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 __init__(self, **kwargs):
BulkTask.__init__(self,
collection=DeltaCodesDFTCollection(),
**kwargs)
self.summary_keys = ['energy', 'fitted energy', 'volume',
'volume error [%]', 'B', 'B error [%]']
def __init__(self, **kwargs):
BulkTask.__init__(self,
collection=HarlSchimkaKresseBulkCollection('PBE'),
**kwargs)
self.summary_keys = ['energy', 'fitted energy', 'volume',
'volume error [%]', 'B', 'B error [%]']
def __init__(self, **kwargs):
BulkTask.__init__(self, collection=DeltaCodesDFTCollection(), **kwargs)
self.summary_keys = [
'energy', 'fitted energy', 'volume', 'volume error [%]', 'B',
'B error [%]'
]
def __init__(self, xc='PBE', **kwargs):
BulkTask.__init__(self,
collection=HaasTranBlahaBulkCollection(xc),
**kwargs)
self.summary_keys = [
'energy', 'fitted energy', 'crystal structure', 'strukturbericht',
'lattice constant', 'lattice constant error [%]', 'volume',
'volume error [%]', 'B', 'B error [%]'
]
def __init__(self, xc='PBE', **kwargs):
BulkTask.__init__(self,
collection=HaasTranBlahaBulkCollection(xc),
**kwargs)
self.summary_keys = ['energy', 'fitted energy',
'crystal structure',
'strukturbericht',
'lattice constant', 'lattice constant error [%]',
'volume', 'volume error [%]',
'B', 'B 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 run(args=sys.argv[1:], calcname='emt', task=None):
if isinstance(args, str):
args = args.split(' ')
argsoriginal = args[:]
if len(args) > 0 and args[0] in calcnames:
calcname = args.pop(0)
if task is None:
taskname = 'molecule'
if (len(args) > 0 and
(args[0] in ['molecule', 'bulk'] or args[0].endswith('.py'))):
taskname = args.pop(0)
if taskname.endswith('.py'):
locals = {}
execfile(taskname, locals, locals)
tasks = [task for task in locals.values() if isinstance(task, Task)]
assert len(tasks) == 1
task = tasks[0]
elif taskname == 'bulk':
task = BulkTask()
else:
task = MoleculeTask()
if len(args) == 0 and task.collection is None:
sys.stderr.write(
usage % textwrap.fill(', '.join(calcnames[:-1]) +
' or ' + calcnames[-1] +
'. Default value is emt.',
initial_indent='calculator: ',
subsequent_indent=' ' * 12))
return
task.set_calculator_factory(calcname)
args = task.parse_args(args)
if task.interactive_python_session:
if '-i' in argsoriginal:
argsoriginal.remove('-i')
if '--interactive-python-session' in argsoriginal:
argsoriginal.remove('--interactive-python-session')
file = tempfile.NamedTemporaryFile()
file.write('import os\n')
file.write('if "PYTHONSTARTUP" in os.environ:\n')
file.write(' execfile(os.environ["PYTHONSTARTUP"])\n')
file.write('from ase.tasks.main import run\n')
file.write('atoms, task = run(%r, %r)\n' % (argsoriginal, calcname))
file.flush()
os.system('python -i %s' % file.name)
return
atoms = task.run(args)
return atoms, task
def run(args=sys.argv[1:], calcname='emt', task=None):
if isinstance(args, str):
# leading/trailing/extra-mid spaces result in weird errors
args = ' '.join(args.split())
args = args.split(' ')
argsoriginal = args[:]
if len(args) > 0 and args[0] in calcnames:
calcname = args.pop(0)
if task is None:
taskname = 'molecule'
if (len(args) > 0 and
(args[0] in ['molecule', 'bulk'] or args[0].endswith('.py'))):
taskname = args.pop(0)
if taskname.endswith('.py'):
locals = {}
exec(compile(open(taskname).read(), taskname, 'exec'), locals, locals)
tasks = [task for task in locals.values() if isinstance(task, Task)]
assert len(tasks) == 1
task = tasks[0]
elif taskname == 'bulk':
task = BulkTask()
else:
task = MoleculeTask()
if len(args) == 0 and task.collection is None:
sys.stderr.write(
usage % textwrap.fill(', '.join(calcnames[:-1]) +
' or ' + calcnames[-1] +
'. Default value is emt.',
initial_indent='calculator: ',
subsequent_indent=' ' * 12))
return
task.set_calculator_factory(calcname)
args = task.parse_args(args)
if task.interactive_python_session:
if '-i' in argsoriginal:
argsoriginal.remove('-i')
if '--interactive-python-session' in argsoriginal:
argsoriginal.remove('--interactive-python-session')
file = tempfile.NamedTemporaryFile()
file.write('import os\n')
file.write('if "PYTHONSTARTUP" in os.environ:\n')
file.write(' execfile(os.environ["PYTHONSTARTUP"])\n')
file.write('from ase.tasks.main import run\n')
file.write('atoms, task = run(%r, %r)\n' % (argsoriginal, calcname))
file.flush()
os.system('python -i %s' % file.name)
return
atoms = task.run(args)
return atoms, task
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 [%]']
def calculate(self, name, atoms):
data = BulkTask.calculate(self, name, atoms)
dexx = atoms.calc.get_xc_difference(HybridXC('EXX', acdf=True))
data['selfconsistent energy'] = data['energy']
data['energy'] += dexx
return data
def __init__(self, **kwargs):
BulkTask.__init__(self,
collection=HarlSchimkaKresseBulkCollection('EXX'),
**kwargs)