Input/output and logging#

The functions and modules described below provide functionality for controlling the verbosity of the output as well as for reading and writing force constant matrices in different formats.

Phonopy and phono3py IO#

This module provides functions for reading and writing data files in phonopy and phono3py formats.

hiphive.input_output.phonopy.read_phonopy_fc2(filename, format=None)[source]#

Parses a second-order force constant file in phonopy format.

Parameters:

  • filename (str) – Input file name.

  • format (str) – Specify the file-format, if None tries to guess the format from filename; possible values: 'text', 'hdf5'.

Returns:

Second-order force constant matrix (N,N,3,3 array) where N is the number of atoms.

Return type:

numpy.ndarray

hiphive.input_output.phonopy.read_phonopy_fc3(filename)[source]#

Parses a third order force constant file in phonopy hdf5 format.

Parameters:

filename (str) – Input file name.

Return type:

ndarray

Returns:

Third-order force constant matrix.

hiphive.input_output.phonopy.write_phonopy_fc2(filename, fc2, format=None)[source]#

Writes second-order force constant matrix in phonopy format.

Parameters:

  • filename (str) – Output file name.

  • fc2 – Second-order force constant matrix as ForceConstants object or as np.ndarray.

  • format (str) – Specify the file-format, if None try to guess the format from filename; possible values: 'text', 'hdf5'.

Return type:

None

hiphive.input_output.phonopy.write_phonopy_fc3(filename, fc3)[source]#

Writes third order force constant matrix in phonopy hdf5 format.

Parameters:

  • filename (str) – Output file name.

  • fc3 – Third-order force constant matrix as ForceConstants object or as np.ndarray.

Return type:

None

ShengBTE IO#

The io.shengBTE module provides functions for reading and writing data files in shengBTE format.

hiphive.input_output.shengBTE.read_shengBTE_fc3(filename, prim, supercell, symprec=1e-05)[source]#

Reads third-order force constants file in shengBTE format.

Parameters:

  • filename (str) – Input file name.

  • prim (Atoms) – Primitive structure for the force constants.

  • supercell (Atoms) – Supercell supercell onto which to map the force constants.

  • symprec (float) – Structural symmetry tolerance.

Returns:

Third-order force constants for the specified supercell as ForceConstants object.

hiphive.input_output.shengBTE.write_shengBTE_fc3(filename, fcs, prim, symprec=1e-05, cutoff=inf, fc_tol=1e-08)[source]#

Writes third-order force constants to file in shengBTE format.

Parameters:

  • filename (str) – Output file name.

  • fcs – Force constants in ForceConstants format; the supercell associated with this object must be based on prim.

  • prim (Atoms) – Primitive structure (must be equivalent to structure used in the shengBTE calculation).

  • symprec (float) – Structural symmetry tolerance.

  • cutoff (float) – All atoms in cluster must be within this cutoff.

  • fc_tol (float) – If the absolute value of the largest entry in a force constant is less than fc_tol it will not be included in the output.

GPUMD IO#

hiphive.input_output.gpumd.write_fcp_txt(fname, path, n_types, max_order, heat_current_order=2)[source]#

Write driver potential file for GPUMD.

Parameters:

  • fname (str) – Output file name.

  • path (str) – Path to directory with force constant file.

  • n_types (int) – Number of atom types.

  • max_order (int) – Maximum order of the force constant potential.

  • heat_current_order (int) – Heat current order used in thermal conductivity.

Return type:

None

Format is a simple file containing the following:

fcp number_of_atom_types
highest_force_order heat_current_order
path_to_force_constant_files

which in practice for a binary system with a sixth order model, consider third-order heat-currents, would mean:

fcp 2
6 3
/path/to/your/folder
hiphive.input_output.gpumd.write_fcs_gpumd(fname_fc, fname_clusters, fcs, order, tol=1e-10)[source]#

Writes force constants of given order in GPUMD format.

Parameters:

  • fname_fc (str) – Name of file which contains the lookup force constants.

  • fname_clusters (str) – Name of file which contains the clusters and the force constant lookup index.

  • fcs – Force constants in ForceConstants format.

  • order (int) – Force constants for this order will be written to file.

  • tol (float) – If the norm of a force constant term is less than this value it will be excluded from the output; if two force-constants differ by this value or less, they are considered equal.

Return type:

None

hiphive.input_output.gpumd.write_r0(fname, atoms)[source]#

Write the GPUMD r0 file with the reference atomic positions.

Parameters:

  • fname (str) – Name of file to which to write the atomic positions.

  • atoms (Atoms) – Input structure.

Logging#

hiphive.input_output.logging_tools.set_config(filename=None, level=None, continuous=None)[source]

Alters the way logging is handled.

Parameters:

  • filename (str) – name of file the log should be sent to

  • level (int) – verbosity level; see Python logging library for details

  • continuous (bool) – if True the progress will be continously updated

Progress bar#

class hiphive.input_output.logging_tools.Progress(tot=None, mode='frac', estimate_remaining=True)[source]

Progress bar like functionality.