OpenScience / Software



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 … Continue reading →

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Posted in Molecular Dynamics | Leave a comment

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 … Continue reading →

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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 … Continue reading →

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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 … Continue reading →

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Posted in Tools | Leave a comment

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 … Continue reading →

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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 … Continue reading →

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Posted in Numerical Methods | Leave a comment

polyXmass

Posted on March 26, 2002 by Dan Gezelter

software for analyzing mass spectrometric data for polymers Find polyXmass at: http://www.polyxmass.org

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Posted in Analytical | Leave a comment

OpenBabel

Posted on March 26, 2002 by Dan Gezelter

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Find … Continue reading →

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Posted in Chemistry | Leave a comment

Gnotide

Posted on March 26, 2002 by Dan Gezelter

Tidal analysis software based on harmonic analysis. It can display the tidal record, calculate the fft and wavelet transforms, the least squares and allow tidal predictions. Additionally it display the moon phases associated with the spring and neap tides. Find … Continue reading →

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Posted in Oceanography | 1 Comment