Phonopy — Phonon Calculations

When to Use

• User needs phonon band structure or phonon DOS
• User wants to check dynamical stability (imaginary phonon modes)
• User needs thermodynamic properties (heat capacity, entropy, free energy) from phonons
• User wants to compute thermal expansion or Gruneisen parameters
• User has a relaxed structure and wants vibrational properties beyond the Gamma point

Prerequisites

1. phonopy installed (phonopy --version)
2. A DFT code (VASP, QE, ABINIT) for computing forces on displaced structures
3. A fully relaxed structure (forces < 0.001 eV/Ang on all atoms)
4. Tight SCF convergence in force calculations (EDIFF=1e-8 for VASP)

Workflow Overview

Phonopy uses the finite-displacement method:

1. Generate supercells with displaced atoms
2. Run DFT force calculations on each displaced supercell
3. Collect forces and compute force constants
4. Post-process: band structure, DOS, thermal properties

Workflow Steps

1. Create supercells with displacements

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "phonopy_displace",
  "command": "phonopy -d --dim 2 2 2 -c POSCAR",
  "input_files": {
    "POSCAR": "<relaxed structure>"
  },
  "system_name": "phonon_setup"
})

This generates POSCAR-001, POSCAR-002, ..., phonopy_disp.yaml.

2. Run DFT on each displaced structure

For each displaced POSCAR, run a VASP single-point calculation:

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "phonon_forces_001",
  "command": "cd disp-001 && vasp_std > vasp.out 2>&1",
  "depends_on": ["phonopy_displace"],
  "system_name": "phonon_disp_001"
})

VASP INCAR for force calculations:

PREC    = Accurate
ENCUT   = 520
EDIFF   = 1e-8      # Must be tight for phonons
IBRION  = -1
NSW     = 0
ISMEAR  = 0
SIGMA   = 0.05
LREAL   = .FALSE.    # Must be FALSE for phonons
LWAVE   = .FALSE.
LCHARG  = .FALSE.

3. Collect forces and compute force constants

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "phonopy_forces",
  "command": "phonopy -f disp-001/vasprun.xml disp-002/vasprun.xml ...",
  "depends_on": ["phonon_forces_001", "phonon_forces_002"],
  "system_name": "phonon_fc"
})

4. Compute phonon band structure

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "phonopy_band",
  "command": "phonopy -p band.conf",
  "input_files": {
    "band.conf": "DIM = 2 2 2\nBAND = AUTO\nBAND_POINTS = 101\nBAND_LABELS = AUTO"
  },
  "depends_on": ["phonopy_forces"],
  "system_name": "phonon_band"
})

Configuration Files

band.conf — Band structure

DIM = 2 2 2
BAND = AUTO
BAND_POINTS = 101

mesh.conf — DOS and thermal properties

DIM = 2 2 2
MP = 20 20 20
TPROP = .TRUE.
TMIN = 0
TMAX = 1000
TSTEP = 10

pdos.conf — Projected DOS

DIM = 2 2 2
MP = 20 20 20
PDOS = 1 2, 3 4 5 6

Atom indices are 1-based. Groups separated by commas.

Python API

import phonopy
from phonopy import Phonopy

ph = phonopy.load("phonopy_disp.yaml")
# Forces already set via phonopy -f

# Band structure
ph.auto_band_structure(plot=True)
ph.save("phonopy_results.yaml")

# Thermal properties
ph.run_mesh([20, 20, 20])
ph.run_thermal_properties(t_min=0, t_max=1000, t_step=10)
tp = ph.get_thermal_properties_dict()
# tp['temperatures'], tp['free_energy'], tp['entropy'], tp['heat_capacity']

Parameter Guidance

Parameter	Typical value	Notes
DIM	2 2 2 or 3 3 3	Supercell size; larger = more accurate but more DFT calcs
MP	20 20 20	q-point mesh for DOS; denser = smoother DOS
BAND	AUTO	Auto high-symmetry path; or specify manually
displacement	0.01 Ang	Default; increase for very stiff materials
TPROP	.TRUE.	Enable thermal property calculation

Interpreting Results

• No imaginary modes — structure is dynamically stable
• Imaginary modes at Gamma — structure is unstable; re-optimize or try different cell
• Imaginary modes at zone boundary — possible CDW or structural phase transition
• Flat acoustic modes — check supercell size; may need larger DIM

Common Pitfalls

1. Structure not fully relaxed — residual forces cause spurious imaginary modes. Relax to < 0.001 eV/Ang.
2. LREAL=Auto in VASP — must use LREAL = .FALSE. for phonon force calculations. Real-space projection introduces noise.
3. Supercell too small — DIM = 1 1 1 gives only Gamma phonons. Use at least 2 2 2 for bulk.
4. SCF not converged — use EDIFF=1e-8 (not 1e-5). Loose SCF causes noisy force constants.
5. Symmetry mismatch — phonopy uses symmetry to reduce displacements. Ensure the input structure has correct symmetry.
6. Many displacements — low-symmetry structures can generate 100+ displaced supercells. Budget DFT time accordingly.
7. Acoustic sum rule — slight violations are normal. Phonopy applies corrections automatically.