrate' the prior distributions, using even the data under consideration. There is an excellent agreement between the 108 HDF spectroscopic redshifts and the predictions of the method, with a rms error Delta z/(1+z_spec) = 0.08 up to z<6 and no systematic biases nor outliers. The results obtained are more reliable than those of standard techniques even when the latter include near-IR colors. The Bayesian formalism developed here can be generalized to deal with a wide range of problems which make use of photometric redshifts, e.g. the estimation of individual galaxy characteristics as the metallicity, dust content, etc., or the study of galaxy evolution and the cosmological parameters from large multicolor surveys. Finally, using Bayesian probability it is possible to develop an integrated statistical method for cluster mass reconstruction which simultaneously considers the information provided by gravitational lensing and photometric redshifts.

[ascl:1108.012]
TITAN: General-purpose Radiation Hydrodynamics Code

TITAN is a general-purpose radiation hydrodynamics code developed at the Laboratory for Computational Astrophysics (NCSA, University of Illinois at Urbana-Champaign). TITAN solves the coupled sets of radiation transfer and fluid dynamics equations on an adaptive mesh in one spatial dimension.

[ascl:1108.013]
STELLA: Multi-group Radiation Hydrodynamics Code

STELLA is a one-dimensional multi-group radiation hydrodynamics code. STELLA incorporates implicit hydrodynamics coupled to a multi-group non-equilibrium radiative transfer for modeling SN II-L light curves. The non-equilibrium description of radiation is crucial for this problem since the presupernova envelope may be of low mass and very dilute. STELLA implicitly treats time dependent equations of the angular moments of intensity averaged over a frequency bin. Local thermodynamic equilibrium is assumed to determine the ionization levels of materials.

[ascl:1108.014]
RADICAL: Multi-purpose 2-D Radiative Transfer Code

RADICAL is a multi-purpose 2-D radiative transfer code for axi-symmetric circumstellar (or circum-black-hole) envelopes /disks / tori etc. It has been extensively tested and found reliable and accurate. The code has recently been supplemented with a Variable Eddington Tensor module which enables it to solve dust continuum radiative transfer problems from very low up to extremely high optical depths with only a few (about 7) iterations at most.

[ascl:1108.015]
DISKSTRUCT: A Simple 1+1-D Disk Structure Code

DISKSTRUCT is a simple 1+1-D code for modeling protoplanetary disks. It is not based on multidimensional radiative transfer! Instead, a flaring-angle recipe is used to compute the irradiation of the disk, while the disk vertical structure at each cylindrical radius is computed in a 1-D fashion; the models computed with this code are therefore approximate. Moreover, this model cannot deal with the dust inner rim.

In spite of these simplifications and drawbacks, the code can still be very useful for disk studies, for the following reasons:

- It allows the disk structure to be studied in a 1-D vertical fashion (one radial cylinder at a time). For understanding the structure of disks, and also for using it as a basis of other models, this can be a great advantage.
- For very optically thick disks this code is likely to be much faster than the RADMC full disk model.
- Viscous internal heating of the disk is implemented and converges quickly, whereas the RADMC code is still having difficulty to deal with high optical depth combined with viscously generated internal heat.

[ascl:1108.016]
RADMC: A 2-D Continuum Radiative Transfer Tool

RADMC is a 2-D Monte-Carlo code for dust continuum radiative transfer circumstellar disks and envelopes. It is based on the method of Bjorkman & Wood (ApJ 2001, 554, 615), but with several modifications to produce smoother results with fewer photon packages.

[ascl:1108.017]
SHELLSPEC: Simple Radiative Transfer along Line of Sight in Moving Media

SHELLSPEC is designed to calculate lightcurves, spectra and images of interacting binaries and extrasolar planets immersed in a moving circumstellar environment which is optically thin. It solves simple radiative transfer along the line of sight in moving media. The assumptions include LTE and optional known state quantities and velocity fields in 3D. Optional (non)transparent objects such as a spot, disc, stream, jet, shell or stars as well as an empty space may be defined (embedded) in 3D and their composite synthetic spectrum calculated. Roche model can be used as a boundary condition for the radiative tranfer. The program does not solve the inverse problem of finding the stellar and orbital parameters.

[ascl:1108.018]
STECKMAP: STEllar Content and Kinematics via Maximum A Posteriori likelihood

STECKMAP stands for STEllar Content and Kinematics via Maximum A Posteriori likelihood. It is a tool for interpreting galaxy spectra in terms of their stellar populations through the derivation of their star formation history, age-metallicity relation, kinematics and extinction. The observed spectrum is projected onto a temporal sequence of models of single stellar populations, so as to determine a linear combination of these models that best fits the observed spectrum. The weights of the various components of this linear combination indicate the stellar content of the population. This procedure is regularized using various penalizing functions. The principles of the method are detailed in Ocvirk et al. 2006.

[ascl:1108.019]
BOREAS: Mass Loss Rate of a Cool, Late-type Star

The basic mechanisms responsible for producing winds from cool, late-type stars are still largely unknown. We take inspiration from recent progress in understanding solar wind acceleration to develop a physically motivated model of the time-steady mass loss rates of cool main-sequence stars and evolved giants. This model follows the energy flux of magnetohydrodynamic turbulence from a subsurface convection zone to its eventual dissipation and escape through open magnetic flux tubes. We show how Alfven waves and turbulence can produce winds in either a hot corona or a cool extended chromosphere, and we specify the conditions that determine whether or not coronal heating occurs. These models do not utilize arbitrary normalization factors, but instead predict the mass loss rate directly from a star's fundamental properties. We take account of stellar magnetic activity by extending standard age-activity-rotation indicators to include the evolution of the filling factor of strong photospheric magnetic fields. We compared the predicted mass loss rates with observed values for 47 stars and found significantly better agreement than was obtained from the popular scaling laws of Reimers, Schroeder, and Cuntz. The algorithm used to compute cool-star mass loss rates is provided as a self-contained and efficient IDL computer code. We anticipate that the results from this kind of model can be incorporated straightforwardly into stellar evolution calculations and population synthesis techniques.

[ascl:1107.001]
SNID: Supernova Identification

We present an algorithm to identify the type of an SN spectrum and to determine its redshift and age. This algorithm, based on the correlation techniques of Tonry & Davis, is implemented in the Supernova Identification (SNID) code. It is used by members of ongoing high-redshift SN searches to distinguish between type Ia and type Ib/c SNe, and to identify "peculiar" SNe Ia. We develop a diagnostic to quantify the quality of a correlation between the input and template spectra, which enables a formal evaluation of the associated redshift error. Furthermore, by comparing the correlation redshifts obtained using SNID with those determined from narrow lines in the SN host galaxy spectrum, we show that accurate redshifts (with a typical error less than 0.01) can be determined for SNe Ia without a spectrum of the host galaxy. Last, the age of an input spectrum is determined with a typical 3-day accuracy, shown here by using high-redshift SNe Ia with well-sampled light curves. The success of the correlation technique confirms the similarity of some SNe Ia at low and high redshifts. The SNID code, which is available to the community, can also be used for comparative studies of SN spectra, as well as comparisons between data and models.

[ascl:1107.002]
GIBIS: Gaia Instrument and Basic Image Simulator

GIBIS is a pixel-level simulator of the Gaia mission. It is intended to simulate how the Gaia instruments will observe the sky, using realistic simulations of the astronomical sources and of the instrumental properties. It is a branch of the global Gaia Simulator under development within the Gaia DPAC CU2 Group (Data Simulations). Access is currently restricted to Gaia DPAC teams.

[ascl:1107.003]
FITSManager: Management of Personal Astronomical Data

Cui, Chenzhou; Fan, Dongwei; Zhao, Yongheng; Kembhavi, Ajit; He, Boliang; Cao, Zihuang; Li, Jian; Nandrekar, Deoyani

With the increase of personal storage capacity, it is easy to find hundreds to thousands of FITS files in the personal computer of an astrophysicist. Because Flexible Image Transport System (FITS) is a professional data format initiated by astronomers and used mainly in the small community, data management toolkits for FITS files are very few. Astronomers need a powerful tool to help them manage their local astronomical data. Although Virtual Observatory (VO) is a network oriented astronomical research environment, its applications and related technologies provide useful solutions to enhance the management and utilization of astronomical data hosted in an astronomer's personal computer. FITSManager is such a tool to provide astronomers an efficient management and utilization of their local data, bringing VO to astronomers in a seamless and transparent way. FITSManager provides fruitful functions for FITS file management, like thumbnail, preview, type dependent icons, header keyword indexing and search, collaborated working with other tools and online services, and so on. The development of the FITSManager is an effort to fill the gap between management and analysis of astronomical data.

[ascl:1107.004]
Flexible DM-NRG

This code combines the spectral sum-conserving methods of Weichselbaum and von Delft and of Peters, Pruschke and Anders (both relying upon the complete basis set construction of Anders and Schiller) with the use of non-Abelian symmetries in a flexible manner: Essentially any non-Abelian symmetry can be taught to the code, and any number of such symmetries can be used throughout the computation for any density of states, and to compute any local operators' correlation function's real and imaginary parts or any thermodynamical expectation value. The code works both at zero and finite temperatures.

[ascl:1107.005]
Sherpa: CIAO Modeling and Fitting Package

Sherpa is the CIAO (ascl:1311.006) modeling and fitting application made available by the Chandra X-ray Center (CXC). It can be used for analysis of images, spectra and time series from many telescopes, including optical telescopes such as Hubble. Sherpa is flexible, modular and extensible. It has an IPython user interface and it is also an importable Python module. Sherpa models, optimization and statistic functions are available via both C++ and Python for software developers wishing to link such functions directly to their own compiled code.

The CIAO 4.3 Sherpa release supports fitting of 1-D X-ray spectra from Chandra and other X-ray missions, as well as 1-D non-X-ray data, including ASCII data arrays, radial profiles, and lightcurves. The options for grating data analysis include fitting the spectrum with multiple response files required for overlapping orders in LETG observations. Modeling of 2-D spatial data is fully supported, including the PSF and exposure maps. User specified models can be added to Sherpa with advanced "user model" functionality.

[ascl:1107.006]
AIRES: AIRshower Extended Simulations

The objective of this work is to report on the influence of muon interactions on the development of air showers initiated by astroparticles. We make a comparative study of the different theoretical approaches to muon bremsstrahlung and muonic pair production interactions. A detailed algorithm that includes all the relevant characteristics of such processes has been implemented in the AIRES air shower simulation system. We have simulated ultra high energy showers in different conditions in order to measure the influence of these muonic electromagnetic interactions. We have found that during the late stages of the shower development (well beyond the shower maximum) many global observables are significantly modified in relative terms when the mentioned interactions are taken into account. This is most evident in the case of the electromagnetic component of very inclined showers. On the other hand, our simulations indicate that the studied processes do not induce significant changes either in the position of the shower maximum or the structure of the shower front surface.

[ascl:1107.007]
AMUSE: Astrophysical Multipurpose Software Environment

AMUSE is an open source software framework for large-scale simulations in astrophysics, in which existing codes for gravitational dynamics, stellar evolution, hydrodynamics and radiative transport can be easily coupled and placed in the appropriate observational context.

[ascl:1107.008]
STARS: A Stellar Evolution Code

Eggleton, P. P.; Tout, Christopher; Pols, Onno; Izzard, Rob; Eldridge, John; Lesaffre, Pierre; Stancliffe, Richard; Church, Ross; Lau, Herbert

We have developed a detailed stellar evolution code capable of following the simultaneous evolution of both stars in a binary system, together with their orbital properties. To demonstrate the capabilities of the code we investigate potential progenitors for the Type IIb supernova 1993J, which is believed to have been an interacting binary system prior to its primary exploding. We use our detailed binary stellar evolution code to model this system to determine the possible range of primary and secondary masses that could have produced the observed characteristics of this system, with particular reference to the secondary. Using the luminosities and temperatures for both stars (as determined by Maund et al. 2004) and the remaining mass of the hydrogen envelope of the primary at the time of explosion, we find that if mass transfer is 100 per cent efficient the observations can be reproduced by a system consisting of a 15 solar mass primary and a 14 solar mass secondary in an orbit with an initial period of 2100 days. With a mass transfer efficiency of 50 per cent, a more massive system consisting of a 17 solar mass primary and a 16 solar mass secondary in an initial orbit of 2360 days is needed. We also investigate some of the uncertainties in the evolution, including the effects of tidal interaction, convective overshooting and thermohaline mixing.

[ascl:1107.009]
REAS3: Modeling Radio Emission from Cosmic Ray Air Showers

The freely available Monte Carlo code REAS for modelling radio emission from cosmic ray air showers has evolved to include the full complexity of air shower physics. REAS3 improves the calculation of the emission contributions, which was not fully consistent in earlier versions of REAS, by incorporating the missing radio emission due to the variation of the number of charged particles during the air shower evolution using an "end-point formalism". With the inclusion of these emission contributions, the structure of the simulated radio pulses changes from unipolar to bipolar, and the azimuthal emission pattern becomes nearly symmetric. Remaining asymmetries can be explained by radio emission due to the variation of the net charge excess in air showers, which is automatically taken into account in the new implementation. REAS3 constitutes the first self-consistent time-domain implementation based on single particle emission taking the full complexity of air shower physics into account, and is freely available for all interested users. REAS3 has been superseded by CoREAS (ascl:1406.003).

[ascl:1107.010]
XDSPRES: CL-based package for Reducing OSIRIS Cross-dispersed Spectra

We present a description of the CL-based package XDSPRES, which aims at being a complete reducing facility for cross-dispersed spectra taken with the Ohio State Infrared Imager/Spectrometer, as installed at the SOAR telescope. This instrument provides spectra in the range between 1.2um and 2.35um in a single exposure, with resolving power of R ~ 1200. XDSPRES consists of two tasks, namely xdflat and doosiris. The former is a completely automated code for preparing normalized flat field images from raw flat field exposures. Doosiris was designed to be a complete reduction pipeline, requiring a minimum of user interaction. General steps towards a fully reduced spectrum are explained, as well as the approach adopted by our code.

[ascl:1107.011]
ARCHANGEL: Galaxy Photometry System

ARCHANGEL is a Unix-based package for the surface photometry of galaxies. While oriented for large angular size systems (i.e. many pixels), its tools can be applied to any imaging data of any size. The package core contains routines to perform the following critical galaxy photometry functions: sky determination; frame cleaning; ellipse fitting; profile fitting; and total and isophotal magnitudes.

The goal of the package is to provide an automated, assembly-line type of reduction system for galaxy photometry of space-based or ground-based imaging data. The procedures outlined in the documentation are flux independent, thus, these routines can be used for non-optical data as well as typical imaging datasets.

ARCHANGEL has been tested on several current OS's (RedHat Linux, Ubuntu Linux, Solaris, Mac OS X). A tarball for installation is available at the download page. The main routines are Python and FORTRAN based, therefore, a current installation of Python and a FORTRAN compiler are required. The ARCHANGEL package also contains Python hooks to the PGPLOT package, an XML processor and network tools which automatically link to data archives (i.e. NED, HST, 2MASS, etc) to download images in a non-interactive manner.

[ascl:1107.012]
LIME: Flexible, Non-LTE Line Excitation and Radiation Transfer Method for Millimeter and Far-infrared Wavelengths

LIME solves the molecular and atomic excitation and radiation transfer problem in a molecular gas and predicting emergent spectra. The code works in arbitrary three dimensional geometry using unstructured Delaunay latices for the transport of photons. Various physical models can be used as input, ranging from analytical descriptions over tabulated models to SPH simulations. To generate the Delaunay grid we sample the input model randomly, but weigh the sample probability with the molecular density and other parameters, and thereby we obtain an average grid point separation that scales with the local opacity. Slow convergence of opaque models becomes traceable; when convergence between the level populations, the radiation field, and the point separation has been obtained, the grid is ray-traced to produced images that can readily be compared to observations. LIME is particularly well suited for modeling of ALMA data because of the high dynamic range in scales that can be resolved using this type of grid, and can furthermore deal with overlapping lines of multiple molecular and atomic species.

[ascl:1107.013]
CASA: Common Astronomy Software Applications

CASA, the Common Astronomy Software Applications package, is being developed with the primary goal of supporting the data post-processing needs of the next generation of radio astronomical telescopes such as ALMA and EVLA. The package can process both interferometric and single dish data. The CASA infrastructure consists of a set of C++ tools bundled together under an iPython interface as a set of data reduction tasks. This structure provides flexibility to process the data via task interface or as a python script. In addition to the data reduction tasks, many post-processing tools are available for even more flexibility and special purpose reduction needs.

[ascl:1107.014]
Clumpfind: Determining Structure in Molecular Clouds

We describe an automatic, objective routine for analyzing the clumpy structure in a spectral line position-position-velocity data cube. The algorithm works by first contouring the data at a multiple of the rms noise of the observations, then searches for peaks of emission which locate the clumps, and then follows them down to lower intensities. No a proiri clump profile is assumed. By creating simulated data, we test the performance of the algorithm and show that a contour map most accurately depicts internal structure at a contouring interval equal to twice the rms noise of the map. Blending of clump emission leads to small errors in mass and size determinations and in severe cases can result in a number of clumps being misidentified as a single unit, flattening the measured clump mass spectrum. The algorithm is applied to two real data sets as an example of its use. The Rosette molecular cloud is a 'typical' star-forming cloud, but in the Maddalena molecular cloud high-mass star formation is completely absent. Comparison of the two clump lists generated by the algorithm show that on a one-to-one basis the clumps in the star-forming cloud have higher peak temperatures, higher average densities, and are more gravitationally bound than in the non-star-forming cloud. Collective properties of the clumps, such as temperature-size-line-width-mass relations appear very similar, however. Contrary to the initial results reported in a previous paper (Williams & Blitz 1993), we find that the current, more thoroughly tested analysis finds no significant difference in the clump mass spectrum of the two clouds.

[ascl:1107.015]
McLuster: A Tool to Make a Star Cluster

The tool McLuster is an open source code that can be used to either set up initial conditions for N-body computations or, alternatively, to generate artificial star clusters for direct investigation. There are two different versions of the code, one basic version for generating all kinds of unevolved clusters (in the following called mcluster) and one for setting up evolved stellar populations at a given age. The former is completely contained in the C file main.c. The latter (dubbed mcluster_sse) is more complex and requires additional FORTRAN routines, namely the Single-Star Evolution (SSE) routines by Hurley, Pols & Tout (ascl:1303.015) that are provided with the McLuster code.

[ascl:1107.016]
SIGPROC: Pulsar Signal Processing Programs

SIGPROC is a package designed to standardize the initial analysis of the many types of fast-sampled pulsar data. Currently recognized machines are the Wide Band Arecibo Pulsar Processor (WAPP), the Penn State Pulsar Machine (PSPM), the Arecibo Observatory Fourier Transform Machine (AOFTM), the Berkeley Pulsar Processors (BPP), the Parkes/Jodrell 1-bit filterbanks (SCAMP) and the filterbank at the Ooty radio telescope (OOTY). The SIGPROC tools should help users look at their data quickly, without the need to write (yet) another routine to read data or worry about big/little endian compatibility (byte swapping is handled automatically).

[ascl:1107.017]
PRESTO: PulsaR Exploration and Search TOolkit

PRESTO is a large suite of pulsar search and analysis software. It was primarily designed to efficiently search for binary millisecond pulsars from long observations of globular clusters (although it has since been used in several surveys with short integrations and to process a lot of X-ray data as well). To date, PRESTO has discovered well over a hundred and fifty pulsars, including approximately 100 recycled pulsars, about 80 of which are in binaries. It is written primarily in ANSI C, with many of the recent routines in Python.

Written with portability, ease-of-use, and memory efficiency in mind, it can currently handle raw data from the following pulsar machines or formats:

- PSRFITS search-format data (as from GUPPI at the GBT and the Mock Spectrometers at Arecibo)
- SPIGOT at the GBT
- Most Wideband Arecibo Pulsar Processor (WAPP) at Arecibo
- The Parkes and Jodrell Bank 1-bit filterbank formats
- Berkeley-Caltech Pulsar Machine (BCPM) at the GBT (may it RIP...)
- 8-bit filterbank format from SIGPROC (other formats will be added if required)
- A time series composed of single precision (i.e. 4-byte) floating point data
- Photon arrival times (or events) in ASCII or double-precision binary formats

[ascl:1107.018]
HEALPix: Hierarchical Equal Area isoLatitude Pixelization of a sphere

HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. Another property of the HEALPix grid is that the pixel centers occur on a discrete number of rings of constant latitude, the number of constant-latitude rings is dependent on the resolution of the HEALPix grid.

[ascl:1107.019]
PSRPOP: Pulsar Population Modelling Programs

PSRPOP is a package developed to model the Galactic population and evolution of radio pulsars. It is a collection of modules written in Fortran77 for an analysis of a large sample of pulsars detected by the Parkes Multibeam Pulsar Survey. The main programs are: 1.) populate, which creates a model Galaxy of pulsars distributed according according to various assumptions; 2.) survey, which searches the model galaxies generated using populate using realistic models of pulsar surveys; and 3.) visualize, a Tk/PGPLOT script to plot various aspects of model detected pulsars from survey. A sample screenshot from visualize can be found here.

[ascl:1106.001]
AlterBBN: A program for calculating the BBN abundances of the elements in alternative cosmologies

AlterBBN evaluates the abundances of the elements generated by Big-Bang nucleosynthesis (BBN). This program computes the abundances of the elements in the standard model of cosmology and allows the user to alter the assumptions of the cosmological model to study their consequences on the abundances of the elements. In particular the baryon-to-photon ratio and the effective number of neutrinos, as well as the expansion rate and the entropy content of the Universe during BBN can be modified in AlterBBN. Such features allow the user to test the cosmological models by confronting them to BBN constraints.

[ascl:1106.002]
PHOEBE: PHysics Of Eclipsing BinariEs

PHOEBE (PHysics Of Eclipsing BinariEs) is a modeling package for eclipsing binary stars, built on top of the widely used WD program (Wilson & Devinney 1971). This introductory paper overviews most important scientific extensions (incorporating observational spectra of eclipsing binaries into the solution-seeking process, extracting individual temperatures from observed color indices, main-sequence constraining and proper treatment of the reddening), numerical innovations (suggested improvements to WD's Differential Corrections method, the new Nelder & Mead's downhill Simplex method) and technical aspects (back-end scripter structure, graphical user interface). While PHOEBE retains 100% WD compatibility, its add-ons are a powerful way to enhance WD by encompassing even more physics and solution reliability.

[ascl:1106.003]
PLplot: Cross-platform Software Package for Scientific Plots

PLplot is a cross-platform software package for creating scientific plots. To help accomplish that task it is organized as a core C library, language bindings for that library, and device drivers which control how the plots are presented in non-interactive and interactive plotting contexts. The PLplot core library can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs (of the same or different sizes) may be placed on a single page, and multiple pages are allowed for those device formats that support them. PLplot has core support for Unicode. This means for our many Unicode-aware devices that plots can be labelled using the enormous selection of Unicode mathematical symbols. A large subset of our Unicode-aware devices also support complex text layout (CTL) languages such as Arabic, Hebrew, and Indic and Indic-derived CTL scripts such as Devanagari, Thai, Lao, and Tibetan. PLplot device drivers support a number of different file formats for non-interactive plotting and a number of different platforms that are suitable for interactive plotting. It is easy to add new device drivers to PLplot by writing a small number of device dependent routines.

[ascl:1106.004]
E3D: The Euro3D Visualization Tool

E3D is a package of tools for the analysis and visualization of IFS data. It is capable of reading, writing, and visualizing reduced data from 3D spectrographs of any kind.

[ascl:1106.005]
R3D: Reduction Package for Integral Field Spectroscopy

R3D was developed to reduce fiber-based integral field spectroscopy (IFS) data. The package comprises a set of command-line routines adapted for each of these steps, suitable for creating pipelines. The routines have been tested against simulations, and against real data from various integral field spectrographs (PMAS, PPAK, GMOS, VIMOS and INTEGRAL). Particular attention is paid to the treatment of cross-talk.

R3D unifies the reduction techniques for the different IFS instruments to a single one, in order to allow the general public to reduce different instruments data in an homogeneus, consistent and simple way. Although still in its prototyping phase, it has been proved to be useful to reduce PMAS (both in the Larr and the PPAK modes), VIMOS and INTEGRAL data. The current version has been coded in Perl, using PDL, in order to speed-up the algorithm testing phase. Most of the time critical algorithms have been translated to C[float=][/float], and it is our intention to translate all of them. However, even in this phase R3D is fast enough to produce valuable science frames in reasonable time.

[ascl:1106.006]
MECI: A Method for Eclipsing Component Identification

We describe an automated method for assigning the most probable physical parameters to the components of an eclipsing binary, using only its photometric light curve and combined colors. With traditional methods, one attempts to optimize a multi-parameter model over many iterations, so as to minimize the chi-squared value. We suggest an alternative method, where one selects pairs of coeval stars from a set of theoretical stellar models, and compares their simulated light curves and combined colors with the observations. This approach greatly reduces the parameter space over which one needs to search, and allows one to estimate the components' masses, radii and absolute magnitudes, without spectroscopic data. We have implemented this method in an automated program using published theoretical isochrones and limb-darkening coefficients. Since it is easy to automate, this method lends itself to systematic analyses of datasets consisting of photometric time series of large numbers of stars, such as those produced by OGLE, MACHO, TrES, HAT, and many others surveys.

[ascl:1106.007]
MIRIAD: Multi-channel Image Reconstruction, Image Analysis, and Display

MIRIAD is a radio interferometry data-reduction package, designed for taking raw visibility data through calibration to the image analysis stage. It has been designed to handle any interferometric array, with working examples for BIMA, CARMA, SMA, WSRT, and ATCA. A separate version for ATCA is available, which differs in a few minor ways from the CARMA version.

[ascl:1106.008]
GRAFIC-2: Multiscale Gaussian Random Fields for Cosmological Simulations

This paper describes the generation of initial conditions for numerical simulations in cosmology with multiple levels of resolution, or multiscale simulations. We present the theory of adaptive mesh refinement of Gaussian random fields followed by the implementation and testing of a computer code package performing this refinement called GRAFIC-2.

[ascl:1106.009]
PARAMESH V4.1: Parallel Adaptive Mesh Refinement

PARAMESH is a package of Fortran 90 subroutines designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity.

The package builds a hierarchy of sub-grids to cover the computational domain, with spatial resolution varying to satisfy the demands of the application. These sub-grid blocks form the nodes of a tree data-structure (quad-tree in 2D or oct-tree in 3D). Each grid block has a logically cartesian mesh. The package supports 1, 2 and 3D models. PARAMESH is released under the NASA-wide Open-Source software license.

[ascl:1106.010]
MAGPHYS: Multi-wavelength Analysis of Galaxy Physical Properties

MAGPHYS is a self-contained, user-friendly model package to interpret observed spectral energy distributions of galaxies in terms of galaxy-wide physical parameters pertaining to the stars and the interstellar medium. MAGPHYS is optimized to derive statistical constraints of fundamental parameters related to star formation activity and dust content (e.g. star formation rate, stellar mass, dust attenuation, dust temperatures) of large samples of galaxies using a wide range of multi-wavelength observations. A Bayesian approach is used to interpret the SEDs all the way from the ultraviolet/optical to the far-infrared.

[ascl:1106.011]
DRAGON: Galactic Cosmic Ray Diffusion Code

DRAGON adopts a second-order Cranck-Nicholson scheme with Operator Splitting and time overrelaxation to solve the diffusion equation. This provides a fast solution that is accurate enough for the average user. Occasionally, users may want to have very accurate solutions to their problem. To enable this feature, users may get close to the accurate solution by using the fast method, and then switch to a more accurate solution scheme featuring the Alternating-Direction-Implicit (ADI) Cranck-Nicholson scheme.

[ascl:1106.012]
SLUG: Stochastically Lighting Up Galaxies

The effects of stochasticity on the luminosities of stellar populations are an often neglected but crucial element for understanding populations in the low mass or low star formation rate regime. To address this issue, we present SLUG, a new code to "Stochastically Light Up Galaxies". SLUG synthesizes stellar populations using a Monte Carlo technique that treats stochastic sampling properly including the effects of clustering, the stellar initial mass function, star formation history, stellar evolution, and cluster disruption. This code produces many useful outputs, including i) catalogs of star clusters and their properties, such as their stellar initial mass distributions and their photometric properties in a variety of filters, ii) two dimensional histograms of color-magnitude diagrams of every star in the simulation, iii) and the photometric properties of field stars and the integrated photometry of the entire simulated galaxy. After presenting the SLUG algorithm in detail, we validate the code through comparisons with starburst99 in the well-sampled regime, and with observed photometry of Milky Way clusters. Finally, we demonstrate the SLUG's capabilities by presenting outputs in the stochastic regime.

[ascl:1106.013]
MGCAMB: Modification of Growth with CAMB

CAMB is a public Fortran 90 code written by Antony Lewis and Anthony Challinor for evaluating cosmological observables. MGCAMB is a modified version of CAMB in which the linearized Einstein equations of General Relativity (GR) are modified. MGCAMB can also be used in CosmoMC to fit different modified-gravity (MG) models to data.

[ascl:1106.014]
Transit Analysis Package (TAP and autoKep): IDL Graphical User Interfaces for Extrasolar Planet Transit Photometry

We present an IDL graphical user interface-driven software package designed for the analysis of extrasolar planet transit light curves. The Transit Analysis Package (TAP) software uses Markov Chain Monte Carlo (MCMC) techniques to fit light curves using the analytic model of Mandel and Agol (2002). The package incorporates a wavelet based likelihood function developed by Carter and Winn (2009) which allows the MCMC to assess parameter uncertainties more robustly than classic chi-squared methods by parameterizing uncorrelated "white" and correlated "red" noise. The software is able to simultaneously analyze multiple transits observed in different conditions (instrument, filter, weather, etc). The graphical interface allows for the simple execution and interpretation of Bayesian MCMC analysis tailored to a user's specific data set and has been thoroughly tested on ground-based and Kepler photometry. AutoKep provides a similar GUI for the preparation of Kepler MAST archive data for analysis by TAP or any other analysis software. This paper describes the software release and provides instructions for its use.

[ascl:1106.015]
OrbFit: Software to Determine Orbits of Asteroids

OrbFit is a software system allowing one to compute the orbits of asteroids starting from the observations, to propagate these orbits, and to compute predictions on the future (and past) position on the celestial sphere. It is a tool to be used to find a well known asteroid, to recover a lost one, to attribute a small group of observations, to identify two orbits with each other, to study the future (and/or past) close approaches to Earth, thus to assess the risk of an impact, and more.

[ascl:1106.016]
Nightfall: Animated Views of Eclipsing Binary Stars

Nightfall is an astronomy application for fun, education, and science. It can produce animated views of eclipsing binary stars, calculate synthetic lightcurves and radial velocity curves, and eventually determine the best-fit model for a given set of observational data of an eclipsing binary star system.

Nightfall comes with a user guide and a set of observational data for several eclipsing binary star systems.

[ascl:1106.017]
CAOS: Code for Adaptive Optics Systems

The CAOS "system" (where CAOS stands for Code for Adaptive Optics Systems) is properly said a Problem Solving Environment (PSE). It is essentially composed of a graphical programming interface (the CAOS Application Builder) which can load different packages (set of modules). Current publicly distributed packages are the Software Package CAOS (the original adaptive optics package), the Software Package AIRY (an image-reconstruction-oriented package - AIRY stands for Astronomical Image Restoration with interferometrY), the Software Package PAOLAC (a simple CAOS interface for the analytic IDL code PAOLA developed by Laurent Jolissaint - PAOLAC stands for PAOLA within Caos), and a couple of private packages (not publicly distributed but restricted to the corresponding consortia): SPHERE (especially developed for the VLT planet finder SPHERE), and AIRY-LN (a specialized version of AIRY for the LBT instrument LINC-NIRVANA). Another package is also being developed: MAOS (that stands for Multiconjugate Adaptive Optics Simulations), developed for multi-reference multiconjugate AO studies purpose but still in a beta-version form.

[ascl:1106.018]
CMB B-modes from Faraday Rotation

This code is a quick and exact calculator of B-mode angular spectrum due to Faraday rotation by stochastic magnetic fields. Faraday rotation induced B-modes can provide a distinctive signature of primordial magnetic fields because of their characteristic frequency dependence and because they are only weakly damped on small scales, allowing them to dominate B-modes from other sources. By numerically solving the full CMB radiative transport equations, we study the B-mode power spectrum induced by stochastic magnetic fields that have significant power on scales smaller than the thickness of the last scattering surface. Constraints on the magnetic field energy density and inertial scale are derived from WMAP 7-year data, and are stronger than the big bang nucleosynthesis (BBN) bound for a range of parameters. Observations of the CMB polarization at smaller angular scales are crucial to provide tighter constraints or a detection.

[ascl:1106.019]
Application of Compressive Sampling to Radio Astronomy I: Deconvolution

Compressive sampling is a new paradigm for sampling, based on sparseness of signals or signal representations. It is much less restrictive than Nyquist-Shannon sampling theory and thus explains and systematises the widespread experience that methods such as the Högbom CLEAN can violate the Nyquist-Shannon sampling requirements. In this paper, a CS-based deconvolution method for extended sources is introduced. This method can reconstruct both point sources and extended sources (using the isotropic undecimated wavelet transform as a basis function for the reconstruction step). We compare this CS-based deconvolution method with two CLEAN-based deconvolution methods: the Högbom CLEAN and the multiscale CLEAN. This new method shows the best performance in deconvolving extended sources for both uniform and natural weighting of the sampled visibilities. Both visual and numerical results of the comparison are provided.

[ascl:1106.020]
CLASS: Cosmic Linear Anisotropy Solving System

Boltzmann codes are used extensively by several groups for constraining cosmological parameters with Cosmic Microwave Background and Large Scale Structure data. This activity is computationally expensive, since a typical project requires from 10'000 to 100'000 Boltzmann code executions. The code CLASS (Cosmic Linear Anisotropy Solving System) incorporates improved approximation schemes leading to a simultaneous gain in speed and precision. We describe here the three approximations used by CLASS for basic LambdaCDM models, namely: a baryon-photon tight-coupling approximation which can be set to first order, second order or to a compromise between the two; an ultra-relativistic fluid approximation which had not been implemented in public distributions before; and finally a radiation streaming approximation taking reionisation into account.

[ascl:1106.021]
StringFast: Fast Code to Compute CMB Power Spectra induced by Cosmic Strings

StringFast implements a method for efficient computation of the C_l spectra induced by a network of strings, which is fast enough to be used in Markov Chain Monte Carlo analyses of future data. This code allows the user to calculate TT, EE, and BB power spectra (scalar [for TT and EE], vector, and tensor modes) for "wiggly" cosmic strings. StringFast uses the output of the public code CMBACT (ascl:1106.023). The properties of the strings are described by four parameters: Gμ—dimensionless string tension; v—rms transverse velocity (as fraction of c); α—"wiggliness"; ξ—comoving correlation length of the string network. It is written as a Fortran 90 module.

[ascl:1106.022]
MPI-Defrost: Extension of Defrost to MPI-based Cluster Environment

MPI-Defrost extends Frolov’s Defrost to an MPI-based cluster environment. This version has been restricted to a single field. Restoring two-field support should be straightforward, but will require some code changes. Some output options may also not be fully supported under MPI.

This code was produced to support our own work, and has been made available for the benefit of anyone interested in either oscillon simulations or an MPI capable version of Defrost, and it is provided on an "as-is" basis. Andrei Frolov is the primary developer of Defrost and we thank him for placing his work under the GPL (GNU Public License), and thus allowing us to distribute this modified version.

[ascl:1106.023]
CMBACT: CMB from ACTive sources

This code is based on the cosmic string model described in this paper by Pogosian and Vachaspati, as well as on the CMBFAST code created by Uros Seljak and Matias Zaldarriaga. It contains an integrator for the vector contribution to the CMB temperature and polarization. The code is reconfigured to make it easier to use with or without active sources. To produce inflationary CMB spectra one simply sets the string tension to zero (gmu=0.0d0). For a non-zero value of tension only the string contribution is calculated.

An option is added to randomize the directions of velocities of consolidated segments as they evolve in time. In the original segment model, which is still the default version (irandomv=0), each segment is given a random velocity initially, but then continues to move in a straight line for the rest of its life. The new option (irandomv=1) allows to additionally randomize velocities of each segment at roughly each Hubble time. However, the merits of this new option are still under investigation. The default version (irandomv=0) is strongly recommended, since it actually gives reasonable unequal time correlators. For each Fourier mode, k, the string stress-energy components are now evaluated on a time grid sufficiently fine for that k.

[ascl:1106.024]
ELMAG: Simulation of Electromagnetic Cascades

A Monte Carlo program for the simulation of electromagnetic cascades initiated by high-energy photons and electrons interacting with extragalactic background light (EBL) is presented. Pair production and inverse Compton scattering on EBL photons as well as synchrotron losses and deflections of the charged component in extragalactic magnetic fields (EGMF) are included in the simulation. Weighted sampling of the cascade development is applied to reduce the number of secondary particles and to speed up computations. As final result, the simulation procedure provides the energy, the observation angle, and the time delay of secondary cascade particles at the present epoch. Possible applications are the study of TeV blazars and the influence of the EGMF on their spectra or the calculation of the contribution from ultrahigh energy cosmic rays or dark matter to the diffuse extragalactic gamma-ray background. As an illustration, we present results for deflections and time-delays relevant for the derivation of limits on the EGMF.

[ascl:1106.025]
CosmoMC: Cosmological MonteCarlo

We present a fast Markov Chain Monte-Carlo exploration of cosmological parameter space. We perform a joint analysis of results from recent CMB experiments and provide parameter constraints, including sigma_8, from the CMB independent of other data. We next combine data from the CMB, HST Key Project, 2dF galaxy redshift survey, supernovae Ia and big-bang nucleosynthesis. The Monte Carlo method allows the rapid investigation of a large number of parameters, and we present results from 6 and 9 parameter analyses of flat models, and an 11 parameter analysis of non-flat models. Our results include constraints on the neutrino mass (m_nu < 0.3eV), equation of state of the dark energy, and the tensor amplitude, as well as demonstrating the effect of additional parameters on the base parameter constraints. In a series of appendices we describe the many uses of importance sampling, including computing results from new data and accuracy correction of results generated from an approximate method. We also discuss the different ways of converting parameter samples to parameter constraints, the effect of the prior, assess the goodness of fit and consistency, and describe the use of analytic marginalization over normalization parameters.

[ascl:1106.026]
RECFAST: Calculate the Recombination History of the Universe

RECFAST calculates the recombination of H, HeI, and HeII in the early Universe; this involves a line-by-line treatment of each atomic level. It differs in comparison to previous calculations in two major ways: firstly, the ionization fraction x_e is approximately 10% smaller for redshifts <~800, due to non-equilibrium processes in the excited states of H, and secondly, HeI recombination is much slower than previously thought, and is delayed until just before H recombines. RECFAST enables fast computation of the ionization history (and quantities such as the power spectrum of CMB anisotropies which depend on it) for arbitrary cosmologies.

[ascl:1105.001]
STILTS: Starlink Tables Infrastructure Library Tool Set

The STIL Tool Set is a set of command-line tools based on STIL, the Starlink Tables Infrastructure Library. It deals with the processing of tabular data; the package has been designed for, but is not restricted to, astronomical tables such as object catalogues. Some of the tools are generic and can work with multiple formats (including FITS, VOTable, CSV, SQL and ASCII), and others are specific to the VOTable format. In some ways, STILTS forms the command-line counterpart of the GUI table analysis tool TOPCAT. The package is robust, fully documented, and designed for efficiency, especially with very large datasets.

Facilities offered include:

- format conversion
- crossmatching
- plotting
- column calculation and rearrangement
- row selections
- data and metadata manipulation and display
- sorting
- statistical calculations
- histogram calculation
- data validation
- VO service access

[ascl:1105.002]
PACCE: Perl Algorithm to Compute Continuum and Equivalent Widths

PACCE (Perl Algorithm to Compute continuum and Equivalent Widths) computes continuum and equivalent widths. PACCE is able to determine mean continuum and continuum at line center values, which are helpful in stellar population studies, and is also able to compute the uncertainties in the equivalent widths using photon statistics.

[ascl:1105.003]
The DTFE public software: The Delaunay Tessellation Field Estimator code

We present the DTFE public software, a code for reconstructing fields from a discrete set of samples/measurements using the maximum of information contained in the point distribution. The code is written in C++ using the CGAL library and is parallelized using OpenMP. The software was designed for the analysis of cosmological data but can be used in other fields where one must interpolate quantities given at a discrete point set. The software comes with a wide suite of options to facilitate the analysis of 2- and 3-dimensional data and of both numerical simulations and galaxy redshift surveys. For comparison purposes, the code also implements the TSC and SPH grid interpolation methods. The code comes with an extensive user guide detailing the program options, examples and the inner workings of the code.

[ascl:1105.004]
SLiM: A Code for the Simulation of Wave Propagation through an Inhomogeneous, Magnetised Solar Atmosphere

The semi-spectral linear MHD (SLiM) code follows the interaction of linear waves through an inhomogeneous three-dimensional solar atmosphere. The background model allows almost arbitrary perturbations of density, temperature, sound speed as well as magnetic and velocity fields. The code is useful in understanding the helioseismic signatures of various solar features, including sunspots.

[ascl:1105.005]
ChaNGa: Charm N-body GrAvity solver

ChaNGa (Charm N-body GrAvity solver) performs collisionless N-body simulations. It can perform cosmological simulations with periodic boundary conditions in comoving coordinates or simulations of isolated stellar systems. It also can include hydrodynamics using the Smooth Particle Hydrodynamics (SPH) technique. It uses a Barnes-Hut tree to calculate gravity, with hexadecapole expansion of nodes and Ewald summation for periodic forces. Timestepping is done with a leapfrog integrator with individual timesteps for each particle.

[ascl:1105.006]
SPARC: Seismic Propagation through Active Regions and Convection

The Seismic Propagation through Active Regions and Convection (SPARC) code was developed by S. Hanasoge. The acoustic wavefield in SPARC is simulated by numerically solving the linearised 3-D Euler equations in Cartesian geometry (e.g., see Hanasoge, Duvall and Couvidat (2007)). Spatial derivatives are calculated using sixth-order compact finite differences (Lele,1992) and time evolution is achieved through the repeated application of an optimized second-order five-stage Runge-Kutta scheme (Hu, 1996). Periodic horizontal boundaries are used.

[ascl:1105.007]
Sunspot Models

This IDL code creates a thick magneto-static structure with parameters of a typical sunspot in a solar like photosphere - chromosphere. The variable parameters are field strength on the axis, radius, and Wilson depression (displacement of the atmosphere on the axis with respect to the field-free atmosphere). Output are magnetic field vector, pressure and density distributions with radius and height. The structure has azimuthal symmetry. The codes are relatively self explanatory and the download packages contain README files.

[ascl:1105.008]
Flux Tube Model

This Fortran code computes magnetohydrostatic flux tubes and sheets according to the method of Steiner, Pneuman, & Stenflo (1986) A&A 170, 126-137. The code has many parameters contained in one input file that are easily modified. Extensive documentation is provided in README files.

[ascl:1105.009]
Ray Tracing Codes: run_tau, run_raypath, and ray_kernel

Time-distance helioseismology aims to measure and interpret the travel times of waves propagating between two points located on the solar surface. The travel times are then inverted to infer sub-surface properties that are encoded in the measurements. The trajectory of the waves generally follows that of the infinite-frequency ray path, although they are sensitive to perturbations off of this path. Finite-frequency sensitivity kernels are thus needed to give more accurate inversion results.

Ray tracing codes calculate travel time kernels for a ray. There are three main codes which calculate the group time as a function of distance, the ray paths as well as the phase and group times along the path, and the ray kernels for the sound speed squared.

[ascl:1105.010]
CASTRO: Multi-dimensional Eulerian AMR Radiation-hydrodynamics Code

Almgren, A. S.; Beckner, V. E.; Bell, J. B.; Day, M. S.; Howell, L. H.; Katz, M; Lijewski, M. J.; Malone, C.; Nonaka, A.; Singer, M.; Zhang, W; Zingale, M.

CASTRO is a multi-dimensional Eulerian AMR radiation-hydrodynamics code that includes stellar equations of state, nuclear reaction networks, and self-gravity. Initial target applications for CASTRO include Type Ia and Type II supernovae. CASTRO supports calculations in 1-d, 2-d and 3-d Cartesian coordinates, as well as 1-d spherical and 2-d cylindrical (r-z) coordinate systems. Time integration of the hydrodynamics equations is based on an unsplit version of the the piecewise parabolic method (PPM) with new limiters that avoid reducing the accuracy of the scheme at smooth extrema. CASTRO can follow an arbitrary number of isotopes or elements. The atomic weights and amounts of these elements are used to calculate the mean molecular weight of the gas required by the equation of state. CASTRO supports several different approaches to solving for self-gravity. The most general is a full Poisson solve for the gravitational potential. CASTRO also supports a monopole approximation for gravity, and a constant gravity option is also available. The CASTRO software is written in C++ and Fortran, and is based on the BoxLib software framework developed by CCSE.

[ascl:1105.011]
Ganalyzer: A tool for automatic galaxy image analysis

Ganalyzer is a model-based tool that automatically analyzes and classifies galaxy images. Ganalyzer works by separating the galaxy pixels from the background pixels, finding the center and radius of the galaxy, generating the radial intensity plot, and then computing the slopes of the peaks detected in the radial intensity plot to measure the spirality of the galaxy and determine its morphological class. Unlike algorithms that are based on machine learning, Ganalyzer is based on measuring the spirality of the galaxy, a task that is difficult to perform manually, and in many cases can provide a more accurate analysis compared to manual observation. Ganalyzer is simple to use, and can be easily embedded into other image analysis applications. Another advantage is its speed, which allows it to analyze ~10,000,000 galaxy images in five days using a standard modern desktop computer. These capabilities can make Ganalyzer a useful tool in analyzing large datasets of galaxy images collected by autonomous sky surveys such as SDSS, LSST or DES.

[ascl:1105.012]
Stagger: MHD Method for Modeling Star Formation

Stagger is an astrophysical MHD code actively used to model star formation. It is equipped with a multi-frequency radiative transfer module and a comprehensive equation of state module that includes a large number of atomic and molecular species, to be able to compute realistic 3-D models of the near-surface layers of stars. The current version of the code allows a discretization that explicitly conserves mass, momentum, energy, and magnetic flux. The tensor formulation of the viscosity ensures that the viscous force is insensitive to the coordinate system orientation, thereby avoiding artificial grid-alignment.

[ascl:1105.013]
CAMB Sources: Number Counts, Lensing & Dark-age 21cm Power Spectra

We relate the observable number of sources per solid angle and redshift to the underlying proper source density and velocity, background evolution and line-of-sight potentials. We give an exact result in the case of linearized perturbations assuming general relativity. This consistently includes contributions of the source density perturbations and redshift distortions, magnification, radial displacement, and various additional linear terms that are small on sub-horizon scales. In addition we calculate the effect on observed luminosities, and hence the result for sources observed as a function of flux, including magnification bias and radial-displacement effects. We give the corresponding linear result for a magnitude-limited survey at low redshift, and discuss the angular power spectrum of the total count distribution. We also calculate the cross-correlation with the CMB polarization and temperature including Doppler source terms, magnification, redshift distortions and other velocity effects for the sources, and discuss why the contribution of redshift distortions is generally small. Finally we relate the result for source number counts to that for the brightness of line radiation, for example 21-cm radiation, from the sources.

[ascl:1105.014]
PSRCHIVE: Development Library for the Analysis of Pulsar Astronomical Data

PSRCHIVE is an Open Source C++ development library for the analysis of pulsar astronomical data. It implements an extensive range of algorithms for use in pulsar timing, polarimetric calibration, single-pulse analyses, RFI mitigation, scintillation studies, etc. These tools are utilized by a powerful suite of user-end programs that come with the library.

[ascl:1104.001]
TomograPy: A Fast, Instrument-Independent, Solar Tomography Software

TomograPy is an open-source software freely available on the Python Package Index that can perform fast tomographic inversions that scale linearly with the number of measurements, linearly with the length of the reconstruction cube (and not the number of voxels) and linearly with the number of cores and can use data from different sources and with a variety of physical models. For performance, TomograPy uses a parallelized-projection algorithm. It relies on the World Coordinate System standard to manage various data sources. A variety of inversion algorithms are provided to perform the tomographic-map estimation. A test suite is provided along with the code to ensure software quality. Since it makes use of the Siddon algorithm it is restricted to rectangular parallelepiped voxels but the spherical geometry of the corona can be handled through proper use of priors.

[ascl:1104.002]
AstroBEAR: Adaptive Mesh Refinement Code for Ideal Hydrodynamics & Magnetohydrodynamics

AstroBEAR is a modular hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications. It uses the BEARCLAW package, a multidimensional, Eulerian computational code used to solve hyperbolic systems of equations. AstroBEAR allows adaptive-mesh-refinment (AMR) simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates. Parallel applications are supported through the MPI architecture. AstroBEAR is written in Fortran 90/95 using standard libraries.

AstroBEAR supports hydrodynamic (HD) and magnetohydrodynamic (MHD) applications using a variety of spatial and temporal methods. MHD simulations are kept divergence-free via the constrained transport (CT) methods of Balsara & Spicer. Three different equation of state environments are available: ideal gas, gas with differing isentropic γ, and the analytic Thomas-Fermi formulation of A.R. Bell.

[ascl:1104.003]
Starburst99: Synthesis Models for Galaxies with Active Star Formation

Leitherer, Claus; Schaerer, Daniel; Goldader, Jeff; Gonzalez-Delgado, Rosa; Robert, Carmelle; Foo Kune, Denis; de Mello, Duilia; Devost, Daniel; Heckman, Timothy M.; Aloisi, Alessandra; Martins, Lucimara; Vazquez, Gerardo

Starburst99 is a comprehensive set of model predictions for spectrophotometric and related properties of galaxies with active star formation. The models are presented in a homogeneous way for five metallicities between Z = 0.040 and 0.001 and three choices of the initial mass function. The age coverage is 10^6 to 10^9 yr. Spectral energy distributions are used to compute colors and other quantities.

[ascl:1104.004]
MASSCLEAN: MASSive CLuster Evolution and ANalysis Package

MASSCLEAN is a sophisticated and robust stellar cluster image and photometry simulation package. This package is able to create color-magnitude diagrams and standard FITS images in any of the traditional optical and near-infrared bands based on cluster characteristics input by the user, including but not limited to distance, age, mass, radius and extinction. At the limit of very distant, unresolved clusters, we have checked the integrated colors created in MASSCLEAN against those from other simple stellar population (SSP) models with consistent results. Because the algorithm populates the cluster with a discrete number of tenable stars, it can be used as part of a Monte Carlo Method to derive the probabilistic range of characteristics (integrated colors, for example) consistent with a given cluster mass and age.

[ascl:1104.005]
GALAXEV: Evolutionary Stellar Population Synthesis Models

GALAXEV is a library of evolutionary stellar population synthesis models computed using the new isochrone synthesis code of Bruzual & Charlot (2003). This code allows one to computes the spectral evolution of stellar populations in wide ranges of ages and metallicities at a resolution of 3 Å across the whole wavelength range from 3200 Å to 9500 Å, and at lower resolution outside this range.

[ascl:1104.006]
LECTOR: Line-strengths in One-dimensional ASCII Spectra

LECTOR is a Fortran 77 code that measures line-strengths in one dimensional ascii spectra. The code returns the values of the Lick indices as well as those of Vazdekis & Arimoto 1999, Vazdekis et al. 2001, Rose 1994, Jones & Worthey 1995 and Cenarro et al. 2001. The code measures as many indices as you wish if the limits of two pseudocontinua (at each side of the feature) and the feature itself (i.e. Lick-style index definition) are provided. The Lick-style indices could be either expressed in pseudo-equivalent widths or in magnitudes. If requested the program provides index error estimates on the basis of photon statistics.

[ascl:1104.007]
ULySS: A Full Spectrum Fitting Package

ULySS (University of Lyon Spectroscopic Analysis Software) is an open-source software package written in the GDL/IDL language to analyze astronomical data. ULySS fits a spectrum with a linear combination of non-linear components convolved with a line-of-sight velocity distribution (LOSVD) and multiplied by a polynomial continuum. ULySS is used to study stellar populations of galaxies and star clusters and atmospheric parameters of stars.

[ascl:1104.008]
Rmodel: Determining Stellar Population Parameters

This program determines stellar population parameters (e.g. age, metallicity, IMF slope,...), using as input a pair of line-strength indices, through the interpolation in SSP model predictions. Both linear and bivariate fits are computed to perform the interpolation.

[ascl:1104.009]
r-Java: An r-process Code and Graphical User Interface for Heavy-Element Nucleosynthesis

r-Java performs r-process nucleosynthesis calculations. It has a simple graphical user interface and is carries out nuclear statistical equilibrium (NSE) as well as static and dynamic r-process calculations for a wide range of input parameters. r-Java generates an abundance pattern based on a general entropy expression that can be applied to degenerate as well as non-degenerate matter, which allows tracking of the rapid density and temperature evolution of the ejecta during the initial stages of ejecta expansion.

[ascl:1104.010]
GALFIT: Detailed Structural Decomposition of Galaxy Images

GALFIT is a two-dimensional (2-D) fitting algorithm designed to extract structural components from galaxy images, with emphasis on closely modeling light profiles of spatially well-resolved, nearby galaxies observed with the Hubble Space Telescope. The algorithm improves on previous techniques in two areas: 1.) by being able to simultaneously fit a galaxy with an arbitrary number of components, and 2.) with optimization in computation speed, suited for working on large galaxy images. 2-D models such as the "Nuker'' law, the Sersic (de Vaucouleurs) profile, an exponential disk, and Gaussian or Moffat functions are used. The azimuthal shapes are generalized ellipses that can fit disky and boxy components. Many galaxies with complex isophotes, ellipticity changes, and position-angle twists can be modeled accurately in 2-D. When examined in detail, even simple-looking galaxies generally require at least three components to be modeled accurately rather than the one or two components more often employed. This is illustrated by way of seven case studies, which include regular and barred spiral galaxies, highly disky lenticular galaxies, and elliptical galaxies displaying various levels of complexities. A useful extension of this algorithm is to accurately extract nuclear point sources in galaxies.

[ascl:1104.011]
DAOPHOT: Crowded-field Stellar Photometry Package

The DAOPHOT program exploits the capability of photometrically linear image detectors to perform stellar photometry in crowded fields. Raw CCD images are prepared prior to analysis, and following the obtaining of an initial star list with the FIND program, synthetic aperture photometry is performed on the detected objects with the PHOT routine. A local sky brightness and a magnitude are computed for each star in each of the specified stellar apertures, and for crowded fields, the empirical point-spread function must then be obtained for each data frame. The GROUP routine divides the star list for a given frame into optimum subgroups, and then the NSTAR routine is used to obtain photometry for all the stars in the frame by means of least-squares profile fits.

[ascl:1104.012]
CHIWEI: A Code of Goodness of Fit Tests for Weighted and Unweighed Histograms

A self-contained Fortran-77 program for goodness of fit tests for histograms with weighted entries as well as with unweighted entries is presented. The code calculates test statistic for case of histogram with normalized weights of events and for case of unnormalized weights of events.

[ascl:1104.013]
BEARCLAW: Boundary Embedded Adaptive Refinement Conservation LAW package

The BEARCLAW package is a multidimensional, Eulerian AMR-capable computational code written in Fortran to solve hyperbolic systems for astrophysical applications. It is part of AstroBEAR, a hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications which allows simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates.

[ascl:1104.014]
A Correction to the Standard Galactic Reddening Map: Passive Galaxies as Standard Crayons

We present corrections to the Schlegel, Finkbeiner, Davis (SFD98) reddening maps over the Sloan Digital Sky Survey northern Galactic cap area. To find these corrections, we employ what we dub the "standard crayon" method, in which we use passively evolving galaxies as color standards by which to measure deviations from the reddening map. We select these passively evolving galaxies spectroscopically, using limits on the H alpha and O II equivalent widths to remove all star-forming galaxies from the SDSS main galaxy catalog. We find that by correcting for known reddening, redshift, color-magnitude relation, and variation of color with environmental density, we can reduce the scatter in color to below 3% in the bulk of the 151,637 galaxies we select. Using these galaxies we construct maps of the deviation from the SFD98 reddening map at 4.5 degree resolution, with 1-sigma error of ~ 1.5 millimagnitudes E(B-V). We find that the SFD98 maps are largely accurate with most of the map having deviations below 3 millimagnitudes E(B-V), though some regions do deviate from SFD98 by as much as 50%. The maximum deviation found is 45 millimagnitudes in E(B-V), and spatial structure of the deviation is strongly correlated with the observed dust temperature, such that SFD98 underpredicts reddening in regions of low dust temperature. The maps of these deviations, as well as their errors, are made available to the scientific community as supplemental correction to SFD98 at the URL below.

[ascl:1103.001]
Difmap: Synthesis Imaging of Visibility Data

Difmap is a program developed for synthesis imaging of visibility data from interferometer arrays of radio telescopes world-wide. Its prime advantages over traditional packages are its emphasis on interactive processing, speed, and the use of Difference mapping techniques.

[ascl:1103.002]
PGPLOT: Device-independent Graphics Package for Simple Scientific Graphs

The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.

The PGPLOT library consists of two major parts: a device-independent part and a set of device-dependent "device handler" subroutines for output on various terminals, image displays, dot-matrix printers, laser printers, and pen plotters. Common file formats supported include PostScript and GIF.

PGPLOT itself is written mostly in standard Fortran-77, with a few non-standard, system-dependent subroutines. PGPLOT subroutines can be called directly from a Fortran-77 or Fortran-90 program. A C binding library (cpgplot) and header file (cpgplot.h) are provided that allow PGPLOT to be called from a C or C++ program; the binding library handles conversion between C and Fortran argument-passing conventions.

[ascl:1103.003]
S2PLOT: Three-dimensional (3D) Plotting Library

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - S2PLOT - is written in C and can be used by C, C++ and FORTRAN programs on GNU/Linux and Apple/OSX systems. S2PLOT draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a PGPLOT inspired interface, S2PLOT provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The S2PLOT architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce S2PLOT to the astronomical community, describe its potential applications, and present some example uses of the library.

[ascl:1103.004]
SPLASH: Interactive Visualization Tool for Smoothed Particle Hydrodynamics Simulations

SPLASH (formerly SUPERSPHPLOT) visualizes output from (astrophysical) simulations using the Smoothed Particle Hydrodynamics (SPH) method in one, two and three dimensions. Written in Fortran 90, it uses the PGPLOT graphics subroutine library for plotting. It is based around a command-line menu structure but utilizes the interactive capabilities of PGPLOT to manipulate data interactively in the plotting window. SPLASH is fully interactive; visualizations can be changed rapidly at the touch of a button (e.g. zooming, rotating, shifting cross section positions etc). Data is read directly from the code dump format giving rapid access to results and the visualization is advanced forwards and backwards through timesteps by single keystrokes. SPLASH uses the SPH kernel to render plots of not only density but other physical quantities, giving a smooth representation of the data.

[ascl:1103.005]
Splotch: Ray Tracer to Visualize SPH Simulations

Splotch is a light and fast, publicly available, ray-tracer software tool which supports the effective visualization of cosmological simulations data. The algorithm it relies on is designed to deal with point-like data, optimizing the ray-tracing calculation by ordering the particles as a function of their 'depth', defined as a function of one of the coordinates or other associated parameters. Realistic three-dimensional impressions are reached through a composition of the final colour in each pixel properly calculating emission and absorption of individual volume elements.

[ascl:1103.006]
GLESP 2.0: Gauss-Legendre Sky Pixelization for CMB Analysis

Doroshkevich, A. G.; Naselsky, P. D.; Verkhodanov, O. V.; Novikov, D. I.; Turchaninov, V. I.; Novikov, I. D.; Christensen, P. R.; Chiang, L.-Y.

GLESP is a pixelization scheme for the cosmic microwave background (CMB) radiation maps. This scheme is based on the Gauss-Legendre polynomials zeros and allows one to create strict orthogonal expansion of the map.

[ascl:1103.007]
VisIt: Interactive Parallel Visualization and Graphical Analysis Tool

VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range. See the table below for more details about the tool’s features.

VisIt was developed by the Department of Energy (DOE) Advanced Simulation and Computing Initiative (ASCI) to visualize and analyze the results of terascale simulations. It was developed as a framework for adding custom capabilities and rapidly deploying new visualization technologies. Although the primary driving force behind the development of VisIt was for visualizing terascale data, it is also well suited for visualizing data from typical simulations on desktop systems.

[ascl:1103.008]
Parallel HOP: A Scalable Halo Finder for Massive Cosmological Data Sets

Modern N-body cosmological simulations contain billions ($10^9$) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory, and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly-employed halo finders, such that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes MPI and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger datasets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit yt, an analysis toolkit for Adaptive Mesh Refinement (AMR) data that includes complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and datasets in excess of $2000^3$ particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable. Parallel HOP is part of yt.

[ascl:1103.009]
SPHRAY: A Smoothed Particle Hydrodynamics Ray Tracer for Radiative Transfer

SPHRAY, a Smoothed Particle Hydrodynamics (SPH) ray tracer, is designed to solve the 3D, time dependent, radiative transfer (RT) equations for arbitrary density fields. The SPH nature of SPHRAY makes the incorporation of separate hydrodynamics and gravity solvers very natural. SPHRAY relies on a Monte Carlo (MC) ray tracing scheme that does not interpolate the SPH particles onto a grid but instead integrates directly through the SPH kernels. Given initial conditions and a description of the sources of ionizing radiation, the code will calculate the non-equilibrium ionization state (HI, HII, HeI, HeII, HeIII, e) and temperature (internal energy/entropy) of each SPH particle. The sources of radiation can include point like objects, diffuse recombination radiation, and a background field from outside the computational volume. The MC ray tracing implementation allows for the quick introduction of new physics and is parallelization friendly. A quick Axis Aligned Bounding Box (AABB) test taken from computer graphics applications allows for the acceleration of the raytracing component. We present the algorithms used in SPHRAY and verify the code by performing all the test problems detailed in the recent Radiative Transfer Comparison Project of Iliev et. al. The Fortran 90 source code for SPHRAY and example SPH density fields are made available online.

[ascl:1103.010]
Hydra: A Parallel Adaptive Grid Code

We describe the first parallel implementation of an adaptive particle-particle, particle-mesh code with smoothed particle hydrodynamics. Parallelisation of the serial code, "Hydra," is achieved by using CRAFT, a Cray proprietary language which allows rapid implementation of a serial code on a parallel machine by allowing global addressing of distributed memory.

The collisionless variant of the code has already completed several 16.8 million particle cosmological simulations on a 128 processor Cray T3D whilst the full hydrodynamic code has completed several 4.2 million particle combined gas and dark matter runs. The efficiency of the code now allows parameter-space explorations to be performed routinely using $64^3$ particles of each species. A complete run including gas cooling, from high redshift to the present epoch requires approximately 10 hours on 64 processors.

[ascl:1103.011]
AP3M: Adaptive Particle-particle, Particle-mesh Code

AP^{3}M is an adaptive particle-particle, particle-mesh code. It is older than Hydra (ascl:1103.010) but faster and more memory-efficient for dark-matter only calculations. The Adaptive P^{3}M technique (AP^{3}M) is built around the standard P^{3}M algorithm. AP^{3}M produces fully equivalent forces to P^{3}M but represents a more efficient implementation of the force splitting idea of P^{3}M. The AP^{3}M program may be used in any of the three modes with an appropriate choice of input parameter.

[ascl:1103.012]
Pyflation: Second Order Perturbations During Inflation Beyond Slow-roll

Pyflation calculates cosmological perturbations during an inflationary expansion of the universe. The modules in the pyflation Python package can be used to run simulations of different scalar field models of the early universe. The main classes are contained in the cosmomodels module and include simulations of background fields and first order and second order perturbations. The sourceterm package contains modules required for the computation of the term required for the evolution of second order perturbations.

Alongside the Python package, the bin directory contains Python scripts which can run first and second order simulations. A helper script called pyflation-qsubstart.py sets up a full second order run (including background, first order and source calculations) to be used on queueing system which contains the qsub executable (e.g. a Rocks cluster).

[ascl:1103.014]
ParaView: Data Analysis and Visualization Application

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

[ascl:1103.015]
Cloudy_3D: Quick Pseudo-3D Photoionization Code

We developed a new quick pseudo-3D photoionization code based on Cloudy (G. Ferland) and IDL (RSI) tools. The code is running the 1D photoionization code Cloudy various times, changing at each run the input parameters (e.g. inner radius, density law) according to an angular law describing the morphology of the object. Then a cube is generated by interpolating the outputs of Cloudy. In each cell of the cube, the physical conditions (electron temperature and density, ionic fractions) and the emissivities of lines are determined. Associated tools (VISNEB and VELNEB_3D) are used to rotate the nebula and to compute surface brightness maps and emission line profiles, given a velocity law and taking into account the effect of the thermal broadening and eventually the turbulence. Integrated emission line profiles are computed, given aperture shapes and positions (seeing and instrumental width effects are included). The main advantage of this tool is the short time needed to compute a model (a few tens minutes).

[ascl:1102.001]
N-MODY: A Code for Collisionless N-body Simulations in Modified Newtonian Dynamics

N-MODY is a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

[ascl:1102.002]
PBL: Particle-Based Lensing for Gravitational Lensing Mass Reconstructions of Galaxy Clusters

We present Particle-Based Lensing (PBL), a new technique for gravitational lensing mass reconstructions of galaxy clusters. Traditionally, most methods have employed either a finite inversion or gridding to turn observational lensed galaxy ellipticities into an estimate of the surface mass density of a galaxy cluster. We approach the problem from a different perspective, motivated by the success of multi-scale analysis in smoothed particle hydrodynamics. In PBL, we treat each of the lensed galaxies as a particle and then reconstruct the potential by smoothing over a local kernel with variable smoothing scale. In this way, we can tune a reconstruction to produce constant signal-noise throughout, and maximally exploit regions of high information density.

PBL is designed to include all lensing observables, including multiple image positions and fluxes from strong lensing, as well as weak lensing signals including shear and flexion. In this paper, however, we describe a shear-only reconstruction, and apply the method to several test cases, including simulated lensing clusters, as well as the well-studied ``Bullet Cluster'' (1E0657-56). In the former cases, we show that PBL is better able to identify cusps and substructures than are grid-based reconstructions, and in the latter case, we show that PBL is able to identify substructure in the Bullet Cluster without even exploiting strong lensing measurements.

[ascl:1102.003]
GRAVLENS: Computational Methods for Gravitational Lensing

Modern applications of strong gravitational lensing require the ability to use precise and varied observational data to constrain complex lens models. Two sets of computational methods for lensing calculations are discussed. The first is a new algorithm for solving the lens equation for general mass distributions. This algorithm makes it possible to apply arbitrarily complicated models to observed lenses. The second is an evaluation of techniques for using observational data including positions, fluxes, and time delays of point-like images, as well as maps of extended images, to constrain models of strong lenses. The techniques presented here are implemented in a flexible and user-friendly software package called gravlens, which is made available to the community.

[ascl:1102.004]
LENSTOOL: A Gravitational Lensing Software for Modeling Mass Distribution of Galaxies and Clusters (strong and weak regime)

We describe a procedure for modelling strong lensing galaxy clusters with parametric methods, and to rank models quantitatively using the Bayesian evidence. We use a publicly available Markov chain Monte-Carlo (MCMC) sampler ('Bayesys'), allowing us to avoid local minima in the likelihood functions. To illustrate the power of the MCMC technique, we simulate three clusters of galaxies, each composed of a cluster-scale halo and a set of perturbing galaxy-scale subhalos. We ray-trace three light beams through each model to produce a catalogue of multiple images, and then use the MCMC sampler to recover the model parameters in the three different lensing configurations. We find that, for typical Hubble Space Telescope (HST)-quality imaging data, the total mass in the Einstein radius is recovered with ~1-5% error according to the considered lensing configuration. However, we find that the mass of the galaxies is strongly degenerated with the cluster mass when no multiple images appear in the cluster centre. The mass of the galaxies is generally recovered with a 20% error, largely due to the poorly constrained cut-off radius. Finally, we describe how to rank models quantitatively using the Bayesian evidence. We confirm the ability of strong lensing to constrain the mass profile in the central region of galaxy clusters in this way. Ultimately, such a method applied to strong lensing clusters with a very large number of multiple images may provide unique geometrical constraints on cosmology.

[ascl:1102.005]
MRLENS: Multi-Resolution methods for gravitational LENSing

The MRLENS package offers a new method for the reconstruction of weak lensing mass maps. It uses the multiscale entropy concept, which is based on wavelets, and the False Discovery Rate which allows us to derive robust detection levels in wavelet space. We show that this new restoration approach outperforms several standard techniques currently used for weak shear mass reconstruction. This method can also be used to separate E and B modes in the shear field, and thus test for the presence of residual systematic effects. We concentrate on large blind cosmic shear surveys, and illustrate our results using simulated shear maps derived from N-Body Lambda-CDM simulations with added noise corresponding to both ground-based and space-based observations.

[ascl:1102.006]
NBODY Codes: Numerical Simulations of Many-body (N-body) Gravitational Interactions

I review the development of direct N-body codes at Cambridge over nearly 40 years, highlighting the main stepping stones. The first code (NBODY1) was based on the simple concepts of a force polynomial combined with individual time steps, where numerical problems due to close encounters were avoided by a softened potential. Fortuitously, the elegant Kustaanheimo-Stiefel two-body regularization soon permitted small star clusters to be studied (NBODY3). Subsequent extensions to unperturbed three-body and four-body regularization proved beneficial in dealing with multiple interactions. Investigations of larger systems became possible with the Ahmad-Cohen neighbor scheme which was used more than 20 years ago for expanding universe models of 4000 galaxies (NBODY2). Combining the neighbor scheme with the regularization procedures enabled more realistic star clusters to be considered (NBODY5). After a period of simulations with no apparent technical progress, chain regularization replaced the treatment of compact subsystems (NBODY3, NBODY5). More recently, the Hermite integration method provided a major advance and has been implemented on the special-purpose HARP computers (NBODY4) together with an alternative version for workstations and supercomputers (NBODY6). These codes also include a variety of algorithms for stellar evolution based on fast lookup functions. The treatment of primordial binaries contains efficient procedures for chaotic two-body motion as well as tidal circularization, and special attention is paid to hierarchical systems and their stability. This family of N-body codes constitutes a powerful tool for dynamical simulations which is freely available to the astronomical community, and the massive effort owes much to collaborators.

[ascl:1102.007]
PixeLens: A Portable Modeler of Lensed Quasars

We introduce and implement two novel ideas for modeling lensed quasars. The first is to require different lenses to agree about H_{0}. This means that some models for one lens can be ruled out by data on a different lens. We explain using two worked examples. One example models 1115+080 and 1608+656 (time-delay quadruple systems) and 1933+503 (a prospective time-delay system) all together, yielding time-delay predictions for the third lens and a 90% confidence estimate of H_{0}^{-1}=14.6+9.4-1.7 Gyr (H_{0}=67+9-26 km s^{-1} Mpc^{-1}) assuming ΩM=0.3 and Ω_{Λ}=0.7. The other example models the time-delay doubles 1520+530, 1600+434, 1830-211, and 2149-275, which gives H_{0}^{-1}=14.5+3.3-1.5 Gyr (H_{0}=67+8-13 km s^{-1} Mpc^{-1}). Our second idea is to write the modeling software as a highly interactive Java applet, which can be used both for coarse-grained results inside a browser and for fine-grained results on a workstation. Several obstacles come up in trying to implement a numerically intensive method thus, but we overcome them.

[ascl:1102.008]
PMFAST: Towards Optimal Parallel PM N-body Codes

The parallel PM N-body code PMFAST is cost-effective and memory-efficient. PMFAST is based on a two-level mesh gravity solver where the gravitational forces are separated into long and short range components. The decomposition scheme minimizes communication costs and allows tolerance for slow networks. The code approaches optimality in several dimensions. The force computations are local and exploit highly optimized vendor FFT libraries. It features minimal memory overhead, with the particle positions and velocities being the main cost. The code features support for distributed and shared memory parallelization through the use of MPI and OpenMP, respectively.

The current release version uses two grid levels on a slab decomposition, with periodic boundary conditions for cosmological applications. Open boundary conditions could be added with little computational overhead. Timing information and results from a recent cosmological production run of the code using a 3712^3 mesh with 6.4 x 10^9 particles are available.

[ascl:1102.009]
AHF: Amiga's Halo Finder

Cosmological simulations are the key tool for investigating the different processes involved in the formation of the universe from small initial density perturbations to galaxies and clusters of galaxies observed today. The identification and analysis of bound objects, halos, is one of the most important steps in drawing useful physical information from simulations. In the advent of larger and larger simulations, a reliable and parallel halo finder, able to cope with the ever-increasing data files, is a must. In this work we present the freely available MPI parallel halo finder AHF. We provide a description of the algorithm and the strategy followed to handle large simulation data. We also describe the parameters a user may choose in order to influence the process of halo finding, as well as pointing out which parameters are crucial to ensure untainted results from the parallel approach. Furthermore, we demonstrate the ability of AHF to scale to high-resolution simulations.

[ascl:1102.010]
SEREN: A SPH code for star and planet formation simulations

Hubber, David; Batty, Chris; McLeod, Andrew; Whitworth, Anthony; Bisbas, Thomas; Stamatellos, Dimitrios; Walch, Stefanie; Rawiraswattana, Krisada; Goodwin, Simon

SEREN is an astrophysical Smoothed Particle Hydrodynamics code designed to investigate star and planet formation problems using self-gravitating hydrodynamics simulations of molecular clouds, star-forming cores, and protostellar disks.

SEREN is written in Fortran 95/2003 with a modular philosophy for adding features into the code. Each feature can be easily activated or deactivated by way of setting options in the Makefile before compiling the code. This has the added benefit of allowing unwanted features to be removed at the compilation stage resulting in a smaller and faster executable program. SEREN is written with OpenMP directives to allow parallelization on shared-memory architecture.

[ascl:1102.011]
Identikit 2: An Algorithm for Reconstructing Galactic Collisions

Using a combination of self-consistent and test-particle techniques, Identikit 1 provided a way to vary the initial geometry of a galactic collision and instantly visualize the outcome. Identikit 2 uses the same techniques to define a mapping from the current morphology and kinematics of a tidal encounter back to the initial conditions. By requiring that various regions along a tidal feature all originate from a single disc with a unique orientation, this mapping can be used to derive the initial collision geometry. In addition, Identikit 2 offers a robust way to measure how well a particular model reproduces the morphology and kinematics of a pair of interacting galaxies. A set of eight self-consistent simulations is used to demonstrate the algorithm's ability to search a ten-dimensional parameter space and find near-optimal matches; all eight systems are successfully reconstructed.

[ascl:1102.012]
CPROPS: Bias-free Measurement of Giant Molecular Cloud Properties

CPROPS, written in IDL, processes FITS data cubes containing molecular line emission and returns the properties of molecular clouds contained within it. Without corrections for the effects of beam convolution and sensitivity to GMC properties, the resulting properties may be severely biased. This is particularly true for extragalactic observations, where resolution and sensitivity effects often bias measured values by 40% or more. We correct for finite spatial and spectral resolutions with a simple deconvolution and we correct for sensitivity biases by extrapolating properties of a GMC to those we would expect to measure with perfect sensitivity. The resulting method recovers the properties of a GMC to within 10% over a large range of resolutions and sensitivities, provided the clouds are marginally resolved with a peak signal-to-noise ratio greater than 10. We note that interferometers systematically underestimate cloud properties, particularly the flux from a cloud. The degree of bias depends on the sensitivity of the observations and the (u,v) coverage of the observations. In the Appendix to the paper we present a conservative, new decomposition algorithm for identifying GMCs in molecular-line observations. This algorithm treats the data in physical rather than observational units, does not produce spurious clouds in the presence of noise, and is sensitive to a range of morphologies. As a result, the output of this decomposition should be directly comparable among disparate data sets.

The CPROPS package contains within it a distribution of the CLUMPFIND code written by Jonathan Williams and described in Williams, de Geus, and Blitz(1994). The package is available as a stand alone package. If you make use of the CLUMPFIND functionality in the CPROPS package for a publication, please cite Jonathan's original article.

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