GARAGe Software

Posted on June 26, 2002 by Dan Gezelter

Genetic Algorithms Research and Applications Group (GARAGe) software: a suite of programs that do genetic algorithms. Includes GALOPPS, the “Genetic ALgorithm Optimized for Portability and Parallelism System”; lilgp, a generic ‘C’ genetic programming tool; and daga, an experimental release of a 2-level genetic algorithm compatible with GALOPPS.
Find GARAGe Software at: http://garage.cse.msu.edu/software/index.html

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Posted in Algorithms And Computational Theory | Leave a comment

AIPS

Posted on April 29, 2002 by Dan Gezelter

Astronomical Image Processing System. This is the classic system used to reduce radio observations.
Find AIPS at: http://www.aoc.nrao.edu/aips/

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Posted in Astronomy | Leave a comment

IRAF

Posted on April 29, 2002 by Dan Gezelter

Image Reduction and Analysis Facility
Find IRAF at: http://iraf.noao.edu/iraf-homepage.html

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GROMACS

Posted on April 18, 2002 by Dan Gezelter

GROMACS is a very fast molecular dynamics code, which comes with lots of features like PME, a variety of cut-offs, non-equilibrium MD and more. The package includes also other algorithms like normal mode analysis and essential dynamics plus a wealth of analysis tools. It is supported by some of the leading trajectory viewers (VMD and gOpenMol). GROMACS is distributed under the GPL.
Find GROMACS at: http://www.gromacs.org

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Scilab

Posted on April 16, 2002 by Dan Gezelter

Scilab is a scientific software package for numerical computations in a user-friendly environment. It features: Elaborate data structures (polynomial, rational and string matrices, lists, multivariable linear systems,…). Sophisticated interpreter and programming language with Matlab-like syntax. Hundreds of built-in math functions (new primitives can easily be added). Stunning graphics (2d, 3d, animation). Open structure (easy interfacing with Fortran and C via online dynamic link). Many built-in libraries: Linear Algebra (including sparse matrices, Kronecker form, ordered Schur,…). Control (Classical, LQG, H-infinity,…). Package for LMI (Linear Matrix Inequalities) optimization. Signal processing. Simulation (various ode’s, dassl,…). Optimization (differentiable and non-differentiable, LQ solver). Scicos, an interactive environment for modeling and simulation of dynamical systems. Metanet (network analysis and optimization). Symbolic capabilities through Maple interface. Parallel Scilab.
Find Scilab at: http://www.scilab.org/

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Posted in Mathematics | Leave a comment

Tessel

Posted on April 15, 2002 by Dan Gezelter

Tessel is a 3D "compiler" to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations. Molecular models combine balls-and-sticks, arrows and coordination polyhedra representations of pure and defective crystals, finite molecules or clusters. The Madelung potential of an ionic system can be computed and depicted on an arbitrary plane or surface. The common crystallographic cell (parallepipedic), as well as the Wigner-Seitz cell or the irreducible components of the WS cell can be easily added to the plot.
Find Tessel at: http://azufre.quimica.uniovi.es/src/tessel/examples/tessel2b.html

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Posted in Molecule Viewers and Editors | Leave a comment

KMatPlot

Posted on April 12, 2002 by Dan Gezelter

KMatplot is a gnuplot-like tool for plotting data sets in either two or three dimensions. It can plot many types of 2d plots, including pixmaps and contours, and 3d surfaces. It offers a full WYSIWYG mode with multiple objects on a single page. As opposite to Gnuplot, KMatplot is very clickable, so easier to use for unexperienced users. It can be used instead of Gnuplot with Octave and Scilab – there are new dll functions installed in those packages, which communicate with KMatplot through an Unix socket. Those functions are named ‘kplot’, ‘kimage’, kmesh’, … and are similar to those found in Octave by default.
Find KMatPlot at: http://kmatplot.sourceforge.net

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ABINIT

Posted on April 12, 2002 by Dan Gezelter

ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulation using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. In addition to the main ABINIT code, different utility programs are provided.
Find ABINIT at: http://www.abinit.org

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Posted in Ab Initio Quantum Chemistry | Leave a comment

Significant Figures

Posted on April 11, 2002 by Dan Gezelter

Libraries for working with scientific numbers in Java programs.
Find Significant Figures at: http://ostermiller.org/utils/SignificantFigures.html

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Posted in Symbolic and Algebraic Manipulation | Leave a comment

JNumeric: Numerical Python for Jython

Posted on March 27, 2002 by Dan Gezelter

Provides the functionality for Jython that Numerical Python does for Python (CPython). As the Numerical Python documentation states, it is "…a collection of extension modules to provide high-performance multidimensional numeric arrays to the Python programming language." JNumeric provides the same functionality as the core of Numeric module and aims to provide all of the standard extensions to Numeric module (FFT, LinearAlgebra, RandomArray).
Find JNumeric: Numerical Python for Jython at: http://jnumerical.sourceforge.net

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Posted in Numerical Methods | Leave a comment