CASINO manual - Theory of Condensed Matter
CASINO manual - Theory of Condensed Matter
CASINO manual - Theory of Condensed Matter
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4<br />
Input geometry<br />
C 0.000000 0.000000 0.000000 5.000000<br />
H -1.407651 -1.138185 0.054434 -1.000000<br />
H 0.894354 0.554315 1.263301 -1.000000<br />
H 0.528074 1.081535 -0.755823 -1.000000<br />
4<br />
Input geometry<br />
C 0.000000 0.000000 0.000000 5.000000<br />
H -1.407651 -1.138185 0.054434 -1.000000<br />
H 0.894354 0.554315 1.263301 -1.000000<br />
H 0.528074 1.081535 -0.755823 -1.000000<br />
(etc.)<br />
Notes:<br />
1. The movie.out file follows the standard (x, y, z) molecular format.<br />
2. Line 1 indicates the total number n <strong>of</strong> ions and particles.<br />
3. Line 2 is a comment.<br />
4. The following n lines consist <strong>of</strong> five columns. Column 1 specifies the type <strong>of</strong> particle (H=electron,<br />
O=hole and C=other atoms). Columns 2, 3 and 4 are the x, y and z coordinates <strong>of</strong> the particle.<br />
Column 5 specifies the charge <strong>of</strong> the particle.<br />
5. This information is then repeated. The total number <strong>of</strong> sets <strong>of</strong> geometry contained in movie.out<br />
is controlled by the keywords vmc equil nstep, vmc nstep and movieplot in the input file.<br />
6. For column 1, the ‘H=electron, O=hole and C=other atoms’ convention is somewhat confusing,<br />
but is necessary because particles have to take on element symbols in order for the standard<br />
visualization programs to read the movie.out file.<br />
7. Column 5 is not read by the visualization programs. It is only there so that different types <strong>of</strong><br />
particle can be distinguished.<br />
11.2 Visualization<br />
Having generated the movie.out file we are able to visualize the results using vmd or jmol. (This<br />
information probably needs updating!)<br />
11.2.1 VMD<br />
vmd (Visual Molecular Dynamics) is a molecular visualization program. It supports computers running<br />
MacOS-X, Unix, or Windows, is distributed free <strong>of</strong> charge, and includes source code. VMC can<br />
be downloaded from www.ks.uiuc.edu/Research/vmd/.<br />
• Type vmd. A ‘VMD console’ and a ‘VMD Display’ window will appear.<br />
• In the ‘VMD console’ window type menu main on. An extra ‘VMD Main’ menu bar will appear.<br />
• On the ‘VMD Main’ menu bar, click on File → New Molecule. A ‘Molecule File Browser’<br />
will appear.<br />
• In the ‘Molecule File Browser’, browse for the file movie.out and choose the file type to be xyz.<br />
Click Load to open the file.<br />
• On ‘VMD Main’, click on Graphics → Representations. A ‘Graphical Representations’ menu<br />
bar will pop up. Choose CPK as the drawing method, the bond resolution to be 1 and the<br />
sphere resolution to be 15. Click Apply.<br />
• On ‘VMD Main’, click on Extensions → vmdmovie. (For version 1.8.3, click on Extensions<br />
→ Visualization → Movie Maker.) A ‘VMD Movie Generator’ will pop up.<br />
120