Output files

The output data are stored in the following files on the current directory.

List of files

band.yaml

Sets of phonon frequencies on band paths calculated by the band-structure mode (e.g. BAND tag) are stored in the YAML format.

band.yaml is viewed using the tool phonopy-bandplot (phonopy-bandplot). phonopy-bandplot can convert the data in the YAML format to that in the gnuplot-style format using the --gnuplot option.

mesh.yaml

A set of frequencies on irreducible q-points of a q-point mesh by the mesh-sampling mode (MESH tag) is stored in the YAML format.

qpoints.yaml

A set of frequencies calculated by the q-points mode (QPOINTS tag) is stored in the YAML format.

thermal_properties.yaml

Thermal properties calculated are stored in the YAML format.

The auxiliary tool phonopy-propplot (phonopy-propplot) can be used to plot the content of thermal_properties.yaml.

thermal_displacements.yaml

Mean square displcements of atoms are stored in the YAML format. Without projecting eigenvectors along a specific direction, the results projected along Cartesianl coordinates, therefore three values for each atom at a temperature, are written into the file.

thermal_displacement_matrices.yaml

Mean square displacement matricies of atoms are stored in the YAML format. Since the matrix for each atom at a temperature is symmetric, only six elements of it, xx, yy, zz, yz, xz, xy, are written in this order.

total_dos.dat and projected_dos.dat

Total and projected DOS are stored in the simple format, respectively.

total_dos.dat and projected_dos.dat are viewed using the auxiliary tool phonopy-pdosplot (phonopy-pdosplot).

File format of projected_dos.dat

The first column is the phonon frequency. The following colums are the projected density of states for atoms in the primitive cell. In the NaCl example, there are two atoms in the primitive cell, which are one Na and one Cl atoms. The order of atoms in the primitive cell is confirmed running phonopy with the -v option. The projected_dos.dat of this example is starting with the following lines:

# Sigma = 0.063253
       -0.6695362607        0.0000000000        0.0000000000
       -0.6379098952        0.0000000000        0.0000000000
       -0.6062835296        0.0000000000        0.0000000000
       -0.5746571641        0.0000000000        0.0000000000
       -0.5430307986        0.0000000000        0.0000000000
       -0.5114044331        0.0000000000        0.0000000000
       -0.4797780675        0.0000000000        0.0000000000
       -0.4481517020        0.0000000000        0.0000000000
       -0.4165253365        0.0000000000        0.0000000000
       -0.3848989710        0.0000000000        0.0000000000
       -0.3532726054        0.0000000004        0.0000000006
       -0.3216462399        0.0000000044        0.0000000066
       -0.2900198744        0.0000000370        0.0000000551
       -0.2583935089        0.0000002410        0.0000003596
       -0.2267671433        0.0000012239        0.0000018260
...

where from the left to right in each line, frequency, PDOS of Na and PDOS of Cl. The first line is just a comment to remember the sigma value used.

With XYZ_PROJECTION tag specified, the format changes to represent x, y, and z components:

# Sigma = 0.063253

       -0.6695362607        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.6315846221        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.5936329834        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.5556813448        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.5177297062        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.4797780675        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.4418264289        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.4038747903        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000        0.0000000000
       -0.3659231516        0.0000000000        0.0000000000        0.0000000000        0.0000000001        0.0000000001        0.0000000001
       -0.3279715130        0.0000000009        0.0000000009        0.0000000009        0.0000000014        0.0000000014        0.0000000014
       -0.2900198744        0.0000000123        0.0000000123        0.0000000123        0.0000000184        0.0000000184        0.0000000184
...

phonopy.yaml and phonopy_disp.yaml

Phonopy configurations and crystal structures are stored in these files when running pre-process (phonopy_disp.yaml) or post-process (phonopy.yaml).

phonopy_disp.yaml contains information used to create supercells with displacements. The format is hopefully understood just looking into it. displacement is written in Cartesian coordinates.

.hdf5 files

See HDF5.

How to read phonopy YAML files

Most phonopy results are written in the YAML format. YAML files are easily translated to the combination of lists and dictionaries in the python case. For each computer language, e.g., Ruby, each YAML parser is prepared and you can use those libraries to parse YAML files and analyze the data easily in conjunction with your favorite language. See http://www.yaml.org/. The basic of the YAML format is found easily on the web. In python, it is very easy to parse phonopy’s yaml files, e.g.,

import yaml
with open("band.yaml") as f:
   data = yaml.load(f)

mesh.yaml, band.yaml, qpoints.yaml

General

Key	Description
nqpoint	Number of q-points calculated.
natom	Number of atoms in the primitive cell.
phonon	Key name of list for q-points.
q-position	Position of q-vector in reduced coordinates.
band	Key name of list for bands.
frequency	Phonon frequency in a specified unit at each phonon mode
eigenvector	Eigenvector at each phonon mode. Each eigenvector \(\mathbf{e}\) of dynamical matrix is shown as sets of three complex values of each atom along the Cartesian axes in the primitive cell. The real and imaginary values correspond to the left and right, respectively. A set of eigenvectors comprising all bands at a q-point forms a unitary matrix obtained as the result of numpy.linalg.eigh, i.e., LAPACK of routine _heevd. Therefore eigenvectors correspond to the column vectors of the unitary matrix.
group_velocity	Group velocity at each phonon mode in the Cartesian coordinates defined in the unit cell.

Mesh sampling mode

Key	Description
mesh	Numbers of mesh sampling points along axes of the primitive cell.
weight	In the mesh sampling mode, only phonons at irreducible q-points are calculated in the default behavior. This value means the multiplicity of a q-point in the reciprocal space of the primitive cell.

Band structure mode

Key	Description
distance	In the band structure mode, this value means the distance from the origin in the reciprocal space of the primitive cell. The unit is the reciprocal of length unit used in the real space.

thermal_properties.yaml

The physical units of the thermal properties are given in the unit section of this YAML file. However the physical units are only correct when phonopy ran with proper physical units. See TPROP.