Energy calculation (bulk and surface)

• In this section, we will see how to do the energy calculation of the bulk material and the surface of the bulk material.
• Please see the energy calculation for molecules if not yet.
• The bulk material is crystal surface, which is periodic in three dimensions (i.e. x-, y-, and z-directions).

Downloading CIF files

• To do the bulk/surface calcuation, Crystal information file (CIF) file is often needed.
• The CIF file can be downloaded from Materials project, ICSD, or others.
• Here, a simple CIF file (Pt.cif) is prepared so please use it.
• The CIF file contains the information of atomic position and unit cell information.

Bulk

• Similar to the calculations for molecules, we need to make POSCAR, POTCAR, INCAR, and KPOINTS files.

Making POSCAR

• Here we will see how to make a POSCAR file from a cif file using VESTA.
• VESTA is the free software for visualization and editing the molecular/bulk/surface structure: https://jp-minerals.org/vesta/jp/
• You can visualize CIF, POSCAR, xyz (and other) files with VESTA.
• To make the POSCAR file for bulk calculation, open the CIF file and then
  1. File -> Export Data and then choose VASP file in File type.
  2. Any name is OK.
  3. Either "fractional coordinate" or "Cartesian coordinate" is OK.
  4. Rename the file to POSCAR.

POTCAR

• Do not forget to make POTCAR file: cat {POTCAR_directory}/Pt/POTCAR > POTCAR.

INCAR

• Actually, INCAR for bulk/surface calculations can be very similar to those of molecules.
• However, we are going to use ISMEAR = 1 instead of ISMEAR = 0 in molecular calculation. This is because Pt is metals, so use of ISMEAR = 1 is recommended for metallic systems.

  SYSTEM = Pt bulk
  ISMEAR =  1
  NSW    =  0
  IBRION = -1
  

KPOINTS

• For the bulk calculation,

  bulk
  0
  Monkhorst Pack
  3 3 3
  0 0 0
  

Executing VASP

• Execution of VASP is the same with the energy calculation of molecule.
  • edit run.sh script (or any name)
  • qsub run.sh

Exercise

• Download the Au (gold) cif file from web (Materials Project etc.) and perform the bulk structure calculation.

Surface

• If you want to do calculations for surfaces, the situation is a little different because the surface loses one periodic direction. Usually this axis is set as z-direction.
• To cut the periodicity of z-direction, a vacant region called vacuum layer in inserted in the surface calculaiton.

Making POSCAR

• It is possible to make the surface file with VESTA; see https://qiita.com/h-nabata/items/290a575e07a2e56c7c94
• It is rather complicated. So we will use Atomic simulation environment (ASE) instead.

ASE

• ASE is useful Python library for theoretical/computational atomic simulations.

• To setup the Python environment, see; https://github.com/ishikawa-group/python_introduction/blob/main/setup.md.

• To make the POSCAR file for surface (e.g. fcc 111 surface), write and execute the following Python script.

  from ase.io import write
  from ase.build import fcc111
  
  surf = fcc111(a=3.92, symbol="Pt", size=[2, 2, 4], vacuum=10.0)
  write("POSCAR", surf)
  

• You can check the structure with VESTA, or using ase gui POSCAR if you've installed the ASE.
• The above script, using the ASE function fcc111, makes the Pt surface with the supercell size of 2x2x4, and introduces the vacuum layer of 10 Angstrom in z-direction. As noted, this vacuum layer is necessary to cut the interaction between upper and lower periodic slabs.
• More details are given in adsorption.md.

Fixing some atoms

• In surface calculations, the lower part of the slab is usually fixed to mimic the bulk structure.
• To fix some atoms, make the POSCAR as following:

  Pt
  1.000
    11.074    0.000    0.000
     0.000   11.495    0.000
     0.000    0.000   29.090
  Pt
  32
  Selective dynamics
  Cartesian
  0.000  2.874  0.100   F F F
  2.768  0.000  0.100   F F F
  0.000  8.621  0.100   T T T
  ...
  

• Put Selective dynamics in after the atomic number section.
• Put F F F at the end of atomic species, to freeze x-, y-, and z-coordinate of that atom.
• F means .FALSE. to move that atom, and T means .TRUE. to move. So open some editor, and put F F F at the atoms you want to freeze.

POTCAR

• Same with bulk or molecular calculations.

KPOINTS

• For the surface calculation, just one k-point is OK for the non-periodic direction. So when the vaccum layer is in the z-direction, following is fine.

  surface
  0
  Monkhorst Pack
  3 3 1
  0 0 0
  

• Using more k-points gives higher accuracy, but larger computational cost.

Executing VASP

• Same with bulk or molecular calculations.

Exercise

1. Perform the Pt surface calculation by yourself.
2. Perform the Pt bulk calculation, and compare the Pt bulk and surface calculations by taking the energy per Pt atom. Which is lower (lower is more stable), bulk or surface?