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.
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.
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.
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-2 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
PARAMESH is a package of Fortran 90 subroutines designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity.
The package builds a hierarchy of sub-grids to cover the computational domain, with spatial resolution varying to satisfy the demands of the application. These sub-grid blocks form the nodes of a tree data-structure (quad-tree in 2D or oct-tree in 3D). Each grid block has a logically cartesian mesh. The package supports 1, 2 and 3D models. PARAMESH is released under the NASA-wide Open-Source software license.
We consider the problem of fitting a parametric model to time-series data that are afflicted by correlated noise. The noise is represented by a sum of two stationary Gaussian processes: one that is uncorrelated in time, and another that has a power spectral density varying as $1/f^gamma$. We present an accurate and fast [O(N)] algorithm for parameter estimation based on computing the likelihood in a wavelet basis. The method is illustrated and tested using simulated time-series photometry of exoplanetary transits, with particular attention to estimating the midtransit time. We compare our method to two other methods that have been used in the literature, the time-averaging method and the residual-permutation method. For noise processes that obey our assumptions, the algorithm presented here gives more accurate results for midtransit times and truer estimates of their uncertainties.
ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.
ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.
PARAVT offers massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition take into account consistent boundary computation between tasks, and support periodic conditions. In addition, the code compute neighbors lists, Voronoi density and Voronoi cell volumes for each particle, and can compute density on a regular grid.
PARSEC (PARametrized Simulation Engine for Cosmic rays) is a simulation engine for fast generation of ultra-high energy cosmic ray data based on parameterizations of common assumptions of UHECR origin and propagation. Implemented are deflections in unstructured turbulent extragalactic fields, energy losses for protons due to photo-pion production and electron-pair production, as well as effects from the expansion of the universe. Additionally, a simple model to estimate propagation effects from iron nuclei is included. Deflections in the Galactic magnetic field are included using a matrix approach with precalculated lenses generated from backtracked cosmic rays. The PARSEC program is based on object oriented programming paradigms enabling users to extend the implemented models and is steerable with a graphical user interface.
ParselTongue is a Python interface to classic AIPS, Obit and possibly other task-based data reduction packages. It serves as the software infrastructure for some of the ALBUS implementation. It allows you to run AIPS tasks, and access AIPS headers and extension tables from Python. There is also support for running Obit tasks and accessing data in FITS files. Full access to the visibilities in AIPS UV data is also available.
Piernik is a multi-fluid grid magnetohydrodynamic (MHD) code based on the Relaxing Total Variation Diminishing (RTVD) conservative scheme. The original code has been extended by addition of dust described within the particle approximation. The dust is now described as a system of interacting particles. The particles can interact with gas, which is described as a fluid. The comparison between the test problem results and the results coming from fluid simulations made with Piernik code shows the most important differences between fluid and particle approximations used to describe dynamical evolution of dust under astrophysical conditions.
In dense clusters a bewildering variety of interactions between stars can be observed, ranging from simple encounters to collisions and other mass-transfer encounters. With faster and special-purpose computers like GRAPE, the amount of data per simulation is now exceeding 1TB. Visualization of such data has now become a complex 4D data-mining problem, combining space and time, and finding interesting events in these large datasets. We have recently starting using the virtual reality simulator, installed in the Hayden Planetarium in the American Museum for Natural History, to tackle some of these problem. partiview is a program that enables you to visualize and animate particle data. partiview runs on relatively simple desktops and laptops, but is mostly compatible with its big brother VirDir.
PASTA performs median stacking of astronomical sources. Written in Python, it can filter sources, provide stack statistics, generate Karma annotations, format source lists, and read information from stacked Flexible Image Transport System (FITS) images. PASTA was originally written to examine polarization stack properties and includes a Monte Carlo modeler for obtaining true polarized intensity from the observed polarization of a stack. PASTA is also useful as a generic stacking tool, even if polarization properties are not being examined.
We present Particle-Based Lensing (PBL), a new technique for gravitational lensing mass reconstructions of galaxy clusters. Traditionally, most methods have employed either a finite inversion or gridding to turn observational lensed galaxy ellipticities into an estimate of the surface mass density of a galaxy cluster. We approach the problem from a different perspective, motivated by the success of multi-scale analysis in smoothed particle hydrodynamics. In PBL, we treat each of the lensed galaxies as a particle and then reconstruct the potential by smoothing over a local kernel with variable smoothing scale. In this way, we can tune a reconstruction to produce constant signal-noise throughout, and maximally exploit regions of high information density.
PBL is designed to include all lensing observables, including multiple image positions and fluxes from strong lensing, as well as weak lensing signals including shear and flexion. In this paper, however, we describe a shear-only reconstruction, and apply the method to several test cases, including simulated lensing clusters, as well as the well-studied ``Bullet Cluster'' (1E0657-56). In the former cases, we show that PBL is better able to identify cusps and substructures than are grid-based reconstructions, and in the latter case, we show that PBL is able to identify substructure in the Bullet Cluster without even exploiting strong lensing measurements.
PBMC (Pre-Conditioned Backward Monte Carlo) solves the vector Radiative Transport Equation (vRTE) and can be applied to planetary atmospheres irradiated from above. The code builds the solution by simulating the photon trajectories from the detector towards the radiation source, i.e. in the reverse order of the actual photon displacements. In accounting for the polarization in the sampling of photon propagation directions and pre-conditioning the scattering matrix with information from the scattering matrices of prior (in the BMC integration order) photon collisions, PBMC avoids the unstable and biased solutions of classical BMC algorithms for conservative, optically-thick, strongly-polarizing media such as Rayleigh atmospheres.
The mid-infrared spectra of ultraluminous infrared galaxies (ULIRGs) contain a variety of spectral features that can be used as diagnostics to characterize the spectra. However, such diagnostics are biased by our prior prejudices on the origin of the features. Moreover, by using only part of the spectrum they do not utilize the full information content of the spectra. Blind statistical techniques such as principal component analysis (PCA) consider the whole spectrum, find correlated features and separate them out into distinct components.
This code, written in IDL, classifies principal components of IRS spectra to define a new classification scheme using 5D Gaussian mixtures modelling. The five PCs and average spectra for the four classifications to classify objects are made available with the code.
PCAT (Probabilistic Cataloger) samples from the posterior distribution of a metamodel, i.e., union of models with different dimensionality, to compare the models. This is achieved via transdimensional proposals such as births, deaths, splits and merges in addition to the within-model proposals. This method avoids noisy estimates of the Bayesian evidence that may not reliably distinguish models when sampling from the posterior probability distribution of each model.
The code has been applied in two different subfields of astronomy: high energy photometry, where transdimensional elements are gamma-ray point sources; and strong lensing, where light-deflecting dark matter subhalos take the role of transdimensional elements.
PCCDPACK analyzes polarimetry data. The set of routines is written in CL-IRAF (including compiled Fortran codes) and analyzes dozens of point objects simultaneously on the same CCD image. A subpackage, specpol, is included to analyze spectropolarimetry data.
Ultraviolet photons from O and B stars strongly influence the structure and emission spectra of the interstellar medium. The UV photons energetic enough to ionize hydrogen (hν > 13.6 eV) will create the H II region around the star, but lower energy UV photons escape. These far-UV photons (6 eV < hν < 13.6 eV) are still energetic enough to photodissociate molecules and to ionize low ionization-potential atoms such as carbon, silicon, and sulfur. They thus create a photodissociation region (PDR) just outside the H II region. In aggregate, these PDRs dominates the heating and cooling of the neutral interstellar medium.
As part of the Web Infrared Tool Shed (WITS) we have developed a web tool, called the PDR Toolbox, that allows users to determine the physical parameters of a PDR from a set of spectral line observations. Typical observations of both Galactic and extragalactic PDRs come from ground-based millimeter and submillimeter telescopes such as CARMA or the CSO, or space-based telescopes such as Spitzer, ISO, SOFIA, and Herschel. Given a set of observations of spectral line intensities, PDR Toolbox will compute best-fit FUV incident intensity and cloud density based on our published models of PDR emission.
PDT removes systematic trends in light curves. It finds clusters of light curves that are highly correlated using machine learning, constructs one master trend per cluster and detrends an individual light curve using the constructed master trends by minimizing residuals while constraining coefficients to be positive.
The PEC (Period Error Calculator) algorithm estimates the period error for eclipsing binaries observed by the Kepler Mission. The algorithm is based on propagation of error theory and assumes that observation of every light curve peak/minimum in a long time-series observation can be unambiguously identified. A simple C implementation of the PEC algorithm is available.
PÉGASE-HR is a code aimed at computing synthetic evolutive optical spectra of galaxies with a very high resolution (R=10 000, or dlambda=0.55) in the range Lambda=[4000, 6800] Angstroms. PÉGASE-HR is the result of combining the code PÉGASE.2 with the high-resolution stellar library ÉLODIE. This code can also be used at low resolution (R=200) over the range covered by the BaSeL library (from far UV to the near IR), and then produces the same results as PÉGASE.2. In PEGASE-HR, the BaSeL library is replaced by a grid of spectra interpolated from the high-resolution ÉLODIE library of stellar spectra. The ÉLODIE library is a stellar database of 1959 spectra for 1503 stars, observed with the echelle spectrograph ÉLODIE on the 193 cm telescope at the Observatoire de Haute Provence.
PÉGASE (Projet d'Étude des GAlaxies par Synthèse Évolutive) is a code to compute the spectral evolution of galaxies. The evolution of the stars, gas and metals is followed for a law of star formation and a stellar initial mass function. The stellar evolutionary tracks extend from the main sequence to the white dwarf stage. The emission of the gas in HII regions is also taken into account. The main improvement in version 2 is the use of evolutionary tracks of different metallicities (from 10-4 to 5×solar). The effect of extinction by dust is also modelled using a radiative transfer code. PÉGASE.2 uses the BaSeL library of stellar spectra and can therefore synthesize low-resolution (R~200) ultraviolet to near-infrared spectra of Hubble sequence galaxies as well as of starbursts.
Pelican is an efficient, lightweight C++ library for quasi-real time data processing. The library provides a framework to separate the acquisition and processing of data, allowing the scalability and flexibility to fit a number of scenarios. Though its origin was in radio astronomy, processing data as it arrives from a telescope, the framework is sufficiently generic to be useful to any application that requires the efficient processing of incoming data streams.
The Pencil code is a high-order finite-difference code for compressible hydrodynamic flows with magnetic fields. It is highly modular and can easily be adapted to different types of problems. The code runs efficiently under MPI on massively parallel shared- or distributed-memory computers, like e.g. large Beowulf clusters. The Pencil code is primarily designed to deal with weakly compressible turbulent flows. To achieve good parallelization, explicit (as opposed to compact) finite differences are used. Typical scientific targets include driven MHD turbulence in a periodic box, convection in a slab with non-periodic upper and lower boundaries, a convective star embedded in a fully nonperiodic box, accretion disc turbulence in the shearing sheet approximation, self-gravity, non-local radiation transfer, dust particle evolution with feedback on the gas, etc. A range of artificial viscosity and diffusion schemes can be invoked to deal with supersonic flows. For direct simulations regular viscosity and diffusion is being used. The code is written in well-commented Fortran90.
PENTACLE calculates gravitational interactions between particles within a cut-off radius and a Barnes-Hut tree method for gravity from particles beyond. It uses FDPS (ascl:1604.011) to parallelize a Barnes-Hut tree algorithm for a memory-distributed supercomputer. The software can handle 1-10 million particles in a high-resolution N-body simulation on CPU clusters for collisional dynamics, including physical collisions in a planetesimal disc.
perfectns performs dynamic nested sampling and standard nested sampling for spherically symmetric likelihoods and priors, and analyses the samples produced. The spherical symmetry allows the nested sampling algorithm to be followed “perfectly” - i.e. without implementation-specific errors correlations between samples. It is intended for use in research into the statistical properties of nested sampling, and to provide a benchmark for testing the performance of nested sampling software packages used for practical problems - which rely on numerical techniques to produce approximately uncorrelated samples.
PERIOD searches for periodicities in data. It is distributed within the Starlink software collection (ascl:1110.012).
Period04 statistically analyzes large astronomical time series containing gaps. It calculates formal uncertainties, can extract the individual frequencies from the multiperiodic content of time series, and provides a flexible interface to perform multiple-frequency fits with a combination of least-squares fitting and the discrete Fourier transform algorithm. Period04, written in Java/C++, supports the SAMP communication protocol to provide interoperability with other applications of the Virtual Observatory. It is a reworked and extended version of Period98 (Sperl 1998) and PERIOD/PERDET (Breger 1990).
PEXO provides a global modeling framework for ns timing, μas astrometry, and μm/s radial velocities. It can account for binary motion and stellar reflex motions induced by planetary companions and also treat various relativistic effects both in the Solar System and in the target system (Roemer, Shapiro, and Einstein delays). PEXO is able to model timing to a precision of 1 ns, astrometry to a precision of 1 μas, and radial velocity to a precision of 1 μm/s.
PFANT computes a synthetic spectrum assuming local thermodynamic equilibrium from a given stellar model atmosphere and lists of atomic and molecular lines; it provides large wavelength coverage and line lists from ultraviolet through the visible and near-infrared. PFANT has been optimized for speed, offers error reporting, and command-line configuration options.
The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.
The PGPLOT library consists of two major parts: a device-independent part and a set of device-dependent "device handler" subroutines for output on various terminals, image displays, dot-matrix printers, laser printers, and pen plotters. Common file formats supported include PostScript and GIF.
PGPLOT itself is written mostly in standard Fortran-77, with a few non-standard, system-dependent subroutines. PGPLOT subroutines can be called directly from a Fortran-77 or Fortran-90 program. A C binding library (cpgplot) and header file (cpgplot.h) are provided that allow PGPLOT to be called from a C or C++ program; the binding library handles conversion between C and Fortran argument-passing conventions.
Phantom-GRAPE is a numerical software library to accelerate collisionless $N$-body simulation with SIMD instruction set on x86 architecture. The Newton's forces and also central forces with an arbitrary shape f(r), which have a finite cutoff radius r_cut (i.e. f(r)=0 at r>r_cut), can be quickly computed.
Phantom is a smoothed particle hydrodynamics and magnetohydrodynamics code focused on stellar, galactic, planetary, and high energy astrophysics. It is modular, and handles sink particles, self-gravity, two fluid and one fluid dust, ISM chemistry and cooling, physical viscosity, non-ideal MHD, and more. Its modular structure makes it easy to add new physics to the code.
phase_space_cosmo_fisher produces Fisher matrix 2D contours from which the constraints on cosmological parameters can be derived. Given a specified redshift array and cosmological case, 2D marginalized contours of cosmological parameters are generated; the code can also plot the derivatives used in the Fisher matrix. In addition, this package can generate 3D plots of qH^2 and other cosmological quantities as a function of redshift and cosmology.
PhAst (Photometry-Astrometry) is an IDL astronomical image viewer based on the existing application ATV which displays and analyzes FITS images. It can calibrate raw images, provide astrometric solutions, and do circular aperture photometry. PhAst allows the user to load, process, and blink any number of images. Analysis packages include image calibration, photometry, and astrometry (provided through an interface with SExtractor, SCAMP, and missFITS). PhAst has been designed to generate reports for Minor Planet Center reporting.
PHOEBE (PHysics Of Eclipsing BinariEs) is a modeling package for eclipsing binary stars, built on top of the widely used WD program (Wilson & Devinney 1971). This introductory paper overviews most important scientific extensions (incorporating observational spectra of eclipsing binaries into the solution-seeking process, extracting individual temperatures from observed color indices, main-sequence constraining and proper treatment of the reddening), numerical innovations (suggested improvements to WD's Differential Corrections method, the new Nelder & Mead's downhill Simplex method) and technical aspects (back-end scripter structure, graphical user interface). While PHOEBE retains 100% WD compatibility, its add-ons are a powerful way to enhance WD by encompassing even more physics and solution reliability.
PHOENIX is a general-purpose state-of-the-art stellar and planetary atmosphere code. It can calculate atmospheres and spectra of stars all across the HR-diagram including main sequence stars, giants, white dwarfs, stars with winds, TTauri stars, novae, supernovae, brown dwarfs and extrasolar giant planets.
The Photon Simulator (PhoSim) is a set of fast photon Monte Carlo codes used to calculate the physics of the atmosphere, telescope, and detector by using modern numerical techniques applied to comprehensive physical models. PhoSim generates images by collecting photons into pixels. The code takes the description of what astronomical objects are in the sky at a particular time (the instance catalog) as well as the description of the observing configuration (the operational parameters) and produces a realistic data stream of images that are similar to what a real telescope would produce. PhoSim was developed for large aperture wide field optical telescopes, such as the planned design of LSST. The initial version of the simulator also targeted the LSST telescope and camera design, but the code has since been broadened to include existing telescopes of a related nature. The atmospheric model, in particular, includes physical approximations that are limited to this general context.
Photo-z-SQL is a flexible template-based photometric redshift estimation framework that can be seamlessly integrated into a SQL database (or DB) server and executed on demand in SQL. The DB integration eliminates the need to move large photometric datasets outside a database for redshift estimation, and uses the computational capabilities of DB hardware. Photo-z-SQL performs both maximum likelihood and Bayesian estimation and handles inputs of variable photometric filter sets and corresponding broad-band magnitudes.
Photodynam facilitates so-called "photometric-dynamical" modeling. This model is quite simple and this is reflected in the code base. A N-body code provides coordinates and the photometric code produces light curves based on coordinates.
PHOTOM performs photometry of digitized images. It has two basic modes of operation: using an interactive display to specify the positions for the measurements, or obtaining those positions from a file. In both modes of operation PHOTOM performs photometry using either the traditional aperture method or via optimal extraction. When using the traditional aperture extraction method the target aperture can be circular or elliptical and its size and shape can be varied interactively on the display, or by entering values from the keyboard. Both methods allow the background sky level to be either sampled interactively by the manual positioning of an aperture, or automatically from an annulus surrounding the target object. PHOTOM is the photometry backend for the GAIA tool (ascl:1403.024) and is part of the Starlink software collection (ascl:1110.012).
PHOTOMETRYPIPELINE (PP) provides calibrated photometry from imaging data obtained with small to medium-sized observatories. PP uses Source Extractor (ascl:1010.064) and SCAMP (ascl:1010.063) to register the image data and perform aperture photometry. Calibration is obtained through matching of field stars with reliable photometric catalogs. PP has been specifically designed for the measurement of asteroid photometry, but can also be used to obtain photometry of fixed sources.
Photon makes simple 1D plots in python. It uses mainly matplotlib and PyQt5 and has been build to be fully customizable, allowing the user to change the fontstyle, fontsize, fontcolors, linewidth of the axes, thickness, and other parameters, and see the changes directly in the plot. Once a customization is created, it can be saved in a configuration file and reloaded for future use, allowing reuse of the customization for other plots. The main tool is a graphical user interface and it is started using a command line interface.
PhotoRApToR (PHOTOmetric Research APplication TO Redshifts) solves regression and classification problems and is specialized for photo-z estimation. PhotoRApToR offers data table manipulation capabilities and 2D and 3D graphics tools for data visualization; it also provides a statistical report for both classification and regression experiments. The code is written in Java; the machine learning model is in C++ to increase the core execution speed.
Photutils provides tools for detecting and performing photometry of astronomical sources. It can estimate the background and background rms in astronomical images, detect sources in astronomical images, estimate morphological parameters of those sources (e.g., centroid and shape parameters), and perform aperture and PSF photometry. Written in Python, it is an affiliated package of Astropy (ascl:1304.002).
PHOX is a novel, virtual X-ray observatory designed to obtain synthetic observations from hydro-numerical simulations. The code is a photon simulator and can be apply to simulate galaxy clusters. In fact, X-ray observations of clusters of galaxies continue to provide us with an increasingly detailed picture of their structure and of the underlying physical phenomena governing the gaseous component, which dominates their baryonic content. Therefore, it is fundamental to find the most direct and faithful way to compare such observational data with hydrodynamical simulations of cluster-like objects, which can currently include various complex physical processes. Here, we present and analyse synthetic Suzaku observations of two cluster-size haloes obtained by processing with PHOX the hydrodynamical simulation of the large-scale, filament-like region in which they reside. Taking advantage of the simulated data, we test the results inferred from the X-ray analysis of the mock observations against the underlying, known solution. Remarkably, we are able to recover the theoretical temperature distribution of the two haloes by means of the multi-temperature fitting of the synthetic spectra. Moreover, the shapes of the reconstructed distributions allow us to trace the different thermal structure that distinguishes the dynamical state of the two haloes.
ISOPHOT is one of the instruments on board the Infrared Space Observatory (ISO). ISOPHOT Interactive Analysis (PIA) is a scientific and calibration interactive data analysis tool for ISOPHOT data reduction. Written in IDL under Xwindows, PIA offers a full context sensitive graphical interface for retrieving, accessing and analyzing ISOPHOT data. It is available in two nearly identical versions; a general observers version omits the calibration sequences.
PIAO is an efficient memory-controlled Python code that uses the standard spherical overdensity (SO) algorithm to identify halos. PIAO employs two additional parameters besides the overdensity Δc. The first is the mesh-box size, which splits the whole simulation box into smaller ones then analyzes them one-by-one, thereby overcoming a possible memory limitation problem that can occur when dealing with high-resolution, large-volume simulations. The second is the smoothed particle hydrodynamics (SPH) neighbors number, which is used for the SPH density calculation.
PICASO (Planetary Intensity Code for Atmospheric Scattering Observations), written in Python, computes the reflected light of exoplanets at any phase geometry using direct and diffuse scattering phase functions and Raman scattering spectral features.
Piccard is a Bayesian-inference pipeline for Pulsar Timing Array (PTA) data and interacts with Tempo2 (ascl:1210.015) through libstempo. The code is used mainly for single-pulsar analysis and gravitational-wave detection purposes of full Pulsar Timing Array datasets. Modeling of the data can include correlated signals per frequency or modeled spectrum, with uniform, dipolar, quadrupolar, or anisotropic correlations; multiple error bars and EFACs per pulsar; and white and red noise. Timing models can be numerically included, either by using the design matrix (linear timing model), or by calling libstempo for the full non-linear timing model. Many types of samplers are included. For common-mode mitigation, the signals can be reconstructed mitigating arbitrary signals simultaneously.
Pico is an algorithm that quickly computes the CMB scalar, tensor and lensed power spectra, the matter transfer function and the WMAP 5 year likelihood. It is intended to accelerate parameter estimation codes; Pico can compute the CMB power spectrum and matter transfer function, as well as any computationally expensive likelihoods, in a few milliseconds. It is extremely fast and accurate over a large volume of parameter space and its accuracy can be improved by using a larger training set. More generally, Pico allows using massively parallel computing resources, including distributed computing projects such as Cosmology@Home, to speed up the slow steps in inherently sequential calculations.
PICsar simulates the magnetosphere of an aligned axisymmetric pulsar and can be used to simulate other arbitrary electromagnetics problems in axisymmetry. Written in Fortran, this special relativistic, electromagnetic, charge conservative particle in cell code features stretchable body-fitted coordinates that follow the surface of a sphere, simplifying the application of boundary conditions in the case of the aligned pulsar; a radiation absorbing outer boundary, which allows a steady state to be set up dynamically and maintained indefinitely from transient initial conditions; and algorithms for injection of charged particles into the simulation domain. PICsar is parallelized using MPI and has been used on research problems with ~1000 CPUs.
pieflag compares bandpass-calibrated data to a clean reference channel and identifies and flags essentially all bad data. pieflag compares visibility amplitudes in each frequency channel to a 'reference' channel that is rfi-free (or manually ensured to be rfi-free). pieflag performs this comparison independently for each correlation on each baseline, but will flag all correlations if threshold conditions are met. To operate effectively, pieflag must be supplied with bandpass-calibrated data. pieflag has two core modes of operation (static and dynamic flagging) with an additional extend mode; the type of data largely determines which mode to choose. Instructions for pre-processing data and selecting the mode of operation are provided in the help file. Once pre-processing and selecting the mode of operation are done, pieflag should work well 'out of the box' with its default parameters.
The pile-up gnuplot script generates a Monte Carlo simulation with a selectable number of randomized drawings (1000 by default, ~1min on a modern laptop). For each realization, the script calculates the torque acting on a hot Jupiter around a young, solar-type star as a function of the star-planet distance. The total torque on the planet is composed of the disk torque in the type II migration regime (that is, the planet is assumed to have opened up a gap in the disk) and of the stellar tidal torque. The model has four free parameters, which are drawn from a normal or lognormal distribution: (1) the disk's gas surface density at 1 astronomical unit, (2) the magnitude of tidal dissipation within the star, (3) the disk's alpha viscosity parameter, and (4) and the mean molecular weight of the gas in the disk midplane. For each realization, the total torque is screened for a distance at which it becomes zero. If present, then this distance would represent a tidal migration barrier to the planet. In other words, the planet would stop migrating. This location is added to a histogram on top of the main torque-over-distance panel and the realization is counted as one case that contributes to the overall survival rate of hot Jupiters. Finally, the script generates an output file (PDF by default) and prints the hot Jupiter survival rate for the assumed parameterization of the star-planet-disk system.
PINGSoft2 visualizes, manipulates and analyzes integral field spectroscopy (IFS) data based on either 3D cubes or Raw Stacked Spectra (RSS) format. Any IFS data can be adapted to work with PINGSoft2, regardless of the original data format and the size/shape of the spaxel. Written in IDL, PINGSoft2 is optimized for fast visualization rendering; it also includes various routines useful for generic astronomy and spectroscopy tasks.
Morphological classification is one of the most demanding challenges in astronomy. With the advent of all-sky surveys, an enormous amount of imaging data is publicly available, and are typically analyzed by experts or encouraged amateur volunteers. For upcoming surveys with billions of objects, however, such an approach is not feasible anymore. PINK (Parallelized rotation and flipping INvariant Kohonen maps) is a simple yet effective variant of a rotation-invariant self-organizing map that is suitable for many analysis tasks in astronomy. The code reduces the computational complexity via modern GPUs and applies the resulting framework to galaxy data for morphological analysis.
PINOCCHIO generates catalogues of cosmological dark matter halos with known mass, position, velocity and merger history. It is able to reproduce, with very good accuracy, the hierarchical formation of dark matter halos from a realization of an initial (linear) density perturbation field, given on a 3D grid. Its setup is similar to that of a conventional N-body simulation, but it is based on the powerful Lagrangian Perturbation Theory. It runs in just a small fraction of the computing time taken by an equivalent N-body simulation, producing promptly the merging histories of all halos in the catalog.
PINT (PINT Is Not Tempo3) analyzes high-precision pulsar timing data, enabling interactive data analysis and providing an extensible and flexible development platform for timing applications. PINT utilizes well-debugged public Python packages and modern software development practices (e.g., the NumPy and Astropy libraries, version control and development with git and GitHub, and various types of testing) for increased development efficiency and enhanced stability. PINT has been developed and implemented completely independently from traditional pulsar timing software such as TEMPO (ascl:1509.002) and Tempo2 (ascl:1210.015) and is a robust tool for cross-checking timing analyses and simulating data.
PINTofALE was originally developed to analyze spectroscopic data from optically-thin coronal plasmas, though much of the software is sufficiently general to be of use in a much wider range of astrophysical data analyses. It is based on a modular set of IDL tools that interact with an atomic database and with observational data. The tools are designed to allow easy identification of spectral features, measure line fluxes, and carry out detailed modeling. The basic philosophy of the package is to provide access to the innards of atomic line databases, and to have flexible tools to interactively compare with the observed data. It is motivated by the large amount of book-keeping, computation and iterative interaction that is required between the researcher and observational and theoretical data in order to derive astrophysical results. The tools link together transparently and automatically the processes of spectral "browsing", feature identification, measurement, and computation and derivation of results. Unlike standard modeling and fitting engines currently in use, PINTofALE opens up the "black box" of atomic data required for UV/X-ray analyses and allows the user full control over the data that are used in any given analysis.
Pippi (parse it, plot it) operates on MCMC chains and related lists of samples from a function or distribution, and can merge, parse, and plot sample ensembles ('chains') either in terms of the likelihood/fitness function directly, or as implied posterior probability densities. Pippi is compatible with ASCII text and hdf5 chains, operates out of core, and can post-process chains on the fly.
PISA (Position, Intensity and Shape Analysis) routines deal with the location and parameterization of objects on an image frame. The core of this package is the routine PISAFIND which performs image analysis on a 2-dimensional data frame. The program searches the data array for objects that have a minimum number of connected pixels above a given threshold and extracts the image parameters (position, intensity, shape) for each object. The image parameters can be determined using thresholding techniques or an analytical stellar profile can be used to fit the objects. In crowded regions deblending of overlapping sources can be performed. PISA is distributed as part of the Starlink software collection (ascl:1110.012).
We introduce and implement two novel ideas for modeling lensed quasars. The first is to require different lenses to agree about H0. This means that some models for one lens can be ruled out by data on a different lens. We explain using two worked examples. One example models 1115+080 and 1608+656 (time-delay quadruple systems) and 1933+503 (a prospective time-delay system) all together, yielding time-delay predictions for the third lens and a 90% confidence estimate of H0-1=14.6+9.4-1.7 Gyr (H0=67+9-26 km s-1 Mpc-1) assuming ΩM=0.3 and ΩΛ=0.7. The other example models the time-delay doubles 1520+530, 1600+434, 1830-211, and 2149-275, which gives H0-1=14.5+3.3-1.5 Gyr (H0=67+8-13 km s-1 Mpc-1). Our second idea is to write the modeling software as a highly interactive Java applet, which can be used both for coarse-grained results inside a browser and for fine-grained results on a workstation. Several obstacles come up in trying to implement a numerically intensive method thus, but we overcome them.
PkdGRAV2 is a high performance N-body treecode for self-gravitating astrophysical simulations. It is designed to run efficiently in serial and on a wide variety of parallel computers including both shared memory and message passing architectures. It can spatially adapt to large ranges in particle densities, and temporally adapt to large ranges in dynamical timescales. The code uses a non-standard data structure for efficiently calculating the gravitational forces, a variant on the k-D tree, and a novel method for treating periodic boundary conditions.
Pkdgrav3 is an 𝒪(N) gravity calculation method; it uses a binary tree algorithm with fifth order fast multipole expansion of the gravitational potential, using cell-cell interactions. Periodic boundaries conditions require very little data movement and allow a high degree of parallelism; the code includes GPU acceleration for all force calculations, leading to a significant speed-up with respect to previous versions (ascl:1305.005). Pkdgrav3 also has a sophisticated time-stepping criterion based on an estimation of the local dynamical time.
PLAN (PLanetesimal ANalyzer) identifies and characterizes planetesimals produced in numerical simulations of the Streaming Instability that includes particle self-gravity with code Athena (ascl:1010.014). PLAN works with the 3D particle output of Athena and finds gravitationally bound clumps robustly and efficiently. PLAN — written in C++ with OpenMP/MPI — is massively parallelized, memory-efficient, and scalable to analyze billions of particles and multiple snapshots simultaneously. The approach of PLAN is based on the dark matter halo finder HOP (ascl:1102.019), but with many customizations for planetesimal formation. PLAN can be easily adapted to analyze other object formation simulations that use Lagrangian particles (e.g., Athena++ simulations). PLAN is also equipped with a toolkit to analyze the grid-based hydro data (VTK dumps of primitive variables) from Athena, which requires the Boost MultiDimensional Array Library.
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