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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 | ||

+ | |||

+ | &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 | ||

+ | |||

+ | &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 | ||

+ | </code> | ||

+ | |||

+ | <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://www.sciencedirect.com/science/article/pii/S0927025610002697|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).</note> | ||

+ | |||

+ | |||

+ | <note important>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.</note> | ||

+ | |||

+ | ====== 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 ''KIND'' section for oxygen). Perform first a single point calculation and second a geometry optimization (as shown in a [[[[geometry_optimization|previous exercise]]) and compare the energy of adsorption for both cases. |

exercises/2018_uzh_cmest/defects_in_graphene.txt · Last modified: 2018/09/17 12:52 (external edit)

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