[ascl:1011.012]
DEFROST: A New Code for Simulating Preheating after Inflation

At the end of inflation, dynamical instability can rapidly deposit the energy of homogeneous cold inflaton into excitations of other fields. This process, known as preheating, is rather violent, inhomogeneous and non-linear, and has to be studied numerically. This paper presents a new code for simulating scalar field dynamics in expanding universe written for that purpose. Compared to available alternatives, it significantly improves both the speed and the accuracy of calculations, and is fully instrumented for 3D visualization. We reproduce previously published results on preheating in simple chaotic inflation models, and further investigate non-linear dynamics of the inflaton decay. Surprisingly, we find that the fields do not want to thermalize quite the way one would think. Instead of directly reaching equilibrium, the evolution appears to be stuck in a rather simple but quite inhomogeneous state. In particular, one-point distribution function of total energy density appears to be universal among various two-field preheating models, and is exceedingly well described by a lognormal distribution. It is tempting to attribute this state to scalar field turbulence.

[ascl:1011.013]
EasyLTB: Code for Testing LTB Models against CosmologyConfronting Lemaitre-Tolman-Bondi Models with Observational Cosmology

The possibility that we live in a special place in the universe, close to the centre of a large void, seems an appealing alternative to the prevailing interpretation of the acceleration of the universe in terms of a LCDM model with a dominant dark energy component. In this paper we confront the asymptotically flat Lemaitre-Tolman-Bondi (LTB) models with a series of observations, from Type Ia Supernovae to Cosmic Microwave Background and Baryon Acoustic Oscillations data. We propose two concrete LTB models describing a local void in which the only arbitrary functions are the radial dependence of the matter density Omega_M and the Hubble expansion rate H. We find that all observations can be accommodated within 1 sigma, for our models with 4 or 5 independent parameters. The best fit models have a chi^2 very close to that of the LCDM model. We perform a simple Bayesian analysis and show that one cannot exclude the hypothesis that we live within a large local void of an otherwise Einstein-de Sitter model.

[ascl:1011.014]
CO5BOLD: COnservative COde for the COmputation of COmpressible COnvection in a BOx of L Dimensions with l=2,3

The code was supplemented with an (optional) MHD version [Schaffenberger et al. (2005)] that can treat magnetic fields. There are also modules for the formation and advection of dust available. The current version now contains the treatment of chemical reaction networks, mostly used for the formation of molecules [Wedemeyer-Böhm et al. (2005)], and hydrogen ionization [Leenaarts & Wedemeyer-Böhm (2005)], too.

Freytag, Bernd; Steffen, Matthias; Wedemeyer-Böhm, Sven; Ludwig, Hans-Günter; Leenaarts, Jorrit; Schaffenberger, Werner; Allard, France; Chiavassa, Andrea; Höfner, Susanne; Kamp, Inga; Steiner, Oskar

CO5BOLD - nickname COBOLD - is the short form of "COnservative COde for the COmputation of COmpressible COnvection in a BOx of L Dimensions with l=2,3''.

It is used to model solar and stellar surface convection. For solar-type stars only a small fraction of the stellar surface layers are included in the computational domain. In the case of red supergiants the computational box contains the entire star. Recently, the model range has been extended to sub-stellar objects (brown dwarfs).

CO5BOLD solves the coupled non-linear equations of compressible hydrodynamics in an external gravity field together with non-local frequency-dependent radiation transport. Operator splitting is applied to solve the equations of hydrodynamics (including gravity), the radiative energy transfer (with a long-characteristics or a short-characteristics ray scheme), and possibly additional 3D (turbulent) diffusion in individual sub steps. The 3D hydrodynamics step is further simplified with directional splitting (usually). The 1D sub steps are performed with a Roe solver, accounting for an external gravity field and an arbitrary equation of state from a table.

The radiation transport is computed with either one of three modules:

- MSrad module: It uses long characteristics. The lateral boundaries have to be periodic. Top and bottom can be closed or open ("solar module'').

- LHDrad module: It uses long characteristics and is restricted to an equidistant grid and open boundaries at all surfaces (old "supergiant module'').

- SHORTrad module: It uses short characteristics and is restricted to an equidistant grid and open boundaries at all surfaces (new "supergiant module'').

The code was supplemented with an (optional) MHD version [Schaffenberger et al. (2005)] that can treat magnetic fields. There are also modules for the formation and advection of dust available. The current version now contains the treatment of chemical reaction networks, mostly used for the formation of molecules [Wedemeyer-Böhm et al. (2005)], and hydrogen ionization [Leenaarts & Wedemeyer-Böhm (2005)], too.

CO5BOLD is written in Fortran90. The parallelization is done with OpenMP directives.

[ascl:1011.015]
Geokerr: Computing Photon Orbits in a Kerr Spacetime

Relativistic radiative transfer problems require the calculation of photon trajectories in curved spacetime. Programmed in Fortran, Geokerr uses a novel technique for rapid and accurate calculation of null geodesics in the Kerr metric. The equations of motion from the Hamilton-Jacobi equation are reduced directly to Carlson's elliptic integrals, simplifying algebraic manipulations and allowing all coordinates to be computed semi-analytically for the first time.

[ascl:1011.016]
Non-LTE Models and Theoretical Spectra of Accretion Disks in Active Galactic Nuclei. III. Integrated Spectra for Hydrogen-Helium Disks

We have constructed a grid of non-LTE disk models for a wide range of black hole mass and mass accretion rate, for several values of viscosity parameter alpha, and for two extreme values of the black hole spin: the maximum-rotation Kerr black hole, and the Schwarzschild (non-rotating) black hole. Our procedure calculates self-consistently the vertical structure of all disk annuli together with the radiation field, without any approximations imposed on the optical thickness of the disk, and without any ad hoc approximations to the behavior of the radiation intensity. The total spectrum of a disk is computed by summing the spectra of the individual annuli, taking into account the general relativistic transfer function. The grid covers nine values of the black hole mass between M = 1/8 and 32 billion solar masses with a two-fold increase of mass for each subsequent value; and eleven values of the mass accretion rate, each a power of 2 times 1 solar mass/year. The highest value of the accretion rate corresponds to 0.3 Eddington. We show the vertical structure of individual annuli within the set of accretion disk models, along with their local emergent flux, and discuss the internal physical self-consistency of the models. We then present the full disk-integrated spectra, and discuss a number of observationally interesting properties of the models, such as optical/ultraviolet colors, the behavior of the hydrogen Lyman limit region, polarization, and number of ionizing photons. Our calculations are far from definitive in terms of the input physics, but generally we find that our models exhibit rather red optical/UV colors. Flux discontinuities in the region of the hydrogen Lyman limit are only present in cool, low luminosity models, while hotter models exhibit blueshifted changes in spectral slope.

[ascl:1011.017]
Occultation and Microlensing

Occultation and microlensing are different limits of the same phenomena of one body passing in front of another body. We derive a general exact analytic expression which describes both microlensing and occultation in the case of spherical bodies with a source of uniform brightness and a non-relativistic foreground body. We also compute numerically the case of a source with quadratic limb-darkening. In the limit that the gravitational deflection angle is comparable to the angular size of the foreground body, both microlensing and occultation occur as the objects align. Such events may be used to constrain the size ratio of the lens and source stars, the limb-darkening coefficients of the source star, and the surface gravity of the lens star (if the lens and source distances are known). Application of these results to microlensing during transits in binaries and giant-star microlensing are discussed. These results unify the microlensing and occultation limits and should be useful for rapid model fitting of microlensing, eclipse, and "microccultation" events.

[ascl:1011.018]
Transit of a Spherical Planet of a Stellar Chromosphere which is Geometrically Thin

Transit light curves for stellar continua have only one minimum and a "U" shape. By contrast, transit curves for optically thin chromospheric emission lines can have a "W" shape because of stellar limb-brightening. We calculate light curves for an optically thin shell of emission and fit these models to time-resolved observations of Si IV absorption by the planet HD209458b. We find that the best fit Si IV absorption model has R_p,SIV/R_*= 0.34+0.07-0.12, similar to the Roche lobe of the planet. While the large radius is only at the limit of statistical significance, we develop formulae applicable to transits of all optically thin chromospheric emission lines.

[ascl:1011.019]
FLY: MPI-2 High Resolution code for LSS Cosmological Simulations

Cosmological simulations of structures and galaxies formations have played a fundamental role in the study of the origin, formation and evolution of the Universe. These studies improved enormously with the use of supercomputers and parallel systems and, recently, grid based systems and Linux clusters. Now we present the new version of the tree N-body parallel code FLY that runs on a PC Linux Cluster using the one side communication paradigm MPI-2 and we show the performances obtained. FLY is included in the Computer Physics Communication Program Library. This new version was developed using the Linux Cluster of CINECA, an IBM Cluster with 1024 Intel Xeon Pentium IV 3.0 Ghz. The results show that it is possible to run a 64 Million particle simulation in less than 15 minutes for each timestep, and the code scalability with the number of processors is achieved. This lead us to propose FLY as a code to run very large N-Body simulations with more than $10^{9}$ particles with the higher resolution of a pure tree code.

[ascl:1011.020]
VisIVO: Integrated Tools and Services for Large-Scale Astrophysical Visualization

Becciani, U.; Costa, A.; Antonuccio-Delogu, V.; Caniglia, G.; Comparato, M.; Gheller, C.; Jin, Z.; Krokos, M.; Massimino, P.

VisIVO is an integrated suite of tools and services specifically designed for the Virtual Observatory. This suite constitutes a software framework for effective visual discovery in currently available (and next-generation) very large-scale astrophysical datasets. VisIVO consists of VisiVO Desktop - a stand alone application for interactive visualization on standard PCs, VisIVO Server - a grid-enabled platform for high performance visualization and VisIVO Web - a custom designed web portal supporting services based on the VisIVO Server functionality. The main characteristic of VisIVO is support for high-performance, multidimensional visualization of very large-scale astrophysical datasets. Users can obtain meaningful visualizations rapidly while preserving full and intuitive control of the relevant visualization parameters. This paper focuses on newly developed integrated tools in VisIVO Server allowing intuitive visual discovery with 3D views being created from data tables. VisIVO Server can be installed easily on any web server with a database repository. We discuss briefly aspects of our implementation of VisiVO Server on a computational grid and also outline the functionality of the services offered by VisIVO Web. Finally we conclude with a summary of our work and pointers to future developments.

[ascl:1011.021]
GRALE: A genetic algorithm for the non-parametric inversion of strong lensing systems

We present a non-parametric technique to infer the projected-mass distribution of a gravitational lens system with multiple strong-lensed images. The technique involves a dynamic grid in the lens plane on which the mass distribution of the lens is approximated by a sum of basis functions, one per grid cell. We used the projected mass densities of Plummer spheres as basis functions. A genetic algorithm then determines the mass distribution of the lens by forcing images of a single source, projected back onto the source plane, to coincide as well as possible. Averaging several tens of solutions removes the random fluctuations that are introduced by the reproduction process of genomes in the genetic algorithm and highlights those features common to all solutions. Given the positions of the images and the redshifts of the sources and the lens, we show that the mass of a gravitational lens can be retrieved with an accuracy of a few percent and that, if the sources sufficiently cover the caustics, the mass distribution of the gravitational lens can also be reliably retrieved. A major advantage of the algorithm is that it makes full use of the information contained in the radial images, unlike methods that minimise the residuals of the lens equation, and is thus able to accurately reconstruct also the inner parts of the lens.

[ascl:1011.022]
yt: A Multi-Code Analysis Toolkit for Astrophysical Simulation Data

yt is an open source, community-developed volumetric analysis and visualization toolkit. Originally designed for handling Enzo's (ascl:1010.072) structure adaptive mesh refinement (AMR) data, yt has been extended to work with numerous simulation methods and simulation codes including Orion, RAMSES (ascl:1011.007), and FLASH (ascl:1010.082). Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to data representation on-disk or in-memory. yt can be used for projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation and topologically-connected isocontour identification.

yt benefits from the contributions of a broad range of community members, and a full list of credits for the code can be found on the yt website or in the source repository.

[ascl:1011.023]
HyRec: A Fast and Highly Accurate Primordial Hydrogen and Helium Recombination Code

We present a state-of-the-art primordial recombination code, HyRec, including all the physical effects that have been shown to significantly affect recombination. The computation of helium recombination includes simple analytic treatments of hydrogen continuum opacity in the He I 2 1P - 1 1S line, the He I] 2 3P - 1 1S line, and treats feedback between these lines within the on-the-spot approximation. Hydrogen recombination is computed using the effective multilevel atom method, virtually accounting for an infinite number of excited states. We account for two-photon transitions from 2s and higher levels as well as frequency diffusion in Lyman-alpha with a full radiative transfer calculation. We present a new method to evolve the radiation field simultaneously with the level populations and the free electron fraction. These computations are sped up by taking advantage of the particular sparseness pattern of the equations describing the radiative transfer. The computation time for a full recombination history is ~2 seconds. This makes our code well suited for inclusion in Monte Carlo Markov chains for cosmological parameter estimation from upcoming high-precision cosmic microwave background anisotropy measurements.

[ascl:1010.001]
CFITSIO: A FITS File Subroutine Library

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CFITSIO provides simple high-level routines for reading and writing FITS files that insulate the programmer from the internal complexities of the FITS format. CFITSIO also provides many advanced features for manipulating and filtering the information in FITS files.

[ascl:1010.002]
fpack: FITS Image Compression Program

fpack is a utility program for optimally compressing images in the FITS data format. The associated funpack program will restore the compressed file back to its original state. These programs may be run from the host operating system command line and are analogous to the gzip and gunzip utility programs, except that they are specifically optimized for FITS format images and offer a wider choice of compression options.

fpack uses the tiled image compression convention for storing the compressed images. This convention can in principle support any number of of different compression algorithms; currently GZIP, Rice, Hcompress, and the IRAF pixel list compression algorithms have been implemented.

The main advantages of fpack compared to the commonly used technique of externally compressing the whole FITS file with gzip are:

- It is generally faster and offers better compression than gzip.
- The FITS header keywords remain uncompressed for fast access.
- Each HDU of a multi-extension FITS file is compressed separately, so it is not necessary to uncompress the entire file to read a single image in a multi-extension file.
- Dividing the image into tiles before compression enables faster access to small subsections of the image.
- The compressed image is itself a valid FITS file and can be manipulated by other general FITS utility software.
- Lossy compression can be used for much higher compression in cases where it is not necessary to exactly preserve the original image.
- The CHECKSUM keywords are automatically updated to help verify the integrity of the files.
- Software that supports the tiled image compression technique can directly read and write the FITS images in their compressed form.

[ascl:1010.003]
AMBER: Data Reduction Software

Malbet, Fabien; Duvert, Gilles; Millour, Florentin; Le Bouquin, Jean-Baptiste; Mella, Guillaume; Halipré, Luc; Chelli, Alain; Lafrasse, Sylvain; Altariba, Evelyne; Zins, Gérard

AMBER data reduction software has an optional graphic interface in a high level language, allowing the user to control the data reduction step by step or in a completely automatic manner. The software has a robust calibration scheme that make use of the full calibration sets available during the night. The output products are standard OI-FITS files, which can be used directly in high level software like model fitting or image reconstruction tools.

[ascl:1010.004]
Needatool: A Needlet Analysis Tool for Cosmological Data Processing

NeedATool (Needlet Analysis Tool) performs data analysis based on needlets, a wavelet rendition powerful for the analysis of fields defined on a sphere. Needlets have been applied successfully to the treatment of astrophysical and cosmological observations, particularly to the analysis of cosmic microwave background (CMB) data. Wavelets have emerged as a useful tool for CMB data analysis, as they combine most of the advantages of both pixel space, where it is easier to deal with partial sky coverage and experimental noise, and the harmonic domain, in which beam treatment and comparison with theoretical predictions are more effective due in large part to their sharp localization.

[ascl:1010.005]
Particle module of Piernik MHD code

Piernik is a multi-fluid grid magnetohydrodynamic (MHD) code based on the Relaxing Total Variation Diminishing (RTVD) conservative scheme. The original code has been extended by addition of dust described within the particle approximation. The dust is now described as a system of interacting particles. The particles can interact with gas, which is described as a fluid. The comparison between the test problem results and the results coming from fluid simulations made with Piernik code shows the most important differences between fluid and particle approximations used to describe dynamical evolution of dust under astrophysical conditions.

[ascl:1010.006]
DSPSR: Digital Signal Processing Software for Pulsar Astronomy

DSPSR, written primarily in C++, is an open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. The library implements an extensive range of modular algorithms for use in coherent dedispersion, filterbank formation, pulse folding, and other tasks. The software is installed and compiled using the standard GNU configure and make system, and is able to read astronomical data in 18 different file formats, including FITS, S2, CPSR, CPSR2, PuMa, PuMa2, WAPP, ASP, and Mark5.

[ascl:1010.007]
JAVELIN: Just Another Vehicle for Estimating Lags In Nuclei (formerly known as SPEAR)

JAVELIN (SPEAR) is a new approach to reverberation mapping that computes the lags between the AGN continuum and emission line light curves and their statistical confidence limits. It uses a damped random walk model to describe the quasar continuum variability and the ansatz that emission line variability is a scaled, smoothed and displaced version of the continuum. While currently configured only to simultaneously fit light curve means, it includes a general linear parameters formalism to fit more complex trends or calibration offsets. The noise matrix can be modified to allow for correlated errors, and the correlation matrix can be modified to use a different stochastic process. The transfer function model is presently a tophat, but this can be altered by changing the line-continuum covariance matrices. It is also able to cope with some problems in traditional reverberation mapping, such as irregular sampling, correlated errors and seasonal gaps.

[ascl:1010.008]
midIR_sensitivity: Mid-infrared astronomy with METIS

Kendrew, Sarah; Jolissaint, Laurent; Brandl, Bernhard; Lenzen, Rainer; Pantin, Eric; Glasse, Alistair; Blommaert, Joris; Venema, Lars; Siebenmorgen, Ralf; Molster, Frank

midIR_sensitivity is IDL code that calculates the sensitivity of a ground-based mid-infrared instrument for astronomy. The code was written for the Phase A study of the instrument METIS (http://www.strw.leidenuniv.nl/metis), the Mid-Infrared E-ELT Imager and Spectrograph, for the 42-m European Extremely Large Telescope. The model uses a detailed set of input parameters for site characteristics and atmospheric profiles, optical design, and thermal background. The code and all input parameters are highly tailored for the particular design parameters of the E-ELT and METIS, however, the program is structured in such a way that the parameters can easily be adjusted for a different system, or alternative input files used.

[ascl:1010.009]
ModeCode: Bayesian Parameter Estimation for Inflation

ModeCode is a publicly available code that computes the primordial scalar and tensor power spectra for single field inflationary models. ModeCode solves the inflationary mode equations numerically, avoiding the slow roll approximation. It provides an efficient and robust numerical evaluation of the inflationary perturbation spectrum, and allows the free parameters in the inflationary potential to be estimated within an MCMC computation. ModeCode also allows the estimation of reheating uncertainties once a potential has been specified. It is interfaced with CAMB and CosmoMC to compute cosmic microwave background angular power spectra and perform likelihood analysis and parameter estimation. It can be run as a standalone code as well. Errors in the results from ModeCode contribute negligibly to the error budget for analyses of data from Planck or other next generation experiments.

[ascl:1010.010]
Fast WMAP Likelihood Code and GSR PC Functions

We place functional constraints on the shape of the inflaton potential from the cosmic microwave background through a variant of the generalized slow roll approximation that allows large amplitude, rapidly changing deviations from scale-free conditions. Employing a principal component decomposition of the source function G'~3(V'/V)^2 - 2V''/V and keeping only those measured to better than 10% results in 5 nearly independent Gaussian constraints that maybe used to test any single-field inflationary model where such deviations are expected. The first component implies < 3% variations at the 100 Mpc scale. One component shows a 95% CL preference for deviations around the 300 Mpc scale at the ~10% level but the global significance is reduced considering the 5 components examined. This deviation also requires a change in the cold dark matter density which in a flat LCDM model is disfavored by current supernova and Hubble constant data and can be tested with future polarization or high multipole temperature data. Its impact resembles a local running of the tilt from multipoles 30-800 but is only marginally consistent with a constant running beyond this range. For this analysis, we have implemented a ~40x faster WMAP7 likelihood method which we have made publicly available.

[ascl:1010.011]
PSpectRe: A Pseudo-Spectral Code for (P)reheating

PSpectRe, written in C++, uses Fourier-space pseudo-spectral methods to evolve interacting scalar fields in an expanding universe. The code is optimized for the analysis of parametric resonance in the post-inflationary universe and provides an alternative to finite differencing codes. PSpectRe has both second- (Velocity-Verlet) and fourth-order (Runge-Kutta) time integrators. In some circumstances PSpectRe obtains reliable results while using substantially fewer points than a finite differencing code by computing the post-resonance equation of state. PSpectRe is designed to be easily extended to other problems in early-universe cosmology, including the generation of gravitational waves during phase transitions and pre-inflationary bubble collisions.

[ascl:1010.012]
glafic: Software Package for Analyzing Gravitational Lensing

glafic is a public software package for analyzing gravitational lensing. It offers many features including computations of various lens properties for many mass models, solving the lens equation using an adaptive grid algorithm, simulations of lensed extended images with PSF convolved, and efficient modeling of observed strong lens systems.

[ascl:1010.013]
AstroGK: Astrophysical Gyrokinetics Code

The gyrokinetic simulation code AstroGK is developed to study fundamental aspects of kinetic plasmas and for applications mainly to astrophysical problems. AstroGK is an Eulerian slab code that solves the electromagnetic Gyrokinetic-Maxwell equations in five-dimensional phase space, and is derived from the existing gyrokinetics code GS2 by removing magnetic geometry effects. Algorithms used in the code are described. The code is benchmarked using linear and nonlinear problems. Serial and parallel performance scalings are also presented.

[ascl:1010.014]
Athena: Grid-based code for astrophysical magnetohydrodynamics (MHD)

Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD). It was developed primarily for studies of the interstellar medium, star formation, and accretion flows. The code has been designed to be easily extensible for use with static and adaptive mesh refinement. It combines higher-order Godunov methods with the constrained transport (CT) technique to enforce the divergence-free constraint on the magnetic field. Discretization is based on cell-centered volume-averages for mass, momentum, and energy, and face-centered area-averages for the magnetic field. Novel features of the algorithm include (1) a consistent framework for computing the time- and edge-averaged electric fields used by CT to evolve the magnetic field from the time- and area-averaged Godunov fluxes, (2) the extension to MHD of spatial reconstruction schemes that involve a dimensionally-split time advance, and (3) the extension to MHD of two different dimensionally-unsplit integration methods. Implementation of the algorithm in both C and Fortran95 is detailed, including strategies for parallelization using domain decomposition. Results from a test suite which includes problems in one-, two-, and three-dimensions for both hydrodynamics and MHD are given, not only to demonstrate the fidelity of the algorithms, but also to enable comparisons to other methods. The source code is freely available for download on the web.

[ascl:1010.015]
Fyris Alpha: Computational Fluid Dynamics Code

Fyris Alpha is a high resolution, shock capturing, multi-phase, up-wind Godunov method hydrodynamics code that includes a variable equation of state and optional microphysics such as cooling, gravity and multiple tracer variables. The code has been designed and developed for use primarily in astrophysical applications, such as galactic and interstellar bubbles, hypersonic shocks, and a range of jet phenomena. Fyris Alpha boasts both higher performance and more detailed microphysics than its predecessors, with the aim of producing output that is closer to the observational domain, such as emission line fluxes, and eventually, detailed spectral synthesis. Fyris Alpha is approximately 75,000 lines of C code; it encapsulates the split sweep semi-lagrangian remap PPM method used by ppmlr (in turn developed from VH1, Blondin et al. 1998) but with an improved Riemann solver, which is derived from the exact solver of Gottlieb and Groth (1988), a significantly faster solution than previous solvers. It has a number of optimisations that have improved the speed so that additional calculations neeed for multi-phase simulations become practical.

[ascl:1010.016]
SpDust/SpDust.2: Code to Calculate Spinning Dust Spectra

SpDust is an IDL program that evaluates the spinning dust emissivity for user-provided environmental conditions. A new version of the code became available in March, 2010.

[ascl:1010.017]
AOFlagger: RFI Software

The RFI software presented here can automatically flag data and can be used to analyze the data in a measurement. The purpose of flagging is to mark samples that are affected by interfering sources such as radio stations, airplanes, electrical fences or other transmitting interferers.

The tools in the package are meant for offline use. The software package contains a graphical interface ("rfigui") that can be used to visualize a measurement set and analyze mitigation techniques. It also contains a console flagger ("rficonsole") that can execute a script of mitigation functions without the overhead of a graphical environment. All tools were written in C++.

The software has been tested extensively on low radio frequencies (150 MHz or lower) produced by the WSRT and LOFAR telescopes. LOFAR is the Low Frequency Array that is built in and around the Netherlands. Higher frequencies should work as well. Some of the methods implemented are the SumThreshold, the VarThreshold and the singular value decomposition (SVD) method. Included also are several surface fitting algorithms.

The software is published under the GNU General Public License version 3.

[ascl:1010.018]
Emu CMB: Power spectrum emulator

Emu CMB is a fast emulator the CMB temperature power spectrum based on CAMB (Jan 2010 version). Emu CMB is based on a "space-filling" Orthogonal Array Latin Hypercube design in a de-correlated parameter space obtained by using a fiducial WMAP5 CMB Fisher matrix as a rotation matrix. This design strategy allows for accurate interpolation with small numbers of simulation design points. The emulator presented here is calibrated with 100 CAMB runs that are interpolated over the design space using a global quadratic polynomial fit.

[ascl:1010.019]
NBSymple: A Double Parallel, Symplectic N-body Code Running on Graphic Processing Units

NBSymple is a numerical code which numerically integrates the equation of motions of N 'particles' interacting via Newtonian gravitation and move in an external galactic smooth field. The force evaluation on every particle is done by mean of direct summation of the contribution of all the other system's particle, avoiding truncation error. The time integration is done with second-order and sixth-order symplectic schemes. NBSymple has been parallelized twice, by mean of the Computer Unified Device Architecture to make the all-pair force evaluation as fast as possible on high-performance Graphic Processing Units NVIDIA TESLA C 1060, while the O(N) computations are distributed on various CPUs by mean of OpenMP Application Program. The code works both in single precision floating point arithmetics or in double precision. The use of single precision allows the use at best of the GPU performances but, of course, limits the precision of simulation in some critical situations. We find a good compromise in using a software reconstruction of double precision for those variables that are most critical for the overall precision of the code.

[ascl:1010.020]
Libpsht: Algorithms for Efficient Spherical Harmonic Transforms

Libpsht (or "library for Performing Spherical Harmonic Transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports transforms of scalars as well as spin-1 and spin-2 quantities, and can be used for a wide range of pixelisations (including HEALPix, GLESP and ECP). It will take advantage of hardware features like multiple processor cores and floating-point vector operations, if available. Even without this additional acceleration, the employed algorithms are among the most efficient (in terms of CPU time as well as memory consumption) currently being used in the astronomical community.

The library is written in strictly standard-conforming C90, ensuring portability to many different hard- and software platforms, and allowing straightforward integration with codes written in various programming languages like C, C++, Fortran, Python etc.

Libpsht is distributed under the terms of the GNU General Public License (GPL) version 2.

Development on this project has ended; its successor is libsharp (ascl:1402.033).

[ascl:1010.021]
velfit: A Code for Modeling Non-Circular Flows in Disk Galaxies

High-quality velocity maps of galaxies frequently exhibit signatures of non-circular streaming motions. velfit yields results that are more easily interpreted than the commonly used procedure. It can estimate the magnitudes of forced non-circular motions over a broad range of bar strengths from a strongly barred galaxy, through cases of mild bar-like distortions to placing bounds on the shapes of halos in galaxies having extended rotation curves.

[ascl:1010.022]
GR1D: Open-Source Code for Spherically-Symmetric Stellar Collapse to Neutron Stars and Black Holes

GR1D is based on the Eulerian formulation of GR hydrodynamics (GRHD) put forth by Romero-Ibanez-Gourgoulhon and employs radial-gauge, polar-slicing coordinates in which the 3+1 equations simplify substantially. GR1D is intended for the simulation of stellar collapse to neutron stars and black holes and will also serve as a testbed for modeling technology to be incorporated in multi-D GR codes. Its GRHD part is coupled to various finite-temperature microphysical equations of state in tabulated form that we make available with GR1D.

[ascl:1010.023]
AstroSim: Collaborative Visualization of an Astrophysics Simulation in Second Life

AstroSim is a Second Life based prototype application for synchronous collaborative visualization targeted at astronomers.

[ascl:1010.024]
ADAPTSMOOTH: A Code for the Adaptive Smoothing of Astronomical Images

ADAPTSMOOTH serves to smooth astronomical images in an adaptive fashion in order to enhance the signal-to-noise ratio (S/N). The adaptive smoothing scheme allows taking full advantage of the spatially resolved photometric information contained in an image in that at any location the minimal smoothing is applied to reach the requested S/N. Support is given to match more images on the same smoothing length, such that proper estimates of local colors can be done, with a big potential impact on multi-wavelength studies of extended sources (galaxies, nebulae). Different modes to estimate local S/N are provided. In addition to classical arithmetic-mean averaging mode, the code can operate in median averaging mode, resulting in a significant enhancement of the final image quality and very accurate flux conservation.

[ascl:1010.025]
SimFast21: Simulation of the Cosmological 21cm Signal

SimFast 21 generates a simulation of the cosmological 21cm signal. While limited to low spatial resolution, the next generation low-frequency radio interferometers that target 21 cm observations during the era of reionization and prior will have instantaneous fields-of-view that are many tens of square degrees on the sky. Predictions related to various statistical measurements of the 21 cm brightness temperature must then be pursued with numerical simulations of reionization with correspondingly large volume box sizes, of order 1000 Mpc on one side. The authors pursued a semi-numerical scheme to simulate the 21 cm signal during and prior to Reionization by extending a hybrid approach where simulations are performed by first laying down the linear dark matter density field, accounting for the non-linear evolution of the density field based on second-order linear perturbation theory as specified by the Zel'dovich approximation, and then specifying the location and mass of collapsed dark matter halos using the excursion-set formalism. The location of ionizing sources and the time evolving distribution of ionization field is also specified using an excursion-set algorithm. They account for the brightness temperature evolution through the coupling between spin and gas temperature due to collisions, radiative coupling in the presence of Lyman-alpha photons and heating of the intergalactic medium, such as due to a background of X-ray photons. The method is capable of producing the required large volume simulations with adequate resolution in a reasonable time so a large number of realizations can be obtained with variations in assumptions related to astrophysics and background cosmology that govern the 21 cm signal.

[ascl:1010.026]
SingLe: A F90-package devoted to Softened Gravity in gaseous discs

**S**often**ingLe**ngth: Because Newton's law of Gravitation diverges as the relative separations |r'-r| tends to zero, it is common to add a positive constant λ also known as the "softening length", i.e. :

|r'-r|² ← |r'-r|² + λ².

SingLe determines the appropriate value of this Softening Length λ for a given disc local structure (thickness 2h and vertical stratification ρ), in the axially symmetric, flat disc limit, preserving at best the Newtonian character of the gravitational potential and associated forces. Mass density ρ(z) is assumed to be locally expandable in the z-direction according to:

ρ(z)= ρ_{0}[1 + a_{1}(z/h)^{2}+...+a_{q} (z/h)^{2q}+...+a_{N} (z/h)^{2 N}].

[ascl:1010.027]
SNANA: A Public Software Package for Supernova Analysis

Kessler, Richard; Bernstein, Joseph P.; Cinabro, David; Dilday, Benjamin; Frieman, Joshua A.; Jha, Saurabh; Kuhlmann, Stephen; Miknaitis, Gajus; Sako, Masao; Taylor, Matt; VanderPlas, Jake

SNANA is a general analysis package for supernova (SN) light curves that contains a simulation, light curve fitter, and cosmology fitter. The software is designed with the primary goal of using SNe Ia as distance indicators for the determination of cosmological parameters, but it can also be used to study efficiencies for analyses of SN rates, estimate contamination from non-Ia SNe, and optimize future surveys. Several SN models are available within the same software architecture, allowing technical features such as K-corrections to be consistently used among multiple models, and thus making it easier to make detailed comparisons between models. New and improved light-curve models can be easily added. The software works with arbitrary surveys and telescopes and has already been used by several collaborations, leading to more robust and easy-to-use code. This software is not intended as a final product release, but rather it is designed to undergo continual improvements from the community as more is learned about SNe.

[ascl:1010.028]
GALPROP: Code for Cosmic-ray Transport and Diffuse Emission Production

GALPROP is a numerical code for calculating the propagation of relativistic charged particles and the diffuse emissions produced during their propagation. The GALPROP code incorporates as much realistic astrophysical input as possible together with latest theoretical developments. The code calculates the propagation of cosmic-ray nuclei, antiprotons, electrons and positrons, and computes diffuse γ-rays and synchrotron emission in the same framework. Each run of the code is governed by a configuration file allowing the user to specify and control many details of the calculation. Thus, each run of the code corresponds to a potentially different "model." The code continues to be developed and is available to the scientific community.

[ascl:1010.029]
DNEST: Diffusive Nested Sampling

This code is a general Monte Carlo method based on Nested Sampling (NS) for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ~e^-1 times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. This method can achieve four times the accuracy of classic MCMC-based Nested Sampling, for the same computational effort; equivalent to a factor of 16 speedup. An additional benefit is that more samples and a more accurate evidence value can be obtained simply by continuing the run for longer, as in standard MCMC.

[ascl:1010.030]
CosmicEmu: Cosmic Emulator for the Dark Matter Power Spectrum

Lawrence, Earl; Heitmann, Katrin; White, Martin; Higdon, David; Wagner, Christian; Habib, Salman; Williams, Brian

Many of the most exciting questions in astrophysics and cosmology, including the majority of observational probes of dark energy, rely on an understanding of the nonlinear regime of structure formation. In order to fully exploit the information available from this regime and to extract cosmological constraints, accurate theoretical predictions are needed. Currently such predictions can only be obtained from costly, precision numerical simulations. The "Coyote Universe'' simulation suite comprises nearly 1,000 N-body simulations at different force and mass resolutions, spanning 38 wCDM cosmologies. This large simulation suite enabled construct of a prediction scheme, or emulator, for the nonlinear matter power spectrum accurate at the percent level out to k~1 h/Mpc. This is the first cosmic emulator for the dark matter power spectrum.

[ascl:1010.031]
DimReduce: Nonlinear Dimensionality Reduction of Very Large Datasets with Locally Linear Embedding (LLE) and its Variants

DimReduce is a C++ package for performing nonlinear dimensionality reduction of very large datasets with Locally Linear Embedding (LLE) and its variants. DimReduce is built for speed, using the optimized linear algebra packages BLAS, LAPACK, and ARPACK. Because of the need for storing very large matrices (1000 by 10000, for our SDSS LLE work), DimReduce is designed to use binary FITS files as inputs and outputs. This means that using the code is a bit more cumbersome. For smaller-scale LLE, where speed of computation is not as much of an issue, the Modular Data Processing toolkit may be a better choice. It is a python toolkit with some LLE functionality, which VanderPlas contributed.

This code has been rewritten and included in scikit-learn and an improved version is included in http://mmp2.github.io/megaman/

[ascl:1010.032]
Extreme Deconvolution: Density Estimation using Gaussian Mixtures in the Presence of Noisy, Heterogeneous and Incomplete Data

Extreme-deconvolution is a general algorithm to infer a d-dimensional distribution function from a set of heterogeneous, noisy observations or samples. It is fast, flexible, and treats the data's individual uncertainties properly, to get the best description possible for the underlying distribution. It performs well over the full range of density estimation, from small data sets with only tens of samples per dimension, to large data sets with hundreds of thousands of data points.

[ascl:1010.033]
GALEV Evolutionary Synthesis Models

GALEV evolutionary synthesis models describe the evolution of stellar populations in general, of star clusters as well as of galaxies, both in terms of resolved stellar populations and of integrated light properties over cosmological timescales of > 13 Gyr from the onset of star formation shortly after the Big Bang until today.

For galaxies, GALEV includes a simultaneous treatment of the chemical evolution of the gas and the spectral evolution of the stellar content, allowing for a chemically consistent treatment using input physics (stellar evolutionary tracks, stellar yields and model atmospheres) for a large range of metallicities and consistently account for the increasing initial abundances of successive stellar generations.

[ascl:1010.034]
iCosmo: An Interactive Cosmology Package

iCosmo is a software package to perform interactive cosmological calculations for the low redshift universe. The computation of distance measures, the matter power spectrum, and the growth factor is supported for any values of the cosmological parameters. It also performs the computation of observables for several cosmological probes such as weak gravitational lensing, baryon acoustic oscillations and supernovae. The associated errors for these observables can be derived for customised surveys, or for pre-set values corresponding to current or planned instruments. The code also allows for the calculation of cosmological forecasts with Fisher matrices which can be manipulated to combine different surveys and cosmological probes. The code is written in the IDL language and thus benefits from the convenient interactive features and scientific library available in this language. iCosmo can also be used as an engine to perform cosmological calculations in batch mode, and forms a convenient evolutive platform for the development of further cosmological modules. With its extensive documentation, it may also serve as a useful resource for teaching and for newcomers in the field of cosmology.

[ascl:1010.035]
SLR: Stellar Locus Regression

Stellar Locus Regression (SLR) is a simple way to calibrate colors at the 1-2% level, and magnitudes at the sub-5% level as limited by 2MASS, without the traditional use of standard stars. With SLR, stars in any field are "standards." This is an entirely new way to calibrate photometry. SLR exploits the simple fact that most stars lie along a well defined line in color-color space called the stellar locus. Cross-match point-sources in flattened images taken through different passbands and plot up all color vs color combinations, and you will see the stellar locus with little effort. SLR calibrates colors by fitting these colors to a standard line. Cross-match with 2MASS on top of that, and SLR will deliver calibrated magnitudes as well.

[ascl:1010.036]
Montage: An Astronomical Image Mosaicking Toolkit

Jacob, Joseph C.; Katz, Daniel S.; Berriman, G. Bruce; Good, John; Laity, Anastasia C.; Deelman, Ewa; Kesselman, Carl; Singh, Gurmeet; Su, Mei-Hui; Prince, Thomas A.; Williams, Roy

Montage is an open source code toolkit for assembling Flexible Image Transport System (FITS) images into custom mosaics. It runs on all common Linux/Unix platforms, on desktops, clusters and computational grids, and supports all World Coordinate System (WCS) projections and common coordinate systems. Montage preserves spatial and calibration fidelity of input images, processes 40 million pixels in up to 32 minutes on 128 nodes on a Linux cluster, and provides independent engines for analyzing the geometry of images on the sky, re-projecting images, rectifying background emission to a common level, and co-adding images. It offers convenient tools for managing and manipulating large image files.

[ascl:1010.037]
FastChi: A Fast Chi-squared Technique For Period Search of Irregularly Sampled Data

The Fast Chi-Squared Algorithm is a fast, powerful technique for detecting periodicity. It was developed for analyzing variable stars, but is applicable to many of the other applications where the Fast Fourier Transforms (FFTs) or other periodograms (such as Lomb-Scargle) are currently used. The Fast Chi-squared technique takes a data set (e.g. the brightness of a star measured at many different times during a series of observations) and finds the periodic function that has the best frequency and shape (to an arbitrary number of harmonics) to fit the data. Among its advantages are:

- Statistical efficiency: all of the data are used, weighted by their individual error bars, giving a result with a significance calibrated in well-understood Chi-squared statistics.
- Sensitivity to harmonic content: many conventional techniques look only at the significance (or the amplitude) of the fundamental sinusoid and discard the power of the higher harmonics.
- Insensitivity to the sample timing: you won't find a period of 24 hours just because you take your observations at night. You do not need to window your data.
- The frequency search is gridded more tightly than the traditional "integer number of cycles over the span of observations", eliminating power loss from peaks that fall between the grid points.
- Computational speed: The complexity of the algorithm is O(NlogN), where N is the number of frequencies searched, due to its use of the FFT.

[ascl:1010.038]
Low Resolution Spectral Templates For AGNs and Galaxies From 0.03 -- 30 microns

Assef, R. J.; Kochanek, C. S.; Brodwin, M.; Cool, R.; Forman, W.; Gonzalez, A. H.; Hickox, R. C.; Jones, C.; Le Floc'h, E.; Moustakas, J.; Murray, S. S.; Stern, D.

We present a set of low resolution empirical SED templates for AGNs and galaxies in the wavelength range from 0.03 to 30 microns based on the multi-wavelength photometric observations of the NOAO Deep-Wide Field Survey Bootes field and the spectroscopic observations of the AGN and Galaxy Evolution Survey. Our training sample is comprised of 14448 galaxies in the redshift range 0<~z<~1 and 5347 likely AGNs in the range 0<~z<~5.58. We use our templates to determine photometric redshifts for galaxies and AGNs. While they are relatively accurate for galaxies, their accuracies for AGNs are a strong function of the luminosity ratio between the AGN and galaxy components. Somewhat surprisingly, the relative luminosities of the AGN and its host are well determined even when the photometric redshift is significantly in error. We also use our templates to study the mid-IR AGN selection criteria developed by Stern et al.(2005) and Lacy et al.(2004). We find that the Stern et al.(2005) criteria suffers from significant incompleteness when there is a strong host galaxy component and at z =~ 4.5, when the broad Halpha emission line is redshifted into the [3.6] band, but that it is little contaminated by low and intermediate redshift galaxies. The Lacy et al.(2004) criterion is not affected by incompleteness at z =~ 4.5 and is somewhat less affected by strong galaxy host components, but is heavily contaminated by low redshift star forming galaxies. Finally, we use our templates to predict the color-color distribution of sources in the upcoming WISE mission and define a color criterion to select AGNs analogous to those developed for IRAC photometry. We estimate that in between 640,000 and 1,700,000 AGNs will be identified by these criteria, but will have serious completeness problems for z >~ 3.4.

[ascl:1010.039]
Parameter Estimation from Time-Series Data with Correlated Errors: A Wavelet-Based Method and its Application to Transit Light Curves

We consider the problem of fitting a parametric model to time-series data that are afflicted by correlated noise. The noise is represented by a sum of two stationary Gaussian processes: one that is uncorrelated in time, and another that has a power spectral density varying as $1/f^gamma$. We present an accurate and fast [O(N)] algorithm for parameter estimation based on computing the likelihood in a wavelet basis. The method is illustrated and tested using simulated time-series photometry of exoplanetary transits, with particular attention to estimating the midtransit time. We compare our method to two other methods that have been used in the literature, the time-averaging method and the residual-permutation method. For noise processes that obey our assumptions, the algorithm presented here gives more accurate results for midtransit times and truer estimates of their uncertainties.

[ascl:1010.040]
Cosmic String Simulations

Complicated cosmic string loops will fragment until they reach simple, non-intersecting ("stable") configurations. Through extensive numerical study, these attractor loop shapes are characterized including their length, velocity, kink, and cusp distributions. An initial loop containing $M$ harmonic modes will, on average, split into 3M stable loops. These stable loops are approximately described by the degenerate kinky loop, which is planar and rectangular, independently of the number of modes on the initial loop. This is confirmed by an analytic construction of a stable family of perturbed degenerate kinky loops. The average stable loop is also found to have a 40% chance of containing a cusp. This new analytic scheme explicitly solves the string constraint equations.

[ascl:1010.041]
FASTLens (FAst STatistics for weak Lensing): Fast Method for Weak Lensing Statistics and Map Making

The analysis of weak lensing data requires to account for missing data such as masking out of bright stars. To date, the majority of lensing analyses uses the two point-statistics of the cosmic shear field. These can either be studied directly using the two-point correlation function, or in Fourier space, using the power spectrum. The two-point correlation function is unbiased by missing data but its direct calculation will soon become a burden with the exponential growth of astronomical data sets. The power spectrum is fast to estimate but a mask correction should be estimated. Other statistics can be used but these are strongly sensitive to missing data. The solution that is proposed by FASTLens is to properly fill-in the gaps with only NlogN operations, leading to a complete weak lensing mass map from which one can compute straight forwardly and with a very good accuracy any kind of statistics like power spectrum or bispectrum.

[ascl:1010.042]
WeightMixer: Hybrid Cross-power Spectrum Estimation

This code, which requires HEALPix 2.x, allows you to generate power spectrum estimators from WMAP 5-year maps and generate hybrid cross- and auto- power spectrum and covariance from general foreground-cleaned maps. In addition, it allows you to simulate combined maps or combinations of maps for individual detectors and do MPI spherical transforms of arrays of maps, calculate coupling matrices etc. The code includes all of LensPix - the MPI framework used for doing spherical transforms (based on HealPix).

[ascl:1010.043]
FSPS: Flexible Stellar Population Synthesis

FSPS is a flexible SPS package that allows the user to compute simple stellar populations (SSPs) for a range of IMFs and metallicities, and for a variety of assumptions regarding the morphology of the horizontal branch, the blue straggler population, the post--AGB phase, and the location in the HR diagram of the TP-AGB phase. From these SSPs the user may then generate composite stellar populations (CSPs) for a variety of star formation histories (SFHs) and dust attenuation prescriptions. Outputs include the "observed" spectra and magnitudes of the SSPs and CSPs at arbitrary redshift. In addition to these fortran routines, several IDL routines are provided that allow easy manipulation of the output. FSPS was designed with the intention that the user would make full use of the provided fortran routines. However, the full FSPS package is quite large, and requires some time for the user to become familiar with all of the options and syntax. Some users may only need SSPs for a range of metallicities and IMFs. For such users, standard SSP sets for several IMFs, evolutionary tracks, and spectral libraries are available here.

[ascl:1010.044]
MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows

Many astrophysical phenomena are highly subsonic, requiring specialized numerical methods suitable for long-time integration. In a series of earlier papers we described the development of MAESTRO, a low Mach number stellar hydrodynamics code that can be used to simulate long-time, low-speed flows that would be prohibitively expensive to model using traditional compressible codes. MAESTRO is based on an equation set derived using low Mach number asymptotics; this equation set does not explicitly track acoustic waves and thus allows a significant increase in the time step. MAESTRO is suitable for two- and three-dimensional local atmospheric flows as well as three-dimensional full-star flows. Here, we continue the development of MAESTRO by incorporating adaptive mesh refinement (AMR). The primary difference between MAESTRO and other structured grid AMR approaches for incompressible and low Mach number flows is the presence of the time-dependent base state, whose evolution is coupled to the evolution of the full solution. We also describe how to incorporate the expansion of the base state for full-star flows, which involves a novel mapping technique between the one-dimensional base state and the Cartesian grid, as well as a number of overall improvements to the algorithm. We examine the efficiency and accuracy of our adaptive code, and demonstrate that it is suitable for further study of our initial scientific application, the convective phase of Type Ia supernovae.

[ascl:1010.045]
PLUTO: A Code for Flows in Multiple Spatial Dimensions

PLUTO is a modular Godunov-type code intended mainly for astrophysical applications and high Mach number flows in multiple spatial dimensions. The code embeds different hydrodynamic modules and multiple algorithms to solve the equations describing Newtonian, relativistic, MHD, or relativistic MHD fluids in Cartesian or curvilinear coordinates. PLUTO is entirely written in the C programming language and can run on either single processor machines or large parallel clusters through the MPI library. A simple user-interface based on the Python scripting language is available to setup a physical problem in a quick and self-explanatory way. Computations may be carried on either static or adaptive (structured) grids, the latter functionality being provided through the Chombo adaptive mesh refinement library.

[ascl:1010.046]
indexf: Line-strength Indices in Fully Calibrated FITS Spectra

This program measures line-strength indices in fully calibrated FITS spectra. By "fully calibrated" one should understand wavelength and relative flux-calibrated data. Note that the different types of line-strength indices that can be measured with indexf (see below) do not require absolute flux calibration. If even a relative flux-calibration is absent (or deficient), the derived indices should be transformed to an appropriate spectrophotometric system. The program can also compute index errors resulting from the propagation of random errors (e.g. photon statistics, read-out noise). This option is only available if the user provides the error spectrum as an additional input FITS file to indexf. The error spectrum must contain the unbiased standard deviation (and not the variance!) for each pixel of the data spectrum. In addition, indexf also estimates the effect of errors on radial velocity. For this purpose, the program performs Monte Carlo simulations by measuring each index using randomly drawn radial velocities (following a Gaussian distribution of a given standard deviation). If no error file is employed, the program can perform numerical simulations with synthetic error spectra, the latter generated from the original data spectra and assuming randomly generated S/N ratios.

[ascl:1010.047]
ISW and Weak Lensing Likelihood Code

ISW and Weak Lensing Likelihood code is the likelihood code that calculates the likelihood of Integrated Sachs Wolfe and Weak Lensing of Cosmic Microwave Background using the WMAP 3year CMB maps with mass tracers such as 2MASS (2-Micron All Sky Survey), SDSS LRG (Sloan Digital Sky Survey Luminous Red Galaxies), SDSS QSOs (Sloan Digital Sky Survey Quasars) and NVSS (NRAO VLA All Sky Survey) radio sources. The details of the analysis (*thus the likelihood code) can be understood by reading the papers ISW paper and Weak lensing paper. The code does brute force theoretical matter power spectrum and calculations with CAMB. See the paper for an introduction, descriptions, and typical results from some pre-WMAP data. The code is designed to be integrated into CosmoMC. For further information concerning the integration, see Code Modification for integration into COSMOMC.

[ascl:1010.048]
OCTGRAV: Sparse Octree Gravitational N-body Code on Graphics Processing Units

Octgrav is a very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The algorithms are based on parallel-scan and sort methods. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way, a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s is achieved. It takes about a second to compute forces on a million particles with an opening angle of $ heta approx 0.5$.

To test the performance and feasibility, we implemented the algorithms in CUDA in the form of a gravitational tree-code which completely runs on the GPU. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second.

The code has a convenient user interface and is freely available for use.

[ascl:1010.049]
Gas-momentum-kinetic SZ cross-correlations

We present a new method for detecting the missing baryons by generating a template for the kinematic Sunyaev-Zel'dovich effect. The template is computed from the product of a reconstructed velocity field with a galaxy field. We provide maps of such templates constructed from SDSS Data Release 7 spectroscopic data (SDSS VAGC sample) along side with their expected two point correlation functions with CMB temperature anisotropies. Codes of generating such coefficients of the two point correlation function are also released to provide users of the gas-momentum map a way to change the parameters such as cosmological parameters, reionization history, ionization parameters, etc.

[ascl:1010.050]
LensPerfect: Gravitational Lens Massmap Reconstructions Yielding Exact Reproduction of All Multiple Images

LensPerfect is a new approach to the massmap reconstruction of strong gravitational lenses. Conventional methods iterate over possible lens models which reproduce the observed multiple image positions well but not exactly. LensPerfect only produces solutions which fit all of the data exactly. Magnifications and shears of the multiple images can also be perfectly constrained to match observations.

[ascl:1010.051]
NEMO: A Stellar Dynamics Toolbox

NEMO is an extendible Stellar Dynamics Toolbox, following an Open-Source Software model. It has various programs to create, integrate, analyze and visualize N-body and SPH like systems, following the pipe and filter architecture. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages. A large growing fraction of NEMO has been contributed by a growing list of authors. The source code consist of a little over 4000 files and a little under 1,000,000 lines of code and documentation, mostly C, and some C++ and Fortran. NEMO development started in 1986 in Princeton (USA) by Barnes, Hut and Teuben. See also ZENO (ascl:1102.027) for the version that Barnes maintains.

[ascl:1010.052]
EAZY: A Fast, Public Photometric Redshift Code

EAZY, Easy and Accurate Zphot from Yale, determines photometric redshifts. The program is optimized for cases where spectroscopic redshifts are not available, or only available for a biased subset of the galaxies. The code combines features from various existing codes: it can fit linear combinations of templates, it includes optional flux- and redshift-based priors, and its user interface is modeled on the popular HYPERZ (ascl:1108.010) code. The default template set, as well as the default functional forms of the priors, are not based on (usually highly biased) spectroscopic samples, but on semi-analytical models. Furthermore, template mismatch is addressed by a novel rest-frame template error function. This function gives different wavelength regions different weights, and ensures that the formal redshift uncertainties are realistic. A redshift quality parameter, Q_z, provides a robust estimate of the reliability of the photometric redshift estimate.

[ascl:1010.053]
Halofitting codes for DGP and Degravitation

We perform N-body simulations of theories with infinite-volume extra dimensions, such as the Dvali-Gabadadze-Porrati (DGP) model and its higher-dimensional generalizations, where 4D gravity is mediated by massive gravitons. The longitudinal mode of these gravitons mediates an extra scalar force, which we model as a density-dependent modification to the Poisson equation. This enhances gravitational clustering, particularly on scales that have undergone mild nonlinear processing. While the standard non-linear fitting algorithm of Smith et al. overestimates this power enhancement on non-linear scales, we present a modified fitting formula that offers a remarkably good fit to our power spectra. Due to the uncertainty in galaxy bias, our results are consistent with precision power spectrum determinations from galaxy redshift surveys, even for graviton Compton wavelengths as small as 300 Mpc. Our model is sufficiently general that we expect it to capture the phenomenology of a wide class of related higher-dimensional gravity scenarios.

[ascl:1010.054]
MagnetiCS.c: Cosmic String Loop Evolution and Magnetogenesis

Large-scale coherent magnetic fields are observed in galaxies and clusters, but their ultimate origin remains a mystery. We reconsider the prospects for primordial magnetogenesis by a cosmic string network. We show that the magnetic flux produced by long strings has been overestimated in the past, and give improved estimates. We also compute the fields created by the loop population, and find that it gives the dominant contribution to the total magnetic field strength on present-day galactic scales. We present numerical results obtained by evolving semi-analytic models of string networks (including both one-scale and velocity-dependent one-scale models) in a Lambda-CDM cosmology, including the forces and torques on loops from Hubble redshifting, dynamical friction, and gravitational wave emission. Our predictions include the magnetic field strength as a function of correlation length, as well as the volume covered by magnetic fields. We conclude that string networks could account for magnetic fields on galactic scales, but only if coupled with an efficient dynamo amplification mechanism.

[ascl:1010.055]
SYNOW: A Highly Parameterized Spectrum Synthesis Code for Direct Analysis of SN Spectra

SYNOW is a highly parameterized spectrum synthesis code used primarily for direct (empirical) analysis of SN spectra. The code is based on simple assumptions : spherical symmetry; homologous expansion; a sharp photosphere that emits a blackbody continuous spectrum; and line formation by resonance scattering, treated in the Sobolev approximation. Synow does not do continuum transport, it does not solve rate equations, and it does not calculate ionization ratios. Its main function is to take line multiple scattering into account so that it can be used in an empirical spirit to make line identifications and estimate the velocity at the photosphere (or pseudo-photosphere) and the velocity interval within which each ion is detected. these quantities provide constraints on the composition structure of the ejected matter.

[ascl:1010.056]
PHOENIX: A General-purpose State-of-the-art Stellar and Planetary Atmosphere Code

PHOENIX is a general-purpose state-of-the-art stellar and planetary atmosphere code. It can calculate atmospheres and spectra of stars all across the HR-diagram including main sequence stars, giants, white dwarfs, stars with winds, TTauri stars, novae, supernovae, brown dwarfs and extrasolar giant planets.

[ascl:1010.057]
Tiny Tim: Simulated Hubble Space Telescope PSFs

Tiny Tim generates simulated Hubble Space Telescope point spread functions (PSFs). It is written in C and distributed as source code and runs on a wide variety of UNIX and VMS systems. Tiny Tim includes mirror zonal errors, time dependent aberrations (for the pre-repair instruments), field dependent obscuration patterns (for WF/PC-1 and WFPC2), and filter passband effects. It can produce a normally sampled or subsampled PSF. Output is a FITS image file.

[ascl:1010.058]
VINE: A numerical code for simulating astrophysical systems using particles

VINE is a particle based astrophysical simulation code. It uses a tree structure to efficiently solve the gravitational N-body problem and Smoothed Particle Hydrodynamics (SPH) to simulate gas dynamical effects. The code has been successfully used for a number of studies on galaxy interactions, galactic dynamics, star formation and planet formation and given the implemented physics, other applications are possible as well.

[ascl:1010.059]
CESAM: A Free Code for Stellar Evolution Calculations

The Cesam code is a consistent set of programs and routines which perform calculations of 1D quasi-hydrostatic stellar evolution including microscopic diffusion of chemical species and diffusion of angular momentum. The solution of the quasi-static equilibrium is performed by a collocation method based on piecewise polynomials approximations projected on a B-spline basis; that allows stable and robust calculations, and the exact restitution of the solution, not only at grid points, even for the discontinuous variables. Other advantages are the monitoring by only one parameter of the accuracy and its improvement by super-convergence. An automatic mesh refinement has been designed for adjusting the localisations of grid points according to the changes of unknowns. For standard models, the evolution of the chemical composition is solved by stiffly stable schemes of orders up to four; in the convection zones mixing and evolution of chemical are simultaneous. The solution of the diffusion equation employs the Galerkin finite elements scheme; the mixing of chemicals is then performed by a strong turbulent diffusion. A precise restoration of the atmosphere is allowed for.

[ascl:1010.060]
Pencil: Finite-difference Code for Compressible Hydrodynamic Flows

The Pencil code is a high-order finite-difference code for compressible hydrodynamic flows with magnetic fields. It is highly modular and can easily be adapted to different types of problems. The code runs efficiently under MPI on massively parallel shared- or distributed-memory computers, like e.g. large Beowulf clusters. The Pencil code is primarily designed to deal with weakly compressible turbulent flows. To achieve good parallelization, explicit (as opposed to compact) finite differences are used. Typical scientific targets include driven MHD turbulence in a periodic box, convection in a slab with non-periodic upper and lower boundaries, a convective star embedded in a fully nonperiodic box, accretion disc turbulence in the shearing sheet approximation, self-gravity, non-local radiation transfer, dust particle evolution with feedback on the gas, etc. A range of artificial viscosity and diffusion schemes can be invoked to deal with supersonic flows. For direct simulations regular viscosity and diffusion is being used. The code is written in well-commented Fortran90.

[ascl:1010.061]
EyE: Enhance Your Extraction

In EyE (Enhance Your Extraction) an artificial neural network connected to pixels of a moving window (retina) is trained to associate these input stimuli to the corresponding response in one or several output image(s). The resulting filter can be loaded in SExtractor to operate complex, wildly non-linear filters on astronomical images. Typical applications of EyE include adaptive filtering, feature detection and cosmetic corrections.

[ascl:1010.062]
MissFITS: Basic Maintenance and Packaging Tasks on FITS Files

MissFITS is a program that performs basic maintenance and packaging tasks on FITS files using an optimized FITS library. MissFITS can:

- add, edit, and remove FITS header keywords;
- split and join Multi-Extension-FITS (MEF) files;
- unpile and pile FITS data-cubes; and,
- create, check, and update FITS checksums, using R. Seaman’s protocol.

[ascl:1010.063]
SCAMP: Automatic Astrometric and Photometric Calibration

Astrometric and photometric calibrations have remained the most tiresome step in the reduction of large imaging surveys. SCAMP has been written to address this problem. The program efficiently computes accurate astrometric and photometric solutions for any arbitrary sequence of FITS images in a completely automatic way. SCAMP is released under the GNU General Public License.

[ascl:1010.064]
SExtractor: Source Extractor

This new software optimally detects, de-blends, measures and classifies sources from astronomical images: SExtractor (Source Extractor). A very reliable star/galaxy separation can be achieved on most images using a neural network trained with simulated images. Salient features of SExtractor include its ability to work on very large images, with minimal human intervention, and to deal with a wide variety of object shapes and magnitudes. It is therefore particularly suited to the analysis of large extragalactic surveys.

[ascl:1010.065]
Higher Post Newtonian Gravity Calculations

Motivated by experimental probes of general relativity, we adopt methods from perturbative (quantum) field theory to compute, up to certain integrals, the effective lagrangian for its n-body problem. Perturbation theory is performed about a background Minkowski spacetime to O[(v/c)^4] beyond Newtonian gravity, where v is the typical speed of these n particles in their center of energy frame. For the specific case of the 2 body problem, the major efforts underway to measure gravitational waves produced by in-spiraling compact astrophysical binaries require their gravitational interactions to be computed beyond the currently known O[(v/c)^7]. We argue that such higher order post-Newtonian calculations must be automated for these field theoretic methods to be applied successfully to achieve this goal. In view of this, we outline an algorithm that would in principle generate the relevant Feynman diagrams to an arbitrary order in v/c and take steps to develop the necessary software. The Feynman diagrams contributing to the n-body effective action at O[(v/c)^6] beyond Newton are derived.

[ascl:1010.066]
SkyMaker: Astronomical Image Simulations Made Easy

SkyMaker is a program that simulates astronomical images. It accepts object lists in ASCII generated by the Stuff program to produce realistic astronomical fields. SkyMaker is part of the EFIGI development project.

[ascl:1010.067]
Stuff: Simulating “Perfect” Astronomical Catalogues

Stuff is a program that simulates “perfect” astronomical catalogues. It generate object lists in ASCII which can read by the SkyMaker program to produce realistic astronomical fields. Stuff is part of the EFIGI development project.

[ascl:1010.068]
SWarp: Resampling and Co-adding FITS Images Together

SWarp is a program that resamples and co-adds together FITS images using any arbitrary astrometric projection defined in the WCS standard. It operates on pre-reduced images and their weight-maps. Based on the astrometric and photometric calibrations derived at an earlier phase of the pipeline, SWarp re-maps ("warps") the pixels to a perfect projection system, and co-adds them in an optimum way, according to their relative weights. SWarp's astrometric engine is based on a customized version of Calabretta's WCSLib 2.6 and supports all of the projections defined in the 2000 version of the WCS proposal.

[ascl:1010.069]
WeightWatcher: Code to Produce Control Maps

WeightWatcher is a program that combines weight-maps, flag-maps and polygon data in order to produce control maps which can directly be used in astronomical image-processing packages like Drizzle, SWarp or SExtractor.

[ascl:1010.070]
Fisher.py: Fisher Matrix Manipulation and Confidence Contour Plotting

Fisher.py allows you to combine constraints from multiple experiments (e.g., weak lensing + supernovae) and add priors (e.g., a flat universe) simply and easily. Calculate parameter uncertainties and plot confidence ellipses. Fisher matrix expectations for several experiments are included as calculated by myself (time delays) and the Dark Energy Task Force (WL/SN/BAO/CL/CMB), or provide your own.

[ascl:1010.071]
WSHAPE: Gravitational Softening and Adaptive Mass Resolution

Pairwise forces between particles in cosmological N-body simulations are generally softened to avoid hard collisions. Physically, this softening corresponds to treating the particles as diffuse clouds rather than point masses. For particles of unequal mass (and hence unequal softening length), computing the softened force involves a nontrivial double integral over the volumes of the two particles. We show that Plummer force softening is consistent with this interpretation of softening while spline softening is not. We provide closed-form expressions and numerical implementation for pairwise gravitational force laws for pairs of particles of general softening scales $epsilon_1$ and $epsilon_2$ assuming the commonly used cloud profiles: NGP, CIC, TSC, and PQS. Similarly, we generalize Plummer force law into pairs of particles of general softenings. We relate our expressions to the gaussian, Plummer and spline force softenings known from literature. Our expressions allow possible inclusions of pointlike particles such as stars or supermassive black holes.

[ascl:1010.072]
Enzo: AMR Cosmology Application

O'Shea, Brian W.; Bryan, Greg; Bordner, James; Norman, Michael L.; Abel, Tom; Harkness, Robert; Kritsuk, Alexei

Enzo is an adaptive mesh refinement (AMR), grid-based hybrid code (hydro + N-Body) which is designed to do simulations of cosmological structure formation. It uses the algorithms of Berger & Collela to improve spatial and temporal resolution in regions of large gradients, such as gravitationally collapsing objects. The Enzo simulation software is incredibly flexible, and can be used to simulate a wide range of cosmological situations with the available physics packages.

Enzo has been parallelized using the MPI message-passing library and can run on any shared or distributed memory parallel supercomputer or PC cluster. Simulations using as many as 1024 processors have been successfully carried out on the San Diego Supercomputing Center's Blue Horizon, an IBM SP.

[ascl:1010.073]
partiview: Immersive 4D Interactive Visualization of Large-Scale Simulations

In dense clusters a bewildering variety of interactions between stars can be observed, ranging from simple encounters to collisions and other mass-transfer encounters. With faster and special-purpose computers like GRAPE, the amount of data per simulation is now exceeding 1TB. Visualization of such data has now become a complex 4D data-mining problem, combining space and time, and finding interesting events in these large datasets. We have recently starting using the virtual reality simulator, installed in the Hayden Planetarium in the American Museum for Natural History, to tackle some of these problem. partiview is a program that enables you to visualize and animate particle data. partiview runs on relatively simple desktops and laptops, but is mostly compatible with its big brother VirDir.

[ascl:1010.074]
StarCrash: 3-d Evolution of Self-gravitating Fluid Systems

StarCrash is a parallel fortran code based on Smoothed Particle Hydrodynamics (SPH) techniques to calculate the 3-d evolution of self-gravitating fluid systems. The code in particularly suited to the study of stellar interactions, such as mergers of binary star systems and stellar collisions. The StarCrash code comes with several important features, including:

- Several routines which construct the initial conditions appropriate to a wide variety of physical systems

- An efficient parallel neighbor-finding algorithm for calculating hydrodynamic quantities

- A parallel gravitational field solver based on FFT convolution techniques, which uses the FFTW software libraries

- Relaxation Techniques for single stars and synchronized binaries

- Three different artificial viscosity treatments to calculate the thermodynamic evolution of the matter

- An optional gravitational radiation back-reaction treatment, which calculates the damping force from gravity wave losses to lowest relativistic order in a spatially accurate way

[ascl:1010.075]
Radex: Fast Non-LTE Analysis of Interstellar Line Spectra

The large quantity and high quality of modern radio and infrared line observations require efficient modeling techniques to infer physical and chemical parameters such as temperature, density, and molecular abundances. Radex calculates the intensities of atomic and molecular lines produced in a uniform medium, based on statistical equilibrium calculations involving collisional and radiative processes and including radiation from background sources. Optical depth effects are treated with an escape probability method. The program makes use of molecular data files maintained in the Leiden Atomic and Molecular Database (LAMDA), which will continue to be improved and expanded. The performance of the program is compared with more approximate and with more sophisticated methods. An Appendix provides diagnostic plots to estimate physical parameters from line intensity ratios of commonly observed molecules. This program should form an important tool in analyzing observations from current and future radio and infrared telescopes.

[ascl:1010.076]
Starlab: A Software Environment for Collisional Stellar Dynamics

Traditionally, a simulation of a dense stellar system required choosing an initial model, running an integrator, and analyzing the output. Almost all of the effort went into writing a clever integrator that could handle binaries, triples and encounters between various multiple systems efficiently. Recently, the scope and complexity of these simulations has increased dramatically, for three reasons: 1) the sheer size of the data sets, measured in Terabytes, make traditional 'awking and grepping' of a single output file impractical; 2) the addition of stellar evolution data brings qualitatively new challenges to the data reduction; 3) increased realism of the simulations invites realistic forms of 'SOS': Simulations of Observations of Simulations, to be compared directly with observations. We are now witnessing a shift toward the construction of archives as well as tailored forms of visualization including the use of virtual reality simulators and planetarium domes, and a coupling of both with budding efforts in constructing virtual observatories. This review describes these new trends, presenting Starlab as the first example of a full software environment for realistic large-scale simulations of dense stellar systems.

[ascl:1010.077]
LAMDA: Leiden Atomic and Molecular Database

LAMDA provides users of radiative transfer codes with the basic atomic and molecular data needed for the excitation calculation. Line data of a number of astrophysically interesting species are summarized, including energy levels, statistical weights, Einstein A-coefficients and collisional rate coefficients. Available collisional data from quantum chemical calculations and experiments are in some cases extrapolated to higher energies. Currently the database contains atomic data for 3 species and molecular data for 28 different species. In addition, several isotopomers and deuterated versions are available. This database should form an important tool in analyzing observations from current and future infrared and (sub)millimetre telescopes. Databases such as these rely heavily on the efforts by the chemical physics community to provide the relevant atomic and molecular data. Further efforts in this direction are strongly encouraged so that the current extrapolations of collisional rate coefficients can be replaced by actual calculations in future releases.

RADEX, a computer program for performing statistical equilibrium calculations is made publicly available as part of the data base.

[ascl:1010.078]
AstroMD: A Multi Dimensional Visualization and Analysis Toolkit for Astrophysics

Over the past few years, the role of visualization for scientific purpose has grown up enormously. Astronomy makes an extended use of visualization techniques to analyze data, and scientific visualization has became a fundamental part of modern researches in Astronomy. With the evolution of high performance computers, numerical simulations have assumed a great role in the scientific investigation, allowing the user to run simulation with higher and higher resolution. Data produced in these simulations are often multi-dimensional arrays with several physical quantities. These data are very hard to manage and to analyze efficiently. Consequently the data analysis and visualization tools must follow the new requirements of the research. AstroMD is a tool for data analysis and visualization of astrophysical data and can manage different physical quantities and multi-dimensional data sets. The tool uses virtual reality techniques by which the user has the impression of travelling through a computer-based multi-dimensional model.

[ascl:1010.079]
Geant4: A Simulation Toolkit for the Passage of Particles through Matter

Geant4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics.

[ascl:1010.080]
GRACOS: Scalable and Load Balanced P3M Cosmological N-body Code

The GRACOS (GRAvitational COSmology) code, a parallel implementation of the particle-particle/particle-mesh (P3M) algorithm for distributed memory clusters, uses a hybrid method for both computation and domain decomposition. Long-range forces are computed using a Fourier transform gravity solver on a regular mesh; the mesh is distributed across parallel processes using a static one-dimensional slab domain decomposition. Short-range forces are computed by direct summation of close pairs; particles are distributed using a dynamic domain decomposition based on a space-filling Hilbert curve. A nearly-optimal method was devised to dynamically repartition the particle distribution so as to maintain load balance even for extremely inhomogeneous mass distributions. Tests using $800^3$ simulations on a 40-processor beowulf cluster showed good load balance and scalability up to 80 processes. There are limits on scalability imposed by communication and extreme clustering which may be removed by extending the algorithm to include adaptive mesh refinement.

[ascl:1010.081]
MGGPOD: A Monte Carlo Suite for Gamma-Ray Astronomy

We have developed MGGPOD, a user-friendly suite of Monte Carlo codes built around the widely used GEANT (Version 3.21) package. The MGGPOD Monte Carlo suite and documentation are publicly available for download. MGGPOD is an ideal tool for supporting the various stages of gamma-ray astronomy missions, ranging from the design, development, and performance prediction through calibration and response generation to data reduction. In particular, MGGPOD is capable of simulating ab initio the physical processes relevant for the production of instrumental backgrounds. These include the build-up and delayed decay of radioactive isotopes as well as the prompt de-excitation of excited nuclei, both of which give rise to a plethora of instrumental gamma-ray background lines in addition to continuum backgrounds.

[ascl:1010.082]
FLASH: Adaptive Mesh Hydrodynamics Code for Modeling Astrophysical Thermonuclear Flashes

Fryxell, B.; Olson, K.; Ricker, P.; Timmes, F. X.; Zingale, M.; Lamb, D. Q.; MacNeice, P.; Rosner, R.; Truran, J. W.; Tufo, H.

The FLASH code, currently in its 4th version, is a publicly available high performance application code which has evolved into a modular, extensible software system from a collection of unconnected legacy codes. FLASH consists of inter-operable modules that can be combined to generate different applications. The FLASH architecture allows arbitrarily many alternative implementations of its components to co-exist and interchange with each other. A simple and elegant mechanism exists for customization of code functionality without the need to modify the core implementation of the source. A built-in unit test framework combined with regression tests that run nightly on multiple platforms verify the code.

[ascl:1010.083]
MESA: Modules for Experiments in Stellar Astrophysics

Stellar physics and evolution calculations enable a broad range of research in astrophysics. Modules for Experiments in Stellar Astrophysics (MESA) is a suite of open source libraries for a wide range of applications in computational stellar astrophysics. A newly designed 1-D stellar evolution module, MESA star, combines many of the numerical and physics modules for simulations of a wide range of stellar evolution scenarios ranging from very-low mass to massive stars, including advanced evolutionary phases. MESA star solves the fully coupled structure and composition equations simultaneously. It uses adaptive mesh refinement and sophisticated timestep controls, and supports shared memory parallelism based on OpenMP. Independently usable modules provide equation of state, opacity, nuclear reaction rates, and atmosphere boundary conditions. Each module is constructed as a separate Fortran 95 library with its own public interface. Examples include comparisons to other codes and show evolutionary tracks of very low mass stars, brown dwarfs, and gas giant planets; the complete evolution of a 1 Msun star from the pre-main sequence to a cooling white dwarf; the Solar sound speed profile; the evolution of intermediate mass stars through the thermal pulses on the He-shell burning AGB phase; the interior structure of slowly pulsating B Stars and Beta Cepheids; evolutionary tracks of massive stars from the pre-main sequence to the onset of core collapse; stars undergoing Roche lobe overflow; and accretion onto a neutron star.

[ascl:1010.084]
WhiskyMHD: Numerical Code for General Relativistic Magnetohydrodynamics

Whisky is a code to evolve the equations of general relativistic hydrodynamics (GRHD) and magnetohydrodynamics (GRMHD) in 3D Cartesian coordinates on a curved dynamical background. It was originally developed by and for members of the EU Network on Sources of Gravitational Radiation and is based on the Cactus Computational Toolkit. Whisky can also implement adaptive mesh refinement (AMR) if compiled together with Carpet.

Whisky has grown from earlier codes such as GR3D and GRAstro_Hydro, but has been rewritten to take advantage of some of the latest research performed here in the EU. The motivation behind Whisky is to compute gravitational radiation waveforms for systems that involve matter. Examples would include the merger of a binary system containing a neutron star, which are expected to be reasonably common in the universe and expected to produce substantial amounts of radiation. Other possible sources are given in the projects list.

[ascl:1010.085]
Network Tools for Astronomical Data Retrieval

The first step in a science project is the acquisition and understanding of the relevant data. The tools range from simple data transfer methods to more complex browser-emulating scripts. When integrated with a defined sample or catalog, these scripts provide seamless techniques to retrieve and store data of varying types. These tools can be used to leapfrog from website to website to acquire multi-wavelength datasets. This project demonstrates the capability to use multiple data websites, in conjunction, to perform the type of calculations once reserved for on-site datasets.

[ascl:1007.001]
PINTofALE: Package for Interactive Analysis of Line Emission

PINTofALE was originally developed to analyze spectroscopic data from optically-thin coronal plasmas, though much of the software is sufficiently general to be of use in a much wider range of astrophysical data analyses. It is based on a modular set of IDL tools that interact with an atomic database and with observational data. The tools are designed to allow easy identification of spectral features, measure line fluxes, and carry out detailed modeling. The basic philosophy of the package is to provide access to the innards of atomic line databases, and to have flexible tools to interactively compare with the observed data. It is motivated by the large amount of book-keeping, computation and iterative interaction that is required between the researcher and observational and theoretical data in order to derive astrophysical results. The tools link together transparently and automatically the processes of spectral "browsing", feature identification, measurement, and computation and derivation of results. Unlike standard modeling and fitting engines currently in use, PINTofALE opens up the "black box" of atomic data required for UV/X-ray analyses and allows the user full control over the data that are used in any given analysis.

[ascl:1007.002]
INFALL: A code for calculating the mean initial and final density profiles around a virialized dark matter halo

Infall is a code for calculating the mean initial and final density profiles around a virialized dark matter halo. The initial profile is derived from the statistics of the initial Gaussian random field, accounting for the problem of peaks within peaks using the extended Press-Schechter model. Spherical collapse then yields the typical density and velocity profiles of the gas and dark matter that surrounds the final, virialized halo. In additional to the mean profile, ±1-σ profiles are calculated and can be used as an estimate of the scatter.

[ascl:1007.003]
GEMINI: A toolkit for analytical models of two-point correlations and inhomogeneous structure formation

Gemini is a toolkit for analytical models of two-point correlations and inhomogeneous structure formation. It extends standard Press-Schechter theory to inhomogeneous situations, allowing a realistic, analytical calculation of halo correlations and bias.

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