GeographicLib is a small set of C++ classes for converting between geographic, UTM, UPS, MGRS, and geocentric coordinates, for gravity (e.g., EGM2008), geoid, and geomagnetic field (e.g., WMM2010) calculations, and for solving geodesic problems. For documentation, visit https://geographiclib.sf.io
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!
Data Analysis, Simulations and Visualization on the Sphere
Software for pixelization, hierarchical indexation, synthesis, analysis, and visualization of data on the sphere. Please acknowledge HEALPix by quoting the web page http://healpix.sourceforge.net and publication: K.M. Gorski et al., 2005, Ap.J., 622, p.759 Full software documentation available at http://healpix.sf.net/documentation.php Wiki Pages: https://sourceforge.net/p/healpix/wiki/Home GDL users should read https://sourceforge.net/p/healpix/wiki/HEALPix%20and%20GDL/
Cross-platform, scientific graphics plotting library
PLplot is a cross-platform, scientific graphics plotting library that supports math symbols and human languages (via UTF-8 user input strings); plot capabilities for multiple non-interactive plot file formats and in multiple interactive environments; and bindings for multiple computer languages.
ffnet is a fast and easy-to-use feed-forward neural network training solution for python. Many nice features are implemented: arbitrary network connectivity, automatic data normalization, very efficient training tools, network export to fortran code. Now ffnet has also a GUI called ffnetui.
AquaTerm is a Mac OS X grahics renderer. It allows command line applications written in ObjC, C, FORTRAN, Lisp, Perl or Python to display vector graphics, text and images using a simple API. Adapters for gnuplot, PGPLOT, and PLplot exists as well.
Software for electromagnetic simulation
MaxFem is an open software package for electromagnetic simulation by using finite element methods. The package can solve problems in electrostatics, direct current, magnetostatics and eddy-currents. We have moved the installers to the MaxFEM website (see below). In order to improve MaxFEM, we will require you to fill out a simple form before downloading them.
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.
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/
Ultrascale Visualization Climate Data Analysis Tools
Ultrascale Visualization Climate Data Analysis Tools (UV-CDAT), is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for climate-data analysis problems.
finFoil is an application to help amateur surfboard fin makers foil their fins properly. Check out the homepage for the latest news and tutorials: http://hrobeers.github.io/finFoil/ hrobeers
AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.
This will be a place to release tools that have not yet been added to SciPy (or will not be added for whatever reason). Currently an interface to ImageMagick is here.
Carbon Fullerene and Capped Nanotube Generator
NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code.
MRCWA - Multilayer Rigorous Coupled Wave Analysis is a fast, flexible optical grating solver. It calculates an exact solution to the Maxwell equations for the diffraction of light from an optical grating with arbitrary profile and materials.
Advanced numerical instruments: adaptive meshing, FE methods, solvers
Ani2D provides portable libraries for each step in the numerical solution of systems of PDEs with variable tensorial coefficients: (1) unstructured adaptive mesh generation, (2) metric-based mesh adaptation, (3) finite element discretization and interpolation, (4) algebraic solvers.
Engineering, analysis and computing tools for marine and coastal science and technology
COmputational fluid dyNamics STRUctured grid CreaTor for 2D airfoils
Construct2D is a grid generator designed to create 2D grids for CFD computations on airfoils. The grids are generated in Plot3D format. The only required input file is the set of coordinates defining the airfoil geometry, using the same format as XFoil, the popular vortex-panel code for airfoil analysis. Construct2D can create grids with O topology (recommended for airfoils with a blunt trailing edge) or C topology (recommended for airfoils with a sharp trailing edge). Now available in version 2.0: hyperbolic grid generation to create higher quality grids in a fraction of the time compared to elliptic grid generation. Elliptic grid generation is still available also. Smooth airfoil surface spacing is handled automatically with user-controlled clustering parameters. Also included is a visualizer written in Python with matplotlib.
Space Science library for Python - contains superposed epoch classes, drift shell tracing, access to magnetic field models, streamline tracing, bootstrap confidence limits, time and coordinate conversions, etc.
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.
2D Frame Analysis, Linear Static Analysis, Mode Shapes
This is a free program for solving linear 2D framed structures under static loading and calculating the mode shapes. It is coupled with an easy-to-use GUI that provides the possibility to design the structure very fast. It calculates reaction forces, diagrams of axial and shear forces, as well as, diagrams of bending moments. Moreover, it calculates the mode shapes of the structure using various methods and it will be cabable of performing dynamic analysis soon. The program is written in FORTRAN90 and the GUI in Python. At the moment it is available only in 64bit version for windows.
This application is intended to be a tool for easy, almost automatic, creation and calculation of gear transmission finite element models. It consists of a geometry and mesh generator based on GMSH and a finite element model based on GETFEM++.
numerical simulation code solving transport equations in 2D
fosite is a generic framework for the numerical solution of 2D hyperbolic conservation laws in generalized orthogonal coordinates. Its main purpose is the simulation of compressible flows with either rotational symmetry or slab symmetry. The underlying numerical solution method belongs to the family of unsplit conservative finite volume TVD schemes. The method is 2nd order accurate in space and uses high order Runge-Kutta and multistep schemes for time evolution. In addition to the pure advection code several source terms have been implemented including viscous diffusion and gravitational acceleration. Due to its modular object-oriented design it is very easy to add new features to the code.
IFEFFIT is a library and set of interactive programs for the analysis of x-ray absorption fine-structure (XAFS) data. IFEFFIT combines state-of-the-art analysis algorithms with graphical display of XAFS data, and general data manipulation. It can be
Computational electromagnetics software. Uses surface Method of Moments, enhanced by using the Multilevel Fast Multipole Method. Code is parallelized and runs on laptops, desktops and clusters. The code precision is adjustable, it is fast and uses little memory. CFIE is used for closed surfaces, and EFIE for open PEC surfaces. Can function on GMSH, GiD and ANSYS meshes.