[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:2001.015]
gnm: The MCMC Jagger

gnm is an implementation of the affine-invariant sampler for Markov chain Monte Carlo (MCMC) that uses the Gauss-Newton-Metropolis (GNM) Algorithm. The GNM algorithm is specialized in sampling highly non-linear posterior probability distribution functions of the form exp(-||f(x)||^2/2). The code includes dynamic hyper-parameter optimization to increase performance of the sampling; other features include the Jacobian tester and an error bars creator.

[ascl:2001.014]
Peasoup: C++/CUDA GPU pulsar searching library

The NVIDIA GPU-based pipeline code peasoup provides a one-step pulsar search, including searching for pulsars with up to moderate accelerations, with only one command. Its features include dedispersion, dereddening in the Fourier domain, resampling, peak detection, and optional time series folding. peasoup's output is the candidate list.

[ascl:2001.013]
RPPPS: Re-analyzing Pipeline for Parkes Pulsar Survey

RPPPS (Re-analysing Pipeline for Parkes Pulsar Survey) uses Linux shell scripts, C language, and python code and two parallel strategies to reorganize the PRESTO (ascl:1107.017) pulsar search pipeline to run multiple processes in parallel, thus accelerating the search for pulsars. Though originally designed for reprocessing PMPS data, the code has also been successfully used with FAST (Five-hundred-meter Aperture Spherical radio Telescope) drift scan data. The pipeline is only CPU-based and can be easily and quickly deployed in computing nodes for testing purposes or data processes.

[ascl:2001.012]
MCMCI: Markov Chain Monte Carlo + Isochrones method for characterizing exoplanetary systems

MCMCI (Markov chain Monte Carlo + isochrones) characterizes a whole exoplanetary system directly by modeling the star and its planets simultaneously. The code, written in Fortran, uses light curves and basic stellar parameters with a transit analysis algorithm that interacts with stellar evolutionary models, thus using both model-dependent and empirical age indicators to characterize the system.

[ascl:2001.011]
ExoTETHyS: Exoplanetary transits and eclipsing binaries modeler

Morello, Giuseppe; Claret, Antonio; Martin-Lagarde, Marine; Cossou, Christophe; Tsiaras, Angelos; Lagage, Pierre-Olivier

ExoTETHyS models exoplanetary transits, eclipsing binaries, and related phenomena. The package calculates stellar limb-darkening coefficients down to <10 parts per million (ppm) and generates an exact transit light-curve based on the entire stellar intensity profile rather than limb-darkening coefficients.

[ascl:2001.010]
CosMOPED: Compressed Planck likelihood

CosMOPED (Cosmological MOPED) uses the MOPED (Multiple/Massively Optimised Parameter Estimation and Data compression) compression scheme to compress the Planck power spectrum. This convenient and lightweight compressed likelihood code is implemented in Python. To compute the likelihood for the LambdaCDM model using CosMOPED, one needs only six compression vectors, one for each parameter, and six numbers from compressing the Planck data using the six compression vectors. Using these, the likelihood of a theory power spectrum given the Planck data is the product of six one-dimensional Gaussians. Extended cosmological models require computing extra compression vectors.

[ascl:2001.009]
ORCS: Analysis engine for SITELLE spectral cubes

ORCS (Outils de Réduction de Cubes Spectraux) is an analysis engine for SITELLE spectral cubes. The software extracts integrated spectra, fits the sinc emission lines, and recalibrates data in wavelength, astrometry and flux. ORCS offers a choice between a Bayesian or a classical fitting algorithm , and also provides automatic source detection and radial velocity correction.

[ascl:2001.008]
DebrisDiskFM: Debris Disk Forward Modeling

DebrisDiskFM provides forward modeling for circumstellar debris disks in scattered light using the MCFOST disk modeling software to generate disk model images using given input parameters and emcee (ascl:1303.002) to obtain the posterior distributions for these parameters.

[ascl:2001.007]
BTS: Behind The Spectrum

Clarke, S. D.; Whitworth, A. P.; Spowage, R. L.; Duarte-Cabral, A.; Suri, S. T.; Jaffa, S. E.; Walch, S.; Clark, P. C.

Behind The Spectrum (BTS) is a fully-automated multiple-component fitter for optically-thin spectra. Written as a python module, the routine uses the first, second and third derivatives to determine thenumber of components in the spectrum. A least-squared fitting routine then determines the best fit with that number of components, checking for over-fitting and over-lapping velocity centroids.

[ascl:2001.006]
Protostellar Evolution: Stellar evolution simulator

Protostellar Evolution simulates the evolution of stellar stellar radius and luminosity from the bound core stage through to the core hydrogen ignition as a zero-age main-sequence (ZAMS) star and beyond. Written in Fortran 90, the code is implemented as a module of the FLASH astrophysical fluid dynamics code (ascl:1010.082).

[ascl:2001.005]
FAKEOBS: Model visibilities generator

The CASA (1107.013) task FAKEOBS generates model visibilities from already-existing measurement sets. This task can be used to substitute all the visibilities of the target with simulations computed from any model image. The measurement can either be with real or simulated data, the target can have been observed in mosaic mode, and there can be several sources (*e.g.*, bandpass calibrator, flux/phase calibrator, and target).

[ascl:2001.004]
FragMent: Fragmentation techniques for studying filaments

FragMent studies fragmentation in filaments by collating a number of different techniques, including nearest neighbour separations, minimum spanning tree, two-point correlation function, and Fourier power spectrum. It also performs model selection using a frequentist and Bayesian approach to find the best descriptor of a filament's fragmentation. While the code was designed to investigate filament fragmentation, the functions are general and may be used for any set of 2D points to study more general cases of fragmentation.

[ascl:2001.003]
sf3dmodels: Star-forming regions 3D modelling package

sf3dmodels models star-forming regions; it brings together analytical models in order to compute their physical properties in a 3-dimensional grid. The package can couple different models in a single grid to recreate complex star forming systems such as those being revealed by current instruments. The output data can be read with LIME (ascl:1107.012) or RADMC-3D (ascl:1108.016) to carry out radiative transfer calculations of the modeled region.

[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.

[ascl:2001.001]
Min-CaLM: Mineral compositional analysis on debris disk spectra

Min-CaLM performs automated mineral compositional analysis on debris disk spectra. The user inputs the debris disk spectrum, and using Min-CaLM's built-in mineralogical library, Min-CaLM calculates the relative mineral abundances within the disk. To do this calculation, Min-CaLM converts the debris disk spectrum and the mineralogical library spectra into a system of linear equations, which it then solves using non-negative least square minimization. This code comes with a GitHub tutorial on how to use the Min-CaLM package.

[submitted]
amber_meta

amber_meta integrates a few routines to launch AMBER (the “Apertif Monitor for Bursts Encountered in Real-time”, https://github.com/AA-ALERT/AMBER) in a systematic manner. To avoid typing a string in the command line manually with all parameters required to launch AMBER, amber_meta generates the command from configuration files, and can directly launch AMBER instances.

[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.

[submitted]
JetSeT: numerical modeling and SED fitting tool for relativistic jets

JetSeT is an open source C/Python framework to reproduce radiative and accelerative processes acting in relativistic jets, allowing to fit the numerical models to observed data. The main features of this framework are:

- Handling observed data: re-binning, definition of data sets, bindings to astropy tables and quantities

definition of complex numerical radiative scenarios: Synchrotron Self-Compton (SSC), external Compton

(EC) and EC against the CMB

- Constraining of the model in the pre-fitting stage, based on accurate and already published

phenomenological trends. In particular, starting from phenomenological parameters, such as spectral indices,

peak fluxes and frequencies, and spectral curvatures, that the code evaluates automatically, the pre-fitting

algorithm is able to provide a good starting model, following the phenomenological trends that I have

implemented. fitting of multiwavelength SEDs using both frequentist approach (iminuit) and bayesian MCMC

sampling (emcee)

- Self-consistent temporal evolution of the plasma under the effect of radiative and accelerative processes,

both first order and second order (stochastic acceleration) processes.

[submitted]
SDSS Dual Active Nuclei Galaxy Detection Pipeline

Dual Active Nuclei Galaxies (DAGNs) are rare occurrences in the sky. Until now, most AGNs have been described to be found serendipitously, or by manual observation. In recent years, there has been an increasing interest in such dual AGNs and their astrophysical properties. Their study is important to the understanding of galaxy formation, star formation and these objects are the precursors to Gravitational Wave Sources.

Hence, we have devised a pipeline, that along with systematic data collection, can detect such dual AGN candidates. A novel algorithm 'Graph-Boosted Gradient Ascent' has been devised to detect whether an R-band image of a galaxy is a potential candidate for a DAGN or not. The pipeline can be cloned to a user's machine, and by joining the AstrIRG_DAGN group on SciServer, astronomers can collectively contribute to the mining of DAGNs.

[submitted]
K2CE: Kepler-K2 Cadence Events

Since early 2018, the Kepler/K2 project has been performing a uniform global reprocessing of data from K2 Campaigns 0 through 14. Subsequent K2 campaigns (C15-C19) are being processed using the same processing pipeline. One of the major benefits of the reprocessing effort is that, for the first time, short-cadence (1-min) light curves are produced in addition to the standard long-cadence (30-min) light curves. Users have been cautioned that the Kepler pipeline detrending module (PDC), developed for use on original Kepler data, has not been tailored for use on short-cadence K2 observations. Systematics due to events on fast timescales, such as thruster firings, are sometimes poorly corrected for many short-cadence targets. A Python data visualization and manipulation tool, called Kepler-K2 Cadence Events, has been developed that identifies and removes cadences associated with problematic thruster events, thus producing better light curves. Kepler-K2 Cadence Events can be used to visualize and manipulate light curve files and target pixel files from the Kepler, K2, and TESS missions. This software is available at the following NASA GitHub repository https://github.com/nasa/K2CE .

[ascl:1912.020]
MRExo: Non-parametric mass-radius relationship for exoplanets

MRExo performs non-parametric fitting and analysis of the mass-radius (M-R) relationship for exoplanets. Written in Python, it offers tools for fitting the M-R relationship to a given data set and also includes predicting (M->R, and R->M) and plotting functions.

[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: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:1912.017]
PTMCMCSampler: Parallel tempering MCMC sampler package written in Python

PTMCMCSampler performs MCMC sampling using advanced techniques. The code implements a variety of proposal schemes, including adaptive Metropolis, differential evolution, and parallel tempering, which can be used together in the same run.

[ascl:1912.016]
GWpy: Python package for studying data from gravitational-wave detectors

Macleod, Duncan; Urban, Alex L.; Coughlin, Scott; Massinger, Thomas; Pitkin, Matt; Altin, Paul; Areeda, Joseph; Quintero, Eric; Leinweber, Katrin

The Python package GWpy analyzes and characterizes gravitational wave data. It provides a user-friendly, intuitive interface to the common time-domain and frequency-domain data produced by the LIGO and Virgo observatories and their analyses. The core Python infrastructure is influenced by, and extends the functionality of, the Astropy (ascl:1304.002) package, and its methodology has been derived from, and augmented by, the LIGO Algorithm Library Suite (LALSuite), a large collection of primarily C99 routines for analysis and manipulation of data from gravitational-wave detectors. These packages use the SWIG program to produce Python wrappings for all C modules, allowing the GWpy package to leverage both the completeness, and the speed, of these libraries.

[ascl:1912.015]
ENTERPRISE: Enhanced Numerical Toolbox Enabling a Robust PulsaR Inference SuitE

ENTERPRISE (Enhanced Numerical Toolbox Enabling a Robust PulsaR Inference SuitE) is a pulsar-timing analysis code which performs noise analysis, gravitational-wave searches, and timing model analysis. It uses Tempo2 (ascl:1210.015) to find the maximum-likelihood fit for the timing parameters and the basis of the fit for the red noise parameters if they are significant.

[ascl:1912.014]
HARMPI: 3D massively parallel general relativictic MHD code

HARMPI is a parallel, 3D version of HARM (ascl:1209.005), which solves hyperbolic partial differential equations in conservative form using high-resolution shock-capturing techniques. The code is parallelized using MPI and is fully operational in 3D. HARMPI, like HARM, is capable of using non-uniform grids and solves the relativistic magnetohydrodynamic equations of motion on a stationary black hole spacetime in Kerr-Schild coordinates to evolve an accretion disk model.

[ascl:1912.013]
GriSPy: Fixed-radius nearest neighbors grid search in Python

Chalela, Martín; Sillero, Emanuel; Pereyra, Luis; Garcia, Mario A.; Cabral, Juan B.; Lares, Marcelo; Merchán, Manuel

GriSPy (Grid Search in Python) uses a regular grid search algorithm for quick fixed-radius nearest-neighbor lookup. It indexes a set of k-dimensional points in a regular grid providing a fast approach for nearest neighbors queries. Optional periodic boundary conditions can be provided for each axis individually. GriSPy implements three types of queries: *bubble*, *shell* and the *nth-nearest*, and offers three different metrics of interest in astronomy: the *Euclidean* and two distance functions in spherical coordinates of varying precision, *haversine* and *Vincenty*. It also provides a custom distance function. GriSPy is particularly useful for large datasets where a brute-force search is not practical.

[ascl:1912.012]
GAME: GAlaxy Machine learning for Emission lines

GAME infers different ISM physical properties by analyzing the emission line intensities in a galaxy spectrum. The code is trained with a large library of synthetic spectra spanning many different ISM phases, including HII (ionized) regions, PDRs, and neutral regions. GAME is based on a Supervised Machine Learning algorithm called AdaBoost with Decision Trees as base learner. Given a set of input lines in a spectrum, the code performs a training on the library and then evaluates the line intensities to give a determination of the physical properties. The errors on the input emission line intensities and the uncertainties on the physical properties determinations are also taken into account. GAME infers gas density, column density, far-ultraviolet (FUV, 6–13.6 eV) flux, ionization parameter, metallicity, escape fraction, and visual extinction. A web interface for using the code is available.

[ascl:1912.011]
QSOSIM: Simulated Quasar Spectrum Generator

QSOSIM realistically simulates high-resolution quasar spectra using a set of basic parameters (magnitude, redshift, and spectral index). The simulated spectra include physical effects seen in the real data: the power-law quasar continuum, the narrow and broad emission lines, absorption by neutral hydrogen (HI) in the Lyman alpha forest, and heavy element transitions along the line of sight. The code uses empirical HI column density, redshift, and b-parameter distributions to simulate absorption in the Lyman alpha forest. All absorbers with column densities larger than log [N(HI)/cm^{2}]>17 have heavy element absorption, for which the column densities are calculated using the plasma simulation code CLOUDY (ascl:9910.001) and the radiative transfer code CUBA. The code also simulates the clustering of the intergalactic medium along the line of sight, the proximity effect of the quasar, and the effect of the cosmic ultraviolet background. Each simulated spectrum is saved in a single FITS file in as a noiseless R=100000 spectrum, as well as a spectrum convolved with Sloan Digital Sky Survey resolution (R=10000) and realistic noise.

[ascl:1912.010]
AstroAccelerate: Accelerated software package for processing time-domain radio astronomy data

AstroAccelerate processes time-domain radio astronomy data. It offers a standalone code that can be used to process filterbank data and a library that performs GPU-accelerated single pulse processing (SPS), Fourier Domain Acceleration Searching (FDAS) and dedispersion in real-time on very large data-sets comparable to those that will be produced by next-generation radio telescopes such as the SKA. AstroAccelerate uses NVIDIAR GPUs, and is configurable, stable, and easily maintained.

[ascl:1912.009]
FORSTAND: Flexible ORbit Superposition Toolbox for ANalyzing Dynamical models

FORSTAND constructs dynamical models of galaxies using the Schwarzschild orbit-superposition method; the method is available as part of the AGAMA (ascl:1805.008) framework. The models created are constrained by line-of-sight kinematic observations and are applicable to galaxies of all morphological types, including disks and triaxial rotating bars.

[submitted]
Exo-MerCat: a merged exoplanet catalog with Virtual Observatory connection.

The heterogeneity of papers dealing with the discovery and characterization of exoplanets makes every attempt to maintain a uniform exoplanet catalog almost impossible. Four sources currently available online (NASA Exoplanet Archive, Exoplanet Orbit Database, Exoplanet Encyclopaedia, and Open Exoplanet Catalogue) are commonly used by the community, but they can hardly be compared, due to discrepancies in notations and selection criteria.

Exo-MerCat is a Python code that collects and selects the most precise measurement for all interesting planetary and orbital parameters contained in the four databases, accounting for the presence of multiple aliases for the same target. It can download information about the host star as well by the use of Virtual Observatory ConeSearch connections to the major archives such as SIMBAD and those available in VizieR. A Graphical User Interface is provided to filter data based on the user's constraints and generate automatic plots that are commonly used in the exoplanetary community.

With Exo-MerCat, we retrieved a unique catalog that merges information from the four main databases, standardizing the output and handling notation differences issues. Exo-MerCat can correct as many issues that prevent a direct correspondence between multiple items in the four databases as possible, with the available data. The catalog is available as a VO resource for everyone to use and it is periodically updated, according to the update rates of the source catalogs.

[submitted]
PyFOSC: a pipeline toolbox for BFOSC/YFOSC long-slit spectroscopy data reduction

PyFOSC is a pipeline toolbox for long-slit spectroscopy data reduction written in Python. It can be used for FOSC (Faint Object Spectrograph and Camera) data from Xinglong/Lijiang 2-meter telescopes in China. This pipeline privodes a neat way for data pre-processing, including updating missing header fileds for BFOSC data, reducing fits file extension for YFOSC data, etc. And it makes the data reduction procedure efficient by using previously identified lamp spectra as re-identification references during wavelength calibration, and applying multiprocessing in some modules. PyFOSC also enables customization for any other long-slit spectroscopy data.

[ascl:1912.008]
PopSyCLE: Population Synthesis for Compact object Lensing Events

PopSyCLE performs compact object population synthesis while taking photometric and astrometric microlensing effects into consideration. It uses Galaxia (ascl:1101.007) to produces a synthetic survey, injects compact objects into the resulting survey, and then produces a list of microlensing events, enabling the discovery of black holes with microlensing. It can be used to examine historical microlensing events from photometric surveys to statistically constrain the abundance of black holes in our galaxy, and to forward model microlensing survey results to constrain, for example, the properties of compact objects, Galactic structure, and the initial-final mass relation.

[ascl:1912.007]
anesthetic: Nested sampling visualization

anesthetic brings together tools for processing nested sampling chains, leveraging standard scientific python libraries. The code provides computation of Bayesian evidences, Kullback-Liebler divergences and Bayesian model dimensionalities, marginalized 1d and 2d plots, and dynamic replaying of nested sampling. anesthetic was designed primarily for use with nested sampling outputs, although it can be used for normal MCMC chains.

[ascl:1912.006]
HSIM: HARMONI simulation pipeline

Zieleniewski, S.; Thatte, N.; Kendrew, S.; Houghton, R. C. W.; Swinbank, A. M.; Tecza, M.; Clarke, F.; Fusco, T.

HSIM simulates observations with HARMONI on the Extremely Large Telescope. HSIM takes high spectral and spatial resolution input data cubes, encoding physical descriptions of astrophysical sources, and generates mock observed data cubes. The simulations incorporate detailed models of the sky, telescope, instrument, and detectors to produce realistic mock data. HSIM performs in-depth simulations for several key science cases as part of the design and development of the HARMONI integral field spectrograph, including the ELT AO performance, atmospheric effects and realistic detector statistics.

[ascl:1912.005]
Athena++: Radiation GR magnetohydrodynamics code

Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code (ascl:1010.014) in C++. Compared to earlier versions, the Athena++ code has much more flexible coordinate and grid options and supports new physics. It also offers significantly improved performance and scalability, and improved source code clarity and modularity. Athena++ supports compressible hydrodynamics and MHD in 1D, 2D, and 3D, and special and general relativistic hydrodynamics and MHD. In addition, it supports Cartesian, cylindrical, or spherical polar coordinates; static or adaptive mesh refinement in any coordinate system; mixed parallelization with both OpenMP and MPI; and a task-based execution model for improved load balancing, scalability and modularity.

[ascl:1912.004]
DALiuGE: Data Activated Liu Graph Engine

Wu, Chen; Tobar, Rodrigo; Vinsen, Kevin; Wicenec, Andreas; Pallot, Dave; Lao, Baoqiang; Wang, Ruonan; An, Tao; Boulton, Mark; Cooper, Ian; Dodson, Richard.; Dolensky, Markus; Mei, Ying; Wang, Feng

DALiuGE provides a distributed data management platform and a scalable pipeline execution environment to support continuous, soft real-time, data-intensive processing for producing radio astronomy data products; it originated from a prototyping activity as part of the SKA SDP Consortium called Data Flow Management System (DFMS). Though the development of DALiuGE is largely based on radio astronomy processing requirements, it has adopted a generic, data-driven framework architecture potentially applicable to many other data-intensive applications.

[ascl:1912.003]
ASKAPsoft: ASKAP science data processor software

Guzman, Juan; Whiting, Matthew; Voronkov, Max; Mitchell, Daniel; Ord, Stephen; Collins, Daniel; Marquarding, Malte; Lahur, Paulus; Maher, Tony; Van Diepen, Ger; Bannister, Keith; Wu, Xinyu; Lenc, Emil; Khoo, Jonathan; Bastholm, Eric

ASKAPsoft provides data processing functionality for Australian Square Kilometre Array Pathfinder, including calibration, spectral line imaging, continuum imaging, source detection and generation of source catalogs, and transient detection. The MPI-based package is the primary software for storing and processing raw data, and initiating the archiving of resulting science data products into the data archive (CASDA). The processing pipelines within ASKAPsoft are largely written in C++ built on top of casacore (ascl:1912.002) and other third party libraries.

[ascl:1912.002]
casacore: Suite of C++ libraries for radio astronomy data processing

The casacore package contains the core libraries of the old AIPS++/CASA (ascl:1107.013) package. This split was made to get a better separation of core libraries and applications. CASA is now built on top of Casacore. The system consists of a set of layered libraries (packages) and includes a library (using Boost-Python) that converts the basic Casacore types (e.g., Array, Record) to and from Python.

Casacore includes the casa package for core functionality and data types like Array and Record; a scimath package for N-dim functions with auto-differentiation and linear or non-linear fitting; and a

tables package for the table data system supporting N-dim arrays with advanced querying. It also includes the measures package to manage values in astronomical reference frames using physical units (Quanta) and the MeasurementSets for storing data in the UV-domain, and also the images package for N-dim images in world coordinates with various analysis operations.

[ascl:1912.001]
Polyspectrum: Computing polyspectra using an FFT estimator

Polyspectrum computes the polyspectrum from 3D grids using a fast Fourier transformation (FFT) estimator. The code, written in C and MPI-parallelized, support the computation of power- and bispectra; it also supports higher-order polyspectra, but streamlining the input data is required.

[ascl:1911.024]
comb: Spectral line data reduction and analysis package

comb is a single-dish radio astronomy spectral line data reduction and analysis package developed at AT&T Bell labs and was used for data reduction for many single-dish telescopes, including Bell Labs 7-m, NRAO 12-m, DSN network, FCRAO 14-m, Arecibo, AST/RO, SEST, BIMA, and in 2011-2012, the Stratospheric Terahertz Observatory. A cookbook for the code is available.

[ascl:1911.023]
miluphcuda: Smooth particle hydrodynamics code

Schaefer, Christoph M.; Riecker, Sven; Wandel, Oliver; Maindl, Thomas I.; Scherrer, Samuel; Werner, Janka; Burger, Christoph; Morlock, Marius

miluphcuda is the CUDA port of the original miluph code; it runs on single Nvidia GPUs with compute capability 5.0 and higher and provides fast and efficient computation. The code can be used for hydrodynamical simulations and collision and impact physics, and features self-gravity via Barnes-Hut trees and porosity models such as P-alpha and epsilon-alpha. It can model solid bodies, including ductile and brittle materials, as well as non-viscous fluids, granular media, and porous continua.

[ascl:1911.022]
FFTLog-and-beyond: Generalized FFTLog algorithm

FFTLog-and-beyond takes the FFTLog algorithm for single-Bessel integrals and generalizes it for integrals containing a derivative of the Bessel function to solve the non-Limber integrals. The full non-Limber angular power spectrum integral is simplified by noting the small contribution from unequal-time nonlinear terms; this significantly reduces the computation and avoids the double-Bessel integral. The original FFTLog algorithm is also extended to compute integrals containing derivatives of Bessel functions, which can be used to efficiently compute angular power spectra including redshift-space distortions (RSD) and Doppler effects. C and Python versions of the code are available.

[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: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:1911.019]
OrbWeaver: Galaxy/(sub)halo orbital processing tool

OrbWeaver extracts orbits from halo catalogs, enabling large statistical studies of their orbital parameters. The code is run in two stages. For the first run, a configuration file is used to modify orbit host selection and the region around orbit host used for the superset of orbiting halos. Each orbit host has a orbit forest (containing halos that passed within the region of interest); the code generates a pre-processed catalog which contains a superset of orbiting halo for each identified orbit host. The second run uses the file list generated in the first stage for the creation of the orbit catalog, which is the final output.

[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:1911.017]
HLattice: Scalar fields and gravity simulator for the early universe

HLattice simulates scalar fields and gravity in the early universe. The code allows the user to select between symplectic integrators, descretization schemes, and metrics such as Minkowski or FRW backgrounds and adaptice schemes in an "all-in-one" configuration file.

[ascl:1911.016]
CLUSTEREASY: Lattice simulator for evolving interacting scalar fields in an expanding universe on parallel computing clusters

CLUSTEREASY is a parallel programming extension of the simulation program LATTICEEASY (ascl:1911.015); running the program in parallel greatly extends the range of scales and times that can be simulated. The program is particularly useful for the study of reheating and thermalization after inflation.

[ascl:1911.015]
LATTICEEASY: Lattice simulator for evolving interacting scalar fields in an expanding universe

LATTICEEASY creates lattice simulations of the evolution of interacting scalar fields in an expanding universe. The program can do runs with different parameters and new models can be easily introduced for evaluation. Simulations can be done in one, two, or three dimensions by resetting a single variable. Mathematica notebooks for plotting the output and a range of models are also available for download; a parallel processing version of LATTICEEASY called CLUSTEREASY (ascl:1911.016) is also available.

[ascl:1911.014]
MORDI: Massively-Overlapped Ring-Diagram Inversion

MORDI (Massively-Overlapped Ring-Diagram Inversion) performs three-dimensional ring-diagram inversions. The code reads in frequency shift measurements and their associated sensitivity kernels and outputs two-dimensional slices of the subsurface flow field at a constant depth and (optionally) the associated averaging kernels. It relies on both distributed-memory (MPI) and shared-memory (OpenMP) parallelism to scale efficiently up to a few thousand processors, but can also run reasonably well on small machines (1-4 cpus). The actions of the code are modified by command-line parameters, which enable a significant amount of flexibility when setting up an inversion.

[ascl:1911.013]
ATLAS: Turning Dopplergram images into frequency shift measurements

ATLAS performs the tracking, projecting, power-spectrum-making, and ring-fitting needed to turn a set of Dopplergram images into a set of frequency shift measurements. This code is essentially a combination of three codes, FRACK (FORTRAN Tracking), PSPEC (Power SPECtrum), and MRF (Multi-Ridge Fitting), included in the ATLAS package. ATLAS reads in a list of longitude/latitude coordinates corresponding to the desired tile centers and a set of full-disk Dopplergram images and outputs frequency shift measurements from each wave mode of each tile. The code relies on both distributed-memory (MPI) and shared-memory (OpenMP) parallelism to scale up to around 1000 processes. Due to the immense volume of data produced by the tracking and projecting steps, the intermediate data products (tiles, power spectra) are never written out.

[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:1911.011]
IDG: Image Domain Gridding

IDG (Image Domain Gridding) is an imager that makes w-term corrections and a-term corrections computationally very cheap. It works with WSClean (ascl:1408.023) and supports the same cleaning and data selections options that WSClean offers in normal mode (such as cotton-schwab, multi-frequency multi-scale cleaning, and auto-masking). IDG also allows gridding with a time-variable beam including the LOFAR, AARTFAAC and MWA beam and can perform full beam or differential correction. The code requires measurement sets with four polarizations (*e.g.* XX/XY/YX/YY), can apply a spatially varying time-variable TEC term that can additionally be different for different antennas and output channels, and performs extremely well on GPUs.

[ascl:1911.010]
Fruitbat: Fast radio burst redshift estimation

Fruitbat estimates the redshift of Fast Radio Bursts (FRB) from their dispersion measure. The code combines various dispersion measure (DM) and redshift relations with the YMW16 galactic dispersion measure model into a single easy to use API.

[ascl:1911.009]
frbpoppy: Fast radio burst population synthesis in Python

frbpoppy conducts fast radio burst population synthesis and continues the work of PSRPOP (ascl:1107.019) and PsrPopPy (ascl:1501.006) in the realm of FRBs. The code replicates observed FRB detection rates and FRB distributions in three steps. It first simulates a cosmic population of one-off FRBs and allows the user to select options such as models for source number density, cosmology, DM host/IGM/Milky Way, luminosity functions, and emission bands as well as maximum redshift and size of the FRB population. The code then generates a survey by adopting a beam pattern using various survey parameters, among them telescope gain, sampling time, receiver temperature, central frequency, channel bandwidth, number of polarizations, and survey region limits. Finally, frbpoppy convolves the generated intrinsic population with the generated survey to simulate an observed FRB population.

[ascl:1911.008]
HeatingRate: Radioactive heating rate and macronova (kilonova) light curve

HeatingRate calculates the nuclear heating rates [erg/s/g] of beta-decay, alpha-decay, and spontaneous fission of r-process nuclei, taking into account for thermalization of gamma-rays and charged decay products in r-process ejecta. It uses the half-lives and injection energy spectra from an evaluated nuclear data library (ENDF/B-VII.1). Each heating rate is computed for given abundances, ejecta mass, velocity, and density profile. HeatingRate also computes the bolometric light curve and the evolution of the effective temperature for given abundances, ejecta mass, velocity, and density profile assuming opacities independent of the wavelength.

[ascl:1911.007]
planetplanet: General photodynamical code for exoplanet light curves

planetplanet models exoplanet transits, secondary eclipses, phase curves, and exomoons, as well as eclipsing binaries, circumbinary planets, and more. The code was originally developed to model planet-planet occultation (PPO) light curves for the TRAPPIST-1 system, but it is generally applicable to any exoplanet system. During a PPO, a planet occults (transits) the disk of another planet in the same planetary system, blocking its thermal (and reflected) light, which can be measured photometrically by a distant observer. planetplanet is coded in C and wrapped in a user-friendly Python interface.

[ascl:1911.006]
ATHOS: A Tool for HOmogenizing Stellar parameters

ATHOS provides on-the-fly stellar parameter determination of FGK stars based on flux ratios from optical spectra. Once configured properly, it will measure flux ratios in the input spectra and deduce the stellar parameters effective temperature, iron abundance (a.k.a [Fe/H]), and surface gravity by employing pre-defined analytical relations. ATHOS can be configured to run in parallel in an arbitrary number of threads, thus enabling the fast and efficient analysis of huge datasets.

[ascl:1911.005]
MARTINI: Mock spatially resolved spectral line observations of simulated galaxies

MARTINI (Mock APERTIF-like Radio Telescope Interferometry of the Neutal ISM) creates synthetic resolved HI line observations (data cubes) of smoothed-particle hydrodynamics simulations of galaxies. The various aspects of the mock-observing process are divided logically into sub-modules handling the data cube, source, beam, noise, spectral model and SPH kernel. MARTINI is object-oriented: each sub-module provides a class (or classes) which can be configured as desired. For most sub-modules, base classes are provided to allow for straightforward customization. Instances of each sub-module class are then given as parameters to the Martini class. A mock observation is then constructed by calling a handful of functions to execute the desired steps in the mock-observing process.

[ascl:1911.004]
PypeIt: Python spectroscopic data reduction pipeline

Prochaska, J. Xavier; Hennawi, Joseph; Cooke, Ryan; Westfall, Kyle; Wang, Feige; Farina, Emanuele Paolo; Hsyu, Tiffany; Wasserman, Asher; Villaume, Alexa; Young, David; Simha, Sunil; Wilde, Matt; Tejos, Nicolas; Isbell, Jacob; Betts, Edward; Holden, Brad

PypeIt reduces data from echelle and low-resolution spectrometers; the code can be run in several modes of reduction that demark the level of sophistication (e.g. quick and dirty vs. MonteCarlo) and also the amount of output written to disk. It also generates numerous data products, including 1D and 2D spectra; calibration images, fits, and meta files; and quality assurance figures.

[ascl:1911.003]
OpenSPH: Astrophysical SPH and N-body simulations and interactive visualization tools

OpenSPH runs hydrodynamical and N-body simulations and was written for asteroid collisions and subsequent gravitational evolution. The code offers SPH and N-body solvers with several different equations of state and material rheologies. It is written in C++14 with a modular object-oriented design, focused on extensibility and maintainability, and it can be used either as a library or as a standalone graphical program that allows to set up the problem in a convenient graphical node editor. The graphical program further allows real-time visualization of the simulation, diagnostics and tools for analysis of the results.

[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:1911.001]
PLAN: A Clump-finder for Planetesimal Formation Simulations

PLAN (PLanetesimal ANalyzer) identifies and characterizes planetesimals produced in numerical simulations of the Streaming Instability that includes particle self-gravity with code Athena (ascl:1010.014). PLAN works with the 3D particle output of Athena and finds gravitationally bound clumps robustly and efficiently. PLAN — written in C++ with OpenMP/MPI — is massively parallelized, memory-efficient, and scalable to analyze billions of particles and multiple snapshots simultaneously. The approach of PLAN is based on the dark matter halo finder HOP (ascl:1102.019), but with many customizations for planetesimal formation. PLAN can be easily adapted to analyze other object formation simulations that use Lagrangian particles (e.g., Athena++ simulations). PLAN is also equipped with a toolkit to analyze the grid-based hydro data (VTK dumps of primitive variables) from Athena, which requires the Boost MultiDimensional Array Library.

[submitted]
Network Flux Transport Demonstration

We have developed a method to efficiently simulate the dynamics of the magnetic flux in the solar network. We call this method Network Flux Transport (NFT). Implemented using a Spherical Centroidal Voronoi Tessellation (SCVT) based network model, magnetic flux is advected by photospheric plasma velocity fields according to the geometry of the SCVT model. We test NFT by simulating the magnetism of the Solar poles. The poles of the sun above 55 deg latitude are free from flux emergence from active regions or ephemeral regions. As such, they are ideal targets for a simplified simulation that relies on the strengths of the NFT model. This simulation method reproduces the magnetic and spatial distributions for the solar poles over two full solar cycles.

[ascl:1910.022]
qnm: Kerr quasinormal modes, separation constants, and spherical-spheroidal mixing coefficients calculator

qnm computes the Kerr quasinormal mode frequencies, angular separation constants, and spherical-spheroidal mixing coefficients. The qnm package includes a Leaver solver with the Cook-Zalutskiy spectral approach to the angular sector, and a caching mechanism to avoid repeating calculations. A large cache of low ℓ, m, n modes is available for download and can be installed with a single function call and interpolated to provide good initial guess for root-polishing at new values of spin.

[ascl:1910.021]
AOtools: Adaptive optics modeling and analysis toolkit

The AOtools package offers generic adaptive optics processing tools in addition to astronomy-specific methods; among these are analyzing data in the pupil plane, images and point spread functions in the focal plane, wavefront sensors, modeling of atmospheric turbulence, physical optical propagation of wavefronts, and conversion functions to convert stellar brightness into photon flux for a given waveband. The software also calculates integrated atmospheric parameters, such as coherence time and isoplanatic angle from atmospheric turbulence and wind speed profile.

[ascl:1910.020]
OCD: O'Connell Effect Detector using push-pull learning

OCD (O'Connell Effect Detector) detects eclipsing binaries that demonstrate the O'Connell Effect. This time-domain signature extraction methodology uses a supporting supervised pattern detection algorithm. The methodology maps stellar variable observations (time-domain data) to a new representation known as Distribution Fields (DF), the properties of which enable efficient handling of issues such as irregular sampling and multiple values per time instance. Using this representation, the code applies a metric learning technique directly on the DF space capable of specifically identifying the stars of interest; the metric is tuned on a set of labeled eclipsing binary data from the Kepler survey, targeting particular systems exhibiting the O’Connell Effect. This code is useful for large-scale data volumes such as that expected from next generation telescopes such as LSST.

[ascl:1910.019]
Cobaya: Bayesian analysis in cosmology

Cobaya (Code for BAYesian Analysis) provides a framework for sampling and statistical modeling and enables exploration of an arbitrary prior or posterior using a range of Monte Carlo samplers, including the advanced MCMC sampler from CosmoMC (ascl:1106.025) and the advanced nested sampler PolyChord (ascl:1502.011). The results of the sampling can be analyzed with GetDist (ascl:1910.018). It supports MPI parallelization and is highly extensible, allowing the user to define priors and likelihoods and create new parameters as functions of other parameters.

It includes interfaces to the cosmological theory codes CAMB (ascl:1102.026) and CLASS (ascl:1106.020) and likelihoods of cosmological experiments, such as Planck, Bicep-Keck, and SDSS. Automatic installers are included for those external modules; Cobaya can also be used as a wrapper for cosmological models and likelihoods, and integrated it in other samplers and pipelines. The interfaces to most cosmological likelihoods are agnostic as to which theory code is used to compute the observables, which facilitates comparison between those codes. Those interfaces are also parameter-agnostic, allowing use of modified versions of theory codes and likelihoods without additional editing of Cobaya’s source.

[ascl:1910.018]
GetDist: Monte Carlo sample analyzer

GetDist analyzes Monte Carlo samples, including correlated samples from Markov Chain Monte Carlo (MCMC). It offers a point and click GUI for selecting chain files, viewing plots, marginalized constraints, and LaTeX tables, and includes a plotting library for making custom publication-ready 1D, 2D, 3D-scatter, triangle and other plots. Its convergence diagnostics include correlation length and diagonalized Gelman-Rubin statistics, and the optimized kernel density estimation provides an automated optimal bandwidth choice for 1D and 2D densities with boundary and bias correction. It is available as a standalong package and with CosmoMC (ascl:1106.025).

[ascl:1910.017]
ChainConsumer: Corner plots, LaTeX tables and plotting walks

ChainConsumer consumes the chains output from Monte Carlo processes such as MCMC to produce plots of the posterior surface inferred from the chain distributions, to plot the chains as walks to check for mixing and convergence, and to output parameter summaries in the form of LaTeX tables. It handles multiple models (chains), allowing for model comparison using AIC, BIC or DIC metrics.

[ascl:1910.016]
MiSTree: Construct and analyze Minimum Spanning Tree graphs

MiSTree quickly constructs minimum spanning tree graphs for various coordinate systems, including Celestial coordinates, by using a k-nearest neighbor graph (k NN, rather than a matrix of pairwise distances) which is then fed to Kruskal's algorithm to create the graph. MiSTree bins the MST statistics into histograms and plots the distributions; enabling the inclusion of high-order statistics information from the cosmic web to provide additional information that improves cosmological parameter constraints. Though MiSTree was designed for use in cosmology, it can be used in any field requiring extracting non-Gaussian information from point distributions.

[ascl:1910.015]
MarsLux: Illumination Mars maps generator

MarsLux generates illumination maps of Mars from Digital Terrain Model (DTM), permitting users to investigate in detail the illumination conditions on Mars based on its topography and the relative position of the Sun. MarsLux consists of two Python codes, SolaPar and MarsLux. SolaPar calculates the matrix with solar parameters for one date or a range between the two. The Marslux code generates the illumination maps using the same DTM and the files generated by SolaPar. The resulting illumination maps show areas that are fully illuminated, areas in total shadow, and areas with partial shade, and can be used for geomorphological studies to examine gullies, thermal weathering, or mass wasting processes as well as for producing energy budget maps for future exploration missions.

[ascl:1910.014]
ANNz2: Estimating photometric redshift and probability density functions using machine learning methods

ANNz2, a newer implementation of ANNz (ascl:1209.009), utilizes multiple machine learning methods such as artificial neural networks, boosted decision/regression trees and k-nearest neighbors to measure photo-zs based on limited spectral data. The code dynamically optimizes the performance of the photo-z estimation and properly derives the associated uncertainties. In addition to single-value solutions, ANNz2 also generates full probability density functions (PDFs) in two different ways. In addition, estimators are incorporated to mitigate possible problems of spectroscopic training samples which are not representative or are incomplete. ANNz2 is also adapted to provide optimized solutions to general classification problems, such as star/galaxy separation.

[ascl:1910.013]
E0102-VR: Virtual Reality application to visualize the optical ejecta in SNR 1E 0102.2-7219

E0102-VR facilitates the characterization of the 3D structure of the oxygen-rich optical ejecta in the young supernova remnant 1E 0102.2-7219 in the Small Magellanic Cloud. This room-scale Virtual Reality application written for the HTC Vive contributes to the exploration of the scientific potential of this technology for the field of observational astrophysics.

[ascl:1910.012]
AOTOOLS: Reduce IR images from Adaptive Optics

AOTOOLS reduces IR images from adaptive optics. It uses effective dithering, either sky subtraction or dark-subtration, and flat-fielding techniques to determine the effect of the instrument on an image of an object. It also performs bad pixel masking, degrades an AO on-axis PSF due to effects of anisoplanicity, and corrects an AO on-axis PSF due to effects of seeing.

[ascl:1910.011]
LEO-Py: Likelihood Estimation of Observational data with Python

LEO-Py uses a novel technique to compute the likelihood function for data sets with uncertain, missing, censored, and correlated values. It uses Gaussian copulas to decouple the correlation structure of variables and their marginal distributions to compute likelihood functions, thus mitigating inconsistent parameter estimates and accounting for non-normal distributions in variables of interest or their errors.

[ascl:1910.010]
PEXO: Precise EXOplanetology

Feng, Fabo; Lisogorskyi, Maksym; Jones, Hugh R. A.; Kopeikin, Sergei M.; Butler, R. Paul; Anglada-Escude, Guillem; Boss, Alan P.

PEXO provides a global modeling framework for ns timing, μas astrometry, and μm/s radial velocities. It can account for binary motion and stellar reflex motions induced by planetary companions and also treat various relativistic effects both in the Solar System and in the target system (Roemer, Shapiro, and Einstein delays). PEXO is able to model timing to a precision of 1 ns, astrometry to a precision of 1 μas, and radial velocity to a precision of 1 μm/s.

[ascl:1910.009]
orbitize: Orbit-fitting for directly imaged objects

Blunt, Sarah; Wang, Jason; Angelo, Isabel; Ngo, Henry; Cody, Devin; De Rosa, Robert J.; Graham, James; Hirsch, Lea; Nagpal, Vighnesh; Nielsen, Eric L.; Pearce, Logan; Rice, Malena; Tejada, Roberto

orbitize fits the orbits of directly-imaged objects by packaging the Orbits for the Impatient (OFTI) algorithm and a parallel-tempered Markov Chain Monte Carlo (MCMC) algorithm into a consistent API. It accepts observations in three measurement formats, which can be mixed in the same input file, generates orbits, and plots the computed orbital parameters. orbitize offers numerous ways to visualize the data, including histograms, corner plots, and orbit plots. Generated orbits can be saved in HDF5 format for future use and analysis.

[ascl:1910.008]
ECLIPS3D: Linear wave and circulation calculations

ECLIPS3D (Eigenvectors, Circulation, and Linear Instabilities for Planetary Science in 3 Dimensions) calculates a posteriori energy equations for the study of linear processes in planetary atmospheres with an arbitrary steady state, and provides both increased robustness and physical meaning to the obtained eigenmodes. It was developed originally for planetary atmospheres and includes python scripts for data analysis. ECLIPS3D can be used to study the initial spin up of superrotation of GCM simulations of hot Jupiters in addition to being applied to other problems.

[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:1910.006]
EMERGE: Empirical ModEl for the foRmation of GalaxiEs

Emerge (Empirical ModEl for the foRmation of GalaxiEs) populates dark matter halo merger trees with galaxies using simple empirical relations between galaxy and halo properties. For each model represented by a set of parameters, it computes a mock universe, which it then compares to observed statistical data to obtain a likelihood. Parameter space can be explored with several advanced stochastic algorithms such as MCMC to find the models that are in agreement with the observations.

[ascl:1910.005]
exoplanet: Probabilistic modeling of transit or radial velocity observations of exoplanets

exoplanet is a toolkit for probabilistic modeling of transit and/or radial velocity observations of exoplanets and other astronomical time series using PyMC3 (ascl:1610.016), a flexible and high-performance model building language and inference engine. exoplanet extends PyMC3's language to support many of the custom functions and distributions required when fitting exoplanet datasets. These features include a fast and robust solver for Kepler's equation; scalable Gaussian processes using celerite (ascl:1709.008); and fast and accurate limb darkened light curves using the code starry (ascl:1810.005). It also offers common reparameterizations for limb darkening parameters, and planet radius and impact parameters.

[ascl:1910.004]
DM_phase: Algorithm for correcting dispersion of radio signals

DM_phase maximizes the coherent power of a radio signal instead of its intensity to calculate the best dispersion measure (DM) for a burst such as those emitted by pulsars and fast radio bursts (FRBs). It is robust to complex burst structures and interference, thus mitigating the limitations of traditional methods that search for the best DM value of a source by maximizing the signal-to-noise ratio (S/N) of the detected signal.

[ascl:1910.003]
a3cosmos-gas-evolution: Galaxy cold molecular gas evolution functions

a3cosmos-gas-evolution calculates galaxies' cold molecular gas properties using gas scaling functions derived from the A3COSMOS project. By known galaxies' redshifts or cosmic age, stellar masses, and star formation enhancement to galaxies' star-forming main sequence (Delta MS), the gas scaling functions predict their stellar mass ratio (gas fraction) and gas depletion time.

[ascl:1910.002]
PreProFit: Pressure Profile Fitter for galaxy clusters in Python

PreProFit fits the pressure profile of galaxy clusters using Markov chain Monte Carlo (MCMC). The software can analyze data from different sources and offers flexible parametrization for the pressure profile. PreProFit accounts for Abel integral, beam smearing, and transfer function filtering when fitting data and returns χ2, model parameters and uncertainties in addition to marginal and joint probability contours, diagnostic plots, and surface brightness radial profiles. The code can be used for analytic approximations for the beam and transfer functions for feasibility studies.

[ascl:1910.001]
PINK: Parallelized rotation and flipping INvariant Kohonen maps

Morphological classification is one of the most demanding challenges in astronomy. With the advent of all-sky surveys, an enormous amount of imaging data is publicly available, and are typically analyzed by experts or encouraged amateur volunteers. For upcoming surveys with billions of objects, however, such an approach is not feasible anymore. PINK (Parallelized rotation and flipping INvariant Kohonen maps) is a simple yet effective variant of a rotation-invariant self-organizing map that is suitable for many analysis tasks in astronomy. The code reduces the computational complexity via modern GPUs and applies the resulting framework to galaxy data for morphological analysis.

[submitted]
Magnetizer: computing magnetic fields of evolving galaxies

Computes time and radial dependent magnetic fields for a sample of galaxies in the output of a semi-analytic model of galaxy formation. The magnetic field is obtained by numerically solving the galactic dynamo equations throughout history of each galaxy. Stokes parameters and Faraday rotation measure can also be computed along a random line-of-sight for each galaxy.

[submitted]
HaloAnalysis: read and analyze halo catalogs and merger trees

HaloAnalysis reads and analyzes halo/galaxy catalogs, generated from Rockstar (ascl:1210.008) or AHF (ascl:1102.009), and merger trees generated from Consistent Trees (ascl:1210.011). Written in Python, it offers the following functionality: reads halo/galaxy/tree catalogs from multiple file formats; assigns baryonic particles and galaxy properties to dark-matter halos; combines and re-generates halo/galaxy/tree files in hdf5 format; analyzes properties of halos/galaxies; selects halos to generate zoom-in initial conditions. Includes a Jupyter notebook tutorial.

[submitted]
GizmoAnalysis: read and analyze Gizmo simulations

GizmoAnalysis reads and analyzes N-body simulations run with the Gizmo code (ascl:1410.003). Written in Python, we developed it primarily to analyze FIRE simulations, though it is useable with any Gizmo snapshot files. It offers the following functionality: reads snapshot files and converts particle data to physical units; provides a flexible dictionary class to store particle data and compute derived quantities on the fly; plots images and properties of particles; generates region files for input to MUSIC (ascl:1311.011) to generate cosmological zoom-in initial conditions; computes rates of supernovae and stellar winds, including their nucleosynthetic yields, as used in FIRE simulations. Includes a Jupyter notebook tutorial.

[ascl:1909.014]
fgivenx: Functional posterior plotter

fgivenx plots a predictive posterior of a function, dependent on sampled parameters, for a Bayesian posterior Post(theta|D,M) described by a set of posterior samples {theta_i}~Post. If there is a function parameterized by theta y=f(x;theta), this script produces a contour plot of the conditional posterior P(y|x,D,M) in the (x,y) plane.

[ascl:1909.013]
EPOS: Exoplanet Population Observation Simulator

EPOS (Exoplanet Population Observation Simulator) simulates observations of exoplanet populations. It provides an interface between planet formation simulations and exoplanet surveys such as Kepler. EPOS can also be used to estimate planet occurrence rates and the orbital architectures of planetary systems.

[ascl:1909.012]
HISS: HI spectra stacker

Healy, J.; Blyth, S. -L.; Elson, E.; van Driel, W.; Butcher, Z.; Schneider, S.; Lehnert, M. D.; Minchin, R.

HISS stacks HI (emission and absorption) spectra in a consistent and reliable manner to enable statistical analysis of average HI properties. It provides plots of the stacked spectrum and reference spectrum with any fitted function, of the stacked noise response, and of the distribution of the integrated fluxes when calculating the uncertainties. It also produces a table containing the integrated flux calculated from the fitted functions and the stacked spectrum, among other output files.

[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:1909.010]
AREPO: Cosmological magnetohydrodynamical moving-mesh simulation code

AREPO is a massively parallel gravity and magnetohydrodynamics code for astrophysics, designed for problems of large dynamic range. It employs a finite-volume approach to discretize the equations of hydrodynamics on a moving Voronoi mesh, and a tree-particle-mesh method for gravitational interactions. AREPO is originally optimized for cosmological simulations of structure formation, but has also been used in many other applications in astrophysics.

[ascl:1909.009]
CLOVER: Convolutional neural network spectra identifier and kinematics predictor

CLOVER (Convnet Line-fitting Of Velocities in Emission-line Regions) is a convolutional neural network (ConvNet) trained to identify spectra with two velocity components along the line of sight and predict their kinematics. It works with Gaussian emission lines (e.g., CO) and lines with hyperfine structure (e.g., NH3). CLOVER has two prediction steps, classification and parameter prediction. For the first step, CLOVER segments the pixels in an input data cube into one of three classes: noise (i.e., no emission), one-component (emission line with single velocity component), and two-component (emission line with two velocity components). For the pixels identified as two-components in the first step, a second regression ConvNet is used to predict centroid velocity, velocity dispersion, and peak intensity for each velocity component.

[ascl:1909.008]
RascalC: Fast code for galaxy covariance matrix estimation

RascalC quickly estimates covariance matrices from two- or three-point galaxy correlation functions. Given an input set of random particle locations and a two-point correlation function (or input set of galaxy positions), RascalC produces an estimate of the associated covariance for a given binning strategy, with non-Gaussianities approximated by a ‘shot-noise-rescaling’ parameter. For the 2PCF, the rescaling parameter can be calibrated by dividing the particles into jackknife regions and comparing sample to theoretical jackknife covariance. RascalC can also be used to compute Legendre-binned covariances and cross-covariances between different two-point correlation functions.

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