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from __future__ import print_function
# Copyright (C) 2010 by CAMd, DTU
# Please see the accompanying LICENSE file for further information.
# This file is taken (almost) verbatim from CMR with D. Landis agreement
FIELD_SEPARATOR = "\\"
PARA_START = "\n\n"
PARA_END = "\\\\@"
names = ['', '', 'Computer_system', 'Type_of_run', 'Method', 'Basis_set',
'Chemical_formula', 'Person', 'Date', '', '', '', '', 'Title', '']
names_compact = ['', '', 'Computer_system', 'Type_of_run', 'Method',
'Basis_set', 'Chemical_formula', 'Person', 'Date', '', '', '',
'', 'Title', '']
charge_multiplicity = 15
class GaussianReader:
def auto_type(self, data):
""" tries to determine type"""
try:
return float(data)
except ValueError:
pass
try:
ds = data.split(",")
array = []
for d in ds:
array.append(float(d))
return array
except ValueError:
pass
return data
def __init__(self, filename):
"""filename is optional; if not set, use parse to set the content"""
if isinstance(filename, str):
fileobj = open(filename, 'r')
else:
fileobj = filename
fileobj.seek(0) # Re-wind fileobj
content = fileobj.read()
# handles the case that users used windows after the calculation:
content = content.replace("\r\n", "\n")
self.parse(content)
def parse(self, content):
from ase.data import atomic_numbers
self.data = []
temp_items = content.split(PARA_START)
seq_count = 0
for i in temp_items:
i = i.replace("\n ", "")
if i.endswith(PARA_END):
i = i.replace(PARA_END, "")
i = i.split(FIELD_SEPARATOR)
new_dict = {}
self.data.append(new_dict)
new_dict['Sequence number'] = seq_count
seq_count += 1
for pos in range(len(names)):
if names[pos] != "":
new_dict[names[pos]] = self.auto_type(i[pos])
chm = i[charge_multiplicity].split(",")
new_dict["Charge"] = int(chm[0])
new_dict["Multiplicity"] = int(chm[1])
# Read atoms
atoms = []
positions = []
position = charge_multiplicity + 1
while position < len(i) and i[position] != "":
s = i[position].split(",")
atoms.append(atomic_numbers[s[0]])
positions.append([float(s[1]), float(s[2]), float(s[3])])
position = position + 1
new_dict["Atomic_numbers"] = atoms
new_dict["Positions"] = positions
# Read more variables
position += 1
while position < len(i) and i[position] != "":
s = i[position].split('=')
if len(s) == 2:
new_dict[s[0]] = self.auto_type(s[1])
else:
print("Warning: unexpected input ", s)
position = position + 1
def __iter__(self):
"""returns an iterator that iterates over all keywords"""
return self.data.__iter__()
def __len__(self):
return len(self.data)
def __getitem__(self, pos):
return self.data[pos]
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