Portable OS X FOSS applications
OS X FOSS portable applications are packaged so you can carry around on any portable device, USB thumb drive, iPod, portable hard drive, memory card, other portable device (or also on your internal hard disk), taking your preferences with you.
Static and Dynamic Structural Analysis of 2D and 3D frames.
FRAME3DD is a program for the static and dynamic structural analysis of two- and three-dimensional frames and trusses with elastic and geometric stiffness.
Dynamics of quantum systems, controlled by external fields
WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics for distinguishable particles. It can be used to solve one or more (i.e. coupled channels) time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can simulate modern experiments using ultrashort light pulses in photo-induced physics or chemistry, including quantum optimal control. The graphical capabilities allow visualization 'on the fly', including Wigner transforms to phase space. A description of WavePacket can be found in our manuscript at http://dx.doi.org/10.1016/j.cpc.2016.12.007. For examples / movies, see also the Wiki pages of the WavePacket main project. First established in 2004, the present Matlab version is in a stable, mature state. Further development mainly by Burkhard Schmidt at Free University Berlin
RYUON : many-particle simulation suite
HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures. Python users may also want to look at PYro at http://pyro.sourceforge.net
Routines for wavefront propagation in IDL, Matlab, and Python
PROPER is a library of routines for the propagation of wavefronts through an optical system using Fourier-based methods. It was developed at the Jet Propulsion Laboratory for modeling stellar coronagraphs, but it can be applied to other optical systems were diffraction propagation is of concern. It is currently available for IDL (Interactive Data Language), Matlab and Python (2.7 & 3.x). It includes routines for generating complex apertures and obscurations and aberrations (Zernike & PSD-defined). It includes a model of a deformable mirror for wavefront control. The routines perform near and far field propagation with automatic selection of propagators. The latest version for IDL and Python is v3.0 released on 7 Aug 2017. For Matlab it is v3.0.1 released on 22 Aug 2017 (bug fix in prop_readmap).
Quantum Information Toolkit is a comprehensive, easy-to-use interactive numerical toolkit for quantum information and computing, available for both MATLAB and Python.
Finite Element Rapid Analysis Lab
FEMM procedures to analyse rotating machines.
QCF is a toolbox of Quantum Computing Functions for Matlab and Octave. It is based on the syntax of Nielsen & Chuang's book 'Quantum Computing and Quantum Information'. It includes simulations of the Grover and Deutsch algorithms and a pdf tutorial.
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
NSB entropy and mutual information estimator; applications to the analysis of neural code.
GUI for fitting 3D single-molecule images using the double-helix PSF
This package of MATLAB routines with accompanying GUI allows scientific users to measure the 3D location of single molecules when using the double-helix point spread function (DH-PSF) widefield microscope. Features - Double-Gaussian estimator is calibrated via an axial scan of bright immobile fluorescent emitters (e.g. beads). - Template-matching and double-helix recognition algorithm is calibrated via setting an image correlation threshold against single-molecule data. - Tiff stacks of SM images are analyzed using template matching followed by double-Gaussian fitting to extract estimates of the molecule positions. - The motion/drift of fiduciaries (e.g. fluorescent beads) during an experiment can tracked and removed form SM localization data. - 3D localization data can be exported to .csv format for post-processing and visualization. - Basic 3D scatterplot and 2D z-projection histogram visualizations are included.
A collection of MATLAB tools for PIV, PTV, particle sizing, and more.
Qi is a collection of MATLAB tools for the quantitative analysis of flow field images. Our Particle Image Velocimetry (PIV) tool, prana, implements a Robust Phase Correlation kernel for PIV analysis, and now includes Particle Tracking Velocimetry and sizing tools. Tools for pressure calculation, proper orthogonal decomposition (POD), and 3d imaging are under development.
IRBEM-LIB provides routines to compute magnetic coordinates for any location in the Earth's magnetic field, to perform coordinate conversions, to evaluate geophysics/space-physics models, and to propagate orbits in time.
Optical ray tracing library based on MATLAB environment Now working on the simple raytracing simulation. Documents are not ready yet. NEW UPDATE : ray generation function, other bug fix and multiple ray treatment
A handle graphics package for Octave, the Free alternative to matlab. OctPlot provides quality postscript(TM) and screen graphics.
Software developed for the analysis of Neutron Reflectivity data.
Software for simulating the flight path of high power rockets in six-degree-of-freedom. This software runs with Octave or Matlab and can simulate a wide range of scenarios including parachute recovery and multiple stage flights.
Heat transfer in a bar and sphere using finite differences.
Simulation of the heat transfer in a bar and a sphere (1D) using finite differences in Matlab. Authors: -Jheyson A. Mogollon R. - email@example.com -Luca Meinardo - firstname.lastname@example.org -Angie Xiomara González - email@example.com Current Version: 2.0 Date: 30/05/2017
An Octave / LUA scripting language project dedicated to modeling electric motors inside the "Finite Element Method Magnetics" (FEMM) 2-D simulation program. Created to design a motor that fits inside a car wheel, experimenting in many degrees of freedo
self-consistent schrodinger-poisson code for core-shell nanowires
PAMELA (Pseudospectral Analysis Method with Exchange & Local Approximations) is a self-contained suite of MATLAB codes that can calculate electronic energies, densities, wavefunctions, and band-bending diagrams within a self-consistent Schrödinger-Poisson formalism.
PRIN-3D (PRoto-code for Internal ﬂows modeled by Navier-Stokes equations in 3-Dimensions) is a CFD code written in MATLAB, with turbulent and reactive capabilities.
Scanning Probe Image Wizard - MATLAB Toolbox
SPIW is a MATLAB toolbox, for automated processing of scanning probe microscope images. Tools are applicable to all SPM images, but the main focus is on images with atomic or molecular resolution. SPIW is primarily a MATLAB toolbox with functions designed to be called in a user's own script. SPIW also has a very basic GUI for browsing and exporting images. For information on SPIW's performance see our publication ( http://dx.doi.org/10.1063/1.4827076 ) in the Review of Scientific Instruments. A related open-source project SPIEPy (https://pypi.python.org/pypi/SPIEPy/) is developing a python library to for automated SPM imaged enhancement. SPIEPy brings many SPIW algorithms to the Python user.
A package for transient and steady state simulation of organic solar cells.
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).