APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>. Please register at http://goo.gl/LGVU5j before downloading!
SWAN is a third-generation wave model, developed at Delft University of Technology, that computes random, short-crested wind-generated waves in coastal regions and inland waters.
Eclim is a set of eclipse and vim plugins to integrate the two projects.
Molecular Dynamics Cell Construction
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/
SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces. It provides a general basis for describing wave transformations from deep water to a beach, port or harbour, complex changes to rapidly varied flows, and density driven flows in coastal seas, estuaries, lakes and rivers.
Graphic molecular dynamic package.
Molecular Graphics, Molecular Dynamics, Optimization, Quantum chemistry. Molecular model building. Explicit and implicit water models. http://www.biomolecular-modeling.com/Products.html
COmputational fluid dyNamics STRUctured grid CreaTor for 2D airfoils
Construct2D is a grid generator designed to create 2D grids for CFD computations on airfoils. The grids are generated in Plot3D format. The only required input file is the set of coordinates defining the airfoil geometry, using the same format as XFoil, the popular vortex-panel code for airfoil analysis. Construct2D can create grids with O topology (recommended for airfoils with a blunt trailing edge) or C topology (recommended for airfoils with a sharp trailing edge). Now available in version 2.0: hyperbolic grid generation to create higher quality grids in a fraction of the time compared to elliptic grid generation. Elliptic grid generation is still available also. Smooth airfoil surface spacing is handled automatically with user-controlled clustering parameters. Also included is a visualizer written in Python with matplotlib.
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.
ProtoFit is software for modeling the acid/base behavior of surfaces. The software is used for parameterizing surface protonation models and for visualization of potentiometric titration data.
is a molecular viewer & model builder for quantum chemistry programs. It has an interface with NWChem, CP2K and PC GAMESS/Firefly quantum programs. http://www.biomolecular-modeling.com/Products.html
Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
IFEFFIT is a library and set of interactive programs for the analysis of x-ray absorption fine-structure (XAFS) data. IFEFFIT combines state-of-the-art analysis algorithms with graphical display of XAFS data, and general data manipulation. It can be
g2 is an easy to use, portable and powerful 2D graphics library. It provides a comprehensive set of functions for simultaneous generation of graphical output on different types of devices.
Modeling and simulation tool for continuous and hybrid systems.
UPDATE: ----------- This repository is no longer maintained, the new version of the QSS Solver is available at: https://github.com/CIFASIS/qss-solver
BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
Sound Propagation and Acoustic Radiation of Turbomachines - Aeroacoustic Noise Suppression Project : A CFD-like CAA code for predicting turbomachines noise.
Simulation of EPR spectra of nitroxide biradicals
The program Orthos is developed to performed simulation (including nonlinear least-squares fitting) of EPR spectra of nitroxide biradicals. The program capabilities include simulation of rigid-limit and slow-motional spectra, of both isotropic and aligned samples. The spectra of multiple paramagnetic species, both bi- and monoradicals can be modeled. NB: Please note that now (as of Nov 2016) the distribution is being updated so that to improve reliability, OS-universality, and the quality of documentation. If you have any troubles installing/compiling/using the software, please contact me. I would be glad to help.
Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
Benefit Your Learning of Climate Modeling
The goal of this project is to provide a couple of Fortran code to those students who selected the course of "Climate Modeling" in the department of atmospheric and oceanic sciences at Peking University. 这个项目的目标是给选择“气候模拟”课程（北京大学大气与海洋科学系）的同学提供与课程学习有关的源代码程序。 We are subject to GNU/GPL license and happy to open the code to the public. 我们遵守GNU/GPL协议，并乐于开放代码给所有需要的人。
Simulation of semiconductor laser optical injection and feedback
External-Cavity Semiconductor Laser Diode simulation is a Fortran implementation of Lang-Kobayashi model of semiconductor lasers subject to optical injection and optical feedback.
Data Processing and Analysis for X-ray Spectroscopy and More
Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. Larch is written in Python and relies heavily on the standard tools for scientific computing with Python (numpy, scipy, matplotlib, and h5py).
Please use the MOHID code official site http://mohid.codeplex.com/, Thank you, The MOHID team
the MMM to HADDOCK tool
MISHAP is the open-source MMM in silico simulated spin label to HADDOCK program. MISHAP aims to take spin labelled proteins and the distance distributions between labels from in silico (MMM) calculations or experimental data (from pulsed electron-electron double resonance experiments which have been analysed with DeerAnalysis) and pass them to the biomolecular docking program HADDOCK as docking restraints.
function library efficiently solving the Nearest Neighbor Problem (also know as the post office problem).