exercises:2018_uzh_cmest:defects_in_graphene
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+ | ======= Analyzing 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: | ||
+ | |||
+ | <code cp2k grapehene.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>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 [[http:// | ||
+ | |||
+ | |||
+ | <note important> | ||
+ | |||
+ | ====== Vacancy in graphene ====== | ||
+ | |||
+ | ===== Comparing energies ===== | ||
+ | |||
+ | 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. | ||
+ | |||
+ | ===== Analyze the PDOS ===== | ||
+ | |||
+ | 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. | ||
+ | |||
+ | ===== Replacement with oxygen ===== | ||
+ | |||
+ | Now, instead of removing one carbon atom from the 6x6x1 supercell, simply replace it with an oxygen atom (remember: you have to a '' |
exercises/2018_uzh_cmest/defects_in_graphene.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1