[ascl:1707.003]
pyaneti: Multi-planet radial velocity and transit fitting

Pyaneti is a multi-planet radial velocity and transit fit software. The code uses Markov chain Monte Carlo (MCMC) methods with a Bayesian approach and a parallelized ensemble sampler algorithm in Fortran which makes the code fast. It creates posteriors, correlations, and ready-to-publish plots automatically, and handles circular and eccentric orbits. It is capable of multi-planet fitting and handles stellar limb darkening, systemic velocities for multiple instruments, and short and long cadence data, and offers additional capabilities.

[ascl:1502.007]
PyBDSF: Python Blob Detection and Source Finder

PyBDSF (Python Blob Detector and Source Finder, formerly PyBDSM) decomposes radio interferometry images into sources and makes their properties available for further use. PyBDSF can decompose an image into a set of Gaussians, shapelets, or wavelets as well as calculate spectral indices and polarization properties of sources and measure the psf variation across an image. PyBDSF uses an interactive environment based on CASA (ascl:1107.013); PyBDSF may also be used in Python scripts.

[ascl:1204.002]
pyBLoCXS: Bayesian Low-Count X-ray Spectral analysis

Siemiginowska, Aneta; Kashyap, Vinay; Refsdal, Brian; van Dyk, David; Connors, Alanna; Park, Taeyoung

pyBLoCXS is a sophisticated Markov chain Monte Carlo (MCMC) based algorithm designed to carry out Bayesian Low-Count X-ray Spectral (BLoCXS) analysis in the Sherpa environment. The code is a Python extension to Sherpa that explores parameter space at a suspected minimum using a predefined Sherpa model to high-energy X-ray spectral data. pyBLoCXS includes a flexible definition of priors and allows for variations in the calibration information. It can be used to compute posterior predictive p-values for the likelihood ratio test. The pyBLoCXS code has been tested with a number of simple single-component spectral models; it should be used with great care in more complex settings.

[ascl:1805.030]
PyCBC: Gravitational-wave data analysis toolkit

PyCBC analyzes data from gravitational-wave laser interferometer detectors, finds signals, and studies their parameters. It contains algorithms that can detect coalescing compact binaries and measure the astrophysical parameters of detected sources. PyCBC was used in the first direct detection of gravitational waves by LIGO and is used in the ongoing analysis of LIGO and Virgo data.

[ascl:1805.032]
PyCCF: Python Cross Correlation Function for reverberation mapping studies

PyCCF emulates a Fortran program written by B. Peterson for use with reverberation mapping. The code cross correlates two light curves that are unevenly sampled using linear interpolation and measures the peak and centroid of the cross-correlation function. In addition, it is possible to run Monto Carlo iterations using flux randomization and random subset selection (RSS) to produce cross-correlation centroid distributions to estimate the uncertainties in the cross correlation results.

[ascl:1304.020]
pyCloudy: Tools to manage astronomical Cloudy photoionization code

PyCloudy is a Python library that handles input and output files of the Cloudy photoionization code (Gary Ferland). It can also generate 3D nebula from various runs of the 1D Cloudy code. pyCloudy allows you to:

- define and write input file(s) for Cloudy code. As you can have it in a code, you may generate automatically sets of input files, changing parameters from one to the other.
- read the Cloudy output files and play with the data: you will be able to plot line emissivity ratio vs. the radius of the nebula, the electron temperature, or any Cloudy output.
- build pseudo-3D models, a la Cloudy_3D, by running a set of models, changing parameters (e.g. inner radius, density) following angular laws, reading the outputs of the set of models and interpolating the results (Te, ne, line emissivities) in a 3D cube.

[ascl:1509.007]
pycola: N-body COLA method code

pycola is a multithreaded Python/Cython N-body code, implementing the Comoving Lagrangian Acceleration (COLA) method in the temporal and spatial domains, which trades accuracy at small-scales to gain computational speed without sacrificing accuracy at large scales. This is especially useful for cheaply generating large ensembles of accurate mock halo catalogs required to study galaxy clustering and weak lensing. The COLA method achieves its speed by calculating the large-scale dynamics exactly using LPT while letting the N-body code solve for the small scales, without requiring it to capture exactly the internal dynamics of halos.

[ascl:1311.002]
PyCOOL: Cosmological Object-Oriented Lattice code

PyCOOL is a Python + CUDA program that solves the evolution of interacting scalar fields in an expanding universe. PyCOOL uses modern GPUs to solve this evolution and to make the computation much faster. The code includes numerous post-processing functions that provide useful information about the cosmological model, including various spectra and statistics of the fields.

[ascl:1210.027]
PyCosmic: Detecting cosmics in CALIFA and other fiber-fed integral-field spectroscopy datasets

The detection of cosmic ray hits (cosmics) in fiber-fed integral-field spectroscopy (IFS) data of single exposures is a challenging task because of the complex signal recorded by IFS instruments. Existing detection algorithms are commonly found to be unreliable in the case of IFS data, and the optimal parameter settings are usually unknown a priori for a given dataset. The Calar Alto legacy integral field area (CALIFA) survey generates hundreds of IFS datasets for which a reliable and robust detection algorithm for cosmics is required as an important part of the fully automatic CALIFA data reduction pipeline. PyCosmic combines the edge-detection algorithm of L.A.Cosmic with a point-spread function convolution scheme. PyCosmic is the only algorithm that achieves an acceptable detection performance for CALIFA data. Only for strongly undersampled IFS data does L.A.Cosmic exceed the performance of PyCosmic by a few percent. Thus, PyCosmic appears to be the most versatile cosmics detection algorithm for IFS data.

[ascl:1509.010]
PyCS : Python Curve Shifting

PyCS is a software toolbox to estimate time delays between multiple images of strongly lensed quasars, from resolved light curves such as obtained by the COSMOGRAIL monitoring program. The pycs package defines a collection of classes and high level functions, that you can script in a flexible way. PyCS makes it easy to compare different point estimators (including your own) without much code integration. The package heavily depends on numpy, scipy, and matplotlib.

[submitted]
pydftools: Distribution function fitting in Python

pydftools is a pure-python port of the dftools R package (ascl:1805.002), which finds the most likely P parameters of a D-dimensional distribution function (DF) generating N objects, where each object is specified by D observables with measurement uncertainties. For instance, if the objects are galaxies, it can fit a MF (P=1), a mass-size distribution (P=2) or the mass-spin-morphology distribution (P=3). Unlike most common fitting approaches, this method accurately accounts for measurement in uncertainties and complex selection functions. Though this package imitates the dftools package quite closely while being as Pythonic as possible, it has not implemented 2D+ nor non-parametric.

[ascl:1401.005]
PyDrizzle: Python version of Drizzle

PyDrizzle provides a semi-automated interface for computing the parameters necessary for running Drizzle. PyDrizzle performs the task of determining the parameters necessary for aligning images based on the WCS information in the input image headers, as well as any supplemental alignment information provided in shift files, and combines the images onto the same WCS. Though it does not identify cosmic rays, it has the ability to ignore pixels flagged as bad, such as pixels identified by other programs as affected by cosmic rays.

[ascl:1112.014]
PyEphem: Astronomical Ephemeris for Python

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

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

[ascl:1609.025]
PYESSENCE: Generalized Coupled Quintessence Linear Perturbation Python Code

PYESSENCE evolves linearly perturbed coupled quintessence models with multiple (cold dark matter) CDM fluid species and multiple DE (dark energy) scalar fields, and can be used to generate quantities such as the growth factor of large scale structure for any coupled quintessence model with an arbitrary number of fields and fluids and arbitrary couplings.

[ascl:1403.002]
pyExtinction: Atmospheric extinction

The Python script/package pyExtinction computes and plots total atmospheric extinction from decomposition into physical components (Rayleigh attenuation, ozone absorption, aerosol extinction). Its default extinction parameters are adapted to mean Mauna Kea summit conditions.

[ascl:1207.009]
PyFITS: Python FITS Module

Barrett, Paul; Hsu, J. C.; Hanley, Chris; Taylor, James; Droettboom, Michael; Bray, Erik M.; Hack, Warren; Greenfield, Perry; Wyckoff, Eric; Jedrzejewski, Robert; De La Pena, Michele; Hodge, Phil

PyFITS provides an interface to FITS formatted files in the Python scripting language and PyRAF, the Python-based interface to IRAF. It is useful both for interactive data analysis and for writing analysis scripts in Python using FITS files as either input or output. PyFITS is a development project of the Science Software Branch at the Space Telescope Science Institute.

**PyFITS has been deprecated. Please see Astropy**

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

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

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

[submitted]
pygad: Analysing Gadget Simulations with Python

pygad provides a framework for dealing with Gadget snapshots. The code reads any of the many different Gadget (ascl:0003.001) formats, allows easy masking snapshots to particles of interest, decorates the data blocks with units, allows to add automatically updating derived blocks, and provides several binning and plotting routines, among other tasks, to provide convenient, intuitive handling of the Gadget data without the need to worry about technical details. pygad provides access to single stellar population (SSP) models, has an interface to Rockstar (ascl:1210.008) output files, provides its own friends-of-friends (FoF) finder, calculates spherical overdensities, and has a sub-module to generate mock absorption lines.

[ascl:1411.001]
pyGadgetReader: GADGET snapshot reader for python

pyGadgetReader is a universal GADGET snapshot reader for python that supports type-1, type-2, HDF5, and TIPSY (ascl:1111.015) binary formats. It additionally supports reading binary outputs from FoF_Special, P-StarGroupFinder, Rockstar (ascl:1210.008), and Rockstar-Galaxies.

[ascl:1402.021]
PyGFit: Python Galaxy Fitter

PyGFit measures PSF-matched photometry from images with disparate pixel scales and PSF sizes; its primary purpose is to extract robust spectral energy distributions (SEDs) from crowded images. It fits blended sources in crowded, low resolution images with models generated from a higher resolution image, thus minimizing the impact of crowding and also yielding consistently measured fluxes in different filters which minimizes systematic uncertainty in the final SEDs.

[ascl:1611.013]
pyGMMis: Mixtures-of-Gaussians density estimation method

pyGMMis is a mixtures-of-Gaussians density estimation method that accounts for arbitrary incompleteness in the process that creates the samples as long as the incompleteness is known over the entire feature space and does not depend on the sample density (missing at random). pyGMMis uses the Expectation-Maximization procedure and generates its best guess of the unobserved samples on the fly. It can also incorporate an uniform "background" distribution as well as independent multivariate normal measurement errors for each of the observed samples, and then recovers an estimate of the error-free distribution from which both observed and unobserved samples are drawn. The code automatically segments the data into localized neighborhoods, and is capable of performing density estimation with millions of samples and thousands of model components on machines with sufficient memory.

[ascl:1603.013]
PyGSM: Python interface to the Global Sky Model

PyGSM is a Python interface for the Global Sky Model (GSM, ascl:1011.010). The GSM is a model of diffuse galactic radio emission, constructed from a variety of all-sky surveys spanning the radio band (e.g. Haslam and WMAP). PyGSM uses the GSM to generate all-sky maps in Healpix format of diffuse Galactic radio emission from 10 MHz to 94 GHz. The PyGSM module provides visualization utilities, file output in FITS format, and the ability to generate observed skies for a given location and date. PyGSM requires Healpy, PyEphem (ascl:1112.014), and AstroPy (ascl:1304.002).

[ascl:1511.005]
pyhrs: Spectroscopic data reduction package for SALT

The pyhrs package reduces data from the High Resolution Spectrograph (HRS) on the Southern African Large Telescope (SALT). HRS is a dual-beam, fiber fed echelle spectrectrograph with four modes of operation: low (R~16000), medium (R~34000), high (R~65000), and high stability (R~65000). pyhrs, written in Python, includes all of the steps necessary to reduce HRS low, medium, and high resolution data; this includes basic CCD reductions, order identification, wavelength calibration, and extraction of the spectra.

[ascl:1208.004]
PyKE: Reduction and analysis of Kepler Simple Aperture Photometry data

PyKE is a python-based PyRAF package that can also be run as a stand-alone program within a unix-based shell without compiling against PyRAF. It is a group of tasks developed for the reduction and analysis of Kepler Simple Aperture Photometry (SAP) data of individual targets with individual characteristics. The main purposes of these tasks are to i) re-extract light curves from manually-chosen pixel apertures and ii) cotrend and/or detrend the data in order to reduce or remove systematic noise structure using methods tunable to user and target-specific requirements. PyKE is an open source project and contributions of new tasks or enhanced functionality of existing tasks by the community are welcome.

[ascl:1506.001]
pyKLIP: PSF Subtraction for Exoplanets and Disks

Wang, Jason J.; Ruffio, Jean-Baptise; De Rosa, Robert J.; Aguilar, Jonathan; Wolff, Schuyler G.; Pueyo, Laurent

pyKLIP subtracts out the stellar PSF to search for directly-imaged exoplanets and disks using a Python implementation of the Karhunen-Loève Image Projection (KLIP) algorithm. pyKLIP supports ADI, SDI, and ADI+SDI to model the stellar PSF and offers a large array of PSF subtraction parameters to optimize the reduction. pyKLIP relies on a minimal amount of dependencies (numpy, scipy, and astropy) and parallelizes the KLIP algorithm to speed up the reduction. pyKLIP supports GPI and P1640 data and can interface with other data sources with the addition of new modules. It also can inject simulated planets and disks as well as automatically search for point sources in PSF-subtracted data.

[ascl:1708.016]
pyLCSIM: X-ray lightcurves simulator

pyLCSIM simulates X-ray lightcurves from coherent signals and power spectrum models. Coherent signals can be specified as a sum of one or more sinusoids, each with its frequency, pulsed fraction and phase shift; or as a series of harmonics of a fundamental frequency (each with its pulsed fraction and phase shift). Power spectra can be simulated from a model of the power spectrum density (PSD) using as a template one or more of the built-in library functions. The user can also define his/her custom models. Models are additive.

[ascl:1510.003]
PyLDTk: Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients for arbitrary filters

PyLDTk automates the calculation of custom stellar limb darkening (LD) profiles and model-specific limb darkening coefficients (LDC) using the library of PHOENIX-generated specific intensity spectra by Husser et al. (2013). It facilitates exoplanet transit light curve modeling, especially transmission spectroscopy where the modeling is carried out for custom narrow passbands. PyLDTk construct model-specific priors on the limb darkening coefficients prior to the transit light curve modeling. It can also be directly integrated into the log posterior computation of any pre-existing transit modeling code with minimal modifications to constrain the LD model parameter space directly by the LD profile, allowing for the marginalization over the whole parameter space that can explain the profile without the need to approximate this constraint by a prior distribution. This is useful when using a high-order limb darkening model where the coefficients are often correlated, and the priors estimated from the tabulated values usually fail to include these correlations.

[ascl:1612.018]
pylightcurve: Exoplanet lightcurve model

pylightcurve is a model for light-curves of transiting planets. It uses the four coefficients law for the stellar limb darkening and returns the relative flux, *F*(*t*), as a function of the limb darkening coefficients, *a _{n}*, the

[submitted]
pyLIMA: An Open Source Package for Microlensing Modeling

pyLIMA is an open source software for microlensing modeling. Based on Python, the goal is to offer to users an efficient and user friendly package to analyze their data. The code is written and tested with professional standards, such as PEP8 or unit testing.

[ascl:1506.005]
PyMC: Bayesian Stochastic Modelling in Python

PyMC is a python module that implements Bayesian statistical models and fitting algorithms, including Markov chain Monte Carlo. Its flexibility and extensibility make it applicable to a large suite of problems. Along with core sampling functionality, PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics.

[ascl:1610.016]
PyMC3: Python probabilistic programming framework

PyMC3 performs Bayesian statistical modeling and model fitting focused on advanced Markov chain Monte Carlo and variational fitting algorithms. It offers powerful sampling algorithms, such as the No U-Turn Sampler, allowing complex models with thousands of parameters with little specialized knowledge of fitting algorithms, intuitive model specification syntax, and optimization for finding the maximum a posteriori (MAP) point. PyMC3 uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed.

[ascl:1505.025]
pyMCZ: Oxygen abundances calculations and uncertainties from strong-line flux measurements

Bianco, Federica B.; Modjaz, Maryam; Oh, Seung Man; Fierroz, David; Liu, Yuqian; Kewley, Lisa; Graur, Or

pyMCZ calculates metallicity according to a number of strong line metallicity diagnostics from spectroscopy line measurements and obtain uncertainties from the line flux errors in a Monte Carlo framework. Given line flux measurements and their uncertainties, pyMCZ produces synthetic distributions for the oxygen abundance in up to 13 metallicity scales simultaneously, as well as for E(B-V), and estimates their median values and their 68% confidence regions. The code can output the full MC distributions and their kernel density estimates.

[ascl:1411.011]
PyMGC3: Finding stellar streams in the Galactic Halo using a family of Great Circle Cell counts methods

PyMGC3 is a Python toolkit to apply the Modified Great Circle Cell Counts (mGC3) method to search for tidal streams in the Galactic Halo. The code computes pole count maps using the full mGC3/nGC3/GC3 family of methods. The original GC3 method (Johnston *et al.*, 1996) uses positional information to search for 'great-circle-cell structures'; mGC3 makes use of full 6D data and nGC3 uses positional and proper motion data.

[ascl:1401.003]
PyMidas: Interface from Python to Midas

PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.

[ascl:1707.005]
PyMOC: Multi-Order Coverage map module for Python

PyMOC manipulates Multi-Order Coverage (MOC) maps. It supports reading and writing the three encodings mentioned in the IVOA MOC recommendation: FITS, JSON and ASCII.

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

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

[ascl:1310.002]
PyMSES: Python modules for RAMSES

PyMSES provides a python solution for getting data out of RAMSES (ascl:1011.007) astrophysical fluid dynamics simulations. It permits transparent manipulation of large simulations and interfaces with common Python libraries and existing code, and can serve as a post-processing toolbox for data analysis. It also does three-dimensional volume rendering with a specific algorithm optimized to work on RAMSES distributed data (Guillet et al. 2011 and Jones et a. 2011).

[ascl:1606.005]
PyMultiNest: Python interface for MultiNest

PyMultiNest provides programmatic access to MultiNest (ascl:1109.006) and PyCuba, integration existing Python code (numpy, scipy), and enables writing Prior & LogLikelihood functions in Python. PyMultiNest can plot and visualize MultiNest's progress and allows easy plotting, visualization and summarization of MultiNest results. The plotting can be run on existing MultiNest output, and when not using PyMultiNest for running MultiNest.

[ascl:1703.009]
PyMVPA: MultiVariate Pattern Analysis in Python

PyMVPA eases statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. It is designed to integrate well with related software packages, such as scikit-learn, shogun, and MDP.

[ascl:1305.002]
pynbody: N-Body/SPH analysis for python

Pynbody is a lightweight, portable, format-transparent analysis package for astrophysical N-body and smooth particle hydrodynamic simulations supporting PKDGRAV/Gasoline, Gadget, N-Chilada, and RAMSES AMR outputs. Written in python, the core tools are accompanied by a library of publication-level analysis routines.

[ascl:1304.021]
PyNeb: Analysis of emission lines

PyNeb (previously PyNebular) is an update and expansion of the IRAF package NEBULAR; rewritten in Python, it is designed to be more user-friendly and powerful, increasing the speed, easiness of use, and graphic visualization of emission lines analysis. In PyNeb, the atom is represented as an n-level atom. For given density and temperature, PyNeb solves the equilibrium equations and determines the level populations. PyNeb can compute physical conditions from suitable diagnostic line ratios and level populations, critical densities and line emissivities, and can compute and display emissivity grids as a function of Te and Ne. It can also deredden line intensities, read and manage observational data, and plot and compare atomic data from different publications, and compute ionic abundances from line intensities and physical conditions and elemental abundances from ionic abundances and icfs.

[ascl:1501.001]
PynPoint: Exoplanet image data analysis

PynPoint uses principal component analysis to detect and estimate the flux of exoplanets in two-dimensional imaging data. It processes many, typically several thousands, of frames to remove the light from the star so as to reveal the companion planet.

[ascl:1612.008]
PyORBIT: Exoplanet orbital parameters and stellar activity

PyORBIT handles several kinds of datasets, such as radial velocity (RV), activity indexes, and photometry, to simultaneously characterize the orbital parameters of exoplanets and the noise induced by the activity of the host star. RV computation is performed using either non-interacting Kepler orbits or n-body integration. Stellar activity can be modeled either with sinusoids at the rotational period and its harmonics or Gaussian process. In addition, the code can model offsets and systematics in measurements from several instruments. The PyORBIT code is modular; new methods for stellar activity modeling or parameter estimation can easily be incorporated into the code.

[ascl:1802.012]
PyOSE: Orbital sampling effect (OSE) simulator

PyOSE is a fully numerical orbital sampling effect (OSE) simulator that can model arbitrary inclinations of the transiting moon orbit. It can be used to search for exomoons in long-term stellar light curves such as those by Kepler and the upcoming PLATO mission.

[ascl:1609.022]
PyPHER: Python-based PSF Homogenization kERnels

Boucaud, Alexandre; Bocchio, Marco; Abergel, Alain; Orieux, François; Dole, Hervé; Amine Hadj-Youcef, Mohamed

PyPHER (Python-based PSF Homogenization kERnels) computes an homogenization kernel between two PSFs; the code is well-suited for PSF matching applications in both an astronomical or microscopy context. It can warp (rotation + resampling) the PSF images (if necessary), filter images in Fourier space using a regularized Wiener filter, and produce a homogenization kernel. PyPHER requires the pixel scale information to be present in the FITS files, which can if necessary be added by using the provided ADDPIXSCL method.

[ascl:1612.005]
PyProfit: Wrapper for libprofit

pyprofit is a python wrapper for libprofit (ascl:1612.003).

[ascl:1706.011]
PyPulse: PSRFITS handler

PyPulse handles PSRFITS files and performs subsequent analyses on pulse profiles.

[ascl:1602.002]
pyraf-dbsp: Reduction pipeline for the Palomar Double Beam Spectrograph

pyraf-dbsp is a PyRAF-based (ascl:1207.011) reduction pipeline for optical spectra taken with the Palomar 200-inch Double Beam Spectrograph. The pipeline provides a simplified interface for basic reduction of single-object spectra with minimal overhead. It is suitable for quicklook classification of transients as well as moderate-precision (few km/s) radial velocity work.

[ascl:1207.011]
PyRAF: Python alternative for IRAF

PyRAF is a command language for running IRAF tasks that is based on the Python scripting language. It gives users the ability to run IRAF tasks in an environment that has all the power and flexibility of Python. PyRAF can be installed along with an existing IRAF installation; users can then choose to run either PyRAF or the IRAF CL.

[ascl:1507.018]
pyro: Python-based tutorial for computational methods for hydrodynamics

pyro is a simple python-based tutorial on computational methods for hydrodynamics. It includes 2-d solvers for advection, compressible, incompressible, and low Mach number hydrodynamics, diffusion, and multigrid. It is written with ease of understanding in mind. An extensive set of notes that is part of the Open Astrophysics Bookshelf project provides details of the algorithms.

[ascl:1207.010]
PySALT: SALT science pipeline

Crawford, S. M.; Still, M.; Schellart, P.; Balona, L.; Buckley, D. A. H.; Gulbis, A. A. S.; Kniazev, A.; Kotze, M.; Loaring, N.; Nordsieck, K. H.; Pickering, T. E.; Potter, S.; Romero Colmenero, E.; Vaisanen, P.; Wiliams, T.; Zietsman, E.

The PySALT user package contains the primary reduction and analysis software tools for the SALT telescope. Currently, these tools include basic data reductions for RSS and SALTICAM in both imaging, spectroscopic, and slot modes. Basic analysis software for slot mode data is also provided. These tools are primarily written in python/PyRAF with some additional IRAF code.

[ascl:1805.026]
PySE: Python Source Extractor for radio astronomical images

Spreeuw, Hanno; Swinbank, John; Molenaar, Gijs; Staley, Tim; Rol, Evert; Sanders, John; Scheers, Bart; Kuiack, Mark

PySE finds and measures sources in radio telescope images. It is run with several options, such as the detection threshold (a multiple of the local noise), grid size, and the forced clean beam fit, followed by a list of input image files in standard FITS or CASA format. From these, PySe provides a list of found sources; information such as the calculated background image, source list in different formats (e.g. text, region files importable in DS9), and other data may be saved. PySe can be integrated into a pipeline; it was originally written as part of the LOFAR Transient Detection Pipeline (TraP, ascl:1412.011).

[ascl:1704.007]
PySM: Python Sky Model

PySM generates full-sky simulations of Galactic foregrounds in intensity and polarization relevant for CMB experiments. The components simulated are thermal dust, synchrotron, AME, free-free, and CMB at a given Nside, with an option to integrate over a top hat bandpass, to add white instrument noise, and to smooth with a given beam. PySM is based on the large-scale Galactic part of Planck Sky Model code and uses some of its inputs

[ascl:1503.008]
pYSOVAR: Lightcurves analysis

The pYSOVAR code calculates properties for a stack of lightcurves, including simple descriptive statistics (mean, max, min, ...), timing (e.g. Lomb-Scargle periodograms), variability indixes (e.g. Stetson), and color properties (e.g. slope in the color-magnitude diagram). The code is written in python and is closely integrated with astropy tables. Initially, pYSOVAR was written specifically for the analysis of two clusters in the YSOVAR project, using the (not publicly released) YSOVAR database as an input. Additional functionality has been added and the code has become more general; it is now useful for other clusters in the YSOVAR dataset or for other projects that have similar data (lightcurves in one or more bands with a few hundred points for a few thousand objects), though may not work out-of-the-box for different datasets.

[ascl:1411.002]
pysovo: A library for implementing alerts triggered by VOEvents

pysovo contains basic tools to work with VOEvents. Though written for specific needs, others interested in VOEvents may find it useful to examine.

[ascl:1109.001]
PySpecKit: Python Spectroscopic Toolkit

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

[ascl:1303.023]
pysynphot: Synthetic photometry software package

pysynphot is a synthetic photometry software package suitable for either library or interactive use. Intended as a modern-language successor to the IRAF/STSDAS synphot package, it provides improved algorithms that address known shortcomings in synphot, and its object-oriented design is more easily extensible than synphot's task-oriented approach. It runs under PyRAF, and a backwards compatibility mode is provided that recognizes all spectral and throughput tables, obsmodes, and spectral expressions used by synphot, to facilitate the transition for legacy code.

[ascl:1612.001]
Python-CPL: Python interface for the ESO Common Pipeline Library

Python-CPL is a framework to configure and execute pipeline recipes written with the Common Pipeline Library (CPL) (ascl:1402.010) with Python2 or Python3. The input, calibration and output data can be specified as FITS files or as astropy.io.fits objects in memory. The package is used to implement the MUSE pipeline in the AstroWISE data management system.

[ascl:1501.003]
python-qucs: Python package for automating QUCS simulations

Characterization of the frequency response of coherent radiometric receivers is a key element in estimating the flux of astrophysical emissions, since the measured signal depends on the convolution of the source spectral emission with the instrument band shape. Python-qucs automates the process of preparing input data, running simulations and exporting results of QUCS (Quasi Universal Circuit Simulator) simulations.

[ascl:1501.010]
PythonPhot: Simple DAOPHOT-type photometry in Python

PythonPhot is a simple Python translation of DAOPHOT-type (ascl:1104.011) photometry procedures from the IDL AstroLib (Landsman 1993), including aperture and PSF-fitting algorithms, with a few modest additions to increase functionality and ease of use. These codes allow fast, easy, and reliable photometric measurements and are currently used in the Pan-STARRS supernova pipeline and the HST CLASH/CANDELS supernova analysis.

[ascl:1505.024]
PyTransit: Transit light curve modeling

PyTransit implements optimized versions of the Giménez and Mandel & Agol transit models for exoplanet transit light-curves. The two models are implemented natively in Fortran with OpenMP parallelization, and are accessed by an object-oriented python interface. PyTransit facilitates the analysis of photometric time series of exoplanet transits consisting of hundreds of thousands of data points, and of multipassband transit light curves from spectrophotometric observations. It offers efficient model evaluation for multicolour observations and transmission spectroscopy, built-in supersampling to account for extended exposure times, and routines to calculate the projected planet-to-star distance for circular and eccentric orbits, transit durations, and more.

[ascl:1710.010]
PyTransport: Calculate inflationary correlation functions

PyTransport calculates the 2-point and 3-point function of inflationary perturbations produced during multi-field inflation. The core of PyTransport is C++ code which is automatically edited and compiled into a Python module once an inflationary potential is specified. This module can then be called to solve the background inflationary cosmology as well as the evolution of correlations of inflationary perturbations. PyTransport includes two additional modules written in Python, one to perform the editing and compilation, and one containing a suite of functions for common tasks such as looping over the core module to construct spectra and bispectra.

[submitted]
PyVO: a package providing access to the Virtual observatory (VO) using Python

Becker, Stefan; Plante, Ray; Boch, Thomas; Brandt, Carlos; Demleitner, Markus; Deil, Christoph; Fitzpatrick, Mike; Graham, Matthew; Muench, Gus; Sipocz, Brigitta; Tody, Doug

PyVO provides access to remote data and services of the Virtual observatory (VO) using Python. It takes advantage VO standards to interface to tens of thousands of catalogs, data archives, information services, and analysis tools. PyVO is built on top of Astropy (and numpy). The VO protocols support by pyVO include the Table Access Protocol TAP, the Simple Image and Spectra Access Protocols (SIAP, SSAP), Simple Cone Search (SCS), the VO services interface VOSI, and Datalink.

[ascl:1402.004]
PyVO: Python access to the Virtual Observatory

PyVO provides access to remote data and services of the Virtual observatory (VO) using Python. It allows archive searches for data of a particular type or related to a particular topic and query submissions to obtain data to a particular archive to download selected data products. PyVO supports querying the VAO registry; simple data access services (DAL) to access images (SIA), source catalog records (Cone Search), spectra (SSA), and spectral line emission/absorption data (SLAP); and object name resolution (for converting names of objects in the sky into positions). PyVO requires both AstroPy and NumPy.

[ascl:1402.034]
PyWiFeS: Wide Field Spectrograph data reduction pipeline

PyWiFeS is a Python-based data reduction pipeline for the Wide Field Spectrograph (WiFeS). Its core data processing routines are built on standard scientific Python packages commonly used in astronomical applications. It includes an implementation of a global optical model of the spectrograph which provides wavelengths solutions accurate to ˜0.05 Å (RMS) across the entire detector. Through scripting, PyWiFeS can enable batch processing of large quantities of data.

[ascl:1608.002]
pyXSIM: Synthetic X-ray observations generator

pyXSIM simulates X-ray observations from astrophysical sources. X-rays probe the high-energy universe, from hot galaxy clusters to compact objects such as neutron stars and black holes and many interesting sources in between. pyXSIM generates synthetic X-ray observations of these sources from a wide variety of models, whether from grid-based simulation codes such as FLASH (ascl:1010.082), Enzo (ascl:1010.072), and Athena (ascl:1010.014), to particle-based codes such as Gadget (ascl:0003.001) and AREPO, and even from datasets that have been created “by hand”, such as from NumPy arrays. pyXSIM can also manipulate the synthetic observations it produces in various ways and export the simulated X-ray events to other software packages to simulate the end products of specific X-ray observatories. pyXSIM is an implementation of the PHOX (ascl:1112.004) algorithm and was initially the photon_simulator analysis module in yt (ascl:1011.022); it is dependent on yt.

[ascl:1806.003]
pyZELDA: Python code for Zernike wavefront sensors

pyZELDA analyzes data from Zernike wavefront sensors dedicated to high-contrast imaging applications. This modular software was originally designed to analyze data from the ZELDA wavefront sensor prototype installed in VLT/SPHERE; simple configuration files allow it to be extended to support several other instruments and testbeds. pyZELDA also includes simple simulation tools to measure the theoretical sensitivity of a sensor and to compare it to other sensors.

[ascl:1712.014]
QATS: Quasiperiodic Automated Transit Search

QATS detects transiting extrasolar planets in time-series photometry. It relaxes the usual assumption of strictly periodic transits by permitting a variable, but bounded, interval between successive transits.

[ascl:1601.015]
QDPHOT: Quick & Dirty PHOTometry

QDPHOT is a fast CCD stellar photometry task which quickly produces CCD stellar photometry from two CCD images of a star field. It was designed to be a data mining tool for finding high-quality stellar observations in the data archives of the National Virtual Observatory. QDPHOT typically takes just a few seconds to analyze two Hubble Space Telescope WFPC2 observations of Local Group star clusters. It is also suitable for real-time data-quality analysis of CCD observations; on-the-fly instrumental color-magnitude diagrams can be produced at the telescope console during the few seconds between CCD readouts.

[ascl:1806.006]
QE: Quantum opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization

Giannozzi, P.; Andreussi, O.; Baroni, S.; Bonini, Nicola; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, Guido L.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dabo, Ismaila; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A., Jr.; Fabris, Stefano; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Gougoussis, Christos; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Martin-Samos, Layla; Marzari, N.; Mauri, F.; Mazzarello, Riccardo; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la-Roza, A.; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Sbraccia, Scandolo, Sandro; Carlo; Schlipf, M.; Sclauzero, Gabriele; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wentzcovitch, Renata M.; Wu, X.

Quantum ESPRESSO (opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization) is an integrated suite of codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. QE performs ground-state calculations such as self-consistent total energies, forces, stresses and Kohn-Sham orbitals, Car-Parrinello and Born-Oppenheimer molecular dynamics, and quantum transport such as ballistic transport, coherent transport from maximally localized Wannier functions, and Kubo-Greenwood electrical conductivity. It can also determine spectroscopic properties and examine time-dependent density functional perturbations and electronic excitations, and has a wide range of other functions.

[ascl:1210.019]
QFitsView: FITS file viewer

QFitsView is a FITS file viewer that can display one, two, and three-dimensional FITS files. It has three modes of operation, depending of what kind of data is being displayed. One-dimensional data are shown in an x-y plot. Two-dimensional images are shown in the main window. Three-dimensional data cubes can be displayed in a variety of ways, with the third dimension shown as a x-y plot at the bottom of the image display. QFitsView was written in C++ and uses the Qt widget library, which makes it available for all major platforms: Windows, MAC OS X, and many Unix variants.

[ascl:1304.016]
Qhull: Quickhull algorithm for computing the convex hull

Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull.

[ascl:1612.011]
QSFit: Quasar Spectral FITting

QSFit performs automatic analysis of Active Galactic Nuclei (AGN) optical spectra. It provides estimates of: AGN continuum luminosities and slopes at several restframe wavelengths; luminosities, widths and velocity offsets of 20 emission lines; luminosities of iron blended lines at optical and UV wavelengths; host galaxy luminosities. The whole fitting process is customizable for specific needs, and can be extended to analyze spectra from other data sources. The ultimate purpose of QSFit is to allow astronomers to run standardized recipes to analyze the AGN data, in a simple, replicable and shareable way.

[ascl:1703.011]
QtClassify: IFS data emission line candidates classifier

QtClassify is a GUI that helps classify emission lines found in integral field spectroscopic data. Input needed is a datacube as well as a catalog with emission lines and a signal-to-noise cube, such at that created by LSDCat (ascl:1612.002). The main idea is to take each detected line and guess what line it could be (and thus the redshift of the object). You would expect to see other lines that might not have been detected but are visible in the cube if you know where to look, which is why parts of the spectrum are shown where other lines are expected. In addition, monochromatic layers of the datacube are displayed, making it easy to spot additional emission lines.

[ascl:1704.006]
Quickclump: Identify clumps within a 3D FITS datacube

Quickclump finds clumps in a 3D FITS datacube. It is a fast, accurate, and automated tool written in Python. Though Quickclump is primarily intended for decomposing observations of interstellar clouds into individual clumps, it can also be used for finding clumps in any 3D rectangular data.

[ascl:1402.012]
QUICKCV: Cosmic variance calculator

QUICKCV is an IDL sample variance/cosmic variance calculator for some geometry.

[ascl:1402.024]
QuickReduce: Data reduction pipeline for the WIYN One Degree Imager

QuickReduce quickly reduces data for ODI and is optimized for a first data inspection during acquisition at the the telescope. When installed on the ODI observer's interface, QuickReduce, coded in Python, performs all basic reduction steps as well as more advanced corrections for pupil-ghost removal, fringe correction and masking of persistent pixels and is capable enough for science-quality data reductions. It can also add an accurate astrometric WCS solution based on the 2MASS reference system as well as photometric zeropoint calibration for frames covered by the SDSS foot-print. The pipeline makes use of multiple CPU-cores wherever possible, resulting in an execution time of only a few seconds per frame, thus offering the ODI observer a convenient way to closely monitor data quality.

[ascl:1210.028]
QYMSYM: A GPU-accelerated hybrid symplectic integrator

QYMSYM is a GPU accelerated 2nd order hybrid symplectic integrator that identifies close approaches between particles and switches from symplectic to Hermite algorithms for particles that require higher resolution integrations. This is a parallel code running with CUDA on a video card that puts the many processors on board to work while taking advantage of fast shared memory.

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

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

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

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

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

[ascl:1502.013]
Rabacus: Analytic Cosmological Radiative Transfer Calculations

Rabacus performs analytic radiative transfer calculations in simple geometries relevant to cosmology and astrophysics; it also contains tools to calculate cosmological quantities such as the power spectrum and mass function. With core routines written in Fortran 90 and then wrapped in Python, the execution speed is thousands of times faster than equivalent routines written in pure Python.

[ascl:1711.015]
rac-2d: Thermo-chemical for modeling water vapor formation in protoplanetary disks

rec-2d models the distribution of water vapor in protoplanetary disks. Given a distribution of gas and dust, rac-2d first solves the dust temperature distribution with a Monte Carlo method and then solves the gas temperature distribution and chemical composition. Although the geometry is symmetric with respect to rotation around the central axis and reflection about the midplane, the photon propagation is done in full three dimensions. After establishing the dust temperature distribution, the disk chemistry is evolved for 1 Myr; the heating and cooling processes are coupled with chemistry, allowing the gas temperature to be evolved in tandem with chemistry based on the heating and cooling rates.

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

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

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

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

[ascl:1308.012]
RADLite: Raytracer for infrared line spectra

RADLite is a raytracer that is optimized for producing infrared line spectra and images from axisymmetric density structures, originally developed to function on top of the dust radiative transfer code RADMC. RADLite can consistently deal with a wide range of velocity gradients, such as those typical for the inner regions of protoplanetary disks. The code is intended as a back-end for chemical and excitation codes, and can rapidly produce spectra of thousands of lines for grids of models for comparison with observations. It includes functionality for simulating telescopic images for optical/IR/midIR/farIR telescopes. It takes advantage of multi-threaded CPUs and includes an escape-probability non-LTE module.

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

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

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

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

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

[ascl:9910.009]
RADPACK: A RADical compression analysis PACKage for fitting to the CMB

The RADPACK package, written in IDL, contains both data and software. The data are the constraints on the cosmic microwave background (CMB) angular power spectrum from all published data as of 9/99. A unique aspect of this compilation is that the non-Gaussianity of the uncertainties has been characterized. The most important program in the package, written in the IDL language, is called chisq.pro and calculates $chi^2$, for an input power spectrum, according to the offset log-normal form of Bond, Jaffe and Knox (astro-ph/9808264). chisq.pro also outputs files that are useful for examining the residuals (the difference between the predictions of the model and the data). There is an sm macro for plotting up the residuals, and a histogram of the residuals. The histogram is actually for the 'whitenend' residuals ---a linear combination of the residuals which leaves them uncorrelated and with unit variance. The expectation is that the whitened residuals will be distributed as a Gaussian with unit variance.

[ascl:1801.012]
RadVel: General toolkit for modeling Radial Velocities

RadVel models Keplerian orbits in radial velocity (RV) time series. The code is written in Python with a fast Kepler's equation solver written in C. It provides a framework for fitting RVs using maximum a posteriori optimization and computing robust confidence intervals by sampling the posterior probability density via Markov Chain Monte Carlo (MCMC). RadVel can perform Bayesian model comparison and produces publication quality plots and LaTeX tables.

[ascl:1411.010]
Raga: Monte Carlo simulations of gravitational dynamics of non-spherical stellar systems

Raga (Relaxation in Any Geometry) is a Monte Carlo simulation method for gravitational dynamics of non-spherical stellar systems. It is based on the SMILE software (ascl:1308.001) for orbit analysis. It can simulate stellar systems with a much smaller number of particles N than the number of stars in the actual system, represent an arbitrary non-spherical potential with a basis-set or spline spherical-harmonic expansion with the coefficients of expansion computed from particle trajectories, and compute particle trajectories independently and in parallel using a high-accuracy adaptive-timestep integrator. Raga can also model two-body relaxation by local (position-dependent) velocity diffusion coefficients (as in Spitzer's Monte Carlo formulation) and adjust the magnitude of relaxation to the actual number of stars in the target system, and model the effect of a central massive black hole.

[ascl:1710.013]
Ramses-GPU: Second order MUSCL-Handcock finite volume fluid solver

RamsesGPU is a reimplementation of RAMSES (ascl:1011.007) which drops the adaptive mesh refinement (AMR) features to optimize 3D uniform grid algorithms for modern graphics processor units (GPU) to provide an efficient software package for astrophysics applications that do not need AMR features but do require a very large number of integration time steps. RamsesGPU provides an very efficient C++/CUDA/MPI software implementation of a second order MUSCL-Handcock finite volume fluid solver for compressible hydrodynamics as a magnetohydrodynamics solver based on the constraint transport technique. Other useful modules includes static gravity, dissipative terms (viscosity, resistivity), and forcing source term for turbulence studies, and special care was taken to enhance parallel input/output performance by using state-of-the-art libraries such as HDF5 and parallel-netcdf.

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

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

[ascl:1803.015]
RAPTOR: Imaging code for relativistic plasmas in strong gravity

Bronzwaer, Thomas; Davelaar, Jordy; Younsi, Ziri; Mościbrodzka, Monika; Falcke, Heino; Kramer, Michael; Rezzolla, Luciano

RAPTOR produces accurate images, animations, and spectra of relativistic plasmas in strong gravity by numerically integrating the equations of motion of light rays and performing time-dependent radiative transfer calculations along the rays. The code is compatible with any analytical or numerical spacetime, is hardware-agnostic and may be compiled and run on both GPUs and CPUs. RAPTOR is useful for studying accretion models of supermassive black holes, performing time-dependent radiative transfer through general relativistic magneto-hydrodynamical (GRMHD) simulations and investigating the expected observational differences between the so-called fastlight and slow-light paradigms.

[ascl:0008.002]
RATRAN: Radiative Transfer and Molecular Excitation in One and Two Dimensions

RATRAN is a numerical method and computer code to calculate the radiative transfer and excitation of molecular lines. The approach is based on the Monte Carlo method, and incorporates elements from Accelerated Lambda Iteration. It combines the flexibility of the former with the speed and accuracy of the latter. Convergence problems known to plague Monte Carlo methods at large optical depth (>100) are avoided by separating local contributions to the radiation field from the overall transfer problem. The random nature of the Monte Carlo method serves to verify the independence of the solution to the angular, spatial, and frequency sampling of the radiation field. This allows the method to be used in a wide variety of astrophysical problems without specific adaptations. Moreover, the code can be applied to all atoms or molecules for which collisional rate coefficients are available and any axially symmetric source model. Continuum emission and absorption by dust is explicitly taken into account but scattering is neglected. We expect this program to be an important tool in analyzing data from present and future infrared and (sub-)millimeter telescopes.

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

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

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

[ascl:1411.006]
RC3 mosaicking pipeline: Creating mosaics for the RC3 Catalogue

The RC3 mosaicking pipeline creates color composite images and scientifically-calibrated FITS mosaics in all SDSS imaging bands for all the RC3 galaxies that lie within the survey’s footprint and on photographic plates taken by the Digitized Palomar Observatory Sky Survey (DPOSS) for the B, R, IR bands. The pipeline uses SExtractor (ascl:1010.064) for extraction and STIFF (ascl:1110.006) to generating color images. The mosaicking program uses a recursive algorithm for positional update first to correct the positional inaccuracy inherent in the RC3 catalog, then conducts the mosaicking procedure using the Astropy (ascl:1304.002) wrapper to IPAC's Montage (ascl:1010.036) software. The program is generalized into a pipeline that can be easily extended to future survey data or other source catalogs; an online interface is available at

http://lcdm.astro.illinois.edu/data/rc3/search.html.

[ascl:1408.017]
RDGEN: Routines for data handling, display, and adjusting

RDGEN is a collection of routines for data handling, display, and adjusting, with a facility which helps to set up files for using with VPFIT (ascl:1408.015); it is included in the VPFIT distribution file. It is useful for setting region boundaries and initial guesses for VPFIT, for displaying the accumulated results, for examining by eye particular redshift systems and fits to them, testing that the error array is a true reflection of the rms scatter in the data, comparing spectra and generally examining and even modifying the data.

[ascl:1506.007]
REALMAF: Magnetic power spectra from Faraday rotation maps

REALMAF is a maximum-a-posteriori code to measure magnetic power spectra from Faraday rotation data. It uses a sophisticated model for the magnetic autocorrelation in real space, thus alleviating the need for simplifying assumptions in the processing. REALMAF treats the divergence relation of the magnetic field with a multiplicative factor in Fourier space, which allows modeling the magnetic autocorrelation as a spherically symmetric function.

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

In recent years, the freely available Monte Carlo code REAS for modelling radio emission from cosmic ray air showers has evolved to include the full complexity of air shower physics. However, it turned out that in REAS2 and all other time-domain models which calculate the radio emission by superposing the radiation of the single air shower electrons and positrons, the calculation of the emission contributions was not fully consistent. In this article, we present a revised implementation in REAS3, which incorporates the missing radio emission due to the variation of the number of charged particles during the air shower evolution using an "end-point formalism". With the inclusion of these emission contributions, the structure of the simulated radio pulses changes from unipolar to bipolar, and the azimuthal emission pattern becomes nearly symmetric. Remaining asymmetries can be explained by radio emission due to the variation of the net charge excess in air showers, which is automatically taken into account in the new implementation. REAS3 constitutes the first self-consistent time-domain implementation based on single particle emission taking the full complexity of air shower physics into account, and is freely available for all interested users.

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