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[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:1902.008] Radynversion: Solar atmospheric properties during a solar flare

Radynversion infers solar atmospheric properties during a solar flare. The code is based on an Invertible Neural Network (INN) that is trained to learn an approximate bijective mapping between the atmospheric properties of electron density, temperature, and bulk velocity (all as a function of altitude), and the observed Hα and Ca II λ8542 line profiles. As information is lost in the forward process of radiation transfer, this information is injected back into the model during the inverse process by means of a latent space; the training allows this latent space to be filled using an n-dimensional unit Gaussian distribution, where n is the dimensionality of the latent space. The code is based on a model trained by simulations made by RADYN, a 1D non-equilibrium radiation hydrodynamic model with good optically thick radiation treatment that does not consider magnetic effects.

[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:2103.016] RAiSERed: Analytic AGN model based code for radio-frequency redshifts

The RAiSERed (Radio AGN in Semi-analytic Environments: Redshifts) code implements the RAiSE analytic model for Fanaroff-Riley type II sources, using a Bayesian prior for their host cosmological environments, to measure the redshift of active galactic nuclei lobes based on radio-frequency observations. The Python code provides a class for the user to store measured attributes for each radio source, and to which model derived redshift probability density functions are returned. Systematic uncertainties in the analytic model can be calibrated by specifying a subset of radio sources with spectroscopic redshifts. Functions are additionally provided to plot the redshift probability density functions and assess the success of the model calibration.

[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:2008.021] ramses2hsim: RAMSES output to 3D data cube for HSIM

The ramses2hsim pipeline converts a simulated galaxy in a RAMSES (ascl:1011.007) output into an 3D input data cube for HSIM (ascl:1912.006). The code incorporates gas kinematics (both bulk and turbulence), line emission and line width for Hα, and accounts for dust extinction.

[ascl:2003.007] RAPID: Real-time Automated Photometric IDentification

RAPID (Real-time Automated Photometric IDentification) classifies multiband photometric light curves into several different transient classes. It uses a deep recurrent neural network to produce time-varying classifications, and because it does not rely on deriving computationally expensive features from the data, it is well suited for processing alerts that wide-field surveys such as the Zwicky Transient Facility (ZTF) and the Large Synoptic Survey Telescope (LSST) will produce.

[ascl:2005.016] RAPP: Robust Automated Photometry Pipeline

RAPP is a robust automated photometry pipeline for blurred images. RAPP requires that the observed images contain at least three stars and applies bias, dark, and flat field correction on blurred observational raw data; it also uses the median of adjacent pixels to eliminate outliers. It also uses star enhancement and robust image matching, extracts stars, and performs aperture photometry to extract information from blurred images.

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

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: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.

[ascl:2002.002] RASCAS: Resonant line transfer in AMR simulations

The massively parallel code RASCAS (RAdiative SCattering in Astrophysical Simulations) performs radiative transfer on an adaptive mesh with an octree structure using the Monte Carlo technique. The code features full MPI parallelization, domain decomposition, adaptive load-balancing, and a standard peeling algorithm to construct mock observations. The radiative transport of resonant line photons through different mixes of species (e.g. HI, SiII, MgII, FeII), including their interaction with dust, is implemented in a modular fashion to allow new transitions to be easily added to the code. RASCAS may also be used to propagate photons at any wavelength (e.g. stellar continuum or fluorescent lines), and has been designed to be easily customizable and to process simulations of arbitrarily large sizes on large supercomputers.

[ascl:2102.022] RASSINE: Normalizing 1D stellar spectra

RASSINE normalizes merged 1D spectra using the concept of convex hulls. The code uses six parameters that can be fine-tuned, and provides an interactive interface, including graphical feedback, for easily choosing the parameters. RASSINE can also provide a first guess for the parameters that are derived directly from the merged 1D spectrum based on previously performed calibrations.

[ascl:1904.014] rate: Reliable Analytic Thermochemical Equilibrium

rate computes thermochemical-equilibrium abundances for a H-C-N-O system with known pressure, temperature, and elemental abundances. The output abundances are H2O, CH4, CO, CO2, NH3, C2H2, C2H4, HCN, and N2, H2, H, and He.

[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:2009.015] rcosmo: Cosmic Microwave Background data analysis

rcosmo provides information processing, visualization, manipulation and spatial statistical analysis of Cosmic Microwave Background (CMB) radiation and other spherical data stored in or converted to HEALPix coordinates. The package has more than 100 different functions, and can perform spherical geometry, manipulate CMB and other spherical data, and visualize HEALPix data. rcosmo can also perform statistical analysis of CMB and spherical data, and transforme spherical data in cartesian and geographic coordinates into HEALPix format.

[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:2007.016] ReadPDS: Visualization tools for PDS4 data

ReadPDS reads in and visualizes data from the Planetary Data System in PDS4 format. Tools are available in Python as PDS4Viewer and in IDL as PDS4-IDL. These tools support PDS4 data, including images, spectra, and arrays and provide multiple views of the data, including summary, image, plot, and table views in addition to easy access to metadata such as structure labels and spectral characteristics.

[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

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. REAS3 improves the calculation of the emission contributions, which was not fully consistent in earlier versions of REAS, by incorporating 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. REAS3 has been superseded by CoREAS (ascl:1406.003).

[ascl:1110.016] REBOUND: Multi-purpose N-body code for collisional dynamics

REBOUND is a multi-purpose N-body code which is freely available under an open-source license. It was designed for collisional dynamics such as planetary rings but can also solve the classical N-body problem. It is highly modular and can be customized easily to work on a wide variety of different problems in astrophysics and beyond.

REBOUND comes with three symplectic integrators: leap-frog, the symplectic epicycle integrator (SEI) and a Wisdom-Holman mapping (WH). It supports open, periodic and shearing-sheet boundary conditions. REBOUND can use a Barnes-Hut tree to calculate both self-gravity and collisions. These modules are fully parallelized with MPI as well as OpenMP. The former makes use of a static domain decomposition and a distributed essential tree. Two new collision detection modules based on a plane-sweep algorithm are also implemented. The performance of the plane-sweep algorithm is superior to a tree code for simulations in which one dimension is much longer than the other two and in simulations which are quasi-two dimensional with less than one million particles.

[ascl:2011.020] REBOUNDx: Adding effects in REBOUND N-body integrations

REBOUNDx incorporates additional physics into REBOUND (ascl:1110.016) simulations. Users can add effects from a list of pre-implemented astrophysical forces or contribute new ones. The main code is written in C, and a Python wrapper is provided for interfacing with other libraries. The REBOUNDx source code is machine independent and a binary format to save REBOUNDx configurations interfaces with the SimulationArchive class in REBOUND, making it possible to share and reproduce results bit by bit.

[ascl:1106.026] RECFAST: Calculate the Recombination History of the Universe

RECFAST calculates the recombination of H, HeI, and HeII in the early Universe; this involves a line-by-line treatment of each atomic level. It differs in comparison to previous calculations in two major ways: firstly, the ionization fraction x_e is approximately 10% smaller for redshifts <~800, due to non-equilibrium processes in the excited states of H, and secondly, HeI recombination is much slower than previously thought, and is delayed until just before H recombines. RECFAST enables fast computation of the ionization history (and quantities such as the power spectrum of CMB anisotropies which depend on it) for arbitrary cosmologies.

[ascl:2005.004] REDFIT: Red-noise spectra directly from unevenly spaced time series

Time series are commonly unevenly spaced in time make it difficult to obtain an accurate estimate of their typical red-noise spectrum. REDFIT overcomes this problem by fitting a first-order autoregressive (AR1) process directly to unevenly spaced time series. Hence, interpolation in the time domain and its inevitable bias can be avoided. The program can be used to test if peaks in the spectrum of a time series are significant against the red-noise background from an AR1 process.

[ascl:2103.004] redshifts: Spectroscopic redshifts search tool

redshifts collects all unique spectroscopic redshifts from online databases such as VizieR and NED. It can perform a flexible search within a radius of a given set of (RA, DEC) coordinates and uses column names and descriptions (including UCD keywords) to identify columns containing spectroscopic redshifts or velocities. It weeds out photometric redshifts and duplicates and returns a unique list of best spectroscopic redshift measurements. redshifts can be used standalone from the terminal, and can take a number of optional command line arguments, or from Python.

[ascl:1507.017] REDSPEC: NIRSPEC data reduction

REDSPEC is an IDL based reduction package designed with NIRSPEC in mind though can be used to reduce data from other spectrographs as well. REDSPEC accomplishes spatial rectification by summing an A+B pair of a calibration star to produce an image with two spectra; the image is remapped on the basis of polynomial fits to the spectral traces and calculation of gaussian centroids to define their separation, producing straight spectral traces with respect to the detector rows. The raw images are remapped onto a coordinate system with uniform intervals in spatial extent along the slit and in wavelength along the dispersion axis.

[ascl:1508.003] REDUCEME: Long-slit spectroscopic data reduction and analysis

The astronomical data reduction package REDUCEME reduces and analyzes long-slit spectroscopic data. The package uses the unformatted FORTRAN raw data format, so requires FITS files be transformed to REDUCEME format; the reverse operation (from REDUCEME to FITS format) is also available. The package is a set of programs written in FORTRAN 77 and includes shell scripts (using the C shell syntax) to perform routine tasks; it can be extended by the inclusion of external programs. REDUCEME uses PGPLOT (ascl:1103.002) for line plots and images, and a subset of subroutines, called BUTTON, enables the user to communicate interactively with the image display employing graphic buttons. One advantage of using REDUCEME is that for each image an associated error image can also be processed throughout the reduction process, allowing for a careful control of the error propagation.

[ascl:1401.004] Reflex: Graphical workflow engine for data reduction

Reflex provides an easy and flexible way to reduce VLT/VLTI science data using the ESO pipelines. It allows graphically specifying the sequence in which the data reduction steps are executed, including conditional stops, loops and conditional branches. It eases inspection of the intermediate and final data products and allows repetition of selected processing steps to optimize the data reduction. The data organization necessary to reduce the data is built into the system and is fully automatic; advanced users can plug their own modules and steps into the data reduction sequence. Reflex supports the development of data reduction workflows based on the ESO Common Pipeline Library. Reflex is based on the concept of a scientific workflow, whereby the data reduction cascade is rendered graphically and data seamlessly flow from one processing step to the next. It is distributed with a number of complete test datasets so users can immediately start experimenting and familiarize themselves with the system.

[ascl:1206.001] RegiStax: Alignment, stacking and processing of images

RegiStax is software for alignment/stacking/processing of images; it was released over 10 years ago and continues to be developed and improved. The current version is RegiStax 6, which supports the following formats: AVI, SER, RFL (RegiStax Framelist), BMP, JPG, TIF, and FIT. This version has a shorter and simpler processing sequence than its predecessor, and optimizing isn't necessary anymore as a new image alignment method optimizes directly. The interface of RegiStax 6 has been simplified to look more uniform in appearance and functionality, and RegiStax 6 now uses Multi-core processing, allowing the user to have up to have multiple cores(recommended to use maximally 4) working simultaneous during alignment/stacking.

[ascl:1404.012] RegPT: Regularized cosmological power spectrum

RegPT computes the power spectrum in flat wCDM class models based on the RegPT treatment when provided with either of transfer function or matter power spectrum. It then gives the multiple-redshift outputs for power spectrum, and optionally provides correlation function data. The Fortran code has two major options for power spectrum calculations; -fast, which quickly computes the power spectrum at two-loop level (typically a few seconds) using the pre-computed data set of PT kernels for fiducial cosmological models, and -direct, in which the code first applies the fast method, and then follows the regularized expression for power spectrum to directly evaluate the multi-dimensional integrals. The output results are the power spectrum of direct calculation and difference of the results between fast and direct method. The code also gives the data set of PT diagrams necessary for power spectrum calculations from which the power spectrum can be constructed.

[ascl:1505.021] relline: Relativistic line profiles calculation

relline calculates relativistic line profiles; it is compatible with the common X-ray data analysis software XSPEC (ascl:9910.005) and ISIS (ascl:1302.002). The two basic forms are an additive line model (RELLINE) and a convolution model to calculate relativistic smearing (RELCONV).

[ascl:2010.015] relxill: Reflection models of black hole accretion disks

relxill self-consistently connects an angle-dependent reflection model constructed with XILLVER (http://www.srl.caltech.edu/personnel/javier/xillver/index.html) with the relativistic blurring code RELLINE (ascl:1505.021). It calculates the proper emission angle of the radiation at each point on the accretion disk and then takes the corresponding reflection spectrum into account.

[ascl:1904.008] repack: Repack and compress line-transition data

repack re-packs and compresses line-transition data for radiative-transfer calculations. It identifies the strong lines that dominate the spectrum from the large-majority of weaker lines, returning a binary line-by-line (LBL) file with the strong lines info (wavenumber, Elow, gf, and isotope ID), and an ASCII file with the combined contribution of the weaker lines compressed into a continuum extinction coefficient (in cm-1 amagat-1) as function of wavenumber and temperature.

[ascl:2011.023] reproject: Python-based astronomical image reprojection

reproject implements image reprojection (resampling) methods for astronomical images using various techniques via a uniform interface. Reprojection re-grids images from one world coordinate system to another (for example changing the pixel resolution, orientation, coordinate system). reproject works on celestial images by interpolation, as well as by finding the exact overlap between pixels on the celestial sphere. It can also reproject to/from HEALPIX projections by relying on the astropy-healpix package.

[ascl:1612.022] REPS: REscaled Power Spectra for initial conditions with massive neutrinos

REPS (REscaled Power Spectra) provides accurate, one-percent level, numerical simulations of the initial conditions for massive neutrino cosmologies, rescaling the late-time linear power spectra to the simulation initial redshift.

[ascl:1809.016] RequiSim: Variance weighted overlap calculator

RequiSim computes the Variance Weighted Overlap, which is a measure of the bias on the lensing signal from power spectrum modelling bias for any non-linear model. It assumes that the bias on the power spectrum is Gaussian with a covariance described by a user-provided knowledge matrix that describes the covariance in the bias on the power spectrum. The data from the Euclid wide-field survey are included.

[ascl:1505.028] RESOLVE: Bayesian algorithm for aperture synthesis imaging in radio astronomy

RESOLVE is a Bayesian inference algorithm for image reconstruction in radio interferometry. It is optimized for extended and diffuse sources. Features include parameter-free Bayesian reconstruction of radio continuum data with a focus on extended and weak diffuse sources, reconstruction with uncertainty propagation dependent on measurement noise, and estimation of the spatial correlation structure of the radio astronomical source. RESOLVE provides full support for measurement sets and includes a simulation tool (if uv-coverage is provided).

[ascl:1907.023] REVOLVER: REal-space VOid Locations from suVEy Reconstruction

REVOLVER reconstructs real space positions from redshift-space tracer data by subtracting RSD through FFT-based reconstruction (optional) and applies void-finding algorithms to create a catalogue of voids in these tracers. The tracers are normally galaxies from a redshift survey but could also be halos or dark matter particles from a simulation box. Two void-finding routines are provided. The first is based on ZOBOV (ascl:1304.005) and uses Voronoi tessellation of the tracer field to estimate the local density, followed by a watershed void-finding step. The second is a voxel-based method, which uses a particle-mesh interpolation to estimate the tracer density, and then uses a similar watershed algorithm. Input data files can be in FITS format, or ASCII- or NPY-formatted data arrays.

[ascl:2005.018] RFCDE: Random Forests for Conditional Density Estimation

RFCDE provides an implementation of random forests designed for conditional density estimation. It computes a kernel density estimate of y with nearest neighbor weightings defined by the location of the evaluation point x relative to the leaves in the random forest.

[ascl:1710.002] rfpipe: Radio interferometric transient search pipeline

rfpipe supports Python-based analysis of radio interferometric data (especially from the Very Large Array) and searches for fast radio transients. This extends on the rtpipe library (ascl:1706.002) with new approaches to parallelization, acceleration, and more portable data products. rfpipe can run in standalone mode or be in a cluster environment.

[ascl:1711.006] RGW: Goodman-Weare Affine-Invariant Sampling

RGW is a lightweight R-language implementation of the affine-invariant Markov Chain Monte Carlo sampling method of Goodman & Weare (2010). The implementation is based on the description of the python package emcee (ascl:1303.002).

[ascl:1502.001] RH 1.5D: Polarized multi-level radiative transfer with partial frequency distribution

RH 1.5D performs Zeeman multi-level non-local thermodynamical equilibrium calculations with partial frequency redistribution for an arbitrary amount of chemical species. Derived from the RH code and written in C, it calculates spectra from 3D, 2D or 1D atmospheric models on a column-by-column basis (or 1.5D). It includes optimization features to speed up or improve convergence, which are particularly useful in dynamic models of chromospheres. While one should be aware of its limitations, the calculation of spectra using the 1.5D or column-by-column is a good approximation in many cases, and generally allows for faster convergence and more flexible methods of improving convergence. RH 1.5D scales well to at least tens of thousands of CPU cores.

[ascl:1611.009] RHOCUBE: 3D density distributions modeling code

RHOCUBE models 3D density distributions on a discrete Cartesian grid and their integrated 2D maps. It can be used for a range of applications, including modeling the electron number density in LBV shells and computing the emission measure. The RHOCUBE Python package provides several 3D density distributions, including a powerlaw shell, truncated Gaussian shell, constant-density torus, dual cones, and spiralling helical tubes, and can accept additional distributions. RHOCUBE provides convenient methods for shifts and rotations in 3D, and if necessary, an arbitrary number of density distributions can be combined into the same model cube and the integration ∫ dz performed through the joint density field.

[ascl:2003.005] RHT: Rolling Hough Transform

The RHT (Rolling Hough Transform) measures linear intensity as a function of orientation in images. This machine vision algorithm works on any image-space (2D) data, and quantifies the presence of linear structure as a function of orientation. The RHT can be used to identify linear features in images, to quantify the orientation of structure in images, and to map image intensity from 2D x-y space to 3D x-y-orientation space. An option in the code allows the user to quantify intensity as a function of direction (modulo 2pi) rather than orientation (modulo pi). The RHT was first used to discover that filamentary structures in neutral hydrogen emission are aligned with the ambient magnetic field.

[ascl:1410.005] RICH: Numerical simulation of compressible hydrodynamics on a moving Voronoi mesh

RICH (Racah Institute Computational Hydrodynamics) is a 2D hydrodynamic code based on Godunov's method. The code, largely based on AREPO (ascl:1909.010), acts on an unstructured moving mesh. It differs from AREPO in the interpolation and time advancement scheme as well as a novel parallelization scheme based on Voronoi tessellation. Though not universally true, in many cases a moving mesh gives better results than a static mesh: where matter moves one way and a sound wave is traveling in the other way (such that relative to the grid the wave is not moving), a static mesh gives better results than a moving mesh. RICH is designed in an object oriented, user friendly way that facilitates incorporation of new algorithms and physical processes.

[ascl:2005.001] RID: Relativistic Image Doubling in water Cherenkov detectors

RID (Relativistic Image Doubling in water Cherenkov detectors) uses Monte Carlo simulations to find the relative fraction of charged, relativistic particles entering a HAWC-like Water Cherenkov Detector that can cause a Relativistic Image Doubling (RID) effect visible to at least one of the internal detectors. The technique is available in C++ and Fortran; RID also includes python code for the horizontal incidence of the muon inside the tank.

[ascl:1811.009] RLOS: Time-resolved imaging of model astrophysical jets

RLOS (Relativistic Line Of Sight) uses hydrocode output data, such as that from PLUTO (ascl:1010.045), to create synthetic images depicting what a model relativistic astrophysical jet looks like to a stationary observer. The approximate time-delayed imaging algorithm used is implemented within existing line-of-sight code. The software has the potential to study a variety of dynamical astrophysical phenomena in collaboration with other imaging and simulation tools.

[ascl:1708.011] RM-CLEAN: RM spectra cleaner

RM-CLEAN reads in dirty Q and U cubes, generates rmtf based on the frequencies given in an ASCII file, and cleans the RM spectra following the algorithm given by Brentjens (2007). The output cubes contain the clean model components and the CLEANed RM spectra. The input cubes must be reordered with mode=312, and the output cubes will have the same ordering and thus must be reordered after being written to disk. RM-CLEAN runs as a MIRIAD (ascl:1106.007) task and a Python wrapper is included with the code.

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