astroPluto is modular Godunov-type code intended mainly for astrophysical applications and high Mach number flows in multiple spatial dimensions. The code embeds different hydrodynamic modules and multiple algorithms to solve the equations describing Newtonian, relativistic, MHD, or relativistic MHD fluids in Cartesian or curvilinear coordinates.
The TIGL Geometry Library can be used for easy processing of geometric data stored inside CPACS data sets. TIGL offers query functions for the geometry structure. These functions can be used, for example, to detect how many segments are attached to a certain segment, which indices these segments have, or how many wings and fuselages the current airplane configuration contains. This functionality is necessary because TIGL targets not only the modeling of simple wings or fuselages but also the description of quite complicated structures with branches or flaps. The library uses the OpenCASCADE software to represent the airplane geometry by B-spline surfaces in order to compute surface points and also to export the geometry in the IGES/VTK format. The library provides external interfaces for C, C++, Python, Java, and FORTRAN.
OpenMPF is a library for solving large, dense, multi-RHS linear systems. It is based on MPI/openMP parallelism, and relies on BLAS/LAPACK/MUMPS for the single node computations. It implements direct and iterative solvers, out-of-core matrices and vectors, and is easily accessible through a Python interface.
GetData is a library that provides an API to interface with dirfile databases. The dirfile database format is designed to provide a fast, scalable format for storing and reading binary, synchronously-sampled, time-ordered data. GetData was originally written for the BOOMERanG and BLAST experiments as a data format suitable for use for both quick-look and data reduction. It is now used by many other cosmological and astrophysical experiments including ACT, Planck, Spider, Keck, as well as other projects.
MathGL is a library for making high-quality scientific graphics under Linux and Windows, fast data plotting and handling of large data arrays, working in window and console modes, and easily embedding into other programs. It has more than 40 general types of graphics for 1d, 2d, and 3d data arrays. It can export graphics to raster and vector (EPS or SVG) formats. It has an OpenGL interface and can be used from console programs. It has functions for data handling and MGL language scripting for simplification of data plotting. It has several types of transparency and smoothed lightning, vector fonts and TeX-like formula drawing, an arbitrary curvilinear coordinate system, and many other useful things.
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.
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.
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.
ffnet is a fast and easy-to-use feed-forward neural network training solution for Python. You can use it to train, test, save, load, and use an artificial neural network with sigmoid activation functions. Any network connectivity without cycles is allowed (not only layered). Training can be performed with several optimization schemes, including genetic alorithm based optimization. There is access to exact partial derivatives of network outputs versus its inputs. Normalization of data is handled automatically by ffnet.