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exercises:2018_uzh_cmest:defects_in_graphene [2018/09/17 12:52] (current)
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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
 +    &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
 +</​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)