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import re
from typing import List, Tuple, Union
import numpy as np
from ase.atoms import Atoms
from ase.calculators.singlepoint import (
SinglePointDFTCalculator,
SinglePointKPoint,
)
def index_startswith(lines: List[str], string: str) -> int:
for i, line in enumerate(lines):
if line.startswith(string):
return i
raise ValueError
def index_pattern(lines: List[str], pattern: str) -> int:
repat = re.compile(pattern)
for i, line in enumerate(lines):
if repat.match(line):
return i
raise ValueError
def read_forces(lines: List[str],
ii: int,
atoms: Atoms) -> Tuple[List[Tuple[float, float, float]], int]:
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) as m:
raise OSError(f'Malformed GPAW log file: {m}')
return f, i
def read_stresses(lines: List[str],
ii: int,) -> Tuple[List[Tuple[float, float, float]], int]:
s = []
for i in range(ii + 1, ii + 4):
try:
x, y, z = lines[i].split()[-3:]
s.append((float(x), float(y), float(z)))
except (ValueError, IndexError) as m:
raise OSError(f'Malformed GPAW log file: {m}')
return s, i
def read_gpaw_out(fileobj, index): # -> Union[Atoms, List[Atoms]]:
"""Read text output from GPAW calculation."""
lines = [line.lower() for line in fileobj.readlines()]
blocks = []
i1 = 0
for i2, line in enumerate(lines):
if line == 'positions:\n':
if i1 > 0:
blocks.append(lines[i1:i2])
i1 = i2
blocks.append(lines[i1:])
images: List[Atoms] = []
for lines in blocks:
try:
i = lines.index('unit cell:\n')
except ValueError:
pass
else:
if lines[i + 2].startswith(' -'):
del lines[i + 2] # old format
cell: List[Union[float, List[float]]] = []
pbc = []
for line in lines[i + 2:i + 5]:
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')
symbols = []
positions = []
magmoms = []
for line in lines[1:]:
words = line.split()
if len(words) < 5:
break
n, symbol, x, y, z = words[:5]
symbols.append(symbol.split('.')[0].title())
positions.append([float(x), float(y), float(z)])
if len(words) > 5:
mom = float(words[-1].rstrip(')'))
magmoms.append(mom)
if len(symbols):
atoms = Atoms(symbols=symbols, positions=positions,
cell=cell, pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
try:
ii = index_pattern(lines, '\\d+ k-point')
word = lines[ii].split()
kx = int(word[2])
ky = int(word[4])
kz = int(word[6])
bz_kpts = (kx, ky, kz)
ibz_kpts = int(lines[ii + 1].split()[0])
except (ValueError, TypeError, IndexError):
bz_kpts = None
ibz_kpts = None
try:
i = index_startswith(lines, 'energy contributions relative to')
except ValueError:
e = energy_contributions = None
else:
energy_contributions = {}
for line in lines[i + 2:i + 13]:
fields = line.split(':')
if len(fields) == 2:
name = fields[0]
energy = float(fields[1])
energy_contributions[name] = energy
if name in ['zero kelvin', 'extrapolated']:
e = energy
break
else: # no break
raise ValueError
try:
ii = index_pattern(lines, '(fixed )?fermi level(s)?:')
except ValueError:
eFermi = None
else:
fields = lines[ii].split()
try:
def strip(string):
for rubbish in '[],':
string = string.replace(rubbish, '')
return string
eFermi = [float(strip(fields[-2])),
float(strip(fields[-1]))]
except ValueError:
eFermi = float(fields[-1])
# 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(w) for w in words])
ii += 1
words = lines[ii].split()
vals = np.array(vals).transpose()
kpts = [SinglePointKPoint(1, 0, 0)]
kpts[0].eps_n = vals[1]
kpts[0].f_n = vals[2]
if vals.shape[0] > 3:
kpts.append(SinglePointKPoint(1, 1, 0))
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])
# read dipole moment
try:
ii = index_startswith(lines, 'dipole moment:')
except ValueError:
dipole = None
else:
line = lines[ii]
for x in '()[],':
line = line.replace(x, '')
dipole = np.array([float(c) for c in line.split()[2:5]])
try:
ii = index_startswith(lines, 'local magnetic moments')
except ValueError:
pass
else:
magmoms = []
for j in range(ii + 1, ii + 1 + len(atoms)):
line = lines[j]
if '#' in line: # new GPAW format
magmom = line.split()[-4].split(']')[0]
else:
magmom = line.split()[-1].rstrip(')')
magmoms.append(float(magmom))
try:
ii = lines.index('forces in ev/ang:\n')
except ValueError:
f = None
else:
f, i = read_forces(lines, ii, atoms)
try:
ii = lines.index('stress tensor:\n')
except ValueError:
stress_tensor = None
else:
stress_tensor, i = read_stresses(lines, ii)
try:
parameters = {}
ii = index_startswith(lines, 'vdw correction:')
except ValueError:
name = 'gpaw'
else:
name = lines[ii - 1].strip()
# save uncorrected values
parameters.update({
'calculator': 'gpaw',
'uncorrected_energy': e,
})
line = lines[ii + 1]
assert line.startswith('energy:')
e = float(line.split()[-1])
f, i = read_forces(lines, ii + 3, atoms)
if len(images) > 0 and e is None:
break
if q is not None and len(atoms) > 0:
n = len(atoms)
atoms.set_initial_charges([q / n] * n)
if magmoms:
atoms.set_initial_magnetic_moments(magmoms)
else:
magmoms = None
if e is not None or f is not None:
calc = SinglePointDFTCalculator(atoms, energy=e, forces=f,
dipole=dipole, magmoms=magmoms,
efermi=eFermi,
bzkpts=bz_kpts, ibzkpts=ibz_kpts,
stress=stress_tensor)
calc.name = name
calc.parameters = parameters
if energy_contributions is not None:
calc.energy_contributions = energy_contributions
if kpts is not None:
calc.kpts = kpts
atoms.calc = calc
images.append(atoms)
if len(images) == 0:
raise OSError('Corrupted GPAW-text file!')
return images[index]
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