exercises:2017_ethz_mmm:surface_cu
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exercises:2017_ethz_mmm:surface_cu [2017/02/22 10:01] – external edit 127.0.0.1 | 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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---- | ---- | ||
- | * Download all the necessary files from from the wiki: {{exercise_3.1.zip|exercise_3.1.zip}} (**all inputs are commented**) in your home directory and unzip it: | + | * Download all the necessary files from from the wiki: {{e4.1.zip|e4.1.zip}} (**all inputs are commented**) in your home directory and unzip it: |
<code bash> | <code bash> | ||
- | you@eulerX ~$ wget http:// | + | you@eulerX ~$ wget http:// |
- | you@eulerX ~$ unzip exercises:2016_ethz_mmm:exercise_3.1.zip | + | you@eulerX ~$ unzip exercises:2017_ethz_mmm:e4.1.zip |
- | you@eulerX ~$ cd exercise_3.1 | + | you@eulerX ~$ cd exercise_4.1 |
</ | </ | ||
+ | |||
+ | If you cannot download with **wget**, you can copy the zip file directly from my directory | ||
+ | <code bash> | ||
+ | you@eulerX ~$ cp / | ||
+ | you@eulerX ~$ unzip e4.1.zip | ||
+ | you@eulerX ~$ cd exercise_4.1 | ||
+ | </ | ||
+ | |||
* Run the optimizations 100.inp, 110.inp, 111.inp and the bulk. | * Run the optimizations 100.inp, 110.inp, 111.inp and the bulk. | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
- | you@eulerX | + | you@eulerX |
- | you@eulerX | + | you@eulerX |
- | you@eulerX | + | you@eulerX |
</ | </ | ||
* While geometry optimization is running you can have a look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. In vmd it is also possible to open a console, and give the command **pbc set { a b c 90 90 90 }** where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization. | * While geometry optimization is running you can have a look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. In vmd it is also possible to open a console, and give the command **pbc set { a b c 90 90 90 }** where a, b, c can be extracted from the cp2k input file. Then you can make several periodic copies for visualization. | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
- | you@eulerX | + | you@eulerX |
- | you@eulerX | + | you@eulerX |
</ | </ | ||
Line 55: | Line 70: | ||
* At this point, you can run the sowos program: | * At this point, you can run the sowos program: | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
</ | </ | ||
* 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.1487757669.txt.gz · Last modified: 2020/08/21 10:15 (external edit)