exercises:2017_uzh_cmest:adsorption
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exercises:2017_uzh_cmest:adsorption [2017/11/03 16:03] – jglan | exercises:2017_uzh_cmest:adsorption [2017/11/07 14:14] – [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 |
- | Adsorb one CO molecule on the top(T), bridge(B) and center(C) sites and optimize the geometry. | + | ===== Lattice constant optimization ===== |
- | The adsorption | + | As you have seen in earlier exercises, the actual |
+ | 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 | ||
+ | PROJECT graphene | ||
+ | RUN_TYPE ENERGY | ||
+ | PRINT_LEVEL MEDIUM | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | METHOD Quickstep | ||
+ | &DFT | ||
+ | BASIS_SET_FILE_NAME | ||
+ | POTENTIAL_FILE_NAME | ||
+ | |||
+ | & | ||
+ | PERIODIC XYZ | ||
+ | &END POISSON | ||
+ | &SCF | ||
+ | SCF_GUESS ATOMIC | ||
+ | EPS_SCF 1.0E-6 | ||
+ | MAX_SCF 300 | ||
+ | |||
+ | # The following settings help with convergence: | ||
+ | ADDED_MOS 100 | ||
+ | CHOLESKY INVERSE | ||
+ | &SMEAR ON | ||
+ | METHOD FERMI_DIRAC | ||
+ | ELECTRONIC_TEMPERATURE [K] 300 | ||
+ | &END SMEAR | ||
+ | & | ||
+ | ALGORITHM STANDARD | ||
+ | EPS_ADAPT 0.01 | ||
+ | &END DIAGONALIZATION | ||
+ | &MIXING | ||
+ | METHOD BROYDEN_MIXING | ||
+ | ALPHA 0.2 | ||
+ | BETA 1.5 | ||
+ | NBROYDEN 8 | ||
+ | &END MIXING | ||
+ | &END SCF | ||
+ | &XC | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | |||
+ | &PDOS | ||
+ | # print all projected DOS available: | ||
+ | NLUMO -1 | ||
+ | # split the density by quantum number: | ||
+ | COMPONENTS | ||
+ | &END | ||
+ | &END | ||
+ | &END DFT | ||
+ | |||
+ | &SUBSYS | ||
+ | &CELL | ||
+ | # create a hexagonal unit cell: | ||
+ | ABC 2.4612 2.4612 15.0 | ||
+ | ALPHA_BETA_GAMMA 90. 90. 60. | ||
+ | SYMMETRY HEXAGONAL | ||
+ | PERIODIC XYZ | ||
+ | &END CELL | ||
+ | &COORD | ||
+ | SCALED | ||
+ | C 1./3. 1./3. 0. | ||
+ | C 2./3. 2./3. 0. | ||
+ | &END | ||
+ | &KIND C | ||
+ | ELEMENT C | ||
+ | BASIS_SET DZVP-MOLOPT-GTH | ||
+ | POTENTIAL GTH-PBE | ||
+ | &END KIND | ||
+ | &END SUBSYS | ||
+ | |||
+ | &END FORCE_EVAL | ||
+ | </ | ||
+ | |||
+ | |||
+ | <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=$(bc -l <<< | ||
+ | </ | ||
+ | |||
+ | Replacing numbers (or any text) inside a file and write the changed file to a new file: | ||
+ | |||
+ | < | ||
+ | a=3.54 | ||
+ | sed -e " | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | <note warning> | ||
+ | Be careful when fitting values for the Birch-Murnaghan EOS: the volume is usually the volume per atom (and the total volume of the cell you can also get from the CP2K output). | ||
+ | </ | ||
+ | ===== CO adsorption on graphene ===== | ||
+ | |||
+ | Adsorb one < | ||
+ | |||
+ | You need change the '' | ||
+ | |||
+ | <note tip> | ||
+ | You can get a 6x6x1 unit cell with absolute coordinates by using '' | ||
+ | |||
+ | < | ||
+ | [...] | ||
+ | | ||
+ | |||
+ | Atom Kind Element | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | [...] | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | |||
+ | The adsorption energy is given by:$ E_{ad} = E_{CO+graphene} - E_{CO} - E_{graphene}$ | ||
+ | |||
+ | This means that you also have to make an auxiliary geometry optimization calculation using < | ||
+ | |||
+ | 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? |
exercises/2017_uzh_cmest/adsorption.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1