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Crystal Animations Resulting from Molecular Dynamics Calculations
Authors

Kazume Nishidate
Organization: Iwate University
Department: Department of Electrical and Electronic Engineering
Yukitoshi Fujimura
Organization: Addison-Wesley Publishing Company Japan
Kiyoshi Nishikawa
Organization: Kanazawa University
Department: Department of Computational Science
Masahiko Suhara
Organization: Kanazawa University
Old MathSource #

0203-397
Revision date

1992-07-01
Description

Mathematica gives us a very useful and simple way to visualize Molecular Dynamics (MD) simulations. Mathematica is used to animate the motion of ions from the results of MD calculations produced by the ANRZR2 and MXDORTO programs, written by K. Nishidate and K. Kawamura, respectively. These notebooks allow us to "look" at the dynamic motion of ions within a crystal from the results of MD calculation. There are many advantages to using Mathematica to analyze the MD simlation. For example, we can easily view not only the animation of crystals, but also the graphics of trajectory of atoms over the MD simulation. Utilizing the graphics object in animation notebooks, stereoscopic views and projections of crystals can also be obtained .
Subjects

*Science > Physics > Crystallography
*Science > Physics > Solid State Physics
*Science > Physics > Thermodynamics and Statistical Mechanics
Keywords

Chemistry, Physics, Molecule, Graphics, Animation, Examples, graphics Presentation, presentation graphics, SiO2 Crystal, Quartz Crystal, Molecular Dynamics, CaTiO3 Crystal, Perovskite Crystal, CaF2 Crystal, Calcium Flouride Crystal, KCl Crystal, Potassium Chloride Crystal, MgF2 Crystal, Magnesium Flouride Crystal, NaCl Crystal, Sodium Chloride Crystal, Stereo Graphics, stereo pair, stereo projection, README.txt, NaCl.ma, KCl.ma, MgF2.ma, CaF2.ma, Perovskite.ma, Quartz.ma, QuartzProjection.ma, QuartzStero.ma
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README.txt (4.2 KB) - Author's notes
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CaF2.nb (74.6 KB) - Mathematica Notebook
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KCl.nb (79.9 KB) - Mathematica Notebook
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MgF2.nb (130.1 KB) - Mathematica Notebook
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NaCl.nb (79.9 KB) - Mathematica Notebook
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Perovskite.nb (83.2 KB) - Mathematica Notebook
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Quartz.nb (33.7 KB) - Mathematica Notebook
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QuartzProjection.nb (33.7 KB) - Mathematica Notebook
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QuartzStero.nb (28.3 KB) - Mathematica Notebook

Files specific to Mathematica 2.2 version:
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CaF2.ma (65.7 KB) - Mathematica Notebook 2.2 or older
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KCl.ma (70.2 KB) - Mathematica Notebook 2.2 or older
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MgF2.ma (113.6 KB) - Mathematica Notebook 2.2 or older
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NaCl.ma (70.2 KB) - Mathematica Notebook 2.2 or older
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Perovskite.ma (73.1 KB) - Mathematica Notebook 2.2 or older
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Quartz.ma (30.7 KB) - Mathematica Notebook 2.2 or older
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QuartzProjection.ma (30.7 KB) - Mathematica Notebook 2.2 or older
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QuartzStero.ma (25.6 KB) - Mathematica Notebook 2.2 or older