octopus is a program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types. Electrons are describe quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.
SEM2DPACK is a simulator of 2D elastic wave propagation and fracture dynamics that applies the Spectral Element Method (SEM, similar to mass-lumped high-order finite element methods). Flexibility and accuracy are the main goals. Although the emphasis is currently on computational seismology and earthquake source dynamics, this tool might attract a wider audience in computational mechanics, research, and engineering.
EXODUS II is a model developed to store and retrieve finite element geometry, topology, and transient data for finite element analyses. It is used for preprocessing, postprocessing, as well as code to code data transfer. ExodusII is based on netcdf. It includes the nemesis parallel extension.
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.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.
Code_Aster offers a full range of multi-physical analysis and modelling methods that go well beyond the standard functions of software for computational thermomechanics: static and dynamic mechanics, linear or not, modal analysis, harmonic and random response, seismic analysis, acoustics, thermics, fracture, damage and fatigue, multiphysics, drying and hydratation, metallurgy analysis ,soil-structure, fluid-structure interactions, geometric and material non linearities, and contact and friction. It has a wide range of material properties (95 constitutive laws): porous media, geomaterials, damage, elastoplasticity, elastoviscoplasticity, etc., a wide range of finite elements (395), and a wide range of loadings.
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.
Electron Gamma Shower (EGS) is a general purpose package for the Monte Carlo simulation of the coupled transport of electrons and photons in an arbitrary geometry for particles with energies from a few keV up to several TeV. Simulations can be performed in arbitrarily complex physical geometries, and a wide range of physical processes are modeled.
The Interactive Spectral Interpretation System (ISIS) is designed to facilitate the interpretation and analysis of high resolution X-ray spectra. It is being developed as a programmable, interactive tool for studying the physics of X-ray spectrum formation, supporting measurement and identification of spectral features and interaction with a database of atomic structure parameters and plasma emission models.