Command options / Setting tags¶

From phonopy v1.12.3, the command option names with underscores _ are replaced by those with dashes -. Those tag names are unchanged.

Command-user-interface of phono3py is operated with a variety of command options. Here those command options are explained.

At the current release v1.14.3, reading configuration file doesn’t work. If this is needed, please try the develop branch of phono3py on github. This will be fixed in the next release. A configuration file with setting tags like phonopy can be used instead of and together with the command options. The setting tags are mostly equivalent to the most command options, but when both are set simultaneously, the command options are preferred. An example of configuration (e.g., saved in a file setting.conf) is as follow:

DIM = 2 2 2
DIM_FC2 = 4 4 4
PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
MESH = 11 11 11
BTERTA = .TRUE.
NAC = .TRUE.
CELL_FILENAME = POSCAR-unitcell


where the setting tag names are case insensitive. This is run by

% phono3py setting.conf [comannd options]


Calculator interface¶

-c: Unit cell filename¶

(Setting tag: CELL_FILENAME)

% phono3py -c POSCAR-unitcell ... (many options)


--pwscf: PWSCF (Quantum espresso) interface¶

Using this option, PWSCF interface is invoked. See the detail at Pwscf & phono3py calculation.

--crystal: CRYSTAL interface¶

Using this option, CRYSTAL interface is invoked. See the detail at CRYSTAL & phono3py calculation.

Force constants¶

-d: Create displacements¶

(Setting tag: CREATE_DISPLACEMENTS)

Supercell with displacements are created. Using with --amplitude option, atomic displacement distances are controlled. With this option, files for supercells with displacements and disp_fc3.yaml file are created.

--amplitude: Amplitude of displacements¶

(Setting tag: DISPLACEMENT_DISTANCE)

Atomic displacement distance is specified using this option. This value may be increased for the weak interaction systems and descreased when the force calculator is numerically very accurate.

The default value depends on calculator. See Default displacement distance created.

--dim: Supercell dimension¶

(Setting tag: DIM)

Supercell size is specified. See the detail at http://atztogo.github.io/phonopy/setting-tags.html#dim .

--dim-fc2: Supercell dimension for 2nd order force constants¶

(Setting tag: DIM_FC2)

A larger and different supercell size for 2nd order force constants than that for 3rd order force constants can be specified with this option. Often interaction between a pair of atoms has longer range in real space than interaction among three atoms. Therefore to reduce computational demand, choosing larger supercell size only for 2nd order force constants may be a good idea.

Using this option with -d option, the structure files (e.g. POSCAR_FC2-xxxxx or equivalent files for the other interfaces) and disp_fc2.yaml are created. These are used to calculate 2nd order force constants for the larger supercell size and these force calculations have to be done in addition to the usual force calculations for 3rd order force constants.

phono3py -d --dim="2 2 2" --dim-fc2="4 4 4" -c POSCAR-unitcell


After the force calculations, --cf2 option is used to create FORCES_FC2.

phono3py --cf2 disp-{001,002}/vasprun.xml


To calculate 2nd order force constants for the larger supercell size, FORCES_FC2 and disp_fc2.yaml are necessary. Whenever running phono3py for the larger 2nd order force constants, --dim-fc2 option has to be specified. fc2.hdf5 created as a result of running phono3py contains the 2nd order force constants with larger supercell size. The filename is the same as that created in the usual phono3py run without --dim-fc2 option.

phono3py --dim="2 2 2" --dim_fc2="4 4 4" -c POSCAR-unitcell ... (many options)


--pa, --primitive-axis: Transformation matrix to primitive cell¶

(Setting tag: PRIMITIVE_AXIS)

Transformation matrix from a non-primitive cell to the primitive cell. See phonopy PRIMITIVE_AXIS tag (--pa option) at http://atztogo.github.io/phonopy/setting-tags.html#primitive-axis

--fc2: Read 2nd order force constants¶

(Setting tag: READ_FC2, .TRUE. or .FALSE.)

Read 2nd order force constants from fc2.hdf5.

--fc3: Read 3nd order force constants¶

(Setting tag: READ_FC3, .TRUE. or .FALSE.)

Read 3rd order force constants from fc3.hdf5.

--cfc or --compact-fc: Compact force constants¶

(Setting tag: COMPACT_FC, .TRUE. or .FALSE.)

When creating force constants from FORCES_FC3 and/or FORCES_FC2, force constants that use smaller data size are created. The shape of the data array is (num_patom, num_satom) for fc2 and (num_patom, num_satom, num_satom) for fc3, where num_patom and num_satom are the numbers of atoms in primtive cell and supercell. In the full size force constants case, num_patom is replaced by num_satom. Therefore if the supercell dimension is large, this reduction of data size becomes large. If the input crystal structure has centring –pa is necessary to have smallest data size. In this case, --pa option has to be specified on reading. Otherwise phono3py can recognize if fc2.hdf5 and fc3.hdf5 are compact or full automatically. When using with --sym-fc, the calculated results will become slightly different due to imperfect symmetrization scheme that phono3py employs.

% phono3py --dim="2 2 2" --cfc --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell


--sym-fc2, --sym-fc3r, --sym-fc: Symmetries force constants¶

(Setting tags: SYMMETRIZE_FC2, .TRUE. or .FALSE.) (Setting tags: SYMMETRIZE_FC3, .TRUE. or .FALSE.) (Setting tags: FC_SYMMETRY, .TRUE. or .FALSE.)

These are used to symmetrize second- and third-order force constants. With --sym-fc2 and --sym-fc3r, the index exchange of real space force constantsand translational invariance symmetry are applied, respectively. --sym-fc is an alias to set both of --sym-fc2 and --sym-fc3r.

When those force constants are not read from the hdf5 files, symmetrized force constants in real space are written into those hdf5 files.

--cf3: Create FORCES_FC3¶

This is used to create FORCES_FC3. disp_fc3.yaml has to be located at the current directory.

% phono3py --cf3 disp-{00001..00755}/vasprun.xml


--cf3-file: Create FORCES_FC3 from file name list¶

This is used to create FORCES_FC3 from a file name list. disp_fc3.yaml has to be located at the current directory.

% phono3py --cf3-file file_list.dat


where file_list.dat contains file names that can be recognized from the current directory and is expected to be like:

disp-00001/vasprun.xml
disp-00002/vasprun.xml
disp-00003/vasprun.xml
disp-00004/vasprun.xml
...


The order of the file names is important. This option may be useful to be used together with --cutoff-pair option.

--cf2: Create FORCES_FC2¶

This is used to create FORCES_FC2. disp_fc2.yaml has to be located at the current directory. This is optional. FORCES_FC2 is necessary to run with --dim_fc2 option.

% phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml


--fs2f2 or --force-sets-to-forces-fc2¶

Using this option, FORCES_FC2 and disp_fc2.yaml are created from phonopy FORCE_SETS file.

% phono3py --fs2f2


--cfs or --create-force-sets¶

Using this option, phonopy’s FORCE_SETS is created from FORCES_FC3 and disp_fc3.yaml.

% phono3py --cfs


In conjunction with –dim-fc2, phonopy’s FORCE_SETS is created from FORCES_FC2 and disp_fc2.yaml instead of FORCES_FC3 and disp_fc3.yaml.

% phono3py --cfs --dim-fc2="x x x"


--cutoff-fc3 or --cutoff-fc3-distance¶

(Setting tag: CUTOFF_FC3_DISTANCE)

This option is not used to reduce number of supercells with displacements, but this option is used to set zero in elements of given third-order force constants. The zero elements are selected by the condition that any pair-distance of atoms in each atom triplet is larger than the specified cut-off distance.

If one wants to reduce number of supercells, the first choice is to reduce the supercell size and the second choice is using --cutoff-pair option.

--cutoff-pair or --cutoff-pair-distance¶

(Setting tag: CUTOFF_PAIR_DISTANCE)

This option is only used together with -d option.

A cutoff pair-distance in a supercell is used to reduce the number of necessary supercells with displacements to obtain third order force constants. As the drawback, a certain number of third-order-force-constants elements are abandoned or computed with less numerical accuracy. More details are found in the following link:

Reciprocal space sampling mesh and grid points, and band indices¶

--mesh: Sampling mesh¶

(Setting tag: MESH or MESH_NUMBERS)

Phonon triples are chosen on the grid points on the sampling mesh specified by this option. This mesh is made along reciprocal axes and is always Gamma-centered.

--gp: Grid points by their ID¶

(Setting tag: GRID_POINTS)

Grid points where imaginary part of self energy is calculated are specified. Indices of grid points are specified by space or comma (,) separated numbers. The mapping table between grid points to its indices is obtained by running with --loglevel=2 option.

% phono3py --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="19 19 19" --fc3 --fc2 --br --write-gamma --gp="0 1 2 3 4 5"


where --gp="0 1 2 3 4 5" can be also written --gp="0,1,2,3,4,5". There is a similar option as this option, –ga option.

--ga option may be also useful when a workload of thermal conductivity calculation is expected to be distributed into different computer nodes.

--ga: Grid points by address with three integer values¶

(Setting tag: GRID_ADDRESSES)

This option is used to specify grid points like --gp option but in the different way. For example with --mesh="16 16 16", a q-point of (0.5, 0.5, 0.5) is given by --ga="8 8 8". The values have to be integers. If you want to specify the point on a path, --ga="0 0 0 1 1 1 2 2 2 3 3 3 ...", where each three values are recogninzed as a grid point. The grid points given by --ga option are translated to grid point indices as given by --gp option, and the values given by --ga option will not be shown in log files.

--wgp: Write grid point information¶

Irreducible grid point indices are written into ir_grid_points.yaml. This information may be used when we want to calculate imaginary part of self energy at each grid point in conjunction with –gp option. grid_address-mxxx.hdf5 is also written. This file contains all the grid points and their grid addresses in integers. Q-points corresponding to grid points are calculated divided these integers by sampling mesh numbers for respective reciprocal axes.

--stp: Show number of triplets to be calculated for each grid point¶

Numbers of q-point triplets to be calculated for irreducible grid points for specified sampling mesh numbers are shown. This can be used to estimate how large a calculation is. Only those for specific grid points are shown by using with --gp or --ga option.

--bi: Specific band index¶

(Setting tag: BAND_INDICES)

Specify band indices. The output file name will be, e.g., gammas-mxxx-gxx(-sx)-bx.dat where bxbx... shows the band indices used to be averaged. The calculated values at indices separated by space are averaged, and those separated by comma are separately calculated.

% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --gp="34" --bi="4 5, 6"


Brillouin zone integration¶

--thm: Tetrahedron method (default choice)¶

(Setting tag: TETRAHEDRON, .TRUE. or .FALSE.)

Tetrahedron method is used for calculation of imaginary part of self energy. This is the default option. Therefore it is not necessary to specify this unless both results by tetrahedron method and smearing method in one time execution are expected.

--sigma: Smearing method¶

(Setting tag: SIGMA)

$$\sigma$$ value of Gaussian function for smearing when calculating imaginary part of self energy. See the detail at Brillouin zone summation.

Multiple $$\sigma$$ values are also specified by space separated numerical values. This is used when we want to test several $$\sigma$$ values simultaneously.

--sigma-cutoff: Cutoff parameter for smearing method¶

(Setting tag: SIGMA_CUTOFF_WIDTH)

The tails of the Guassian functions that are used to replace delta functions in the equation shown at –full-pp are cut with this option. The value is specified in number of standard deviation. --sigma-cutoff=5 gives the Gaussian functions to be cut at $$5\sigma$$. Using this option scarifies the numerical accuracy. So the number has to be carefully tested. But computation of phonon-phonon interaction strength becomes much faster in exchange for it.

--full-pp: Calculate all elements of phonon-phonon interaction strength¶

(Setting tag: FULL_PP, .TRUE. or .FALSE.)

For thermal conductivity calculation using the linear tetrahedron method (from version 1.10.5) and smearing method with --simga-cutoff (from version 1.12.3), only necessary elements (i.e., that have non-zero delta functions) of phonon-phonon interaction strength, $$\bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2$$, is calculated due to delta functions in calculation of $$\Gamma_\lambda(\omega)$$,

$\Gamma_\lambda(\omega) = \frac{18\pi}{\hbar^2} \sum_{\lambda' \lambda''} \bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2 \left\{(n_{\lambda'}+ n_{\lambda''}+1) \delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right. + (n_{\lambda'}-n_{\lambda''}) \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''}) - \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''}) \right]\right\}.$

But using this option, full elements of phonon-phonon interaction strength are calculated and averaged phonon-phonon interaction strength ($$P_{\mathbf{q}j}$$, see –ave-pp) is also given and stored.

Physical properties¶

--br: Thermal conductivity with relaxation time approximation¶

(Setting tag: BTERTA, .TRUE. or .FALSE.)

Run calculation of lattice thermal conductivity tensor with the single mode relaxation time approximation (RTA) and linearized phonon Boltzmann equation. Without specifying --gp (or --ga) option, all necessary phonon lifetime calculations for grid points are sequentially executed and then thermal conductivity is calculated under RTA. The thermal conductivity and many related properties are written into kappa-mxxx.hdf5.

With --gp (or --ga) option, phonon lifetimes on the specified grid points are calculated. To save the results, --write-gamma option has to be specified and the physical properties belonging to the grid points are written into kappa-mxxx-gx(-sx).hdf5.

--lbte: Thermal conductivity with direct solution of LBTE¶

(Setting tag: BTERTA, .TRUE. or .FALSE.)

Run calculation of lattice thermal conductivity tensor with a direct solution of linearized phonon Boltzmann equation. The basis usage of this option is equivalent to that of --br. More detail is documented at Direct solution of linearized phonon Boltzmann equation.

--isotope: Phonon-isotope scattering¶

(Setting tag: ISOTOPE, .TRUE. or .FALSE.)

Phonon-isotope scattering is calculated based on the formula by Shin-ichiro Tamura, Phys. Rev. B, 27, 858 (1983). Mass variance parameters are read from database of the natural abundance data for elements, which refers Laeter et al., Pure Appl. Chem., 75, 683 (2003).

% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --isotope


--mass-variances or --mv: Parameter for phonon-isotope scattering¶

(Setting tag: MASS_VARIANCES)

This option is used to include isotope effect by reading specified mass variance parameters. For example of GaN, this may be set like --mv="1.97e-4 1.97e-4 0 0". The number of elements has to correspond to the number of atoms in the primitive cell.

Isotope effect to thermal conductivity may be checked first running without isotope calculation:

% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br


Then running with isotope calculation:

% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --mv="1.97e-4 1.97e-4 0 0"


In the result hdf5 file, currently isotope scattering strength is not written out, i.e., gamma is still imaginary part of self energy of ph-ph scattering.

--boundary-mfp, --bmfp: Very simple phonon-boundary scattering model¶

(Setting tag: BOUNDARY_MFP)

A most simple boundary scattering treatment is implemented. $$v_g/L$$ is just used as the scattering rate, where $$v_g$$ is the group velocity and $$L$$ is the boundary mean free path. The value is given in micrometre. The default value, 1 metre, is just used to avoid divergence of phonon lifetime and the contribution to the thermal conducitivity is considered negligible.

--tmax, --tmin, --tstep: Temperature range¶

(Setting tag: TMAX, TMIN, TSTEP)

Temperatures at equal interval are specified by --tmax, --tmin, --tstep. See phonopy’s document for the same tags at http://atztogo.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep .

% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --tmin=100 --tmax=1000 --tstep=50


--ts: Temperatures¶

(Setting tag: TEMPERATURES)

Specific temperatures are specified by --ts.

% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="11 11 11" -c POSCAR-unitcell --br --ts="200 300 400"


--nac: Non-analytical term correction¶

(Setting tag: NAC, .TRUE. or .FALSE.)

Non-analytical term correction for harmonic phonons. Like as phonopy, BORN file has to be put on the same directory. Always the default value of unit conversion factor is used even if it is written in the first line of BORN file.

--q-direction: Direction for non-analytical term correction at $$\mathbf{q}\rightarrow \mathbf{0}$$¶

(Setting tag: Q_DIRECTION)

This is used with --nac to specify the direction to polarize in reciprocal space. See the detail at http://atztogo.github.io/phonopy/setting-tags.html#q-direction .

--nu: Normal and Umklapp processes¶

(Setting tag: N_U, .TRUE. or .FALSE.)

Integration over q-point triplets for the calculation of $$\Gamma_\lambda(\omega_\lambda)$$ is made separately for normal and Umklapp processes, therefore the sum of them is usual $$\Gamma_\lambda(\omega_\lambda)$$. The separation, i.e., the choice of G-vector, is made based on the first Brillouin zone.

--write-gamma¶

(Setting tag: WRITE_GAMMA, .TRUE. or .FALSE.)

Imaginary parts of self energy at harmonic phonon frequencies $$\Gamma_\lambda(\omega_\lambda)$$ are written into file in hdf5 format. The result is written into kappa-mxxx-gx(-sx-sdx).hdf5 or kappa-mxxx-gx-bx(-sx-sdx).hdf5 with --bi option. With --sigma and --sigma-cutoff options, -sx and --sdx are inserted, respectively, in front of .hdf5.

--read-gamma¶

(Setting tag: READ_GAMMA, .TRUE. or .FALSE.)

Imaginary parts of self energy at harmonic phonon frequencies $$\Gamma_\lambda(\omega_\lambda)$$ are read from kappa file in hdf5 format. Initially the usual result file of kappa-mxxx(-sx-sdx).hdf5 is searched. Unless it is found, it tries to read kappa file for each grid point, kappa-mxxx-gx(-sx-sdx).hdf5. Then, similarly, kappa-mxxx-gx(-sx-sdx).hdf5 not found, kappa-mxxx-gx-bx(-sx-sdx).hdf5 files for band indices are searched.

--write-gamma-detail¶

(Setting tag: WRITE_GAMMA_DETAIL, .TRUE. or .FALSE.)

Each q-point triplet contribution to imaginary part of self energy is written into gamma_detail-mxxx-gx(-sx-sdx).hdf5 file. Be careful that this is large data.

In the output file in hdf5, following keys are used to extract the detailed information.

 gamma_detail for --ise (temperature, sampling frequency point, symmetry reduced set of triplets at a grid point, band1, band2, band3) in THz (without $$2\pi$$) gamma_detail for --br (temperature, symmetry reduced set of triplets at a grid point, band1, band2, band3) in THz (without $$2\pi$$) mesh Numbers of sampling mesh along reciprocal axes. frequency_point for --ise Sampling frequency points in THz (without $$2\pi$$), i.e., $$\omega$$ in $$\Gamma_\lambda(\omega)$$ temperature (temperature,), Temperatures in K triplet (symmetry reduced set of triplets at a grid point, 3), Triplets are given by the grid point indices (see below). weight (symmetry reduced set of triplets at a grid point,), Weight of each triplet to imaginary part of self energy

Imaginary part of self energy (linewidth/2) is recovered by the following script:

import h5py
import numpy as np

gd = h5py.File("gamma_detail-mxxx-gx.hdf5")
temp_index = 30 # index of temperature
temperature = gd['temperature'][temp_index]
gamma_tp = gd['gamma_detail'][:].sum(axis=-1).sum(axis=-1)
weight = gd['weight'][:]
gamma = np.dot(weight, gamma_tp[temp_index])


For example, for --br, this gamma gives $$\Gamma_\lambda(\omega_\lambda)$$ of the band indices at the grid point indicated by $$\lambda$$ at the temperature of index 30. If any bands are degenerated, those gamma in kappa-mxxx-gx(-sx-sdx).hdf5 or gamma-mxxx-gx(-sx-sdx).hdf5 type file are averaged, but the gamma obtained here in this way are not symmetrized. Apart from this symmetrization, the values must be equivalent between them.

To understand each contribution of triptle to imaginary part of self energy, reading phonon-mxxx.hdf5 is useful (see --write-phonon). For example, phonon triplets of three phonon scatterings are obtained by

import h5py
import numpy as np

gd = h5py.File("gamma_detail-mxxx-gx.hdf5", 'r')
ph = h5py.File("phonon-mxxx.hdf5", 'r')
gp1 = gd['grid_point'][()]
triplets = gd['triplet'][:] # Sets of (gp1, gp2, gp3) where gp1 is fixed
mesh = gd['mesh'][:]
q_triplets = grid_address[triplets] / mesh.astype('double')
# Phonons of triplets[2]
phonon_tp = [(ph['frequency'][i], ph['eigenvector'][i]) for i in triplets[2]]
# Fractions of contributions of tripltes at this grid point and temperture index 30
gamma_sum_over_bands = np.dot(weight, gd['gamma_detail'][30].sum(axis=-1).sum(axis=-1).sum(axis=-1))
contrib_tp = [gd['gamma_detail'][30, i].sum() / gamma_sum_over_bands for i in range(len(weight))]
np.dot(weight, contrib_tp) # is one


--write-phonon¶

Phonon frequencies, eigenvectors, and grid point addresses are stored in phonon-mxxx.hdf5 file. After writing phonons, phono3py stops without going to calculation. –pa and –nac may be required depending on calculation setting.

% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-phoonon


Contents of phonon-mxxx.hdf5 are watched by:

In [1]: import h5py

In [2]: ph = h5py.File("phonon-m111111.hdf5", 'r')

In [3]: list(ph)
Out[3]: ['eigenvector', 'frequency', 'grid_address', 'mesh']

In [4]: ph['mesh'][:]
Out[4]: array([11, 11, 11], dtype=int32)

Out[5]: (1367, 3)

In [6]: ph['frequency'].shape
Out[6]: (1367, 6)

In [7]: ph['eigenvector'].shape
Out[7]: (1367, 6, 6)


The first axis of ph['grid_address'], ph['frequency'], and ph['eigenvector'] corresponds to the number of q-points where phonons are calculated. Here the number of phonons may not be equal to product of mesh numbers ($$1367 \neq 11^3$$). This is because all q-points on Brillouin zone boundary are included, i.e., even if multiple q-points are translationally equivalent, those phonons are stored separately though these phonons are physically equivalent within the equations employed in phono3py. Here Brillouin zone is defined by Wigner–Seitz cell of reciprocal primitive basis vectors. This is convenient to categorize phonon triplets into Umklapp and Normal scatterings based on the Brillouin zone.

--read-phonon¶

Phonon frequencies, eigenvectors, and grid point addresses are read from phonon-mxxx.hdf5 file and the calculation is continued using these phonon values. This is useful when we want to use fixed phonon eigenvectors that can be different for degenerate bands when using different eigenvalue solvers or different CPU architectures. –pa and –nac may be required depending on calculation setting.

% phono3py --fc2 --fc3 --dim="2 2  2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-phoonon --br


--write-pp and --read-pp¶

Phonon-phonon (ph-ph) intraction strengths are written to and read from pp-mxxx-gx.hdf5. This works only in the calculation of lattice thermal conductivity, i.e., usable only with --br or --lbte. The stored data are different with and without specifying --full-pp option. In the former case, all the ph-ph interaction strengths among considered phonon triplets are stored in a simple manner, but in the later case, only necessary elements to calculate collisions are stored in a complicated way. In the case of RTA conductivity calculation, in writing and reading, ph-ph interaction strength has to be stored in memory, so there is overhead in memory than usual RTA calculation.

% phono3py --fc2 --fc3 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --write-pp --br --gp=1

% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --mesh="11 11 11" -c POSCAR-unitcell --nac --read-pp --br --gp=1


--ise: Imaginary part of self energy¶

(Setting tag: IMAG_SELF_ENERGY, .TRUE. or .FALSE.)

Imaginary part of self energy $$\Gamma_\lambda(\omega)$$ is calculated with respect to $$\omega$$. The output is written to gammas-mxxx-gx(-sx)-tx-bx.dat in THz (without $$2\pi$$) with respect to frequency in THz (without $$2\pi$$).

% phono3py --fc3 --fc2 --dim="2 2 2" --mesh="16 16 16" -c POSCAR-unitcell --nac --q-direction="1 0 0" --gp=0 --ise --bi="4 5, 6"


--jdos: Joint density of states¶

(Setting tag: JOINT_DOS, .TRUE. or .FALSE.)

Two classes of joint density of states (JDOS) are calculated. The result is written into jdos-mxxx-gx(-sx-sdx).dat in $$\text{THz}^{-1}$$ (without $$(2\pi)^{-1}$$) with respect to frequency in THz (without $$2\pi$$). The first column is the frequency, and the second and third columns are the values given as follows, respectively,

$\begin{split}&D_2^{(1)}(\mathbf{q}, \omega) = \frac{1}{N} \sum_{\lambda',\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''}) + \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''}) \right], \\ &D_2^{(2)}(\mathbf{q}, \omega) = \frac{1}{N} \sum_{\lambda',\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') \delta(\omega-\omega_{\lambda'} -\omega_{\lambda''}).\end{split}$
% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8"


When temperatures are specified, two classes of weighted JDOS are calculated. The result is written into jdos-mxxx-gx(-sx)-txxx.dat in $$\text{THz}^{-1}$$ (without $$(2\pi)^{-1}$$) with respect to frequency in THz (without $$2\pi$$). In the file name, txxx shows the temperature. The first column is the frequency, and the second and third columns are the values given as follows, respectively,

$\begin{split}&N_2^{(1)}(\mathbf{q}, \omega) = \frac{1}{N} \sum_{\lambda'\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') (n_{\lambda'} - n_{\lambda''}) [ \delta( \omega + \omega_{\lambda'} - \omega_{\lambda''}) - \delta( \omega - \omega_{\lambda'} + \omega_{\lambda''})], \\ &N_2^{(2)}(\mathbf{q}, \omega) = \frac{1}{N} \sum_{\lambda'\lambda''} \Delta(-\mathbf{q}+\mathbf{q}'+\mathbf{q}'') (n_{\lambda'}+ n_{\lambda''}+1) \delta( \omega - \omega_{\lambda'} - \omega_{\lambda''}).\end{split}$
% phono3py --fc2 --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8" --ts=300


This is an example of Si-PBEsol.

--num-freq-points, --freq-pitch: Sampling frequency for distribution functions¶

(Setting tag: NUM_FREQUENCY_POINTS)

For spectrum like calculations of imaginary part of self energy and JDOS, number of sampling frequency points is controlled by --num-freq-points or --freq-pitch.

--ave-pp: Use averaged phonon-phonon interaction strength¶

(Setting tag: USE_AVE_PP, .TRUE. or .FALSE.)

Averaged phonon-phonon interaction strength ($$P_{\mathbf{q}j}=P_\lambda$$) is used to calculate imaginary part of self energy in thermal conductivity calculation. $$P_\lambda$$ is defined as

$P_\lambda = \frac{1}{(3n_\text{a})^2}\sum_{\lambda' \lambda''}|\Phi_{\lambda \lambda' \lambda''}|^2,$

where $$n_\text{a}$$ is the number of atoms in unit cell. This is roughly constant with respect to the sampling mesh density for converged $$|\Phi_{\lambda \lambda' \lambda''}|^2$$. Then for all $$\mathbf{q}',j',j''$$,

$|\Phi_{\mathbf{q}j,\mathbf{q}'j',\mathbf{G-q-q'}j''}|^2 := P_{\mathbf{q}j} / N,$

where $$N$$ is the number of grid points on the sampling mesh. $$\Phi_{\lambda \lambda' \lambda''} \equiv 0$$ unless $$\mathbf{q} + \mathbf{q}' + \mathbf{q}'' = \mathbf{G}$$.

This option works only when --read-gamma and --br options are activated where the averaged phonon-phonon interaction that is read from kappa-mxxx(-sx-sdx).hdf5 file is used if it exists in the file. Therefore the averaged phonon-phonon interaction has to be stored before using this option (see –full-pp). The calculation result overwrites kappa-mxxx(-sx-sdx).hdf5 file. Therefore to use this option together with -o option is strongly recommended.

First, run full conductivity calculation,

% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br


Then

% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --read-gamma --ave-pp -o ave_pp


--const-ave-pp: Use constant phonon-phonon interaction strength¶

(Setting tag: CONST_AVE_PP, .TRUE. or .FALSE.)

Averaged phonon-phonon interaction ($$P_{\mathbf{q}j}$$) is replaced by this constant value and $$|\Phi_{\lambda \lambda' \lambda''}|^2$$ are set as written in –ave-pp for thermal conductivity calculation. This option works only when --br options are activated. Therefore third-order force constants are not necessary to input. The physical unit of the value is $$\text{eV}^2$$.

% phono3py --dim="3 3 2" -v --mesh="32 32 20" -c POSCAR-unitcell --br --const-ave-pp=1e-10


--gruneisen: Mode-Gruneisen parameter from 3rd order force constants¶

(Setting tag: GRUNEISEN, .TRUE. or .FALSE.)

Mode-Gruneisen-parameters are calculated from fc3.

Mesh sampling mode:

% phono3py --fc3 --fc2 --dim="2 2 2" -v --mesh="16 16 16" -c POSCAR-unitcell --nac --gruneisen


Band path mode:

% phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0  0 0 1/2"


File I/O¶

--hdf5-compression: Choice of HDF5 compression filter¶

Most of phono3py HDF5 output file is compressed by default with the gzip compression filter. To avoid compression, --hdf5-compression=None has to be set. Other filters (lzf or integer values of 0 to 9) may be used, see h5py documentation (http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline).

-o: Arranging output file names¶

Using this option, output file names are slightly modified. For example, specifying -o iso, a file name kappa-m191919.hdf5 is changed to kappa-m191919.iso.hdf5.

This rule is applied to

• fc3.hdf5
• fc2.hdf5
• kappa-xxx.hdf5
• disp_fc3.yaml
• disp_fc2.yaml

-i: Arranging input file names¶

Using this option, input file names are slightly modified. For example, specifying -i iso --fc3, a file name fc3.iso.hdf5 is read instead of fc3.hdf5.

This rule is applied to

• fc3.hdf5
• fc2.hdf5
• kappa-xxx.hdf5
• disp_fc3.yaml
• disp_fc2.yaml