"""
This module provides functions for reading and writing data files
in phonopy and phono3py formats.
"""
import os
import warnings
from itertools import product
import numpy as np
import hiphive
from .logging_tools import logger
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=FutureWarning)
import h5py
logger = logger.getChild('io_phonopy')
def _filename_to_format(filename: str) -> str:
""" Tries to guess the format from the filename. """
basename = os.path.basename(filename)
if basename == 'FORCE_CONSTANTS':
return 'text'
if '.' in basename:
extension = basename.split('.')[-1]
if extension == 'hdf5':
return 'hdf5'
raise ValueError('Could not guess file format')
[docs]
def read_phonopy_fc2(filename: str, format: str = None) -> np.ndarray:
"""Parses a second-order force constant file in phonopy format.
Parameters
----------
filename
Input file name.
format
Specify the file-format, if `None` tries to guess the format from filename;
possible values: `'text'`, `'hdf5'`.
Returns
-------
numpy.ndarray
Second-order force constant matrix (`N,N,3,3` array)
where `N` is the number of atoms.
"""
fc2_readers = {
'text': _read_phonopy_fc2_text,
'hdf5': _read_phonopy_fc2_hdf5
}
if format is None:
format = _filename_to_format(filename)
if format not in fc2_readers.keys():
raise ValueError('Did not recognize format {}'.format(format))
return fc2_readers[format](filename)
[docs]
def write_phonopy_fc2(filename: str,
fc2,
format: str = None) -> None:
"""Writes second-order force constant matrix in phonopy format.
Parameters
----------
filename
Output file name.
fc2
Second-order force constant matrix as :class:`ForceConstants` object or as `np.ndarray`.
format
Specify the file-format, if `None` try to guess the format from filename;
possible values: `'text'`, `'hdf5'`.
"""
fc2_writers = {
'text': _write_phonopy_fc2_text,
'hdf5': _write_phonopy_fc2_hdf5
}
# get fc2_array
if isinstance(fc2, hiphive.ForceConstants):
fc2_array = fc2.get_fc_array(order=2)
elif isinstance(fc2, np.ndarray):
fc2_array = fc2
else:
raise TypeError('fc2 should be a ForceConstants object or a NumPy array.')
# check that fc2 has correct shape
n_atoms = fc2_array.shape[0]
if fc2_array.shape != (n_atoms, n_atoms, 3, 3):
raise ValueError('fc2 has wrong shape')
# write
if format is None:
format = _filename_to_format(filename)
if format not in fc2_writers.keys():
raise ValueError('Did not recognize format {}'.format(format))
fc2_writers[format](filename, fc2_array)
[docs]
def read_phonopy_fc3(filename: str) -> np.ndarray:
"""Parses a third order force constant file in phonopy hdf5 format.
Parameters
----------
filename
Input file name.
Returns
-------
Third-order force constant matrix.
"""
with h5py.File(filename, 'r') as hf:
if 'fc3' in hf.keys():
fc3 = hf['fc3'][:]
else:
raise IOError('Could not find fc3 in file {}'.format(filename))
return fc3
[docs]
def write_phonopy_fc3(
filename: str,
fc3,
) -> None:
"""Writes third order force constant matrix in phonopy hdf5 format.
Parameters
----------
filename
Output file name.
fc3
Third-order force constant matrix as :class:`ForceConstants` object or as `np.ndarray`.
"""
if isinstance(fc3, hiphive.ForceConstants):
fc3_array = fc3.get_fc_array(order=3)
elif isinstance(fc3, np.ndarray):
fc3_array = fc3
else:
raise TypeError('fc3 should be a ForceConstants object or a NumPy array.')
# check that fc3 has correct shape
n_atoms = fc3_array.shape[0]
if fc3_array.shape != (n_atoms, n_atoms, n_atoms, 3, 3, 3):
raise ValueError('fc3 has wrong shape')
with h5py.File(filename, 'w') as hf:
hf.create_dataset('fc3', data=fc3_array, compression='gzip')
hf.flush()
def _read_phonopy_fc2_text(filename: str) -> np.ndarray:
""" Reads phonopy-fc2 file in text format. """
with open(filename, 'r') as f:
# read shape of force constants
line = f.readline()
line_ints = [int(x) for x in line.split()]
if len(line_ints) == 1:
n_atoms = line_ints[0]
elif len(line_ints) == 2:
assert line_ints[0] == line_ints[1]
n_atoms = line_ints[0]
else:
raise ValueError('Unsupported or incorrect phonopy format')
fc2 = np.full((n_atoms, n_atoms, 3, 3), np.nan)
# read force constants
lines = f.readlines()
for n, line in enumerate(lines):
flds = line.split()
if len(flds) == 2:
i = int(flds[0]) - 1 # phonopy index starts with 1
j = int(flds[1]) - 1
for x in range(3):
fc_row = lines[n + x + 1].split()
for y in range(3):
fc2[i][j][x][y] = float(fc_row[y])
return fc2
def _read_phonopy_fc2_hdf5(filename: str) -> np.ndarray:
""" Reads phonopy-fc2 file in hdf5 format. """
with h5py.File(filename, 'r') as hf:
if 'force_constants' in hf.keys():
fc2 = hf['force_constants'][:]
elif 'fc2' in hf.keys():
fc2 = hf['fc2'][:]
else:
raise IOError('Could not find fc2 in file {}'.format(filename))
return fc2
def _write_phonopy_fc2_text(filename: str, fc2: np.ndarray) -> None:
""" Writes second-order force constants to file in text format. """
n_atoms = fc2.shape[0]
with open(filename, 'w') as f:
f.write('{:5d} {:5d}\n'.format(n_atoms, n_atoms))
for i, j in product(range(n_atoms), repeat=2):
fc2_ij = fc2[(i, j)]
if fc2_ij.shape != (3, 3):
raise ValueError('Invalid shape for fc2[({},{})]'.format(i, j))
f.write('{:-5d}{:5d}\n'.format(i + 1, j + 1))
for row in fc2_ij:
f.write((3*' {:22.15f}'+'\n').format(*tuple(row)))
def _write_phonopy_fc2_hdf5(filename: str, fc2: np.ndarray) -> None:
""" Writes second-order force constants to file in hdf5 format. """
with h5py.File(filename, 'w') as hf:
hf.create_dataset('fc2', data=fc2, compression='gzip')
hf.flush()
