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!
Open-Source Multiphysics FEA (FEM) Package
CalculiX Binaries for MS Windows, made with CYGWIN and ARPACK libraries. CalculiX is most popular FEA open-source package (like Code-Aster and Elmer-FEM). it is comparable in features with most known commercial packages like ANSYS, NASTRAN, Abaqus, etc. Good for structural, mechanical, thermal and fluid applications (trusses, plates, frames, shells, solid bodies). It has powerful nonlinear capabilities (including tension/compression only material like concrete) and most types of analysis (modal, thermal, buckling, coupled, etc) . See home page at http://www.dhondt.de New versions can be obtauned here: http://calculixforwin.blogspot.com/2015/05/calculix-launcher.html
The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.
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/
Unit testing framework for Fortran with MPI extensions
pFUnit is a Fortran testing framework created by developers from NASA and NGC TASC. pFUnit offers a convenient, lightweight mechanism for Fortran developers to create and run software tests that specify the desired behavior for a given piece of code. See the website or wiki for more information.
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
PHIGS (Programmer's Hierarchical Interactive Graphics System)
PHIGS is an API standard for rendering 3D computer graphics. During the 1990's OpenGL became a more popular 3D API for professionals, and it still is today. PHIGS remains to be widely used in the film industry. Open PHIGS uses OpenGL for rendering graphics rather than implementing it's own abstraction layer to the graphics hardware, or using the PHIGS Extension to X (PEX). The reason for doing so is that today every graphics card manufacturer provides their own OpenGL implementation, which takes full advantage of the accelerated drawing capabilities in the hardware. PHIGS is a higher level API than OpenGL that works with a hierarchical scene graph. Models are built up in a Centralized Structure Store (CSS), a database containing the drawing primitives and their attributes (color, line style, etc.). CSSes cand be shared among a number of views, known under PHIGS as a workstation. PHIGS is defined by the ISO standards ISO/IEC 9592 & 9593. Open PHIGS provides a library for C.
The allRound pocket sized CodeEditor.
Refurbished Scintilla.orgs/SciTE with some additional patches. -- Features -- - Full MinGW and GTK SDKs Autocomplete.(190+) - Do system scripting (bash, applescript, cmd, powershell, perl, j/vbscript, awk) - Examine all sorts of data files (sql, regedit, mib, xml, yaml, json, vcard ...) - Review difference and patch files - Create makefiles (gnu make / cmake) - Edit html, css and config files (with calltips) - Describe circuits in vhdl and spice. ... - And finally; read & write source code: - [ Syntax highlighted ] - go, vala, pike, swift, flash, ch, rust - [ Calltip assisted ] - c/cpp11, js&jQuery, python, php, ruby, lua, c#, java, perl --Others-- - Restructured config files with inline docs - Scriptable via lua Extension. - Provides theming, a customizeable toolbar, a sidebar with a File Browser and a cleaned up options Menu. --- Summary --- Enjoy your vlc for sourceCode lecture ;) (30Langs)
PCP (Pattern Classification Program) is an open-source machine learning program for supervised classification of patterns. PCP is a binary executable running on Linux and Windows (under Cygwin environment).
Parallel finite element analysis
ParaFEM is an open source platform for parallel finite element analysis. The source code and philosophy are documented in the text book Smith, Griffiths and Margetts, "Programming the Finite Element Method", 5th Edition, Wiley, 2014. The software is written in modern Fortran and uses MPI for message passing.
Real Space Multigrid based electronic structure code.
News: V2.2.2 released on 10/14/2017 with minor bug fixes. News: V2.2 with performance enhancements, bug fixes and new features released on 06/26/2017. Sources are available with binaries to follow soon. News: V2.1 with many improvements released on 07/15/2016. Sources and binaries are available. RMG is a density functional theory (DFT) based electronic structure code that uses real space grids to represent wavefunctions, charge densities and ionic potentials. Designed for scaleability it has been run successfully on systems with thousands of nodes and hundreds of thousands of CPU cores. It is currently under active development and contributions are gladly accepted.
CFD (computational fluid dynamics) software. Numerical 2d-solver for compressible ideal gases. Sophisticated turbulence and numerical approach which captures laminar-turbulent transition and aero-acoustic features.
DAXCAD is an easy to use PC based CAD system. It was originally written in 1984 for Apollo workstations and runs today under Cygwin.
OpenEnsemble is advanced object-based middleware software for distributing modelling and simulation across networks and the Internet.
Open-GMF is an open Ground Water Modeling Framework for hydrogeologists and reservoir engineers. It is an extensible development environment for finite-difference, finite-element, and finite-volume models tailored to specific problems.
tool for inverse modeling of the semiconductor devices
The PROFILE  is a tool for inverse modeling of the semiconductor devices using 2D data and advanced optimization driver. All the files and its documentation is available at the official homepage of Profile: http://profile.ewi.tudelft.nl/ REF:  G.J.L. Ouwerling. Inverse modelling with the PROFILE optimization driver. NASECODE VI Software Forum, Dublin, July 1989.
Yet Another Finite Element Method Solver
YAFEMS (Yet Another Finite Element Method Solver) is a FEM solver for Linux and WIndows that reads a MED mesh file produced by Salome (http://www.salome-platform.org/) with certain groups created into the mesh, and with the help of an input text file (.yaf), performs a 3D or 2D plane stress or plane strain analysis and creates results in plain text format and in MED format. This way a complete analysis can be carried inside Salome, where a mesh file can be created, exported and read by YAFEMS with the help of a .yaf input file and post-processed within Salome using ParaView. New in v0.4 - More performance boost due to the implementation of the Cuthill-McKee algorithm.
This project looks at the development of a set of generic models (box,chamber, photo-chemical trajectory) to use with the MCM (www.mcm.leeds.ac.uk). The software provides a tailored FORTRAN interface to the CVODE solver (http://www.llnl.gov/CASC/sundials