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
ATLAS (Automatically Tuned Linear Algebra Software) provides highly optimized Linear Algebra kernels for arbitrary cache-based architectures. ATLAS provides ANSI C and Fortran77 interfaces for the entire BLAS API, and a small portion of the LAPACK AP
CFD-related Fortran libraries and applications
The CFD Utility Software Library (previously known as the Aerodynamics Division Software Library at NASA Ames Research Center) contains nearly 30 libraries of generalized subroutines and close to 100 applications built upon those libraries. These utilities have accumulated during four decades or so of software development in the aerospace field. All are written in Fortran 90 or FORTRAN 77 with potential reuse in mind. The only exception is the C translations of a dozen or so numerics routines grouped as C_utilities. David Saunders and Robert Kennelly are the primary authors, but miscellaneous contributions by others are gratefully acknowledged. See 1-line summaries of the libraries and applications under the Files menu. Each library folder also contains 1-line summaries of the grouped subroutines, while each application folder contains READMEs adapted from the main program headers. NASA permission to upload actual software was granted on Jan. 24, 2014.
Open source finite element software for multiphysical problems
Elmer is a finite element software for numerical solution of partial differential equations and multiphysical problems. It includes models of structural mechanics, fluid dynamics, heat transfer, electromagnetics etc. Elmer home is www.csc.fi/elmer
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!
Eclim is a set of eclipse and vim plugins to integrate the two projects.
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.
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/
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.
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).
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.
Open-Source Multiphysics FEA (FEM) Package
CalculiX Binaries for MS Windows, made with CYGWIN and ARPACK libraries. CalculiX is most popular FEA open-source package (like Code-Aster and Elmer-FEM). it is comparable in features with most known commercial packages like ANSYS, NASTRAN, Abaqus, etc. Good for structural, mechanical, thermal and fluid applications (trusses, plates, frames, shells, solid bodies). It has powerful nonlinear capabilities (including tension/compression only material like concrete) and most types of analysis (modal, thermal, buckling, coupled, etc) . See home page at http://www.dhondt.de New versions can be obtauned here: http://calculixforwin.blogspot.com/2015/05/calculix-launcher.html
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.
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.
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.
The Earth System Modeling Framework provides high-performance software infrastructure and superstructure for the construction and coupling of climate, weather, and data assimilation applications.
The CFD General Notation System (CGNS) provides a standard for recording and recovering computer data associated with the numerical solution of fluid dynamics equations. We are in process of moving! Old stable releases can still be found here, but the new repository is at https://github.com/CGNS
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/
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.
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.
The purpose of this project was to prepare gfortran for integration into gcc. Since this integration was completed in the summer of 2003, this project is now finished. You can find information about gfortran on http://gcc.gnu.org/wiki/GFortran/
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.
This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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.