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:

• 1 - all atoms in the cell will be displaced to a new position, the displacement vector will be asked in units corresponding to the setting An
• 2 - similar, but the displacement vector will be calculated from the atomic masses
• 3 - a rotation of the coordinate system is specified by giving new directions for a pair of two existing primitive lattice vectors using the existing coordinate system; of course, the angle between them should be preserved! This may be an inconvenience, but in some cases the choice is obvious
• 4 - move an atom to an equivalent position by adding lattice vectors to its current coordinate; this may be e.g. useful when building up a slab
• Rf - some codes such as VASP change atomic positions in the cell in such a way that their fractional coordinates become between 0 and 1; this may be not really wanted since after the relaxation (with VASP) it may be very difficult to recognise the cell; a cure is here: in this option upi will be prompted again to the Input-menu (Section 2.4) to read in another input file (e.g. before the relaxation) the atomic coordinates in the two geometries will be compared and proper lattice vectors applied to the relaxed atoms to ``return'' them to the original unit cell
• 44 - atoms in the system around a given point (atom) are shown that cluster around it; more specifically, the displayed atoms have fractional coordinates between -0.5 and 0.5 if the centre of the coordinate system is positioned at the chosen atom
• 6 - after specifying three Miller indices, a new equivalent set of primitive translations for the cell is given in which the first two vectors $\mathbf{A}_{1}$and $\mathbf{A}_{2}$ lie within the plane characterised by the Miller indices; use the option 3 above to rotate the whole cell so that your plane becomes perpendicular to the $z$ axes (if desired)
• Ex - extend you cell by elongating the three current primitive translations, i.e. the transformation matrix of Eq. (2.6.4) is diagonal: $T_{ij}=\delta_{ij}n_{i}$; the three integers $n_{i}$are to be specified
• Su - the current cell is extended using a general transformation matrix $\mathbf{T}$
• 8 - the third lattice vector can be arbitrarily changed here; this is necessary in creating a slab out of a bulk cell assuming that the vacuum gap is opened via the third lattice vector; note that atomic positions in the cell will not change
• 9 - all three lattice vectors can be changed; this may be useful in calculating a molecule or a cluster, if the distance between images must be changed; of course, atomic positions inside the cell do not change
• 10 - an additional atom is added to the cell; its position must be unique, otherwise, the atom is not added
• Ad - similar, but in this case all atoms from another file (that may be written even in a different format) can be added to the current system; the Input-menu (Section 2.4) is called here
• 11, 12 - these two options remove a set of atoms from the cell
• 13 - this renames a set of atoms, i.e. it changes their species into another species; this may be useful, e.g. in changing the lowermost atoms of the slab into hydrogens to terminate properly the slab and thus simulate the bulk at the lower surface
• Mv - move a set of atoms to another position (Section 2.6.11.2)
• Rt - rotate a set of atoms (Section 2.6.11.3)

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:

• U - undo the last transformation
• UU - restore the original geometry (the one with which you entered the M-menu initially)

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).