exercises:2017_uzh_cmest:adsorption
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exercises:2017_uzh_cmest:adsorption [2017/11/06 08:52] – jglan | exercises:2017_uzh_cmest:adsorption [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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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:// | + | |
- | =====Lattice constant optimization===== | + | In this exercise, you will be asked to calculate |
- | Take the input from the last exercise | + | |
- | <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 94: | ||
&END FORCE_EVAL | &END FORCE_EVAL | ||
</ | </ | ||
- | <note tip>You can use bash script for loop | ||
- | < | ||
- | for i in `seq 0.95 0.025 1.05` | ||
- | do | ||
- | mkdir $i | + | <note tip>The following commands may be useful. |
- | cd $i | + | Doing calculations on the command line using the '' |
- | i=$(echo $i * 2.4612 | bc) | + | |
- | cp ../bulk.inp . | + | |
- | | + | < |
+ | bc -l <<< | ||
- | mv grapehene.inp bulk-$i.inp | + | # you can also use variables and capture the output again in a variable: |
+ | x=1.025 | ||
+ | a=$(bc | ||
+ | </ | ||
- | | + | Replacing numbers (or any text) inside a file and write the changed file to a new file: |
- | cd .. | + | |
- | done | + | < |
+ | a=3.54 | ||
+ | sed -e "s|2.4612|$a|g" graphene.inp > " | ||
</ | </ | ||
</ | </ | ||
- | =====CO adsorption on graphene===== | + | <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 '' | ||
- | Adsorb one CO molecule on the graphene 6X6X1 supercell at the top(T), bridge(B) and center(C) sites and optimize the geometry. | ||
- | You need change the RUN_TYPE to GEO_OPT and also specify the coordinate by yourself. One can get 6x6x1 unit cell by using MULTIPLE_UNT_CELL which was mentioned in previous exercises. | ||
< | < | ||
- | &GLOBAL | + | [...] |
- | | + | MODULE QUICKSTEP: |
- | | + | |
- | | + | |
- | &END GLOBAL | + | |
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | [...] | ||
</ | </ | ||
+ | </ | ||
+ | |||
+ | |||
+ | The adsorption energy is given by:$ E_{ad} = E_{CO+graphene} - E_{CO} - E_{graphene}$ | ||
- | The adsorption energy is given by:$ E_{ad} = E_{CO-graphene} - E_{CO} - E_{graphene}$ | + | This means that you also have to run an auxiliary geometry optimization calculation for < |
- | Find the most stable adsorption site and study the coverage effect such like 1/2 and 1. What do you observe when increasing the coverage? | + | Which one is the most stable adsorption site? |
exercises/2017_uzh_cmest/adsorption.1509958365.txt.gz · Last modified: 2020/08/21 10:15 (external edit)