def parse_castep_file(file_name, ir_or_raman):
"""
Read frequencies from a <>.castep file
@param file_name - file path of the file to read
@return the frequencies, infra red and raman intensities and weights of frequency blocks
"""
file_data = {}
# Get Regex strings from load_helper
header_regex = re.compile(load_helper.CASTEP_HEADER_REGEX)
data_regex = re.compile(load_helper.CASTEP_DATA_REGEX)
bond_regex = re.compile(load_helper.CASTEP_BOND_REGEX)
block_count = 0
frequencies, ir_intensities, raman_intensities, weights, q_vectors, bonds = [], [], [], [], [], []
data_lists = (frequencies, ir_intensities, raman_intensities)
with open(file_name, 'rU') as f_handle:
file_data.update(_parse_castep_file_header(f_handle))
while True:
line = f_handle.readline()
# Check we've reached the end of file
if not line:
break
# Check if we've found a block of frequencies
header_match = header_regex.match(line)
if header_match:
block_count += 1
weight, q_vector = load_helper._parse_block_header(header_match, block_count)
weights.append(weight)
q_vectors.append(q_vector)
# Move file pointer forward to start of intensity data
_find_castep_freq_block(f_handle, data_regex)
# Parse block of frequencies
for line_data in _parse_castep_freq_block(f_handle, file_data['num_branches'], ir_or_raman):
for data_list, item in zip(data_lists, line_data):
data_list.append(item)
# Check if we've found a bond
bond_match = bond_regex.match(line)
if bond_match:
bonds.append(_parse_castep_bond(bond_match))
frequencies = np.asarray(frequencies)
ir_intensities = np.asarray(ir_intensities)
raman_intensities = np.asarray(raman_intensities)
warray = np.repeat(weights, file_data['num_branches'])
file_data.update({
'frequencies': frequencies,
'ir_intensities': ir_intensities,
'raman_intensities': raman_intensities,
'weights': warray,
'q_vectors':q_vectors
})
if len(bonds) > 0:
file_data['bonds'] = bonds
return file_data
def parse_phonon_file(file_name, record_eigenvectors):
"""
Read frequencies from a <>.phonon file
@param file_name - file path of the file to read
@return the frequencies, infra red and raman intensities and weights of frequency blocks
"""
file_data = {}
# Get regex strings from load_helper
header_regex = re.compile(load_helper.PHONON_HEADER_REGEX)
eigenvectors_regex = re.compile(load_helper.PHONON_EIGENVEC_REGEX)
block_count = 0
frequencies, ir_intensities, raman_intensities, weights, q_vectors, eigenvectors = [], [], [], [], [], []
data_lists = (frequencies, ir_intensities, raman_intensities)
with open(file_name, 'rU') as f_handle:
file_data.update(_parse_phonon_file_header(f_handle))
while True:
line = f_handle.readline()
# Check we've reached the end of file
if not line:
break
# Check if we've found a block of frequencies
header_match = header_regex.match(line)
if header_match:
block_count += 1
weight, q_vector = load_helper._parse_block_header(
header_match, block_count)
weights.append(weight)
q_vectors.append(q_vector)
# Parse block of frequencies
for line_data in _parse_phonon_freq_block(
f_handle, file_data['num_branches']):
for data_list, item in zip(data_lists, line_data):
data_list.append(item)
vector_match = eigenvectors_regex.match(line)
if vector_match:
if record_eigenvectors:
# Parse eigenvectors for partial dos
vectors = _parse_phonon_eigenvectors(
f_handle, file_data['num_ions'],
file_data['num_branches'])
eigenvectors.append(vectors)
else:
# Skip over eigenvectors
for _ in range(file_data['num_ions'] *
file_data['num_branches']):
line = f_handle.readline()
if not line:
raise IOError(
"Bad file format. Uexpectedly reached end of file."
)
frequencies = np.asarray(frequencies)
ir_intensities = np.asarray(ir_intensities)
raman_intensities = np.asarray(raman_intensities)
warray = np.repeat(weights, file_data['num_branches'])
eigenvectors = np.asarray(eigenvectors)
file_data.update({
'frequencies': frequencies,
'ir_intensities': ir_intensities,
'raman_intensities': raman_intensities,
'weights': warray,
'q_vectors': q_vectors,
'eigenvectors': eigenvectors
})
return file_data, element_isotope
def parse_castep_file(file_name, ir_or_raman):
"""
Read frequencies from a <>.castep file
@param file_name - file path of the file to read
@return the frequencies, infra red and raman intensities and weights of frequency blocks
"""
file_data = {}
# Get Regex strings from load_helper
header_regex = re.compile(load_helper.CASTEP_HEADER_REGEX)
data_regex = re.compile(load_helper.CASTEP_DATA_REGEX)
bond_regex = re.compile(load_helper.CASTEP_BOND_REGEX)
block_count = 0
frequencies, ir_intensities, raman_intensities, weights, q_vectors, bonds = [], [], [], [], [], []
data_lists = (frequencies, ir_intensities, raman_intensities)
with open(file_name, 'rU') as f_handle:
file_data.update(_parse_castep_file_header(f_handle))
while True:
line = f_handle.readline()
# Check we've reached the end of file
if not line:
break
# Check if we've found a block of frequencies
header_match = header_regex.match(line)
if header_match:
block_count += 1
weight, q_vector = load_helper._parse_block_header(header_match, block_count)
weights.append(weight)
q_vectors.append(q_vector)
# Move file pointer forward to start of intensity data
_find_castep_freq_block(f_handle, data_regex)
# Parse block of frequencies
for line_data in _parse_castep_freq_block(f_handle, file_data['num_branches'], ir_or_raman):
for data_list, item in zip(data_lists, line_data):
data_list.append(item)
# Check if we've found a bond
bond_match = bond_regex.match(line)
if bond_match:
bonds.append(_parse_castep_bond(bond_match))
frequencies = np.asarray(frequencies)
ir_intensities = np.asarray(ir_intensities)
raman_intensities = np.asarray(raman_intensities)
warray = np.repeat(weights, file_data['num_branches'])
file_data.update({
'frequencies': frequencies,
'ir_intensities': ir_intensities,
'raman_intensities': raman_intensities,
'weights': warray,
'q_vectors':q_vectors
})
if len(bonds) > 0:
file_data['bonds'] = bonds
return file_data
def parse_phonon_file(file_name, record_eigenvectors):
"""
Read frequencies from a <>.phonon file
@param file_name - file path of the file to read
@return the frequencies, infra red and raman intensities and weights of frequency blocks
"""
file_data = {}
# Get regex strings from load_helper
header_regex = re.compile(load_helper.PHONON_HEADER_REGEX)
eigenvectors_regex = re.compile(load_helper.PHONON_EIGENVEC_REGEX)
block_count = 0
frequencies, ir_intensities, raman_intensities, weights, q_vectors, eigenvectors = [], [], [], [], [], []
data_lists = (frequencies, ir_intensities, raman_intensities)
with open(file_name, 'rU') as f_handle:
file_data.update(_parse_phonon_file_header(f_handle))
while True:
line = f_handle.readline()
# Check we've reached the end of file
if not line:
break
# Check if we've found a block of frequencies
header_match = header_regex.match(line)
if header_match:
block_count += 1
weight, q_vector = load_helper._parse_block_header(header_match, block_count)
weights.append(weight)
q_vectors.append(q_vector)
# Parse block of frequencies
for line_data in _parse_phonon_freq_block(f_handle,
file_data['num_branches']):
for data_list, item in zip(data_lists, line_data):
data_list.append(item)
vector_match = eigenvectors_regex.match(line)
if vector_match:
if record_eigenvectors:
# Parse eigenvectors for partial dos
vectors = _parse_phonon_eigenvectors(f_handle,
file_data['num_ions'],
file_data['num_branches'])
eigenvectors.append(vectors)
else:
# Skip over eigenvectors
for _ in range(file_data['num_ions'] * file_data['num_branches']):
line = f_handle.readline()
if not line:
raise IOError("Bad file format. Uexpectedly reached end of file.")
frequencies = np.asarray(frequencies)
ir_intensities = np.asarray(ir_intensities)
raman_intensities = np.asarray(raman_intensities)
warray = np.repeat(weights, file_data['num_branches'])
eigenvectors = np.asarray(eigenvectors)
file_data.update({
'frequencies': frequencies,
'ir_intensities': ir_intensities,
'raman_intensities': raman_intensities,
'weights': warray,
'q_vectors':q_vectors,
'eigenvectors': eigenvectors
})
return file_data, element_isotope