PE - PES: move atoms keeping the symmetry

An atom can be displaced from its positions, and all other atoms of the orbit^2.4 this atom belongs to (see Section 2.6.8.3) will be moved in concert to keep the symmetry. Atoms of the orbit are detected automatically. This is useful if one wants to calculate the potential energy surface (PES) with respect to full-symmetry displacements of atoms in the system. See also Sections 2.5.1 about symmetry.

First of all, you will arrive at the point group generator menu (Section 2.6.11.4). Use it to accept the group automatically detected or build a new one. Then the following menu will appear:

______ So, your system point group is C2h

       with elements:

           UNIT I P1 C21

Choose an option:

>>>>>> atoms are numbered across species <<<<<<<

1. Specify atom to be moved and show all equivalent

2. Choose the method of displacing atoms

M. Move it!

------- g e n e r a l s e t t i n g s --------

UU. ****** RESTORE the original serting ******

U. ********** UNDO *********** the last step

XY. Produce <geom.xyz> file after every change for Xmol

Hs. H atoms to be added to <geom.xyz> file: NO

An. [For input] Coordinates are specified in: <AtomNumber>

Sy. Check the symmetry after distortion

Co. Show current atomic positions in fractional/Cartesian

Bb. Set the size of the breeding box for visualisation

>>>>> Current setting for the breeding box: <<<<<

     [ 0... 0] x [ 0... 0] x [ 0... 0]

>>>>> extension = 1, # of atoms= 65

W. Write <geom.xyz> file to preview using current breeding

S. Save.

Q. Proceed/Quit

-----> Choose the appropriate option:

Apart from the self-explanatory options in the settings, the first tree options do the actual job:

• 1 - specify an atom that represents the orbit you wnat to displace
• 2 - choose how to displace and by what amount
• M - displace atoms of tbhis orbit

The new geometry can be written into a file with the desired format in a usual way (Section 2.6.11.1) via option S. After this is done, you can run the DFT code of your choice to calculate the energy.