def read_gpaw_out(fileobj, index):
notfound = []
def index_startswith(lines, string):
if not isinstance(string, str):
# assume it's a list
for entry in string:
try:
return index_startswith(lines, entry)
except ValueError:
pass
raise ValueError
if string in notfound:
raise ValueError
for i, line in enumerate(lines):
if line.startswith(string):
return i
notfound.append(string)
raise ValueError
def index_pattern(lines, pattern):
repat = re.compile(pattern)
if pattern in notfound:
raise ValueError
for i, line in enumerate(lines):
if repat.match(line):
return i
notfound.append(pattern)
raise ValueError
def read_forces(lines, ii):
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 IOError('Malformed GPAW log file: %s' % m)
return f, i
lines = [line.lower() for line in fileobj.readlines()]
images = []
while True:
try:
i = index_startswith(lines, 'reference energy:')
Eref = float(lines[i].split()[-1])
except ValueError:
Eref = None
try:
i = lines.index('unit cell:\n')
except ValueError:
pass
else:
if lines[i + 2].startswith(' -'):
del lines[i + 2] # old format
cell = []
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')
try:
i = lines.index('positions:\n')
except ValueError:
break
symbols = []
positions = []
for line in lines[i + 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(symbols):
atoms = Atoms(symbols=symbols,
positions=positions,
cell=cell,
pbc=pbc)
else:
atoms = Atoms(cell=cell, pbc=pbc)
lines = lines[i + 5:]
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 + 8]:
fields = line.split(':')
energy_contributions[fields[0]] = float(fields[1])
line = lines[i + 10]
assert (line.startswith('zero kelvin:')
or line.startswith('extrapolated:'))
e = float(line.split()[-1])
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:
magmoms = None
else:
magmoms = []
for j in range(ii + 1, ii + 1 + len(atoms)):
magmom = lines[j].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)
try:
ii = index_startswith(lines, 'vdw correction:')
except ValueError:
pass
else:
line = lines[ii + 1]
assert line.startswith('energy:')
e = float(line.split()[-1])
f, i = read_forces(lines, ii + 3)
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 is not None:
atoms.set_initial_magnetic_moments(magmoms)
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)
calc.eref = Eref
calc.name = 'gpaw'
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)
lines = lines[i:]
if len(images) == 0:
raise IOError('Corrupted GPAW-text file!')
return images[index]
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 + 8]:
fields = line.split(':')
energy_contributions[fields[0]] = float(fields[1])
line = lines[i + 10]
assert (line.startswith('zero kelvin:') or
line.startswith('extrapolated:'))
e = float(line.split()[-1])
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)):
magmom = lines[j].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:
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)
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 IOError('Corrupted GPAW-text file!')
return images[index]
