Electron poor materials research group
Group meeting Nov 11, 2010
Theory- Si an exploration of
what is a bond via charge
density.
Procedure
• Static Calculations of the 4 FCC structures were computed from
accurate relaxation (see previous weeks precentation)
– Calculations were done on a Gamma 11X11X11 grid
– USED NG(X,Y,Z)F of 6XNG(X,Y,Z) for accurate charge density grid.
– An extra flag was used in the INCAR file: LAECHG = .TRUE.
•
•
•
•
Turns on All Electron CHGCAR file outputs and outputs 3 files
AECCAR0: core charge density
AECCAR1: atomic AE charge density (overlapping atomic charge density)
AECCAR2: AE charge density
• The files AECCAR0 and AECCAR2 are added together for bader
analysis per instructions:
http://theory.cm.utexas.edu/bader/vasp.php
– chgsum.sh AECCAR0 AECCAR2, chsum is a shellscript
• Outputs CHGCAR_sum
• Bader analysis is done on the vasp CHGCAR from the static run
– bader.x -p atom_index -p bader_index CHGCAR -ref CHGCAR_sum
• atom_index: Write the atomic volume index to a charge density file
• bader_index: Write the Bader volume index to a charge density file
Si - Atom location and charge
Bader analysis
ACF.dat :
#
X
Y
Z
CHARGE MIN DIST ATOMIC VOL
-------------------------------------------------------------------------------1
0.0000
0.0000
0.0000
3.9681
1.1316 20.2891
2
1.3672
1.3672
1.3672
4.0319
1.1051 20.6007
-------------------------------------------------------------------------------VACUUM CHARGE:
0.0000
VACUUM VOLUME:
0.0000
NUMBER OF ELECTRONS:
8.0000
Bader charge shift = 0.0319
Si atomic bounding box according to Bader
Charge density Isosurfaces
High charge density of
valence electrons. 0.24
electrons/Å3 (I think :P)
Vesta claims 0.08
Subtracted Charge density
• Calculate charge density of crystal. CHGCAR
• Now calculate the charge density of each of the atoms within
the crystal individually using the same lattice constants and
same input parameters.
• Subtract the charge density of individual (CHGCAR-1,
CHGCAR-2 …) atoms from the charge density of the crystal.
Giving a resultant charge denstiy ρf.
N
 f  C   i
N
 f  0;
C 
i 1
i 1
 f  0;
N
C 

i 1
i
 f  0;
N
C 

i 1

i
i
Subtracted charge density. ρf > 0
Here the
isosurface lies
in line directly
between
bonded Si
Atoms
Subtracted charge density. ρf < 0
Here the
isosurface lies
in a line with
the Si-Si bonds
but on the
opposite side
of the nearest
bonding atom.
Subtracted charge density. ρf > 0 is yellow,
ρf < 0 is blue
Subtracted charge density. Slice of charge
density.
Subtracted charge density. Slices of charge
density.