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!
Eclim is a set of eclipse and vim plugins to integrate the two projects.
FORTRAN Unit Test Framework FRUIT - TDD in FORTRAN
FORTRAN Unit Test Framework, written in FORTRAN 95. So that all FORTRAN features can be tested. FRUIT has assertion, fixture, setup, teardown, report, spec, driver generation. Rake used as build tool. Tutorials at http://fortranxunit.wiki.sourceforge.net The core testing part is in FORTRAN, this part can be used independent of the Ruby codes. The Ruby code is to make fixtures and reports easier. Rake is to build the project elegantly. This project also demonstrate a new way to build mixed language code in an alternative way than Make. Most of the FORTRAN are important in nature, used in nuclear and aerospace codes, etc, and maintained and written actively. Please help to bring TDD practices to the FORTRAN community. The change could be very hard, personally, I quit, since I could not make the change. I hope your organization will be successful. Enjoy a cup of fruit while maintaining FORTRAN ! Andrew Hang Chen and other maintainers who feel importance of TDD in cr
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
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 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/
MieConScat is a GUI/Console program for generating MIE SCATtering data as a table of cross sections. It can generate scattering cross sections over specified angular ranges and total absorption cross sections. It was initially developed to aid work with optical particle counters (OPC) especially when CONverting data between cross section and diameter space. These methods are described in Rosenberg et al. 2012, Particle sizing calibration with refractive index correction for light scattering optical particle counters and impacts upon PCASP and CDP data collected during the Fennec campaign and CDP data collected during the Fennec campaign, http://www.atmos-meas-tech.net/5/1147/2012/amt-5-1147-2012.html
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
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
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.
sparse linear algebra library, with emphasis on preconditioned Krylov subspace methods for the solution of linear systems of equations
Yurix es un Entorno de desarrollo de modelos matemáticos, nos da la posibilidad de realizar cálculos numéricos utilizando un lenguaje orientado a objetos de alto nivel interpretado.
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.
Real-time interactive 3D graphics API for scientific simulations
OpenFrames is an Application Programming Interface (API) that provides the ability to add interactive 3D graphics to any scientific simulation. A simulation developer can use OpenFrames to specify what they want to visualize, without having to know any details of computer graphics programming. Visualizations created using OpenFrames are cross-platform, hardware accelerated with OpenGL, and designed specifically to minimize computational overhead. They can be embedded within an existing GUI framework (e.g. Qt, wxWidgets, Winteracter) or created in independent OS-native windows. The OpenFrames API itself is written in C++, and bindings are available for C and Fortran.
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.
A Spectral Element Solver for Structural Health Monitoring Application
A solver based on the spectral element method, used in conjunction with FEMAP, as a pre- and post- processor. It solves the elastic wave propagation problem, and the coupling with a piezoelectric materials for excitation and sensing. It is currently in 2D and has both static and transient capabilities.
The software is developed for calculations of hierarchy big circuits by methods of the tensor analysis of networks and diakoptic. It is planned also to application for joint calculation of circuits and the fields presented by electrical equivalent circuits. For input of circuits editor KiCAD is used.
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
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).
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。
Please use the MOHID code official site http://mohid.codeplex.com/, Thank you, The MOHID team
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.
A library collection of FORTRAN 90 subroutines and functions for the handling of raster images and for remote sensing applications. The 'fwtools' name evolved from 'framework tools'.
This is a collection of small fortran tools to perform various operations on raster images: projection, upscaling, downscaling, algebraic calculations etc. IDRISI binary raster format is assumed.
Fully automatic h, p, and hp-adaptive finite element package supporting different physics modes.