[submitted]
millennium-tap-query: A Python Tool to Query the Millennium Simulation UWS/TAP client

millennium-tap-query is a simple wrapper for the Python package requests to deal with connections to the Millennium TAP Web Client. With this tool you can perform basic or advanced queries to the Millennium Simulation database and download the data products. millennium-tap-query is similar to the TAP query tool in the German Astrophysical Virtual Observatory (GAVO) VOtables package.

[ascl:0101.001]
MILLISEARCH: A Search for Millilensing in BATSE GRB Data

The millisearch.for code was used to generate a new search for the gravitational lens effects of a significant cosmological density of supermassive compact objects (SCOs) on gamma-ray bursts. No signal attributable to millilensing was found. We inspected the timing data of 774 BATSE-triggered GRBs for evidence of millilensing: repeated peaks similar in light-curve shape and spectra. Our null detection leads us to conclude that, in all candidate universes simulated, Omega_{SCO} < 0.1 is favored for 10^{5} < M_{SCO}/M_{odot} < 10^{9}, while in some universes and mass ranges the density limits are as much as 10 times lower. Therefore, a cosmologically significant population of SCOs near globular cluster mass neither came out of the primordial universe, nor condensed at recombination.

[ascl:1911.023]
miluphcuda: Smooth particle hydrodynamics code

Schaefer, Christoph M.; Riecker, Sven; Wandel, Oliver; Maindl, Thomas I.; Scherrer, Samuel; Werner, Janka; Burger, Christoph; Morlock, Marius

miluphcuda is the CUDA port of the original miluph code; it runs on single Nvidia GPUs with compute capability 5.0 and higher and provides fast and efficient computation. The code can be used for hydrodynamical simulations and collision and impact physics, and features self-gravity via Barnes-Hut trees and porosity models such as P-alpha and epsilon-alpha. It can model solid bodies, including ductile and brittle materials, as well as non-viscous fluids, granular media, and porous continua.

[ascl:2001.001]
Min-CaLM: Mineral compositional analysis on debris disk spectra

Min-CaLM performs automated mineral compositional analysis on debris disk spectra. The user inputs the debris disk spectrum, and using Min-CaLM's built-in mineralogical library, Min-CaLM calculates the relative mineral abundances within the disk. To do this calculation, Min-CaLM converts the debris disk spectrum and the mineralogical library spectra into a system of linear equations, which it then solves using non-negative least square minimization. This code comes with a GitHub tutorial on how to use the Min-CaLM package.

[ascl:1302.006]
Minerva: Cylindrical coordinate extension for Athena

Minerva is a cylindrical coordinate extension of the Athena astrophysical MHD code of Stone, Gardiner, Teuben, and Hawley. The extension follows the approach of Athena's original developers and has been designed to alter the existing Cartesian-coordinates code as minimally and transparently as possible. The numerical equations in cylindrical coordinates are formulated to maintain consistency with constrained transport (CT), a central feature of the Athena algorithm, while making use of previously implemented code modules such as the Riemann solvers. Angular momentum transport, which is critical in astrophysical disk systems dominated by rotation, is treated carefully.

[submitted]
MiraPy: Python package for Deep Learning in Astronomy

MiraPy is a Python package for problem-solving in astronomy using Deep Learning for astrophysicist, researchers and students. Current applications of MiraPy are X-Ray Binary classification, ATLAS variable star feature classification, OGLE variable star light-curve classification, HTRU1 dataset classification and Astronomical image reconstruction using encoder-decoder network. It also contains modules for loading various datasets, curve-fitting, visualization and other utilities. It is built using Keras for developing ML models to run on CPU and GPU seamlessly.

[ascl:1106.007]
MIRIAD: Multi-channel Image Reconstruction, Image Analysis, and Display

MIRIAD is a radio interferometry data-reduction package, designed for taking raw visibility data through calibration to the image analysis stage. It has been designed to handle any interferometric array, with working examples for BIMA, CARMA, SMA, WSRT, and ATCA. A separate version for ATCA is available, which differs in a few minor ways from the CARMA version.

[ascl:1110.025]
MIS: A Miriad Interferometry Singledish Toolkit

MIS is a pipeline toolkit using the package MIRIAD to combine Interferometric and Single Dish data. This was prompted by our observations made with the Combined Array For Research in Millimeter-wave Astronomy (CARMA) interferometer of the star-forming region NGC 1333, a large survey highlighting the new 23-element and singledish observing modes. The project consists of 20 CARMA datasets each containing interferometric as well as simultaneously obtained single dish data, for 3 molecular spectral lines and continuum, in 527 different pointings, covering an area of about 8 by 11 arcminutes. A small group of collaborators then shared this toolkit and their parameters via CVS, and scripts were developed to ensure uniform data reduction across the group. The pipeline was run end-to-end each night that new observations were obtained, producing maps that contained all the data to date. This approach could serve as a model for repeated calibration and mapping of large mixed-mode correlation datasets from ALMA.

[ascl:1010.062]
MissFITS: Basic Maintenance and Packaging Tasks on FITS Files

MissFITS is a program that performs basic maintenance and packaging tasks on FITS files using an optimized FITS library. MissFITS can:

- add, edit, and remove FITS header keywords;
- split and join Multi-Extension-FITS (MEF) files;
- unpile and pile FITS data-cubes; and,
- create, check, and update FITS checksums, using R. Seaman’s protocol.

[ascl:1505.011]
missForest: Nonparametric missing value imputation using random forest

missForest imputes missing values particularly in the case of mixed-type data. It uses a random forest trained on the observed values of a data matrix to predict the missing values. It can be used to impute continuous and/or categorical data including complex interactions and non-linear relations. It yields an out-of-bag (OOB) imputation error estimate without the need of a test set or elaborate cross-validation and can be run in parallel to save computation time. missForest has been used to, among other things, impute variable star colors in an All-Sky Automated Survey (ASAS) dataset of variable stars with no NOMAD match.

[ascl:1910.016]
MiSTree: Construct and analyze Minimum Spanning Tree graphs

MiSTree quickly constructs minimum spanning tree graphs for various coordinate systems, including Celestial coordinates, by using a k-nearest neighbor graph (k NN, rather than a matrix of pairwise distances) which is then fed to Kruskal's algorithm to create the graph. MiSTree bins the MST statistics into histograms and plots the distributions; enabling the inclusion of high-order statistics information from the cosmic web to provide additional information that improves cosmological parameter constraints. Though MiSTree was designed for use in cosmology, it can be used in any field requiring extracting non-Gaussian information from point distributions.

[ascl:1409.001]
mixT: single-temperature fit for a multi-component thermal plasma

mixT accurately predicts T derived from a single-temperature fit for a multi-component thermal plasma. It can be applied in the deprojection analysis of objects with the temperature and metallicity gradients, for correction of the PSF effects, for consistent comparison of numerical simulations of galaxy clusters and groups with the X-ray observations, and for estimating how emission from undetected components can bias the global X-ray spectral analysis.

[ascl:1206.010]
mkj_libs: Helper routines for plane-fitting & analysis tools

mkj_libs provides a set of helper routines (vector operations, astrometry, statistical analysis of spherical data) for the main plane-fitting and analysis tools.

[ascl:0104.001]
MLAPM: Simulating Structure Formation from Collisionless Matter

MLAPM simulates structure formation from collisionless matter. The code, written in C, is purely grid-based and uses a recursively refined Cartesian grid to solve Poisson's equation for the potential, rather than obtaining the potential from a Green's function. Refinements can have arbitrary shapes and in practice closely follow the complex morphology of the density field that evolves. The timestep shortens by a factor two with each successive refinement. It is argued that an appropriate choice of softening length is of great importance and that the softening should be at all points an appropriate multiple of the local inter-particle separation. Unlike tree and P3M codes, multigrid codes automatically satisfy this requirement.

[ascl:1403.003]
MLZ: Machine Learning for photo-Z

The parallel Python framework MLZ (Machine Learning and photo-Z) computes fast and robust photometric redshift PDFs using Machine Learning algorithms. It uses a supervised technique with prediction trees and random forest through TPZ that can be used for a regression or a classification problem, or a unsupervised methods with self organizing maps and random atlas called SOMz. These machine learning implementations can be efficiently combined into a more powerful one resulting in robust and accurate probability distributions for photometric redshifts.

[ascl:1412.010]
MMAS: Make Me A Star

Make Me A Star (MMAS) quickly generates stellar collision remnants and can be used in combination with realistic dynamical simulations of star clusters that include stellar collisions. The code approximates the merger process (including shock heating, hydrodynamic mixing, mass ejection, and angular momentum transfer) with simple algorithms based on conservation laws and a basic qualitative understanding of the hydrodynamics. These simple models agree very well with those from SPH (smoothed particle hydrodynamics) calculations of stellar collisions, and the subsequent stellar evolution of these models also matches closely that of the more accurate hydrodynamic models.

[ascl:1905.005]
MMIRS-DRP: MMIRS Data Reduction Pipeline

The MMIRS data reduction pipeline provides complete and flexible data reduction for long-slit and multi-slit spectroscopic observations collected using the MMT and Magellan Infrared Spectrograph (MMIRS). Written in IDL, it offers sky subtraction, correction for telluric absorpition, and is fast enough to permit real-time data reduction for quality control.

[ascl:1110.010]
MOCASSIN: MOnte CArlo SimulationS of Ionized Nebulae

MOCASSIN is a fully 3D or 2D photoionisation and dust radiative transfer code which employs a Monte Carlo approach to the transfer of radiation through media of arbitrary geometry and density distribution. Written in Fortran, it was originally developed for the modelling of photoionised regions like HII regions and planetary nebulae and has since expanded and been applied to a variety of astrophysical problems, including modelling clumpy dusty supernova envelopes, star forming galaxies, protoplanetary disks and inner shell fluorence emission in the photospheres of stars and disk atmospheres. The code can deal with arbitrary Cartesian grids of variable resolution, it has successfully been used to model complex density fields from SPH calculations and can deal with ionising radiation extending from Lyman edge to the X-ray. The dust and gas microphysics is fully coupled both in the radiation transfer and in the thermal balance.

[ascl:1010.009]
ModeCode: Bayesian Parameter Estimation for Inflation

ModeCode is a publicly available code that computes the primordial scalar and tensor power spectra for single field inflationary models. ModeCode solves the inflationary mode equations numerically, avoiding the slow roll approximation. It provides an efficient and robust numerical evaluation of the inflationary perturbation spectrum, and allows the free parameters in the inflationary potential to be estimated within an MCMC computation. ModeCode also allows the estimation of reheating uncertainties once a potential has been specified. It is interfaced with CAMB and CosmoMC to compute cosmic microwave background angular power spectra and perform likelihood analysis and parameter estimation. It can be run as a standalone code as well. Errors in the results from ModeCode contribute negligibly to the error budget for analyses of data from Planck or other next generation experiments.

[ascl:1109.023]
MOKA: A New Tool for Strong Lensing Studies

MOKA simulates the gravitational lensing signal from cluster-sized haloes. This algorithm implements recent results from numerical simulations to create realistic lenses with properties independent of numerical resolution and can be used for studies of the strong lensing cross section in dependence of halo structure.

[ascl:1501.013]
Molecfit: Telluric absorption correction tool

Smette, A.; Kausch, W; Sana, H; Noll, S.; Horst, H.; Kimeswenger, S.; Barden, M; Szyszka, C.; Jones, A. M.; Gallene, A.; Vinther, J.; Ballester, P.; Kerber, F.

Molecfit corrects astronomical observations for atmospheric absorption features based on fitting synthetic transmission spectra to the astronomical data, which saves a significant amount of valuable telescope time and increases the instrumental efficiency. Molecfit can also estimate molecular abundances, especially the water vapor content of the Earth’s atmosphere. The tool can be run from a command-line or more conveniently through a GUI.

[ascl:1212.004]
MOLIERE-5: Forward and inversion model for sub-mm wavelengths

MOLIERE-5 (Microwave Observation LIne Estimation and REtrieval) is a versatile forward and inversion model for the millimeter and submillimeter wavelengths range and includes an inversion model. The MOLIERE-5 forward model includes modules for the calculation of absorption coefficients, radiative transfer, and instrumental characteristics. The radiative transfer model is supplemented by a sensitivity module for estimating the contribution to the spectrum of each catalog line at its center frequency enabling the model to effectively filter for small spectral lines. The instrument model consists of several independent modules, including the calculation of the convolution of spectra and weighting functions with the spectrometer response functions. The instrument module also provides several options for modeling of frequency-switched observations. The MOLIERE-5 inversion model calculates linear Optimal Estimation, a least-squares retrieval method which uses statistical apriori knowledge on the retrieved parameters for the regularization of ill-posed inversion problems and computes diagnostics such as the measurement and smoothing error covariance matrices along with contribution and averaging kernel functions.

[ascl:1907.012]
molly: 1D astronomical spectra analyzer

molly analyzes 1D astronomical spectra. Its prime purpose is for handling large numbers of similar spectra (*e.g.,* time series spectroscopy), but it contains many of the standard operations used for normal spectrum analysis as well. It overlaps with the various similar programs such as dipso (ascl:1405.016) and has strengths (particularly for time series spectra) and weaknesses compared to them.

[ascl:1206.004]
MOLSCAT: MOLecular SCATtering

MOLSCAT is a FORTRAN code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem and was developed to obtain collision rates for molecules in the interstellar gas which are needed to understand microwave and infrared astronomical observations. The code is implemented for various types of collision partners. In addition to the essentially exact close coupling method several approximate methods, including the Coupled States and Infinite Order Sudden approximations, are provided.

[ascl:1908.002]
Molsoft: Molonglo Telescope Observing Software

Molsoft operates, monitors and schedules observations, both through predetermined schedule files and fully dynamically, at the refurbished Molonglo Observatory Synthesis Radio Telescope (MOST). It was developed as part of the UTMOST upgrade of the facility. The software runs a large-scale pulsar timing program; the autonomous observing system and the dynamic scheduler have increased the observing efficiency by a factor of 2-3 in comparison with static scheduling.

[ascl:1010.036]
Montage: An Astronomical Image Mosaicking Toolkit

Jacob, Joseph C.; Katz, Daniel S.; Berriman, G. Bruce; Good, John; Laity, Anastasia C.; Deelman, Ewa; Kesselman, Carl; Singh, Gurmeet; Su, Mei-Hui; Prince, Thomas A.; Williams, Roy

Montage is an open source code toolkit for assembling Flexible Image Transport System (FITS) images into custom mosaics. It runs on all common Linux/Unix platforms, on desktops, clusters and computational grids, and supports all World Coordinate System (WCS) projections and common coordinate systems. Montage preserves spatial and calibration fidelity of input images, processes 40 million pixels in up to 32 minutes on 128 nodes on a Linux cluster, and provides independent engines for analyzing the geometry of images on the sky, re-projecting images, rectifying background emission to a common level, and co-adding images. It offers convenient tools for managing and manipulating large image files.

[ascl:1502.006]
Montblanc: GPU accelerated Radio Interferometer Measurement Equations in support of Bayesian Inference for Radio Observations

Montblanc, written in Python, is a GPU implementation of the Radio interferometer measurement equation (RIME) in support of the Bayesian inference for radio observations (BIRO) technique. The parameter space that BIRO explores results in tens of thousands of computationally expensive RIME evaluations before reduction to a single *X ^{2}* value. The RIME is calculated over four dimensions, time, baseline, channel and source and the values in this 4D space can be independently calculated; therefore, the RIME is particularly amenable to a parallel implementation accelerated by Graphics Programming Units (GPUs). Montblanc is implemented for NVIDIA's CUDA architecture and outperforms MeqTrees (ascl:1209.010) and OSKAR.

[ascl:1307.002]
Monte Python: Monte Carlo code for CLASS in Python

Monte Python is a parameter inference code which combines the flexibility of the python language and the robustness of the cosmological code CLASS into a simple and easy to manipulate Monte Carlo Markov Chain code.

This version has been archived and replaced by MontePython 3 (ascl:1805.027).

[ascl:1805.027]
MontePython 3: Parameter inference code for cosmology

MontePython 3 provides numerous ways to explore parameter space using Monte Carlo Markov Chain (MCMC) sampling, including Metropolis-Hastings, Nested Sampling, Cosmo Hammer, and a Fisher sampling method. This improved version of the Monte Python (ascl:1307.002) parameter inference code for cosmology offers new ingredients that improve the performance of Metropolis-Hastings sampling, speeding up convergence and offering significant time improvement in difficult runs. Additional likelihoods and plotting options are available, as are post-processing algorithms such as Importance Sampling and Adding Derived Parameter.

[ascl:1202.009]
MOOG: LTE line analysis and spectrum synthesis

MOOG performs a variety of LTE line analysis and spectrum synthesis tasks. The typical use of MOOG is to assist in the determination of the chemical composition of a star. The basic equations of LTE stellar line analysis are followed. The coding is in various subroutines that are called from a few driver routines; these routines are written in standard FORTRAN. The standard MOOG version has been developed on unix, linux and macintosh computers.

One of the chief assets of MOOG is its ability to do on-line graphics. The plotting commands are given within the FORTRAN code. MOOG uses the graphics package SM, chosen for its ease of implementation in FORTRAN codes. Plotting calls are concentrated in just a few routines, and it should be possible for users of other graphics packages to substitute other appropriate FORTRAN commands.

[ascl:1308.018]
MoogStokes: Zeeman polarized radiative transfer

MOOGStokes is a version of the MOOG one-dimensional local thermodynamic equilibrium radiative transfer code that incorporates a Stokes vector treatment of polarized radiation through a magnetic medium. It consists of three complementary programs that together can synthesize the disk-averaged emergent spectrum of a star with a magnetic field. The MOOGStokes package synthesizes emergent spectra of stars with magnetic fields in a familiar computational framework and produces disk-averaged spectra for all Stokes vectors ( I, Q, U, V ), normalized by the continuum.

[ascl:1111.006]
MOPEX: MOsaicker and Point source EXtractor

MOPEX (MOsaicker and Point source EXtractor) is a package for reducing and analyzing imaging data, as well as MIPS SED data. MOPEX includes the point source extraction package, APEX.

MOPEX is designed to allow the user to:

- perform sophisticated background matching of individual data frames
- mosaic the individual frames downloaded from the Spitzer archive
- perform both temporal and spatial outlier rejection during mosaicking
- apply offline pointing refinement for MIPS data (refinement is already applied to IRAC data)
- perform source detection on the mosaics using APEX
- compute aperture photometry or PRF-fitting photometry for point sources
- perform interpolation, coaddition, and spectrum extraction of MIPS SED images.

[ascl:1303.011]
MOPSIC: Extended Version of MOPSI

MOPSIC was created to analyze bolometer data but can be used for much more versatile tasks. It is an extension of MOPSI; this software had been merged with the command interpreter of GILDAS. For data reduction, MOPSIC uses a special method to calculate the chopped signal. This gives much better results than the straight difference of the signals obtained at both chopper positions. In addition there are also scripts to reduce pointings, skydips, and to calculate the RCPs (Receiver Channel Parameters) from calibration maps. MOPSIC offers a much broader range of applications including advanced planning functions for mapping and onoff observations, post-reduction data analysis and processing and even reduction of non-bolometer data (optical, IR, spectroscopy).

[ascl:1911.014]
MORDI: Massively-Overlapped Ring-Diagram Inversion

MORDI (Massively-Overlapped Ring-Diagram Inversion) performs three-dimensional ring-diagram inversions. The code reads in frequency shift measurements and their associated sensitivity kernels and outputs two-dimensional slices of the subsurface flow field at a constant depth and (optionally) the associated averaging kernels. It relies on both distributed-memory (MPI) and shared-memory (OpenMP) parallelism to scale efficiently up to a few thousand processors, but can also run reasonably well on small machines (1-4 cpus). The actions of the code are modified by command-line parameters, which enable a significant amount of flexibility when setting up an inversion.

[ascl:1906.013]
MORPHEUS: A 3D Eulerian Godunov MPI-OpenMP hydrodynamics code with multiple grid geometries

MORPHEUS (Manchester Omni-geometRical Program for Hydrodynamical EUlerian Simulations) is a 3D hydrodynamical code used to simulate astrophysical fluid flows. It has three different grid geometries (cartesian, spherical, and cylindrical) and uses a second-order Godunov method to solve the equations of hydrodynamics. Physical modules also include radiative cooling and gravity, and a hybrid MPI-OpenMP parallelization allows computations to be run on large-scale architectures. MORPHEUS is written in Fortran90 and does not require any libraries (apart from MPI) to run.

[ascl:1906.012]
Morpheus: Library to generate morphological semantic segmentation maps of astronomical images

Morpheus generates pixel level morphological classifications of astronomical sources by leveraging advances in deep learning to perform source detection, source segmentation, and morphological classification pixel-by-pixel via a semantic segmentation algorithm adopted from the field of computer vision. By utilizing morphological information about the flux of real astronomical sources during object detection, Morpheus shows resiliency to false positive identifications of sources.

[ascl:1908.007]
MosfireDRP: MOSFIRE Data Reduction Pipeline

MosfireDRP reduces data from the MOSFIRE spectrograph of the Keck Observatory; it produces flat-fielded, wavelength calibrated, rectified, and stacked 2D spectrograms for each slit on a given mask in nearly real time. Background subtraction is performed in two states: a simple pairwise subtraction of interleaved stacks, and then fitting a 2D b-spline model to the background residuals.

[ascl:1710.006]
MOSFiT: Modular Open-Source Fitter for Transients

Guillochon, James; Nicholl, Matt; Villar, V. Ashley; Mockler, Brenna; Narayan, Gautham; Mandel, Kaisey S.; Berger, Edo; Williams, Peter K. G.

MOSFiT (Modular Open-Source Fitter for Transients) downloads transient datasets from open online catalogs (e.g., the Open Supernova Catalog), generates Monte Carlo ensembles of semi-analytical light curve fits to those datasets and their associated Bayesian parameter posteriors, and optionally delivers the fitting results back to those same catalogs to make them available to the rest of the community. MOSFiT helps bridge the gap between observations and theory in time-domain astronomy; in addition to making the application of existing models and creation of new models as simple as possible, MOSFiT yields statistically robust predictions for transient characteristics, with a standard output format that includes all the setup information necessary to reproduce a given result.

[ascl:1611.003]
MPDAF: MUSE Python Data Analysis Framework

MPDAF, the MUSE Python Data Analysis Framework, provides tools to work with MUSE-specific data (for example, raw data and pixel tables), and with more general data such as spectra, images, and data cubes. Originally written to work with MUSE data, it can also be used for other data, such as that from the Hubble Space Telescope. MPDAF also provides MUSELET, a SExtractor-based tool to detect emission lines in a data cube, and a format to gather all the information on a source in one FITS file. MPDAF was developed and is maintained by CRAL (Centre de Recherche Astrophysique de Lyon).

[ascl:1208.019]
MPFIT: Robust non-linear least squares curve fitting

These IDL routines provide a robust and relatively fast way to perform least-squares curve and surface fitting. The algorithms are translated from MINPACK-1, which is a rugged minimization routine found on Netlib, and distributed with permission. This algorithm is more desirable than CURVEFIT because it is generally more stable and less likely to crash than the brute-force approach taken by CURVEFIT, which is based upon Numerical Recipes.

[ascl:1304.014]
MPgrafic: A parallel MPI version of Grafic-1

MPgrafic is a parallel MPI version of Grafic-1 which can produce large cosmological initial conditions on a cluster without requiring shared memory. The real Fourier transforms are carried in place using fftw while minimizing the amount of used memory (at the expense of performance) in the spirit of Grafic-1. The writing of the output file is also carried in parallel. In addition to the technical parallelization, it provides three extensions over Grafic-1:

- it can produce power spectra with baryon wiggles (DJ Eisenstein and W. Hu, Ap. J. 496);
- it has the optional ability to load a lower resolution noise map corresponding to the low frequency component which will fix the larger scale modes of the simulation (extra flag 0/1 at the end of the input process) in the spirit of Grafic-2;
- it can be used in conjunction with constrfield, which generates initial conditions phases from a list of local constraints on density, tidal field density gradient and velocity.

[ascl:1712.002]
MPI_XSTAR: MPI-based parallelization of XSTAR program

MPI_XSTAR parallelizes execution of multiple XSTAR runs using Message Passing Interface (MPI). XSTAR (ascl:9910.008), part of the HEASARC's HEAsoft (ascl:1408.004) package, calculates the physical conditions and emission spectra of ionized gases. MPI_XSTAR invokes XSTINITABLE from HEASoft to generate a job list of XSTAR commands for given physical parameters. The job list is used to make directories in ascending order, where each individual XSTAR is spawned on each processor and outputs are saved. HEASoft's XSTAR2TABLE program is invoked upon the contents of each directory in order to produce table model FITS files for spectroscopy analysis tools.

[ascl:1208.014]
MPI-AMRVAC: MPI-Adaptive Mesh Refinement-Versatile Advection Code

van der Holst, Bar; Keppens, Rony; Meliani, Zakaria; Porth, Oliver; van Marle, Allard Jan; Delmont, Peter; Xia, Chun

MPI-AMRVAC is an MPI-parallelized Adaptive Mesh Refinement code, with some heritage (in the solver part) to the Versatile Advection Code or VAC, initiated by Gábor Tóth at the Astronomical Institute at Utrecht in November 1994, with help from Rony Keppens since 1996. Previous incarnations of the Adaptive Mesh Refinement version of VAC were of restricted use only, and have been used for basic research in AMR strategies, or for well-targeted applications. This MPI version uses a full octree block-based approach, and allows for general orthogonal coordinate systems. MPI-AMRVAC aims to advance any system of (primarily hyperbolic) partial differential equations by a number of different numerical schemes. The emphasis is on (near) conservation laws, with shock-dominated problems as a main research target. The actual equations are stored in separate modules, can be added if needed, and they can be selected by a simple configuration of the VACPP preprocessor. The dimensionality of the problem is also set through VACPP. The numerical schemes are able to handle discontinuities and smooth flows as well.

[ascl:1106.022]
MPI-Defrost: Extension of Defrost to MPI-based Cluster Environment

MPI-Defrost extends Frolov’s Defrost to an MPI-based cluster environment. This version has been restricted to a single field. Restoring two-field support should be straightforward, but will require some code changes. Some output options may also not be fully supported under MPI.

This code was produced to support our own work, and has been made available for the benefit of anyone interested in either oscillon simulations or an MPI capable version of Defrost, and it is provided on an "as-is" basis. Andrei Frolov is the primary developer of Defrost and we thank him for placing his work under the GPL (GNU Public License), and thus allowing us to distribute this modified version.

[ascl:1212.003]
MPWide: Light-weight communication library for distributed computing

MPWide is a light-weight communication library for distributed computing. It is specifically developed to allow message passing over long-distance networks using path-specific optimizations. An early version of MPWide was used in the Gravitational Billion Body Project to allow simulations across multiple supercomputers.

[ascl:1912.020]
MRExo: Non-parametric mass-radius relationship for exoplanets

MRExo performs non-parametric fitting and analysis of the mass-radius (M-R) relationship for exoplanets. Written in Python, it offers tools for fitting the M-R relationship to a given data set and also includes predicting (M->R, and R->M) and plotting functions.

[ascl:1102.005]
MRLENS: Multi-Resolution methods for gravitational LENSing

The MRLENS package offers a new method for the reconstruction of weak lensing mass maps. It uses the multiscale entropy concept, which is based on wavelets, and the False Discovery Rate which allows us to derive robust detection levels in wavelet space. We show that this new restoration approach outperforms several standard techniques currently used for weak shear mass reconstruction. This method can also be used to separate E and B modes in the shear field, and thus test for the presence of residual systematic effects. We concentrate on large blind cosmic shear surveys, and illustrate our results using simulated shear maps derived from N-Body Lambda-CDM simulations with added noise corresponding to both ground-based and space-based observations.

[ascl:1809.015]
MrMoose: Multi-Resolution Multi-Object/Origin Spectral Energy distribution fitting procedure

MrMoose (Multi-Resolution Multi-Object/Origin Spectral Energy) fits user-defined models onto a set of multi-wavelength data using a Bayesian framework. The code can handle blended sources, large variation in resolution, and even upper limits consistently. It also generates a series of outputs allowing for an quick interpretation of the results. The code uses emcee (ascl:1303.002), and saves the emcee sampler object, thus allowing users to transfer the output to a personal graphical interface.

[ascl:1802.015]
mrpy: Renormalized generalized gamma distribution for HMF and galaxy ensemble properties comparisons

mrpy calculates the MRP parameterization of the Halo Mass Function. It calculates basic statistics of the truncated generalized gamma distribution (TGGD) with the TGGD class, including mean, mode, variance, skewness, pdf, and cdf. It generates MRP quantities with the MRP class, such as differential number counts and cumulative number counts, and offers various methods for generating normalizations. It can generate the MRP-based halo mass function as a function of physical parameters via the mrp_b13 function, and fit MRP parameters to data in the form of arbitrary curves and in the form of a sample of variates with the SimFit class. mrpy also calculates analytic hessians and jacobians at any point, and allows the user to alternate parameterizations of the same form via the reparameterize module.

[ascl:1504.016]
MRrelation: Posterior predictive mass distribution

MRrelation calculates the posterior predictive mass distribution for an individual planet. The probabilistic mass-radius relationship (M-R relation) is evaluated within a Bayesian framework, which both quantifies this intrinsic dispersion and the uncertainties on the M-R relation parameters.

[ascl:1112.010]
MRS3D: 3D Spherical Wavelet Transform on the Sphere

Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D Spherical Fourier-Bessel (SFB) analysis is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. We present a new fast Discrete Spherical Fourier-Bessel Transform (DSFBT) based on both a discrete Bessel Transform and the HEALPIX angular pixelisation scheme. We tested the 3D wavelet transform and as a toy-application, applied a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and found we can successfully remove noise without much loss to the large scale structure. The new spherical 3D isotropic wavelet transform, called MRS3D, is ideally suited to analysing and denoising future 3D spherical cosmological surveys; it uses a novel discrete spherical Fourier-Bessel Transform. MRS3D is based on two packages, IDL and Healpix and can be used only if these two packages have been installed.

[ascl:1709.007]
MSSC: Multi-Source Self-Calibration

Multi-Source Self-Calibration (MSSC) provides direction-dependent calibration to standard phase referencing. The code combines multiple faint sources detected within the primary beam to derive phase corrections. Each source has its CLEAN model divided into the visibilities which results in multiple point sources that are stacked in the uv plane to increase the S/N, thus permitting self-calibration. This process applies only to wide-field VLBI data sets that detect and image multiple sources within one epoch.

[ascl:1701.006]
MSWAVEF: Momentum-Space Wavefunctions

MSWAVEF calculates hydrogenic and non-hydrogenic momentum-space electronic wavefunctions. Such wavefunctions are often required to calculate various collision processes, such as excitation and line broadening cross sections. The hydrogenic functions are calculated using the standard analytical expressions. The non-hydrogenic functions are calculated within quantum defect theory according to the method of Hoang Binh and van Regemorter (1997). Required Hankel transforms have been determined analytically for angular momentum quantum numbers ranging from zero to 13 using Mathematica. Calculations for higher angular momentum quantum numbers are possible, but slow (since calculated numerically). The code is written in IDL.

[ascl:1710.011]
mTransport: Two-point-correlation function calculator

mTransport computes the 2-point-correlation function of the curvature and tensor perturbations in multifield models of inflation in the presence of a curved field space. It is a Mathematica implementation of the transport method which encompasses scenarios with violations of slow-roll conditions and turns of the trajectory in field space. It can be used for an arbitrary mass spectrum, including massive modes, particle production and models with quasi-single-field dynamics.

[ascl:1811.012]
muLAn: gravitational MICROlensing Analysis Software

muLAn analyzes and fits light curves of gravitational microlensing events. The code includes all classical microlensing models (for example, single and binary microlenses, ground- and space-based parallax effects, orbital motion, finite-source effects, and limb-darkening); these can be combined into several time intervals of the analyzed light curve. Minimization methods include an Affine-Invariant Ensemble Sampler to generate a multivariate proposal function while running several Markov Chain Monte Carlo (MCMC) chains, for the set of parameters which is chosen to be fit; non-fitting parameters can be either kept fixed or set on a grid defined by the user. Furthermore, the software offers a model-free option to align all data sets together and allow inspection the light curve before any modeling work. It also comes with many useful routines (export publication-quality figures, data formatting and cleaning) and state-of-the-art statistical tools.

Modeling results can be interpreted using an interactive html page which contains all information about the light curve model, caustics, source trajectory, best-fit parameters and chi-square. Parameters uncertainties and statistical properties (such as multi-modal features of the posterior density) can be assessed from correlation plots. The code is modular, allowing the addition of other computation or minimization routines by directly adding their Python files without modifying the main code. The software has been designed to be easy to use even for the newcomer in microlensing, with external, synthetic and self-explanatory setup files containing all important commands and option settings. The user may choose to launch the code through command line instructions, or to import muLAn within another Python project like any standard Python package.

[ascl:1803.006]
MulensModel: Microlensing light curves modeling

MulensModel calculates light curves of microlensing events. Both single and binary lens events are modeled and various higher-order effects can be included: extended source (with limb-darkening), annual microlensing parallax, and satellite microlensing parallax. The code is object-oriented and written in Python3, and requires AstroPy (ascl:1304.002).

[ascl:1506.004]
multiband_LS: Multiband Lomb-Scargle Periodograms

The multiband periodogram is a general extension of the well-known Lomb-Scargle approach for detecting periodic signals in time-domain data. In addition to advantages of the Lomb-Scargle method such as treatment of non-uniform sampling and heteroscedastic errors, the multiband periodogram significantly improves period finding for randomly sampled multiband light curves (e.g., Pan-STARRS, DES and LSST). The light curves in each band are modeled as arbitrary truncated Fourier series, with the period and phase shared across all bands.

[ascl:1909.002]
MultiColorFits: Colorize and combine multiple fits images for visually aesthetic scientific plots

MultiColorFits is a tool to colorize and combine multiple fits images for making visually aesthetic scientific plots. The standard method to make color composites by combining fits images programmatically in python is to assign three images as separate red, green, and blue channels. This can produce unsatisfactory results for a variety of reasons, such as when less than three images are available, or additional images are desired to be shown. MultiColorFits breaks these limitations by allowing users to apply any color to a given image, not just red, green, or blue. Composites can then be created from an arbitrary number of images. Controls are included for stretching brightness scales with common functions.

[ascl:1109.006]
MultiNest: Efficient and Robust Bayesian Inference

We present further development and the first public release of our multimodal nested sampling algorithm, called MultiNest. This Bayesian inference tool calculates the evidence, with an associated error estimate, and produces posterior samples from distributions that may contain multiple modes and pronounced (curving) degeneracies in high dimensions. The developments presented here lead to further substantial improvements in sampling efficiency and robustness, as compared to the original algorithm presented in Feroz & Hobson (2008), which itself significantly outperformed existing MCMC techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MultiNest algorithm is demonstrated by application to two toy problems and to a cosmological inference problem focusing on the extension of the vanilla $Lambda$CDM model to include spatial curvature and a varying equation of state for dark energy. The MultiNest software is fully parallelized using MPI and includes an interface to CosmoMC (ascl:1106.025). It will also be released as part of the SuperBayeS package (ascl:1109.007) for the analysis of supersymmetric theories of particle physics.

[ascl:1109.008]
Multipole Vectors: Decomposing Functions on a Sphere

We propose a novel representation of cosmic microwave anisotropy maps, where each multipole order l is represented by l unit vectors pointing in directions on the sky and an overall magnitude. These "multipole vectors and scalars" transform as vectors under rotations. Like the usual spherical harmonics, multipole vectors form an irreducible representation of the proper rotation group SO(3). However, they are related to the familiar spherical harmonic coefficients, alm, in a nonlinear way, and are therefore sensitive to different aspects of the CMB anisotropy. Nevertheless, it is straightforward to determine the multipole vectors for a given CMB map and we present an algorithm to compute them. Using the WMAP full-sky maps, we perform several tests of the hypothesis that the CMB anisotropy is statistically isotropic and Gaussian random. We find that the result from comparing the oriented area of planes defined by these vectors between multipole pairs 2<=l1!=l2<=8 is inconsistent with the isotropic Gaussian hypothesis at the 99.4% level for the ILC map and at 98.9% level for the cleaned map of Tegmark et al. A particular correlation is suggested between the l=3 and l=8 multipoles, as well as several other pairs. This effect is entirely different from the now familiar planarity and alignment of the quadrupole and octupole: while the aforementioned is fairly unlikely, the multipole vectors indicate correlations not expected in Gaussian random skies that make them unusually likely. The result persists after accounting for pixel noise and after assuming a residual 10% dust contamination in the cleaned WMAP map. While the definitive analysis of these results will require more work, we hope that multipole vectors will become a valuable tool for various cosmological tests, in particular those of cosmic isotropy.

[ascl:1704.014]
Multipoles: Potential gain for binary lens estimation

Multipoles, written in Python, calculates the quadrupole and hexadecapole approximations of the finite-source magnification: quadrupole (Wk,rho,Gamma) and hexadecapole (Wk,rho,Gamma). The code is efficient and faster than previously available methods, and could be generalized for use on large portions of the light curves.

[ascl:1402.006]
Munipack: General astronomical image processing software

Munipack provides easy-to-use tools for all astronomical astrometry and photometry, access to Virtual Observatory as well as FITS files operations and a simple user interface along with a powerful processing engine. Its many features include a FITS images viewer that allows for basic (astronomical) operations with frames, advanced image processor supporting an infinite dynamic range and advanced color management, and astrometric calibration of images. The astrometry module uses robust statistical estimators and algorithms. The photometry module provides the classical method detection of stars and implements the aperture photometry, calibrated on the basis of photon statistics, and allows for the automatic detection and aperture photometry of stars; calibration on absolute fluxes is possible. The software also provides a standard way to correct for all the bias, dark and flat-field frames, and many other features.

[ascl:1605.007]
MUSCLE: MUltiscale Spherical-ColLapse Evolution

MUSCLE (MUltiscale Spherical ColLapse Evolution) produces low-redshift approximate N-body realizations accurate to few-Megaparsec scales. It applies a spherical-collapse prescription on multiple Gaussian-smoothed scales. It achieves higher accuracy than perturbative schemes (Zel'dovich and second-order Lagrangian perturbation theory - 2LPT), and by including the void-in-cloud process (voids in large-scale collapsing regions), solves problems with a single-scale spherical-collapse scheme.

[ascl:1610.004]
MUSE-DRP: MUSE Data Reduction Pipeline

The MUSE pipeline turns the complex raw data of the MUSE integral field spectrograph into a ready-to-use datacube for scientific analysis.

[ascl:1311.011]
MUSIC: MUlti-Scale Initial Conditions

MUSIC generates multi-scale initial conditions with multiple levels of refinements for cosmological ‘zoom-in’ simulations. The code uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). MUSIC achieves rms relative errors of the order of 10−4 for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier space-induced interference ringing.

[ascl:1203.009]
MYRIAD: N-body code for simulations of star clusters

MYRIAD is a C++ code for collisional N-body simulations of star clusters. The code uses the Hermite fourth-order scheme with block time steps, for advancing the particles in time, while the forces and neighboring particles are computed using the GRAPE-6 board. Special treatment is used for close encounters, binary and multiple sub-systems that either form dynamically or exist in the initial configuration. The structure of the code is modular and allows the appropriate treatment of more physical phenomena, such as stellar and binary evolution, stellar collisions and evolution of close black-hole binaries. Moreover, it can be easily modified so that the part of the code that uses GRAPE-6 could be replaced by another module that uses other accelerating-hardware like the Graphics Processing Units (GPUs). Appropriate choice of the free parameters give a good accuracy and speed for simulations of star clusters up to and beyond core collapse. The code accuracy becomes comparable and even better than the accuracy of existing codes when a number of close binary systems is dynamically created in a simulation; this is due to the high accuracy of the method that is used for close binary and multiple sub-systems. The code can be used for evolving star clusters containing equal-mass stars or star clusters with an initial mass function (IMF) containing an intermediate mass black hole (IMBH) at the center and/or a fraction of primordial binaries, which are systems of particular astrophysical interest.

[ascl:1502.003]
N-GenIC: Cosmological structure initial conditions

N-GenIC is an initial conditions code for cosmological structure formation that can be used to set-up random N-body realizations of Gaussian random fields with a prescribed power spectrum in a homogeneously sampled periodic box. The code creates cosmological initial conditions based on the Zeldovich approximation, in a format directly compatible with GADGET or AREPO.

[ascl:1102.001]
N-MODY: A Code for Collisionless N-body Simulations in Modified Newtonian Dynamics

N-MODY is a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

[ascl:1411.014]
NAFE: Noise Adaptive Fuzzy Equalization

NAFE (Noise Adaptive Fuzzy Equalization) is an image processing method allowing for visualization of fine structures in SDO AIA high dynamic range images. It produces artifact-free images and gives significantly better results than methods based on convolution or Fourier transform.

[ascl:1409.009]
Nahoon: Time-dependent gas-phase chemical model

Nahoon is a gas-phase chemical model that computes the chemical evolution in a 1D temperature and density structure. It uses chemical networks downloaded from the KInetic Database for Astrochemistry (KIDA) but the model can be adapted to any network. The program is written in Fortran 90 and uses the DLSODES (double precision) solver from the ODEPACK package (ascl:1905.021) to solve the coupled stiff differential equations. The solver computes the chemical evolution of gas-phase species at a fixed temperature and density and can be used in one dimension (1D) if a grid of temperature, density, and visual extinction is provided. Grains, both neutral and negatively charged, and electrons are considered as chemical species and their concentrations are computed at the same time as those of the other species. Nahoon contains a test to check the temperature range of the validity of the rate coefficients and avoid extrapolations outside this range. A test is also included to check for duplication of chemical reactions, defined over complementary ranges of temperature.

[ascl:1708.022]
Naima: Derivation of non-thermal particle distributions through MCMC spectral fitting

Naima computes non-thermal radiation from relativistic particle populations. It includes tools to perform MCMC fitting of radiative models to X-ray, GeV, and TeV spectra using emcee (ascl:1303.002), an affine-invariant ensemble sampler for Markov Chain Monte Carlo. Naima is an Astropy (ascl:1304.002) affiliated package.

[ascl:1803.004]
nanopipe: Calibration and data reduction pipeline for pulsar timing

nanopipe is a data reduction pipeline for calibration, RFI removal, and pulse time-of-arrival measurement from radio pulsar data. It was developed primarily for use by the NANOGrav project. nanopipe is written in Python, and depends on the PSRCHIVE (ascl:1105.014) library.

[ascl:1905.020]
NAPLES: Numerical Analysis of PLanetary EncounterS

NAPLES (Numerical Analysis of PLanetary EncounterS) performs batch propagations of close encounters in the three-body problem and computes the numerical error with respect to reference trajectories computed in quadruple precision. It uses the LSODAR integrator from ODEPACK (ascl:1905.021) and the equations of motion correspond to several regularized formulations.

[ascl:1102.006]
NBODY Codes: Numerical Simulations of Many-body (N-body) Gravitational Interactions

I review the development of direct N-body codes at Cambridge over nearly 40 years, highlighting the main stepping stones. The first code (NBODY1) was based on the simple concepts of a force polynomial combined with individual time steps, where numerical problems due to close encounters were avoided by a softened potential. Fortuitously, the elegant Kustaanheimo-Stiefel two-body regularization soon permitted small star clusters to be studied (NBODY3). Subsequent extensions to unperturbed three-body and four-body regularization proved beneficial in dealing with multiple interactions. Investigations of larger systems became possible with the Ahmad-Cohen neighbor scheme which was used more than 20 years ago for expanding universe models of 4000 galaxies (NBODY2). Combining the neighbor scheme with the regularization procedures enabled more realistic star clusters to be considered (NBODY5). After a period of simulations with no apparent technical progress, chain regularization replaced the treatment of compact subsystems (NBODY3, NBODY5). More recently, the Hermite integration method provided a major advance and has been implemented on the special-purpose HARP computers (NBODY4) together with an alternative version for workstations and supercomputers (NBODY6). These codes also include a variety of algorithms for stellar evolution based on fast lookup functions. The treatment of primordial binaries contains efficient procedures for chaotic two-body motion as well as tidal circularization, and special attention is paid to hierarchical systems and their stability. This family of N-body codes constitutes a powerful tool for dynamical simulations which is freely available to the astronomical community, and the massive effort owes much to collaborators.

[ascl:1502.010]
nbody6tt: Tidal tensors in N-body simulations

nbody6tt, based on Aarseth's nbody6 (ascl:1102.006) code, includes the treatment of complex galactic tides in a direct N-body simulation of a star cluster through the use of tidal tensors (tt) and offers two complementary methods. The first allows consideration of any kind of galaxy and orbit, thus offering versatility; this method cannot be used to study tidal debris, as it relies on the tidal approximation (linearization of the tidal force). The second method is not limited by this and does not require a galaxy simulation; the user defines a numerical function which takes position and time as arguments, and the galactic potential is returned. The space and time derivatives of the potential are used to (i) integrate the motion of the cluster on its orbit in the galaxy (starting from user-defined initial position and velocity vector), and (ii) compute the tidal acceleration on the stars.

[ascl:1904.027]
nbodykit: Massively parallel, large-scale structure toolkit

nbodykit provides algorithms for analyzing cosmological datasets from N-body simulations and large-scale structure surveys, and takes advantage of the abundance and availability of large-scale computing resources. The package provides a unified treatment of simulation and observational datasets by insulating algorithms from data containers, and reduces wall-clock time by scaling to thousands of cores. All algorithms are parallel and run with Message Passing Interface (MPI); the code is designed to be deployed on large super-computing facilities. nbodykit offers an interactive user interface that performs as well in a Jupyter notebook as on super-computing machines.

[ascl:1010.019]
NBSymple: A Double Parallel, Symplectic N-body Code Running on Graphic Processing Units

NBSymple is a numerical code which numerically integrates the equation of motions of N 'particles' interacting via Newtonian gravitation and move in an external galactic smooth field. The force evaluation on every particle is done by mean of direct summation of the contribution of all the other system's particle, avoiding truncation error. The time integration is done with second-order and sixth-order symplectic schemes. NBSymple has been parallelized twice, by mean of the Computer Unified Device Architecture to make the all-pair force evaluation as fast as possible on high-performance Graphic Processing Units NVIDIA TESLA C 1060, while the O(N) computations are distributed on various CPUs by mean of OpenMP Application Program. The code works both in single precision floating point arithmetics or in double precision. The use of single precision allows the use at best of the GPU performances but, of course, limits the precision of simulation in some critical situations. We find a good compromise in using a software reconstruction of double precision for those variables that are most critical for the overall precision of the code.

[ascl:1411.023]
NDF: Extensible N-dimensional Data Format Library

The Extensible N-Dimensional Data Format (NDF) stores bulk data in the form of N-dimensional arrays of numbers. It is typically used for storing spectra, images and similar datasets with higher dimensionality. The NDF format is based on the Hierarchical Data System (HDS) and is extensible; not only does it provide a comprehensive set of standard ancillary items to describe the data, it can also be extended indefinitely to handle additional user-defined information of any type. The NDF library is used to read and write files in the NDF format. It is distributed with the Starlink software (ascl:1110.012).

[ascl:1101.002]
NDSPMHD Smoothed Particle Magnetohydrodynamics Code

This paper presents an overview and introduction to Smoothed Particle Hydrodynamics and Magnetohydrodynamics in theory and in practice. Firstly, we give a basic grounding in the fundamentals of SPH, showing how the equations of motion and energy can be self-consistently derived from the density estimate. We then show how to interpret these equations using the basic SPH interpolation formulae and highlight the subtle difference in approach between SPH and other particle methods. In doing so, we also critique several `urban myths' regarding SPH, in particular the idea that one can simply increase the `neighbour number' more slowly than the total number of particles in order to obtain convergence. We also discuss the origin of numerical instabilities such as the pairing and tensile instabilities. Finally, we give practical advice on how to resolve three of the main issues with SPMHD: removing the tensile instability, formulating dissipative terms for MHD shocks and enforcing the divergence constraint on the particles, and we give the current status of developments in this area. Accompanying the paper is the first public release of the NDSPMHD SPH code, a 1, 2 and 3 dimensional code designed as a testbed for SPH/SPMHD algorithms that can be used to test many of the ideas and used to run all of the numerical examples contained in the paper.

[ascl:1411.013]
NEAT: Nebular Empirical Analysis Tool

NEAT is a fully automated code which carries out a complete analysis of lists of emission lines to estimate the amount of interstellar extinction, calculate representative temperatures and densities, compute ionic abundances from both collisionally excited lines and recombination lines, and finally to estimate total elemental abundances using an ionization correction scheme. NEAT uses a Monte Carlo technique to robustly propagate uncertainties from line flux measurements through to the derived abundances.

[ascl:1809.009]
NEBULA: Radiative transfer code of ionized nebulae at radio wavelengths

NEBULA performs the radiative transfer of the 3He+ hyperfine transition, radio recombination lines (RRLs), and free-free continuum emission through a model nebula. The model nebula is composed of only H and He within a three-dimension Cartesian grid with arbitrary density, temperature, and ionization structure. The 3He+ line is assumed to be in local thermodynamic equilibrium (LTE), but non-LTE effects and pressure broadening from electron impacts can be included for the RRLs. All spectra are broadened by thermal and microturbulent motions.

[ascl:1608.019]
NEBULAR: Spectrum synthesis for mixed hydrogen-helium gas in ionization equilibrium

NEBULAR synthesizes the spectrum of a mixed hydrogen helium gas in collisional ionization equilibrium. It is not a spectral fitting code, but it can be used to resample a model spectrum onto the wavelength grid of a real observation. It supports a wide range of temperatures and densities. NEBULAR includes free-free, free-bound, two-photon and line emission from HI, HeI and HeII. The code will either return the composite model spectrum, or, if desired, the unrescaled atomic emission coefficients. It is written in C++ and depends on the GNU Scientific Library (GSL).

[ascl:1010.004]
Needatool: A Needlet Analysis Tool for Cosmological Data Processing

NeedATool (Needlet Analysis Tool) performs data analysis based on needlets, a wavelet rendition powerful for the analysis of fields defined on a sphere. Needlets have been applied successfully to the treatment of astrophysical and cosmological observations, particularly to the analysis of cosmic microwave background (CMB) data. Wavelets have emerged as a useful tool for CMB data analysis, as they combine most of the advantages of both pixel space, where it is easier to deal with partial sky coverage and experimental noise, and the harmonic domain, in which beam treatment and comparison with theoretical predictions are more effective due in large part to their sharp localization.

[ascl:1010.051]
NEMO: A Stellar Dynamics Toolbox

NEMO is an extendible Stellar Dynamics Toolbox, following an Open-Source Software model. It has various programs to create, integrate, analyze and visualize N-body and SPH like systems, following the pipe and filter architecture. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages. A large growing fraction of NEMO has been contributed by a growing list of authors. The source code consist of a little over 4000 files and a little under 1,000,000 lines of code and documentation, mostly C, and some C++ and Fortran. NEMO development started in 1986 in Princeton (USA) by Barnes, Hut and Teuben. See also ZENO (ascl:1102.027) for the version that Barnes maintains.

[ascl:1307.017]
NEST: Noble Element Simulation Technique

Szydagis, M.; Barry, N.; Kazkaz, K.; Mock, J.; Stolp, D.; Sweany, M.; Tripathi, M.; Uvarov, S.; Walsh, N.; Woods, M.

NEST (Noble Element Simulation Technique) offers comprehensive, accurate, and precise simulation of the excitation, ionization, and corresponding scintillation and electroluminescence processes in liquid noble elements, useful for direct dark matter detectors, double beta decay searches, PET scans, and general radiation detection technology. Written in C++, NEST is an add-on module for the Geant4 simulation package that incorporates more detailed physics than is currently available into the simulation of scintillation. NEST is of particular use for low-energy nuclear recoils. All available liquid xenon data on nuclear recoils and electron recoils to date have been taken into consideration in arriving at the current models. NEST also handles the magnitude of the light and charge yields of nuclear recoils, including their electric field dependence, thereby shedding light on the possibility of detection or exclusion of a low-mass dark matter WIMP by liquid xenon detectors.

[ascl:1809.012]
nestcheck: Nested sampling calculations analysis

Nestcheck analyzes nested sampling runs and estimates numerical uncertainties on calculations using them. The package can load results from a number of nested sampling software packages, including MultiNest (ascl:1109.006), PolyChord (ascl:1502.011), dynesty (ascl:1809.013) and perfectns (ascl:1809.005), and offers the flexibility to add input functions for other nested sampling software packages. Nestcheck utilities include error analysis, diagnostic tests, and plots for nested sampling calculations.

[submitted]
Network Flux Transport Demonstration

We have developed a method to efficiently simulate the dynamics of the magnetic flux in the solar network. We call this method Network Flux Transport (NFT). Implemented using a Spherical Centroidal Voronoi Tessellation (SCVT) based network model, magnetic flux is advected by photospheric plasma velocity fields according to the geometry of the SCVT model. We test NFT by simulating the magnetism of the Solar poles. The poles of the sun above 55 deg latitude are free from flux emergence from active regions or ephemeral regions. As such, they are ideal targets for a simplified simulation that relies on the strengths of the NFT model. This simulation method reproduces the magnetic and spatial distributions for the solar poles over two full solar cycles.

[ascl:1010.085]
Network Tools for Astronomical Data Retrieval

The first step in a science project is the acquisition and understanding of the relevant data. The tools range from simple data transfer methods to more complex browser-emulating scripts. When integrated with a defined sample or catalog, these scripts provide seamless techniques to retrieve and store data of varying types. These tools can be used to leapfrog from website to website to acquire multi-wavelength datasets. This project demonstrates the capability to use multiple data websites, in conjunction, to perform the type of calculations once reserved for on-site datasets.

[ascl:1807.011]
nfield: Stochastic tool for QFT on inflationary backgrounds

nfield uses a stochastic formalism to compute the IR correlation functions of quantum fields during cosmic inflation in n-field dimensions. This is a necessary 1-loop resummation of the correlation functions to render them finite. The code supports the implementation of n-numbers of coupled test fields (energetically sub-dominant) as well as non-test fields.

[ascl:1903.013]
NFWdist: Density, distribution function, quantile function and random generation for the 3D NFW profile

Available in R and Python, the simple analytic scheme NFWdist performs highly efficient and exact sampling of the Navarro, Frenk & White (NFW) profile as a true probability distribution function, with the only variable being the concentration.

[ascl:1508.008]
NGMIX: Gaussian mixture models for 2D images

NGMIX implements Gaussian mixture models for 2D images. Both the PSF profile and the galaxy are modeled using mixtures of Gaussians. Convolutions are thus performed analytically, resulting in fast model generation as compared to methods that perform the convolution in Fourier space. For the galaxy model, NGMIX supports exponential disks and de Vaucouleurs and Sérsic profiles; these are implemented approximately as a sum of Gaussians using the fits from Hogg & Lang (2013). Additionally, any number of Gaussians can be fit, either completely free or constrained to be cocentric and co-elliptical.

[ascl:1608.016]
NICIL: Non-Ideal magnetohydrodynamics Coefficients and Ionisation Library

NICIL (Non-Ideal magnetohydrodynamics Coefficients and Ionisation Library) calculates the ionization values and the coefficients of the non-ideal magnetohydrodynamics terms of Ohmic resistivity, the Hall effect, and ambipolar diffusion. Written as a standalone Fortran90 module that can be implemented in existing codes, NICIL is fully parameterizable, allowing the user to choose which processes to include and decide the values of the free parameters. The module includes both cosmic ray and thermal ionization; the former includes two ion species and three species of dust grains (positively charged, negatively charged and neutral), and the latter includes five elements which can be doubly ionized.

[ascl:1508.002]
NICOLE: NLTE Stokes Synthesis/Inversion Code

NICOLE, written in Fortran 90, seeks the model atmosphere that provides the best fit to the Stokes profiles (in a least-squares sense) of an arbitrary number of simultaneously-observes spectral lines from solar/stellar atmospheres. The inversion core used for the development of NICOLE is the LORIEN engine (the Lovely Reusable Inversion ENgine), which combines the SVD technique with the Levenberg-Marquardt minimization method to solve the inverse problem.

[ascl:1302.013]
NIFTY: A versatile Python library for signal inference

Selig, Marco; Bell, Michael R.; Junklewitz, Henrik; Oppermann, Niels; Reinecke, Martin; Greiner, Maksim; Pachajoa, Carlos; Ensslin, Torsten A.

NIFTY (Numerical Information Field TheorY) is a versatile library enables the development of signal inference algorithms that operate regardless of the underlying spatial grid and its resolution. Its object-oriented framework is written in Python, although it accesses libraries written in Cython, C++, and C for efficiency. NIFTY offers a toolkit that abstracts discretized representations of continuous spaces, fields in these spaces, and operators acting on fields into classes. Thereby, the correct normalization of operations on fields is taken care of automatically. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTY permits rapid prototyping of algorithms in 1D and then the application of the developed code in higher-dimensional settings of real world problems. NIFTY operates on point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those.

[ascl:1903.008]
NIFTy5: Numerical Information Field Theory v5

Arras, Philipp; Baltac, Mihai; Ensslin, Torsten A.; Frank, Philipp; Hutschenreuter, Sebastian; Knollmueller, Jakob; Leike, Reimar; Newrzella, Max-Niklas; Platz, Lukas; Reinecke, Martin; Stadler, Julia

NIFTy (Numerical Information Field Theory) facilitates the construction of Bayesian field reconstruction algorithms for fields being defined over multidimensional domains. A NIFTy algorithm can be developed for 1D field inference and then be used in 2D or 3D, on the sphere, or on product spaces thereof. NIFTy5 is a complete redesign of the previous framework (ascl:1302.013), and requires only the specification of a probabilistic generative model for all involved fields and the data in order to be able to recover the former from the latter. This is achieved via Metric Gaussian Variational Inference, which also provides posterior samples for all unknown quantities jointly.

[ascl:1106.016]
Nightfall: Animated Views of Eclipsing Binary Stars

Nightfall is an astronomy application for fun, education, and science. It can produce animated views of eclipsing binary stars, calculate synthetic lightcurves and radial velocity curves, and eventually determine the best-fit model for a given set of observational data of an eclipsing binary star system.

Nightfall comes with a user guide and a set of observational data for several eclipsing binary star systems.

[ascl:1501.002]
NIGO: Numerical Integrator of Galactic Orbits

NIGO (Numerical Integrator of Galactic Orbits) predicts the orbital evolution of test particles moving within a fully-analytical gravitational potential generated by a multi-component galaxy. The code can simulate the orbits of stars in elliptical and disc galaxies, including non-axisymmetric components represented by a spiral pattern and/or rotating bar(s).

[ascl:1101.006]
NIRVANA: A Numerical Tool for Astrophysical Gas Dynamics

The NIRVANA code is capable of the simulation of multi-scale self-gravitational magnetohydrodynamics problems in three space dimensions employing the technique of adaptive mesh refinement. The building blocks of NIRVANA are (i) a fully conservative, divergence-free Godunov-type central scheme for the solution of the equations of magnetohydrodynamics; (ii) a block-structured mesh refinement algorithm which automatically adds and removes elementary grid blocks whenever necessary to achieve adequate resolution and; (iii) an adaptive mesh Poisson solver based on multigrid philosophy which incorporates the so-called elliptic matching condition to keep the gradient of the gravitational potential continous at fine/coarse mesh interfaces.

[ascl:1711.024]
NOD3: Single dish reduction software

NOD3 processes and analyzes maps from single-dish observations affected by scanning effects from clouds, receiver instabilities, or radio-frequency interference. Its “basket-weaving” tool combines orthogonally scanned maps into a final map that is almost free of scanning effects. A restoration tool for dual-beam observations reduces the noise by a factor of about two compared to the NOD2 version. Combining single-dish with interferometer data in the map plane ensures the full recovery of the total flux density.

[ascl:1305.013]
Non-Gaussian Realisations

Non-Gaussian Realisations provides code based on a spectral distortion/quantile transformation that generates a realization of a field on a cubic grid that has a specified probability distribution function and a specified power spectrum.

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