Phonons and reaction paths

This chapter is a map, not a manual. ph.x and neb.x are each a book-sized topic, so here we only fix when you will need them and where to start.

ph.x: phonons (DFPT)

Computes dynamical matrices by density-functional perturbation theory. You will need it when:

• Validating structural stability: is the optimized structure a true minimum (no imaginary frequencies)?
• Vibrational spectra, thermodynamic quantities (free energy, entropy), thermal expansion (with thermo_pw).
• Electron-phonon coupling.

The skeleton of the workflow:

pw.x (scf, very tight conv_thr) → ph.x (&INPUTPH, ldisp=.true., nq grid)
  → q2r.x (real-space force constants) → matdyn.x (dispersion and DOS at any q)

The essentials of &INPUTPH: tr2_ph (response threshold, typically 1.0d-14), ldisp with nq1/nq2/nq3 (the q-grid), epsil (dielectric tensor, needed for LO-TO splitting in polar insulators), fildyn. The cost is heavy, so image parallelism (-ni) and start_q/last_q splitting are standard practice.

Start with PHonon/examples/ and a thoroughly converged structure, as in Example E6. Phonons on an under-optimized structure are full of imaginary modes, and those are a symptom of non-convergence, not physics.

neb.x: reaction paths and barriers

Nudged Elastic Band finds the minimum-energy path and transition state between two structures. It is the central tool for oxidation mechanisms, diffusion barriers, and surface reactions.

Its input format differs from pw.x: path settings (&PATH) and an engine input (identical to a pw.x input) sit together inside BEGIN/END blocks.

BEGIN
BEGIN_PATH_INPUT
&PATH
  string_method = 'neb'
  num_of_images = 7
  nstep_path    = 100
  opt_scheme    = 'broyden'
  CI_scheme     = 'auto'      ! climbing image: nails the saddle point
  path_thr      = 0.05        ! eV/Å
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
 ...                          ! same as a pw.x input
/
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS (crystal)
 ...
LAST_IMAGE
ATOMIC_POSITIONS (crystal)
 ...
END_POSITIONS
END_ENGINE_INPUT
END

Practical notes:

• Fully optimize both endpoints first, then hand them to NEB.
• Start with an odd number of images (5–9) and parallelize over images with -ni.
• Turn on CI_scheme='auto' (climbing image) if you care about the barrier height.

The wider map