Bader charges of two Zr atoms
Posted: Tue Feb 17, 2009 8:47 pm
Dear all,
I am applying the code bader to a simple model system, two Zr atoms in a cubic box with a side of 4 A.
To compute the electron density, a Zr pseudpotential is used with 12 valence electrons: two 4s, six 4p, two 4d, and two 5s.
The electron density is written to a Gaussian .cube file whose starting point is (0,0,0).
For the first test, the two Zr atoms are given fractional coordinates of (0,0,0) and (0.5,0.5,0.5).
As expected, bader produces the following output in ACF:
1 0.0000 0.0000 0.0000 11.9945 3.1678 224.5750
2 3.7795 3.7795 3.7795 12.0057 3.1640 218.2087
That is, both Zr atoms are assigned 12 electrons.
For the second test, the two Zr atoms are given fractional coordinates of (0.25,0.25,0.25) and (0.75,0.75,0.75).
The following is produced in ACF:
1 1.8897 1.8897 1.8897 11.9302 2.7616 215.6611
2 5.6692 5.6692 5.6692 12.0700 2.6725 227.1226
That is, only 11.93 electrons are assigned to one of the Zr atoms, while the other one receives 12.07 electrons.
This error does not rapidly reduce if the grid resolution is increased.
In the .cube files, a zero is assigned to the grid points at x=L, y=L, or z=L that are periodically repeated.
Might this error arise from the fact that the zeroed points are not distributed in a more uniform fashion along the sides of the box?
If so, would you be able to recommend a program that reformats the .cube file in order to eliminate this error?
Sincerely,
Yves
I am applying the code bader to a simple model system, two Zr atoms in a cubic box with a side of 4 A.
To compute the electron density, a Zr pseudpotential is used with 12 valence electrons: two 4s, six 4p, two 4d, and two 5s.
The electron density is written to a Gaussian .cube file whose starting point is (0,0,0).
For the first test, the two Zr atoms are given fractional coordinates of (0,0,0) and (0.5,0.5,0.5).
As expected, bader produces the following output in ACF:
1 0.0000 0.0000 0.0000 11.9945 3.1678 224.5750
2 3.7795 3.7795 3.7795 12.0057 3.1640 218.2087
That is, both Zr atoms are assigned 12 electrons.
For the second test, the two Zr atoms are given fractional coordinates of (0.25,0.25,0.25) and (0.75,0.75,0.75).
The following is produced in ACF:
1 1.8897 1.8897 1.8897 11.9302 2.7616 215.6611
2 5.6692 5.6692 5.6692 12.0700 2.6725 227.1226
That is, only 11.93 electrons are assigned to one of the Zr atoms, while the other one receives 12.07 electrons.
This error does not rapidly reduce if the grid resolution is increased.
In the .cube files, a zero is assigned to the grid points at x=L, y=L, or z=L that are periodically repeated.
Might this error arise from the fact that the zeroed points are not distributed in a more uniform fashion along the sides of the box?
If so, would you be able to recommend a program that reformats the .cube file in order to eliminate this error?
Sincerely,
Yves