# Open SourceMolecular Dynamics

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exercises:2018_uzh_cmest:defects_in_graphene

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 — exercises:2018_uzh_cmest:defects_in_graphene [2018/09/17 12:52] (current) Line 1: Line 1: + ======= 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: + + ​ + &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 [[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).​ + + + ​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.​ + + ====== 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.