Here, it is possible to modify the electron density on the grid3.11 by taking away (setting to zero) the density at all grid points that are inside spheres build around specified atoms. This might be useful if, for instance, one is interested in some local region in the cell, e.g. a defect. In this case the density associated with the atoms around that region can be removed to isolate the density in the region of interest. Sometimes, some of the density inside that region (e.g. around specific atoms) can also be removed. This way it is easy, for example, to get the ``pure'' F-centre density localised in the vacancy which can be then (see Section ) simulated by point charges.
The spheres radii are calculated inside the code from the charges that to be cut off around each atom; the charges are specified by the user. The initial menu:
..............MENU for CUT ...........................
......... Change these parameters if necessary:.......
>>>>> Representation of results: through number of electrons
>>>>> Algorithm for the charge integration: <nonconserving>
1. Specify atoms/electrons to be cut out of the density:
2. The smallest radius (Angstroms): 5.00000
3. The largest radius (Angstroms): 10.00000
4. The number of points between these radii: ... undefined ...
5. X,Y,Z integration grid inside the sphere: 30
6. Scan atoms to obtain the radii using charge to cut
---- A t o m i c p o s i t i o n s -----
Co. Show current atomic positions in fractional/Cartesian
--- L e a v e t h e m e n u -------
Q. Return to the previous menu
---> Choose the item and press ENTER:
In option 1 you can specify a range of atoms (e.g. 5-10) that carry the same charges and which should be removed. At the same time, you will be asked about the (positive) charge to be associated with the atoms. It is not possible to specify several lists of atoms. However, when using option 1 several times, it is possible to update and complement the existing list of atoms, and add other atoms with different charges. For example, in the case of a MgO cell, you can first enter a list of Mg atoms with nearly zero electron charge, and then (the second time) - the list of O atoms with the charge of, say, 7.8.
The next step is to specify the radii (options 2 and 3) and the number of points (option 4). This information will be used for interpolation of the charge around the atoms listed in option 1. Then, perform the scan of all specified atoms in 6, and the radii for each set of atoms of equal charge will be calculated. The menu grows:
..............MENU for CUT ...........................
......... Change these parameters if necessary:.......
>>>>> Representation of results: through number of electrons
>>>>> Algorithm for the charge integration: <nonconserving>
1. Atoms to be cut out of the density:
To be cut 2 atoms with numbers(electrons):
1( 0.10) 2( 0.50)
2. The smallest radius (Angstroms): 0.10000
3. The largest radius (Angstroms): 2.00000
4. The number of points between these radii: 10
5. X,Y,Z integration grid inside the sphere: 30
6. Scan atoms to obtain the radii using charge to cut <= DONE!
7. Show the list of atoms and their radii + exact charge to be cut out
8. The threshhold: the smallest density allowed: 0.000000E+00
9. Cut atoms out (current density (in memory) is destroyed!)
---- A t o m i c p o s i t i o n s -----
Co. Show current atomic positions in fractional/Cartesian
--- L e a v e t h e m e n u -------
Q. Return to the previous menu
---> Choose the item and press ENTER:
The calculated information can be previewed in 7, e.g.
Please, wait, scanning the charge density again ...
>>>>>>>> Radii + charges for chosen atoms <<<<<<<<
# atom radius charge(asked) charge(estimate) charge(actual)
1 1 0.76386 0.10000000 0.09044981 0.08987854
2 2 0.23717 0.50000000 0.30739785 0.30747416
Press ENTER when ready ...
Here one can see for each atom the sphere radius found by interpolation from the target charge, an estimate of the charge calculated using the nonconserving algorithm (Section 3.5) for the same radius, and, finally, the actual charge inside the sphere calculated using the conserving algorithm.
It is also possible to remove the density from the grid points where the density is smaller than some specified threshold in 8.
Finally, option 9 sets all grid points of the density that are found inside either of the specified spheres to zero. After the calculation, the following information is displayed:
9. Cut atoms out (current density (in memory) is destroyed!)
Out of the total original density = 8.00338
... grid points removed due to radii = 4870
... with the density cut out = 0.39735
... add. grid points removed due to threshold = 0
... with the density cut out = 0.000000E+00
... so that the TOTAL density left is = 7.60602
10. Write charges cut out + core charges into a file
Some information about the charges on removed atoms can be obtained and then saved in a file charges.cut in a new option 10.