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GPS
This is a candidate for deletion: Links broken. No links to page. Email to maintainer broken. Poppy-one (talk) 12:14, 31 July 2018 (EDT) Gravitational Particle Simulator uses numerical methods to simulate the behaviour of particles that obey the gravitational laws of motion. The numerical method used to approximate the differential equations is a 4th order Runge Kutta method. Home page is in Italian only, but the README and the comments in the code are in English.
Gnome Flow
Gnome Flow calculates and visualizes simple steady-state fluid flows. It uses the relaxation method, and can calculate flows past symmetric objects. Steady-state means it calculates the flow at a given time and that the physical parameters are constant in time.
Goptical Heckert gnu.tiny.png
Goptical is a C++ optical design and simulation library. It provides model classes for optical components, surfaces and materials. It enables building optical systems by creating and placing various optical components in a 3d space and simulates light propagation through the system. Classical optical design analysis tools can be used on optical systems.
Gpiv
'Gpiv' is a graphic user interface for analyzing images obtained from a fluid flow that has been seeded with tracer particles by the so-called Particle Image Velocimetry technique (PIV). It is meant to have a quick overview of the parameters of all piv processes, easily changing them, running the processes and visualizing their results interactively.
Gpivtools
Gpiv-tools is a package that contains command-line driven programs for the so-called (Digital) Particle Image Velocimetry technique (PIV). The programs perform image evaluation, resulting into a velocity field of the flow, validation programs and post-processing programs to manipulate the data or to extract information from the data (statistics, derivatives). There are some additional programs and scripts for data and image format conversions, chain-processing, batch-processing and for generating graphical output. Though the command-line driven tools are mainly intended for non-graphic processing, its outputs may be visualized in a graphical way by displaying with the aid of gnuplot.
INFOTOPO
Programs for Information Topology Data Analysis Information Topology is a program written in Python (compatible with Python 3.4.x), with a graphic interface built using TKinter [1], plots drawn using Matplotlib [2], calculations made using NumPy [3], and scaffold representations drawn using NetworkX [4]. It computes all the results on information presented in the study [5], that is all the usual information functions: entropy, joint entropy between k random variables (Hk), mutual informations between k random variables (Ik), conditional entropies and mutual informations and provides their cohomological (and homotopy) visualisation in the form of information landscapes and information paths together with an approximation of the minimum information energy complex [5]. It is applicable on any set of empirical data that is data with several trials-repetitions-essays (parameter m), and also allows to compute the undersampling regime, the degree k above which the sample size m is to small to provide good estimations of the information functions [5]. The computational exploration is restricted to the simplicial sublattice of random variable (all the subsets of k=n random variables) and has hence a complexity in O(2^n). In this simplicial setting we can exhaustively estimate information functions on the simplicial information structure, that is joint-entropy Hk and mutual-informations Ik at all degrees k=<n and for every k-tuple, with a standard commercial personal computer (a laptop with processor Intel Core i7-4910MQ CPU @ 2.90GHz * 8) up to k=n=21 in reasonable time (about 3 hours). Using the expression of joint-entropy and the probability obtained using equation and marginalization [5], it is possible to compute the joint-entropy and marginal entropy of all the variables. The alternated expression of n-mutual information given by equation then allows a direct evaluation of all of these quantities. The definitions, formulas and theorems are sufficient to obtain the algorithm [5]. We will further develop a refined interface (help welcome) but for the moment it works like this, and requires minimum Python use knowledge. Please contact pierre.baudot [at] gmail.com for questions, request, developments (etc.): [1] J.W. Shipman. Tkinter reference: a gui for python. . New Mexico Tech Computer Center, Socorro, New Mexico, 2010. [2] J.D. Hunter. Matplotlib: a 2d graphics environment. Comput. Sci. Eng., 9:22–30, 2007. [3] S. Van Der Walt, C. Colbert, and G. Varoquaux. The numpy array: a structure for efficient numerical computation. Comput. Sci. Eng., 13:22– 30, 2011. [4] A.A. Hagberg, D.A. Schult, and P.J. Swart. Exploring network structure, dynamics, and function using networkx. Proceedings of the 7th Python in Science Conference (SciPy2008). Gel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pages 11–15, 2008. [5] M. Tapia, P. Baudot, M. Dufour, C. Formisano-Tréziny, S. Temporal, M. Lasserre, J. Gabert, K. Kobayashi, JM. Goaillard . Information topology of gene expression profile in dopaminergic neurons doi: https://doi.org/10.1101/168740 http://www.biorxiv.org/content/early/2017/07/26/168740
Libgpiv
'LIBGPIV' is a library for the (Digital) Particle Image Velocimetry technique (PIV), an image analyzing technology that obtains a velocity field from a fluid flow (gas or liquid) that has been seeded with small tracer particles or smoke. 'LIBGPIV' contains the core functions for image evaluation (resulting into estimators of particle image displacements, i.e. PIV data), validation (on peak-locking effects, erroneous vectors or outliers), post-processing, input/output functions, utility functions like memory allocation etc. The project is designed for maximum flexibility for extending and adapting the code for different applications.
Libquantum
'libquantum' is a simulation of a quantum computer. It provides an interface for a quantum register and for all important quantum operations. An efficient model for decoherence allows an analysis of quantum computation in a realistic environment. Features include the simulation of arbitrary algorithms, high performance and low memory consumption and interfaces for quantum error correction (QEC) and the density operator formalism. The package includes implementations of Shor's factoring algorithm and Grover's search algorithm.
Librsb
librsb is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. The most common operations necessary to iterative solvers are available, e.g.: matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants. On these variants, librsb has been found to be faster than Intel MKL's implementation for CSR. Most numerical kernels code is auto generated, and the supported numerical types can be chosen by the user at build time. librsb implements the Sparse BLAS standard, as specified in the BLAS Forum documents.
Light Speed!
Light Speed! is an OpenGL-based program which illustrates the effects of special relativity on the appearance of moving objects. When an object accelerates past a few million meters per second, these effects begin to grow noticeable, becoming more and more pronounced as the speed of light is approached. These relativistic effects are viewpoint-dependent, and include shifts in length, object hue, brightness and shape. The moving object is, by default, a geometric lattice. 3D Studio and LightWave 3D objects may be imported as well. Best of all, the simulator is completely interactive, rendering the exotic distortions in real-time!
MIT Photonic Bands
MIT Photonic Bands (MPB) computes the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, and is applicable both to photonic crystals (photonic band-gap materials) and other optical problems. Its features include: fully-vectorial, 3D computations; a flexible user-interface based upon the GNU Guile scripting language; output in HDF format; and iterative, targeted eigensolver methods to address very large problems by solving for only a few states near a specified frequency.
McStas
McStas lets you model very precisely a neutron instrument described as a series of various components. A source component shoots each neutron randomly (Monte-Carlo), and the particle is then propagated through the different instrument components. These later act on the neutron characteristics (position, speed, direction, spin, etc.). Usually, one installs some detectors along the neutron path to monitor its characteristics and flux.
Meep
Meep is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. It supports distributed-memory parallelism, dispersive and nonlinear materials, PML absorbing boundaries, 1d/2d/3d/cylindrical problems, and arbitrary material and source geometries. It is completely scriptable via either C++ or a Scheme (GNU Guile) interface.
Minfx
The minfx project is a Python package for numerical optimisation, being a large collection of standard minimisation algorithms. This includes the line search methods: steepest descent, back-and-forth coordinate descent, quasi-Newton BFGS, Newton, Newton-CG; the trust-region methods: Cauchy point, dogleg, CG-Steihaug, exact trust region; the conjugate gradient methods: Fletcher-Reeves, Polak-Ribiere, Polak-Ribiere +, Hestenes-Stiefel; the miscellaneous methods: Grid search, Simplex, Levenberg-Marquardt; and the augmented function constraint algorithms: logarithmic barrier and method of multipliers (or augmented Lagrangian method).
Mpc Heckert gnu.tiny.png
GNU MPC is a complex floating-point library with exact rounding. It is based on the GNU MPFR floating-point library, which is itself based on the GNU MP library. This is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
MuTE Toolbox
A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. We propose a freeware MATLAB toolbox, MuTE (Multivariate Transfer Entropy), that implements four both Granger causality and transfer entropy estimators according to uniform and non-uniform embedding frameworks. The resulting eight methods can be easily compared showing all the pros and cons of the methodologies used to detect the directed dynamical information transfers. The toolbox provides a completely brand-new approach that bridges machine learning and information theory fields. MuTE is also able to perform bivariate and fully multivariate analyses. Furthermore, users can easily implement their own methods or change some features of the already existing approaches due to the modularity of the toolbox.
NMod nBody Modelling Toolkit
nMod nbody toolkit is a collection of tools designed to enable researchers to perform experiments using a particle-particle nBody model that runs on standard home computers.
The toolkit contains a particle-particle model, functions to enable the simulation of spacecraft flight, and an opengl viewer to display the resulting time series data.
Nano-archimedes Heckert gnu.tiny.png
nano-archimedes is for the simulation of quantum systems. It is based on the Wigner equation, a formulation of quantum mechanics in terms of a phase-space which is mathematically equivalent to the Schroedinger equation. GNU nano-archimedes implements the Wigner Monte Carlo method. The code can be easily extended to density functional theory (DFT) and time-dependent ab-initio simulations.
Network Extraction from Images
NEFI is an extensible computer vision tool that analyzes images that contain networks and extracts the graph. Examples are leaf venations, insect wings, slime molds, mud crack patterns etc. It determines topological information as well as properties such as edge length and width.
OOF
'OOF' helps materials scientists calculate macroscopic properties from images of real or simulated microstructures. It consists of two cooperating parts: 'ppm2oof' and 'oof'. 'ppm2oof' reads images in the ppm (Portable Pixel Map) format and assigns material properties to features in the image. 'oof' conducts virtual experiments on the data structures created by ppm2oof to determine the macroscopic properties of the microstructure. There are now two separate versions of OOF available. The original version solves elasticity problems. The new thermal version solves elasticity and thermal diffusion problems. Plans are to include eventually include electric and magnetic field calculations as well.


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