# Semantic search

- 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
**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
**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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