Results 901-950 of 2372 (2337 ASCL, 35 submitted)
Modern N-body cosmological simulations contain billions ($10^9$) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory, and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly-employed halo finders, such that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes MPI and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger datasets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit yt, an analysis toolkit for Adaptive Mesh Refinement (AMR) data that includes complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and datasets in excess of $2000^3$ particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable. Parallel HOP is part of yt.
Pangloss reconstructs all the mass within a light cone through the Universe. Understanding complex mass distributions like this is important for accurate time delay lens cosmography, and also for accurate lens magnification estimation. It aspires to use all available data in an attempt to make the best of all mass maps.
PandExo generates instrument simulations of JWST’s NIRSpec, NIRCam, NIRISS and NIRCam and HST WFC3 for planning exoplanet observations. It uses throughput calculations from STScI’s Exposure Time Calculator, Pandeia, and offers both an online tool and a python package.
PampelMuse analyzes integral-field spectroscopic observations of crowded stellar fields and provides several subroutines to perform the individual steps of the data analysis. All analysis steps assume that the IFS data has been properly reduced and that all the instrumental artifacts have been removed. PampelMuse is designed to correctly handle IFS data regardless of which instrument was used to observe the data. In addition to the actual data, the software also requires an estimate of the variances for the analysis; optionally, it can use a bad pixel mask. The analysis relies on the presence of a reference catalogue, containing coordinates and magnitudes of the stars in and around the observed field.
PAMELA is an implementation of the optimal extraction algorithm for long-slit CCD spectroscopy and is well suited for time-series spectroscopy. It properly implements the optimal extraction algorithm for curved spectra, including on-the-fly cosmic ray rejection as well as proper calculation and propagation of the errors. The software is distributed as part of the Starlink software collection (ascl:1110.012).
The PAL library is a partial re-implementation of Pat Wallace's popular SLALIB library written in C using a Gnu GPL license and layered on top of the IAU's SOFA library (or the BSD-licensed ERFA) where appropriate. PAL attempts to stick to the SLA C API where possible.
PAHFIT is an IDL tool for decomposing Spitzer IRS spectra of PAH emission sources, with a special emphasis on the careful recovery of ambiguous silicate absorption, and weak, blended dust emission features. PAHFIT is primarily designed for use with full 5-35 micron Spitzer low-resolution IRS spectra. PAHFIT is a flexible tool for fitting spectra, and you can add or disable features, compute combined flux bands, change fitting limits, etc., without changing the code.
PAHFIT uses a simple, physically-motivated model, consisting of starlight, thermal dust continuum in a small number of fixed temperature bins, resolved dust features and feature blends, prominent emission lines (which themselves can be blended with dust features), as well as simple fully-mixed or screen dust extinction, dominated by the silicate absorption bands at 9.7 and 18 microns. Most model components are held fixed or are tightly constrained. PAHFIT uses Drude profiles to recover the full strength of dust emission features and blends, including the significant power in the wings of the broad emission profiles. This means the resulting feature strengths are larger (by factors of 2-4) than are recovered by methods which estimate the underlying continuum using line segments or spline curves fit through fiducial wavelength anchors.
PACSman provides an alternative for several reduction and analysis steps performed in HIPE (ascl:1111.001) on PACS spectroscopic data; it is written in IDL. Among the operations possible with it are transient correction, line fitting, map projection, and map analysis, and unchopped scan, chop/nod, and the decommissioned wavelength switching observation modes are supported.
Pacerman, written in IDL, is a new method to calculate Faraday rotation measure maps from multi-frequency polarisation angle data. In order to solve the so called n-pi-ambiguity problem which arises from the observationally ambiguity of the polarisation angle which is only determined up to additions of n times pi, where n is an integer, we suggest using a global scheme. Instead of solving the n-pi-ambiguity for each data point independently, our algorithm, which we chose to call Pacerman solves the n-pi-ambiguity for a high signal-to-noise region "democratically" and uses this information to assist computations in adjacent low signal-to-noise areas.
PACCE (Perl Algorithm to Compute continuum and Equivalent Widths) computes continuum and equivalent widths. PACCE is able to determine mean continuum and continuum at line center values, which are helpful in stellar population studies, and is also able to compute the uncertainties in the equivalent widths using photon statistics.
p3d is semi-automatic data-reduction tool designed to be used with fiber-fed integral-field spectrographs. p3d is a highly general and freely available tool based on IDL but can be used with full functionality without an IDL license. It is easily extended to include improved algorithms, new visualization tools, and support for additional instruments. It uses a novel algorithm for automatic finding and tracing of spectra on the detector, and includes two methods of optimal spectrum extraction in addition to standard aperture extraction. p3d also provides tools to combine several images, perform wavelength calibration and flat field data.
P2SAD computes the Particle Phase Space Average Density (P2SAD) in galactic haloes. The model for the calculation is based on the stable clustering hypothesis in phase space, the spherical collapse model, and tidal disruption of substructures. The multiscale prediction for P2SAD computed by this IDL code can be used to estimate signals sensitive to the small scale structure of dark matter distributions (e.g. dark matter annihilation). The code computes P2SAD averaged over the whole virialized region of a Milky-Way-size halo at redshift zero.
P2DFFT is a parallelized version of 2DFFT (ascl:1608.015). It isolates and measures the spiral arm pitch angle of galaxies. The code allows direct input of FITS images, offers the option to output inverse Fourier transform FITS images, and generates idealized logarithmic spiral test images of a specified size that have 1 to 6 arms with pitch angles of -75 degrees to 75 degrees. Further, it can output Fourier amplitude versus inner radius and pitch angle versus inner radius for each Fourier component (m = 0 to m = 6), and calculates the Fourier amplitude weighted mean pitch angle across m = 1 to m = 6 versus inner radius.
oxkat semi-automatically performs calibration and imaging of data from the MeerKAT radio telescope. Taking as input raw visibilities in Measurement Set format, the entire processing workflow is covered, from flagging and reference calibration, to imaging and self-calibration, and (optionally) direction-dependent calibration. The oxkat scripts use Python, and draw on numerous existing radio astronomy packages, including CASA (ascl:1107.013), WSClean (ascl:1408.023), and CubiCal (ascl:1805.031), among others, that are containerized using Singularity. Submission scripts for slurm and PBS job schedulers are automatically generated where necessary, catering for HPC facilities that are commonly used for processing MeerKAT data.
OXAF provides a simplified model of Seyfert Active Galactic Nucleus (AGN) continuum emission designed for photoionization modeling. It removes degeneracies in the effects of AGN parameters on model spectral shapes and reproduces the diversity of spectral shapes that arise in physically-based models. OXAF accepts three parameters which directly describe the shape of the output ionizing spectrum: the energy of the peak of the accretion disk emission Epeak, the photon power-law index of the non-thermal X-ray emission Γ, and the proportion of the total flux which is emitted in the non-thermal component pNT. OXAF accounts for opacity effects where the accretion disk is ionized because it inherits the ‘color correction’ of OPTXAGNF, the physical model upon which OXAF is based.
Comparing properties of discovered trans-Neptunian Objects (TNOs) with dynamical models is impossible due to the observational biases that exist in surveys. The OSSOS Survey Simulator takes an intrinsic orbital model (from, for example, the output of a dynamical Kuiper belt emplacement simulation) and applies the survey biases, so the biased simulated objects can be directly compared with real discoveries.
OSPEX (Object Spectral Executive) is an object-oriented interface for X-ray spectral analysis of solar data. The next generation of SPEX (ascl:2007.017), it reads and displays input data, selects and subtracts background, selects time intervals of interest, selects a combination of photon flux model components to describe the data, and fits those components to the spectrum in each time interval selected. During the fitting process, the response matrix is used to convert the photon model to the model counts to compare with the input count data. The resulting time-ordered fit parameters are stored and can be displayed and analyzed with OSPEX. The entire OSPEX session can be saved in the form of a script and the fit results stored in the form of a FITS file. Part of the SolarSoft (ascl:1208.013) package, OSPEX works with any type of data structured in the form of time-ordered count spectra; RHESSI, Fermi, SOXS, MESSENGER, Yohkoh, SMM, and SMART data analysis have all been implemented in OSPEX.
OSIRIS Toolbox reduces data for the Keck OSIRIS instrument, an integral field spectrograph that works with the Keck Adaptive Optics System. It offers real-time reduction of raw frames into cubes for display and basic analysis. In this real-time mode, it takes about one minute for a preliminary data cube to appear in the “quicklook” display package. The reduction system also includes a growing set of final reduction steps including correction of telluric absorption and mosaicing of multiple cubes.
oscode solves oscillatory ordinary differential equations efficiently. It is designed to deal with equations of the form x¨(t)+2γ(t)x˙(t)+ω2(t)x(t)=0, where γ(t) and ω(t) can be given as explicit functions or sequence containers (Eigen::Vectors, arrays, std::vectors, lists) in C++ or as numpy.arrays in Python. oscode makes use of an analytic approximation of x(t) embedded in a stepping procedure to skip over long regions of oscillations, giving a reduction in computing time. The approximation is valid when the frequency changes slowly relative to the timescales of integration, it is therefore worth applying when this condition holds for at least some part of the integration range.
ORSA is an interactive tool for scientific grade Celestial Mechanics computations. Asteroids, comets, artificial satellites, solar and extra-solar planetary systems can be accurately reproduced, simulated, and analyzed. The software uses JPL ephemeris files for accurate planets positions and has a Qt-based graphical user interface. It offers an advanced 2D plotting tool and 3D OpenGL viewer and the standalone numerical library liborsa and can import asteroids and comets from all the known databases (MPC, JPL, Lowell, AstDyS, and NEODyS). In addition, it has an integrated download tool to update databases.
ORIGIN performs blind detection of faint emitters in MUSE datacubes. The algorithm is tuned to detect faint spatial-spectral emission signatures while allowing for a stable false detection rate over the data cube, and providing in the same time an automated and reliable estimation of the purity. ORIGIN implements a nuisance removal part based on a continuum subtraction combining a Discrete Cosine Transform and an iterative Principal Component Analysis and a detection part based on the local maxima of Generalized Likelihood Ratio test statistics obtained for a set of spatial-spectral profiles of emission line emitters. In addition, it performs a purity estimation in which the proportion of true emission lines is estimated from the data itself: the distribution of the local maxima in the noise only configuration is estimated from that of the local minima.
ORIGAMI is a dynamical method of determining the morphology of particles in a cosmological simulation by checking for whether, and in how many dimensions, a particle has undergone shell-crossing. The code is written in C and makes use of the Delaunay tessellation calculation routines from the VOBOZ package (which relies on the Qhull package).
ORCS (Outils de Réduction de Cubes Spectraux) is an analysis engine for SITELLE spectral cubes. The software extracts integrated spectra, fits the sinc emission lines, and recalibrates data in wavelength, astrometry and flux. ORCS offers a choice between a Bayesian or a classical fitting algorithm , and also provides automatic source detection and radial velocity correction.
OrbWeaver extracts orbits from halo catalogs, enabling large statistical studies of their orbital parameters. The code is run in two stages. For the first run, a configuration file is used to modify orbit host selection and the region around orbit host used for the superset of orbiting halos. Each orbit host has a orbit forest (containing halos that passed within the region of interest); the code generates a pre-processed catalog which contains a superset of orbiting halo for each identified orbit host. The second run uses the file list generated in the first stage for the creation of the orbit catalog, which is the final output.
ORBS merges, corrects, transforms and calibrates interferometric data cubes and produces a spectral cube of the observed region for analysis. It is a fully automatic data reduction software for use with SITELLE (installed at the Canada-France-Hawaii Telescope) and SpIOMM (a prototype attached to the Observatoire du Mont Mégantic); these imaging Fourier transform spectrometers obtain a hyperspectral data cube which samples a 12 arc-minutes field of view into 4 millions of visible spectra. ORBS is highly parallelized; its core classes (ORB) have been designed to be used in a suite of softwares for data analysis (ORCS and OACS), data simulation (ORUS) and data acquisition (IRIS).
orbitize fits the orbits of directly-imaged objects by packaging the Orbits for the Impatient (OFTI) algorithm and a parallel-tempered Markov Chain Monte Carlo (MCMC) algorithm into a consistent API. It accepts observations in three measurement formats, which can be mixed in the same input file, generates orbits, and plots the computed orbital parameters. orbitize offers numerous ways to visualize the data, including histograms, corner plots, and orbit plots. Generated orbits can be saved in HDF5 format for future use and analysis.
orbit-estimation tests and evaluates the Stäckel approximation method for estimating orbit parameters in galactic potentials. It relies on the approximation of the Galactic potential as a Stäckel potential, in a prolate confocal coordinate system, under which the vertical and horizontal motions decouple. By solving the Hamilton Jacobi equations at the turning points of the horizontal and vertical motions, it is possible to determine the spatial boundary of the orbit, and hence calculate the desired orbit parameters.
OrbFit is a software system allowing one to compute the orbits of asteroids starting from the observations, to propagate these orbits, and to compute predictions on the future (and past) position on the celestial sphere. It is a tool to be used to find a well known asteroid, to recover a lost one, to attribute a small group of observations, to identify two orbits with each other, to study the future (and/or past) close approaches to Earth, thus to assess the risk of an impact, and more.
Orbfit determines positions and orbital elements, and associated uncertainties, of outer solar system planets. The orbit-fitting procedure is greatly streamlined compared with traditional methods because acceleration can be treated as a perturbation to the inertial motion of the body. Orbfit quickly and accurately calculates orbital elements and ephemerides and their associated uncertainties for targets ≳ 10 AU from the Sun and produces positional estimates and uncertainty ellipses even in the face of the substantial degeneracies of short-arc orbit fits; the sole a priori assumption is that the orbit should be bound or nearly so.
ORBE performs numerical integration of an arbitrary planetary system composed by a central star and up to 100 planets and minor bodies. ORBE calculates the orbital evolution of a system of bodies by means of the computation of the time evolution of their orbital elements. It is easy to use and is suitable for educational use by undergraduate students in the classroom as a first approach to orbital integrators.
ORBADV adopts a ZEUS-like scheme to solve magnetohydrodynamic equations of motion in a shearing sheet. The magnetic field is discretized on a staggered mesh, and magnetic field variables represent fluxes through zone faces. The code uses obital advection to ensure fast and accurate integration in a large shearing box.
ORAC-DR is a generic data reduction pipeline infrastructure; it includes specific data processing recipes for a number of instruments. It is used at the James Clerk Maxwell Telescope, United Kingdom Infrared Telescope, AAT, and LCOGT. This pipeline runs at the JCMT Science Archive hosted by CADC to generate near-publication quality data products; the code has been in use since 1998.
optBINS (optimal binning) determines the optimal number of bins in a uniform bin-width histogram by deriving the posterior probability for the number of bins in a piecewise-constant density model after assigning a multinomial likelihood and a non-informative prior. The maximum of the posterior probability occurs at a point where the prior probability and the the joint likelihood are balanced. The interplay between these opposing factors effectively implements Occam's razor by selecting the most simple model that best describes the data.
The Opik method gives the mean probability of collision of a small body with a given planet. It is a statistical value valid for an orbit with given (a,e,i) and undefined argument of perihelion. In some cases, the planet can eject the small body from the solar system; in these cases, the program estimates the mean time for the ejection. The Opik method does not take into account other perturbers than the planet considered, so it only provides an idea of the timescales involved.
OPERA (Open-source Pipeline for Espadons Reduction and Analysis) is an open-source collaborative software reduction pipeline for ESPaDOnS data. ESPaDOnS is a bench-mounted high-resolution echelle spectrograph and spectro-polarimeter designed to obtain a complete optical spectrum (from 370 to 1,050 nm) in a single exposure with a mode-dependent resolving power between 68,000 and 81,000. OPERA is fully automated, calibrates on two-dimensional images and reduces data to produce one-dimensional intensity and polarimetric spectra. Spectra are extracted using an optimal extraction algorithm. Though designed for CFHT ESPaDOnS data, the pipeline is extensible to other echelle spectrographs.
OPERA (Objective Prism Enhanced Reduction Algorithms) automatically analyzes astronomical images using the objective-prism (OP) technique to register thousands of low resolution spectra in large areas. It detects objects in an image, extracts one-dimensional spectra, and identifies the emission line feature. The main advantages of this method are: 1) to avoid subjectivity inherent to visual inspection used in past studies; and 2) the ability to obtain physical parameters without follow-up spectroscopy.
OpenSPH runs hydrodynamical and N-body simulations and was written for asteroid collisions and subsequent gravitational evolution. The code offers SPH and N-body solvers with several different equations of state and material rheologies. It is written in C++14 with a modular object-oriented design, focused on extensibility and maintainability, and it can be used either as a library or as a standalone graphical program that allows to set up the problem in a convenient graphical node editor. The graphical program further allows real-time visualization of the simulation, diagnostics and tools for analysis of the results.
OpenOrb (OOrb) contains tools for rigorously estimating the uncertainties resulting from the inverse problem of computing orbital elements using scarce astrometry. It uses the least-squares method and also contains both Monte-Carlo (MC) and Markov-Chain MC versions of the statistical ranging method. Ranging obtains sampled, non-Gaussian orbital-element probability-density functions and is optimized for cases where the amount of astrometry is scarce or spans a relatively short time interval.
OpenMHD is a Godunov-type finite-volume code for ideal/resistive magnetohydrodynamics (MHD). It is written in Fortran 90 and is parallelized by using MPI-3 and OpenMP. The code was originally developed for studying magnetic reconnection problems and has been made publicly available in the hope that others may find it useful.
OoT (Out-of-Transit) calculates the light curves and radial velocity signals due to a planet orbiting a star. It explicitly models the effects of tides, orbital motion. relativistic beaming, and reflection of the stars light by the planet. The code can also be used to model secondary eclipses.
OMNICAL calibrates antennas in the redundant subset of the array. The code consists of two algorithms, a logarithmic method (logcal) and a linearized method (lincal). OMNICAL makes visibilities from physically redundant baselines agree with each other and also explicitly minimizes the variance within redundant visibilities.
OMEGA (One-zone Model for the Evolution of GAlaxies) calculates the global chemical evolution trends of galaxies. From an input star formation history, it uses SYGMA to create as a function of time multiple simple stellar populations with different masses, ages, and initial compositions. OMEGA offers several prescriptions for modeling the star formation efficiency and the evolution of galactic inflows and outflows. OMEGA is part of the NuGrid (ascl:1610.015) chemical evolution package.
In the context of optical interferometry, only undersampled power spectrum and bispectrum data are accessible, creating an ill-posed inverse problem for image recovery. Recently, a tri-linear model was proposed for monochromatic imaging, leading to an alternated minimization problem; in that work, only a positivity constraint was considered, and the problem was solved by an approximated Gauss–Seidel method.
The Optical-Interferometry-Trilinear code improves the approach on three fundamental aspects. First, the estimated image is defined as a solution of a regularized minimization problem, promoting sparsity in a fixed dictionary using either an l1 or a (re)weighted-l1 regularization term. Second, the resultant non-convex minimization problem is solved using a block-coordinate forward–backward algorithm. This algorithm is able to deal both with smooth and non-smooth functions, and benefits from convergence guarantees even in a non-convex context. Finally, the model and algorithm are generalized to the hyperspectral case, promoting a joint sparsity prior through an l2,1 regularization term.
Odyssey is a GPU-based General Relativistic Radiative Transfer (GRRT) code for computing images and/or spectra in Kerr metric describing the spacetime around a rotating black hole. Odyssey is implemented in CUDA C/C++. For flexibility, the namespace structure in C++ is used for different tasks; the two default tasks presented in the source code are the redshift of a Keplerian disk and the image of a Keplerian rotating shell at 340GHz. Odyssey_Edu, an educational software package for visualizing the ray trajectories in the Kerr spacetime that uses Odyssey, is also available.
ODUSSEAS (Observing Dwarfs Using Stellar Spectroscopic Energy-Absorption Shapes) uses machine learning to derive the Teff and [Fe/H] of M dwarf stars by using their optical spectra obtained by different spectrographs with different resolutions. The software uses the measurement of the pseudo equivalent widths for more than 4000 stellar absorption lines and the machine learning Python package scikit-learn (https://scikit-learn.org/stable/) to predict the stellar parameters.
ODTBX (Orbit Determination Toolbox) provides orbit determination analysis, advanced mission simulation, and analysis for concept exploration, proposal, early design phase, and/or rapid design center environments. The core ODTBX functionality is realized through a set of estimation commands that incorporate Monte Carlo data simulation, linear covariance analysis, and measurement processing at a generic level; its functions and utilities are combined in a flexible architecture to allow modular development of navigation algorithms and simulations. ODTBX is written in Matlab and Java.
ODEPACK solves for the initial value problem for ordinary differential equation systems. It consists of nine solvers, a basic solver called LSODE and eight variants of it: LSODES, LSODA, LSODAR, LSODPK, LSODKR, LSODI, LSOIBT, and LSODIS. The collection is suitable for both stiff and nonstiff systems. It includes solvers for systems given in explicit form, dy/dt = f(t,y), and also solvers for systems given in linearly implicit form, A(t,y) dy/dt = g(t,y). The ODEPACK solvers are written in standard Fortran and there are separate double and single precision versions. Each solver consists of a main driver subroutine having the same name as the solver and some number of subordinate routines. For each solver, there is also a demonstration program, which solves one or two simple problems in a somewhat self-checking manner.
Octgrav is a very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The algorithms are based on parallel-scan and sort methods. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way, a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s is achieved. It takes about a second to compute forces on a million particles with an opening angle of $ heta approx 0.5$.
To test the performance and feasibility, we implemented the algorithms in CUDA in the form of a gravitational tree-code which completely runs on the GPU. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second.
The code has a convenient user interface and is freely available for use.
The OctApps library provides various functions, written in Octave, for performing searches for the weak signatures of continuous gravitational waves from rapidly-rotating neutron stars amidst the instrumental noise of the LIGO and Virgo detectors.
OCFit fits and analyzes O-C diagrams using Genetic Algorithms and Markov chain Monte Carlo methods. The MC method is used to determine a very good estimation of errors of the parameters. Unlike some other fitting routines, OCFit does not need any initial values of fitted parameters. An intuitive graphic user interface is provided for ease of fitting, and nine common models of periodic O-C changes are included.
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