# Open SourceMolecular Dynamics

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exercises:2017_ethz_mmm:surface_cu

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 exercises:2017_ethz_mmm:surface_cu [2017/03/17 04:47]dpasserone exercises:2017_ethz_mmm:surface_cu [2017/03/17 10:34]dpasserone Both sides previous revision Previous revision 2017/03/17 14:59 dpasserone 2017/03/17 10:34 dpasserone 2017/03/17 04:47 dpasserone 2017/03/17 04:39 dpasserone 2017/03/17 04:39 dpasserone 2017/03/17 04:26 dpasserone 2017/03/17 04:25 dpasserone 2017/03/17 04:24 dpasserone 2017/03/17 04:20 dpasserone 2017/02/22 10:01 external edit 2017/03/17 14:59 dpasserone 2017/03/17 10:34 dpasserone 2017/03/17 04:47 dpasserone 2017/03/17 04:39 dpasserone 2017/03/17 04:39 dpasserone 2017/03/17 04:26 dpasserone 2017/03/17 04:25 dpasserone 2017/03/17 04:24 dpasserone 2017/03/17 04:20 dpasserone 2017/02/22 10:01 external edit Last revision Both sides next revision Line 67: Line 67: * There will be many output files. Important are: * There will be many output files. Important are: - the atomistic model **out.atomistic-inside-gnuplot.xyz** which will contain many atoms if you chose a proportionality constant in the file DP which is too large. Unfortunately this file does NOT have a proper structure of an xyz file. - the atomistic model **out.atomistic-inside-gnuplot.xyz** which will contain many atoms if you chose a proportionality constant in the file DP which is too large. Unfortunately this file does NOT have a proper structure of an xyz file. + - This can be solved by using a simple m_* function that adds the atomic symbol at the beginning of each line, and adding two lines at the beginning of the resulting file (number of atoms; comment): + + you@eulerX exercise_4.1$m_addcolumn Au < out.atomistic-inside-gnuplot.xyz > cluster.xyz + you@eulerX exercise_4.1$ nano cluster.xyz # Add two lines at the beginning. + ​ - the **out.plot-gnuplot.plt** file. You can open it with gnuplot - the **out.plot-gnuplot.plt** file. You can open it with gnuplot