[ascl:1902.011]
SpecViz: 1D Spectral Visualization Tool

SpecViz interactively visualizes and analyzes 1D astronomical spectra. It reads data from FITS and ASCII tables and allows spectra to be easily plotted and examined. It supports instrument-specific data quality handling, flexible spectral units conversions, custom plotting attributes, plot annotations, tiled plots, among other features. SpecViz includes a measurement tool for spectral lines for performing and recording measurements and a model fitting capability for creating simple (e.g., single Gaussian) or multi-component models (e.g., multiple Gaussians for emission and absorption lines in addition to regions of flat continua). SpecViz is built on top of the Specutils (ascl:1902.012) Astropy-affiliated python library, providing a visual, interactive interface to the analysis capabilities in that library.

[ascl:1310.008]
SPECX: Spectral Line Data Reduction Package

SPECX is a general purpose line data reduction system. It can read and write FITS data cubes but has specialist support for the GSD format data from the James Clerk Maxwell Telescope. It includes commands to store and retrieve intermediate spectra in storage registers and perform the fitting and removal of polynomial, harmonic and Gaussian baselines.

SPECX can filter and edit spectra and list and display spectra on a graphics terminal. It is able to perform Fourier transform and power spectrum calculations, process up to eight spectra (quadrants) simultaneously with either the same or different center, and assemble a number of reduced individual spectra into a map file and contour or greyscale any plane or planes of the resulting cube.

Two versions of SPECX are distributed. Version 6.x is the VMS and Unix version and is distributed as part of the Starlink software collection. Version 7.x is a complete rewrite of SPECX distributed for Windows.

[ascl:1807.014]
SPEGID: Single-Pulse Event Group IDentification

SPEGID (Single-Pulse Event Group IDentification) identifies astrophysical pulse candidates as trial single-pulse event groups (SPEGs) by first applying Density Based Spatial Clustering of Applications with Noise (DBSCAN) on trial single-pulse events and then merging the clusters that fall within the expected DM (Dispersion Measure) and time span of astrophysical pulses. SPEGID also calculates the peak score for each SPEG in the S/N versus DM space to identify the expected peak-like shape in the signal-to-noise (S/N) ratio versus DM curve of astrophysical pulses. Additionally, SPEGID groups SPEGs that appear at a consistent DM and therefore are likely emitted from the same source. After running SPEGID, periocity.py can be used to find (or verify) the underlying periodicity among a group of SPEGs (i.e., astrophysical pulse candidates).

[ascl:1308.014]
SPEX: High-resolution cosmic X-ray spectra analysis

SPEX is optimized for the analysis and interpretation of high-resolution cosmic X-ray spectra. The software is especially suited for fitting spectra obtained by current X-ray observatories like XMM-Newton, Chandra, and Suzaku. SPEX can fit multiple spectra with different model components simultaneously and handles highly complex models with many free parameters.

[ascl:1404.017]
Spextool: Spectral EXtraction tool

Spextool (Spectral EXtraction tool) is an IDL-based data reduction package for SpeX, a medium resolution near-infrared spectrograph on the NASA IRTF. It performs all of the steps necessary to produce spectra ready for analysis and publication including non-linearity corrections, flat fielding, wavelength calibration, telluric correction, flux calibration, and order merging.

[ascl:9912.001]
SPH_1D: Hierarchical gravity/SPH treecode for simulations of interacting galaxies

We describe a fast tree algorithm for gravitational N-body simulation on SIMD parallel computers. The tree construction uses fast, parallel sorts. The sorted lists are recursively divided along their x, y and z coordinates. This data structure is a completely balanced tree (i.e., each particle is paired with exactly one other particle) and maintains good spatial locality. An implementation of this tree-building algorithm on a 16k processor Maspar MP-1 performs well and constitutes only a small fraction (approximately 15%) of the entire cycle of finding the accelerations. Each node in the tree is treated as a monopole. The tree search and the summation of accelerations also perform well. During the tree search, node data that is needed from another processor is simply fetched. Roughly 55% of the tree search time is spent in communications between processors. We apply the code to two problems of astrophysical interest. The first is a simulation of the close passage of two gravitationally, interacting, disk galaxies using 65,636 particles. We also simulate the formation of structure in an expanding, model universe using 1,048,576 particles. Our code attains speeds comparable to one head of a Cray Y-MP, so single instruction, multiple data (SIMD) type computers can be used for these simulations. The cost/performance ratio for SIMD machines like the Maspar MP-1 make them an extremely attractive alternative to either vector processors or large multiple instruction, multiple data (MIMD) type parallel computers. With further optimizations (e.g., more careful load balancing), speeds in excess of today's vector processing computers should be possible.

[ascl:1806.023]
Spheral++: Coupled hydrodynamical and gravitational numerical simulations

Spheral++ provides a steerable parallel environment for performing coupled hydrodynamical and gravitational numerical simulations. Hydrodynamics and gravity are modeled using particle-based methods (SPH and N-Body). It uses an Adaptive Smoothed Particle Hydrodynamics (ASPH) algorithm, provides a total energy conserving compatible hydro mode, and performs fluid and solid material modeling and damage and fracture modeling in solids.

[ascl:1309.004]
Spherical: Geometry operations and searches on spherical surfaces

The Spherical Library provides an efficient and accurate mathematical representation of shapes on the celestial sphere, such as sky coverage and footprints. Shapes of arbitrary complexity and size can be dynamically created from simple building blocks, whose exact area is also analytically computed. This methodology is also perfectly suited for censoring problematic parts of datasets, e.g., bad seeing, satellite trails or diffraction spikes of bright stars.

[ascl:1311.005]
Spheroid: Electromagnetic Scattering by Spheroids

Spheroid determines the size distribution of polarizing interstellar dust grains based on electromagnetic scattering by spheroidal particles. It contains subroutines to treat the case of complex refractive indices, and also includes checks for some limiting cases.

[ascl:1502.012]
SPHGR: Smoothed-Particle Hydrodynamics Galaxy Reduction

SPHGR (Smoothed-Particle Hydrodynamics Galaxy Reduction) is a python based open-source framework for analyzing smoothed-particle hydrodynamic simulations. Its basic form can run a baryonic group finder to identify galaxies and a halo finder to identify dark matter halos; it can also assign said galaxies to their respective halos, calculate halo & galaxy global properties, and iterate through previous time steps to identify the most-massive progenitors of each halo and galaxy. Data about each individual halo and galaxy is collated and easy to access.

SPHGR supports a wide range of simulations types including N-body, full cosmological volumes, and zoom-in runs. Support for multiple SPH code outputs is provided by pyGadgetReader (ascl:1411.001), mainly Gadget (ascl:0003.001) and TIPSY (ascl:1111.015).

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

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

[ascl:1709.001]
SPHYNX: SPH hydrocode for subsonic hydrodynamical instabilities and strong shocks

SPHYNX addresses subsonic hydrodynamical instabilities and strong shocks; it is Newtonian, grounded on the Euler-Lagrange formulation of the smoothed-particle hydrodynamics technique, and density based. SPHYNX uses an integral approach for estimating gradients, a flexible family of interpolators to suppress pairing instability, and incorporates volume elements to provides better partition of the unity.

[ascl:1903.015]
SPICE: Observation Geometry System for Space Science Missions

The SPICE (Spacecraft Planet Instrument C-matrix [“Camera matrix”] Events) toolkit offers a set of building blocks for constructing tools supporting multi-mission, international space exploration programs and research in planetary science, heliophysics, Earth science, and for observations from terrestrial observatories. It computes many kinds of observation geometry parameters, including the ephemerides, orientations, sizes, and shapes of planets, satellites, comets and asteroids. It can also compute the orientation of a spacecraft, its various moving structures, and an instrument's field-of-view location on a planet's surface or atmosphere. It can determine when a specified geometric event occurs, such as when an object is in shadow or is in transit across another object. The SPICE toolkit is available in FORTRAN 77, ANSI C, IDL, and MATLAB.

[ascl:1903.016]
SpiceyPy: Python wrapper for the NAIF C SPICE Toolkit

Annex, Andrew; Carcich, Brian; Murakami, Shin-ya; Kulumani, Shankar; de Val-Borro, Miguel; Stefko, Marcel; Diaz del Rio, Jorge; Seignovert, B.

SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (ascl:1903.015). It is compatible with Python 2 and 3, and was written using ctypes.

[ascl:1711.019]
SPIDERMAN: Fast code to simulate secondary transits and phase curves

SPIDERMAN calculates exoplanet phase curves and secondary eclipses with arbitrary surface brightness distributions in two dimensions. The code uses a geometrical algorithm to solve exactly the area of sections of the disc of the planet that are occulted by the star. Approximately 1000 models can be generated per second in typical use, which makes making Markov Chain Monte Carlo analyses practicable. The code is modular and allows comparison of the effect of multiple different brightness distributions for a dataset.

[ascl:1608.020]
SPIDERz: SuPport vector classification for IDEntifying Redshifts

SPIDERz (SuPport vector classification for IDEntifying Redshifts) applies powerful support vector machine (SVM) optimization and statistical learning techniques to custom data sets to obtain accurate photometric redshift (photo-z) estimations. It is written for the IDL environment and can be applied to traditional data sets consisting of photometric band magnitudes, or alternatively to data sets with additional galaxy parameters (such as shape information) to investigate potential correlations between the extra galaxy parameters and redshift.

[ascl:1710.004]
SPIPS: Spectro-Photo-Interferometry of Pulsating Stars

SPIPS (Spectro-Photo-Interferometry of Pulsating Stars) combines radial velocimetry, interferometry, and photometry to estimate physical parameters of pulsating stars, including presence of infrared excess, color excess, Teff, and ratio distance/p-factor. The global model-based parallax-of-pulsation method is implemented in Python. Derived parameters have a high level of confidence; statistical precision is improved (compared to other methods) due to the large number of data taken into account, accuracy is improved by using consistent physical modeling and reliability of the derived parameters is strengthened by redundancy in the data.

[ascl:1512.015]
Spirality: Spiral arm pitch angle measurement

Shields, Douglas W.; Boe, Benjamin; Pfountz, Casey; Davis, Benjamin L.; Hartley, Matthew; Pour Imani, Hamed; Slade, Zac; Kennefick, Daniel; Kennefick, Julia

Spirality measures spiral arm pitch angles by fitting galaxy images to spiral templates of known pitch. Written in MATLAB, the code package also includes GenSpiral, which produces FITS images of synthetic spirals, and SpiralArmCount, which uses a one-dimensional Fast Fourier Transform to count the spiral arms of a galaxy after its pitch is determined.

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

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

[ascl:1402.008]
SPLAT-VO: Spectral Analysis Tool for the Virtual Observatory

SPLAT-VO is an extension of the SPLAT (Spectral Analysis Tool, ascl:1402.007) graphical tool for displaying, comparing, modifying and analyzing astronomical spectra; it includes facilities that allow it to work as part of the Virtual Observatory (VO). SPLAT-VO comes in two different forms, one for querying and downloading spectra from SSAP servers and one for interoperating with VO tools, such as TOPCAT (ascl:1101.010).

[ascl:1402.007]
SPLAT: Spectral Analysis Tool

SPLAT is a graphical tool for displaying, comparing, modifying and analyzing astronomical spectra stored in NDF, FITS and TEXT files as well as in NDX format. It can read in many spectra at the same time and then display these as line plots. Display windows can show one or several spectra at the same time and can be interactively zoomed and scrolled, centered on specific wavelengths, provide continuous coordinate readout, produce printable hardcopy and be configured in many ways. Analysis facilities include the fitting of a polynomial to selected parts of a spectrum, the fitting of Gaussian, Lorentzian and Voigt profiles to emission and absorption lines and the filtering of spectra using average, median and line-shape window functions as well as wavelet denoising. SPLAT also supports a full range of coordinate systems for spectra, which allows coordinates to be displayed and aligned in many different coordinate systems (wavelength, frequency, energy, velocity) and transformed between these and different standards of rest (topocentric, heliocentric, dynamic and kinematic local standards of rest, etc). SPLAT is distributed as part of the Starlink (ascl:1110.012) software collection.

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

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

[ascl:1809.006]
spops: Spinning black-hole binary population synthesis

Gerosa, Davide; Berti, Emanuele; O'Shaughnessy, Richard; Belczynski, Krzysztof; Kesden, Michael; Wysocki, Daniel; Gladysz, Wojciech

spops is a database of populations synthesis simulations of spinning black-hole binary systems, together with a python module to query it. Data are obtained with the startrack and precession [ascl:1611.004] numerical codes to consistently evolve binary stars from formation to gravitational-wave detection. spops allows quick exploration of the interplay between stellar physics and black-hole spin dynamics.

[ascl:1411.015]
SPOTROD: Semi-analytic model for transits of spotted stars

SPOTROD is a model for planetary transits of stars with an arbitrary limb darkening law and a number of homogeneous, circular spots on their surface. It facilitates analysis of anomalies due to starspot eclipses, and is a free, open source implementation written in C with a Python API.

[ascl:1506.008]
SPRITE: Sparsity-based super-resolution algorithm

SPRITE (Sparse Recovery of InstrumenTal rEsponse) computes a well-resolved compact source image from several undersampled and noisy observations. The algorithm is based on sparse regularization; adding a sparse penalty in the recovery leads to far better accuracy in terms of ellipticity error, especially at low S/N.

[ascl:1806.013]
SpS: Single-pulse Searcher

The presence of human-made interference mimicking the behavior of celestial radio pulses is a major challenge when searching for radio pulses emitted on millisecond timescales by celestial radio sources such as pulsars and fast radio bursts due to the highly imbalanced samples. Single-pulse Searcher (SpS) reduces the presence of radio interference when processing standard output from radio single-pulse searches to produce diagnostic plots useful for selecting good candidates. The modular software allows modifications for specific search characteristics. LOTAAS Single-pulse Searcher (L-SpS) is an implementation of different features of the software (such as a machine-learning approach) developed for a particular study: the LOFAR Tied-Array All-Sky Survey (LOTAAS).

[ascl:1201.013]
SPS: SPIRE Photometer Simulator

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

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

[ascl:1411.025]
SPT Lensing Likelihood: South Pole Telescope CMB lensing likelihood code

The SPT lensing likelihood code, written in Fortran90, performs a Gaussian likelihood based upon the lensing potential power spectrum using a file from CAMB (ascl:1102.026) which contains the normalization required to get the power spectrum that the likelihood call is expecting.

[ascl:1705.005]
SPTCLASS: SPecTral CLASSificator code

SPTCLASS assigns semi-automatic spectral types to a sample of stars. The main code includes three spectral classification schemes: the first one is optimized to classify stars in the mass range of TTS (K5 or later, hereafter LATE-type scheme); the second one is optimized to classify stars in the mass range of IMTTS (F late to K early, hereafter Gtype scheme), and the third one is optimized to classify stars in the mass range of HAeBe (F5 or earlier, hereafter HAeBe scheme). SPTCLASS has an interactive module that allows the user to select the best result from the three schemes and analyze the input spectra.

[ascl:1303.015]
SSE: Single Star Evolution

SSE is a rapid single-star evolution (SSE) code; these analytical formulae cover all phases of evolution from the zero-age main-sequence up to and including remnant phases. It is valid for masses in the range 0.1-100 Msun and metallicity can be varied. The SSE package contains a prescription for mass loss by stellar winds. It also follows the evolution of rotational angular momentum for the star.

[submitted]
sslf: A simple spectral-line finder

sslf is designed to be a dead-simple, effective and useful spectral line finder for 1D data. It utilizes the continuous wavelet transform from scipy, which is a productive way to find even weak spectral lines.

[ascl:1807.032]
SSMM: Slotted Symbolic Markov Modeling for classifying variable star signatures

SSMM (Slotted Symbolic Markov Modeling) reduces time-domain stellar variable observations to classify stellar variables. The method can be applied to both folded and unfolded data, and does not require time-warping for waveform alignment. Written in Matlab, the performance of the supervised classification code is quantifiable and consistent, and the rate at which new data is processed is dependent only on the computational processing power available.

[ascl:1901.006]
ssos: Solar system objects detection pipeline

The ssos pipeline detects and identifies known and unknown Solar System Objects (SSOs) in astronomical images. ssos requires at least 3 images with overlapping field-of-views in the sky taken within a reasonable amount of time (*e.g.*, 2 hours, 1 night). SSOs are detected mainly by judging the apparent motion of all sources in the images. The pipeline serves as a wrapper for the SExtractor (ascl:1010.064) and SCAMP (ascl:1010.063) software suites and allows different source extraction strategies to be chosen. All sources in the images are subject to a highly configurable filter pipeline. ssos is a versatile, light-weight, and easy-to-use software for surveys or PI-observation campaigns lacking a dedicated SSO detection pipeline.

[ascl:1912.019]
STACKER: Stack sources in interferometric data

STACKER stacks sources in interferometric data, *i.e.*, averaging emission from different sources. The library allows stacking to be done directly on visibility data as well as in the image domain. The code is in format of a CASA (ascl:1107.013) task and implements uv- and image-stacking algorithms; it also provides several useful tasks for stacking related data processing. It allows introduction and stacking of random sources to estimate bias and noise, and also allows removal of a model of bright sources from the data.

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

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

[ascl:1801.003]
Stan: Statistical inference

Stan facilitates statistical inference at the frontiers of applied statistics and provides both a modeling language for specifying complex statistical models and a library of statistical algorithms for computing inferences with those models. These components are exposed through interfaces in environments such as R, Python, and the command line.

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

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

[ascl:1805.009]
STARBLADE: STar and Artefact Removal with a Bayesian Lightweight Algorithm from Diffuse Emission

STARBLADE (STar and Artefact Removal with a Bayesian Lightweight Algorithm from Diffuse Emission) separates superimposed point-like sources from a diffuse background by imposing physically motivated models as prior knowledge. The algorithm can also be used on noisy and convolved data, though performing a proper reconstruction including a deconvolution prior to the application of the algorithm is advised; the algorithm could also be used within a denoising imaging method. STARBLADE learns the correlation structure of the diffuse emission and takes it into account to determine the occurrence and strength of a superimposed point source.

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

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

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

[submitted]
StarburstPy: Python Wrapper for Starburst99

StarburstPy is a python wrapper for Starburst99 (ascl:1104.003). The code contains methods for setting all inputs, running Starburst99, and reading output data into python dictionaries.

[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:2004.009]
stardate: Measure precise stellar ages

stardate measures precise stellar ages by combining isochrone fitting with gyrochronology (rotation-based ages) to increase the precision of stellar ages on the main sequence. The best possible ages provided by stardate will be for stars with rotation periods, though ages can also be predicted for stars without rotation periods. stardate is an extension to isochrones that incorporates gyrochronology and the code reverts back to isochrones when no rotation period is provided.

[ascl:0011.001]
StarFinder: A code for stellar field analysis

Diolaiti, Emiliano; Bendinelli, Orazio; Bonaccini, Domenico; Close, Laird M.; Currie, Doug G.; Parmeggiani, Gianluigi

StarFinder is an IDL code for the deep analysis of stellar fields, designed for Adaptive Optics well-sampled images with high and low Strehl ratio. The Point Spread Function is extracted directly from the frame, to take into account the actual structure of the instrumental response and the atmospheric effects. The code is written in IDL language and organized in the form of a self-contained widget-based application, provided with a series of tools for data visualization and analysis. A description of the method and some applications to Adaptive Optics data are presented.

[ascl:1204.008]
StarFISH: For Inferring Star-formation Histories

StarFISH is a suite of programs designed to determine the star formation history (SFH) of a stellar population, given multicolor stellar photometry and a library of theoretical isochrones. It constructs a library of synthetic color-magnitude diagrams from the isochrones, which includes the effects of extinction, photometric errors and completeness, and binarity. A minimization routine is then used to determine the linear combination of synthetic CMDs that best matches the observed photometry. The set of amplitudes modulating each synthetic CMD describes the star formation history of the observed stellar population.

[ascl:1505.007]
Starfish: Robust spectroscopic inference tools

Starfish is a set of tools used for spectroscopic inference. It robustly determines stellar parameters using high resolution spectral models and uses Markov Chain Monte Carlo (MCMC) to explore the full posterior probability distribution of the stellar parameters. Additional potential applications include other types of spectra, such as unresolved stellar clusters or supernovae spectra.

[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:1108.006]
STARLIGHT: Spectral Synthesis Code

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

[ascl:1411.022]
Starlink Figaro: Starlink version of the Figaro data reduction software package

Shortridge, Keith; Meyerdierks, Horst; Currie, Malcolm J.; Davenhall, Clive; Jenness, Tim; Clayton, Martin

Starlink Figaro is an independently-maintained fork of Figaro (ascl:1203.013) that runs in the Starlink software environment (ascl:1110.012). It is a general-purpose data reduction package targeted mainly at optical/IR spectroscopy. It uses the NDF data format and the ADAM libraries for parameters and messaging.

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

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

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

[ascl:1406.020]
STARMAN: Stellar photometry and image/table handling

STARMAN is a stellar photometry package designed for the reduction of data from imaging systems. Its main components are crowded-field photometry programs, aperture photometry programs, a star finding program, and a CCD reduction program.

Image and table handling are served by a large number of programs which have a general use in photometry and other types of work. The package is a coherent whole, for use in the entire process of stellar photometry from raw images to the final standard-system magnitudes and their plotting as color-magnitude and color-color diagrams. It was distributed as part of the Starlink software collection (ascl:1110.012).

[ascl:1609.002]
StarPy: Quenched star formation history parameters of a galaxy using MCMC

Smethurst, R. J.; Lintott, C. J.; Simmons, B. D.; Schawinski, K.; Marshall, P. J.; Bamford, S.; Fortson, L.; Kaviraj, S.; Masters, K. L.; Melvin, T.; Nichol, R. C.; Skibba, R. A.; Willett, K. W.

StarPy derives the quenching star formation history (SFH) of a single galaxy through the Bayesian Markov Chain Monte Carlo method code *emcee* (ascl:1303.002). The sample function implements the emcee EnsembleSampler function for the galaxy colors input. Burn-in is run and calculated for the length specified before the sampler is reset and then run for the length of steps specified. StarPy provides the ability to use the look-up tables provided or creating your own.

[ascl:1810.005]
STARRY: Analytic computation of occultation light curves

Luger, Rodrigo; Agol, Eric; Foreman-Mackey, Daniel; Fleming, David P.; Lustig-Yaeger, Jacob; Deitrick, Russell

STARRY computes light curves for various applications in astronomy: transits and secondary eclipses of exoplanets, light curves of eclipsing binaries, rotational phase curves of exoplanets, light curves of planet-planet and planet-moon occultations, and more. By modeling celestial body surface maps as sums of spherical harmonics, STARRY does all this analytically and is therefore fast, stable, and differentiable. Coded in C++ but wrapped in Python, STARRY is easy to install and use.

[ascl:1107.008]
STARS: A Stellar Evolution Code

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

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

[ascl:1703.005]
starsense_algorithms: Performance evaluation of various star sensors

Sarpotdar, Mayuresh; Mathew, Joice; Sreejith, A. G.; Nirmal, K.; Ambily, S.; Prakash, Ajin; Safonova, Margarita; Murthy, Jayant

The Matlab starsense_algorithms package evaluates the performance of various star sensors through the implementation of centroiding, geometric voting and QUEST algorithms. The physical parameters of a star sensor are parametrized and by changing these parameters, performance estimators such as sky coverage, memory requirement, and timing requirements can be estimated for the selected star sensor.

[ascl:1805.010]
StarSmasher: Smoothed Particle Hydrodynamics code for smashing stars and planets

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle method that approximates a continuous fluid as discrete nodes, each carrying various parameters such as mass, position, velocity, pressure, and temperature. In an SPH simulation the resolution scales with the particle density; StarSmasher is able to handle both equal-mass and equal number-density particle models. StarSmasher solves for hydro forces by calculating the pressure for each particle as a function of the particle's properties - density, internal energy, and internal properties (e.g. temperature and mean molecular weight). The code implements variational equations of motion and libraries to calculate the gravitational forces between particles using direct summation on NVIDIA graphics cards. Using a direct summation instead of a tree-based algorithm for gravity increases the accuracy of the gravity calculations at the cost of speed. The code uses a cubic spline for the smoothing kernel and an artificial viscosity prescription coupled with a Balsara Switch to prevent unphysical interparticle penetration. The code also implements an artificial relaxation force to the equations of motion to add a drag term to the calculated accelerations during relaxation integrations. Initially called StarCrash, StarSmasher was developed originally by Rasio.

[ascl:1704.004]
STATCONT: Statistical continuum level determination method for line-rich sources

STATCONT determines the continuum emission level in line-rich spectral data by inspecting the intensity distribution of a given spectrum by using different statistical approaches. The sigma-clipping algorithm provides the most accurate continuum level determination, together with information on the uncertainty in its determination; this uncertainty is used to correct the final continuum emission level. In general, STATCONT obtains accuracies of < 10 % in the continuum determination, and < 5 % in most cases. The main products of the software are the continuum emission level, together with its uncertainty, and data cubes containing only spectral line emission, i.e. continuum-subtracted data cubes. STATCONT also includes the option to estimate the spectral index or variation of the continuum emission with frequency.

[ascl:1206.006]
statpl: Goodness-of-fit for power-law distributed data

statpl estimates the parameter of power-law distributed data and calculates goodness-of-fit tests for them. Many objects studied in astronomy follow a power-law distribution function (DF), for example the masses of stars or star clusters. Such data is often analyzed by generating a histogram and fitting a straight line to it. The parameters obtained in this way can be severely biased, and the properties of the underlying DF, such as its shape or a possible upper limit, are difficult to extract. statpl is an (effectively) bias-free estimator for the exponent and the upper limit.

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

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

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

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

[ascl:1505.009]
StellaR: Stellar evolution tracks and isochrones tools

stellaR accesses and manipulates publicly available stellar evolutionary tracks and isochrones from the Pisa low-mass database. It retrieves and plots the required calculations from CDS, constructs by interpolation tracks or isochrones of compositions different to the ones available in the database, constructs isochrones for age not included in the database, and extracts relevant evolutionary points from tracks or isochrones.

[ascl:1303.028]
Stellarics: Inverse Compton scattering from stellar heliospheres

Cosmic ray electrons scatter on the photon fields around stars, including the sun, to create gamma rays by the inverse Compton effect. Stellarics computes the spectrum and angular distribution of this emission. The software also includes general-purpose routines for inverse Compton scattering on a given electron spectrum, for example for interstellar or astrophysical source modelling.

[ascl:1901.012]
stellarWakes: Dark matter subhalo searches using stellar kinematic data

stellarWakes uses stellar kinematic data to search for dark matter (DM) subhalos through their gravitational perturbations to the stellar phase-space distribution.

[ascl:1907.018]
StePar: Inferring stellar atmospheric parameters using the EW method

StePar computes the stellar atmospheric parameters T_{eff}, log g, [Fe/H], and ξ of FGK-type stars using the Equivalent Width (*EW*) method. The code implements a grid of MARCS model atmospheres and uses the MOOG radiative transfer code (ascl:1202.009) and TAME (ascl:1503.003). StePar uses a Downhill Simplex minimization algorithm, running it twice for any given star, to compute the stellar atmospheric parameters.

[ascl:1809.014]
stepped_luneburg: Stacked-based ray tracing code to model a stepped Luneburg lens

stepped_luneburg investigates the scattered light properties of a Luneburg lens approximated as a series of concentric shells with discrete refractive indices. The optical Luneburg lens has promising applications for low-cost, continuous all-sky monitoring to obtain transit light curves of bright, nearby stars. This code implements a stack-based algorithm that tracks all reflected and refracted rays generated at each optical interface of the lens as described by Snell's law. The Luneburg lens model parameters, such as number of lens layers, the power-law that describes the refractive indices, the number of incident rays, and the initial direction of the incident wavefront can be altered to optimize lens performance. The stepped_luneburg module can be imported within the Python environment or used with scripting, and it is accompanied by two other modules, enc_int and int_map, that help the user to determine the resolving power of the lens and the strength of scattered light haloes for the purpose of quality assessment.

[ascl:1805.006]
StePS: Stereographically Projected Cosmological Simulations

StePS (Stereographically Projected Cosmological Simulations) compactifies the infinite spatial extent of the Universe into a finite sphere with isotropic boundary conditions to simulate the evolution of the large-scale structure. This eliminates the need for periodic boundary conditions, which are a numerical convenience unsupported by observation and which modifies the law of force on large scales in an unrealistic fashion. StePS uses stereographic projection for space compactification and naive O(N2) force calculation; this arrives at a correlation function of the same quality more quickly than standard (tree or P3M) algorithms with similar spatial and mass resolution. The N2 force calculation is easy to adapt to modern graphics cards, hence StePS can function as a high-speed prediction tool for modern large-scale surveys.

[ascl:1306.009]
STF: Structure Finder

STF is a general structure finder designed to find halos, subhaloes, and tidal debris in N-body simulations. The current version is designed to read in "particle data" (that is SPH N-body data), but a simple modification of the I/O can have it read grid data from Grid based codes.

This code has been updated and renamed to VELOCIraptor-STF (ascl:1911.020).

[submitted]
stginga: Ginga for STScI

stginga customizes Ginga to aid data analysis for the data supported by STScI (e.g., HST or JWST). For instance, it provides plugins and configuration files that understand HST and JWST data products.

[ascl:1810.014]
STiC: Stockholm inversion code

STiC is a MPI-parallel non-LTE inversion code for observed full-Stokes observations. The code processes lines from multiple atoms in non-LTE, including partial redistribution effects of scattered photons in angle and frequency of scattered photons (PRD), and can be used with model atmospheres that have a complex depth stratification without introducing artifacts.

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

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

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

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

Facilities offered include:

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

[ascl:1608.001]
Stingray: Spectral-timing software

Stingray is a spectral-timing software package for astrophysical X-ray (and more) data. The package merges existing efforts for a (spectral-)timing package in Python and is composed of a library of time series methods (including power spectra, cross spectra, covariance spectra, and lags); scripts to load FITS data files from different missions; a simulator of light curves and event lists that includes different kinds of variability and more complicated phenomena based on the impulse response of given physical events (e.g. reverberation); and a GUI to ease the learning curve for new users.

[ascl:1204.009]
STOKES: Modeling Radiative Transfer and Polarization

STOKES was designed to perform three-dimensional radiative transfer simulations for astronomical applications. The code also considers the polarization properties of the radiation. The program is based on the Monte-Carlo method and treats optical and ultraviolet polarization induced by scattering off free electrons or dust grains. Emission and scattering regions can be arranged in various geometries within the model space, the computed continuum and line spectra can be evaluated at different inclinations and azimuthal viewing angles.

[ascl:1708.005]
STools: IDL Tools for Spectroscopic Analysis

STools contains a variety of simple tools for spectroscopy, such as reading an IRAF-formatted (multispec) echelle spectrum in FITS, measuring the wavelength of the center of a line, Gaussian convolution, deriving synthetic photometry from an input spectrum, and extracting and interpolating a MARCS model atmosphere (standard composition).

[ascl:1702.009]
stream-stream: Stellar and dark-matter streams interactions

Stream-stream analyzes the interaction between a stellar stream and a disrupting dark-matter halo. It requires galpy (ascl:1411.008), NEMO (ascl:1010.051), and the usual common scientific Python packages.

[ascl:1702.010]
streamgap-pepper: Effects of peppering streams with many small impacts

streamgap-pepper computes the effect of subhalo fly-bys on cold tidal streams based on the action-angle representation of streams. A line-of-parallel-angle approach is used to calculate the perturbed distribution function of a given stream segment by undoing the effect of all impacts. This approach allows one to compute the perturbed stream density and track in any coordinate system in minutes for realizations of the subhalo distribution down to 10^5 Msun, accounting for the stream's internal dispersion and overlapping impacts. This code uses galpy (ascl:1411.008) and the streampepperdf.py galpy extension, which implements the fast calculation of the perturbed stream structure.

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

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

[ascl:1206.003]
STSDAS: IRAF Tools for Hubble Space Telescope data reduction

The Space Telescope Science Data Analysis System (STSDAS) is a software package for reducing and analyzing astronomical data. It is layered on top of IRAF and provides general-purpose tools for astronomical data analysis as well as routines specifically designed for HST data. In particular, STSDAS contains all the programs used for the calibration and reduction of HST data in the STScI post-observation processing pipelines.

[submitted]
stsynphot: synphot for HST and JWST

An extension to synphot (ascl:1811.001), stsynphot implements synthetic photometry package for HST and JWST support. The software constructs spectra from various grids of model atmosphere spectra, parameterized spectrum models, and atlases of stellar spectrophotometry. It also simulates observations specific to HST and JWST, computes photometric calibration parameters for any supported instrument mode, and plots instrument-specific sensitivity curves and calibration target spectra.

[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:1401.010]
SunPy: Python for Solar Physicists

SunPy is a community-developed free and open-source software package for solar physics and is an alternative to the SolarSoft data analysis environment. SunPy provides data structures for representing the most common solar data types (images, lightcurves, and spectra) and integration with the Virtual Solar Observatory (VSO) and the Heliophysics Event Knowledgebase (HEK) for data acquisition.

[ascl:1303.030]
Sunrise: Radiation transfer through interstellar dust

Sunrise is a Monte Carlo radiation transfer code for calculating absorption and scattering of light to study the effects of dust in hydrodynamic simulations of interacting galaxies. It uses an adaptive mesh refinement grid to describe arbitrary geometries of emitting and absorbing/scattering media, with spatial dynamical range exceeding 10^{4}; it can efficiently generate images of the emerging radiation at arbitrary points in space and spectral energy distributions of simulated galaxies run with the Gadget, Gasoline, Arepo, Enzo or ART codes. In addition to the monochromatic radiative transfer typically used by Monte Carlo codes, Sunrise can propagate a range of wavelengths simultaneously. This "polychromatic" algorithm gives significant improvements in efficiency and accuracy when spectral features are calculated.

[ascl:1105.007]
Sunspot Models

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

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

SuperBayeS is a package for fast and efficient sampling of supersymmetric theories. It uses Bayesian techniques to explore multidimensional SUSY parameter spaces and to compare SUSY predictions with observable quantities, including sparticle masses, collider observables, dark matter abundance, direct detection cross sections, indirect detection quantities etc. Scanning can be performed using Markov Chain Monte Carlo (MCMC) technology or even more efficiently by employing a new scanning technique called MultiNest (ascl:1109.006). which implements the nested sampling algorithm. Using MultiNest, a full 8-dimensional scan of the CMSSM takes about 12 hours on 10 2.4GHz CPUs. There is also an option for old-style fixed-grid scanning. A discussion forum for SuperBayeS is available.

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

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

[ascl:1609.019]
SuperBoL: Module for calculating the bolometric luminosities of supernovae

SuperBoL calculates the bolometric lightcurves of Type II supernovae using observed photometry; it includes three different methods for calculating the bolometric luminosity: quasi-bolometric, direct, and bolometric correction. SuperBoL propagates uncertainties in the input data through the calculations made by the code, allowing for error bars to be included in plots of the lightcurve.

[ascl:1507.002]
SUPERBOX: Particle-multi-mesh code to simulate galaxies

SUPERBOX is a particle-mesh code that uses moving sub-grids to track and resolve high-density peaks in the particle distribution and a nearest grid point force-calculation scheme based on the second derivatives of the potential. The code implements a fast low-storage FFT-algorithm and allows a highly resolved treatment of interactions in clusters of galaxies, such as high-velocity encounters between elliptical galaxies and the tidal disruption of dwarf galaxies, as sub-grids follow the trajectories of individual galaxies. SUPERBOX is efficient in that the computational overhead is kept as slim as possible and is also memory efficient since it uses only one set of grids to treat galaxies in succession.

[ascl:1511.001]
SuperFreq: Numerical determination of fundamental frequencies of an orbit

SuperFreq numerically estimates the fundamental frequencies and orbital actions of pre-computed orbital time series. It is an implementation of a version of the Numerical Analysis of Fundamental Frequencies close to that by Monica Valluri, which itself is an implementation of an algorithm first used by Jacques Laskar.

[ascl:1109.014]
Supernova Flux-averaging Likelihood Code

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

[ascl:1705.017]
supernovae: Photometric classification of supernovae

Supernovae classifies supernovae using their light curves directly as inputs to a deep recurrent neural network, which learns information from the sequence of observations. Observational time and filter fluxes are used as inputs; since the inputs are agnostic, additional data such as host galaxy information can also be included.

[ascl:1612.015]
Superplot: Graphical interface for plotting and analyzing data

Superplot calculates and plots statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space produced by codes such as MultiNest (ascl:1109.006), BAYES-X (ascl:1505.027), and PolyChord (ascl:1502.011). It offers a graphical interface for browsing a chain of many variables quickly and can produce numerous kinds of publication quality plots, including one- and two-dimensional profile likelihood, three-dimensional scatter plots, and confidence intervals and credible regions. Superplot can also save plots in PDF format, create a summary text file, and export a plot as a pickled object for importing and manipulating in a Python interpreter.

[ascl:1403.008]
SURF: Submm User Reduction Facility

SURF reduces data from the SCUBA instrument from the James Clerk Maxwell Telescope. Facilities are provided for reducing all the SCUBA observing modes including jiggle, scan and photometry modes. SURF uses the Starlink environment (ascl:1110.012).

[ascl:1809.007]
surfinBH: Surrogate final black hole properties for mergers of binary black holes

surfinBH predicts the final mass, spin and recoil velocity of the remnant of a binary black hole merger. Trained directly against numerical relativity simulations, these models are extremely accurate, reproducing the results of the simulations at the same level of accuracy as the simulations themselves. Fits such as these play a crucial role in waveform modeling and tests of general relativity with gravitational waves, performed by LIGO.

[ascl:1605.017]
Surprise Calculator: Estimating relative entropy and Surprise between samples

The Surprise is a measure for consistency between posterior distributions and operates in parameter space. It can be used to analyze either the compatibility of separately analyzed posteriors from two datasets, or the posteriors from a Bayesian update. The Surprise Calculator estimates relative entropy and Surprise between two samples, assuming they are Gaussian. The software requires the R package CompQuadForm to estimate the significance of the Surprise, and rpy2 to interface R with Python.

[ascl:1804.016]
surrkick: Black-hole kicks from numerical-relativity surrogate models

surrkick quickly and reliably extract recoils imparted to generic, precessing, black hole binaries. It uses a numerical-relativity surrogate model to obtain the gravitational waveform given a set of binary parameters, and from this waveform directly integrates the gravitational-wave linear momentum flux. This entirely bypasses the need of fitting formulae which are typically used to model black-hole recoils in astrophysical contexts.

[ascl:1208.012]
Swarm-NG: Parallel n-body Integrations

Dindar, Saleh; Ford, Eric B.; Juric, Mario; Young, In Yeo; Gao, Jianwei; Boley, Aaron C.; Nelson, Benjamin; Peters, Jorg

Swarm-NG is a C++ library for the efficient direct integration of many n-body systems using highly-parallel Graphics Processing Units (GPU). Swarm-NG focuses on many few-body systems, e.g., thousands of systems with 3...15 bodies each, as is typical for the study of planetary systems; the code parallelizes the simulation, including both the numerical integration of the equations of motion and the evaluation of forces using NVIDIA's "Compute Unified Device Architecture" (CUDA) on the GPU. Swarm-NG includes optimized implementations of 4th order time-symmetrized Hermite integration and mixed variable symplectic integration as well as several sample codes for other algorithms to illustrate how non-CUDA-savvy users may themselves introduce customized integrators into the Swarm-NG framework. Applications of Swarm-NG include studying the late stages of planet formation, testing the stability of planetary systems and evaluating the goodness-of-fit between many planetary system models and observations of extrasolar planet host stars (e.g., radial velocity, astrometry, transit timing). While Swarm-NG focuses on the parallel integration of many planetary systems,the underlying integrators could be applied to a wide variety of problems that require repeatedly integrating a set of ordinary differential equations many times using different initial conditions and/or parameter values.

[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:1303.001]
SWIFT: A solar system integration software package

SWIFT follows the long-term dynamical evolution of a swarm of test particles in the solar system. The code efficiently and accurately handles close approaches between test particles and planets while retaining the powerful features of recently developed mixed variable symplectic integrators. Four integration techniques are included: Wisdom-Holman Mapping; Regularized Mixed Variable Symplectic (RMVS) method; fourth order T+U Symplectic (TU4) method; and Bulirsch-Stoer method. The package is designed so that the calls to each of these look identical so that it is trivial to replace one with another. Complex data manipulations and results can be analyzed with the graphics packace SwiftVis.

[ascl:1805.020]
SWIFT: SPH With Inter-dependent Fine-grained Tasking

SWIFT runs cosmological simulations on peta-scale machines for solving gravity and SPH. It uses the Fast Multipole Method (FMM) to calculate gravitational forces between nearby particles, combining these with long-range forces provided by a mesh that captures both the periodic nature of the calculation and the expansion of the simulated universe. SWIFT currently uses a single fixed but time-variable softening length for all the particles. Many useful external potentials are also available, such as galaxy haloes or stratified boxes that are used in idealised problems. SWIFT implements a standard LCDM cosmology background expansion and solves the equations in a comoving frame; equations of state of dark-energy evolve with scale-factor. The structure of the code allows implementation for modified-gravity solvers or self-interacting dark matter schemes to be implemented. Many hydrodynamics schemes are implemented in SWIFT and the software allows users to add their own.

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

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

[ascl:1606.001]
SWOC: Spectral Wavelength Optimization Code

SWOC (Spectral Wavelength Optimization Code) determines the wavelength ranges that provide the optimal amount of information to achieve the required science goals for a spectroscopic study. It computes a figure-of-merit for different spectral configurations using a user-defined list of spectral features, and, utilizing a set of flux-calibrated spectra, determines the spectral regions showing the largest differences among the spectra.

[ascl:1707.007]
swot: Super W Of Theta

SWOT (Super W Of Theta) computes two-point statistics for very large data sets, based on “divide and conquer” algorithms, mainly, but not limited to data storage in binary trees, approximation at large scale, parellelization (open MPI), and bootstrap and jackknife resampling methods “on the fly”. It currently supports projected and 3D galaxy auto and cross correlations, galaxy-galaxy lensing, and weighted histograms.

[ascl:1904.001]
sxrbg: ROSAT X-Ray Background Tool

The ROSAT X-Ray Background Tool (sxrbg) calculates the average X-ray background count rate and statistical uncertainty in each of the six standard bands of the ROSAT All-Sky Survey (RASS) diffuse background maps (R1, R2, R4, R5, R6, R7) for a specified astronomical position and a search region consisting of either a circle with a specified radius or an annulus with specified inner and outer radii centered on the position. The values returned by the tool are in units of 10^-6 counts/second/arcminute^2. sxrbg can also create a count-rate-based spectrum file which can be used with XSpec (ascl:9910.005) to calculate fluxes and offers support for counts statistics (cstat), an alternative method for generating a background spectrum. HEASoft (ascl:1408.004) is a prerequisite for building. The code is in the public domain.

[ascl:1806.019]
SYGMA: Modeling stellar yields for galactic modeling

SYGMA (Stellar Yields for Galactic Modeling Applications) follows the ejecta of simple stellar populations as a function of time to model the enrichment and feedback from simple stellar populations. It is the basic building block of the galaxy code One-zone Model for the Evolution of GAlaxies (OMEGA, ascl:1806.018) and is part of the NuGrid Python Chemical Evolution Environment (NuPyCEE, ascl:1610.015). Stellar yields of AGB and massive stars are calculated with the same nuclear physics and are provided by the NuGrid collaboration.

[ascl:1308.008]
SYN++: Standalone SN spectrum synthesis

SYN++ is a standalone SN spectrum synthesis program. It is a rewrite of the original SYNOW (ascl:1010.055) code in modern C++. It offers further enhancements, a new structured input control file format, and the atomic data files have been repackaged and are more complete than those of SYNOW.

[ascl:1308.007]
SYNAPPS: Forward-modeling of supernova spectroscopy data sets

SYNAPPS is a spectrum fitter embedding a highly parameterized synthetic SN spectrum calculation within a parallel asynchronous optimizer. This open-source code is aimed primarily at the problem of systematically interpreting large sets of SN spectroscopy data.

[ascl:1302.014]
SYNMAG Photometry: Catalog-level Matched Colors of Extended Sources

Bundy, Kevin; Hogg, David W.; Higgs, Tim D.; Nichol, Robert C.; Yasuda, Naoki; Masters, Karen L.; Lang, Dustin; Wake, David A.

SYNMAG is a tool for producing synthetic aperture magnitudes to enable fast matched photometry at the catalog level without reprocessing imaging data. Aperture magnitudes are the most widely tabulated flux measurements in survey catalogs; obtaining reliable, matched photometry for galaxies imaged by different observatories represents a key challenge in the era of wide-field surveys spanning more than several hundred square degrees. Methods such as flux fitting, profile fitting, and PSF homogenization followed by matched-aperture photometry are all computationally expensive. An alternative solution called "synthetic aperture photometry" exploits galaxy profile fits in one band to efficiently model the observed, point-spread-function-convolved light profile in other bands and predict the flux in arbitrarily sized apertures.

[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:1811.001]
synphot: Synthetic photometry using Astropy

Synphot simulates photometric data and spectra, observed or otherwise. It can incorporate the user's filters, spectra, and data, and use of a pre-defined standard star (Vega), bandpass, or extinction law. synphot can also construct complicated composite spectra using different models, simulate observations, and compute photometric properties such as count rate, effective wavelength, and effective stimulus. It can manipulate a spectrum by, for example, applying redshift, or normalize it to a given flux value in a given bandpass. Synphot can also sample a spectrum at given wavelengths, plot a quick-view of a spectrum, and perform repetitive operations such as simulating the observations of multiple type of sources through multiple bandpasses. Synphot understands Astropy (ascl:1304.002) models and units and is an Astropy affiliated package.

[ascl:1109.022]
Synspec: General Spectrum Synthesis Program

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

[ascl:1212.010]
Synth3: Non-magnetic spectrum synthesis code

Synth3 is a non-magnetic spectrum synthesis code. It works with model atmospheres in Kurucz format and VALD Sf line lists and features element stratification, molecular equilibrium and individual microturbulence for each line. Disk integration can be done with s3di which is included in the archive. Synth3 computes spectra emergent from the stellar atmospheres with a depth-dependent chemical composition if depth-dependent abundance is provided in the input model atmosphere file.

[ascl:1210.018]
Systemic Console: Advanced analysis of exoplanetary data

Systemic Console is a tool for advanced analysis of exoplanetary data. It comprises a graphical tool for fitting radial velocity and transits datasets and a library of routines for non-interactive calculations. Among its features are interactive plotting of RV curves and transits, combined fitting of RV and transit timing (primary and secondary), interactive periodograms and FAP estimation, and bootstrap and MCMC error estimation. The console package includes public radial velocity and transit data.

[ascl:1304.018]
SZpack: Computation of Sunyaev-Zeldovich (SZ) signals

SZpack is a numerical library which allows fast and precise computation of the Sunyaev-Zeldovich (SZ) signal for hot, moving clusters of galaxies. Both explicit numerical integration as well as approximate representation of the SZ signals can be obtained. Variations of the electron temperature and bulk velocity along the line-of-sight can be included. SZpack allows very fast and precise (<~0.001% at frequencies h nu <~ 30kT_g and electron temperature kTe ~ 75 keV) computation and its accuracy practically eliminates uncertainties related to more expensive numerical evaluation of the Boltzmann collision term. It furthermore cleanly separates kinematic corrections from scattering physics, effects that previously have not been clarified.

[ascl:1511.006]
T-Matrix: Codes for Computing Electromagnetic Scattering by Nonspherical and Aggregated Particles

The T-Matrix package includes codes to compute electromagnetic scattering by homogeneous, rotationally symmetric nonspherical particles in fixed and random orientations, randomly oriented two-sphere clusters with touching or separated components, and multi-sphere clusters in fixed and random orientations. All codes are written in Fortran-77. LAPACK-based, extended-precision, Gauss-elimination- and NAG-based, and superposition codes are available, as are double-precision superposition, parallelized double-precision, double-precision Lorenz-Mie codes, and codes for the computation of the coefficients for the generalized Chebyshev shape.

[ascl:1609.001]
T-PHOT: PSF-matched, prior-based, multiwavelength extragalactic deconfusion photometry

Merlin, E.; Fontana, A.; Ferguson, H. C.; Dunlop, J. S.; Elbaz, D.; Bourne, N.; Bruce, V. A.; Buitrago, F.; Castellano, M.; Schreiber, C.; Grazian, A.; McLure, R. J.; Okumura, K.; Shu, X.; Wang, T.; Amorín, R.; Boutsia, K.; Cappelluti, N.; Comastri, A.; Derriere, S.; Faber, S. M.; Santini, P.

T-PHOT extracts accurate photometry from low-resolution images of extragalactic fields, where the blending of sources can be a serious problem for accurate and unbiased measurement of fluxes and colors. It gathers data from a high-resolution image of a region of the sky and uses the source positions and morphologies to obtain priors for the photometric analysis of the lower resolution image of the same field. T-PHOT handles different types of datasets as input priors, including a list of objects that will be used to obtain cutouts from the real high-resolution image, a set of analytical models (as .fits stamps), and a list of unresolved, point-like sources, useful for example for far-infrared wavelength domains. T-PHOT yields accurate estimations of fluxes within the intrinsic uncertainties of the method when systematic errors are taken into account (which can be done using a flagging code given in the output), and handles multiwavelength optical to far-infrared image photometry. T-PHOT was developed as part of the ASTRODEEP project (www.astrodeep.eu).

[ascl:1906.008]
T-RECS: Tiered Radio Extragalactic Continuum Simulation

Bonaldi, Anna; Bonato, Matteo; Galluzzi, Vincenzo; Harrison, Ian; Massardi, Marcella; Kay, Scott; De Zotti, Gianfranco; Brown, Michael L.

T-RECS produces radio sources catalogs with user-defined frequencies, area and depth. It models two main populations of radio galaxies, Active Galactic Nuclei (AGNs) and Star-Forming Galaxies (SFGs), and corresponding sub-populations. T-RECS is not computationally demanding and can be run multiple times, using the same catalog inputs, to project the simulated sky onto different fields.

[ascl:1403.014]
T(dust) as a function of sSFR

This IDL code returns the dust temperature of a galaxy from its redshift, SFR and stellar mass; it can also predict the observed monochromatic fluxes of the galaxy. These monochromatic fluxes correspond to those of a DH SED template with the appropriate dust temperature and the appropriate normalization. Dust temperatures and fluxes predictions are only valid and provided in the redshift, stellar mass, SSFR and wavelength ranges 0 < z < 2.5, Mstar> 10^10 Msun, 10^-11 < SSFR[yr-1]< 10^-7 and 30um < lambda_rest < 2mm.

[ascl:1210.006]
TA-DA: A Tool for Astrophysical Data Analysis

TA-DA is a pre-compiled IDL widget-based application which greatly simplifies and improves the analysis of stellar photometric data in comparison with theoretical models and allows the derivation of stellar parameters from multi-band photometry. It is flexible and can address a number of problems, from the interpolation of stellar models or sets of stellar physical parameters in general to the computation of synthetic photometry in arbitrary filters or units. It also analyzes observed color-magnitude diagrams and allows a Bayesian derivation of stellar parameters (and extinction) based on multi-band data.

[ascl:1303.010]
TAC-maker: Transit Analytical Curve maker

TAC-maker allows for rapid and interactive calculation of synthetic planet transits by numerical computations of the integrals, allowing the use of an arbitrary limb-darkening law of the host star. This advantage together with the practically arbitrary precision of the calculations makes the code a valuable tool for the continuously increasing photometric precision of ground-based and space observations.

[ascl:1512.020]
TACT: The Action Computation Tool

The Action Computation Tool (TACT) tests methods for estimating actions, angles and frequencies of orbits in both axisymmetric and triaxial potentials, including general spherical potentials, analytic potentials (Isochrone and Harmonic oscillator), axisymmetric Stackel fudge, average generating function from orbit (AvGF), and others. It is written in C++; code is provided to compile the routines into a Python library. TM (ascl:1512.014) and LAPACK are required to access some features.

[ascl:1602.013]
TailZ: Redshift distributions estimator of photometric samples of galaxies

TailZ estimates redshift distributions of photometric samples of galaxies selected photometrically given a subsample with measured spectroscopic redshifts. The approach uses a non-parametric Voronoi tessellation density estimator to interpolate the galaxy distribution in the redshift and photometric color space. The Voronoi tessellation estimator performs well at reconstructing the tails of the redshift distribution of individual galaxies and gives unbiased estimates of the first and second moments.

[submitted]
taktent: A Python framework for agent-based simulations of SETI observations

This Python package allows the user to setup and run an agent-based simulation of a SETI survey. The package allows the creation of a population of observing and transmitting civilisations. Each transmitter and observer conducts their activities according to an input strategy. The success of observers and transmitters can then be recorded, and multiple simulations can be run for Monte Carlo Realisation.

This package is therefore a flexible framework in which to simulate and test different SETI strategies, both as an Observer and as a Transmitter. It is primarily designed with radio SETI in mind, but is sufficiently flexible to simulate all forms of electromagnetic SETI, and potentially neutrino and gravitational wave SETI.

[ascl:1202.004]
TALYS: Nuclear Reaction Simulator

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

[ascl:1503.003]
TAME: Tool for Automatic Measurement of Equivalent-width

TAME measures the equivalent width (EWs) in high-resolution spectra. Written by IDL, TAME provides the EWs of spectral lines by profile fitting in an automatic or interactive mode and is reliable for measuring EWs in a spectrum with a spectral resolution of R ≳ 20000. It offers an interactive mode for more flexible measurement of the EW and a fully automatic mode that can simultaneously measure the EWs for a large set of lines.

[ascl:1912.018]
Tangos: Framework and web interface for database-driven analysis of numerical structure formation simulations

Tangos builds databases (along the lines of Eagle or MultiDark) for cosmological and zoom simulations. Its

modular system generates and queries databases. It is designed to store and manage results from a user's own analysis code, provides web and python interfaces, and allows users to construct science-focused queries, including across entire merger trees, without requiring knowledge of SQL. Tangos manages the process of populating the database with science data, including auto-parallelizing the analysis. It can be customized to work with multiple python modules such as pynbody (ascl:1305.002) or yt (ascl:1011.022) to process raw simulation data; it defaults to using SQLite, but allows use of other databases as the underlying store through the use of SQLAlchemy.

[ascl:2004.002]
Tangra: Software for video photometry and astrometry

Tangra performs scientific grade data reduction of GPS time-tagged video observations, including reduction of stellar occultation light curves and astrometry of close flybys of Near Earth Objects. It offers Dark and Flat frame image correction, PSF and aperture photometry, multiple methods for deriving a background as well as extensibility via add-ins. Tangra is actively developed for Windows and the current version of the software supports UCAC2, UCAC3, UCAC4, NOMAD, PPMXL and Gaia DR2 star catalogues for astrometry. The software can perform motion-fitting for fast objects and derive a mini-normal astrometric positions. The supported video file formats are AVI, SER, ADV and AAV. Tangra can be also used with observations recorded as a sequence of FITS files. There are also versions for Linux and OS-X with more limited functionality.

[ascl:1306.007]
Tapir: A web interface for transit/eclipse observability

Tapir is a set of tools, written in Perl, that provides a web interface for showing the observability of periodic astronomical events, such as exoplanet transits or eclipsing binaries. The package provides tools for creating finding charts for each target and airmass plots for each event. The code can access target lists that are stored on-line in a Google spreadsheet or in a local text file.

[ascl:1402.018]
TARDIS: Temperature And Radiative Diffusion In Supernovae

TARDIS creates synthetic spectra for supernova ejecta and is sufficiently fast to allow exploration of the complex parameter spaces of models for SN ejecta. TARDIS uses Monte Carlo methods to obtain a self-consistent description of the plasma state and to compute a synthetic spectrum. It is written in Python with a modular design that facilitates the implementation of a range of physical approximations that can be compared to assess both accuracy and computational expediency; this allows users to choose a level of sophistication appropriate for their application.

[ascl:2006.019]
TATOO : Tidal-chronology Age TOOl

TATOO (Tidal-chronology Age TOOl) estimates the age of massive close-in planetary systems, even those subject to tidal spin-up, using the systems' observed properties: the mass of the planet and the star, stellar rotational, and planetary orbital periods. It can also be used as a classical gyrochronological tool and offers first order correction of the impact of tidal interaction on gyrochronology.

[ascl:2006.007]
TATTER: Two-sAmple TesT EstimatoR

TATTER (Two-sAmple TesT EstimatoR) performs two-sample hypothesis test. The two-sample hypothesis test is concerned with whether distributions p(x) and q(x) are different on the basis of finite samples drawn from each of them. This ubiquitous problem appears in a legion of applications, ranging from data mining to data analysis and inference. This implementation can perform the Kolmogorov-Smirnov test (for one-dimensional data only), Kullback-Leibler divergence, and Maximum Mean Discrepancy (MMD) test. The module performs a bootstrap algorithm to estimate the null distribution and compute p-value.

[ascl:1305.014]
TAU: 1D radiative transfer code for transmission spectroscopy of extrasolar planet atmospheres

TAU is a 1D line-by-line radiative transfer code for modeling transmission spectra of close-in extrasolar planets. The code calculates the optical path through the planetary atmosphere of the radiation from the host star and quantifies the absorption due to the modeled composition in a transmission spectrum of transit depth as a function of wavelength. The code is written in C++ and is parallelized using OpenMP.

[ascl:1807.024]
TBI: Three-Body Integration

Three-Body Integration performs numerical n-body simulations for mapping conditions for close approaches for the relevant parameter space of configurations and mass values of two white dwarfs and a third star. Low tertiary masses of 0.1M⊙ can be studied, and the collision probability can be estimated with good confidence for the case of nearly equal mass white dwarfs.

[ascl:1505.031]
TEA: Thermal Equilibrium Abundances

TEA (Thermal Equilibrium Abundances) calculates gaseous molecular abundances under thermochemical equilibrium conditions. Given a single T,P point or a list of T,P pairs (the thermal profile of an atmosphere) and elemental abundances, TEA calculates mole fractions of the desired molecular species. TEA uses 84 elemental species and thermodynamical data for more then 600 gaseous molecular species, and can adopt any initial elemental abundances.

[ascl:1405.002]
TelFit: Fitting the telluric absorption spectrum

TelFit calculates the best-fit telluric absorption spectrum in high-resolution optical and near-IR spectra. The best-fit model can then be divided out to remove the telluric contamination. Written in Python, TelFit is essentially a wrapper to LBLRTM, the Line-By-Line Radiative Transfer Model, and simplifies the process of generating a telluric model.

[ascl:1509.002]
Tempo: Pulsar timing data analysis

Nice, D; Demorest, P.; Stairs, I.; Manchester, R.; Taylor, J.; Peters, W.; Weisberg, J.; Irwin, A.; Wex, N.; Huang, Y.

Tempo analyzes pulsar timing data. Pulse times of arrival (TOAs), pulsar model parameters, and coded instructions are read from one or more input files. The TOAs are fitted by a pulse timing model incorporating transformation to the solar-system barycenter, pulsar rotation and spin-down and, where necessary, one of several binary models. Program output includes parameter values and uncertainties, residual pulse arrival times, chi-squared statistics, and the covariance matrix of the model. In prediction mode, ephemerides of pulse phase behavior (in the form of polynomial expansions) are calculated from input timing models. Tempo is the basis for the Tempo2 (ascl:1210.015) code.

[ascl:1210.015]
Tempo2: Pulsar Timing Package

Tempo2 is a pulsar timing package developed to be used both for general pulsar timing applications and also for pulsar timing array research in which data-sets from multiple pulsars need to be processed simultaneously. It was initially developed by George Hobbs and Russell Edwards as part of the Parkes Pulsar Timing Array project. Tempo2 is based on the original Tempo (ascl:1509.002) code and can be used (from the command-line) in a similar fashion. It is very versatile and can be extended by plugins.

[ascl:2003.001]
TESS-Point: High precision TESS pointing tool

Burke, Christopher J.; Levine, Alan; Fausnaugh, Michael; Vanderspek, Roland; Barclay, Thomas; Libby-Roberts, Jessica E.; Morris, Brett; Sipocz, Brigitta; Owens, Martin; Feinstein, Adina D.; Camacho, Joao

TESS-Point converts astronomical target coordinates given in right ascension and declination to detector pixel coordinates for the MIT-led NASA Transiting Exoplanet Survey Satellite (TESS) spacecraft. The program can also provide detector pixel coordinates for a star by TESS input catalog identifier number and common astronomical name. Tess-point outputs the observing sector number, camera number, detector number, and pixel column and row.

[ascl:1611.002]
tf_unet: Generic convolutional neural network U-Net implementation in Tensorflow

tf_unet mitigates radio frequency interference (RFI) signals in radio data using a special type of Convolutional Neural Network, the U-Net, that enables the classification of clean signal and RFI signatures in 2D time-ordered data acquired from a radio telescope. The code is not tied to a specific segmentation and can be used, for example, to detect radio frequency interference (RFI) in radio astronomy or galaxies and stars in widefield imaging data. This U-Net implementation can outperform classical RFI mitigation algorithms.

[ascl:1505.019]
TFIT: Mixed-resolution data set photometry package

Laidler, Victoria G.; Papovich, Casey; Grogin, Norman A.; Idzi, Rafal; Dickinson, Mark; Ferguson, Henry C.; Hilbert, Bryan; Clubb, Kelsey; Ravindranath, Swara

TFIT measures galaxy photometry using prior knowledge of sources in a deep, high‐resolution image (HRI) to improve photometric measurements of objects in a corresponding low‐resolution image (LRI) of the same field, usually at a different wavelength. For background‐limited data, this technique produces optimally weighted photometry that maximizes signal‐to‐noise ratio (S/N). For objects not significantly detected in the low‐resolution image, it provides useful and quantitative information for setting upper limits.

This code is no longer updated and has been superseded by T-PHOT (ascl:1609.001).

[ascl:1303.012]
TGCat: Chandra Transmission Grating Catalog and Archive

TGCat is an archive of Chandra transmission grating spectra and a suite of software for processing such data. Users can browse and categorize Chandra gratings observations quickly and easily, generate custom plots of resulting response corrected spectra on-line without the need for special software and download analysis ready products from multiple observations in one convenient operation. Data processing for the catalog is done with a suite of ISIS/S-Lang scripts; the software is available for download. These ISIS scripts wrap and call CIAO tools for reprocessing from "Level 1" (acis_process_events or hrc_process_events) through "Level 2" (binned spectra, via tg_resolve_events and tgextract), compute responses (grating "RMFs" and "ARFs", via mkgrmf and mkgarf), and make summary plots.

[ascl:1905.018]
THALASSA: Orbit propagator for near-Earth and cislunar space

THALASSA (Tool for High-Accuracy, Long-term Analyses for SSA) propagates orbits for bodies in the Earth-Moon-Sun system. Written in Fortran, it integrates either Newtonian equations in Cartesian coordinates or regularized equations of motion with the LSODAR (Livermore Solver for Ordinary Differential equations with Automatic Root-finding). THALASSA is a command-line tool; the repository also includes some Python3 scripts to perform batch propagations.

[ascl:1602.010]
The Cannon: Data-driven method for determining stellar parameters and abundances from stellar spectra

The Cannon is a data-driven method for determining stellar labels (physical parameters and chemical abundances) from stellar spectra in the context of vast spectroscopic surveys. It fits for the spectral model given training spectra and labels, with the polynomial order for the spectral model decided by the user, infers labels for the test spectra, and provides diagnostic output for monitoring and evaluating the process. It offers SNR-independent continuum normalization, performs well at lower signal-to-noise, and is very accurate.

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

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

[ascl:1906.004]
The Exo-Striker: Transit and radial velocity interactive fitting tool for orbital analysis and N-body simulations

The Exo-Striker analyzes exoplanet orbitals, performs N-body simulations, and models the RV stellar reflex motion caused by dynamically interacting planets in multi-planetary systems. It offers a broad range of tools for detailed analysis of transit and Doppler data, including power spectrum analysis for Doppler and transit data; Keplerian and dynamical modeling of multi-planet systems; MCMC and nested sampling; Gaussian Processes modeling; and a long-term stability check of multi-planet systems. The Exo-Striker can also analyze Mean Motion Resonance (MMR) analysis, create fast fully interactive plots, and export ready-to-use LaTeX tables with best-fit parameters, errors, and statistics. It combines Fortran efficiency and Python flexibility and is cross-platform compatible (MAC OS, Linux, Windows). The tool relies on a number of open-source packages, including RVmod engine, emcee (ascl:1303.002), batman (ascl:1510.002), celerite (ascl:1709.008), and dynesty (ascl:1809.013).

[ascl:1405.003]
The Hammer: An IDL Spectral Typing Suite

The Hammer can classify spectra in a variety of formats with targets spanning the MK spectral sequence. It processes a list of input spectra by automatically estimating each object's spectral type and measuring activity and metallicity tracers in late type stars. Once automatic processing is complete, an interactive interface allows the user to manually tweak the final assigned spectral type through visual comparison with a set of templates.

[ascl:1701.001]
The Joker: A custom Monte Carlo sampler for binary-star and exoplanet radial velocity data

Given sparse or low-quality radial-velocity measurements of a star, there are often many qualitatively different stellar or exoplanet companion orbit models that are consistent with the data. The consequent multimodality of the likelihood function leads to extremely challenging search, optimization, and MCMC posterior sampling over the orbital parameters. The Joker is a custom-built Monte Carlo sampler that can produce a posterior sampling for orbital parameters given sparse or noisy radial-velocity measurements, even when the likelihood function is poorly behaved. The method produces correct samplings in orbital parameters for data that include as few as three epochs. The Joker can therefore be used to produce proper samplings of multimodal pdfs, which are still highly informative and can be used in hierarchical (population) modeling.

[ascl:1407.001]
The Starfish Diagram: Statistical visualization tool

The Starfish Diagram is a statistical visualization tool that simultaneously displays the properties of an individual and its parent sample through a series of histograms. The code is useful for large datasets for which one needs to understand the standing or significance of a single entry.

[ascl:1604.008]
The Tractor: Probabilistic astronomical source detection and measurement

The Tractor optimizes or samples from models of astronomical objects. The approach is generative: given astronomical sources and a description of the image properties, the code produces pixel-space estimates or predictions of what will be observed in the images. This estimate can be used to produce a likelihood for the observed data given the model: assuming the model space actually includes the truth (it doesn’t, in detail), then if we had the optimal model parameters, the predicted image would differ from the actually observed image only by noise. Given a noise model of the instrument and assuming pixelwise independent noise, the log-likelihood is the negative chi-squared difference: (image - model) / noise.

[ascl:1706.008]
the-wizz: Clustering redshift estimation code

the-wizz clusters redshift estimates for any photometric unknown sample in a survey. The software is composed of two main parts: a pair finder and a pdf maker. The pair finder finds spatial pairs and stores the indices of all closer pairs around target reference objects in an output HDF5 data file. Users then query this data file using the indices of their unknown sample to produce an output clustering-z.

[ascl:1308.013]
THELI GUI: Optical, near- & mid-infrared imaging data reduction

THELI is an easy-to-use, end-to-end pipeline for the reduction of any optical, near-IR and mid-IR imaging data. It combines a variety of processing algorithms and third party software into a single, homogeneous tool. Over 90 optical and infrared instruments at observatories world-wide are pre-configured; more can be added by the user. The code's online appendix contains three walk-through examples using public data (optical, near-IR and mid-IR) and additional online documentation is available for training and troubleshooting.

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

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

[ascl:1711.016]
Thindisk: Protoplanetary disk model

Thindisk computes the line emission from a geometrically thin protoplanetary disk. It creates a datacube in FITS format that can be processed with a data reduction package (such as GILDAS, ascl:1305.010) to produce synthetic images and visibilities. These synthetic data can be compared with observations to determine the properties (e.g. central mass or inclination) of an observed disk. The disk is assumed to be in Keplerian rotation at a radius lower than the centrifugal radius (which can be set to a large value, for a purely Keplerian disk), and in infall with rotation beyond the centrifugal radius.

[ascl:1807.010]
THOR: Global Circulation Model for planetary atmospheres

THOR solves the three-dimensional nonhydrostatic Euler equations. The code implements an icosahedral grid for the poles where converging meridians lead to increasingly smaller time steps; irregularities in the grid are smoothed using spring dynamics. THOR is designed to run on graphics processing units (GPUs) and is part of the open-source Exoclimes Simulation Platform.

[ascl:1212.014]
Thrust: Productivity-Oriented Library for CUDA

Thrust is a parallel algorithms library which resembles the C++ Standard Template Library (STL). Thrust's high-level interface greatly enhances programmer productivity while enabling performance portability between GPUs and multicore CPUs. Interoperability with established technologies (such as CUDA, TBB, and OpenMP) facilitates integration with existing software.

[ascl:1609.021]
TIDEV: Tidal Evolution package

TIDEV (Tidal Evolution package) calculates the evolution of rotation for tidally interacting bodies using Efroimsky-Makarov-Williams (EMW) formalism. The package integrates tidal evolution equations and computes the rotational and dynamical evolution of a planet under tidal and triaxial torques. TIDEV accounts for the perturbative effects due to the presence of the other planets in the system, especially the secular variations of the eccentricity. Bulk parameters include the mass and radius of the planet (and those of the other planets involved in the integration), the size and mass of the host star, the Maxwell time and Andrade's parameter. TIDEV also calculates the time scale that a planet takes to be tidally locked as well as the periods of rotation reached at the end of the spin-orbit evolution.

[ascl:1206.012]
Time Utilities

Time Utilities are software tools that, in principal, allow one to calculate BJD to a precision of 1 μs for any target from anywhere on Earth or from any spacecraft. As the quality and quantity of astrophysical data continue to improve, the precision with which certain astrophysical events can be timed becomes limited not by the data themselves, but by the manner, standard, and uniformity with which time itself is referenced. While some areas of astronomy (most notably pulsar studies) have required absolute time stamps with precisions of considerably better than 1 minute for many decades, recently new areas have crossed into this regime. In particular, in the exoplanet community, we have found that the (typically unspecified) time standards adopted by various groups can differ by as much as a minute. Left uncorrected, this ambiguity may be mistaken for transit timing variations and bias eccentricity measurements. We recommend using BJD_TDB, the Barycentric Julian Date in the Barycentric Dynamical Time standard for any astrophysical event. The BJD_TDB is the most practical absolute time stamp for extraterrestrial phenomena, and is ultimately limited by the properties of the target system. We compile a general summary of factors that must be considered in order to achieve timing precisions ranging from 15 minutes to 1 μs, and provide software for download and online webapps for use.

[submitted]
Time-domain astronomy sandbox

Time-domain astronomy sandbox consists in a series of classes to simulate and process time-domain astronomy data products in Python. The code was originally developed to model Fast Radio Burst (FRB) and Radio Frequency Interference (RFI), and evaluate different RFI mitigation methods and their effect on FRB search.

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

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

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

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

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

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

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

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

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

[ascl:1208.008]
TiRiFiC: Tilted Ring Fitting Code

Tilted Ring Fitting Code (TiRiFiC) is a prototype computer program to construct simulated (high-resolution) astronomical spectroscopic 3d-observations (data cubes) of simple kinematical and morphological models of rotating (galactic) disks. It is possible to automatically optimize the parameterizations of constructed model disks to fit spectroscopic (3d-) observations via a χ2 minimization. TiRiFiC is currently implemented as an add-on to the Groningen Image Processing System (GIPSY) software package and attempts to provide a method to automatically fit an extended tilted-ring model directly to a data cube.

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

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

[ascl:1910.007]
TLS: Transit Least Squares

TLS is an optimized transit-fitting algorithm to search for periodic transits of small planets. In contrast to BLS: Box Least Squares (ascl:1607.008), which searches for rectangular signals in stellar light curves, TLS searches for transit-like features with stellar limb-darkening and including the effects of planetary ingress and egress. TLS also analyses the entire, unbinned data of the phase-folded light curve. TLS yields a ~10% higher detection efficiency (and similar false alarm rates) compared to BLS though has a higher computational load. This load is partly compensated for by applying an optimized period sampling and transit duration sampling constrained to the physically plausible range.

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

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

[ascl:1512.014]
TM: Torus Mapper

TM (Torus Mapper) produces models for orbits in action-angle coordinates in axisymmetric potentials using torus mapping, a non-perturbative technique for creating orbital tori for specified values of the action integrals. It can compute a star's position at any time given an orbital torus and a star’s position at a reference time, and also provides a way to choose initial conditions for N-body simulations of realistic disc galaxies that start in perfect equilibrium. TM provides some advantages over use of a standard time-stepper to create orbits.

[ascl:1212.015]
TMAP: Tübingen NLTE Model-Atmosphere Package

The Tübingen NLTE Model-Atmosphere Package (TMAP) is a tool to calculate stellar atmospheres in spherical or plane-parallel geometry in hydrostatic and radiative equilibrium allowing departures from local thermodynamic equilibrium (LTE) for the population of atomic levels. It is based on the Accelerated Lambda Iteration (ALI) method and is able to account for line blanketing by metals. All elements from hydrogen to nickel may be included in the calculation with model atoms which are tailored for the aims of the user.

[ascl:1605.005]
TMBIDL: Single dish radio astronomy data reduction package

The IDL package reduces and analyzes radio astronomy data. It translates SDFITS files into TMBIDL format, and can average and display spectra, remove baselines, and fit Gaussian models.

[ascl:1209.007]
TMCalc: Fast estimation of stellar metallicity [Fe/H]

TMCalc is a C code developed as an extension to ARES. Using the line list given, the code can be used as a precise and fast indicator of the spectroscopic temperature and metallicity for dwarf FKG stars with effective temperatures ranging from 4500 K to 6500 K and with [Fe/H] ranging from -0.8 dex to 0.4 dex.

[ascl:2003.009]
TOASTER: Times-Of-Arrival Tracker

Lazarus, Patrick; Bassa, Cees; Desvignes, Greg; Hessels, Jason; Verbiest, Joris; Karuppusamy, Ramesh

TOASTER is a pulse times-of-arrival (TOA) tracker. It stores reduced/folded observations, meta data, templates, parfiles, TOAs, and timefiles in an organized manner using an SQL database. TOASTER also provides a full-featured python toolkit for reliably interacting with the data and database, and provides scripts that, for example, list and summarize the TOAs in the data base, and generate TOA files in multiple formats. The framework can also be used to generate TOAs from observations using flexible and reproducible plugins referred to as "manipulators".

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

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

[ascl:1101.010]
TOPCAT: Tool for OPerations on Catalogues And Tables

TOPCAT is an interactive graphical viewer and editor for tabular data. Its aim is to provide most of the facilities that astronomers need for analysis and manipulation of source catalogues and other tables, though it can be used for non-astronomical data as well. It understands a number of different astronomically important formats (including FITS and VOTable) and more formats can be added.

It offers a variety of ways to view and analyse tables, including a browser for the cell data themselves, viewers for information about table and column metadata, and facilities for 1-, 2-, 3- and higher-dimensional visualisation, calculating statistics and joining tables using flexible matching algorithms. Using a powerful and extensible Java-based expression language new columns can be defined and row subsets selected for separate analysis. Table data and metadata can be edited and the resulting modified table can be written out in a wide range of output formats.

It is a stand-alone application which works quite happily with no network connection. However, because it uses Virtual Observatory (VO) standards, it can cooperate smoothly with other tools in the VO world and beyond, such as VODesktop, Aladin and ds9. Between 2006 and 2009 TOPCAT was developed within the AstroGrid project, and is offered as part of a standard suite of applications on the AstroGrid web site, where you can find information on several other VO tools.

The program is written in pure Java and available under the GNU General Public Licence. It has been developed in the UK within the Starlink and AstroGrid projects, and under PPARC and STFC grants. Its underlying table processing facilities are provided by STIL.

[ascl:2003.014]
Torch: Coupled gas and N-body dynamics simulator

Wall, Joshua E.; Tran, Aaron; Mac Low, Mordecai-Mark; McMillan, Stephen L. W.; Klessen, Ralf S.; Portegies Zwart, Simon; Pellegrino, Andrew

Torch simulates coupled gas and N-body dynamics in astrophysical systems such as newly forming star clusters. It combines the FLASH (ascl:1010.082) code for gas dynamics and the ph4 code for direct N-body evolution via the AMUSE framework.

[ascl:1404.006]
TORUS: Radiation transport and hydrodynamics code

TORUS is a flexible radiation transfer and radiation-hydrodynamics code. The code has a basic infrastructure that includes the AMR mesh scheme that is used by several physics modules including atomic line transfer in a moving medium, molecular line transfer, photoionization, radiation hydrodynamics and radiative equilibrium. TORUS is useful for a variety of problems, including magnetospheric accretion onto T Tauri stars, spiral nebulae around Wolf-Rayet stars, discs around Herbig AeBe stars, structured winds of O supergiants and Raman-scattered line formation in symbiotic binaries, and dust emission and molecular line formation in star forming clusters. The code is written in Fortran 2003 and is compiled using a standard Gnu makefile. The code is parallelized using both MPI and OMP, and can use these parallel sections either separately or in a hybrid mode.

[ascl:1507.006]
Toyz: Large datasets and astronomical images analysis framework

Toyz is a python web framework that allows scientists to interact with large images and data sets stored on a remote server. A web application is run on the server containing the data and clients are run from web browsers on the user's computer. Toyz displays large FITS images also also renders any image format supported by Pillow (a fork of the Python Imaging Library), contains a GUI to interact with linked plots, and offers a customizable framework that allows students and researchers to create their own work spaces inside a Toyz environment. Astro-Toyz extends the features of the Toyz image viewer, allowing users to view world coordinates and align images based on their WCS.

[ascl:1904.021]
TP2VIS: Total Power Map to Visibilities

TP2VIS creates visibilities from a single dish cube; the TP visibilities can be combined with the interferometric visibilities in a joint deconvolution using, for example, CASA's tclean() method. TP2VIS requires CASA 5.4 (ascl:1107.013) or above.

[ascl:1909.004]
TPI: Test Particle Integrator

TPI computes the gravitational dynamics of particles orbiting a supermassive black hole (SBH). A distinction is made to two types of particles: test particles and field particles. Field particles are assumed to move in quasi-static Keplerian orbits around the SBH that precess due to the enclosed mass (Newtonian 'mass precession') and relativistic effects. Otherwise, field-particle-field-particle interactions are neglected. Test particles are integrated in the time-dependent potential of the field particles and the SBH. Relativistic effects are included in the equations of motion (including the effects of SBH spin), and test-particle-test-particle interactions are neglected.

[ascl:1603.012]
tpipe: Searching radio interferometry data for fast, dispersed transients

Visibilities from radio interferometers have not traditionally been used to study the fast transient sky. Millisecond transients (e.g., fast radio bursts) and periodic sources (e.g., pulsars) have been studied with single-dish radio telescopes and a software stack developed over the past few decades. tpipe is an initial attempt to develop the fast transient algorithms for visibility data. Functions exist for analysis of visibilties, such as reading data, flagging data, applying interferometric gain calibration, and imaging. These functions are given equal footing as time-domain techniques like filters and dedispersion.

tpipe has been largely superseded by rtpipe (ascl:1706.002).

[ascl:1305.003]
TPM: Tree-Particle-Mesh code

TPM carries out collisionless (dark matter) cosmological N-body simulations, evolving a system of N particles as they move under their mutual gravitational interaction. It combines aspects of both Tree and Particle-Mesh algorithms. After the global PM forces are calculated, spatially distinct regions above a given density contrast are located; the tree code calculates the gravitational interactions inside these denser objects at higher spatial and temporal resolution. The code is parallel and uses MPI for message passing.

[ascl:1304.011]
TPZ: Trees for Photo-Z

TPZ, a parallel code written in python, produces robust and accurate photometric redshift PDFs by using prediction tree and random forests. The code also produces ancillary information about the sample used, such as prior unbiased errors estimations (giving an estimation of performance) and a ranking of importance of variables as well as a map of performance indicating where extra training data is needed to improve overall performance. It is designed to be easy to use and a tutorial is available.

[ascl:1601.001]
TRADES: TRAnsits and Dynamics of Exoplanetary Systems

TRADES (TRAnsits and Dynamics of Exoplanetary Systems) simultaneously fits observed radial velocities and transit times data to determine the orbital parameters of exoplanetary systems from observational data. It uses a dynamical simulator for N-body systems that also fits the available data during the orbital integration and determines the best combination of the orbital parameters using grid search, χ2 minimization, genetic algorithms, particle swarm optimization, and bootstrap analysis.

[ascl:1501.011]
transfer: The Sloan Digital Sky Survey Data Transfer Infrastructure

The Sloan Digital Sky Survey (SDSS) produces large amounts of data daily. transfer, written in Python, provides the effective automation needed for daily data transfer operations and management and operates essentially free of human intervention. This package has been tested and used successfully for several years.

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

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

[ascl:1611.008]
Transit Clairvoyance: Predicting multiple-planet systems for TESS

Transit Clairvoyance uses Artificial Neural Networks (ANNs) to predict the most likely short period transiters to have additional transiters, which may double the discovery yield of the TESS (Transiting Exoplanet Survey Satellite). Clairvoyance is a simple 2-D interpolant that takes in the number of planets in a system with period less than 13.7 days, as well as the maximum radius amongst them (in Earth radii) and orbital period of the planet with maximum radius (in Earth days) in order to predict the probability of additional transiters in this system with period greater than 13.7 days.

[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:1704.008]
Transit: Radiative-transfer code for planetary atmospheres

Cubillos, Patricio; Blecic, Jasmina; Harrington, Joe; Rojo, Patricio; Foster, Austin J.; Stemm, Madison; Challener,Ryan; Foster, Andrew S. D.

Transit calculates the transmission or emission spectrum of a planetary atmosphere with application to extrasolar-planet transit and eclipse observations, respectively. It computes the spectra by solving the one-dimensional line-by-line radiative-transfer equation for an atmospheric model.

[ascl:1703.010]
TransitSOM: Self-Organizing Map for Kepler and K2 transits

A self-organizing map (SOM) can be used to identify planetary candidates from Kepler and K2 datasets with accuracies near 90% in distinguishing known Kepler planets from false positives. TransitSOM classifies a Kepler or K2 lightcurve using a self-organizing map (SOM) created and pre-trained using PyMVPA (ascl:1703.009). It includes functions for users to create their own SOMs.

[ascl:2001.002]
TRANSPHERE: 1-D spherical continuum radiative transfer

TRANSPHERE is a simple dust continuum radiative transfer code for spherically symmetric circumstellar envelopes. It handles absorption and re-emission and computes the dust temperature self-consistently; it does not, however, deal with scattering. TRANSPHERE uses a variable eddington factor method for the radiative transfer. The RADMD code (ascl:1108.016) is more versatile, but for a spherically symmetric problem for which scattering is of much concern, it may be easier to use a simple code such as TRANSPHERE.

Please note that this code has not been updated since 2006.

[ascl:1412.011]
TraP: Transients discovery pipeline for image-plane surveys

The TraP is a pipeline for detecting and responding to transient and variable sources in a stream of astronomical images. Images are initially processed using a pure-Python source-extraction package, PySE (ascl:1805.026), which is bundled with the TraP. Source positions and fluxes are then loaded into a SQL database for association and variability detection. The database structure allows for estimation of past upper limits on newly detected sources, and for forced fitting of previously detected sources which have since dropped below the blind-extraction threshold. Developed with LOFAR data in mind, the TraP has been used with data from other radio observatories.

[ascl:1508.007]
TreeCorr: Two-point correlation functions

TreeCorr efficiently computes two-point correlation functions. It can compute correlations of regular number counts, weak lensing shears, or scalar quantities such as convergence or CMB temperature fluctuations. Two-point correlations may be auto-correlations or cross-correlations, including any combination of shear, kappa, and counts. Two-point functions can be done with correct curved-sky calculation using RA, Dec coordinates, on a Euclidean tangent plane, or in 3D using RA, Dec and a distance. The front end is written in Python, which can be used as a Python module or as a standalone executable using configuration files; the actual computation of the correlation functions is done in C++ using ball trees (similar to kd trees), making the calculation extremely efficient, and when available, OpenMP is used to run in parallel on multi-core machines.

[ascl:1911.021]
TreeFrog: Construct halo merger trees and compare halo catalogs

TreeFrog reads in particle IDs information between various structure catalogs and cross matches catalogs, assuming that particle IDs are unique and constant across snapshots. Though it is built as a cross correlator (in that it can match particles across several different catalogs), its principle use is as halo merger tree builder. TreeFrog produces links between objects found at different snapshots (or catalogs) and uses several possible functions to evaluate the merit of a link between one object at a given snapshot (or in a given catalog) to another object in a previous snapshot (or different catalog). It can also produce a full graph. The code utilizes MPI and OpenMP. It is optimzed for reading VELOCIraptor (ascl:1911.020) output but can also read output from other structure finders such as AHF (ascl:1102.009).

[ascl:2002.004]
triceratops: Candidate exoplanet rating tool

triceratops (Tool for Rating Interesting Candidate Exoplanets and Reliability Analysis of Transits Originating from Proximate Stars) validates planet candidates from the Transiting Exoplanet Survey Satellite (TESS). The code calculates the probabilities of a wide range of transit-producing scenarios using the primary transit of the planet candidate and preexisting knowledge of its host and nearby stars. It then uses the known properties of these stars to calculate star-specific priors for each scenario with estimates of stellar multiplicity and planet occurrence rates.

[ascl:1612.019]
Trident: Synthetic spectrum generator

Trident creates synthetic absorption-line spectra from astrophysical hydrodynamics simulations. It uses the yt package (ascl:1011.022) to read in simulation datasets and extends it to provide realistic synthetic observations appropriate for studies of the interstellar, circumgalactic, and intergalactic media.

[ascl:1508.009]
Trilogy: FITS image conversion software

Trilogy automatically scales and combines FITS images to produce color or grayscale images using Python scripts. The user assigns images to each color channel (RGB) or a single image to grayscale luminosity. Trilogy determines the intensity scaling automatically and independently in each channel to display faint features without saturating bright features. Each channel's scaling is determined based on a sample of the image (or summed images) and two input parameters. One parameter sets the output luminosity of "the noise," currently determined as 1-sigma above the sigma-clipped mean. The other parameter sets what fraction of the data (if any) in the sample region should be allowed to saturate. Default values for these parameters (0.15% and 0.001%, respectively) work well, but the user is able to adjust them. The scaling is accomplished using the logarithmic function y = a log(kx + 1) clipped between 0 and 1, where a and k are constants determined based on the data and desired scaling parameters as described above.

[ascl:1210.014]
TRIP: General computer algebra system for celestial mechanics

TRIP is an interactive computer algebra system that is devoted to perturbation series computations, and specially adapted to celestial mechanics. Its development started in 1988, as an upgrade of the special purpose FORTRAN routines elaborated by J. Laskar for the demonstration of the chaotic behavior of the Solar System. TRIP is a mature and efficient tool for handling multivariate generalized power series, and embeds two kernels, a symbolic and a numerical kernel. This numerical kernel communicates with Gnuplot or Grace to plot the graphics and allows one to plot the numerical evaluation of symbolic objects.

[ascl:1405.008]
TRIPP: Time Resolved Imaging Photometry Package

Geckeler, Ralf D.; Schuh, Sonja; Dreizler, Stefan; Deetjen, Jochen; Gleissner, Thomas; Risse, Patrick; Rauch, Thomas; Göhler, Eckart; Hügelmeyer, Simon; Husser, Tim-Oliver; Israel, Holger; Benlloch-Garcia, Sara; Pottschmidt, Katja; Wilms, Jörn

Written in IDL, TRIPP performs CCD time series reduction and analysis. It provides an on-line check of the incoming frames, performs relative aperture photometry and provides a set of time series tools, such as calculation of periodograms including false alarm probability determination, epoc folding, sinus fitting, and light curve simulations.

[ascl:1605.010]
TRIPPy: Python-based Trailed Source Photometry

Fraser, Wesley C.; Alexandersen, Mike; Schwamb, Megan E.; Marsset, Michael E.; Pike, Rosemary E.; Kavelaars, JJ; Bannister, Michele T.; Benecchi, Susan; Delsanti, Audrey

TRIPPy (TRailed Image Photometry in Python) uses a pill-shaped aperture, a rectangle described by three parameters (trail length, angle, and radius) to improve photometry of moving sources over that done with circular apertures. It can generate accurate model and trailed point-spread functions from stationary background sources in sidereally tracked images. Appropriate aperture correction provides accurate, unbiased flux measurement. TRIPPy requires numpy, scipy, matplotlib, Astropy (ascl:1304.002), and stsci.numdisplay; emcee (ascl:1303.002) and SExtractor (ascl:1010.064) are optional.

[ascl:1908.008]
TRISTAN-MP: TRIdimensional STANford - Massively Parallel code

TRISTAN-MP is a fully relativistic Particle-In-Cell (PIC) code for plasma physics computations and self-consistently solves the full set of Maxwell’s equations, along with the relativistic equations of motion for the charged particles. Fields are discretized on a finite 3D or 2D mesh, the computational grid; the code then uses time-centered and space-centered finite difference schemes to advance the equations in time via the Lorentz force equation, and to calculate spatial derivatives, so that the algorithm is second order accurate in space and time. The charges and currents derived from the particles' velocities and positions are then used as source terms to re-calculate the electromagnetic fields. TRISTAN-MP is based on the original TRISTAN code by O. Buneman (1999).

[ascl:1509.005]
TRUVOT: True Background Technique for the Swift UVOT Grisms

TRUVOT decontaminates Swift UVOT grism spectra for transient objects. The technique makes use of template images in a process similar to image subtraction.

[ascl:1406.011]
TSP: Time-Series/Polarimetry Package

TSP is an astronomical data reduction package that handles time series data and polarimetric data from a variety of different instruments, and is distributed as part of the Starlink software collection (ascl:1110.012).

[ascl:1409.002]
Tsyganenko Geomagnetic Field Models

The Tsyganenko models are semi-empirical best-fit representations for the magnetic field, based on a large number of satellite observations (IMP, HEOS, ISEE, POLAR, Geotail, GOES, etc). The models include the contributions from major external magnetospheric sources: ring current, magnetotail current system, magnetopause currents, and large-scale system of field-aligned currents.

[ascl:1404.015]
TTVFast: Transit timing inversion

TTVFast efficiently calculates transit times for n-planet systems and the corresponding radial velocities. The code uses a symplectic integrator with a Keplerian interpolator for the calculation of transit times (Nesvorny et al. 2013); it is available in both C and Fortran.

[ascl:1604.012]
TTVFaster: First order eccentricity transit timing variations (TTVs)

TTVFaster implements analytic formulae for transit time variations (TTVs) that are accurate to first order in the planet–star mass ratios and in the orbital eccentricities; the implementations are available in several languages, including IDL, Julia, Python and C. These formulae compare well with more computationally expensive N-body integrations in the low-eccentricity, low mass-ratio regime when applied to simulated and to actual multi-transiting Kepler planet systems.

[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:1906.006]
turboSETI: Python-based SETI search algorithm

TurboSETI analyzes filterbank data (frequency vs. time) for narrow band drifting signals; its main purpose is to search for signals of extraterrestrial origin. TurboSETI can search the data for hundreds of drift rates (in Hz/sec) and handles either .fil or .h5 file formats. It has several dependencies, including Blimpy (ascl:1906.002) and Astropy (ascl:1304.002).

[ascl:1205.004]
Turbospectrum: Code for spectral synthesis

Turbospectrum is a 1D LTE spectrum synthesis code which covers 600 molecules, is fast with many lines, and uses the treatment of line broadening described by Barklem & O’Mara (1998).

[ascl:1907.015]
TurbuStat: Turbulence statistics in spectral-line data cubes

Koch, Eric W.; Rosolowsky, Erik W.; Boyden, Ryan D.; Burkhart, Blakesley; Ginsburg, Adam; Loeppky, Jason L.; Offner, Stella S. R.

TurbuStat implements a variety of turbulence-based statistics described in the astronomical literature and defines distance metrics for each statistic to quantitatively compare spectral-line data cubes, as well as column density, integrated intensity, or other moment maps. The software can simulate observations of fractional Brownian Motion fields, including 2-D images and optically thin H I data cubes. TurbuStat also offers multicore fast-Fourier-transform support and provides a segmented linear model for fitting lines with a break point.

[ascl:1304.015]
TVD: Total Variation Diminishing code

TVD solves the magnetohydrodynamic (MHD) equations by updating the fluid variables along each direction using the flux-conservative, second-order, total variation diminishing (TVD), upwind scheme of Jin & Xin. The magnetic field is updated separately in two-dimensional advection-constraint steps. The electromotive force (EMF) is computed in the advection step using the TVD scheme, and this same EMF is used immediately in the constraint step in order to preserve ∇˙B=0 without the need to store intermediate fluxes. The code is extended to three dimensions using operator splitting, and Runge-Kutta is used to get second-order accuracy in time. TVD offers high-resolution per grid cell, second-order accuracy in space and time, and enforcement of the ∇˙B=0 constraint to machine precision. Written in Fortran, It has no memory overhead and is fast. It is also available in a fully scalable message-passing parallel MPI implementation.

[ascl:1708.015]
TWO-POP-PY: Two-population dust evolution model

TWO-POP-PY runs a two-population dust evolution model that follows the upper end of the dust size distribution and the evolution of the dust surface density profile and treats dust surface density, maximum particle size, small and large grain velocity, and fragmentation. It derives profiles that describe the dust-to-gas ratios and the dust surface density profiles well in protoplanetary disks, in addition to the radial flux by solid material rain out.

[ascl:1407.002]
TWODSPEC: Long-slit and optical fiber array spectra extensions for FIGARO

TWODSPEC offers programs for the reduction and analysis of long-slit and optical fiber array spectra, implemented as extensions to the FIGARO package (ascl:1203.013). The software are currently distributed as part of the Starlink software collection (ascl:1110.012). These programs are designed to do as much as possible for the user, to assist quick reduction and analysis of data; for example, LONGSLIT can fit multiple Gaussians to line profiles in batch and decides how many components to fit.

[ascl:1210.025]
TwoDSSM: Self-gravitating 2D shearing sheet

TwoDSSM solves the equations of self-gravitating hydrodynamics in the shearing sheet, with cooling. TwoDSSM is configured to use a simple, exponential cooling model, although it contains code for a more complicated (and perhaps more realistic) cooling model based on a one-zone vertical model. The complicated cooling model can be switched on using a flag.

[ascl:1303.008]
TYCHO: Stellar evolution code

TYCHO is a general, one dimensional (spherically symmetric) stellar evolution code written in structured Fortran 77; it is designed for hydrostatic and hydrodynamic stages including mass loss, accretion, pulsations and explosions. Mixing and convection algorithms are based on 3D time-dependent simulations. It offers extensive on-line graphics using Tim Pearson's PGPLOT with X-windows and runs effectively on Linux and Mac OS X laptop and desktop computers.

NOTE: This code is no longer being supported.

[ascl:1303.004]
UCL_PDR: Time dependent photon-dissociation regions model

UCL_PDR is a time dependent photon-dissociation regions model that calculates self consistently the thermal balance. It can be used with gas phase only species as well as with surface species. It is very modular, has the possibility of accounting for density and pressure gradients and can be coupled with UCL_CHEM as well as with SMMOL. It has been used to model small scale (e.g. knots in proto-planetary nebulae) to large scale regions (high redshift galaxies).

[ascl:1303.006]
UCLCHEM: time and depth dependent gas-grain chemical model

UCLCHEM is a time and depth dependent gas-grain chemical model that can be used to estimate the fractional abundances (with respect to hydrogen) of gas and surface species in every environment where molecules are present. The model includes both gas and surface reactions. The code starts from the most diffuse state where all the gas is in atomic form and evolve sthe gas to its final density. Depending on the temperature, atoms and molecules from the gas freeze on to the grains and they hydrogenate where possible. The advantage of this approach is that the ice composition is not assumed but it is derived by a time-dependent computation of the chemical evolution of the gas-dust interaction process. The code is very modular, has been used to model a variety of regions and can be coupled with the UCL_PDR and SMMOL codes.

[ascl:1704.002]
UDAT: A multi-purpose data analysis tool

UDAT is a pattern recognition tool for mass analysis of various types of data, including image and audio. Based on its WND-CHARM (ascl:1312.002) prototype, UDAT computed a large set of numerical content descriptors from each file it analyzes, and selects the most informative features using statistical analysis. The tool can perform automatic classification of galaxy images by training with annotated galaxy images. It also has unsupervised learning capabilities, such as query-by-example of galaxies based on morphology. That is, given an input galaxy image of interest, the tool can search through a large database of images to retrieve the galaxies that are the most similar to the query image. The downside of the tool is its computational complexity, which in most cases will require a small or medium cluster.

[ascl:1611.001]
UltraNest: Pythonic Nested Sampling Development Framework and UltraNest

This three-component package provides a Pythonic implementation of the Nested Sampling integration algorithm for Bayesian model comparison and parameter estimation. It offers multiple implementations for constrained drawing functions and a test suite to evaluate the correctness, accuracy and efficiency of various implementations. The three components are:

- a modular framework for nested sampling algorithms (nested_sampling) and their development;
- a test framework to evaluate the performance and accuracy of algorithms (testsuite); and
- UltraNest, a fast C implementation of a mixed RadFriends/MCMC nested sampling algorithm.

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

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

[ascl:1804.022]
UniDAM: Unified tool to estimate Distances, Ages, and Masses

UniDAM obtains a homogenized set of stellar parameters from spectrophotometric data of different surveys. Parallax and extinction data can be incorporated into the isochrone fitting method used in UniDAM to reduce distance and age estimate uncertainties for TGAS stars for distances up to 1 kpc and decrease distance Gaia end-of-mission parallax uncertainties by about a factor of 20 and age uncertainties by a factor of two for stars up to 10 kpc away from the Sun.

[ascl:1403.007]
Unified EOS for neutron stars

The equation of state (EOS) of dense matter is a crucial input for the neutron-star structure calculations. This Fortran code can obtain a "unified EOS" in the many-body calculations based on a single effective nuclear Hamiltonian, and is valid in all regions of the neutron star interior. For unified EOSs, the transitions between the outer crust and the inner crust and between the inner crust and the core are obtained as a result of many-body calculations.

[ascl:1503.007]
UniPOPS: Unified data reduction suite

Maddalena, Ronald J.; Garwood, Robert W.; Salter, Christopher J.; Stobie, Elizabeth B; Cram, Thomas R.; Morgan, Lorrie; Vance, Bob; Hudson, Jerome

UniPOPS, a suite of programs and utilities developed at the National Radio Astronomy Observatory (NRAO), reduced data from the observatory's single-dish telescopes: the Tucson 12-m, the Green Bank 140-ft, and archived data from the Green Bank 300-ft. The primary reduction programs, 'line' (for spectral-line reduction) and 'condar' (for continuum reduction), used the People-Oriented Parsing Service (POPS) as the command line interpreter. UniPOPS unified previous analysis packages and provided new capabilities; development of UniPOPS continued within the NRAO until 2004 when the 12-m was turned over to the Arizona Radio Observatory (ARO). The submitted code is version 3.5 from 2004, the last supported by the NRAO.

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

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

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

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

[ascl:1901.004]
unwise_psf: PSF models for unWISE coadds

The unwise_psf Python module renders point spread function (PSF) models appropriate for use in modeling of unWISE coadd images. unwise_psf translates highly detailed single-exposure WISE PSF models in detector coordinates to the corresponding pixelized PSF models in coadd space, accounting for subtleties including the WISE scan direction and its considerable variation near the ecliptic poles. Applications of the unwise_psf module include performing forced photometry on unWISE coadds, constructing WISE-selected source catalogs based on unWISE coadds and masking unWISE coadd regions contaminated by bright stars.

[ascl:1504.001]
UPMASK: Unsupervised Photometric Membership Assignment in Stellar Clusters

UPMASK, written in R, performs membership assignment in stellar clusters. It uses photometry and spatial positions, but can take into account other types of data. UPMASK takes into account arbitrary error models; the code is unsupervised, data-driven, physical-model-free and relies on as few assumptions as possible. The approach followed for membership assessment is based on an iterative process, principal component analysis, a clustering algorithm and a kernel density estimation.

[ascl:1512.019]
UPSILoN: AUtomated Classification of Periodic Variable Stars using MachIne LearNing

UPSILoN (AUtomated Classification of Periodic Variable Stars using MachIne LearNing) classifies periodic variable stars such as Delta Scuti stars, RR Lyraes, Cepheids, Type II Cepheids, eclipsing binaries, and long-period variables (i.e. superclasses), and their subclasses (e.g. RR Lyrae ab, c, d, and e types) using well-sampled light curves from any astronomical time-series surveys in optical bands regardless of their survey-specific characteristics such as color, magnitude, and sampling rate. UPSILoN consists of two parts, one which extracts variability features from a light curve, and another which classifies a light curve, and returns extracted features, a predicted class, and a class probability. In principle, UPSILoN can classify any light curves having arbitrary number of data points, but using light curves with more than ~80 data points provides the best classification quality.

[ascl:1412.009]
URCHIN: Reverse ray tracer

URCHIN is a Smoothed Particle Hydrodynamics (SPH) reverse ray tracer (i.e. from particles to sources). It calculates the amount of shielding from a uniform background that each particle experiences. Preservation of the adaptive density field resolution present in many gas dynamics codes and uniform sampling of gas resolution elements with rays are two of the benefits of URCHIN; it also offers preservation of Galilean invariance, high spectral resolution, and preservation of the standard uniform UV background in optically thin gas.

[ascl:1411.012]
util_2comp: Planck-based two-component dust model utilities

The util_2comp software utilities generate predictions of far-infrared Galactic dust emission and reddening based on a two-component dust emission model fit to Planck HFI, DIRBE and IRAS data from 100 GHz to 3000 GHz. These predictions and the associated dust temperature map have angular resolution of 6.1 arcminutes and are available over the entire sky. Implementations in IDL and Python are included.

[ascl:1412.003]
UTM: Universal Transit Modeller

The Universal Transit Modeller (UTM) is a light-curve simulator for all kinds of transiting or eclipsing configurations between arbitrary numbers of several types of objects, which may be stars, planets, planetary moons, and planetary rings. A separate fitting program, UFIT (Universal Fitter) is part of the UTM distribution and may be used to derive best fits to light-curves for any set of continuously variable parameters. UTM/UFIT is written in IDL code and its source is released in the public domain under the GNU General Public License.

[ascl:1606.006]
uvmcmcfit: Parametric models to interferometric data fitter

Uvmcmcfit fits parametric models to interferometric data. It is ideally suited to extract the maximum amount of information from marginally resolved observations with interferometers like the Atacama Large Millimeter Array (ALMA), Submillimeter Array (SMA), and Plateau de Bure Interferometer (PdBI). uvmcmcfit uses emcee (ascl:1303.002) to do Markov Chain Monte Carlo (MCMC) and can measure the goodness of fit from visibilities rather than deconvolved images, an advantage when there is strong gravitational lensing and in other situations. uvmcmcfit includes a pure-Python adaptation of Miriad’s (ascl:1106.007) uvmodel task to generate simulated visibilities given observed visibilities and a model image and a simple ray-tracing routine that allows it to account for both strongly lensed systems (where multiple images of the lensed galaxy are detected) and weakly lensed systems (where only a single image of the lensed galaxy is detected).

[ascl:1402.017]
UVMULTIFIT: Fitting astronomical radio interferometric data

UVMULTIFIT, written in Python, is a versatile library for fitting models directly to visibility data. These models can depend on frequency and fitting parameters in an arbitrary algebraic way. The results from the fit to the visibilities of sources with sizes smaller than the diffraction limit of the interferometer are superior to the output obtained from a mere analysis of the deconvolved images. Though UVMULTIFIT is based on the CASA package, it can be easily adapted to other analysis packages that have a Python API.

[ascl:1410.004]
UVOTPY: Swift UVOT grism data reduction

The two Swift UVOT grisms provide uv (170.0-500.0 nm) and visible (285.0-660.0 nm) spectra with a resolution of R~100 and 75. To reduce the grism data, UVOTPY extracts a spectrum given source sky position, and outputs a flux calibrated spectrum. UVOTPY is a replacement for the UVOTIMGRISM FTOOL (ascl:9912.002) in the HEADAS Swift package. Its extraction uses a curved aperture for the uv spectra, accounts the coincidence losses in the detector, provides more accurate anchor positions for the wavelength scale, and is valid for the whole detector.

[ascl:1911.002]
uvplot: Interferometric visibilities plotter

uvplot makes nice plots of deprojected interferometric visibilities (often called uvplots). It implements plotting functionality, handles MS tables with spectral windows with different number of channels, and can import visibilities from ASCII to MS Table. It also allows export of specific channels. uvplot can be installed inside the NRAO CASA package (ascl:1107.013).

[ascl:1207.003]
VAC: Versatile Advection Code

The Versatile Advection Code (VAC) is a freely available general hydrodynamic and magnetohydrodynamic simulation software that works in 1, 2 or 3 dimensions on Cartesian and logically Cartesian grids. VAC runs on any Unix/Linux system with a Fortran 90 (or 77) compiler and Perl interpreter. VAC can run on parallel machines using either the Message Passing Interface (MPI) library or a High Performance Fortran (HPF) compiler.

[ascl:1406.009]
VADER: Viscous Accretion Disk Evolution Resource

VADER is a flexible, general code that simulates the time evolution of thin axisymmetric accretion disks in time-steady potentials. VADER handles arbitrary viscosities, equations of state, boundary conditions, and source and sink terms for both mass and energy.

[ascl:1810.004]
VaeX: Visualization and eXploration of Out-of-Core DataFrames

VaeX (Visualization and eXploration) interactively visualizes and explores big tabular datasets. It can calculate statistics such as mean, sum, count, and standard deviation on an N-dimensional grid up to a billion (10^{9}) objects/rows per second. Visualization is done using histograms, density plots, and 3d volume rendering, allowing interactive exploration of big data. VaeX uses memory mapping, zero memory copy policy and lazy computations for best performance, and integrates well with the Jupyter/IPython notebook/lab ecosystem.

[ascl:1702.004]
Validation: Codes to compare simulation data to various observations

Validation provides codes to compare several observations to simulated data with stellar mass and star formation rate, simulated data stellar mass function with observed stellar mass function from PRIMUS or SDSS-GALEX in several redshift bins from 0.01-1.0, and simulated data B band luminosity function with observed stellar mass function, and to create plots for various attributes, including stellar mass functions, and stellar mass to halo mass. These codes can model predictions (in some cases alongside observational data) to test other mock catalogs.

[ascl:1309.002]
VAPHOT: Precision differential aperture photometry package

VAPHOT is an aperture photometry package for precise time−series photometry of uncrowded fields, geared towards the extraction of target lightcurves of eclipsing or transiting systems. Its photometric main routine works within the IRAF (ascl:9911.002) environment and is built upon the standard aperture photometry task 'phot' from IRAF, using optimized aperture sizes. The associated analysis program 'VANALIZ' works in the IDL environment. It performs differential photometry with graphical and numerical output. VANALIZ produces plots indicative of photometric stability and permits the interactive evaluation and weighting of comparison stars. Also possible is the automatic or manual suppression of data-points and the output of statistical analyses. Several methods for the calculation of the reference brightness are offered. Specific routines for the analysis of transit 'on'-'off' photometry, comparing the target brightness inside against outside a transit are also available.

[ascl:1506.010]
VAPID: Voigt Absorption-Profile [Interstellar] Dabbler

VAPID (Voigt Absorption Profile [Interstellar] Dabbler) models interstellar absorption lines. It predicts profiles and optimizes model parameters by least-squares fitting to observed spectra. VAPID allows cloud parameters to be optimized with respect to several different data set simultaneously; those data sets may include observations of different transitions of a given species, and may have different S/N ratios and resolutions.

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

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

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

[ascl:1208.016]
VARTOOLS: Light Curve Analysis Program

The VARTOOLS program is a command line utility that provides tools for analyzing time series astronomical data. It implements a number of routines for calculating variability/periodicity statistics of light curves, as well as tools for modifying and filtering light curves.

[ascl:1704.005]
VaST: Variability Search Toolkit

VaST (Variability Search Toolkit) finds variable objects on a series of astronomical images in FITS format. The software performs object detection and aperture photometry using SExtractor (ascl:1010.064) on each image, cross-matches lists of detected stars, performs magnitude calibration with respect to the first (reference) image and constructs a lightcurve for each object. The sigma-magnitude, Stetson's L variability index, Robust Median Statistic (RoMS) and other plots may be used to visually identify variable star candidates. The two distinguishing features of VaST are its ability to perform accurate aperture photometry of images obtained with non-linear detectors and to handle complex image distortions. VaST can be used in cases of unstable PSF (e.g., bad guiding or with digitized wide-field photographic images), and has been successfully applied to images obtained with telescopes ranging from 0.08 to 2.5m in diameter equipped with a variety of detectors including CCD, CMOS, MIC and photographic plates.

[ascl:1809.004]
VBBINARYLENSING: Microlensing light-curve computation

Bozza, Valerio; Bachelet, Etienne; Bartolić, Fran; Heintz, Tyler M.; Hoag, Ava R.; Hundertmark, Markus

VBBinaryLensing forward models gravitational microlensing events using the advanced contour integration method; it supports single and binary lenses. The lens map is inverted on a collection of points on the source boundary to obtain a corresponding collection of points on the boundaries of the images from which the area of the images can be recovered by use of Green’s theorem. The code takes advantage of a number of techniques to make contour integration much more efficient, including using a parabolic correction to increase the accuracy of the summation, introducing an error estimate on each arc of the boundary to enable defining an optimal sampling, and allowing the inclusion of limb darkening. The code is written as a C++ library and wrapped as a Python package, and can be called from either C++ or Python.

[ascl:1610.009]
velbin: radial velocity corrected for binary orbital motions

Velbin convolves the radial velocity offsets due to binary orbital motions with a Gaussian to model an observed velocity distribution. This can be used to measure the mean velocity and velocity dispersion from an observed radial velocity distribution, corrected for binary orbital motions. Velbin fits single- or multi-epoch data with any arbitrary binary orbital parameter distribution (as long as it can be sampled properly), however it always assumes that the intrinsic velocity distribution (i.e. corrected for binary orbital motions) is a Gaussian. Velbin samples (and edits) a binary orbital parameter distribution, fits an observed radial velocity distribution, and creates a mock radial velocity distribution that can be used to provide the fitted radial velocities in the single_epoch or multi_epoch methods.

[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.

This code is no longer maintained and has been superseded by DiskFit (ascl:1209.011).

[ascl:1911.020]
VELOCIraptor-STF: Six-dimensional Friends-of-Friends phase space halo finder

VELOCIraptor-STF, formerly STructure Finder (ascl:1306.009), is a 6-Dimensional Friends-of-Friends (6D-FoF) phase space halo finder and constructs halo catalogs. The code uses using MPI and OpenMP APIs and can be compiled as a library for on-the-fly halo finding within an N-body/hydrodynamnical code. There is an associated halo merger tree code TreeFrog (ascl:1911.021).

[ascl:1802.002]
venice: Mask utility

venice reads a mask file (DS9 or fits type) and a catalogue of objects (ascii or fits type) to create a pixelized mask, find objects inside/outside a mask, or generate a random catalogue of objects inside/outside a mask. The program reads the mask file and checks if a point, giving its coordinates, is inside or outside the mask, *i.e.* inside or outside at least one polygon of the mask.

[ascl:1802.005]
Verne: Earth-stopping effect for heavy dark matter

Verne calculates the Earth-stopping effect for super-heavy Dark Matter (DM). The code allows you to calculate the speed distribution (and DM signal rate) at an arbitrary detector location on the Earth. The calculation takes into account the full anisotropic DM velocity distribution and the full velocity dependence of the DM-nucleus cross section. Results can be obtained for any DM mass and cross section, though the results are most reliable for very heavy DM particles.

[ascl:1503.011]
VESPA: False positive probabilities calculator

Validation of Exoplanet Signals using a Probabilistic Algorithm (VESPA) calculates false positive probabilities and statistically validates transiting exoplanets. Written in Python, it uses isochrones [ascl:1503.010] and the package simpledist.

[ascl:1904.019]
Vevacious: Global minima of one-loop effective potentials generator

Vevacious takes a generic expression for a one-loop effective potential energy function and finds all the tree-level extrema, which are then used as the starting points for gradient-based minimization of the one-loop effective potential. The tunneling time from a given input vacuum to the deepest minimum, if different from the input vacuum, can be calculated. The parameter points are given as files in the SLHA format (though is not restricted to supersymmetric models), and new model files can be easily generated automatically by the Mathematica package SARAH (ascl:1904.020).

[ascl:1204.007]
VH-1: Multidimensional ideal compressible hydrodynamics code

VH-1 is a multidimensional ideal compressible hydrodynamics code written in FORTRAN for use on any computing platform, from desktop workstations to supercomputers. It uses a Lagrangian remap version of the Piecewise Parabolic Method developed by Paul Woodward and Phil Colella in their 1984 paper. VH-1 comes in a variety of versions, from a simple one-dimensional serial variant to a multi-dimensional version scalable to thousands of processors.

[ascl:1306.015]
VHD: Viscous pseudo-Newtonian accretion

VHD is a numerical study of viscous fluid accretion onto a black hole. The flow is axisymmetric and uses a pseudo-Newtonian potential to model relativistic effects near the event horizon. VHD is based on ZEUS-2D (Stone & Norman 1992) with the addition of an explicit scheme for the viscosity.

[ascl:1404.010]
VictoriaReginaModels: Stellar evolutionary tracks

The Victoria–Regina stellar models are comprised of seventy-two grids of stellar evolutionary tracks accompanied by complementary zero-age horizontal branches and are presented in “equivalent evolutionary phase” (.eep) files. This Fortran 77 software interpolates isochrones, isochrone population functions, luminosity functions, and color functions of stellar evolutionary tracks.

[ascl:1407.014]
VIDE: The Void IDentification and Examination toolkit

Sutter, P. M.; Lavaux, Guilhem; Hamaus, Nico; Pisani, Alice; Wandelt, Benjamin D.; Warren, Michael S.; Villaescusa-Navarro, Francisco; Zivick, Paul; Mao, Qingqing; Thompson, Benjamin B.

The Void IDentification and Examination toolkit (VIDE) identifies voids using a modified version of the parameter-free void finder ZOBOV (ascl:1304.005); a Voronoi tessellation of the tracer particles is used to estimate the density field followed by a watershed algorithm to group Voronoi cells into zones and subsequently voids. Output is a summary of void properties in plain ASCII; a Python API is provided for analysis tasks, including loading and manipulating void catalogs and particle members, filtering, plotting, computing clustering statistics, stacking, comparing catalogs, and fitting density profiles.

[ascl:1403.016]
Viewpoints: Fast interactive linked plotting of large multivariate data sets

Viewpoints is an interactive tool for exploratory visual analysis of large high-dimensional (multivariate) data. It uses linked scatterplots to find relations in a few seconds that can take much longer with other plotting tools. Its features include linked scatter plots with brushing, dynamic histograms, normalization, and outlier detection/removal.

[ascl:1201.006]
VIM: Visual Integration and Mining

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

[ascl: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:1603.003]
VIP: Vortex Image Processing pipeline for high-contrast direct imaging of exoplanets

Gomez Gonzalez, Carlos Alberto; Wertz, Olivier; Christiaens, Valentin; Absil, Olivier; Mawet, Dimitri

VIP (Vortex Image Processing pipeline) provides pre- and post-processing algorithms for high-contrast direct imaging of exoplanets. Written in Python, VIP provides a very flexible framework for data exploration and image processing and supports high-contrast imaging observational techniques, including angular, reference-star and multi-spectral differential imaging. Several post-processing algorithms for PSF subtraction based on principal component analysis are available as well as the LLSG (Local Low-rank plus Sparse plus Gaussian-noise decomposition) algorithm for angular differential imaging. VIP also implements the negative fake companion technique coupled with MCMC sampling for rigorous estimation of the flux and position of potential companions.

[ascl:1204.012]
VirGO: A Visual Browser for the ESO Science Archive Facility

VirGO is the next generation Visual Browser for the ESO Science Archive Facility developed by the Virtual Observatory (VO) Systems Department. It is a plug-in for the popular open source software Stellarium adding capabilities for browsing professional astronomical data. VirGO gives astronomers the possibility to easily discover and select data from millions of observations in a new visual and intuitive way. Its main feature is to perform real-time access and graphical display of a large number of observations by showing instrumental footprints and image previews, and to allow their selection and filtering for subsequent download from the ESO SAF web interface. It also allows the loading of external FITS files or VOTables, the superimposition of Digitized Sky Survey (DSS) background images, and the visualization of the sky in a `real life' mode as seen from the main ESO sites. All data interfaces are based on Virtual Observatory standards which allow access to images and spectra from external data centers, and interaction with the ESO SAF web interface or any other VO applications supporting the PLASTIC messaging system.

[ascl:1804.019]
ViSBARD: Visual System for Browsing, Analysis and Retrieval of Data

Roberts, D. Aaron; Boller, Ryan; Rezapkin, V.; Coleman, J.; McGuire, R.; Goldstein, M.; Kalb, V.; Kulkarni, R.; Luckyanova, M.; Byrnes, J.; Kerbel, U.; Candey, R.; Holmes, C.; Chimiak, R.; Harris, B.

ViSBARD interactively visualizes and analyzes space physics data. It provides an interactive integrated 3-D and 2-D environment to determine correlations between measurements across many spacecraft. It supports a variety of spacecraft data products and MHD models and is easily extensible to others. ViSBARD provides a way of visualizing multiple vector and scalar quantities as measured by many spacecraft at once. The data are displayed three-dimesionally along the orbits which may be displayed either as connected lines or as points. The data display allows the rapid determination of vector configurations, correlations between many measurements at multiple points, and global relationships. With the addition of magnetohydrodynamic (MHD) model data, this environment can also be used to validate simulation results with observed data, use simulated data to provide a global context for sparse observed data, and apply feature detection techniques to the simulated data.

[ascl:1802.006]
VISIBLE: VISIbility Based Line Extraction

Loomis, Ryan A.; Oberg, Karin I.; Andrews, Sean M.; Walsh, Catherine; Czekala, Ian; Huang, Jane; Rosenfeld, Katherine A.

VISIBLE applies approximated matched filters to interferometric data, allowing line detection directly in visibility space. The filter can be created from a FITS image or RADMC3D output image, and the weak line data can be a CASA MS or uvfits file. The filter response spectrum can be output either to a .npy file or returned back to the user for scripting.

[ascl:1408.010]
VisiOmatic: Celestial image viewer

VisiOmatic is a web client for IIPImage (ascl:1408.009) and is used to visualize and navigate through large science images from remote locations. It requires STIFF (ascl:1110.006), is based on the Leaflet Javascript library, and works on both touch-based and mouse-based devices.

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

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

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

[ascl: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:1402.001]
Vissage: ALMA VO Desktop Viewer

Vissage (VISualisation Software for Astronomical Gigantic data cubEs) is a FITS browser primarily targeting FITS data cubes obtained from ALMA. Vissage offers basic functionality for viewing three-dimensional data cubes, integrated intensity map, flipbook, channel map, and P-V diagram. It has several color sets and color scales available, offers panning and zooming, and can connect with the ALMA WebQL system and the JVO Subaru Image Cutout Service.

[ascl:1701.002]
Vizic: Jupyter-based interactive visualization tool for astronomical catalogs

Vizic is a Python visualization library that builds the connection between images and catalogs through an interactive map of the sky region. The software visualizes catalog data over a custom background canvas using the shape, size and orientation of each object in the catalog and displays interactive and customizable objects in the map. Property values such as redshift and magnitude can be used to filter or apply colormaps, and objects can be selected for further analysis through standard Python functions from inside a Jupyter notebook.

Vizic allows custom overlays to be appended dynamically on top of the sky map; included are Voronoi, Delaunay, Minimum Spanning Tree and HEALPix layers, which are helpful for visualizing large-scale structure. Overlays can be generated, added or removed dynamically with one line of code. Catalog data is kept in a non-relational database. The Jupyter Notebook allows the user to create scripts to analyze and plot the data selected/displayed in the interactive map, making Vizic a powerful and flexible interactive analysis tool. Vizic be used for data inspection, clustering analysis, galaxy alignment studies, outlier identification or simply large-scale visualizations.

[ascl:1908.014]
Vlasiator: Hybrid-Vlasov simulation code

von Alfthan, Sebastian; Pfau-Kempf, Yann; Sandroos, Arto; Hannuksela, Otto Akseli; Ganse, Urs; Battarbee, Markus; Pokhotelov, Dimitry

Vlasiator is a 6-dimensional Vlasov theory-based simulation. It simulates the entire near-Earth space at a global scale using the kinetic hybrid-Vlasov approach, to study fundamental plasma processes (reconnection, particle acceleration, shocks), and to gain a deeper understanding of space weather.

[submitted]
vlt-sphere: Automatic VLT/SPHERE data reduction and analysis

The high-contrast imager SPHERE at the Very Large Telescope is a new generation instrument combining extreme adaptive optics and coronagraphy to directly image exoplanets in the near-infrared. The vlt-sphere package enables easy reduction of the data coming from IRDIS and IFS, the two near-infrared subsystems of SPHERE. The package relies on the official ESO pipeline (ascl:1402.010) which must be installed separately.

[ascl:1304.005]
VOBOZ/ZOBOV: Halo-finding and Void-finding algorithms

VOBOZ (VOronoi BOund Zones) is an algorithm to find haloes in an N-body dark matter simulation which has little dependence on free parameters.

ZOBOV (ZOnes Bordering On Voidness) is an algorithm that finds density depressions in a set of points without any free parameters or assumptions about shape. It uses the Voronoi tessellation to estimate densities to find both voids and subvoids. It also measures probabilities that each void or subvoid arises from Poisson fluctuations.

[ascl:1411.003]
voevent-parse: Parse, manipulate, and generate VOEvent XML packets

voevent-parse, written in Python, parses, manipulates, and generates VOEvent XML packets; it is built atop lxml.objectify. Details of transients detected by many projects, including Fermi, Swift, and the Catalina Sky Survey, are currently made available as VOEvents, which is also the standard alert format by future facilities such as LSST and SKA. However, working with XML and adhering to the sometimes lengthy VOEvent schema can be a tricky process. voevent-parse provides convenience routines for common tasks, while allowing the user to utilise the full power of the lxml library when required. An earlier version of voevent-parse was part of the pysovo (ascl:1411.002) library.

[ascl:1811.016]
VoigtFit: Absorption line fitting for Voigt profiles

VoigtFit fits Voigt profiles to absorption lines. It fits multiple components for various atomic lines simultaneously, allowing parameters to be tied and fixed, and can automatically fit a polynomial continuum model together with the line profiles. A physical model can be used to constrain thermal and turbulent broadening of absorption lines as well as implementing molecular excitation models. The code uses a χ2 minimization approach to find the best solution and offers interactive features such as manual continuum placement locally around each line, manual masking of undesired fitting regions, and interactive definition of velocity components for various elements, improving the ease of estimating initial guesses.

[ascl:1309.007]
VOMegaPlot: Plotting millions of points

Urunkar, Nilesh; Kembhavi, Ajit K.; Navelkar, Ameya; Pandya, Jagruti; Moosani, Vivekananda; Nair, Prameela; Shaikh, Mohasin

VOMegaPlot, a Java based tool, has been developed for visualizing astronomical data that is available in VOTable format. It has been specifically optimized for handling large number of points (in the range of millions). It has the same look and feel as VOPlot (ascl:1309.006) and both these tools have certain common functionality.

[ascl:1309.006]
VOPlot: Toolkit for Scientific Discovery using VOTables

Kale, Sonali; Vijayaraman, T. M.; Kembhavi, Ajit; Krishnan, P. R.; Navelkar, Amey, Hedge, Hrishikesh; Kulkarni, Pallavi; Balaji, K. D.

VOPlot is a tool for visualizing astronomical data. It was developed in Java and acts on data available in VOTABLE, ASCII and FITS formats. VOPlot is available as a stand alone version, which is to be installed on the user's machine, or as a web-based version fully integrated with the VizieR database.

[ascl:1211.006]
Voronoi binning method

The Voronoi binning method is an IDL program to bin two-dimensional data to a constant signal-to-noise ratio per bin. It optimally solves the problem of preserving the maximum spatial resolution of general two-dimensional data, given a constraint on the minimum signal-to-noise ratio.

[ascl:1205.011]
VOSpec: VO Spectral Analysis Tool

VOSpec is a multi-wavelength spectral analysis tool with access to spectra, theoretical models and atomic and molecular line databases registered in the VO. The standard tools of VOSpec include line and continuum fitting, redshift and reddening correction, spectral arithmetic and convolution between spectra, equivalent width and flux calculations, and a best fitting algorithm for fitting selected SEDs to a TSAP service. VOSpec offers several display modes (tree vs table) and organising functionalities according to the available metadata for each service, including distance from the observation position.

[ascl:1309.008]
VOStat: Statistical analysis of astronomical data

VOStat allows astronomers to use both simple and sophisticated statistical routines on large datasets. This tool uses the large public-domain statistical computing package R. Datasets can be uploaded in either ASCII or VOTABLE (preferred) format. The statistical computations are performed by the VOStat and results are returned to the user.

[ascl:1408.015]
VPFIT: Voigt profile fitting program

The VPFIT program fits multiple Voigt profiles (convolved with the instrument profiles) to spectroscopic data that is in FITS or an ASCII file. It requires CFITSIO (ascl:1010.001) and PGPLOT (ascl:1103.002); the tarball includes RDGEN (ascl:1408.017), which can be used with VPFIT to set up the fits, fit the profiles, and examine the result in interactive mode for setting up initial guesses; vpguess (ascl:1408.016) can also be used to set up an initial file.

[ascl:1408.016]
vpguess: Fitting multiple Voigt profiles to spectroscopic data

vpguess facilitates the fitting of multiple Voigt profiles to spectroscopic data. It is a graphical interface to VPFIT (ascl:1408.015). Originally meant to simplify the process of setting up first guesses for a subsequent fit with VPFIT, it has developed into a full interface to VPFIT. It may also be used independently of VPFIT for displaying data, playing around with data and models, "chi-by-eye" fits, displaying the result of a proper fit, pretty plots, etc. vpguess is written in C, and the graphics are based on PGPLOT (ascl:1103.002).

[ascl:1811.017]
Vplanet: Virtual planet simulator

Barnes, Rory; Deitrick, Russell; Luger, Rodrigo; Driscoll, Peter; Fleming, David; Quinn, Thomas; Smotherman, Hayden; Garcia, Rodolfo; McDonald, Diego; Wilhelm, Caitlyn; Guyer, Benjamin

Vplanet simulates planetary system evolution with a focus on habitability. Physical models, typically consisting of ordinary differential equations for stellar, orbital, tidal, rotational, atmospheric, internal, magnetic, climate, and galactic evolution, are coupled together to simulate evolution for the age of a system.

[ascl:1407.013]
VStar: Variable star data visualization and analysis tool

VStar is a multi-platform, easy-to-use variable star data visualization and analysis tool. Data for a star can be read from the AAVSO (American Association of Variable Star Observers) database or from CSV and TSV files. VStar displays light curves and phase plots, can produce a mean curve, and analyzes time-frequency with Weighted Wavelet Z-Transform. It offers tools for period analysis, filtering, and other functions.

[ascl:1704.011]
VULCAN: Chemical Kinetics For Exoplanetary Atmospheres

VULCAN describes gaseous chemistry from 500 to 2500 K using a reduced C-H-O chemical network with about 300 reactions. It uses eddy diffusion to mimic atmospheric dynamics and excludes photochemistry, and can be used to examine the theoretical trends produced when the temperature-pressure profile and carbon-to-oxygen ratio are varied.

[ascl:1710.001]
vysmaw: Fast visibility stream muncher

The vysmaw client library facilitates the development of code for processes to tap into the fast visibility stream on the National Radio Astronomy Observatory's Very Large Array correlator back-end InfiniBand network. This uses the vys protocol to allow loose coupling to clients that need to remotely access memory over an Infiniband network.

[ascl:1807.002]
Warpfield: Winds And Radiation Pressure: Feedback Induced Expansion, colLapse and Dissolution

Warpfield (Winds And Radiation Pressure: Feedback Induced Expansion, colLapse and Dissolution) calculates shell dynamics and shell structure simultaneously for isolated massive clouds (≥10^{5} M_{☉}). This semi-analytic 1D feedback model scans a large range of physical parameters (gas density, star formation efficiency, and metallicity) to estimate escape fractions of ionizing radiation f_{esc, I}, the minimum star formation efficiency ∊_{min} required to drive an outflow, and recollapse time-scales for clouds that are not destroyed by feedback.

[ascl:1108.003]
WCSLIB and PGSBOX

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

[ascl:1109.015]
WCSTools: Image Astrometry Toolkit

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

[ascl:2004.004]
WD: Wilson-Devinney binary star modeling

Wilson-Devinney binary star modeling code (WD) is a complete package for modeling binary stars and their eclipes and consists of two main modules. The LC module generates light and radial velocity curves, spectral line profiles, images, conjunction times, and timing residuals; the DC module handles differential corrections, performing parameter adjustment of light curves, velocity curves, and eclipse timings by the Least Squares criterion. WD handles eccentric orbits and asynchronous rotation, and can compute velocity curves (with proximity and eclipse effects). It offers options for detailed reflection and nonlinear (logarithmic law) limb darkening, adjustment of spot parameters, an optional provision for spots to drift over the surface, and can follow light curve development over large numbers of orbits. Absolute flux solution allow Direct Distance Estimation (DDE) and there are improved solutions for ellipsoidal variables and for eclipsing binaries (EBs) with very shallow eclipses. Absolute flux solutions also can estimate temperatures of both EB components under suitable circumstances.

[ascl:1806.012]
WDEC: White Dwarf Evolution Code

WDEC (White Dwarf Evolution Code), written in Fortran, offers a fast and fairly easy way to produce models of white dwarfs. The code evolves hot (~100,000 K) input models down to a chosen effective temperature by relaxing the models to be solutions of the equations of stellar structure. The code can also be used to obtain g-mode oscillation modes for the models.

[ascl:1807.020]
wdmerger: Simulate white dwarf mergers with CASTRO

wdmerger simulates binary white dwarf mergers (and related events) in CASTRO (ascl:1105.010) and provides useful information on the viability of mergers of white dwarfs as a progenitor for Type Ia supernovae.

[ascl:1504.007]
WebbPSF: James Webb Space Telescope PSF Simulation Tool

Perrin, Marshall D.; Long, Joseph; Sivaramakrishnan, Anand; Lajoie, Charles-Phillipe; Elliot, Erin; Pueyo, Laurent; Albert, Loic

WebbPSF provides a PSF simulation tool in a flexible and easy-to-use software package implemented in Python. Functionality includes support for spectroscopic modes of JWST NIRISS, MIRI, and NIRSpec, including modeling of slit losses and diffractive line spread functions.

[ascl:1609.007]
Weighted EMPCA: Weighted Expectation Maximization Principal Component Analysis

Weighted EMPCA performs principal component analysis (PCA) on noisy datasets with missing values. Estimates of the measurement error are used to weight the input data such that the resulting eigenvectors, when compared to classic PCA, are more sensitive to the true underlying signal variations rather than being pulled by heteroskedastic measurement noise. Missing data are simply limiting cases of weight = 0. The underlying algorithm is a noise weighted expectation maximization (EM) PCA, which has additional benefits of implementation speed and flexibility for smoothing eigenvectors to reduce the noise contribution.

[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:1010.069]
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:1705.015]
WeirdestGalaxies: Outlier Detection Algorithm on Galaxy Spectra

WeirdestGalaxies finds the weirdest galaxies in the Sloan Digital Sky Survey (SDSS) by using a basic outlier detection algorithm. It uses an unsupervised Random Forest (RF) algorithm to assign a similarity measure (or distance) between every pair of galaxy spectra in the SDSS. It then uses the distance matrix to find the galaxies that have the largest distance, on average, from the rest of the galaxies in the sample, and defined them as outliers.

[ascl:1404.013]
WFC3UV_GC: WFC3 UVIS geometric-distortion correction

WFC3UV_GC is an improved geometric-distortion solution for the Hubble Space Telescope UVIS channel of Wide Field Camera 3 for ten broad-band filters. The solution is made up of three parts:

1.) a 3rd-order polynomial to deal with the general optical distortion;

2.) a table of residuals that accounts for both chip-related anomalies and fine-structure introduced by the filter; and,

3.) a linear transformation to put the two chips into a convenient master frame.

[ascl:1911.018]
WhereWolf: Galaxy/(sub)Halo ghosting tool for N-body simulations

WhereWolf tracks (sub)haloes even if they have been lost by a halo finder in cosmological simulations and supplements halo catalogs such as VELOCIraptor (ascl:1911.020) with these recovered (sub)haloes. The code can improve measurements of the subhalo/halo mass function and present estimates of the distribution of radii at which subhaloes merge.

[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:9910.007]
WINGSPAN: A WINdows Gamma-ray SPectral Analysis program

WINGSPAN is a program written to analyze spectral data from the Burst and Transient Source Experiment (BATSE) on NASA's Compton Gamma-Ray Observatory. Data files in the FITS (BFITS) format are suitable for input into the program. WINGSPAN can be used to view and manipulate event time histories or count spectra, and also has the capability to perform spectral deconvolution via a standard forward folding model fitting technique (Levenberg-Marquardt algorithm). Although WINGSPAN provides many functions for data manipulation, the program was designed to allow users to easily plug in their own external IDL routines. These external routines have access to all data read from the FITS files, as well as selection intervals created in the main part of WINGSPAN (background intervals and model, etc).

[ascl:1806.004]
WiseView: Visualizing motion and variability of faint WISE sources

WiseView renders image blinks of Wide-field Infrared Survey Explorer (WISE) coadds spanning a multi-year time baseline in a browser. The software allows for easy visual identification of motion and variability for sources far beyond the single-frame detection limit, a key threshold not surmounted by many studies. WiseView transparently gathers small image cutouts drawn from many terabytes of unWISE coadds, facilitating access to this large and unique dataset. Users need only input the coordinates of interest and can interactively tune parameters including the image stretch, colormap and blink rate. WiseView was developed in the context of the Backyard Worlds: Planet 9 citizen science project, and has enabled hundreds of brown dwarf candidate discoveries by citizen scientists and professional astronomers.

[ascl:1812.001]
WISP: Wenger Interferometry Software Package

WISP (Wenger Interferometry Software Package) is a radio interferometry calibration, reduction, imaging, and analysis package. WISP is a collection of Python code implemented through CASA (ascl:1107.013). Its generic and modular framework is designed to handle any continuum or spectral line radio interferometry data.

[ascl:1204.001]
WM-basic: Modeling atmospheres of hot stars

WM-basic is an easy-to-use interface to a program package which models the atmospheres of Hot Stars (and also SN and GN). The release comprises all programs required to calculate model atmospheres which especially yield ionizing fluxes and synthetic spectra. WM-basic is a native 32-bit application, conforming to the Multiple Documents Interface (MDI) standards for Windows XP/2000/NT/9x. All components of the program package have been compiled with Digital Visual Fortran V6.6(Pro) and Microsoft Visual C++.

[ascl:1312.002]
WND-CHARM: Multi-purpose image classifier

WND-CHARM quantitatively analyzes morphologies of galaxy mergers and associate galaxies by their morphology. It computes a large set (up to ~2700) of image features for each image based on the WND-CHARM algorithm. It can then split the images into training and test sets and classify them. The software extracts the image content descriptor from raw images, image transforms, and compound image transforms. The most informative features are then selected, and the feature vector of each image is used for classification and similarity measurement using Fisher discriminant scores and a variation of Weighted Nearest Neighbor analysis. WND-CHARM's results comparable favorably to the performance of task-specific algorithms developed for tested datasets. The simple user interface allows researchers who are not knowledgeable in computer vision methods and have no background in computer programming to apply image analysis to their data.

[ascl:1212.007]
WOLF: FITS file processor

WOLF processes FITS files and generates photometry files, annotated JPGs, opacity maps, background, transient detection and luminance changes detection. This software was used to process data for the Night Sky Live project.

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

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

[ascl:1907.030]
Wōtan: Stellar detrending methods

Wōtan provides free and open source algorithms to remove trends from time-series data automatically as an aid to to search efficiently for transits in stellar light curves from surveys. The toolkit helps determine empirically the best tool for a given job, serving as a one-stop solution for various smoothing tasks.

[ascl:1304.004]
Wqed: Lightcurve Analysis Suite

Wqed (pronounced "Wicked") is a set of tools developed by the Delaware Asteroseismic Research Center (DARC) to simplify the process of reducing time-series CCD data on variable stars. It does not provide tools to measure the brightness of stars in individual frames, focusing instead on what comes next:

- - selecting and removing data lost to cloud,

- removing the effects of light cloud and seeing variations,

- keeping track of what star a given data set refers to, and when that data was taken, and

- performing barycentric corrections to data.

[ascl:1408.023]
WSClean: Widefield interferometric imager

Offringa, A. R.; McKinley, B.; Hurley-Walker, N.; Briggs, F. H.; Wayth, R. B.; Kaplan, D. L.; Bell, M. E.; Feng, L.; Neben, A. R.; Hughes, J. D.; Rhee, J.; Murphy, T.; Bhat, N. D. R.; Bernardi, G.; Bowman, J. D.; Cappallo, R. J.; Corey, B. E.; Deshpande, A. A.; Emrich, D.; Ewall-Wice, A.; Gaensler, B. M.; Goeke, R.; Greenhill, L. J.; Hazelton, B. J.; Hindson, L.; Johnston-Hollitt, M.; Jacobs, D. C.; Kasper, J. C.; Kratzenberg, E.; Lenc, E.; Lonsdale, C. J.; Lynch, M. J.; McWhirter, S. R.; Mitchell, D. A.; Morales, M. F.; Morgan, E.; Kudryavtseva, N.; Oberoi, D.; Ord, S. M.; Pindor, B.; Procopio, P.; Prabu, T.; Riding, J.; Roshi, D. A.; Shankar, N. Udaya; Srivani, K. S.; Subrahmanyan, R.; Tingay, S. J.; Waterson, M.; Webster, R. L.; Whitney, A. R.; Williams, A.; Williams, C. L.

WSClean (w-stacking clean) is a fast generic widefield imager. It uses the w-stacking algorithm and can make use of the w-snapshot algorithm. It supports full-sky imaging and proper beam correction for homogeneous dipole arrays such as the MWA. WSClean allows Hogbom and Cotton-Schwab cleaning, and can clean polarizations joinedly. All operations are performed on the CPU; it is not specialized for GPUs.

[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:1402.029]
wssa_utils: WSSA 12 micron dust map utilities

wssa_utils contains utilities for accessing the full-sky, high-resolution maps of the WSSA 12 micron data release. Implementations in both Python and IDL are included. The code allows users to sample values at (longitude, latitude) coordinates of interest with ease, transparently mapping coordinates to WSSA tiles and performing interpolation. The wssa_utils software also serves to define a unique WSSA 12 micron flux at every location on the sky.

[ascl:1207.014]
wvrgcal: Correction of atmospheric phase fluctuations in ALMA observations

wvrgcal is a command line front end to LibAIR, the atmospheric inference library for phase correction of ALMA data using water vapour radiometers, and is the user-facing application for calculating atmospheric phase correction from WVR data. wvrgcal outputs a CASA gain calibration table which can then be applied to the observed data in the usual way.

[ascl:1211.003]
WVT Binning: Spatially adaptive 2-D binning

WVT Binning is a spatially adaptive 2-dimensional binning algorithm designed to bin sparse X-ray data. It can handle background subtracted, exposure corrected data to produce intensity images, hardness ratio maps, or temperature maps. The algorithm is an extension of Cappellari & Copin's (2003) Voronoi binning code and uses Weighted Voronoi Tesselations (WVT) to produce a very compact binning structure with a constant S/N per bin. The bin size adjusts to the required resolution in single-pixel steps, which minimizes the scatter around the target S/N. The code is very versatile and can in principle be applied to any type of data. The user manual contains instructions on how to apply the WVT binning code to X-ray data and how to extend the algorithm to other problems.

[ascl:1909.011]
WVTICs: SPH initial conditions using Weighted Voronoi Tesselations

Arth, Alexander; Donnert, Julius; Steinwandel, Ulrich; Böss, Ludwig; Halbesma, Timo; Pütz, Martin; Hubber, David; Dolag, Klaus

WVTICs generates glass-like initial conditions for Smoothed Particle Hydrodynamics. Relaxation of the particle distribution is done using an algorithm based on Weighted Voronoi Tesselations; additional particle reshuffling can be enabled to improve over- and undersampled maxima/minima. The WBTICs package includes a full suite of analytical test problems.

[ascl:1601.019]
WzBinned: Binned and uncorrelated estimates of dark energy EOS extractor

WzBinned extracts binned and uncorrelated estimates of dark energy equation of state w(z) using Type Ia supernovae Hubble diagram and other cosmological probes and priors. It can handle an arbitrary number of input distance modulus data (entered as an input file SNdata.dat) and various existing cosmological information.

[ascl:1312.005]
XAssist: Automatic analysis of X-ray astrophysics data

XAssist provides automation of X-ray astrophysics, specifically data reprocessing, source detection, and preliminary spatial, temporal and spectral analysis for each source with sufficient counts, with an emphasis on galaxies. It has been used for data from Chandra, ROSAT, XMM-Newton, and other various projects.

[ascl:1810.016]
XCLASS: eXtended CASA Line Analysis Software Suite

XCLASS (eXtended CASA Line Analysis Software Suite) extends CASA (ascl:1107.013) with new functions for modeling interferometric and single dish data. It provides a tool for calculating synthetic spectra by solving the radiative transfer equation for an isothermal object in one dimension, taking into account the finite source size and dust attenuation. It also includes an interface for MAGIX (ascl:1303.009) to find the parameter set that most closely reproduces the data.

[ascl:1907.029]
XDF-GAN: Mock astronomical survey generator

XDF-GAN generates mock galaxy surveys with a Spatial Generative Adversarial Network (SGAN)-like architecture. Mock galaxy surveys are generated from data that is preprocessed as little as possible (preprocessing is only a 99.99th percentile clipping). The outputs can also be tessellated together to create a very large survey, limited in size only by the RAM of the generation machine.

[ascl:1708.026]
XDGMM: eXtreme Deconvolution Gaussian Mixture Modeling

XDGMM uses Gaussian mixtures to do density estimation of noisy, heterogenous, and incomplete data using extreme deconvolution (XD) algorithms which is compatible with the scikit-learn machine learning methods. It implements both the astroML and Bovy et al. (2011) algorithms, and extends the BaseEstimator class from scikit-learn so that cross-validation methods work. It allows the user to produce a conditioned model if values of some parameters are known.

[ascl:1302.016]
XDQSO: Photometic quasar probabilities and redshifts

Bovy, Jo; Hennawi, Joseph F.; Hogg, David W.; Myers, Adam D.; Kirkpatrick, Jessica A.; Schlegel, David J.; Ross, Nicholas P.; Sheldon, Erin S.; McGreer, Ian D.; Schneider, Donald P.; Weaver, Benjamin A.

XDQSO, written in IDL, calculates photometric quasar probabilities to mimick SDSS-III’s BOSS quasar target selection or photometric redshifts for quasars, whether in three redshift ranges (z < 2.2; 2.2 leq z leq 3.5; z > 3.5) or arbitrary redshift ranges.

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

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

[ascl:1112.013]
XEphem: Interactive Astronomical Ephemeris

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

[ascl:1502.018]
XFGLENSES: Gravitational lens visualizer

XFGL visualizes gravitational lenses. It has an XFORM GUI and is completely interactive with the mouse. It uses OpenGL for the simulations.

[ascl:1807.031]
xGDS: Exploration Ground Data Systems

xGDS (Exploration Ground Data Systems) synthesizes real world data (from sensors, robots, ROVs, mobile devices, etc) and human observations into rich, digital maps and displays for analysis, decision making, and collaboration. xGDS processes and maps data (including video) in real-time during operations and uses it to support live role-based geolocated note taking. Notes can be used to search for and display important data. The software enables real-time analysis of data, permitting one to make inferences and plan new data collection operations while still in the field.

[ascl:1511.004]
Xgremlin: Interferograms and spectra from Fourier transform spectrometers analysis

Xgremlin is a hardware and operating system independent version of the data analysis program Gremlin used for Fourier transform spectrometry. Xgremlin runs on PCs and workstations that use the X11 window system, including cygwin in Windows. It is used to Fourier transform interferograms, plot spectra, perform phase corrections, perform intensity and wavenumber calibration, and find and fit spectral lines. It can also be used to construct synthetic spectra, subtract continua, compare several different spectra, and eliminate ringing around lines.

[ascl:1704.012]
XID+: Next generation XID development

XID+ is a prior-based source extraction tool which carries out photometry in the Herschel SPIRE (Spectral and Photometric Imaging Receiver) maps at the positions of known sources. It uses a probabilistic Bayesian framework that provides a natural framework in which to include prior information, and uses the Bayesian inference tool Stan to obtain the full posterior probability distribution on flux estimates.

[ascl:1303.021]
Xmatch: GPU Enhanced Astronomic Catalog Cross-Matching

Xmatch is a cross-platform, multi-GPU tool which allows for extremely fast cross-matching between two Astronomic catalogs. It is capable of asyncronously managing multiple GPUs, ideal for workstation and cluster environments.

[ascl:1402.020]
XNS: Axisymmetric equilibrium configuration of neutron stars

XNS solves for the axisymmetric equilibrium configuration of neutron stars in general relativity. It can model differentially rotating and magnetic fields that are either purely toroidal, purely poloidal or in the mixed twisted torus configuration. Einsten's equations are solved using the XCFC approximation for the metric in spherical coordinates.

[ascl:1502.019]
XPCell: Convective plasma cells simulator

XPCell simulates convective plasma cells. The program is implemented in two versions, one using GNUPLOT and the second OpenGL. XPCell offers a GUI to introduce the parameter required by the program.

[ascl:1212.002]
XPHOT: Estimation of properties of weak X-ray sources

XPHOT is an IDL implementation of a non-parametric method for estimating the apparent and intrinsic broad-band fluxes and absorbing X-ray column densities of weak X-ray sources. XPHOT is intended for faint sources with greater than ∼5-7 counts but fewer than 100-300 counts where parametric spectral fitting methods will be superior. This method is similar to the long-standing use of color-magnitude diagrams in optical and infrared astronomy, with X-ray median energy replacing color index and X-ray source counts replacing magnitude. Though XPHOT was calibrated for thermal spectra characteristic of stars in young stellar clusters, recalibration should be possible for some other classes of faint X-ray sources such as extragalactic active galactic nuclei.

[ascl:1509.001]
XSHPipelineManager: Wrapper for the VLT/X-shooter Data Reduction Pipeline

XSHPipelineManager provides a framework for reducing spectroscopic observations taken by the X-shooter spectrograph at the Very Large Telescope. This Python code wraps recipes developed by the European Southern Observatory and runs the full X-shooter data reduction pipeline. The code offers full flexibility in terms of what data reduction recipes to include and which calibration files to use. During the data reduction chain restart-files are saved, making it possible to restart at any step in the chain.

[submitted]
Xsmurf - Measuring multifractal properties with the continuous wavelet transform modulus maxima (WTMM) method

Xsmurf is a software package written in C/Tcl/Tk that implements the continuous wavelet transform modulus maxima method, an image processing tool for measuring fractal and multifractal properties in experimental and simulation data.

Multifractal analysis is described in the following page: http://www.scholarpedia.org/article/Wavelet-based_multifractal_analysis

Xsmurf has been used in multiple applications in astrophysics, e.g. :

- analysis of solar magnetograms for characterizing complexity of evolving regions

- fractal/multifractal nature and anisotropic structure of Galactic atomic hydrogen (H I)

- analysis of simulation data (velocity field, ...) of turbulent flow

[ascl:1207.008]
xSonify: Sonification software

xSonify maps scientific data to acoustic sequences. Listening to data can help discover patterns in huge amounts of data. Written in Java, xSonify allows visually impaired people to examine numerical data for patterns. The data can be imported from local files or from remote databases via the Internet. Single results of measurements from spacecraft instruments can be selected by their corresponding variables in a specific time frame. The results are transformed into MIDI sequences which can be played with a selection of different instruments from a soundbank. Another software module enables xSonify to convert the sonified data into other sound formats to make it easier to archive and exchange the Sonification results with other scientists.

[ascl:1805.016]
xspec_emcee: XSPEC-friendly interface for the emcee package

XSPEC_EMCEE is an XSPEC-friendly interface for emcee (ascl:1303.002). It carries out MCMC analyses of X-ray spectra in the X-ray spectral fitting program XSPEC (ascl:9910.005). It can run multiple xspec processes simultaneously, speeding up the analysis, and can switch to parameterizing norm

parameters in log space.

[ascl:9910.005]
XSPEC: An X-ray spectral fitting package

It has been over a decade since the first paper was published containing results determined using the general X-ray spectral-fitting program XSPEC. Since then XSPEC has become the most widely used program for this purpose, being the de facto standard for the ROSAT and the de jure standard for the ASCA and XTE satellites. Probably the most important features of XSPEC are the large number of theoretical models available and the facilities for adding new models.

[ascl:9910.008]
XSTAR: A program for calculating conditions and spectra of photoionized gases

XSTAR is a command-driven, interactive, computer program for calculating the physical conditions and emission spectra of photoionized gases. It may be applied in a wide variety of astrophysical contexts. Stripped to essentials, its job may be described simply: A spherical gas shell surrounding a central source of ionizing radiation absorbs some of this radiation and reradiates it in other portions of the spectrum; XSTAR computes the effects on the gas of absorbing this energy, and the spectrum of reradiated light. The user supplies the shape and strength of the incident continuum, the elemental abundances in the gas, its density or pressure, and its thickness; the code can be directed to return any of a large number of derived quantities, including (but not limited to) the ionization balance and temperature, opacity tables, and emitted line and continuum fluxes.

[ascl:1306.016]
Yaxx: Yet another X-ray extractor

Yaxx is a Perl script that facilitates batch data processing using Perl open source software and commonly available software such as CIAO/Sherpa, S-lang, SAS, and FTOOLS. For Chandra and XMM analysis it includes automated spectral extraction, fitting, and report generation. Yaxx can be run without climbing an extensive learning curve; even so, yaxx is highly configurable and can be customized to support complex analysis. yaxx uses template files and takes full advantage of the unique Sherpa / S-lang environment to make much of the processing user configurable. Although originally developed with an emphasis on X-ray data analysis, yaxx evolved to be a general-purpose pipeline scripting package.

[ascl:1908.022]
YMW16: Electron-density model

YMW16 models the distribution of free electrons in the Galaxy, the Magellanic Clouds and the inter-galactic medium and can be used to estimate distances for real or simulated pulsars and fast radio bursts (FRBs) based on their position and dispersion measure. The Galactic model is based on 189 pulsars that have independently determined distances as well as dispersion measures, whereas simpler models are used for the electron density in the MC and the IGM.

[ascl:1305.008]
YNOGK: Calculating null geodesics in the Kerr spacetime

YNOGK, written in Fortran, calculates the null geodesics in the Kerr spacetime. It uses Weierstrass' and Jacobi's elliptic functions to express all coordinates and affine parameters as analytical and numerical functions of a parameter $p$, which is an integral value along the geodesic. The information about the turning points do not need to be specified in advance by the user, allowing applications such as imaging, the calculation of line profiles or the observer-emitter problem to become root finding problems. Elliptic integrations are computed by Carlson's elliptic integral method, which allows fast computation.

[ascl:1403.012]
YNOGKM: Time-like geodesics in the Kerr-Newmann Spacetime calculations

YNOGKM (Yun-Nan observatories geodesic in a Kerr-Newman spacetime for massive particles) performs fast calculation of time-like geodesics in the Kerr-Newman (K-N) spacetime; it is a direct extension of YNOGK (Yun-Nan observatories geodesic Kerr) calculating null geodesics in a Kerr spacetime. The four Boyer-Lindquis coordinates and proper time are expressed as functions of a parameter p semi-analytically by using the Weierstrass' and Jacobi's elliptic functions and integrals. The elliptic integrals are computed by Carlson's elliptic integral method, which guarantees the fast speed of the code. The source Fortran file ynogkm.f90 contains three modules: constants, rootfind, ellfunction, and blcoordinates.

[ascl:1312.009]
YODA: Yet another Object Detection Application

YODA, implemented in C++, performs object detection, photometry and star-galaxy classification on astronomical images. Developed specifically to cope with the multi-band imaging data common in modern extragalactic imaging surveys, it is modular and therefore easily adaptable to specific needs. YODA works under conditions of inhomogeneous background noise across the detection frame, and performs accurate aperture photometry in image sets not sharing a common coordinate system or pixel scale as is often the case in present-day extragalactic survey work.

[ascl:1203.010]
Youpi: YOUr processing PIpeline

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

[ascl: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:1602.003]
ZAP: Zurich Atmosphere Purge

ZAP (Zurich Atmosphere Purge) provides sky subtraction for integral field spectroscopy; its approach is based on principal component analysis (PCA) developed for the Multi Unit Spectrographic Explorer (MUSE) integral field spectrograph. ZAP employs filtering and data segmentation to enhance the inherent capabilities of PCA for sky subtraction. ZAP reduces sky emission residuals while robustly preserving the flux and line shapes of astronomical sources; this method works in a variety of observational situations from sparse fields with a low density of sources to filled fields in which the target source fills the field of view. With the inclusion of both of these situations the method is generally applicable to many different science cases and should also be useful for other instrumentation.

[ascl:1607.012]
ZASPE: Zonal Atmospheric Stellar Parameters Estimator

ZASPE (Zonal Atmospheric Stellar Parameters Estimator) computes the atmospheric stellar parameters (Teff, log(g), [Fe/H] and vsin(i)) from echelle spectra via least squares minimization with a pre-computed library of synthetic spectra. The minimization is performed only in the most sensitive spectral zones to changes in the atmospheric parameters. The uncertainities and covariances computed by ZASPE assume that the principal source of error is the systematic missmatch between the observed spectrum and the sythetic one that produces the best fit. ZASPE requires a grid of synthetic spectra and can use any pre-computed library minor modifications.

[ascl:1807.017]
ZBARYCORR: Barycentric redshift calculator

ZBARYCORR determines the barycentric redshift (*z _{B}*) for a given star. It calculates the positions and velocities of solar system objects, applies the rotation, precession, nutation, and polar motion of the Earth, applies the stellar motion using the Markwardt library (ascl:1807.016), Shapiro delay, and light-travel term, and finally calculates the quantity

[ascl:1907.017]
ZChecker: Zwicky Transient Facility moving target checker for short object lists

Kelley, Michael S.P.; Bodewits, Dennis; Ye, Qaunzhi; Laher, Russ R.; Masci, Frank J.; Monkewitz, Serge; Riddle, Reed; Rusholme, Ben; Shupe, David L; Soumagnac, Maayane T.

ZChecker finds, measures, and visualizes known comets in the Zwicky Transient Facility time-domain survey. Images of targets are identified using on-line ephemeris generation and survey metadata. The photometry of the targets are measured and the images are processed with temporal filtering to highlight morphological variations in time.

[ascl:1404.002]
ZDCF: Z-Transformed Discrete Correlation Function

The cross-correlation function (CCF) is commonly employed in the study of AGN, where it is used to probe the structure of the broad line region by line reverberation, to study the continuum emission mechanism by correlating multi-waveband light curves and to seek correlations between the variability and other AGN properties. The z -transformed discrete correlation function (ZDCF) is a method for estimating the CCF of sparse, unevenly sampled light curves. Unlike the commonly used interpolation method, it does not assume that the light curves are smooth and it does provide errors on its estimates.

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

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

[ascl:1605.016]
zeldovich-PLT: Zel'dovich approximation initial conditions generator

zeldovich-PLT generates Zel'dovich approximation (ZA) initial conditions (i.e. first-order Lagrangian perturbation theory) for cosmological N-body simulations, optionally applying particle linear theory (PLT) corrections.

[ascl:1512.016]
ZeldovichRecon: Halo correlation function using the Zeldovich approximation

ZeldovichRecon computes the halo correlation function using the Zeldovich approximation. It includes 3 variants:

- zelrecon.cpp, which computes the various contributions to the correlation function;

- zelrecon_ctypes.cpp, which is designed to be called from Python using the ctypes library; and

- a version which implements the "ZEFT" formalism of "A Lagrangian effective field theory" [arxiv:1506.05264] including the alpha term described in that paper.

[ascl:1911.012]
Zeltron: Explicit 3D relativistic electromagnetic Particle-In-Cell code

Zeltron is an explicit 3D relativistic electromagnetic Particle-In-Cell code suited for modeling particle acceleration in astrophysical plasmas. The code is efficiently parallelized with the Message Passing Interface, and can be run on a laptop computer or on multiple cores on current supercomputers. Zeltron takes into account the effect of the radiation reaction force on the motion of the particles; it assigns variable weights to the macro-particles to model particle density gradients, and does not strictly conserve the total energy. The code uses linear interpolation to deposit the charges and currents generated by each particle at the nodes of the computational grid, and computes the charge and current densities for Maxwell's equations. Zeltron contains a large set of analysis tools, including plasma density, particle spectrum, optically thin synchrotron and inverse Compton spectra, angular distributions, and stress-energy tensor.

[ascl:1102.027]
ZENO: N-body and SPH Simulation Codes

The ZENO software package integrates N-body and SPH simulation codes with a large array of programs to generate initial conditions and analyze numerical simulations. Written in C, the ZENO system is portable between Mac, Linux, and Unix platforms. It is in active use at the Institute for Astronomy (IfA), at NRAO, and possibly elsewhere.

Zeno programs can perform a wide range of simulation and analysis tasks. While many of these programs were first created for specific projects, they embody algorithms of general applicability and embrace a modular design strategy, so existing code is easily applied to new tasks. Major elements of the system include structured data file utilities facilitate basic operations on binary data, including import/export of ZENO data to other systems; snapshot generation routines to create particle distributions with various properties; systems with user-specified density profiles can be realized in collisionless or gaseous form; multiple spherical and disk components may be set up in mutual equilibrium; and snapshot manipulation routines permit the user to sift, sort, and combine particle arrays, translate and rotate particle configurations, and assign new values to data fields associated with each particle.

Simulation codes include both pure N-body and combined N-body/SPH programs. Pure N-body codes are available in both uniprocessor and parallel versions. SPH codes offer a wide range of options for gas physics, including isothermal, adiabatic, and radiating models. Snapshot analysis programs calculate temporal averages, evaluate particle statistics, measure shapes and density profiles, compute kinematic properties, and identify and track objects in particle distributions. Visualization programs generate interactive displays and produce still images and videos of particle distributions; the user may specify arbitrary color schemes and viewing transformations.

[ascl:1306.014]
ZEUS-2D: Simulation of fluid dynamical flows

ZEUS-2D is a hydrodynamics code based on ZEUS which adds a covariant differencing formalism and algorithms for compressible hydrodynamics, MHD, and radiation hydrodynamics (using flux-limited diffusion) in Cartesian, cylindrical, or spherical polar coordinates.

[ascl:1102.028]
ZEUS-MP/2: Computational Fluid Dynamics Code

Hayes, John C.; Norman, Michael L.; Fiedler, Robert A.; Bordner, James O.; Li, Pak Shing; Clark, Stephen E.; Ud-Doula, Asif; Mac Low, Mordecai-Mark

ZEUS-MP is a multiphysics, massively parallel, message-passing implementation of the ZEUS code. ZEUS-MP offers an MHD algorithm that is better suited for multidimensional flows than the ZEUS-2D module by virtue of modifications to the method of characteristics scheme first suggested by Hawley & Stone. This MHD module is shown to compare quite favorably to the TVD scheme described by Ryu et al. ZEUS-MP is the first publicly available ZEUS code to allow the advection of multiple chemical (or nuclear) species. Radiation hydrodynamic simulations are enabled via an implicit flux-limited radiation diffusion (FLD) module. The hydrodynamic, MHD, and FLD modules can be used, singly or in concert, in one, two, or three space dimensions. In addition, so-called 1.5D and 2.5D grids, in which the "half-D'' denotes a symmetry axis along which a constant but nonzero value of velocity or magnetic field is evolved, are supported. Self-gravity can be included either through the assumption of a GM/r potential or through a solution of Poisson's equation using one of three linear solver packages (conjugate gradient, multigrid, and FFT) provided for that purpose. Point-mass potentials are also supported.

Because ZEUS-MP is designed for large simulations on parallel computing platforms, considerable attention is paid to the parallel performance characteristics of each module in the code. Strong-scaling tests involving pure hydrodynamics (with and without self-gravity), MHD, and RHD are performed in which large problems (2563 zones) are distributed among as many as 1024 processors of an IBM SP3. Parallel efficiency is a strong function of the amount of communication required between processors in a given algorithm, but all modules are shown to scale well on up to 1024 processors for the chosen fixed problem size.

[ascl:1511.022]
ZInCo: Zoomed Initial Conditions

ZInCo manipulates existing initial conditions (ICs) compatible with GADGET-2/3 (ascl:0003.001) ICs, allowing different flavors of zoom-in simulations rather then producing new ICs from scratch. The code can manipulate initial conditions with multiple types of particles, unlike the vast majority of zoom-in ICs codes available, preserving their properties and random field. This allows ZInCo to take advantage of other codes that produce ICs featuring a broad range of different cosmologies; it can be used also on existing ICs even in the unlikely case nothing is known about their properties. The code is written in C++ and parallelized using MPI.

[ascl:1202.002]
ZODIPIC: Zodiacal Cloud Image Synthesis

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

[ascl: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.

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