6. API

This is the Python API for phonoLAMMPS

class phonolammps.PhonoBase

Base class for PhonoLAMMPS This class is not designed to be called directly. To use it make a subclass and implement the following methods:

• __init__()
• get_forces()

get_force_constants(include_data_set=False)

calculate the force constants with phonopy using lammps to calculate forces

Returns:ForceConstants type object containing force constants

get_path_using_seek_path()

Obtain the path in reciprocal space to plot the phonon band structure

Returns:dictionary with list of q-points and labels of high symmetry points

get_phonopy_phonon()

Return phonopy phonon object with unitcell, primitive cell and the force constants set.

Returns:

get_supercell_matrix()

Get the supercell matrix

Return supercell:  the supercell 3x3 matrix (list of lists)

get_unitcell()

Get unit cell structure

Return unitcell:  unit cell 3x3 matrix (lattice vectors in rows)

plot_phonon_dispersion_bands(bands_and_labels=None)

Plot phonon band structure using seekpath automatic k-path Warning: The labels may be wrong if the structure is not standarized

Parameters:bands_and_labels – Custom energy band path

write_force_constants(filename='FORCE_CONSTANTS', hdf5=False)

Write the force constants in a file in phonopy plain text format

Parameters:filename – Force constants filename

write_force_sets(filename='FORCE_SETS')

Write the force sets in a file in phonopy plain text format

Parameters:filename – Force sets filename

write_unitcell_POSCAR(filename='POSCAR')

Write unit cell in VASP POSCAR type file

Parameters:filename – POSCAR file name (Default: POSCAR)

class phonolammps.PhonoGromacs(gro_file, supercell_matrix=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), primitive_matrix=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), displacement_distance=0.01, show_log=False, show_progress=False, use_NAC=False, symmetrize=True, gmx_params=None, base_ff='charmm27.ff/forcefield.itp', itp_file=None, silent=True, omp_num_threads=1)

cell_angles(cell)

Get the angles between the cell lattice vectors in degrees.

cell_lengths(cell)

Get the lengths of cell lattice vectors in angstroms.

get_forces(cell_with_disp)

Calculate the forces of a supercell using tinker :param cell_with_disp: supercell (PhonopyAtoms) from which determine the forces :return array: numpy array matrix with forces of atoms [Natoms x 3]

class phonolammps.PhonoTinker(txyz_input_file, key_input_file, force_field_file, supercell_matrix=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), primitive_matrix=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), displacement_distance=0.01, show_log=False, show_progress=False, use_NAC=False, symmetrize=True)

get_forces(cell_with_disp)

Calculate the forces of a supercell using tinker :param cell_with_disp: supercell (PhonopyAtoms) from which determine the forces :return array: numpy array matrix with forces of atoms [Natoms x 3]

class phonolammps.Phonolammps(lammps_input, supercell_matrix=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), primitive_matrix=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), displacement_distance=0.01, show_log=False, show_progress=False, use_NAC=False, symmetrize=True)

get_forces(cell_with_disp)

Calculate the forces of a supercell using lammps

Parameters:cell_with_disp – supercell from which determine the forces Returns:numpy array matrix with forces of atoms [Natoms x 3]

get_units(commands_list)

Get the units label for LAMMPS “units” command from a list of LAMMPS input commands

Parameters:commands_list – list of LAMMPS input commands (strings) Return units:string containing the units

optimize_unitcell(energy_tol=0, force_tol=1e-10, max_iter=1000000, max_eval=1000000)

Optimize atoms position of the unitcell using lammps minimizer. Check https://docs.lammps.org/minimize.html for details

Parameters:

• energy_tol – stopping tolerance for energ
• force_tol – stopping tolerance for force (force units)
• max_iter – max iterations of minimizer
• max_eval – max number of force/energy evaluations

end