def analyse(self, atomsfile=None):
BulkTask.analyse(self)
for name, data in self.data.items():
if 'strains' in data:
atoms = self.create_system(name)
volume = atoms.get_volume()
data['volume error [%]'] = (data['volume'] / volume - 1) * 100
if self.collection.xc == 'PBE':
B = self.collection.data[name][-1] * units.kJ * 1e-24
data['B error [%]'] = (data['B'] / B - 1) * 100
if atomsfile:
atomdata = read_json(atomsfile)
for name, data in self.data.items():
atoms = self.create_system(name)
e = -data['energy']
for atom in atoms:
e += atomdata[atom.symbol]['energy']
e /= len(atoms)
data['cohesive energy'] = e
if self.collection.xc == 'PBE':
eref = self.collection.data[name][7]
else:
eref = self.collection.data[name][9]
data['cohesive energy error [%]'] = (e / eref - 1) * 100
self.summary_keys += ['cohesive energy',
'cohesive energy error [%]']
def analyse(self, atomsfile=None):
try:
BulkTask.analyse(self)
except ValueError: # allow fit outside of range
pass
for name, data in self.data.items():
if 'strains' in data:
atoms = self.create_system(name)
# full equation of state
# use relaxed volume if present
if 'relaxed volume' in data:
volume = data['relaxed volume']
else:
volume = atoms.get_volume()
volumes = data['strains']**3 * volume
energies = data['energies']
eos = FullEquationOfState(volumes, energies)
try:
v, e, B0, B1, R = eos.fit()
except ValueError:
pass
else:
data['dcdft fitted energy'] = e / len(atoms)
data['dcdft volume'] = v / len(atoms)
data['dcdft B0'] = B0
data['dcdft B1'] = B1
data['dcdft R'] = R
if atomsfile:
# MDTMP: TODO
atomdata = read_json(atomsfile)
for name, data in self.data.items():
atoms = self.create_system(name)
e = -data['energy']
for atom in atoms:
e += atomdata[atom.symbol]['energy']
e /= len(atoms)
data['cohesive energy'] = e
if self.collection.xc == 'PBE':
eref = self.collection.data[name][7]
else:
eref = self.collection.data[name][9]
data['cohesive energy error [%]'] = (e / eref - 1) * 100
self.summary_keys += [
'cohesive energy', 'cohesive energy error [%]'
]
def analyse(self, atomsfile=None):
try:
BulkTask.analyse(self)
except ValueError: # allow fit outside of range
pass
for name, data in self.data.items():
if 'strains' in data:
atoms = self.create_system(name)
# full equation of state
# use relaxed volume if present
if 'relaxed volume' in data:
volume = data['relaxed volume']
else:
volume = atoms.get_volume()
volumes = data['strains']**3 * volume
energies = data['energies']
eos = FullEquationOfState(volumes, energies)
try:
v, e, B0, B1, R = eos.fit()
except ValueError:
pass
else:
data['dcdft fitted energy'] = e / len(atoms)
data['dcdft volume'] = v / len(atoms)
data['dcdft B0'] = B0
data['dcdft B1'] = B1
data['dcdft R'] = R
if atomsfile:
# MDTMP: TODO
atomdata = read_json(atomsfile)
for name, data in self.data.items():
atoms = self.create_system(name)
e = -data['energy']
for atom in atoms:
e += atomdata[atom.symbol]['energy']
e /= len(atoms)
data['cohesive energy'] = e
if self.collection.xc == 'PBE':
eref = self.collection.data[name][7]
else:
eref = self.collection.data[name][9]
data['cohesive energy error [%]'] = (e / eref - 1) * 100
self.summary_keys += ['cohesive energy',
'cohesive energy error [%]']
def analyse(self, atomsfile=None):
try:
BulkTask.analyse(self)
except ValueError: # allow fit outside of range
pass
for name, data in self.data.items():
if 'strains' in data:
atoms = self.create_system(name)
# use relaxed volume if present
if 'relaxed volume' in data:
volume = data['relaxed volume']
else:
volume = atoms.get_volume()
volumes = data['strains']**3 * volume
energies = data['energies']
# allow selection of eos type independent of data
if self.eos is not None:
eos = EquationOfState(volumes, energies, self.eos)
else:
eos = EquationOfState(volumes, energies)
try:
v, e, B = eos.fit()
except ValueError:
pass
else:
data['fitted energy'] = e
data['volume'] = v
data['B'] = B
# with respect tot the reference volume
data['volume error [%]'] = (
data['volume'] / atoms.get_volume() - 1) * 100
if self.collection.B:
i = self.collection.labels.index(self.collection.xc) - 1
B = self.collection.B[name][i] * units.kJ * 1e-24
data['B error [%]'] = (data['B'] / B - 1) * 100
else:
data['B error [%]'] = None
data['strukturbericht'] = self.collection.data[name][0]
data['crystal structure'] = strukturbericht[
data['strukturbericht']]
# calculate lattice constant from volume
cs = data['crystal structure']
if cs == 'bcc':
a0 = (volume * 2)**(1 / 3.)
a = (data['volume'] * 2)**(1 / 3.)
elif cs == 'cesiumchloride':
a0 = (volume)**(1 / 3.)
a = (data['volume'])**(1 / 3.)
elif cs in [
'fcc', 'diamond', 'zincblende', 'rocksalt', 'fluorite'
]:
a0 = (volume * 4)**(1 / 3.)
a = (data['volume'] * 4)**(1 / 3.)
i = self.collection.labels.index(self.collection.xc) - 1
a0_ref = self.collection.data[name][i]
if 'relaxed volume' not in data:
# no volume relaxation performed - volume equals the reference one
assert abs(a0 - a0_ref) < 1.e-4
data['lattice constant'] = a
data['lattice constant error [%]'] = (a -
a0_ref) / a0_ref * 100
if atomsfile:
# MDTMP: TODO
atomdata = read_json(atomsfile)
for name, data in self.data.items():
atoms = self.create_system(name)
e = -data['energy']
for atom in atoms:
e += atomdata[atom.symbol]['energy']
e /= len(atoms)
data['cohesive energy'] = e
if self.collection.xc == 'PBE':
eref = self.collection.data[name][7]
else:
eref = self.collection.data[name][9]
data['cohesive energy error [%]'] = (e / eref - 1) * 100
self.summary_keys += [
'cohesive energy', 'cohesive energy error [%]'
]
def analyse(self, atomsfile=None):
try:
BulkTask.analyse(self)
except ValueError: # allow fit outside of range
pass
for name, data in self.data.items():
if 'strains' in data:
atoms = self.create_system(name)
# use relaxed volume if present
if 'relaxed volume' in data:
volume = data['relaxed volume']
else:
volume = atoms.get_volume()
volumes = data['strains']**3 * volume
energies = data['energies']
# allow selection of eos type independent of data
if self.eos is not None:
eos = EquationOfState(volumes, energies, self.eos)
else:
eos = EquationOfState(volumes, energies)
try:
v, e, B = eos.fit()
except ValueError:
pass
else:
data['fitted energy'] = e
data['volume'] = v
data['B'] = B
# with respect tot the reference volume
data['volume error [%]'] = (data['volume'] / atoms.get_volume() - 1) * 100
if self.collection.B:
i = self.collection.labels.index(self.collection.xc) - 1
B = self.collection.B[name][i] * units.kJ * 1e-24
data['B error [%]'] = (data['B'] / B - 1) * 100
else:
data['B error [%]'] = None
data['strukturbericht'] = self.collection.data[name][0]
data['crystal structure'] = strukturbericht[data['strukturbericht']]
# calculate lattice constant from volume
cs = data['crystal structure']
if cs == 'bcc':
a0 = (volume*2)**(1/3.)
a = (data['volume']*2)**(1/3.)
elif cs == 'cesiumchloride':
a0 = (volume)**(1/3.)
a = (data['volume'])**(1/3.)
elif cs in ['fcc',
'diamond',
'zincblende',
'rocksalt',
'fluorite']:
a0 = (volume*4)**(1/3.)
a = (data['volume']*4)**(1/3.)
i = self.collection.labels.index(self.collection.xc) - 1
a0_ref = self.collection.data[name][i]
if 'relaxed volume' not in data:
# no volume relaxation performed - volume equals the reference one
assert abs(a0 - a0_ref) < 1.e-4
data['lattice constant'] = a
data['lattice constant error [%]'] = (a - a0_ref) / a0_ref * 100
if atomsfile:
# MDTMP: TODO
atomdata = read_json(atomsfile)
for name, data in self.data.items():
atoms = self.create_system(name)
e = -data['energy']
for atom in atoms:
e += atomdata[atom.symbol]['energy']
e /= len(atoms)
data['cohesive energy'] = e
if self.collection.xc == 'PBE':
eref = self.collection.data[name][7]
else:
eref = self.collection.data[name][9]
data['cohesive energy error [%]'] = (e / eref - 1) * 100
self.summary_keys += ['cohesive energy',
'cohesive energy error [%]']
