exercises:2018_uzh_cmest:defects_in_graphene

Now we are going to draw our attention towards surfaces and the effect of defects on them.

Use the following input file as a starting point for this exercise, noting that you will have to make some modifications to it:

- grapehene.inp
&GLOBAL PROJECT graphene RUN_TYPE ENERGY PRINT_LEVEL MEDIUM &END GLOBAL &FORCE_EVAL METHOD Quickstep &DFT BASIS_SET_FILE_NAME BASIS_MOLOPT POTENTIAL_FILE_NAME POTENTIAL &POISSON 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 &DIAGONALIZATION 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 &XC_FUNCTIONAL PBE &END XC_FUNCTIONAL &END XC &PRINT &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

When comparing scaled coordinates between papers and code input scripts, always make sure that they use the same coordinate systems and definitions for a unit cell (both real and reciprocal space). For example while many sources (like the paper of Curtarolo, Setyawan) assume a 120° degree angle between $a$ and $b$ for a hexagonal cell, you can also define it to be a 60° angle (like the default in CP2K).

Once you have verified that your calculation setup works, use

`nohup mpirun -np 4 cp2k.popt … &`

again to run the calculations in parallel and in the background since they may take longer to complete than before.
Use the provided template and its initial geometry to setup a single point energy calculation for a 6x6x1 supercell of graphene.

Create a vacancy by removing one carbon atom from this supercell and perform the energy calculation again.

Quick question: Does it matter which carbon atom you remove? (hint: what kind of boundary conditions do we impose?)

Calculate the energy of the vacancy formation, that is $E_v = E_2 - \frac{N-1}{N} \cdot E_1$ where $E_1$ is the energy of the complete system, $E_2$ that of the system with a vacancy and $N$ the number of atoms.

Would you expect the vacancy to haven any influence on the projected density of states? Check whether your assumption was right by visualizing the PDOS.

Now, instead of removing one carbon atom from the 6x6x1 supercell, simply replace it with an oxygen atom (remember: you have to a `KIND`

section for oxygen). Perform first a single point calculation and second a geometry optimization (as shown in a previous exercise) and compare the energy of adsorption for both cases.

exercises/2018_uzh_cmest/defects_in_graphene.txt · Last modified: 2018/09/17 14:52 (external edit)

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