exercises:2015_ethz_mmm:surface_cu
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exercises:2015_ethz_mmm:surface_cu [2015/03/04 00:49] – dpasserone | exercises:2015_ethz_mmm:surface_cu [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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- | ====== Generation of slab with high symmetry surfaces ====== | ||
- | |||
====== 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> | ||
+ | |||
+ | <code bash> | ||
+ | you@eulerX ~$ module load new cp2k | ||
+ | </ | ||
+ | |||
+ | **and to submit the job:** | ||
+ | |||
+ | <code bash> | ||
+ | you@eulerX ~$ bsub < jobname | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | |||
+ | {{: | ||
+ | |||
+ | ---- | ||
+ | |||
+ | {{: | ||
+ | |||
+ | ---- | ||
+ | |||
+ | {{: | ||
+ | |||
+ | |||
In this exercise we will compute the surface energies of Cu using the EAM potential. | In this exercise we will compute the surface energies of Cu using the EAM potential. | ||
As a reference, we report the table from the Gross book: | As a reference, we report the table from the Gross book: | ||
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{{screen_shot_2014-03-07_at_6.55.49_am.png? | {{screen_shot_2014-03-07_at_6.55.49_am.png? | ||
+ | ---- | ||
+ | * 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> | ||
+ | you@eulerX ~$ wget http:// | ||
+ | you@eulerX ~$ unzip exercises: | ||
+ | you@eulerX ~$ cd exercise_3.1 | ||
+ | </ | ||
+ | * Run the optimizations 100.inp, 110.inp, 111.inp and the bulk. | ||
+ | <code bash> | ||
+ | you@eulerX exercise_3.1$ bsub cp2k.popt -i 100.inp -o 100.out | ||
+ | you@eulerX exercise_3.1$ bsub cp2k.popt -i 110.inp -o 110.out | ||
+ | you@eulerX exercise_3.1$ bsub cp2k.popt -i 111.inp -o 111.out | ||
+ | you@eulerX exercise_3.1$ bsub cp2k.popt -i bulk.inp -o bulk.out | ||
+ | </ | ||
+ | * 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> | ||
+ | you@eulerX exercise_3.1$ vmd 100.xyz | ||
+ | you@eulerX exercise_3.1$ vmd 110.xyz | ||
+ | you@eulerX exercise_3.1$ vmd 111.xyz | ||
+ | </ | ||
- | | + | * Compute the three surface energies: you need to compute the area, subtract bulk contribution, |
- | - Use the batch **run_cp2k_lattice** to run a chain of simulations on a Cu bulk system. From the output **lat.out** check the lattice constant corresponding to minimum cohesive energy **PER ATOM** (divide by the number of particles, find it out!), you will need it later | + | |
- | - Run the optimizations 100.inp, 110.inp, 111.inp ---- look at the corresponding initial coordinate files 100.xyz, 110.xyz, 111.xyz. | + | |
- | - In vmd, you can also 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. | + | |
- | - Compute the three surface energies: you need to compute the area, subtract bulk contribution, | + | <code bash> |
- | | + | you@eulerX exercise_3.1$ |
- | | + | </ |
- | | + | |
- | | + | - 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. If you appropriately modify it (how?) you can have a xyz file to be opened in vmd. |
- | - * 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. If you appropriately modify it (how?) you can have a xyz file to be opened in vmd. | + | - the **out.plot-gnuplot.plt** file. You can open it with gnuplot: |
- | - * the **out.plot-gnuplot.plt** file. If you launch | + | <code bash> |
- | | + | you@eulerX exercise_3.1$ |
+ | gnuplot> | ||
+ | gnuplot> | ||
+ | gnuplot> | ||
+ | gnuplot> | ||
+ | gnuplot> | ||
+ | </ | ||
+ | * you can rotate with the mouse! | ||
- | < | + | < |
+ | 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! | ||
+ | </ | ||
<note tip> | <note tip> |
exercises/2015_ethz_mmm/surface_cu.1425430172.txt.gz · Last modified: 2020/08/21 10:14 (external edit)