APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.
ESMF is software for building and coupling weather, climate, and related models. The premise is that complicated applications should be broken up into smaller pieces, or components. A component is a unit of software composition that has a coherent function, and a standard calling interface and behavior. Components can be assembled to create multiple applications, and different implementations of a component may be available.
Fenris is a multipurpose tracer, debugger, and code analysis tool that detects and documents high-level language constructions, can recover symbols, graph program execution flow, detect internal functions, recover symbol tables, and deal with anti-debugging protection. It features a command-line interface as well as a SoftICE-alike GUI and Web frontend.
GSEGYView is a viewer for seismic data in SEG-Y format, its modifications, and many other related formats aimed to store either petroleum exploration data or seismology data. GSEGYView features graphics hardware acceleration via OpenGL for seismic data rendering, wiggle, variable area and variable density seismic traces representation, two-level sorting of seismic traces by arbitratry keys in trace headers, multiple windows for multiple files with separate display parameters, easy seismic section navigation and zoom with mouse wheel support, and more.
GetDP is a general finite element solver using mixed elements to discretize de Rham-type complexes in one, two, and three dimensions. The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems.