FYSM350,  MD PART
<hr><br>
<a href="./generalinfo.pdf"> General info </a>
<br><br>
Lecture notes:
<a href="./Lecture1.pdf"> L1 </a> 
<br>
<a href="./Lecture2.pdf"> L2 </a>
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On L3 we'll discuss some material used in the corresponding course
(Kuronen and Nordlund) in HY: from the
<a href="http://www.acclab.helsinki.fi/~akuronen/atomistiset/">
	link </a> see Lectures 5,8,9
<br>
<a href="./Lecture4.pdf"> L4 </a>
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YOUR MD PROJECT IS DESCRIBED IN LECTURE 5:
<a href="./Lecture5.pdf"> L5 </a>
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A sample fortran MD code from openmp.org web site is 
<a href="./openmpmd.f"> here. </a>  We will discuss 28.3. a structure of a "good" MD program using this
code as an example. One can take this code as platform for your project (if you are using fortran)  but it
will need several modifications and additions. (Do not care about the OpenMP
directives - they would make the calculation run parallel if you would try
this code in a machine where OpenMP works. This is off the topic of our course.
Anyway this code works and can be run in serial CPU, the directives are
then ignored as comments.)
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Just for fun - visualisation
<a href="./N26.avi">(avi-file)  </a>
of the dynamcis of 26 Coulomb particles in a harmonic trap. The temperature is increased during the run and the system "melts " in an interesting way. Matlab - simulation by Timo Santa-Nokki 2004. The visualisation works at least with QuickTime viewer.
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Bits and pieces, sample f90 routines are discussed 
<a href="./f90samples.pdf">here.  </a>
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Simple tests for a MD code are found
<a href="./testingMD.pdf">here.  </a>
We will discuss these tests during the lecture Tuesday 4.4.
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Coordinate files for:  
<br><br>
<a href="./fcc-32.txt">
	32-atom fcc lattice in internal LJ units</a>, rho=1, corresponding to the lattice parameter
a = sqrt(2)*r0,  r0=2**(1/6)sigma (r0=position of the bottom of the LJ well) in
LJ units (sigma = 1) for MD test # 1,
<br>
the same  converted to  
<a href="./fcc-vmd-32.xyz">
	xyz format </a>
for VMD (sigma=3.4 A for Argon).
<br><br>
<a href="./fcc-256.txt">
	        256-atom fcc lattice </a> with the same lattice parameter
	<br>
	the same  converted to  
	<a href="./fcc-vmd-256.xyz">
		        xyz format </a>
		for VMD .
		<br><br>
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 <a href="http://www.phys.jyu.fi/homepages/merikosk/Simu2006.html"> homepage. </a>