exercises:2017_uzh_cmest:adsorption
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exercises:2017_uzh_cmest:adsorption [2017/11/06 15:21] – tmueller | exercises:2017_uzh_cmest:adsorption [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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===== Lattice constant optimization ===== | ===== 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 | + | 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 |
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 $B_1$: | 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 $B_1$: | ||
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\end{align*} | \end{align*} | ||
- | Use the following input file as a starting point, and an adapted version of the script you documented in a [[exercises: | + | 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. | 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. | ||
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< | < | ||
a=3.54 | a=3.54 | ||
- | sed -e "s/2.4612/$a/g" graphene.inp > " | + | sed -e "s|2.4612|$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_UNIT_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.1509981718.txt.gz · Last modified: 2020/08/21 10:15 (external edit)