5. Advanced topics

5.1. Use non-analytical corrections (NAC) in phonon band structure

Non-analytical corrections (NAC) can be used in phonoLAMMPS during the plot of the phononn band structure preview. To use them a file named BORN containing the Born charges anf the dielectric tensor should exist in the working directory. This file is formated in phonopy format (check phonopy documentation for further information). To activate this options –use_NAC flag is used

$ phonolammps in.lammps --dim 2 2 2 --use_NAC -p

Notice that this option does not modify the calculated force constants written in FORCE_CONSTANTS file. It is only used in the phonon band structure plot, therefore it makes no effect without -p flag.

5.2. Atomic position optimization

The atomic positions of the unit cell can be optimized using –optimization flag. This uses LAMMPS minimize to perform a minimization of atomic forces at constant volume. The forces tolerance for the convergence criterion is defined by –force_tol flag.

$ phonolammps in.lammps --dim 2 2 2 --optimization --force_tol 1e-10 -p

This option performs a simple minimization. If a more sophisticated optimization is required then use LAMMPS directly. This option is best used to refine the atomic positions of an already optimized unit cell.

5.3. Finite temperature force constants

Finite temperature force constants can be calculated from molecular dynamics using dynaphopy software (http://abelcarreras.github.io/DynaPhoPy). This software implements the normal mode projection technique to obtain the renormalized force constants at finite temperature based on quasiparticle theory. Phonolammps provide a minimum functionality to make this process automatic using both LAMMPS and dynaphopy python API. To use this feature dynaphopy must be installed (for further details check dynaphopy documentation).

In command line script temperature is defined by -t flag. By default this value is 0 and usual 2n order force constants are calculated. If the temperature is higher than 0 then a molecular dynamics (MD) simulation is calculated with LAMMPS using a supercell defined by –dim flag. By default the length of the MD if 20 ps with time step of 0.001 ps and a relaxation time of 5 ps, but these parameters can be tweaked using –total_time, –relaxation_time and –relaxation_time flags.

example for silicon:

$ phonolammps in.lammps --dim 2 2 2 -pa 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 -t 300 -p

to have more control over the simulation and the renormalization precedure you will have to use the two software separately.