Open Source MATLAB Physics Software for Linux - Page 3

RYUON : many-particle simulation suite

Acquisition software for electron microscopes. Runs on FEI Tecnai and Titan microscopes and is usable in material and life science applications

This project is used to share code between collaborators on several projects pertaining to a class Numerical Physics class taken at Université Laval during the semester of Winter 2012.

VibroToolbox is a tool for research and education in vibrometry. Test your audio equipment, describe responses to vibratory stimulation and analyze directionality. It works with precision i/o hardware or simple sound cards, various sensors and speakers.

WavePacket is a program package for numerical quantum-mechanics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, as well as classical or quantum-classical Liouville equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern experiments involving ultrashort light pulses in photo-induced physics or chemistry, including quantum optimal control. With its visualization of quantum dynamics generated 'on the fly', WavePacket is suitable for teaching quantum mechanics as well as for research projects, see also the numerous demonstration examples . While the Matlab/Octave version is already in a mature state, the C++/Python version is still under construction. Using tensor train techniques, the additional WaveTrain package aims at beating the curse of dimensionality.

This toolkit allows complete control of a microscopy setup from Labview, Matlab, Scilab, Python, .Net, VB, IgorPro, Mathematica and more. Included is a standalone program for image acquisition and scripting control of a scientific microscope.

The dwi-toolbox provides a set of free and open-source Matlab routines for the simulation and analysis of Diffusion-Weighted Magnetic Resonance Imaging data. It includes data-fitting, simulation, visualization and statistical components.

This package includes a collection of MATLAB files which are designed to: 1. Given a calibration scan of the image of a point emitter with an engineered point spread function (PSF), 2. Perform a phase retrieval algorithm based on maximum likelihood estimation (MLE) of a phase aberration term which is added to the theoretical pupil function of the imaging system. 3. Use the phase-retrieved pupil function to perform single-emitter localization. Accompanying publication available here: https://doi.org/10.1364/OE.25.007945

At the moment this code can calculate free electron gas and the SIAM (single-impurity-anderson-model) In this version, the only thing computed by the code is the energy flow. There is no calculation for any thermodynamic quantaties. The implementation is very slow and rather for educational purposes to get an idea of the NRG-method. For example: it is not considered, that only matrix elements between states, whos occupation number differs by one and S_z differs by 1/2. There is only implicit parallelisation implemented by vectorizing the time consuming parts of the code. This code is licensed under the CC BY-SA 3.0 license (http://creativecommons.org/licenses/by-sa/3.0/, http://creativecommons.org/licenses/by-sa/3.0/legalcode)

A MatLab toolbox with many simple and useful functions for analyzing data from Cluster, Champ and the future Swarm missions. Other functions for space science, magnetospheric and ionospheric research are included. The toolbox is designed to be as simple as possible. Each function can be learned and used individually. Check the webpage for the list of functions: http://eugen-library.sourceforge.net/

With the support of the NSF and ONR over the past few years we have developed a MATLAB tool that calculates the internal wave field generated by barotropic tidal flow of a nonlinearly stratified fluid past any arbitrary two-dimensional topography of finite extent You can download a recent version as a .zip file or get up-to-date version via the svn version (svn checkout svn://svn.code.sf.net/p/itides/svn/trunk itides-svn).

Software for clustering networks as described in "Information-theoretic approach to network modularity" (Phys. Rev. E 71, 046117 (2005); http://link.aps.org/abstract/PRE/v71/e046117).

Lottie Vectors is an application for Matlab that alows you to do some pretty neat things -with vectors. More exactly -displaying them in ways that hopefully will allow you to explore and better understand your vector data. The basic idea is simple, take a vector defined in one of a few different types of data formats and map it on the screen. Add another vector and you start to form a 'route'. Each route or position vector can be accompanied with a 'force' vector. This can be used to show something acting on a position with direction and magnitude. Finally you can give each position a tag to display on screen. This could be a common math symbol or greek letter, start/end signposts, or a number of the position either from the begining or after a reset. After all the information has been loaded for your dataset. Either passed over the command line, or as a text file. Lottie Vectors displays inside a figure that you can resize, rotate and turn 2D positions into a 3D picture.

Magnetostatic finite differences simulation tool based on GNU Octave and a Perl/Tk user interface.

Program for solving pnp equations

This site hosts code investigating the role of spatial heterogeneity in biochemical signaling. Motivated by several biological examples, we study the behavior of covalent modification networks when the activating component is localized to a planar membrane in either a random or clustered configuration. Reactions and diffusion are implemented on a three-dimensional lattice.

SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.

software for identifying modules in networks (e.g. "community detection"), as described in "a bayesian approach to network modularity" (physical review letters 100, 258701 (2008); http://link.aps.org/abstract/PRL/v100/e258701).