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!
Unit testing framework for Fortran with MPI extensions
pFUnit is a Fortran testing framework created by developers from NASA and NGC TASC. pFUnit offers a convenient, lightweight mechanism for Fortran developers to create and run software tests that specify the desired behavior for a given piece of code. See the website or wiki for more information.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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.
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.
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.
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.
SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces. It provides a general basis for describing wave transformations from deep water to a beach, port or harbour, complex changes to rapidly varied flows, and density driven flows in coastal seas, estuaries, lakes and rivers.
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.
Intellect Modeling Kit ~ AI intellect-based apps development suite
Intellect Modeling Kit is an alternative to traditional Artificial Intelligence, intended to build apps assisting human intellect on the steps of its activity: * Observation * Producing propositions based on knowledge * Elimination of impossible propositions * Selection and verification of the most appropriate propositions * Memorizing - converting data to information and new knowledge item creation * Abstraction finding – building artificial objects, representing group of real objects featuring typical signs of group Any human knowledge written and spoken can be uploaded to IMK in a straight way by any expert not familiar with software coding. The IMK components are designed to create ready-to-use software application using simple text files provided by people. IMK accepts human knowledge and develops new knowledge together with people. The activity of IMK could be verified by human expert on every stage. IMK assists intellectual activity, but does not replace us.
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.
Command-line tools for astronomy and astrophysics
Command-line tools for astronomy and astrophysics, written in Fortran.
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
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
PARAMESH is a package of Fortran 90 subroutines designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement(AMR).
Stress intensity factor (SIF) calculation from crack tip displacements
The code implements Muskhelishvili's complex function approach to calculate 2D stress intensity factors (modes I+II) from crack tip displacement fields. Surface displacements can be used with a plane stress elastic model. The code uses power/Fourier series expansion and a conformal mapping of an ellipse onto a circle.
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD.
Quantum Chemistry: Excited States Topology
An open source code for the analysis of electronic excited states: Natural Transition Orbitals; Detachment and Attachment Density Matrices; Quantum Chemical Charge-Transfer Descriptors. The code is intended to postprocess Gaussian 03 and 09 outputs. Important Note: A new release with better compilation option has been released on November the 9th 2015. We strongly advise to use this one since the previous option may have led to some unexpected bugs.
Python library to perform electronic structure calculations with tight binding models in different types of lattices and different dimensionalities. It allows to include different terms in the Hamiltonian as sublattice, exchange field or magnetic field. Provides functions to calculate different Green functions, band structure, density of states, transport using Landauer formula, topological invariants, etc.
Implementation of HYCOM physical ocean model with coupled biogeochemical component to study nitrogen fixation in the Amazon plume. This project is still in development, the code may not be functional at this time.
Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
A cross platform audio inteface
CIOS Audio Core is the infrastructure and subsystem in Collective Intelligence Operation System. It is a cross platforms audio abstract interface, supports including Mac OS X, Linux, Android, iPhone OS and Windows 7.
Benefit Your Learning of Climate Modeling
The goal of this project is to provide a couple of Fortran code to those students who selected the course of "Climate Modeling" in the department of atmospheric and oceanic sciences at Peking University. 这个项目的目标是给选择“气候模拟”课程（北京大学大气与海洋科学系）的同学提供与课程学习有关的源代码程序。 We are subject to GNU/GPL license and happy to open the code to the public. 我们遵守GNU/GPL协议，并乐于开放代码给所有需要的人。