V3 - Vibrations => application [DOS, masses]

This option works similarly to the previous one, V2, although the initial part is very different. At the beginning, all the necessary files (including forces) are read in. The data must be available for all representation, otherwise, you cannot proceed. Once everything is read in, the following V3-menu appears:

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

MOLECULE: lattice translations IGNORED

========= CHOOSE an OPTION:

Am. Change atomic masses for a range of atoms

--- A c t i o n s w i t h v i b r a t i o n s -----

Ei. Solve the eigenvalue problem

------------ p h o n o n D O S ---------

pD. Choose atoms for projected phonon DOS

------- G e n e r a l I n f o r m a t i o n ------

Co. Show information about atoms

Sy. Show the point symmetry group info

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

XY. Format of <movie.xyz> file is for Xmol

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

Da. Distortion amplitude for movies: 0.05000

Nd. Number of dispersions: 1

Sg. Dispersion for DOS (cm-1): 10.00000

St. Step for DOS (cm-1): 0.10000

Up. Upper limit for DOS: not set

W. Write <geom.xyz> file to preview current geometry

Q. Proceed/Quit

-----> Choose an appropriate option:

At this point the FCM in the Cartesian representation, $\Phi=\left\Vert \Phi_{ij}\right\Vert$ is available via Eq. (2.10). Change masses^2.3 in Am (symmetry is not used, therefore, division of atoms into orbits is irrelevant here), and then solve the eigenproblem in Ei. After you are done, the natural logarithm of the product of all real nonzero frequencies will be shown just under Ei. This is useful for the calculation of the transition rates prefactors. Also, three new options appear just under ``Actions with vibrations'':

Am. Change atomic masses for a range of atoms

--- A c t i o n s w i t h v i b r a t i o n s -----

Ei. Solve the eigenvalue problem <= Done!

    Nat. logarithm of product of frequencies = 170.087612

Sv. Show eigenvalues/vectors

Sa. Show frequencies and normal modes

Vs. Write xyz movie file for a mode

These are similar to those of the V2-menu:

• Sv - show eigenvalues/eigenvectors
• Sa - show frequencies and the normal coordinates
• Vs - make the movie file movie.xyz for the chosen normal coordinate

Under ``phonon DOS'', a new option D1 appeared that allows one to calculate and preview (gnuplot is called from inside tetr) the total phonon DOS. When calculating DOS, each eigenfrequency is smeared out by a single Gaussian function with dispersion shown under Sg. It is possible to select the appropriate dispersion by displaying several DOS curves with different dispersions: use option Nd for this, and then D1.

If a set of atoms is chosen via pD, the phonon DOS projected on these atoms can be previewed using D2. In this case only a single dispersion (the first one if there are many) will be used.

Some other miscellaneous options controlling DOS:

• St - frequency step when calculating the DOS
• Up - upper limit for the DOS (the vertical axis on the DOS graphs)

You can also preview the current geometry, use W for this: a geom.xyz file will be written that can be previewed using Xmol or a similar viewer.