Glossary ======== .. glossary:: AB magnitude An astronomical magnitude system in which the apparent magnitude is defined as :math:`m=-2.5\log_{10}f-48.60` for a flux density, :math:`f`, measured in ergs per second per square centimeter per hertz ADAF An advection-dominated accretion flow (ADAF) is a particular solution for an accretion flow around a black hole, star or compact object in which energy liberated by viscous forces is stored within the accretion flow and advected inward to the central object (see :cite:author:`narayan_advection-dominated_1998` :cite:year:`narayan_advection-dominated_1998`) AHF `Amiga's Halo Finder `_ (AHF) is a software package which identifies dark matter halos in N-body simulations. Full details are given by :cite:t:`gill_evolution_2004` and :cite:t:`knollmann_ahf:_2009` Approximate Nearest Neighbor The `Approximate Nearest Neighbor `_ library is a software package used finding the closest set of points to a given point, approximately AxionCAMB `AxionCAMB `_ is a code to compute anisotropies in the cosmic microwave background, and the linear theory power spectra of matter and radiation including an axion component in the dark matter backward descendant The :term:`primary progenitor` of a node. This type of descendant is usually relevant when building merger trees and should be distinguished from a :term:`forward descendant` which is relevant when considering how halos and galaxies evolve forward in time Bernoulli distribution A discrete probability distribution which takes value :math:`1` with success probability :math:`p` and value :math:`0` with failure probability :math:`q = 1-p`. Read more on `Wikipedia `_ CAMB `CAMB `_ is a code to compute anisotropies in the cosmic microwave background, and the linear theory power spectra of matter and radiation CDF `Cumulative Distribution Function `_ (CDF) is a function which describes the cumulative probability for a random variable to be equal to or less than a given value. CDM `Cold dark matter `_ (CDM) is a hypothesized type of dark matter in which the particles move slowly compared to the speed of light CGM circum-galactic medium CIE collisional ionization equilibrium CLASS `CLASS `_ is a code to compute anisotropies in the cosmic microwave background, and the linear theory power spectra of matter and radiation Cloudy `Cloudy `_ is a code to compute the ionization structure of HII regions CMB cosmic microwave background component An individual physical system within a :term:`node`, such as a dark matter halo, a galactic disk or a supermassive black hole dark matter-only universe Masses of nodes/halos are often defined as the mass which the node/halo would have in a dark matter-only universe in which the total matter density is the same as the actual model universe, but in which no baryons are present (i.e. all matter is dark matter) deadlock A deadlock describes a situation in which no node in a merger tree (or forest) can be evolved further forward in time due to the existence of circular dependencies between nodes. Deadlocks can occur due to incompatible parameter choices, or may indicate a bug in Galacticus. DSL `Domain-specific languages `_ (DSL) are a type of programming language dedicated to a particular problem. In Galacticus a DSL is used to specify the structure of :term:`component` ENZO `Enzo `_ is an adaptive mesh refinement hydrodynamics code FDM `Fuzzy dark matter `_ (FDM) is a hypothesized type of dark matter consisting of extremely light scalar particles with masses on the order of :math:`10^{-22}` eV FFTLog `FFTLog `_ is a code to compute fast Fourier transforms of discrete periodic sequences of logarithmically spaced data forest A collection of merger trees that are linked together by virtue of nodes which jump between trees forward descendant The node with which the mass (or majority of the mass) of a node will become associated with at a later time. This type of descendant is usually relevant when considering how halos and galaxies evolve forward in time and should be distinguished from a :term:`backward descendant` which is relevant when building merger trees GAMA The `Galaxy and Mass Assembly `_ (GAMA) survey is a spectroscopic survey of :math:`\approx 300,000` galaxies down to r :math:`<` 19.8 mag over :math:`\approx 286` deg\ :math:`^2`. GNU `GNU `_ is a free software collection used extensively on Unix-like operating systems GraphViz `GraphViz `_ is an open source graph visualization package. It is used by Galacticus in making diagrams of merger trees. GSL `GNU Scientific Library `_ (GSL) is a library providing a variety of numerical algorithms. HDF5 The `hierarchical data format `_ (version 5; HDF5) is a file format designed for storing scientific data. HOD A halo occupation distribution (HOD) is a mathematical model describing the distribution of the number of galaxies (of some given physical properties) found in a dark matter halo of given mass. IGM intergalactic medium IMF initial mass function IRATE `IRATE `_ is file format designed for N-body simulation particle, halo, merger tree, and galaxy data ISCO innermost stable circular orbit ISM interstellar medium Latin hypercube A `Latin hypercube `_ is a construct for generating a sample of plausible collections of parameter values from a multidimensional distribution Lyman continuum The part of the electromagnetic spectrum which is capable of ionizing hydrogen, i.e. photons with wavelengths shorter than 91.1267 nanometers and with energy above 13.6 eV maggie A unit of luminosity defined to be equal to the luminosity of a zeroth magnitude object in the :term:`AB magnitude` system mangle `mangle `_ is a software package used for defining angular masks on the surface of a sphere. It is used primarily for defining the geometry of galaxy surveys maximin In :term:`Latin hypercube` design, the "maximin" approach generates a large number of :term:`Latin hypercube` and selects the one which has the greatest minimum distance between all pairs of points in the hypercube MCMC Markov Chain Monte Carlo MD5 hash The `MD5 Message-Digest Algorithm `_ is a widely used cryptographic hash function that produces a 128-bit (16-byte) hash value. In Galacticus it is used to encode unique labels for modules which are incorporated into file names. Galacticus uses the `glibc `_ `crypt() `_ function to compute MD5 hashes, but switches "``/``" for "``@``" in the hash (since "``/``" is inconvenient for use in file names) mergee For a given node in a merger tree, the set of mergee nodes consists of all nodes which will undergo a galaxy merger with the node at some point in the future Millennium Simulation The `Millennium Simulation `_ is a high-resolution N-body simulation of structure formation in a cold dark matter universe. MPI `Message Passing Interface `_ (MPI) is a standard for passing messages between processes on parallel computers. NFW Navarro-Frenk-White (dark matter halo profile) node A single point in a merger tree, consisting of a dark matter halo and associated baryons NSC `Nuclear star clusters `_ (NSC) are high-density star clusters found in the centers of some galaxies ODE ordinary differential equation OpenMP `OpenMP `_ is an API for shared memory parallel programming. PAH `Polycyclic aromatic hydrocarbons `_ (PAH) are large organic molecules consisting of fused aromatic rings parent In a merger tree, the parent node of any given node that exists at time :math:`t_0` is that node to which it is directly connected in the tree at time :math:`t_1>t_0` PBS `Portable Batch System `_ (PBS) is a job scheduler used on many compute cluster environments. PDF `Probability Density Function `_ (PDF) is a function which describes the probability for a random variable to take on a given value. primary progenitor The progenitor of a given :term:`node` which is regarding as the direct descendant of that :term:`node` (often, but not always, the most massive progenitor). Other progenitors are considered to merge into this primary progenitor RecFast `RecFast `_ is a code to calculate the recombination history of the universe SAM Semi-analytic models (SAMs) are a type of galaxy formation model utilizing simple parameterizations of physical processes to follow the evolution of galaxies through a merging hierarchy of galaxies. SDSS Sloan Digital Sky Survey SED spectral energy distribution SNe supernovae UUID A `universally unique identifier `_---this is a label which uniquely identifies some object (in this case, a Galacticus model) WDM `Warm dark matter `_ (WDM) is a hypothesized type of dark matter in which the particle has non-negligible thermal velocity at decoupling XML `XML `_ is a markup language, used for Galacticus parameter files