exercises:2017_uzh_cmest:adsorption
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exercises:2017_uzh_cmest:adsorption [2017/11/05 22:00] – jglan | exercises:2017_uzh_cmest:adsorption [2017/11/07 14:36] – [CO adsorption on graphene] tmueller | ||
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- | In this exercise, you will be asked to calculate the adsorption energy of CO molecule | + | ====== Adsorption |
- | The reference paper you can find in [[https:// | + | |
- | Take the input from the last exercise | + | In this exercise, you will be asked to calculate |
- | <code cp2k grapehene.inp> | + | ===== Lattice constant optimization ===== |
+ | |||
+ | As you have seen in earlier exercises, the actual energy -- and therefore also the stress tensor -- depends on many parameters, like the selected functional. This means that geometrical parameters like the lattice constant may also vary and therefore need to be optimized first when building a new geometry. While this could be done using CP2K's '' | ||
+ | |||
+ | What we are using to determine the center volume (the volume for which the energy is minimal) is the Birch–Murnaghan equation of state (to be precise: the BM equation integrated over pressure), which links the energy and the volume using the minimal energy $E_0$, the center volume $V_0$, the bulk modulus $B_0$ and its derivative $B_1$: | ||
+ | |||
+ | \begin{align*} | ||
+ | E(V) = E_0 + \frac{9 V_0 B_0}{16} \Bigg\{ | ||
+ | \left[ \left(\frac{V_0}{V}\right)^{2/ | ||
+ | \Bigg\} | ||
+ | \end{align*} | ||
+ | |||
+ | Use the following input file as a starting point, and an adapted version of the script you documented in a [[exercises: | ||
+ | |||
+ | Extract the energies and fit $E_0$, $V_0$, $B_0$, $B_1$ using the Birch–Murnaghan EOS and using the new $V0$ determine the lattice constant. | ||
+ | |||
+ | <code cp2k graphene.inp> | ||
&GLOBAL | &GLOBAL | ||
PROJECT graphene | PROJECT graphene | ||
Line 80: | Line 95: | ||
</ | </ | ||
- | Adsorb one CO molecule on the graphene 6X6X1 supercell at the top(T), bridge(B) and center(C) sites and optimize the geometry. | ||
- | The adsorption energy is given by:$ E_{ad} | + | <note tip>The following commands may be useful. |
+ | |||
+ | Doing calculations on the command line using the '' | ||
+ | |||
+ | < | ||
+ | bc -l <<< | ||
+ | |||
+ | # you can also use variables and capture the output again in a variable: | ||
+ | x=1.025 | ||
+ | a=$(bc -l <<< | ||
+ | </ | ||
+ | |||
+ | Replacing numbers (or any text) inside a file and write the changed file to a new file: | ||
+ | |||
+ | < | ||
+ | a=3.54 | ||
+ | sed -e " | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | <note warning> | ||
+ | Be careful when fitting values for the Birch-Murnaghan EOS: the volume is usually the volume per atom (and the total volume of the cell you can also get from the CP2K output). | ||
+ | </ | ||
+ | ===== CO adsorption on graphene | ||
+ | |||
+ | Adsorb one < | ||
+ | |||
+ | You need change the '' | ||
+ | |||
+ | <note tip> | ||
+ | You can get a 6x6x1 unit cell with absolute coordinates by using '' | ||
+ | |||
+ | < | ||
+ | [...] | ||
+ | | ||
+ | |||
+ | Atom Kind Element | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | [...] | ||
+ | </ | ||
+ | </ | ||
- | Find the most stable | + | The adsorption |
+ | This means that you also have to run an auxiliary geometry optimization calculation for < | ||
+ | Which one is the most stable adsorption site? |
exercises/2017_uzh_cmest/adsorption.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1