Phonopy API for Python

Phonopy API for Python#

Three unit cells#

In the Phonopy class, mainly three different unit cells are used, unitcell, supercell, and primitive, which can be accessed with these attributes in the instance. unitcell is the initial input crystal structure. From unitcell, supercell is created by supercell_matrix (Supercell matrix). Then primitive is created from supercell with supercell_matrix and primitive_matrix (Primitive matrix).

Having the supercell_matrix (\(\mathrm{M}_\mathrm{s}\)) and the primitive matrix (\(\mathrm{M}_\mathrm{p}\)), for example,

\[\begin{split}\mathrm{M}_\mathrm{s} = \begin{pmatrix} 2 & 0 & 0 \\ 0 & 2 & 0 \\ 0 & 0 & 2 \end{pmatrix} \;\text{and}\;\; \mathrm{M}_\mathrm{p} = \begin{pmatrix} 0 & 1/2 & 1/2 \\ 1/2 & 0 & 1/2 \\ 1/2 & 1/2 & 0 \end{pmatrix},\end{split}\]

respectively, the basis vectors of supercell are built from those of unitcell by

\[( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \; \mathbf{c}_\mathrm{s} ) = ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \; \mathbf{c}_\mathrm{u} ) \mathrm{M}_\mathrm{s}\]

and the basis vectors of primitive are built from those of supercell by

\[( \mathbf{a}_\mathrm{p} \; \mathbf{b}_\mathrm{p} \; \mathbf{c}_\mathrm{p} ) = ( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \; \mathbf{c}_\mathrm{s} ) \mathrm{M}_\mathrm{s}^{-1} \mathrm{M}_\mathrm{p}.\]

Once supercell and primitive are made, unitcell will not be used basically.

Import modules#

After setting the phonopy python path, the phonopy module is imported by:

from phonopy import Phonopy

Crystal structure is defined by the PhonopyAtoms class. The PhonopyAtoms module is imported by:

from phonopy.structure.atoms import PhonopyAtoms

The instance of PhonopyAtoms can be made by reading a crystal structure in a variety of calculator formats found at Interfaces to calculators.

from phonopy.interface.calculator import read_crystal_structure
unitcell, _ = read_crystal_structure("POSCAR-unitcell", interface_mode='vasp')

For VASP format, the keyword argument of interface_mode can be omitted. For QE,

unitcell, optional_structure_info = read_crystal_structure("NaCl.in", interface_mode='qe')

Note that read_crystal_structure returns a tuple and the first element is the PhonopyAtoms instance.

Work flow#

The work flow is schematically shown in Work flow.

Pre-process#

The first step is to create a Phonopy object with at least two arguments, a unit cell (PhonopyAtoms object, see PhonopyAtoms class) and a supercell matrix (3x3 array, see Supercell matrix). In the following example, a \(2\times 2\times 2\) supercell is created. The displacements to be introduced to the supercell are internally generated by the generate_displacements() method with the distance keyword argument. The supercells with displacements are obtained by get_supercells_with_displacements() method as a list of PhonopyAtoms objects.

import numpy as np
from phonopy import Phonopy
from phonopy.structure.atoms import PhonopyAtoms

a = 5.404
unitcell = PhonopyAtoms(symbols=['Si'] * 8,
                        cell=(np.eye(3) * a),
                        scaled_positions=[[0, 0, 0],
                                          [0, 0.5, 0.5],
                                          [0.5, 0, 0.5],
                                          [0.5, 0.5, 0],
                                          [0.25, 0.25, 0.25],
                                          [0.25, 0.75, 0.75],
                                          [0.75, 0.25, 0.75],
                                          [0.75, 0.75, 0.25]])
phonon = Phonopy(unitcell,
                 supercell_matrix=[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
                 primitive_matrix=[[0, 0.5, 0.5],
                                   [0.5, 0, 0.5],
                                   [0.5, 0.5, 0]])
phonon.generate_displacements(distance=0.03)
supercells = phonon.supercells_with_displacements

In this example, the displacement distance is set to 0.03 (0.01 by default). The units are determined by the calculator used (See Physical unit system for calculator for the complete list). This example uses the default calculator for the instance of Phonopy—VASP—which uses Angstroms for distance. The supercells with displacements are given as a list of PhonopyAtoms. See Read and write crystal structures to write those into files in a crystal structure format.

Calculators#

If not using the default calculator ("vasp"), the calculator keyword argument must also be set in your instance of Phonopy (e.g. Phonopy(..., calculator="qe")).

The range of supported calculators use different units internally. If not using VASP, set set_factor_by_calculator to True for correct unit conversion. Some more information on physical unit conversion is found at FREQUENCY_CONVERSION_FACTOR, Physical unit conversion, and Interfaces to calculators.

Pre-processing Example#

import numpy as np
from phonopy import Phonopy
from phonopy.interface.calculator import (
    read_crystal_structure,
    write_crystal_structure,
)

calc = "qe"  # Quantum Espresso
unitcell, optional_structure_info = read_crystal_structure("pw.in",
    interface_mode=calc)

phonon = Phonopy(unitcell, supercell_matrix=np.eye(3), calculator=calc,
    set_factor_by_calculator=True)

phonon.generate_displacements(distance=0.03)
supercells = phonon.supercells_with_displacements

for i, supercell in enumerate(supercells):
    write_crystal_structure(
        f"supercell-{i}.in",
        supercell,
        interface_mode=calc,
        optional_structure_info=optional_structure_info,
    )

phonon.save("phonopy_disp.yaml")

Post process#

Forces on atoms are supposed to be obtained by running force calculator (e.g. VASP) with each supercell with a displacement. Then the forces in the calculation outputs have to be collected by users. However output parsers for selected calculators are found under phonopy.interface, which may be useful. The forces have to be stored in a specific structure: a numpy array (or nested list) as follows:

[ [ [ f_1x, f_1y, f_1z ], [ f_2x, f_2y, f_2z ], ... ], # first supercell
  [ [ f_1x, f_1y, f_1z ], [ f_2x, f_2y, f_2z ], ... ], # second supercell
  ...                                                   ]

This array (sets_of_forces) is set to the Phonopy object by:

phonon.forces = sets_of_forces

This is the case when the set of atomic displacements is generated internally. The information of displacements is already stored in the Phonopy object. But if you want to input the forces together with the corresponding custom set of displacements, displacement_dataset has to be prepared as a python dictionary as follows:

displacement_dataset =
   {'natom': number_of_atoms_in_supercell,
    'first_atoms': [
      {'number': atom index of displaced atom (starting with 0),
       'displacement': displacement in Cartesian coordinates,
       'forces': forces on atoms in supercell},
      {...}, ...]}

This is set to the Phonopy object by:

phonon.dataset = displacement_dataset

From the set of displacements and forces, force constants internally with calculated supercell sets of forces by

phonon.produce_force_constants()

If you have force constants and don’t need to create force constants from forces and displacements, simply set your force constants by

phonon.force_constants = force_constants

The force constants matrix is given in 4 dimensional array (better to be a numpy array of dtype='double', order='C'). The shape of force constants matrix is (N, N, 3, 3) where N is the number of atoms in the supercell and 3 gives Cartesian axes. The compact force constants matrix with (Np, N, 3, 3) where Np is the number of atoms in the primitive cell is also supported. See the details at FORCE_CONSTANTS and force_constants.hdf5.

Phonon calculation#

Save parameters (`phonopy.save`)#

Basic information and parameters needed for phonon calculation are saved into a file by phonopy.save.

phonon.save()

Force sets, displacements, Born effective charges, and dielectric constant are written in the default behaviour.

The default file name is phonopy_params.yaml, but this can be changed with the filename keword argument, which may be necessary if using certain CUI commands that expect a particular filename

The force constants can be written as follows:

phonon.save(settings={'force_constants': True})

Band structure#

Set band paths (run_band_structure()) and get the results (get_band_structure_dict()).

A dictionary with qpoints, distances, frequencies, eigenvectors, group_velocities is returned by get_band_structure_dict(). Eigenvectors can be obtained when with_eigenvectors=True at run_band_structure(). See the details at docstring of Phonopy.get_band_structure_dict. Phonon frequency is sqrt(eigenvalue). A negative eigenvalue has to correspond to the imaginary frequency, but for the plotting, it is set as the negative value in the above example. In addition, you need to multiply by your unit conversion factor. In the case of VASP to transform to THz, the factor is 15.633302.

In example/NaCl, the phonopy is executed from python script, e.g.,

import phonopy
from phonopy.phonon.band_structure import get_band_qpoints_and_path_connections

path = [[[0, 0, 0], [0.5, 0, 0.5], [0.625, 0.25, 0.625]],
        [[0.375, 0.375, 0.75], [0, 0, 0], [0.5, 0.5, 0.5], [0.5, 0.25, 0.75]]]
labels = ["$\\Gamma$", "X", "U", "K", "$\\Gamma$", "L", "W"]
qpoints, connections = get_band_qpoints_and_path_connections(path, npoints=51)
phonon = phonopy.load("phonopy_disp.yaml")
phonon.run_band_structure(qpoints, path_connections=connections, labels=labels)
phonon.plot_band_structure().show()

# To plot DOS next to band structure
phonon.run_mesh([20, 20, 20])
phonon.run_total_dos()
phonon.plot_band_structure_and_dos().show()

# To plot PDOS next to band structure
phonon.run_mesh([20, 20, 20], with_eigenvectors=True, is_mesh_symmetry=False)
phonon.run_projected_dos()
phonon.plot_band_structure_and_dos(pdos_indices=[[0], [1]]).show()

path_connections and labels are optional unless nice looking plotting is needed. To obtain eigenvectors, the corresponding keyword argument must be set:

phonon.run_band_structure(bands, with_eigenvectors=True)

To obtain group velocities:

phonon.run_band_structure(bands, with_group_velocities=True)

Automatic selection of band paths using SeeK-path is invoked by

phonon.auto_band_structure()

and to plot

phonon.auto_band_structure(plot=True).show()

To use this method, seekpath python module is needed.

Mesh sampling#

Set sampling mesh (set_mesh) in reciprocal space. The irreducible q-points and corresponding q-point weights, eigenvalues, and eigenvectors are obtained by get_mesh_dict(). mesh gives the sampling mesh with Monkhorst-Pack scheme. The keyword shift gives the fractional mesh shift with respect to the neighboring grid points.

mesh = [20, 20, 20]
phonon.run_mesh(mesh)
mesh_dict = phonon.get_mesh_dict()
qpoints = mesh_dict['qpoints']
weights = mesh_dict['weights']
frequencies = mesh_dict['frequencies']
eigenvectors = mesh_dict['eigenvectors']
group_velocities = mesh_dict['group_velocities']

To obtain eigenvectors, the corresponding keyword argument must be set:

phonon.run_mesh([20, 20, 20], with_eigenvectors=True)

and for group velocities:

phonon.run_mesh([20, 20, 20], with_group_velocities=True)

The first argument of run_mesh() can be a float value, which is a length measure as explained at MESH, MP, or MESH_NUMBERS, for example:

phonon.run_mesh(100.0)

DOS and PDOS#

Before starting mesh sampling has to be finished. Then set parameters (run_total_dos() or run_projected_dos()) and write the results into files (write_total_dos() and write_projected_dos()). In the case of PDOS, the eigenvectors have to be calculated in the mesh sampling. To get the results get_total_dos_dict() and get_projected_dos_dict() can be used.

To plot total DOS,

phonon.run_mesh([20, 20, 20]) phonon.run_total_dos()
phonon.plot_total_dos().show()

and projected DOS

phonon.run_mesh([20, 20, 20], with_eigenvectors=True, is_mesh_symmetry=False)
phonon.run_projected_dos()
phonon.plot_projected_dos().show()

Convenient shortcuts exist as follows:

phonon.auto_total_dos(plot=True).show()

and

phonon.auto_projected_dos(plot=True).show()

Thermal properties#

Before starting the thermal property calculation, the mesh sampling calculation has to be done in the THz unit. The unit conversion factor for phonon frequency is set in the pre-process of Phonopy with the factor keyword. Calculation range of temperature is set by the parameters run_thermal_properties. Helmholtz free energy, entropy, heat capacity at constant volume at temperatures are obtained by get_thermal_properties_dict, where the results are given as a dictionary of temperatures, Helmholtz free energy, entropy, and heat capacity with keys temperatures, free_energy, entropy, and heat_capacity, respectively.

phonon.run_mesh([20, 20, 20])
phonon.run_thermal_properties(t_step=10,
                              t_max=1000,
                              t_min=0)
tp_dict = phonon.get_thermal_properties_dict()
temperatures = tp_dict['temperatures']
free_energy = tp_dict['free_energy']
entropy = tp_dict['entropy']
heat_capacity = tp_dict['heat_capacity']

for t, F, S, cv in zip(temperatures, free_energy, entropy, heat_capacity):
    print(("%12.3f " + "%15.7f" * 3) % ( t, F, S, cv ))

phonon.plot_thermal_properties().show()

Non-analytical term correction#

To apply non-analytical term correction, Born effective charge tensors for all atoms in primitive cell, dielectric constant tensor, and the unit conversion factor have to be correctly set. The tensors are given in Cartesian coordinates.

born = [[[1.08878299, 0, 0],
         [0, 1.08878299, 0],
         [0, 0, 1.08878299]],
        [[-1.08878299, 0, 0],
         [0, -1.08878299, 0],
         [0, 0, -1.08878299]]]
epsilon = [[2.56544559, 0, 0],
           [0, 2.56544559, 0],
           [0, 0, 2.56544559]]
factors = 14.400
phonon.nac_params = {'born': born,
                     'factor': factors,
                     'dielectric': epsilon}

Data structure#

Eigenvectors#

Eigenvectors are given as the column vectors. Internally phonopy uses numpy.linalg.eigh and eigh is a wrapper of LAPACK. So eigenvectors follow the convention of LAPACK, which can be shown at http://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.eigh.html

Eigenvectors corresponding to phonopy yaml output are obtained as follows.

Band structure#

if eigvecs is not None:
    for eigvecs_on_path in eigvecs:
        for eigvecs_at_q in eigvecs_on_path:
            for vec in eigvecs_at_q.T:
                print(vec)

Mesh sampling#

if eigvecs is not None:
    for eigvecs_at_q in eigvecs:
        for vec in eigvecs_at_q.T:
            print(vec)

`PhonopyAtoms` class#

Initialization#

The usable keywords in the initialization are:

cell=None,
scaled_positions=None,
positions=None,
numbers=None,
symbols=None,
masses=None,
magnetic_moments=None,
species_table=None,
species_ids=None,

At least three arguments have to be given at the initialization, which are

cell
positions or scaled_positions
symbols, or numbers, or (species_table and species_ids)

symbols, numbers, and species_table are mutually exclusive. The species_table / species_ids pair is the canonical internal representation and is required to construct cells with mixed-species sites such as those arising from the Virtual Crystal Approximation; see Mixed-species sites and the Virtual Crystal Approximation.

Variables#

The following variables are implemented in the PhonopyAtoms class in phonopy/structure/atoms.py.

`cell`#

Basis vectors are given in the matrix form in Cartesian coordinates.

[ [ a_x, a_y, a_z ], [ b_x, b_y, b_z ], [ c_x, c_y, c_z ] ]

`scaled_positions`#

Atomic positions in fractional coordinates.

[ [ x1_a, x1_b, x1_c ], [ x2_a, x2_b, x2_c ], [ x3_a, x3_b, x3_c ], ... ]

`positions`#

Cartesian positions of atoms.

positions = np.dot(scaled_positions, cell)

where np means the numpy module (import numpy as np).

`symbols`#

Chemical symbols, e.g.,

['Zn', 'Zn', 'O', 'O']

for the ZnO unit cell.

`numbers`#

Atomic numbers, e.g.,

[30, 30, 8, 8]

for the ZnO unit cell.

For cells that contain mixed-species sites (e.g. VCA), cell.numbers raises RuntimeError because a mixture has no single atomic number; use cell.species_ids instead.

`species_ids`#

Per-atom indices into cell.species_table. Each id is an opaque non-negative integer that refers to a _Species entry; two atoms share an id iff they are the same chemical species (including any suffix index or mixture content). Available on every cell, including those without mixed sites.

`species_table`#

Deduplicated list of _Species entries indexed by species_ids. Each entry holds either a single-element species (atomic_number set) or a mixed-species site (mixture set to a tuple of (symbol, weight) pairs summing to 1.0). The list is a shallow copy on each access; entries are frozen and safe to share.

`has_mixtures`#

Boolean property. True when any species in the cell is a weighted mixture of constituents (e.g. a VCA virtual-crystal site).

`masses`#

Atomic masses, e.g.,

[65.38, 65.38, 15.9994, 15.9994]

for the ZnO unit cell.

Attributes#

cell
positions
scaled_positions
masses
magnetic_moments
symbols
numbers
species_ids
species_table
has_mixtures
volume

where volume is the getter only.

Methods#

unitcell.get_number_of_atoms() is equivalent to len(unitcell). An instance can be deep-copied by unitcell.copy(). Human-readable crystal structure in Yaml format is shown by print(unitcell). unitcell.to_tuple converts to spglib crystal structure (https://spglib.github.io/spglib/python-spglib.html#crystal-structure-cell).

Mixed-species sites and the Virtual Crystal Approximation#

Warning

Experimental. The mixed-species / Virtual Crystal Approximation (VCA) support — including species_table / species_ids / has_mixtures on PhonopyAtoms, apply_site_mixture, build_species_table_from_mixtures, the --site-mixture CLI option, the FC-time mixture-force reduction, and the VASP expand_mixtures writer — is experimental. APIs, file layouts (including the expanded FORCE_SETS format), and CLI flags may change without notice in upcoming releases. Currently only the VASP calculator interface is wired for mixture-expanded I/O.

Each PhonopyAtoms instance owns a deduplicated species table plus a per-atom index list (species_ids). A species can either be an ordinary chemical element or a weighted mixture of elements; the latter represents a single crystallographic site shared by several species in fixed proportions (e.g. a Virtual Crystal Approximation site for a Ge/Sn alloy). Mixed-site masses are the weight-averaged sum of constituent atomic masses.

Building a cell with mixed sites#

build_species_table_from_mixtures packs a per-atom list of (symbol, weight) tuples into the canonical (species_table, species_ids) pair:

from phonopy.structure.atoms import (
    PhonopyAtoms,
    build_species_table_from_mixtures,
)

species_table, species_ids = build_species_table_from_mixtures(
    [
        [("Si", 1.0)],                  # ordinary Si
        [("Ge", 0.5), ("Sn", 0.5)],     # GeSn mixed-species site
    ]
)
cell = PhonopyAtoms(
    cell=[[a, 0, 0], [0, a, 0], [0, 0, a]],
    scaled_positions=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
    species_table=species_table,
    species_ids=species_ids,
)
assert cell.has_mixtures

Constituent weights of each entry must sum to 1.0; a single-component entry of weight 1.0 is canonicalized to a normal (single-element) species. Mixed species carry composite labels formed by concatenating constituent symbols in input order (“GeSn”); two distinct mixtures that would share the same composite label still get distinct ids because the underlying (symbol, weight) tuples differ.

`apply_site_mixture` utility#

phonopy.structure.cells.apply_site_mixture collapses overlapping atoms in an ordinary cell into mixed-species sites. The Virtual Crystal Approximation (VCA) is the typical use case.

from phonopy.structure.cells import apply_site_mixture

mixed_cell = apply_site_mixture(cell, weights=[0.5, 0.5, 0.5, 0.5])

weights must have one entry per atom in the input order. Atoms whose fractional positions agree (modulo lattice translations) within symprec are merged into a single site whose weights must sum to 1.0; isolated atoms must carry weight 1.0. When several distinct mixtures within the same cell would collide on the same composite label, all colliding sites get 1-based suffixes ("GeSn1", "GeSn2", …). The returned cell can be fed to Phonopy(...) as a unit cell.

The per-atom convention here is distinct from VASP’s INCAR VCA tag, which lists one weight per element row in POSCAR; see the CLI section below for how phonopy generates a VASP-compatible POSCAR/INCAR pair.

CLI: `--site-mixture`#

The same merge can be requested at the command line:

phonopy --dim "2 2 2" --site-mixture "0.5 0.5 0.5 0.5" -d

--site-mixture takes a space-separated list of per-atom weights in the input order, with the same validation rules as apply_site_mixture. The merge is applied immediately after the unit cell is read, so the rest of the workflow (displacement generation, supercell construction, force-constant building) sees only the merged cell.

When the calculator is VASP, the supercell and displaced supercells are written with each mixed-species site expanded into one POSCAR row per constituent at the same fractional coordinates, and a hint is printed showing the matching POTCAR concatenation order and the INCAR VCA = ... line. For example, a 50/50 GeSn cell with --dim "2 2 2" produces SPOSCAR with Ge Sn / 16 16 and prints INCAR: VCA = 0.5 0.5.

Forces for mixed-species cells#

A VASP run on a mixture-expanded supercell returns one force vector per expanded constituent row (n_expanded per displacement). Because every constituent at a shared crystallographic site is governed by its own POTCAR, those forces differ between constituents and carry the raw single-potential information from the SCF calculation.

Phonopy preserves this raw output: parse_set_of_forces (and get_forces_vasprunxml) for a mixed-species cell return forces of shape (num_supercells, n_expanded, 3) and store them as-is in the Phonopy.dataset. The corresponding displacement entries remain on a per-site basis in 1..n_sites, so the dataset is asymmetric in shape between displacements and forces; this is intentional and preserved by phonopy.yaml round-trips and by the expanded FORCE_SETS format.

The conversion to per-site forces is deferred to immediately before force-constant calculation. The reduction utility is phonopy.structure.cells.reduce_mixture_forces(forces, cell, mode=...), which supports two conventions selected through the mode keyword:

mode="sum" produces the plain sum,
```
F_site = sum_k F_k
```
used for VASP because its vasprun.xml per-row forces already incorporate the VCA weights through the averaged potential.
mode="weighted_sum" (the default) produces the weighted sum,
```
F_site = sum_k (w_k * F_k)
```
where w_k is the constituent weight stored in the mixture entry of cell.species_table. Use this when the calculator returns single-potential forces that have not yet been folded with mixture weights.

The Phonopy FC pipeline picks the convention based on Phonopy.calculator: VASP (and the default None calculator) maps to "sum"; all other interfaces map to "weighted_sum". Because the raw forces are preserved in the dataset, applying a different reduction convention or different weights only requires re-running the reduction and the force-constant build, not the calculator.

Expansion ordering#

The mapping from expanded row indices back to phonopy sites is fixed by the same routine that writes the VASP POSCAR: for each entry in cell.species_table, the atoms belonging to that entry are emitted once per constituent (in mixture order) at the original site coordinates. The shared helper phonopy.structure.cells.get_mixture_expansion(cell) returns the ordered list of (site_index, weight) pairs that this row order corresponds to, and is used by both the writer and the force/FORCE_SETS parser so the two stay in lockstep.

Definitions of variables#

Supercell matrix#

Supercell matrix \(\mathrm{M}_\mathrm{s}\) is a transformation matrix from lattice vectors to those of a super cell. Following a crystallography convention, the transformation is given by

\[( \mathbf{a}_\mathrm{s} \; \mathbf{b}_\mathrm{s} \; \mathbf{c}_\mathrm{s} ) = ( \mathbf{a}_\mathrm{u} \; \mathbf{b}_\mathrm{u} \; \mathbf{c}_\mathrm{u} ) \mathrm{M}_\mathrm{s}\]

where \(\mathbf{a}_\mathrm{u}\), \(\mathbf{b}_\mathrm{u}\), and \(\mathbf{c}_\mathrm{u}\) are the column vectors of the original lattice vectors, and \(\mathbf{a}_\mathrm{s}\), \(\mathbf{b}_\mathrm{s}\), and \(\mathbf{c}_\mathrm{s}\) are the column vectors of the supercell lattice vectors. Be careful that the lattice vectors of the PhonopyAtoms class are the row vectors (cell). Therefore the phonopy code, which relies on the PhonopyAtoms class, is usually written such as

supercell_lattice = (original_lattice.T @ supercell_matrix).T,

Primitive matrix#

Primitive matrix \(\mathrm{M}_\mathrm{p}\) is a tranformation matrix from lattice vectors to those of a primitive cell if there exists the primitive cell in the lattice vectors. Following a crystallography convention, the transformation is given by

where \(\mathbf{a}_\mathrm{p}\), \(\mathbf{b}_\mathrm{p}\), and \(\mathbf{c}_\mathrm{p}\) are the column vectors of the primitive lattice vectors. Be careful that the lattice vectors of the PhonopyAtoms class are the row vectors (cell). Therefore the phonopy code, which relies on the PhonopyAtoms class, is usually written such as

primitive_lattice = (supercell_lattice.T @ np.linalg.inv(supercell_matrix) @ primitive_matrix).T,

Symmetry search tolerance#

Symmetry search tolerance (often the name symprec is used in phonopy) is used to determine symmetry operations of the crystal structures. The physical unit follows that of input crystal structure.

Load phonopy settings `phonopy.load`#

phonopy.load is a convenient function that creates a Phonopy instance by loading data from a phonopy_xxx.yaml file, which may include all the necessary information to run phonopy. A typical usage is:

import phonopy
phonon = phonopy.load("phonopy_params.yaml")

If phonopy_params.yaml contains a displacement-force dataset and you want to avoid producing force constants, set produce_fc=False:

phonon = phonopy.load("phonopy_params.yaml", produce_fc=False)

Alternatively, if you have either phonopy.yaml (or phonopy_disp.yaml) along with a FORCE_SETS file, you can create a Phonopy object like this:

phonon = phonopy.load("phonopy.yaml", force_sets_filename="FORCE_SETS")

In this case, the command reads the structure information from phonopy.yaml and the displacement-force data from FORCE_SETS to create the Phonopy instance.

If your current directory contains the following files:

% ls
BORN  FORCE_SETS  phonopy.yaml

then both the BORN and FORCE_SETS files will be read automatically by

phonon = phonopy.load("phonopy.yaml")

For more details, see the function’s docstring:

In [1]: import phonopy
In [2]: help(phonopy.load)

Read and write crystal structures#

There is a function to write the PhonopyAtoms instance into crystal structure formats of different force calculators, write_crystal_structure. This works as a partner of read_crystal_structure. Taking an example of QE interface, how to use these functions is shown below.

In [1]: from phonopy.interface.calculator import read_crystal_structure, write_crystal_structure

In [2]: !cat "NaCl.in"
 &control
    calculation = 'scf'
    tprnfor = .true.
    tstress = .true.
    pseudo_dir = '/home/togo/espresso/pseudo/'
 /
 &system
    ibrav = 0
    nat = 8
    ntyp = 2
    ecutwfc = 70.0
 /
 &electrons
    diagonalization = 'david'
    conv_thr = 1.0d-9
 /
ATOMIC_SPECIES
 Na  22.98976928 Na.pbe-spn-kjpaw_psl.0.2.UPF
 Cl  35.453      Cl.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS crystal
 Na   0.0000000000000000  0.0000000000000000  0.0000000000000000
 Na   0.0000000000000000  0.5000000000000000  0.5000000000000000
 Na   0.5000000000000000  0.0000000000000000  0.5000000000000000
 Na   0.5000000000000000  0.5000000000000000  0.0000000000000000
 Cl   0.5000000000000000  0.5000000000000000  0.5000000000000000
 Cl   0.5000000000000000  0.0000000000000000  0.0000000000000000
 Cl   0.0000000000000000  0.5000000000000000  0.0000000000000000
 Cl   0.0000000000000000  0.0000000000000000  0.5000000000000000
CELL_PARAMETERS angstrom
 5.6903014761756712 0 0
 0 5.6903014761756712 0
 0 0 5.6903014761756712
K_POINTS automatic
 8 8 8 1 1 1

In [3]: cell, optional_structure_info = read_crystal_structure("NaCl.in", interface_mode='qe')

In [4]: optional_structure_info
Out[4]:
('NaCl.in',
 {'Na': 'Na.pbe-spn-kjpaw_psl.0.2.UPF', 'Cl': 'Cl.pbe-n-kjpaw_psl.0.1.UPF'})

In [5]: write_crystal_structure("NaCl-out.in", cell, interface_mode='qe', optional_structure_info=optional_structure_info)

In [6]: !cat "NaCl-out.in"
!    ibrav = 0, nat = 8, ntyp = 2
CELL_PARAMETERS bohr
   10.7531114272216008    0.0000000000000000    0.0000000000000000
    0.0000000000000000   10.7531114272216008    0.0000000000000000
    0.0000000000000000    0.0000000000000000   10.7531114272216008
ATOMIC_SPECIES
 Na   22.98977   Na.pbe-spn-kjpaw_psl.0.2.UPF
 Cl   35.45300   Cl.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS crystal
 Na   0.0000000000000000  0.0000000000000000  0.0000000000000000
 Na   0.0000000000000000  0.5000000000000000  0.5000000000000000
 Na   0.5000000000000000  0.0000000000000000  0.5000000000000000
 Na   0.5000000000000000  0.5000000000000000  0.0000000000000000
 Cl   0.5000000000000000  0.5000000000000000  0.5000000000000000
 Cl   0.5000000000000000  0.0000000000000000  0.0000000000000000
 Cl   0.0000000000000000  0.5000000000000000  0.0000000000000000
 Cl   0.0000000000000000  0.0000000000000000  0.5000000000000000

Depending on calculator interfaces, all the information can not be recovered from the information obtained from read_crystal_structure. More details about how write_crystal_structure works may need to read directly the code.

Getting parameters for non-analytical term correction#

Parameters for non-analytical term correction may be made as follows. This example assumes that the user knows what are the unit cell and primitive cell and that the Born effective charge and dielectric constant were calculated using VASP code by the unit cell.

import io
import numpy as np
from phonopy.physical_units import get_physical_units
from phonopy.structure.symmetry import symmetrize_borns_and_epsilon
from phonopy.interface.vasp import VasprunxmlExpat

with io.open("vasprun.xml", "rb") as f:
    vasprun = VasprunxmlExpat(f)
    vasprun.parse():
    epsilon = vasprun.epsilon
    borns = vasprun.born
    unitcell = vasprun.cell

borns_, epsilon_ = symmetrize_borns_and_epsilon(
    borns,
    epsilon,
    unitcell,
    primitive_matrix=[[0, 0.5, 0.5],
                      [0.5, 0, 0.5],
                      [0.5, 0.5, 0]],
    supercell_matrix=np.diag([2, 2, 2]),
    symprec=1e-5)

units = get_physical_units()
nac_params = {'born': borns_,
              'factor': units.Hartree * units.Bohr,
              'dielectric': epsilon_}

Phonopy API for Python

Contents

Phonopy API for Python#

Three unit cells#

Import modules#

Work flow#

Pre-process#

Calculators#

Pre-processing Example#

Post process#

Phonon calculation#

Save parameters (phonopy.save)#

Band structure#

Mesh sampling#

DOS and PDOS#

Thermal properties#

Non-analytical term correction#

Data structure#

Eigenvectors#

Band structure#

Mesh sampling#

PhonopyAtoms class#

Initialization#

Variables#

cell#

scaled_positions#

positions#

symbols#

numbers#

species_ids#

species_table#

has_mixtures#

masses#

Attributes#

Methods#

Mixed-species sites and the Virtual Crystal Approximation#

Building a cell with mixed sites#

apply_site_mixture utility#

CLI: --site-mixture#

Forces for mixed-species cells#

Expansion ordering#

Definitions of variables#

Supercell matrix#

Primitive matrix#

Symmetry search tolerance#

Load phonopy settings phonopy.load#

Read and write crystal structures#

Getting parameters for non-analytical term correction#

Save parameters (`phonopy.save`)#

`PhonopyAtoms` class#

`cell`#

`scaled_positions`#

`positions`#

`symbols`#

`numbers`#

`species_ids`#

`species_table`#

`has_mixtures`#

`masses`#

`apply_site_mixture` utility#

CLI: `--site-mixture`#

Load phonopy settings `phonopy.load`#