Fimex is a the File Interpolation, Manipulation, and EXtraction library for gridded geospatial data. It converts between different, extensible data formats (currently netcdf, NcML, grib1/2, metgm, wdb, and felt). It enables you to change the projection and interpolation of scalar and vector grids. It makes it possible to subset the gridded data and to extract only parts of the files. For simple usage, Fimex also comes with the command line program fimex.
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.
San Le's Free Computational Electromagnetics (SLFCEM) is a package of scientific software for use in computational electromagnetics. Command-line driven calculation engines are separate from the GUI components and can be used independently. It includes two of the basic finite elements types, 4 node quad and 3 node triangle. Each element type has a unique GUI specific to the element. Modal analysis for solving the waveguide problem is done using edge based elements. There is also code for generating edge connectivity. The algorithm used is a combination of Lanczos for tridiagonalization of the system, as well as QR to calculate the resulting eigenvalues. In addition to skyline storage and LU decomposition, calculations are also made using the Conjugate Gradient Method.
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.
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.