/usr/share/pyshared/ase/io/gpawtext.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 | import numpy as np
from ase.atoms import Atom, Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.calculators.singlepoint import SinglePointKPoint
def read_gpaw_text(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
def index_startswith(lines, string):
for i, line in enumerate(lines):
if line.startswith(string):
return i
raise ValueError
lines = fileobj.readlines()
images = []
while True:
try:
i = lines.index('Unit Cell:\n')
except ValueError:
pass
else:
cell = []
pbc = []
for line in lines[i + 3:i + 6]:
words = line.split()
if len(words) == 5: # old format
cell.append(float(words[2]))
pbc.append(words[1] == 'yes')
else: # new format with GUC
cell.append([float(word) for word in words[3:6]])
pbc.append(words[2] == 'yes')
try:
i = lines.index('Positions:\n')
except ValueError:
break
atoms = Atoms(cell=cell, pbc=pbc)
for line in lines[i + 1:]:
words = line.split()
if len(words) != 5:
break
n, symbol, x, y, z = words
symbol = symbol.split('.')[0]
atoms.append(Atom(symbol, [float(x), float(y), float(z)]))
lines = lines[i + 5:]
try:
i = lines.index('-------------------------\n')
except ValueError:
e = None
else:
line = lines[i + 9]
assert line.startswith('Zero Kelvin:')
e = float(line.split()[-1])
try:
ii = index_startswith(lines, 'Fermi Level:')
except ValueError:
eFermi = None
else:
try:
eFermi = float(lines[ii].split()[2])
except ValueError: # we have two Fermi levels
fields = lines[ii].split()
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[2])),
float(strip(fields[3])) ]
# read Eigenvalues and occupations
ii1 = ii2 = 1e32
try:
ii1 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
try:
ii2 = index_startswith(lines, ' Band Eigenvalues Occupancy')
except ValueError:
pass
ii = min(ii1, ii2)
if ii == 1e32:
kpts = None
else:
ii += 1
words = lines[ii].split()
vals = []
while(len(words) > 2):
vals.append([float(word) for word in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(0, 1))
kpts[1].eps_n = vals[3]
kpts[1].f_n = vals[4]
# read charge
try:
ii = index_startswith(lines, 'Total Charge:')
except ValueError:
q = None
else:
q = float(lines[ii].split()[2])
try:
ii = index_startswith(lines, 'Local Magnetic Moments')
except ValueError:
magmoms = None
else:
magmoms = []
for i in range(ii + 1, ii + 1 + len(atoms)):
iii, magmom = lines[i].split()[:2]
magmoms.append(float(magmom))
try:
ii = lines.index('Forces in eV/Ang:\n')
except ValueError:
f = None
else:
f = []
for i in range(ii + 1, ii + 1 + len(atoms)):
try:
x, y, z = lines[i].split()[-3:]
f.append((float(x), float(y), float(z)))
except (ValueError, IndexError), m:
raise IOError('Malformed GPAW log file: %s' % m)
if len(images) > 0 and e is None:
break
if e is not None or f is not None:
calc = SinglePointDFTCalculator(e, f, None, magmoms, atoms, eFermi)
if kpts is not None:
calc.kpts = kpts
atoms.set_calculator(calc)
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_charges([q / n] * n)
images.append(atoms)
lines = lines[i:]
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]
|