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Astrophysics Source Code Library

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[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 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

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

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:1011.001] Identikit 1: A Modeling Tool for Interacting Disk Galaxies

By combining test-particle and self-consistent techniques, we have developed a method to rapidly explore the parameter space of galactic encounters. Our method, implemented in an interactive graphics program, can be used to find the parameters required to reproduce the observed morphology and kinematics of interacting disk galaxies. We test this system on an artificial data-set of 36 equal-mass merging encounters, and show that it is usually possible to reproduce the morphology and kinematics of these encounters and that a good match strongly constrains the encounter parameters.

[ascl:1011.002] DAOSPEC: An Automatic Code for Measuring Equivalent Widths in High-resolution Stellar Spectra

DAOSPEC is a Fortran code for measuring equivalent widths of absorption lines in stellar spectra with minimal human involvement. It works with standard FITS format files and it is designed for use with high resolution (R>15000) and high signal-to-noise-ratio (S/N>30) spectra that have been binned on a linear wavelength scale. First, we review the analysis procedures that are usually employed in the literature. Next, we discuss the principles underlying DAOSPEC and point out similarities and differences with respect to conventional measurement techniques. Then experiments with artificial and real spectra are discussed to illustrate the capabilities and limitations of DAOSPEC, with special attention given to the issues of continuum placement; radial velocities; and the effects of strong lines and line crowding. Finally, quantitative comparisons with other codes and with results from the literature are also presented.

[ascl:1011.003] ZPEG: An Extension of the Galaxy Evolution Model PEGASE.2

Photometric redshifts are estimated on the basis of template scenarios with the help of the code ZPEG, an extension of the galaxy evolution model PEGASE.2 and available on the PEGASE web site. The spectral energy distribution (SED) templates are computed for nine spectral types including starburst, irregular, spiral and elliptical. Dust, extinction and metal effects are coherently taken into account, depending on evolution scenarios. The sensitivity of results to adding near-infrared colors and IGM absorption is analyzed. A comparison with results of other models without evolution measures the evolution factor which systematically increases the estimated photometric redshift values by $Delta z$ > 0.2 for z > 1.5. Moreover we systematically check that the evolution scenarios match observational standard templates of nearby galaxies, implying an age constraint of the stellar population at z=0 for each type. The respect of this constraint makes it possible to significantly improve the accuracy of photometric redshifts by decreasing the well-known degeneracy problem. The method is applied to the HDF-N sample. From fits on SED templates by a $chi^2$-minimization procedure, not only is the photometric redshift derived but also the corresponding spectral type and the formation redshift $z_for$ when stars first formed. Early epochs of galaxy formation z > 5 are found from this new method and results are compared to faint galaxy count interpretations.

[ascl:1011.004] MARS: The MAGIC Analysis and Reconstruction Software

With the commissioning of the second MAGIC gamma-ray Cherenkov telescope situated close to MAGIC-I, the standard analysis package of the MAGIC collaboration, MARS, has been upgraded in order to perform the stereoscopic reconstruction of the detected atmospheric showers. MARS is a ROOT-based code written in C++, which includes all the necessary algorithms to transform the raw data recorded by the telescopes into information about the physics parameters of the observed targets. An overview of the methods for extracting the basic shower parameters is presented, together with a description of the tools used in the background discrimination and in the estimation of the gamma-ray source spectra.

[ascl:1011.005] Shape of Cosmic String Loops

Complicated cosmic string loops will fragment until they reach simple, non-intersecting ("stable") configurations. Through extensive numerical study we characterize these attractor loop shapes including their length, velocity, kink, and cusp distributions. We find that 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. We examine the properties of stable loops of different lengths and find only slight variation. Finally we develop a new analytic scheme to explicitly solve the string constraint equations.

[ascl:1011.006] DAME: A Web Oriented Infrastructure for Scientific Data Mining & Exploration

DAME (DAta Mining & Exploration) is an innovative, general purpose, Web-based, VObs compliant, distributed data mining infrastructure specialized in Massive Data Sets exploration with machine learning methods. Initially fine tuned to deal with astronomical data only, DAME has evolved in a general purpose platform which has found applications also in other domains of human endeavor.

[ascl:1011.007] RAMSES: A new N-body and hydrodynamical code

A new N-body and hydrodynamical code, called RAMSES, is presented. It has been designed to study structure formation in the universe with high spatial resolution. The code is based on Adaptive Mesh Refinement (AMR) technique, with a tree based data structure allowing recursive grid refinements on a cell-by-cell basis. The N-body solver is very similar to the one developed for the ART code (Kravtsov et al. 97), with minor differences in the exact implementation. The hydrodynamical solver is based on a second-order Godunov method, a modern shock-capturing scheme known to compute accurately the thermal history of the fluid component. The accuracy of the code is carefully estimated using various test cases, from pure gas dynamical tests to cosmological ones. The specific refinement strategy used in cosmological simulations is described, and potential spurious effects associated to shock waves propagation in the resulting AMR grid are discussed and found to be negligible. Results obtained in a large N-body and hydrodynamical simulation of structure formation in a low density LCDM universe are finally reported, with 256^3 particles and 4.1 10^7 cells in the AMR grid, reaching a formal resolution of 8192^3. A convergence analysis of different quantities, such as dark matter density power spectrum, gas pressure power spectrum and individual haloes temperature profiles, shows that numerical results are converging down to the actual resolution limit of the code, and are well reproduced by recent analytical predictions in the framework of the halo model.

[ascl:1011.008] Binsim: Visualising Interacting Binaries in 3D

Binsim produces images of interacting binaries for any system parameters. Though not suitable for modeling light curves or spectra, the resulting images are helpful in visualizing the geometry of a given system and are also helpful in talks and educational work. The code uses the OpenGL API to do the 3D rendering. The software can produce images of cataclysmic variables and X-ray binaries, and can render the mass donor star, an axisymmetric disc (without superhumps, warps or spirals), the accretion stream and hotspot, and a "corona."

[ascl:1011.009] DRAGON: Monte Carlo Generator of Particle Production from a Fragmented Fireball in Ultrarelativistic Nuclear Collisions

A Monte Carlo generator of the final state of hadrons emitted from an ultrarelativistic nuclear collision is introduced. An important feature of the generator is a possible fragmentation of the fireball and emission of the hadrons from fragments. Phase space distribution of the fragments is based on the blast wave model extended to azimuthally non-symmetric fireballs. Parameters of the model can be tuned and this allows to generate final states from various kinds of fireballs. A facultative output in the OSCAR1999A format allows for a comprehensive analysis of phase-space distributions and/or use as an input for an afterburner. DRAGON's purpose is to produce artificial data sets which resemble those coming from real nuclear collisions provided fragmentation occurs at hadronisation and hadrons are emitted from fragments without any further scattering. Its name, DRAGON, stands for DRoplet and hAdron GeneratOr for Nuclear collisions. In a way, the model is similar to THERMINATOR, with the crucial difference that emission from fragments is included.

[ascl:1011.010] Global Sky Model (GSM): A Model of Diffuse Galactic Radio Emission from 10 MHz to 100 GHz

Understanding diffuse Galactic radio emission is interesting both in its own right and for minimizing foreground contamination of cosmological measurements. Cosmic Microwave Background experiments have focused on frequencies > 10 GHz, whereas 21 cm tomography of the high redshift universe will mainly focus on < 0.2 GHz, for which less is currently known about Galactic emission. Motivated by this, we present a global sky model derived from all publicly available total power large-area radio surveys, digitized with optical character recognition when necessary and compiled into a uniform format, as well as the new Villa Elisa data extending the 1.4 GHz map to the entire sky. We quantify statistical and systematic uncertainties in these surveys by comparing them with various global multi-frequency model fits. We find that a principal component based model with only three components can fit the 11 most accurate data sets (at 10, 22, 45 & 408 MHz and 1.4, 2.3, 23, 33, 41, 61, 94 GHz) to an accuracy around 1%-10% depending on frequency and sky region. The data compilation and software returning a predicted all-sky map at any frequency from 10 MHz to 100 GHz are publicly available in the archive file at the link below.

[ascl:1011.011] turboGL: Accurate Modeling of Weak Lensing

turboGL is a fast Mathematica code based on a stochastic approach to cumulative weak lensing. It can easily compute the lensing PDF relative to arbitrary halo mass distributions, selection biases, number of observations, halo profiles and evolutions, making it a useful tool to study how lensing depends on cosmological parameters and impact on observations.

[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

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

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.

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