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Author Archives: Dan Gezelter
OOPSE
OOPSE is a new molecular dynamics simulation program which is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded … Continue reading
Posted in Molecular Dynamics
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The Molecular Workbench Software
The Molecular Workbench is a set of tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using classical dynamics and applicable forces, including van der … Continue reading
Posted in Molecular Dynamics
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Metro
Metro is an open source tool designed to evaluate the hausdorff distance between two triangular meshes. Metro adopts an approximated approach based on surface sampling and point-to-surface distance computation. Find Metro at: https://github.com/cnr-isti-vclab/vcglib/tree/master/apps/metro
Posted in Geometry
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EChem++
a problem solving environment (PSE) for electrochemical experiments. This PSE is intended to provide support for the definition of electrochemical experiments, their control, simulation, and analysis. Find EChem++ at: http://www.echem.uni-tuebingen.de/~bs/echem/software/EChem++/echem++.shtml
Posted in Electrochemistry
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PAL: Phylogenetic Analysis Library
The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces … Continue reading
Posted in Genetics
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JabRef bibliography manager
JabRef is a graphical application for managing bibliographical databases. The main focus is on BibTeX databases, but other database formats will be supported as well. JabRef is distributed under the terms of the Gnu General Public License, runs on all … Continue reading
Posted in Tools
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Nuclear Simulation Java Class Libraries
The class libraries here provide infrastructure for creating simulations of low energy nuclear physics experiments, as well as some useful working programs that do simple simulations and analysis of experiments performed with magnetic spectrographs. Find Nuclear Simulation Java Class Libraries … Continue reading
Posted in Nuclear
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Jam: A Java-based Data Acquisition System for Nuclear Physics
Jam is an easy-to-use self-contained data acquisition and analysis system for VME-based (or CAMAC-based) nuclear physics experiments. Jam has an easy, standard GUI for taking and sorting multi-parameter event-based data into 1-d and 2-d histograms. Find Jam: A Java-based Data … Continue reading
Posted in Nuclear
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XmdS
xmds – the eXtensible Multi-Dimensional Simulator – is a program for solving equations – fast. It is a tool to simplify the computer modelling of various systems, and is currently being developed within the Australian Centre for Quantum-Atom Optics at … Continue reading
Posted in Partial
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Quickplot
Quickplot is a fast interactive 2D plotter with infinite zooming, value picking, pipe input, and unlimited plots displayed. Quickplot is meant for looking at your data quickly and of secondary importance is making static pictures of your data. It’s a … Continue reading
Posted in Tools
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