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[ascl:1506.002] dmdd: Dark matter direct detection

The dmdd package enables simple simulation and Bayesian posterior analysis of recoil-event data from dark-matter direct-detection experiments under a wide variety of scattering theories. It enables calculation of the nuclear-recoil rates for a wide range of non-relativistic and relativistic scattering operators, including non-standard momentum-, velocity-, and spin-dependent rates. It also accounts for the correct nuclear response functions for each scattering operator and takes into account the natural abundances of isotopes for a variety of experimental target elements.

[ascl:1705.002] DMATIS: Dark Matter ATtenuation Importance Sampling

DMATIS (Dark Matter ATtenuation Importance Sampling) calculates the trajectories of DM particles that propagate in the Earth's crust and the lead shield to reach the DAMIC detector using an importance sampling Monte-Carlo simulation. A detailed Monte-Carlo simulation avoids the deficiencies of the SGED/KS method that uses a mean energy loss description to calculate the lower bound on the DM-proton cross section. The code implementing the importance sampling technique makes the brute-force Monte-Carlo simulation of moderately strongly interacting DM with nucleons computationally feasible. DMATIS is written in Python 3 and MATHEMATICA.

[submitted] DM phase: A novel algorithm for correcting dispersion of radio signals

Radio waves propagating in space are subject to frequency-dependent delay due to interactions with cold free electrons, which gives coherent radio emissions a unique structure known as dispersion. The study of impulsive radio signals from astronomical sources, such as those emitted by pulsars and fast radio bursts (FRBs), requires proper corrections for this effect. Moreover, the ionized medium itself can be characterized by sensitive measurements of this dispersion.
Signal dispersion is proportional to the integrated column density of free electrons along the line of sight, a quantity known as dispersion measure (DM), and inversely proportional to the observing frequency squared. Traditional methods search for the best DM value of a source by maximizing the signal-to-noise ratio (S/N) of the detected signal. While sensitive and efficient algorithms have been designed for this purpose, they are affected by two limitations. Firstly, they implicitly assume a broadband emission across the entire observing frequency bandwidth. While this is normally true for pulsars, some FRBs have been observed to have complex spectra which returned incorrect DM values. Secondly, these traditional algorithms are highly sensitive to large-amplitude events such as large noise spikes and radio interference. In order to overcome these limitations, we developed a new algorithm to maximize the coherent power of the signal instead of its intensity. Since the structure of the signal is coherent at different frequencies, this method is relatively insensitive to complex spectro-temporal shapes of the pulses. In addition, this method is more robust to noise and interference because these normally have incoherent structures and the amplitude information in each frequency channel is discarded.

[ascl:1812.012] distlink: Minimum orbital intersection distance (MOID) computation library

distlink computes the minimum orbital intersection distance (MOID), or global minimum of the distance between the points lying on two Keplerian ellipses by finding all stationary points of the distance function, based on solving an algebraic polynomial equation of 16th degree. The program tracks numerical errors and carefully treats nearly degenerate cases, including practical cases with almost circular and almost coplanar orbits. Benchmarks confirm its high numeric reliability and accuracy, and even with its error-controlling overheads, this algorithm is a fast MOID computation method that may be useful in processing large catalogs. Written in C++, the library also includes auxiliary functions.

[ascl:1302.015] DisPerSE: Discrete Persistent Structures Extractor

DisPerSE is open source software for the identification of persistent topological features such as peaks, voids, walls and in particular filamentary structures within noisy sampled distributions in 2D, 3D. Using DisPerSE, structure identification can be achieved through the computation of the discrete Morse-Smale complex. The software can deal directly with noisy datasets via the concept of persistence (a measure of the robustness of topological features). Although developed for the study of the properties of filamentary structures in the cosmic web of galaxy distribution over large scales in the Universe, the present version is quite versatile and should be useful for any application where a robust structure identification is required, such as for segmentation or for studying the topology of sampled functions (for example, computing persistent Betti numbers). Currently, it can be applied can work indifferently on many kinds of cell complex (such as structured and unstructured grids, 2D manifolds embedded within a 3D space, discrete point samples using delaunay tesselation, and Healpix tesselations of the sphere). The only constraint is that the distribution must be defined over a manifold, possibly with boundaries.

[ascl:1708.006] DISORT: DIScrete Ordinate Radiative Transfer

DISORT (DIScrete Ordinate Radiative Transfer) solves the problem of 1D scalar radiative transfer in a single optical medium, such as a planetary atmosphere. The code correctly accounts for multiple scattering by an isotropic or plane-parallel beam source, internal Planck sources, and reflection from a lower boundary. Provided that polarization effects can be neglected, DISORT efficiently calculates accurate fluxes and intensities at any user-specified angle and location within the user-specified medium.

[ascl:1108.015] DISKSTRUCT: A Simple 1+1-D Disk Structure Code

DISKSTRUCT is a simple 1+1-D code for modeling protoplanetary disks. It is not based on multidimensional radiative transfer! Instead, a flaring-angle recipe is used to compute the irradiation of the disk, while the disk vertical structure at each cylindrical radius is computed in a 1-D fashion; the models computed with this code are therefore approximate. Moreover, this model cannot deal with the dust inner rim.

In spite of these simplifications and drawbacks, the code can still be very useful for disk studies, for the following reasons:

  • It allows the disk structure to be studied in a 1-D vertical fashion (one radial cylinder at a time). For understanding the structure of disks, and also for using it as a basis of other models, this can be a great advantage.
  • For very optically thick disks this code is likely to be much faster than the RADMC full disk model.
  • Viscous internal heating of the disk is implemented and converges quickly, whereas the RADMC code is still having difficulty to deal with high optical depth combined with viscously generated internal heat.

[ascl:1811.013] DiskSim: Modeling Accretion Disk Dynamics with SPH

DiskSim is a source-code distribution of the SPH accretion disk modeling code previously released in a Windows executable form as FITDisk (ascl:1305.011). The code released now is the full research code in Fortran and can be modified as needed by the user.

[ascl:1603.011] DiskJockey: Protoplanetary disk modeling for dynamical mass derivation

DiskJockey derives dynamical masses for T Tauri stars using the Keplerian motion of their circumstellar disks, applied to radio interferometric data from the Atacama Large Millimeter Array (ALMA) and the Submillimeter Array (SMA). The package relies on RADMC-3D (ascl:1202.015) to perform the radiative transfer of the disk model. DiskJockey is designed to work in a parallel environment where the calculations for each frequency channel can be distributed to independent processors. Due to the computationally expensive nature of the radiative synthesis, fitting sizable datasets (e.g., SMA and ALMA) will require a substantial amount of CPU cores to explore a posterior distribution in a reasonable timeframe.

[ascl:1209.011] DiskFit: Modeling Asymmetries in Disk Galaxies

DiskFit implements procedures for fitting non-axisymmetries in either kinematic or photometric data. DiskFit can analyze H-alpha and CO velocity field data as well as HI kinematics to search for non-circular motions in the disk galaxies. DiskFit can also be used to constrain photometric models of the disc, bar and bulge. It deprecates an earlier version, by a subset of these authors, called velfit.

[ascl:1605.011] DISCO: 3-D moving-mesh magnetohydrodynamics package

DISCO evolves orbital fluid motion in two and three dimensions, especially at high Mach number, for studying astrophysical disks. The software uses a moving-mesh approach with a dynamic cylindrical mesh that can shear azimuthally to follow the orbital motion of the gas, thus removing diffusive advection errors and permitting longer timesteps than a static grid. DISCO uses an HLLD Riemann solver and a constrained transport scheme compatible with the mesh motion to implement magnetohydrodynamics.

[ascl:1403.020] disc2vel: Tangential and radial velocity components derivation

Disc2vel derives tangential and radial velocity components in the equatorial plane of a barred stellar disc from the observed line-of-sight velocity, assuming geometry of a thin disc. The code is written in IDL, and the method assumes that the bar is close to steady state (i.e. does not evolve fast) and that both morphology and kinematics are symmetrical with respect to the major axis of the bar.

[ascl:1102.021] DIRT: Dust InfraRed Toolbox

DIRT is a Java applet for modelling astrophysical processes in circumstellar dust shells around young and evolved stars. With DIRT, you can select and display over 500,000 pre-run model spectral energy distributions (SEDs), find the best-fit model to your data set, and account for beam size in model fitting. DIRT also allows you to manipulate data and models with an interactive viewer, display gas and dust density and temperature profiles, and display model intensity profiles at various wavelengths.

[ascl:1806.016] DirectDM-py: Dark matter direct detection

DirectDM, written in Python, takes the Wilson coefficients of relativistic operators that couple DM to the SM quarks, leptons, and gauge bosons and matches them onto a non-relativistic Galilean invariant EFT in order to calculate the direct detection scattering rates. A Mathematica implementation of DirectDM is also available (ascl:1806.015).

[ascl:1806.015] DirectDM-mma: Dark matter direct detection

The Mathematica code DirectDM takes the Wilson coefficients of relativistic operators that couple DM to the SM quarks, leptons, and gauge bosons and matches them onto a non-relativistic Galilean invariant EFT in order to calculate the direct detection scattering rates. A Python implementation of DirectDM is also available (ascl:1806.016).

[ascl:1405.016] DIPSO: Spectrum analysis code

DIPSO plots spectroscopic data rapidly and combines analysis and high-quality graphical output in a simple command-line driven interactive environment. It can be used, for example, to fit emission lines, measure equivalent widths and fluxes, do Fourier analysis, and fit models to spectra. A macro facility allows convenient execution of regularly used sequences of commands, and a simple Fortran interface permits "personal" software to be integrated with the program. DIPSO is part of the Starlink software collection (ascl:1110.012).

[ascl:1908.005] dips: Detrending periodic signals in timeseries

dips detrends timeseries of strictly periodic signals. It does not assume any functional form for the signal or the background or the noise; it disentangles the strictly periodic component from everything else. It has been used for detrending Kepler, K2 and TESS timeseries of periodic variable stars, eclipsing binary stars, and exoplanets.

[ascl:1010.031] DimReduce: Nonlinear Dimensionality Reduction of Very Large Datasets with Locally Linear Embedding (LLE) and its Variants

DimReduce is a C++ package for performing nonlinear dimensionality reduction of very large datasets with Locally Linear Embedding (LLE) and its variants. DimReduce is built for speed, using the optimized linear algebra packages BLAS, LAPACK, and ARPACK. Because of the need for storing very large matrices (1000 by 10000, for our SDSS LLE work), DimReduce is designed to use binary FITS files as inputs and outputs. This means that using the code is a bit more cumbersome. For smaller-scale LLE, where speed of computation is not as much of an issue, the Modular Data Processing toolkit may be a better choice. It is a python toolkit with some LLE functionality, which VanderPlas contributed.

This code has been rewritten and included in scikit-learn and an improved version is included in http://mmp2.github.io/megaman/

[ascl:1904.023] digest2: NEO binary classifier

digest2 classifies Near-Earth Object (NEO) candidates by providing a score, D2, that represents a pseudo-probability that a tracklet belongs to a given solar system orbit type. The code accurately and precisely distinguishes NEOs from non-NEOs, thus helping to identify those to be prioritized for follow-up observation. This fast, short-arc orbit classifier for small solar system bodies code is built upon the Pangloss code developed by Robert McNaught and further developed by Carl Hergenrother and Tim Spahr and Robert Jedicke's 223.f code.

[ascl:1102.024] DiFX2: A more flexible, efficient, robust and powerful software correlator

Software correlation, where a correlation algorithm written in a high-level language such as C++ is run on commodity computer hardware, has become increasingly attractive for small to medium sized and/or bandwidth constrained radio interferometers. In particular, many long baseline arrays (which typically have fewer than 20 elements and are restricted in observing bandwidth by costly recording hardware and media) have utilized software correlators for rapid, cost-effective correlator upgrades to allow compatibility with new, wider bandwidth recording systems and improve correlator flexibility. The DiFX correlator, made publicly available in 2007, has been a popular choice in such upgrades and is now used for production correlation by a number of observatories and research groups worldwide. Here we describe the evolution in the capabilities of the DiFX correlator over the past three years, including a number of new capabilities, substantial performance improvements, and a large amount of supporting infrastructure to ease use of the code. New capabilities include the ability to correlate a large number of phase centers in a single correlation pass, the extraction of phase calibration tones, correlation of disparate but overlapping sub-bands, the production of rapidly sampled filterbank and kurtosis data at minimal cost, and many more. The latest version of the code is at least 15% faster than the original, and in certain situations many times this value. Finally, we also present detailed test results validating the correctness of the new code.

[ascl:1103.001] Difmap: Synthesis Imaging of Visibility Data

Difmap is a program developed for synthesis imaging of visibility data from interferometer arrays of radio telescopes world-wide. Its prime advantages over traditional packages are its emphasis on interactive processing, speed, and the use of Difference mapping techniques.

[ascl:1304.008] Diffusion.f: Diffusion of elements in stars

Diffusion.f is an exportable subroutine to calculate the diffusion of elements in stars. The routine solves exactly the Burgers equations and can include any number of elements as variables. The code has been used successfully by a number of different groups; applications include diffusion in the sun and diffusion in globular cluster stars. There are many other possible applications to main sequence and to evolved stars. The associated README file explains how to use the subroutine.

[ascl:1512.012] DiffuseModel: Modeling the diffuse ultraviolet background

DiffuseModel calculates the scattered radiation from dust scattering in the Milky Way based on stars from the Hipparcos catalog. It uses Monte Carlo to implement multiple scattering and assumes a user-supplied grid for the dust distribution. The output is a FITS file with the diffuse light over the Galaxy. It is intended for use in the UV (900 - 3000 A) but may be modified for use in other wavelengths and galaxies.

[ascl:1704.013] Difference-smoothing: Measuring time delay from light curves

The Difference-smoothing MATLAB code measures the time delay from the light curves of images of a gravitationally lendsed quasar. It uses a smoothing timescale free parameter, generates more realistic synthetic light curves to estimate the time delay uncertainty, and uses X2 plot to assess the reliability of a time delay measurement as well as to identify instances of catastrophic failure of the time delay estimator. A systematic bias in the measurement of time delays for some light curves can be eliminated by applying a correction to each measured time delay.

[ascl:1801.010] DICE/ColDICE: 6D collisionless phase space hydrodynamics using a lagrangian tesselation

DICE is a C++ template library designed to solve collisionless fluid dynamics in 6D phase space using massively parallel supercomputers via an hybrid OpenMP/MPI parallelization. ColDICE, based on DICE, implements a cosmological and physical VLASOV-POISSON solver for cold systems such as dark matter (CDM) dynamics.

[ascl:1607.002] DICE: Disk Initial Conditions Environment

DICE models initial conditions of idealized galaxies to study their secular evolution or their more complex interactions such as mergers or compact groups using N-Body/hydro codes. The code can set up a large number of components modeling distinct parts of the galaxy, and creates 3D distributions of particles using a N-try MCMC algorithm which does not require a prior knowledge of the distribution function. The gravitational potential is then computed on a multi-level Cartesian mesh by solving the Poisson equation in the Fourier space. Finally, the dynamical equilibrium of each component is computed by integrating the Jeans equations for each particles. Several galaxies can be generated in a row and be placed on Keplerian orbits to model interactions. DICE writes the initial conditions in the Gadget1 or Gadget2 (ascl:0003.001) format and is fully compatible with Ramses (ascl:1011.007).

[ascl:1410.001] DIAMONDS: high-DImensional And multi-MOdal NesteD Sampling

DIAMONDS (high-DImensional And multi-MOdal NesteD Sampling) provides Bayesian parameter estimation and model comparison by means of the nested sampling Monte Carlo (NSMC) algorithm, an efficient and powerful method very suitable for high-dimensional and multi-modal problems; it can be used for any application involving Bayesian parameter estimation and/or model selection in general. Developed in C++11, DIAMONDS is structured in classes for flexibility and configurability. Any new model, likelihood and prior PDFs can be defined and implemented upon a basic template.

[ascl:1805.002] dftools: Distribution function fitting

dftools, written in R, finds the most likely P parameters of a D-dimensional distribution function (DF) generating N objects, where each object is specified by D observables with measurement uncertainties. For instance, if the objects are galaxies, it can fit a mass function (D=1), a mass-size distribution (D=2) or the mass-spin-morphology distribution (D=3). Unlike most common fitting approaches, this method accurately accounts for measurement in uncertainties and complex selection functions.

[ascl:1904.017] dfitspy: A dfits/fitsort implementation in Python

dfitspy searches and displays metadata contained in FITS files. Written in Python, it displays the results of a metadata search and is able to grep certain values of keywords inside large samples of files in the terminal. dfitspy can be used directly with the command line interface and can also be imported as a python module into other python code or the python interpreter.

[ascl:1112.015] Dexter: Data Extractor for scanned graphs

The NASA Astrophysics Data System (ADS) now holds 1.3 million scanned pages, containing numerous plots and figures for which the original data sets are lost or inaccessible. The availability of scans of the figures can significantly ease the regeneration of the data sets. For this purpose, the ADS has developed Dexter, a Java applet that supports the user in this process. Dexter's basic functionality is to let the user manually digitize a plot by marking points and defining the coordinate transformation from the logical to the physical coordinate system. Advanced features include automatic identification of axes, tracing lines and finding points matching a template.

[ascl:1402.022] DexM: Semi-numerical simulations for very large scales

DexM (Deus ex Machina) efficiently generates density, halo, and ionization fields on very large scales and with a large dynamic range through seminumeric simulation. These properties are essential for reionization studies, especially those involving rare, massive QSOs, since one must be able to statistically capture the ionization field. DexM can also generate ionization fields directly from the evolved density field to account for the ionizing contribution of small halos. Semi-numerical simulations use more approximate physics than numerical simulations, but independently generate 3D cosmological realizations. DexM is portable and fast, and allows for explorations of wide swaths of astrophysical parameter space and an unprecedented dynamic range.

[ascl:1907.008] Dewarp: Distortion removal and on-sky orientation solution for LBTI detectors

Dewarp constructs pipelines to remove distortion from a detector and find the orientation with true North. It was originally written for the LBTI LMIRcam detector, but is generalizable to any project with reference sources and/or an astrometric field paired with a machine-readable file of astrometric target locations.

[ascl:1304.007] DESPOTIC: Derive the Energetics and SPectra of Optically Thick Interstellar Clouds

DESPOTIC (Derive the Energetics and SPectra of Optically Thick Interstellar Clouds), written in Python, represents optically thick interstellar clouds using a one-zone model and calculates line luminosities, line cooling rates, and in restricted cases line profiles using an escape probability formalism. DESPOTIC calculates clouds' equilibrium gas and dust temperatures and their time-dependent thermal evolution. The code allows rapid and interactive calculation of clouds' characteristic temperatures, identification of their dominant heating and cooling mechanisms, and prediction of their observable spectra across a wide range of interstellar environments.

[ascl:1804.011] DESCQA: Synthetic Sky Catalog Validation Framework

The DESCQA framework provides rigorous validation protocols for assessing the quality of high-quality simulated sky catalogs in a straightforward and comprehensive way. DESCQA enables the inspection, validation, and comparison of an inhomogeneous set of synthetic catalogs via the provision of a common interface within an automated framework. An interactive web interface is also available at portal.nersc.gov/project/lsst/descqa.

[ascl:1511.017] DES exposure checker: Dark Energy Survey image quality control crowdsourcer

DES exposure checker renders science-grade images directly to a web browser and allows users to mark problematic features from a set of predefined classes, thus allowing image quality control for the Dark Energy Survey to be crowdsourced through its web application. Users can also generate custom labels to help identify previously unknown problem classes; generated reports are fed back to hardware and software experts to help mitigate and eliminate recognized issues. These problem reports allow rapid correction of artifacts that otherwise may be too subtle or infrequent to be recognized.

[ascl:1904.009] deproject: Deprojection of two-dimensional annular X-ray spectra

Deproject extends Sherpa (ascl:1107.005) to facilitate deprojection of two-dimensional annular X-ray spectra to recover the three-dimensional source properties. For typical thermal models, this includes the radial temperature and density profiles. This basic method is used for X-ray cluster analysis and is the basis for the XSPEC (ascl:9910.005) model project. The deproject module is written in Python and is straightforward to use and understand. The basic physical assumption of deproject is that the extended source emissivity is constant and optically thin within spherical shells whose radii correspond to the annuli used to extract the specta. Given this assumption, one constructs a model for each annular spectrum that is a linear volume-weighted combination of shell models.

[ascl:1705.003] demc2: Differential evolution Markov chain Monte Carlo parameter estimator

demc2, also abbreviated as DE-MCMC, is a differential evolution Markov Chain parameter estimation library written in R for adaptive MCMC on real parameter spaces.

[ascl:1602.012] DELightcurveSimulation: Light curve simulation code

DELightcurveSimulation simulates light curves with any given power spectral density and any probability density function, following the algorithm described in Emmanoulopoulos et al. (2013). The simulated products have exactly the same variability and statistical properties as the observed light curves. The code is a Python implementation of the Mathematica code provided by Emmanoulopoulos et al.

[ascl:1011.012] DEFROST: A New Code for Simulating Preheating after Inflation

At the end of inflation, dynamical instability can rapidly deposit the energy of homogeneous cold inflaton into excitations of other fields. This process, known as preheating, is rather violent, inhomogeneous and non-linear, and has to be studied numerically. This paper presents a new code for simulating scalar field dynamics in expanding universe written for that purpose. Compared to available alternatives, it significantly improves both the speed and the accuracy of calculations, and is fully instrumented for 3D visualization. We reproduce previously published results on preheating in simple chaotic inflation models, and further investigate non-linear dynamics of the inflaton decay. Surprisingly, we find that the fields do not want to thermalize quite the way one would think. Instead of directly reaching equilibrium, the evolution appears to be stuck in a rather simple but quite inhomogeneous state. In particular, one-point distribution function of total energy density appears to be universal among various two-field preheating models, and is exceedingly well described by a lognormal distribution. It is tempting to attribute this state to scalar field turbulence.

[ascl:1405.004] Defringeflat: Fringe pattern removal

The IDL package Defringeflat identifies and removes fringe patterns from images such as spectrograph flat fields. It uses a wavelet transform to calculate the frequency spectrum in a region around each point of a one-dimensional array. The wavelet transform amplitude is reconstructed from (smoothed) parameters obtaining the fringe's wavelet transform, after which an inverse wavelet transform is performed to obtain the computed fringe pattern which is then removed from the flat.

[ascl:1805.029] DeepMoon: Convolutional neural network trainer to identify moon craters

DeepMoon trains a convolutional neural net using data derived from a global digital elevation map (DEM) and catalog of craters to recognize craters on the Moon. The TensorFlow-based pipeline code is divided into three parts. The first generates a set images of the Moon randomly cropped from the DEM, with corresponding crater positions and radii. The second trains a convnet using this data, and the third validates the convnet's predictions.

[ascl:1603.015] Dedalus: Flexible framework for spectrally solving differential equations

Dedalus solves differential equations using spectral methods. It implements flexible algorithms to solve initial-value, boundary-value, and eigenvalue problems with broad ranges of custom equations and spectral domains. Its primary features include symbolic equation entry, multidimensional parallelization, implicit-explicit timestepping, and flexible analysis with HDF5. The code is written primarily in Python and features an easy-to-use interface. The numerical algorithm produces highly sparse systems for many equations which are efficiently solved using compiled libraries and MPI.

[ascl:1801.006] DecouplingModes: Passive modes amplitudes

DecouplingModes calculates the amplitude of the passive modes, which requires solving the Einstein equations on superhorizon scales sourced by the anisotropic stress from the magnetic fields (prior to neutrino decoupling), and the magnetic and neutrino stress (after decoupling). The code is available as a Mathematica notebook.

[ascl:1501.005] DECA: Decomposition of images of galaxies

DECA performs photometric analysis of images of disk and elliptical galaxies having a regular structure. It is written in Python and combines the capabilities of several widely used packages for astronomical data processing such as IRAF, SExtractor, and the GALFIT code to perform two-dimensional decomposition of galaxy images into several photometric components (bulge+disk). DECA can be applied to large samples of galaxies with different orientations with respect to the line of sight (including edge-on galaxies) and requires minimum human intervention.

[ascl:1510.004] DEBiL: Detached Eclipsing Binary Light curve fitter

DEBiL rapidly fits a large number of light curves to a simple model. It is the central component of a pipeline for systematically identifying and analyzing eclipsing binaries within a large dataset of light curves; the results of DEBiL can be used to flag light curves of interest for follow-up analysis.

[ascl:0008.001] DDSCAT: The discrete dipole approximation for scattering and absorption of light by irregular particles

DDSCAT is a freely available software package which applies the "discrete dipole approximation" (DDA) to calculate scattering and absorption of electromagnetic waves by targets with arbitrary geometries and complex refractive index. The DDA approximates the target by an array of polarizable points. DDSCAT.5a requires that these polarizable points be located on a cubic lattice. DDSCAT allows accurate calculations of electromagnetic scattering from targets with "size parameters" 2 pi a/lambda < 15 provided the refractive index m is not large compared to unity (|m-1| < 1). The DDSCAT package is written in Fortran and is highly portable. The program supports calculations for a variety of target geometries (e.g., ellipsoids, regular tetrahedra, rectangular solids, finite cylinders, hexagonal prisms, etc.). Target materials may be both inhomogeneous and anisotropic. It is straightforward for the user to import arbitrary target geometries into the code, and relatively straightforward to add new target generation capability to the package. DDSCAT automatically calculates total cross sections for absorption and scattering and selected elements of the Mueller scattering intensity matrix for specified orientation of the target relative to the incident wave, and for specified scattering directions. This User Guide explains how to use DDSCAT to carry out EM scattering calculations. CPU and memory requirements are described.

[ascl:1810.020] DDS: Debris Disk Radiative Transfer Simulator

DDS simulates scattered light and thermal reemission in arbitrary optically dust distributions with spherical, homogeneous grains where the dust parameters (optical properties, sublimation temperature, grain size) and SED of the illuminating/ heating radiative source can be arbitrarily defined. The code is optimized for studying circumstellar debris disks where large grains (i.e., with large size parameters) are expected to determine the far-infrared through millimeter dust reemission spectral energy distribution. The approach to calculate dust temperatures and dust reemission spectra is only valid in the optically thin regime. The validity of this constraint is verified for each model during the runtime of the code. The relative abundances of different grains can be arbitrarily chosen, but must be constant outside the dust sublimation region., i.e., the shape of the (arbitrary) radial dust density distribution outside the dust sublimation region is the same for all grain sizes and chemistries.

[ascl:1212.012] ddisk: Debris disk time-evolution

ddisk is an IDL script that calculates the time-evolution of a circumstellar debris disk. It calculates dust abundances over time for a debris-disk that is produced by a planetesimal disk that is grinding away due to collisional erosion.

[ascl:1207.006] dcr: Cosmic Ray Removal

This code provides a method for detecting cosmic rays in single images. The algorithm is based on a simple analysis of the histogram of the image data and does not use any modeling of the picture of the object. It does not require a good signal-to-noise ratio in the image data. Identification of multiple-pixel cosmic-ray hits is realized by running the procedure for detection and replacement iteratively. The method is very effective when applied to the images with spectroscopic data, and is also very fast in comparison with other single-image algorithms found in astronomical data-processing packages. Practical implementation and examples of application are presented in the code paper.

[ascl:1709.006] DCMDN: Deep Convolutional Mixture Density Network

Deep Convolutional Mixture Density Network (DCMDN) estimates probabilistic photometric redshift directly from multi-band imaging data by combining a version of a deep convolutional network with a mixture density network. The estimates are expressed as Gaussian mixture models representing the probability density functions (PDFs) in the redshift space. In addition to the traditional scores, the continuous ranked probability score (CRPS) and the probability integral transform (PIT) are applied as performance criteria. DCMDN is able to predict redshift PDFs independently from the type of source, e.g. galaxies, quasars or stars and renders pre-classification of objects and feature extraction unnecessary; the method is extremely general and allows the solving of any kind of probabilistic regression problems based on imaging data, such as estimating metallicity or star formation rate in galaxies.

[ascl:1903.012] DAVE: Discovery And Vetting of K2 Exoplanets

DAVE implements a pipeline to find and vet planets planets using data from NASA's K2 mission. The pipeline contains several modules tailored to particular aspects of the vetting procedures, using photocenter analysis to rule out background eclipsing binaries and flux time-series analysis to rule out odd–even differences, secondary eclipses, low-S/N events, variability other than a transit, and size of the transiting object.

[ascl:1405.011] DATACUBE: A datacube manipulation package

DATACUBE is a command-line package for manipulating and visualizing data cubes. It was designed for integral field spectroscopy but has been extended to be a generic data cube tool, used in particular for sub-millimeter data cubes from the James Clerk Maxwell Telescope. It is part of the Starlink software collection (ascl:1110.012).

[ascl:1402.027] Darth Fader: Galaxy catalog cleaning method for redshift estimation

Darth Fader is a wavelet-based method for extracting spectral features from very noisy spectra. Spectra for which a reliable redshift cannot be measured are identified and removed from the input data set automatically, resulting in a clean catalogue that gives an extremely low rate of catastrophic failures even when the spectra have a very low S/N. This technique may offer a significant boost in the number of faint galaxies with accurately determined redshifts.

[ascl:1110.002] DarkSUSY: Supersymmetric Dark Matter Calculations

DarkSUSY, written in Fortran, is a publicly-available advanced numerical package for neutralino dark matter calculations. In DarkSUSY one can compute the neutralino density in the Universe today using precision methods which include resonances, pair production thresholds and coannihilations. Masses and mixings of supersymmetric particles can be computed within DarkSUSY or with the help of external programs such as FeynHiggs, ISASUGRA and SUSPECT. Accelerator bounds can be checked to identify viable dark matter candidates. DarkSUSY also computes a large variety of astrophysical signals from neutralino dark matter, such as direct detection in low-background counting experiments and indirect detection through antiprotons, antideuterons, gamma-rays and positrons from the Galactic halo or high-energy neutrinos from the center of the Earth or of the Sun.

[ascl:1706.004] Dark Sage: Semi-analytic model of galaxy evolution

DARK SAGE is a semi-analytic model of galaxy formation that focuses on detailing the structure and evolution of galaxies' discs. The code-base, written in C, is an extension of SAGE (ascl:1601.006) and maintains the modularity of SAGE. DARK SAGE runs on any N-body simulation with trees organized in a supported format and containing a minimum set of basic halo properties.

[ascl:1011.002] DAOSPEC: An Automatic Code for Measuring Equivalent Widths in High-resolution Stellar Spectra

DAOSPEC is a Fortran code for measuring equivalent widths of absorption lines in stellar spectra with minimal human involvement. It works with standard FITS format files and it is designed for use with high resolution (R>15000) and high signal-to-noise-ratio (S/N>30) spectra that have been binned on a linear wavelength scale. First, we review the analysis procedures that are usually employed in the literature. Next, we discuss the principles underlying DAOSPEC and point out similarities and differences with respect to conventional measurement techniques. Then experiments with artificial and real spectra are discussed to illustrate the capabilities and limitations of DAOSPEC, with special attention given to the issues of continuum placement; radial velocities; and the effects of strong lines and line crowding. Finally, quantitative comparisons with other codes and with results from the literature are also presented.

[ascl:1104.011] DAOPHOT: Crowded-field Stellar Photometry Package

The DAOPHOT program exploits the capability of photometrically linear image detectors to perform stellar photometry in crowded fields. Raw CCD images are prepared prior to analysis, and following the obtaining of an initial star list with the FIND program, synthetic aperture photometry is performed on the detected objects with the PHOT routine. A local sky brightness and a magnitude are computed for each star in each of the specified stellar apertures, and for crowded fields, the empirical point-spread function must then be obtained for each data frame. The GROUP routine divides the star list for a given frame into optimum subgroups, and then the NSTAR routine is used to obtain photometry for all the stars in the frame by means of least-squares profile fits.

[ascl:1709.005] DanIDL: IDL solutions for science and astronomy

DanIDL provides IDL functions and routines for many standard astronomy needs, such as searching for matching points between two coordinate lists of two-dimensional points where each list corresponds to a different coordinate space, estimating the full-width half-maximum (FWHM) and ellipticity of the PSF of an image, calculating pixel variances for a set of calibrated image data, and fitting a 3-parameter plane model to image data. The library also supplies astrometry, general image processing, and general scientific applications.

[ascl:1807.023] DAMOCLES: Monte Carlo line radiative transfer code

The Monte Carlo code DAMOCLES models the effects of dust, composed of any combination of species and grain size distributions, on optical and NIR emission lines emitted from the expanding ejecta of a late-time (> 1 yr) supernova. The emissivity and dust distributions follow smooth radial power-law distributions; any arbitrary distribution can be specified by providing the appropriate grid. DAMOCLES treats a variety of clumping structures as specified by a clumped dust mass fraction, volume filling factor, clump size and clump power-law distribution, and the emissivity distribution may also initially be clumped. The code has a large number of variable parameters ranging from 5 dimensions in the simplest models to > 20 in the most complex cases.

[ascl:1412.004] DAMIT: Database of Asteroid Models from Inversion Techniques

DAMIT (Database of Asteroid Models from Inversion Techniques) is a database of three-dimensional models of asteroids computed using inversion techniques; it provides access to reliable and up-to-date physical models of asteroids, i.e., their shapes, rotation periods, and spin axis directions. Models from DAMIT can be used for further detailed studies of individual objects as well as for statistical studies of the whole set. The source codes for lightcurve inversion routines together with brief manuals, sample lightcurves, and the code for the direct problem are available for download.

[ascl:1011.006] DAME: A Web Oriented Infrastructure for Scientific Data Mining & Exploration

DAME (DAta Mining & Exploration) is an innovative, general purpose, Web-based, VObs compliant, distributed data mining infrastructure specialized in Massive Data Sets exploration with machine learning methods. Initially fine tuned to deal with astronomical data only, DAME has evolved in a general purpose platform which has found applications also in other domains of human endeavor.

[ascl:1706.003] DaMaSCUS: Dark Matter Simulation Code for Underground Scatterings

DaMaSCUS calculates the density and velocity distribution of dark matter (DM) at any detector of given depth and latitude to provide dark matter particle trajectories inside the Earth. Provided a strong enough DM-matter interaction, the particles scatter on terrestrial atoms and get decelerated and deflected. The resulting local modifications of the DM velocity distribution and number density can have important consequences for direct detection experiments, especially for light DM, and lead to signatures such as diurnal modulations depending on the experiment's location on Earth. The code involves both the Monte Carlo simulation of particle trajectories and generation of data as well as the data analysis consisting of non-parametric density estimation of the local velocity distribution functions and computation of direct detection event rates.

[ascl:1803.001] DaMaSCUS-CRUST: Dark Matter Simulation Code for Underground Scatterings - Crust Edition

DaMaSCUS-CRUST determines the critical cross-section for strongly interacting DM for various direct detection experiments systematically and precisely using Monte Carlo simulations of DM trajectories inside the Earth's crust, atmosphere, or any kind of shielding. Above a critical dark matter-nucleus scattering cross section, any terrestrial direct detection experiment loses sensitivity to dark matter, since the Earth crust, atmosphere, and potential shielding layers start to block off the dark matter particles. This critical cross section is commonly determined by describing the average energy loss of the dark matter particles analytically. However, this treatment overestimates the stopping power of the Earth crust; therefore, the obtained bounds should be considered as conservative. DaMaSCUS-CRUST is a modified version of DaMaSCUS (ascl:1706.003) that accounts for shielding effects and returns a precise exclusion band.

[ascl:1507.015] DALI: Derivative Approximation for LIkelihoods

DALI (Derivative Approximation for LIkelihoods) is a fast approximation of non-Gaussian likelihoods. It extends the Fisher Matrix in a straightforward way and allows for a wider range of posterior shapes. The code is written in C/C++.

[ascl:1804.005] DaCHS: Data Center Helper Suite

DaCHS, the Data Center Helper Suite, is an integrated package for publishing astronomical data sets to the Virtual Observatory. Network-facing, it speaks the major VO protocols (SCS, SIAP, SSAP, TAP, Datalink, etc). Operator-facing, many input formats, including FITS/WCS, ASCII files, and VOTable, can be processed to publication-ready data. DaCHS puts particular emphasis on integrated metadata handling, which facilitates a tight integration with the VO's Registry

[ascl:1612.007] dacapo_calibration: Photometric calibration code

dacapo_calibration implements the DaCapo algorithm used in the Planck/LFI 2015 data release for photometric calibration. The code takes as input a set of TODs and calibrates them using the CMB dipole signal. DaCapo is a variant of the well-known family of destriping algorithms for map-making.

[ascl:1504.018] D3PO: Denoising, Deconvolving, and Decomposing Photon Observations

D3PO (Denoising, Deconvolving, and Decomposing Photon Observations) addresses the inference problem of denoising, deconvolving, and decomposing photon observations. Its primary goal is the simultaneous but individual reconstruction of the diffuse and point-like photon flux given a single photon count image, where the fluxes are superimposed. A hierarchical Bayesian parameter model is used to discriminate between morphologically different signal components, yielding a diffuse and a point-like signal estimate for the photon flux components.

[ascl:1606.003] Cygrid: Cython-powered convolution-based gridding module for Python

The Python module Cygrid grids (resamples) data to any collection of spherical target coordinates, although its typical application involves FITS maps or data cubes. The module supports the FITS world coordinate system (WCS) standard; its underlying algorithm is based on the convolution of the original samples with a 2D Gaussian kernel. A lookup table scheme allows parallelization of the code and is combined with the HEALPix tessellation of the sphere for fast neighbor searches. Cygrid's runtime scales between O(n) and O(nlog n), with n being the number of input samples.

[submitted] cuvarbase: fast period finding utilities for GPU's (Python)

cuvarbase provides a Python (2.7+) library for performing period finding (Lomb-Scargle, Phase Dispersion Minimization, Conditional Entropy, Box-least squares) on astronomical time-series datasets. Speedups over CPU implementations depend on the algorithm, dataset, and GPU capabilities but are typically ~1-2 orders of magnitude and are especially high for BLS and Lomb-Scargle. Unit tested and available via pip or from source at GitHub.

[ascl:1708.018] CUTEX: CUrvature Thresholding EXtractor

CuTEx analyzes images in the infrared bands and extracts sources from complex backgrounds, particularly star-forming regions that offer the challenges of crowding, having a highly spatially variable background, and having no-psf profiles such as protostars in their accreting phase. The code is composed of two main algorithms, the first an algorithm for source detection, and the second for flux extraction. The code is originally written in IDL language and it was exported in the license free GDL language. CuTEx could be used in other bands or in scientific cases different from the native case.

This software is also available as an on-line tool from the Multi-Mission Interactive Archive web pages dedicated to the Herschel Observatory.

[ascl:1505.016] CUTE: Correlation Utilities and Two-point Estimation

CUTE (Correlation Utilities and Two-point Estimation) extracts any two-point statistic from enormous datasets with hundreds of millions of objects, such as large galaxy surveys. The computational time grows with the square of the number of objects to be correlated; technology provides multiple means to massively parallelize this problem and CUTE is specifically designed for these kind of calculations. Two implementations are provided: one for execution on shared-memory machines using OpenMP and one that runs on graphical processing units (GPUs) using CUDA.

[ascl:1405.015] CURSA: Catalog and Table Manipulation Applications

The CURSA package manipulates astronomical catalogs and similar tabular datasets. It provides facilities for browsing or examining catalogs; selecting subsets from a catalog; sorting and copying catalogs; pairing two catalogs; converting catalog coordinates between some celestial coordinate systems; and plotting finding charts and photometric calibration. It can also extract subsets from a catalog in a format suitable for plotting using other Starlink packages such as PONGO. CURSA can access catalogs held in the popular FITS table format, the Tab-Separated Table (TST) format or the Small Text List (STL) format. Catalogs in the STL and TST formats are simple ASCII text files. CURSA also includes some facilities for accessing remote on-line catalogs via the Internet. It is part of the Starlink software collection (ascl:1110.012).

[ascl:1311.008] CUPID: Customizable User Pipeline for IRS Data

Written in c, the Customizable User Pipeline for IRS Data (CUPID) allows users to run the Spitzer IRS Pipelines to re-create Basic Calibrated Data and extract calibrated spectra from the archived raw files. CUPID provides full access to all the parameters of the BCD, COADD, BKSUB, BKSUBX, and COADDX pipelines, as well as the opportunity for users to provide their own calibration files (e.g., flats or darks). CUPID is available for Mac, Linux, and Solaris operating systems.

[ascl:1311.007] CUPID: Clump Identification and Analysis Package

The CUPID package allows the identification and analysis of clumps of emission within 1, 2 or 3 dimensional data arrays. Whilst targeted primarily at sub-mm cubes, it can be used on any regularly gridded 1, 2 or 3D data. A variety of clump finding algorithms are implemented within CUPID, including the established ClumpFind (ascl:1107.014) and GaussClumps algorithms. In addition, two new algorithms called FellWalker and Reinhold are also provided. CUPID allows easy inter-comparison between the results of different algorithms; the catalogues produced by each algorithm contains a standard set of columns containing clump peak position, clump centroid position, the integrated data value within the clump, clump volume, and the dimensions of the clump. In addition, pixel masks are produced identifying which input pixels contribute to each clump. CUPID is distributed as part of the Starlink (ascl:1110.012) software collection.

[ascl:1109.013] CULSP: Fast Calculation of the Lomb-Scargle Periodogram Using Graphics Processing Units

I introduce a new code for fast calculation of the Lomb-Scargle periodogram, that leverages the computing power of graphics processing units (GPUs). After establishing a background to the newly emergent field of GPU computing, I discuss the code design and narrate key parts of its source. Benchmarking calculations indicate no significant differences in accuracy compared to an equivalent CPU-based code. However, the differences in performance are pronounced; running on a low-end GPU, the code can match 8 CPU cores, and on a high-end GPU it is faster by a factor approaching thirty. Applications of the code include analysis of long photometric time series obtained by ongoing satellite missions and upcoming ground-based monitoring facilities; and Monte-Carlo simulation of periodogram statistical properties.

[ascl:1810.015] cuFFS: CUDA-accelerated Fast Faraday Synthesis

cuFFS (CUDA-accelerated Fast Faraday Synthesis) performs Faraday rotation measure synthesis; it is particularly well-suited for performing RM synthesis on large datasets. Compared to a fast single-threaded and vectorized CPU implementation, depending on the structure and format of the data cubes, cuFFs achieves an increase in speed of up to two orders of magnitude. The code assumes that the pixels values are IEEE single precision floating points (BITPIX=-32), and the input cubes must have 3 axes (2 spatial dimensions and 1 frequency axis) with frequency axis as NAXIS1. A package is included to reformat data with individual stokes Q and U channel maps to the required format. The code supports both the HDFITS format and the standard FITS format, and is written in C with GPU-acceleration achieved using Nvidia's CUDA parallel computing platform.

[ascl:1111.007] CUBISM: CUbe Builder for IRS Spectra Maps

CUBISM, written in IDL, constructs spectral cubes, maps, and arbitrary aperture 1D spectral extractions from sets of mapping mode spectra taken with Spitzer's IRS spectrograph. CUBISM is optimized for non-sparse maps of extended objects, e.g. the nearby galaxy sample of SINGS, but can be used with data from any spectral mapping AOR (primarily validated for maps which are designed as suggested by the mapping HOWTO).

[ascl:1805.031] CubiCal: Suite for fast radio interferometric calibration

CubiCal implements several accelerated gain solvers which exploit complex optimization for fast radio interferometric gain calibration. The code can be used for both direction-independent and direction-dependent self-calibration. CubiCal is implemented in Python and Cython, and multiprocessing is fully supported.

[ascl:1208.018] CUBEP3M: High performance P3M N-body code

CUBEP3M is a high performance cosmological N-body code which has many utilities and extensions, including a runtime halo finder, a non-Gaussian initial conditions generator, a tuneable accuracy, and a system of unique particle identification. CUBEP3M is fast, has a memory imprint up to three times lower than other widely used N-body codes, and has been run on up to 20,000 cores, achieving close to ideal weak scaling even at this problem size. It is well suited and has already been used for a broad number of science applications that require either large samples of non-linear realizations or very large dark matter N-body simulations, including cosmological reionization, baryonic acoustic oscillations, weak lensing or non-Gaussian statistics.

[ascl:1512.010] CubeIndexer: Indexer for regions of interest in data cubes

CubeIndexer indexes regions of interest (ROIs) in data cubes reducing the necessary storage space. The software can process data cubes containing megabytes of data in fractions of a second without human supervision, thus allowing it to be incorporated into a production line for displaying objects in a virtual observatory. The software forms part of the Chilean Virtual Observatory (ChiVO) and provides the capability of content-based searches on data cubes to the astronomical community.

[ascl:1805.018] CUBE: Information-optimized parallel cosmological N-body simulation code

CUBE, written in Coarray Fortran, is a particle-mesh based parallel cosmological N-body simulation code. The memory usage of CUBE can approach as low as 6 bytes per particle. Particle pairwise (PP) force, cosmological neutrinos, spherical overdensity (SO) halofinder are included.

[ascl:1609.010] CuBANz: Photometric redshift estimator

CuBANz is a photometric redshift estimator code for high redshift galaxies that uses the back propagation neural network along with clustering of the training set, making it very efficient. The training set is divided into several self learning clusters with galaxies having similar photometric properties and spectroscopic redshifts within a given span. The clustering algorithm uses the color information (i.e. u-g, g-r etc.) rather than the apparent magnitudes at various photometric bands, as the photometric redshift is more sensitive to the flux differences between different bands rather than the actual values. The clustering method enables accurate determination of the redshifts. CuBANz considers uncertainty in the photometric measurements as well as uncertainty in the neural network training. The code is written in C.

[ascl:1608.008] Cuba: Multidimensional numerical integration library

The Cuba library offers four independent routines for multidimensional numerical integration: Vegas, Suave, Divonne, and Cuhre. The four algorithms work by very different methods, and can integrate vector integrands and have very similar Fortran, C/C++, and Mathematica interfaces. Their invocation is very similar, making it easy to cross-check by substituting one method by another. For further safeguarding, the output is supplemented by a chi-square probability which quantifies the reliability of the error estimate.

[ascl:1601.005] ctools: Cherenkov Telescope Science Analysis Software

ctools provides tools for the scientific analysis of Cherenkov Telescope Array (CTA) data. Analysis of data from existing Imaging Air Cherenkov Telescopes (such as H.E.S.S., MAGIC or VERITAS) is also supported, provided that the data and response functions are available in the format defined for CTA. ctools comprises a set of ftools-like binary executables with a command-line interface allowing for interactive step-wise data analysis. A Python module allows control of all executables, and the creation of shell or Python scripts and pipelines is supported. ctools provides cscripts, which are Python scripts complementing the binary executables. Extensions of the ctools package by user defined binary executables or Python scripts is supported. ctools are based on GammaLib (ascl:1110.007).

[ascl:1307.015] CTI Correction Code

Charge Transfer Inefficiency (CTI) due to radiation damage above the Earth's atmosphere creates spurious trailing in images from Charge-Coupled Device (CCD) imaging detectors. Radiation damage also creates unrelated warm pixels, which can be used to measure CTI. This code provides pixel-based correction for CTI and has proven effective in Hubble Space Telescope Advanced Camera for Surveys raw images, successfully reducing the CTI trails by a factor of ~30 everywhere in the CCD and at all flux levels. The core is written in java for speed, and a front-end user interface is provided in IDL. The code operates on raw data by returning individual electrons to pixels from which they were unintentionally dragged during readout. Correction takes about 25 minutes per ACS exposure, but is trivially parallelisable to multiple processors.

[ascl:0104.002] CSENV: A code for the chemistry of CircumStellar ENVelopes

CSENV is a code that computes the chemical abundances for a desired set of species as a function of radius in a stationary, non-clumpy, CircumStellar ENVelope. The chemical species can be atoms, molecules, ions, radicals, molecular ions, and/or their specific quantum states. Collisional ionization or excitation can be incorporated through the proper chemical channels. The chemical species interact with one another and can are subject to photo-processes (dissociation of molecules, radicals, and molecular ions as well as ionization of all species). Cosmic ray ionization can be included. Chemical reaction rates are specified with possible activation temperatures and additional power-law dependences. Photo-absorption cross-sections vs. wavelength, with appropriate thresholds, can be specified for each species, while for H2+ a photoabsorption cross-section is provided as a function of wavelength and temperature. The photons originate from both the star and the external interstellar medium. The chemical species are shielded from the photons by circumstellar dust, by other species and by themselves (self-shielding). Shielding of continuum-absorbing species by these species (self and mutual shielding), line-absorbing species, and dust varies with radial optical depth. The envelope is spherical by default, but can be made bipolar with an opening solid-angle that varies with radius. In the non-spherical case, no provision is made for photons penetrating the envelope from the sides. The envelope is subject to a radial outflow (or wind), constant velocity by default, but the wind velocity can be made to vary with radius. The temperature of the envelope is specified (and thus not computed self-consistently).

[ascl:1308.011] CRUSH: Comprehensive Reduction Utility for SHARC-2 (and more...)

CRUSH is an astronomical data reduction/imaging tool for certain imaging cameras, especially at the millimeter, sub-millimeter, and far-infrared wavelengths. It supports the SHARC-2, LABOCA, SABOCA, ASZCA, p-ArTeMiS, PolKa, GISMO, MAKO and SCUBA-2 instruments. The code is written entirely in Java, allowing it to run on virtually any platform. It is normally run from the command-line with several arguments.

[ascl:1202.007] CRUNCH3D: Three-dimensional compressible MHD code

CRUNCH3D is a massively parallel, viscoresistive, three-dimensional compressible MHD code. The code employs a Fourier collocation spatial discretization, and uses a second-order Runge-Kutta temporal discretization. CRUNCH3D can be applied to MHD turbulence and magnetic fluxtube reconnection research.

[ascl:1412.013] CRPropa: Numerical tool for the propagation of UHE cosmic rays, gamma-rays and neutrinos

CRPropa computes the observable properties of UHECRs and their secondaries in a variety of models for the sources and propagation of these particles. CRPropa takes into account interactions and deflections of primary UHECRs as well as propagation of secondary electromagnetic cascades and neutrinos. CRPropa makes use of the public code SOPHIA (ascl:1412.014), and the TinyXML, CFITSIO (ascl:1010.001), and CLHEP libraries. A major advantage of CRPropa is its modularity, which allows users to implement their own modules adapted to specific UHECR propagation models.

[ascl:1110.020] CROSS_CMBFAST: ISW-correlation Code

This code is an extension of CMBFAST4.5.1 to compute the ISW-correlation power spectrum and the 2-point angular ISW-correlation function for a given galaxy window function. It includes dark energy models specified by a constant equation of state (w) or a linear parameterization in the scale factor (w0,wa) and a constant sound speed (c2de). The ISW computation is limited to flat geometry. Differently from the original CMBFAST4.5 version dark energy perturbations are implemented for a general dark energy fluid specified by w(z) and c2de in synchronous gauge. For time varying dark energy models it is suggested not to cross the w=-1 line, as Dr. Wenkman says: "never cross the streams", bad things can happen.

[ascl:1708.003] CRISPRED: CRISP imaging spectropolarimeter data reduction pipeline

CRISPRED reduces data from the CRISP imaging spectropolarimeter at the Swedish 1 m Solar Telescope (SST). It performs fitting routines, corrects optical aberrations from atmospheric turbulence as well as from the optics, and compensates for inter-camera misalignments, field-dependent and time-varying instrumental polarization, and spatial variation in the detector gain and in the zero level offset (bias). It has an object-oriented IDL structure with computationally demanding routines performed in C subprograms called as dynamically loadable modules (DLMs).

[ascl:1612.009] CRETE: Comet RadiativE Transfer and Excitation

CRETE (Comet RadiativE Transfer and Excitation) is a one-dimensional water excitation and radiation transfer code for sub-millimeter wavelengths based on the RATRAN code (ascl:0008.002). The code considers rotational transitions of water molecules given a Haser spherically symmetric distribution for the cometary coma and produces FITS image cubes that can be analyzed with tools like MIRIAD (ascl:1106.007). In addition to collisional processes to excite water molecules, the effect of infrared radiation from the Sun is approximated by effective pumping rates for the rotational levels in the ground vibrational state.

[ascl:1308.009] CReSyPS: Stellar population synthesis code

CReSyPS (Code Rennais de Synthèse de Populations Stellaires) is a stellar population synthesis code that determines core overshooting amount for Magellanic clouds main sequence stars.

[ascl:1111.002] CRBLASTER: A Parallel-Processing Computational Framework for Embarrassingly-Parallel Image-Analysis Algorithms

The development of parallel-processing image-analysis codes is generally a challenging task that requires complicated choreography of interprocessor communications. If, however, the image-analysis algorithm is embarrassingly parallel, then the development of a parallel-processing implementation of that algorithm can be a much easier task to accomplish because, by definition, there is little need for communication between the compute processes. I describe the design, implementation, and performance of a parallel-processing image-analysis application, called CRBLASTER, which does cosmic-ray rejection of CCD (charge-coupled device) images using the embarrassingly-parallel L.A.COSMIC algorithm. CRBLASTER is written in C using the high-performance computing industry standard Message Passing Interface (MPI) library. The code has been designed to be used by research scientists who are familiar with C as a parallel-processing computational framework that enables the easy development of parallel-processing image-analysis programs based on embarrassingly-parallel algorithms. The CRBLASTER source code is freely available at the official application website at the National Optical Astronomy Observatory. Removing cosmic rays from a single 800x800 pixel Hubble Space Telescope WFPC2 image takes 44 seconds with the IRAF script lacos_im.cl running on a single core of an Apple Mac Pro computer with two 2.8-GHz quad-core Intel Xeon processors. CRBLASTER is 7.4 times faster processing the same image on a single core on the same machine. Processing the same image with CRBLASTER simultaneously on all 8 cores of the same machine takes 0.875 seconds -- which is a speedup factor of 50.3 times faster than the IRAF script. A detailed analysis is presented of the performance of CRBLASTER using between 1 and 57 processors on a low-power Tilera 700-MHz 64-core TILE64 processor.

[ascl:1101.008] CRASH: A Block-Adaptive-Mesh Code for Radiative Shock Hydrodynamics

We describe the CRASH (Center for Radiative Shock Hydrodynamics) code, a block adaptive mesh code for multi-material radiation hydrodynamics. The implementation solves the radiation diffusion model with the gray or multigroup method and uses a flux limited diffusion approximation to recover the free-streaming limit. The electrons and ions are allowed to have different temperatures and we include a flux limited electron heat conduction. The radiation hydrodynamic equations are solved in the Eulerian frame by means of a conservative finite volume discretization in either one, two, or three-dimensional slab geometry or in two-dimensional cylindrical symmetry. An operator split method is used to solve these equations in three substeps: (1) solve the hydrodynamic equations with shock-capturing schemes, (2) a linear advection of the radiation in frequency-logarithm space, and (3) an implicit solve of the stiff radiation diffusion, heat conduction, and energy exchange. We present a suite of verification test problems to demonstrate the accuracy and performance of the algorithms. The CRASH code is an extension of the Block-Adaptive Tree Solarwind Roe Upwind Scheme (BATS-R-US) code with this new radiation transfer and heat conduction library and equation-of-state and multigroup opacity solvers. Both CRASH and BATS-R-US are part of the publicly available Space Weather Modeling Framework (SWMF).

[submitted] CR-SISTEM: Symplectic integrator for lunar core-mantle and orbital dynamics

This integrator is based on the algorithm of Touma and Wisdom (2001, http://ui.adsabs.harvard.edu/abs/2001AJ....122.1030T). The triaxial Moon has a triaxial liquid core, and is perturbed by the Sun and Earth's oblateness. Orbits of the Moon and Earth are fully integrated, and other planets (or additional point-mass satellites) may be included in the integration. Lunar and solar tides on Earth, eccentricity and obliquity tides on the Moon, and lunar core-mantle friction and all included. The tides on Earth and the Moon are treated in the same way Cuk et al (2016, http://ui.adsabs.harvard.edu/abs/2016Natur.539..402C) and many details of their closely-related code can be found in the online supplement of that paper. In the posted version, the lunar core-mantle friction torque is directly proportional to the core-mantle differential rotation, with a fixed damping timescale of 10,000 present-day sidereal months (120 yrs, after Pavlov et al. (2016, https://ui.adsabs.harvard.edu/abs/2016CeMDA.126...61P).

[ascl:1102.012] CPROPS: Bias-free Measurement of Giant Molecular Cloud Properties

CPROPS, written in IDL, processes FITS data cubes containing molecular line emission and returns the properties of molecular clouds contained within it. Without corrections for the effects of beam convolution and sensitivity to GMC properties, the resulting properties may be severely biased. This is particularly true for extragalactic observations, where resolution and sensitivity effects often bias measured values by 40% or more. We correct for finite spatial and spectral resolutions with a simple deconvolution and we correct for sensitivity biases by extrapolating properties of a GMC to those we would expect to measure with perfect sensitivity. The resulting method recovers the properties of a GMC to within 10% over a large range of resolutions and sensitivities, provided the clouds are marginally resolved with a peak signal-to-noise ratio greater than 10. We note that interferometers systematically underestimate cloud properties, particularly the flux from a cloud. The degree of bias depends on the sensitivity of the observations and the (u,v) coverage of the observations. In the Appendix to the paper we present a conservative, new decomposition algorithm for identifying GMCs in molecular-line observations. This algorithm treats the data in physical rather than observational units, does not produce spurious clouds in the presence of noise, and is sensitive to a range of morphologies. As a result, the output of this decomposition should be directly comparable among disparate data sets.

The CPROPS package contains within it a distribution of the CLUMPFIND code written by Jonathan Williams and described in Williams, de Geus, and Blitz(1994). The package is available as a stand alone package. If you make use of the CLUMPFIND functionality in the CPROPS package for a publication, please cite Jonathan's original article.

[ascl:1710.009] CppTransport: Two- and three-point function transport framework for inflationary cosmology

CppTransport solves the 2- and 3-point functions of the perturbations produced during an inflationary epoch in the very early universe. It is implemented for models with canonical kinetic terms, although the underlying method is quite general and could be scaled to handle models with a non-trivial field-space metric or an even more general non-canonical Lagrangian.

[ascl:1402.010] CPL: Common Pipeline Library

The Common Pipeline Library (CPL) is a set of ISO-C libraries that provide a comprehensive, efficient and robust software toolkit to create automated astronomical data reduction pipelines. Though initially developed as a standardized way to build VLT instrument pipelines, the CPL may be more generally applied to any similar application. The code also provides a variety of general purpose image- and signal-processing functions, making it an excellent framework for the creation of more generic data handling packages. The CPL handles low-level data types (images, tables, matrices, strings, property lists, etc.) and medium-level data access methods (a simple data abstraction layer for FITS files). It also provides table organization and manipulation, keyword/value handling and management, and support for dynamic loading of recipe modules using programs such as EsoRex (ascl:1504.003).

[ascl:1808.003] CPF: Corral Pipeline Framework

Corral generates astronomical pipelines. Data processing pipelines represent an important slice of the astronomical software library that include chains of processes that transform raw data into valuable information via data reduction and analysis. Written in Python, Corral features a Model-View-Controller design pattern on top of an SQL Relational Database capable of handling custom data models, processing stages, and communication alerts. It also provides automatic quality and structural metrics based on unit testing. The Model-View-Controller provides concept separation between the user logic and the data models, delivering at the same time multi-processing and distributed computing capabilities.

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