exercise_1 - Molecular Dynamics Simulations 2011 Exercise 1...

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Unformatted text preview: Molecular Dynamics Simulations 2011 Exercise 1: Suggested solutions Eero Holmstrom ¨ September 14, 2011 1. The program ex1, given in both C and Fortran, as are all model solutions to come, performs the desired functions. The program is compiled by typing make in a linux or unix terminal. After compiling, the program can be used to create a 4 × 4 × 4 FCC lattice of Cu by the command ./ex1 1 4 4 4 > fcc.xyz. Here the program prints out the coordinates in xyz format, and we redirect the output to the file fcc.xyz. Then we can use e.g. RasMol to visualize the system. The results are presented in Figs 1 and 2. 2. For visualizing the (111) surface, the program ex1 can be used to either cut the cube in the (111) plane (mode 2), or the system can be built out of unit cells with the xy -side in the (111) plane (mode 3). Results using the former approach, ./ex1 2 4 4 4 > fcc_cut.xyz, are visualized in Figs 3 and 4. Instructions for constructing a rectangular unit cell with the xy -side in the (111) plane are presented in Fig. 5. Figure 1: Visualization of the FCC lattice using a ’ball and stick’ representation, i.e. plotting atoms and the bonds between them (determined simply by interatomic distance). 2 Figure 2: Visualization of the FCC lattice using a ’spacefill’ representation, i.e. plotting the atoms as solid spheres of the Van der Waals radius. 3 Figure 3: Visualization of the (111) surface of the FCC lattice using a ’ball and stick’ representation, i.e. plotting atoms and the bonds between them (determined simply by interatomic distance). 4 Figure 4: Visualization of the (111) surface of the FCC lattice using a ’spacefill’ representation, i.e. plotting the atoms as solid spheres of the Van der Waals radius. 5 Figure 5: A rectangular FCC unit cell with the xy -side in the (111) plane is spanned by the vectors bx , by , and bz shown here. 6 ...
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This note was uploaded on 02/14/2012 for the course CSE 6590 taught by Professor Kotakoski during the Winter '12 term at York University.

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exercise_1 - Molecular Dynamics Simulations 2011 Exercise 1...

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