exercises:2017_ethz_mmm:surface_cu
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exercises:2017_ethz_mmm:surface_cu [2017/03/17 04:39] – dpasserone | exercises:2017_ethz_mmm:surface_cu [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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====== Surface energies of Copper high-symmetry surfaces ====== | ====== Surface energies of Copper high-symmetry surfaces ====== | ||
+ | <note warning> | ||
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
+ | |||
+ | you@eulerX ~$ module load courses mmm vmd | ||
+ | |||
+ | you@eulerX ~$ mmm-init | ||
+ | </ | ||
<note important> | <note important> | ||
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If you cannot download with **wget**, you can copy the zip file directly from my directory | If you cannot download with **wget**, you can copy the zip file directly from my directory | ||
<code bash> | <code bash> | ||
- | you@eulerX ~$ cp /Users/ | + | you@eulerX ~$ cp /cluster/ |
+ | you@eulerX ~$ unzip e4.1.zip | ||
+ | you@eulerX ~$ cd exercise_4.1 | ||
</ | </ | ||
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* 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): | ||
+ | <code bash> | ||
+ | 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 | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
gnuplot> load " | gnuplot> load " | ||
gnuplot> set xrange [-80:80] | gnuplot> set xrange [-80:80] |
exercises/2017_ethz_mmm/surface_cu.1489725564.txt.gz · Last modified: 2020/08/21 10:15 (external edit)