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M - Complex cell modifications

An extremely powerful option! It allows you to modify your existing geometry in a number of ways and build up your final periodic cell. You will be given an extended menu with self-explanatory options. You should be able to change your lattice vectors; extend your cell; rotate, shift the system; add, remove, shift atoms; change their species; construct a slab for the surface calculation using e.g. Millers indices, etc. What is more, after every step a geom.xyz (xyz-format) file with the system geometry is written in the current directory so that you can preview your cell on the fly as you build it using a molecular viewer (e.g. Xmol)! In fact, you can even preview it as an extended cell (the option Bb). Every step can also be undone.

The M-menu looks like this:

>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<

... CURRENT lattice vectors for the supercell ARE...

AJ(1): 10.88160 0.00000 0.00000

AJ(2): 0.00000 10.88160 0.00000

AJ(3): 0.00000 0.00000 10.88160

>>>>>>>>>>>>>>>> Current species are: <<<<<<<<<<<<<<

Si O

========= CHOOSE AN OPTION:

/==================================================\\

|| HELP: a complex transformation is obtained by ||

|| applying elementary operations one after another||

\\==================================================/

1. General shift of the system (new origin)

2. Shift the system to the center of mass

3. Rotate the system (the same origin)

4. Move an atom to an equivalent position

Rf. Choose equivalent positions wrt reference input file

44. Cluster atoms around particular point

6. Choose unit cell with respect to Miller indices:

1st 2 lattice vectors will be in the (hkl) plane

Ex. Diagonal "breeding": construct a supercell

Su. General "breeding": construct a supercell

8. Create/modify SLAB: change the 3rd(z) lattice vector

9. Arbitrarily change lattice vectors (e.g. for molecules)

10. Manually add an atom to the cell

Ad. Add atoms from another file

/11. Remove a range of atoms from the cell

\12. Keep a range of atoms in the cell: remove the rest

13. Rename a range of atoms: change species

Mv. Move a range of atoms to another general position

Rt. Rotate a range of atoms about the X,Y,Z axes

----- operations with multiple lists of atoms ------

T. Tag atoms (specify multiple lists): currently OFF

------- 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>

Co. Show current atomic positions in fractional/Cartesian

Sy. Show the point symmetry

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 an appropriate option:

At the top, the current lattice vectors and species are shown. What you can do is explained below:

Normally, a set of atoms is chosen by two atomic numbers, in which case all atoms with the numbers in between are also chosen. If it is required to have a more complex non-contagious set of atoms in the list, use the option T, that allows you to do this (see Section 1.2). Note that all atoms added to the system from another file (option Ad) are tagged automatically, so that you can move and/or rotate them.

Other useful options (in seetings) include:

Once the necessary geometry is created (the lattice vectors, number of atoms in species and their positions in space), it can be saved using option S (Section 2.6.11.1).


next up previous contents
Next: KP - k-points generation Up: Detailed description of options Previous: Cl - Build up   Contents
Lev Kantorovich 2006-05-08