Charge analysis - Bader charge

• The atomic charge can be calculted with Bader's method. This charge is called Bader charge.
• The positive charge means atoms are positively charged (cationic), and negative charge means anionic atoms.

INCAR

• It is always better to calculate the Bader charge with all-electron charge density, i.e. valence and core electrons.
• VASP usually doesn't give all electron charge density (valence only) so following INCAR tag is needed.
  • LCHARG = .TRUE.
  • LAECHG = .TRUE.
• This generates the files AECCAR0 and AECCAR2.

Making Bader charge sum with VTST script

Preparation

VTST script

1. Download VTST scripts from Henkelman group (in University of Texas): https://theory.cm.utexas.edu/code/vtstscripts.tgz
2. Extract by tar zxvf vtstscripts.tgz

Bader

1. Download bader: https://theory.cm.utexas.edu/henkelman/code/bader/download/bader.tar.gz
2. Extract by tar zxvf bader.tar.gz
3. cd bader
4. cp makefile.lnx_ifort Makefile
5. make
6. module load intel (when using supercomputer)
7. Done. Command file for Bader analysis is bader in that directory.

Making CHGCAR_sum

• Make all-electron CHGCAR by vtstscript/chgsum.pl AECCAR0 AECCAR2
  • CHGCAR_sum should be generated

• bader CHGCAR -ref CHGCAR_sum

  • Files like ACF.dat or BCF.dat are generated.
  • Bader charge is written in ACF.dat.
  • "CHARGE" colum gives the number of valence electrons for each atom in that system (so the value is "electron population" rather than "charge").
  • To calculate the charge, the number of valence electrons (in atom) should be subtracted.

  • This value is written in ZVAL in POTCAR.

    $${\rm charge} = -(N_{\text{calculated number of electron}} - {\rm ZVAL})$$

Charge density

Visualizing charge density

• Charge density can be visualized by using VESTA and CHGCAR file, which is generated by VASP calculation.

• With VESTA, open CHGCAR

• Adjust isosurface values with "Objects" --> "Property" --> "Isosurface". Positive means negative charge.

• The unit of charge densities input by VESTA is $\rm{Bohr}^{-3}$.

2 dimensional (plane) plot

• "Utilities" --> "2D Data Display"
• Define the plane with "Slice". Select three atoms in the plane. Miller index also can be used.

Charge density difference with VESTA

• Calculate "adsorbate + surface", "adsorbate", and "surface".
• Prepare CHGCAR files for each.
• "Edit" --> "Edit Data" --> "Volumetric data" -> "Import" then import CHGCAR file for "adsorbate + surface".
• After that, subtract the CHGCAR file of adsrobate. Repeat the same thing for surface CHGCAR.
• You need to define temporary directory because VESTA only accept the CHGCAR-named file.

Ref: http://renqinzhang.weebly.com/uploads/9/6/1/9/9619514/charge_density_difference.pdf

Plotting the spin density with VESTA

Generating spin density

• You can use either VTST script or Vaspkit to generate spin density file.

VTST script

1. Do spin-polarized calculation by setting ISPIN = 2 and LCHARG = .TRUE. in INCAR.
2. Confirm that CHGCAR is generated.
3. vtstscripts/chgsplit.pl CHGCAR --> CHGCAR_tot and CHGCAR_mag are generated
4. Copy CHGCAR_mag to tmpCHGCAR (any xxxCHGCAR filename is OK) and load with VESTA.

Vaspkit

• Type vaspkit to go interactive mode, and choose 31 and then 312.
• Althernatively, executure vaspkit -task 312 to do the same thing.