CrystalsMotion Package (July 1992)

Author: K. Nishidate, Y. Fujimura*, K. Nishikawa, M. Suhara
   Department of Chemistry, Faculty of Science, Kanazawa University,
    Kanazawa, 920, Japan
 * Addison-Wesley Publishing Company Japan

Copyright 1992 Permission is granted to modify and/or make copies of 
this package(CrystalsMotion) for any purpose other than direct 
profit, or as part of a commercial product, provided this copyright 
notice is left intact and incorporated in the modified version. 

Overview

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 to 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 .

FILE DESCRIPTION
NaCl.ma		Mathematica Notebook containing animation of the NaCl crystal
		from the MD calculation.
KCl.ma		Mathematica Notebook containing animation of the KCl crystal
		from the MD calculation.
MgF2.ma		Mathematica Notebook containing animation of the MgF2 crystal
		from the MD calculation.
CaF2.ma		Mathematica Notebook containing animation of the CaF2 crystal
		from the MD calculation.
Perovskite.ma	Mathematica Notebook containing animation of Perovskite
		(CaTiO3) crystal from the MD calculation.
Quartz.ma	Mathematica Notebook containing animation of the Quartz
		(SiO2) crystal from the MD calculation. 
QuartzProjection.ma
		Mathematica Notebook containing projection view of Quartz
		(SiO2) crystal. (MD-unit cell version)
QuartzStereo.ma	 Mathematica Notebook containing stereoscopic view of Quartz
		(SiO2) crystal. (MD-unit cell version)

# Program creating the Mathematica-animation package : ANRZR2(K. Nishidate)
# MD-Calclation Program : MXDORTO(K. Kawamura), 
  [ Japan Chemistry Program Exchange(JCPE), P029. ]
# ComputerSystem: HP Apollo 730

References

Mathematica packages (MathSource library)
0200-316: Crystal Structure Graphics (August 1991)
          Produces a nice picture of the crystal structure of diamond.
0202-059: Gallium Arsenide Crystal Graphics (February 1992)
          Author: Alastair McLean
          Renders the GaAs(110) surface within Mathematica. 

MD simulation
[3] Matsui, Y. & Kawamura, K.:Instantaneous structure of an MgSiO/sub 3/
    melt simulated by molecular dynamics, Nature 285(5767), 648-649(1980)
[4] Matsui, Y. & Kawamura, K. & Syono, Y.: Molecular dynamics calculations
    applied to silicate systems: Molten and vitreous MgSiO/sub 3/ and 
    Mg/sub 2/Si O/sub 4/ under low and high pressures, High Pressure Research
    in Geophysics (Akimoto & Manghani eds), 511-524
[5] Matui, Y. & Kawamura, K.: Computer simulation of structures of silicate
    melts and glasses, "Materials Science of the Earth's Interior" 
    (Sunagawa ed.) 3-23(1984)
[6] Tsuneyuki, S., Tukada, M., Aoki, H. & Matsui, Y.:First-priciples interatomic
    potential of silica applied to molecular dynamics, Phys. Rev. Lett., 61
    (7), 869-872(1988)
[7] Matsui, M. and Price, G. D.:Computer simlation of the MgSiO/sub 3/ 
    polymorphs, Phys. Chem. Minerals, 18(1992), 365-372.
[8] L. Verlet : Phys. Rev., 159(1967), 98.
[9] H. C. Andersen: J. Chem. Phys., 72(1980), 2384.
[10] M. Parrinello and A. Rahman : J. Appl. Phys., 52(1981), 7182.
[11] S. Nose: J. Chem. Phys., 81(1984), 511
[12] Y. Kaneko, A. Ueda and Y. Hiwatari.: J. Phys. Soc. Jpn.,55(1986), 1244.
[13] Ciccotti, G. Hoover, W. G.(Eds): Molecular Dynamics Simulation of 
     Statistical-Mechanical Systems,North-Holland(1986)
[14] Ciccotti, G. Frenkel, D. and McDonald(Eds): Simulation of liquids and solids
     (Molecular Dynamics and Monte Carlo Methods in Statistical Mechanics),
     North-Holland Personal Library(1987)

If you have any comments, you could contact us at
	nisidate@hep.s.kanazawa-u.ac.jp

Enjoy the dynamic motion of crystals in computer! 
Another type of animation coming soon.