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.
MESA: Modules for Experiments in Stellar Astrophysics -- a set of thread-safe fortran 95 libraries for stellar astrophysics, including physics (e.g., eos, opacities, nuclear nets) and algorithms (e.g., ODE solvers). Available by svn checkout or as zip file. See project webpage (http://mesa.sourceforge.net/).
gputils is a collection of tools for Microchip PIC microcontrollers. Its goal is to be fully compatible with Microchip's tools, MPASM, MPLINK, and MPLIB.
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.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
Free cross-platform viewer for seismic data in SEG-Y format (Revision 1 draft 6 and its modifications).
qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.
Simple tools for working with gravitational waves
GWtool: simple tools for working with gravitational waves
The Ocean Land Atmosphere Model (OLAM) is a new global general circulation/climate prediction model that will allow to “nest down” to any desired resolution using a flexible mesh refinement technique that works on either triangular or hexagonal g
SWAN is a third-generation wave model, developed at Delft University of Technology, that computes random, short-crested wind-generated waves in coastal regions and inland waters.
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.
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.
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.
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
A Suite of Programs implementing a fast approach to the Debye Function Analysis (DFA) of powder diffraction data from nanocrystalline and/or non-ordered materials. See J. Appl. Cryst. 2015, 48, 2026-2032
Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
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.
Massively parallel software for quantum chemistry calculations
Scalable Molecular Analysis Solver for High-performance computing systems (SMASH) is open-source software for massively parallel quantum chemistry calculations. It is currently capable of energy, analytical gradient, and geometry optimization calculations of Hartree-Fock theory and Density Functional Theory (DFT), and energy calculations of Second-order Moller-Plesset (MP2) perturbation theory. DFT calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
Generic data-assimilation toolbox written in java, with native (c and fortran) libraries for high performance computing. Provides tools to couple to your own model and a wide range of algorithms, ranging from parameter calibration to Kalman filters.
The Open-source Pseudopotential Interface / Unification Module (OPIUM) allows to generate pseudopotentials in an interactive way, perform ghost checks, Kleinman-Bylander transformation, and output in many different pseudopotential file formats.
MMTL, the Multilayer Multiconductor Transmission Line 2-D and 2.5-D electromagnetic modeling tool suite, generates transmission parameters and SPICE models from descriptions of electronics interconnect dimensions and materials properties.
RINGS "Rigorous Investigation of Networks Generated using Simulations" is a scientific code developed in Fortran90/MPI to analyze the results of molecular dynamics simulations. Its main feature is the analysis of the connectivity using ring statistics.