split_freq

This program handles VASP frequency calculations. They can be evaluated, giving molden files for the visualization of spectra and normal modes with intensities, and they can be prepared, by splitting a calculation into parts.

VASP frequency calculations cannot be restarted! Therefore, large systems can lead to problems with the wall time limit of a cluster. This program can split the frequency calculations for those systems into an arbitrary number of parts, where in each parts, only a subset of all activated atoms are shifted numerically. The evaluate option than can recombine the results from the parts to a full output and gives the spectrum (with intensities) and the normal modes of the full system.

Preparation

If you want to split the frequency calculation for a large system into parts, generate a folder with the usual input files and commands (look into the frequency section for details). In this folder, start the program with the command:

split_freq -setup -chunks=[number of chunks]

where [number of chunks] need to be replaced by the desired number of parts, into which the full calculation is divided. If your system for example contains 100 atoms in total, of which 50 are activated for the frequency calculation (T T T in selective dynamics. see in the general input section), choosing 4 chunks would result in four calculations, in which calculation 1 to 3 are calculating 13 atoms and calculation 4 calculates 11 atoms (the last one always less atoms, if the number of actviated atoms cannot be divided by the number of chunks), according to the ordering in the POSCAR file. Chunk 1 then calculates the first activated atom until the 13th activated atom and so on. Each calculation calculates of course still the full system, but only the described number of atoms is activated for the dynamics (T T T) in each part. After the command has been executed, one folder is generated for each part, named chunk1, chunk2, ... until the chosen number of chunks.

Now, all calculations can be run independently!

Note that a queue management script like a slurm_script is not copied into the chunk folders from the main folder, it must therefore be copied manually!

Evaluation

After you have ran a VASP frequency calculation (either a usual one for a subdivided one as described in the previous section), you can use this program to evaluate its results.

For a usual calculation with one part, simply go into the calculation folder and execute the command:

split_freq -eval

and the calculation is evaluated. Two files are generated, that can be opened by programs like molden or avogadro:

• combined_full.molden contains the IR spectrum and the normal modes of the full system, including atoms set to F F F in the POSCAR file. In the normal modes, these will simply not move.
• combined_active.molden contains the same IR spectrum as combined_full.molden but the normal modes only include the active atoms, such that, e.g., for an adsorbate on a metal surface, where only the atoms of the adsorbates are set to T T T, the metal surface is not seen in the normal modes at all (but its influence on the adsorbate is of course still enshrined into the normal modes and the IR spectrum, e.g., the metal surface selection rule).

For a calculation of several parts, go to the main folder containing the folders chunk1, chunk2, ... and execute the program with the same command:

split_freq -eval

and the calculation is evaluated in the usual way. Again, the files combined_full.molden and combined_active.molden are generated with the same contents as described above.