exercises:2016_ethz_mmm:surface_cu
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exercises:2016_ethz_mmm:surface_cu [2016/02/03 09:54] – external edit 127.0.0.1 | exercises:2016_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 ====== | ||
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- | <note warning> | ||
- | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
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- | you@eulerX ~$ module load courses mmm vmd | ||
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- | you@eulerX ~$ mmm-init | ||
- | </ | ||
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</ | </ | ||
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- | {{: | + | |
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- | ---- | + | |
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- | {{: | + | |
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- | ---- | + | |
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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: {{exercise_3.1.zip|exercise_3.1.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:2015_ethz_mmm: | + | you@eulerX ~$ unzip exercises:2016_ethz_mmm: |
you@eulerX ~$ cd exercise_3.1 | you@eulerX ~$ cd exercise_3.1 | ||
</ | </ | ||
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</ | </ | ||
- | * Compute the three surface energies: you need to compute the area, subtract bulk contribution, | + | |
- | * Unordered List ItemIn the class we will learn how to compute the Wulff crystal from these three numbers. | + | <note tip> |
- | * Basically, you should edit the input file " | + | Assignments: |
+ | - Without calculating the surface energies but just looking at the structures, could you guess which surface will be the most stable one? And the least stable one? Why? (Quite often a simple logic could tell you already how your results should look like.) | ||
+ | - Have a look into the files, containing the optimization trajectory (100-pos-1.xyz, | ||
+ | - Compute the three surface energies: you need to compute the area, subtract bulk contribution, | ||
+ | </ | ||
+ | Now we will learn how to compute the Wulff crystal from these three numbers. Basically, you should edit the input file " | ||
* At this point, you can run the sowos program: | * At this point, you can run the sowos program: | ||
<code bash> | <code bash> | ||
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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. | + | - 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. |
- | - 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 exercise_3.1$ gnuplot | you@eulerX exercise_3.1$ gnuplot | ||
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gnuplot> replot | gnuplot> replot | ||
</ | </ | ||
- | * you can rotate with the mouse! | + | you can rotate with the mouse! |
+ | |||
+ | |||
<note tip> | <note tip> | ||
- | Assignment: use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system! | + | Assignments: |
+ | - What is the proper structure of a XYZ file? Try to appropriately modify **out.atomistic-inside-gnuplot.xyz** and open it in vmd. Make a nice snapshot and add it to your report. | ||
+ | - Use the cluster generated with SOWOS as an input configuration for a cluster optimization with cp2k. Comment on the final geometry. BEWARE OF THE CELL! It is not a periodic system! | ||
</ | </ | ||
<note tip> | <note tip> |
exercises/2016_ethz_mmm/surface_cu.1454493256.txt.gz · Last modified: 2020/08/21 10:15 (external edit)