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.
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/
Cellular Automata library for SUPercomputers (CASUP)
CASUP is a Fortran 2018 cellular automata library for HPC and supercomputers. It can be used in materials science (microstructure evolution, grain coarsening, fracture etc.), physics (Ising magnetisation) and for many other CA. CASUP project page: http://cgpack.sf.net. (The old project name was CGPACK). If you use the library, please reference it as: A. Shterenlikht, L. Margetts, Three-dimensional cellular automata modelling of cleavage propagation across crystal boundaries in polycrystalline microstructures, Proc. Roy. Soc. A 471:20150039, DOI: http://dx.doi.org/10.1098/rspa.2015.0039. CASUP can be linked with FE (e.g. MPI FE library ParaFEM, http://parafem.org.uk) for a multi-scale multi-physics CA-FE framework. CASUP extensively uses Fortran 2008 and 2018 coarrays, as well as MPI, OpenMP and do concurrent. CASUP can be used with Cray, Intel and GCC/OpenCoarrays compilers. Scaling beyond 100,000 cores on Cray XC30 was achieved.
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.
hydrological model for simulation of water and water quality over time
Please go to project home (http://hypecode.smhi.se) for more information. The hydrological model HYPE is developed at the Swedish Meteorological and Hydrological Institute (SMHI). The model simulates water, nutrients and other substances in small and large river catchments. Included in the project is HYSS, which is needed to run the model. It handles input and output and the simuation over time.
A FOTRAN 90 Numerical library (AFNL) is a set of MODULES containing definitions of Fourier series and polynomials, and able to perform linear (multi-)dimensional fittings, integrals, sorting data, compute roots of functions, and other numerical tasks.
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
function library efficiently solving the Nearest Neighbor Problem (also know as the post office problem).
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
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/
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.
The Earth System Modeling Framework provides high-performance software infrastructure and superstructure for the construction and coupling of climate, weather, and data assimilation applications.
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.
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.
ISAAC (Integrated Solution Algorithm for Arbitrary Configurations) is a computational fluid dynamics (CFD) code developed to test and apply high order turbulence models for compressible flows around complex geometric configurations.
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.
Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
FORTRAN Unit Test Framework FRUIT - TDD in FORTRAN
FORTRAN Unit Test Framework, written in FORTRAN 95. So that all FORTRAN features can be tested. FRUIT has assertion, fixture, setup, teardown, report, spec, driver generation. Rake used as build tool. Tutorials at http://fortranxunit.wiki.sourceforge.net The core testing part is in FORTRAN, this part can be used independent of the Ruby codes. The Ruby code is to make fixtures and reports easier. Rake is to build the project elegantly. This project also demonstrate a new way to build mixed language code in an alternative way than Make. Most of the FORTRAN are important in nature, used in nuclear and aerospace codes, etc, and maintained and written actively. Please help to bring TDD practices to the FORTRAN community. The change could be very hard, personally, I quit, since I could not make the change. I hope your organization will be successful. Enjoy a cup of fruit while maintaining FORTRAN ! Andrew Hang Chen and other maintainers who feel importance of TDD in cr
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.
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.
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.
Airfoil optimization with Xfoil
Airfoil optimization using the highly-regarded Xfoil engine for aerodynamic calculations. Starting with a seed airfoil, Xoptfoil uses particle swarm, genetic algorithm and direct search methodologies to perturb the geometry and maximize performance. The user selects a number of operating points over which to optimize, desired constraints, and the optimizer does the rest.
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.