def read_run(self, taskname, tag, run):
if tag is not None:
tag += '_%s' % run
else:
tag = run
return read_json(taskname + '-' + tag + '.json')
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 read_run(self, taskname, tag, run):
if tag is not None:
tag += '_%s' % run
else:
tag = run
return read_json(taskname + '-' + tag + '.json')
def write(self, name, data):
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
if os.path.isfile(filename):
alldata = read_json(filename)
else:
alldata = {}
alldata[name] = data
write_json(filename, alldata)
finally:
self.lock.release()
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_single(self, name):
self.log('Running', name)
try:
atoms = self.create_system(name)
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
atoms.calc = self.calcfactory(self.get_filename(name), atoms)
tstart = time()
try:
data = self.calculate(name, atoms)
if self.after:
exec self.after
except KeyboardInterrupt:
raise
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
tstop = time()
data['time'] = tstop - tstart
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
if os.path.isfile(filename):
alldata = read_json(filename)
else:
alldata = {}
alldata[name] = data
write_json(filename, alldata)
finally:
self.lock.release()
for write in self.write_funcs:
filenamebase = self.get_filename(name)
write(filenamebase, atoms, data)
return atoms
def run_single(self, name):
self.log('Running', name)
try:
atoms = self.create_system(name)
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
atoms.calc = self.calcfactory(self.get_filename(name), atoms)
tstart = time()
try:
data = self.calculate(name, atoms)
if self.after:
exec self.after
except KeyboardInterrupt:
raise
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
return
tstop = time()
data['time'] = tstop - tstart
filename = self.get_filename(ext='json')
try:
self.lock.acquire()
if os.path.isfile(filename):
alldata = read_json(filename)
else:
alldata = {}
alldata[name] = data
write_json(filename, alldata)
finally:
self.lock.release()
for write in self.write_funcs:
filenamebase = self.get_filename(name)
write(filenamebase, atoms, data)
return atoms
def run(self, atoms, name):
args = self.args
if self.lock is None:
# Create lock object:
if args.use_lock_file:
self.lock = Lock(self.get_filename(ext='lock'))
else:
self.lock = OpenLock()
skip = False
if args.use_lock_file:
try:
filename = self.get_filename(ext='json')
self.lock.acquire()
if os.path.isfile(filename):
data = read_json(filename)
if name in data:
skip = True
else:
data[name] = {}
write_json(filename, data)
else:
write_json(filename, {name: {}})
finally:
self.lock.release()
if not skip:
self.set_calculator(atoms, name)
tstart = time.time()
try:
data = self.calculate(atoms, name)
except KeyboardInterrupt:
raise
except Exception:
self.log(name, 'FAILED')
traceback.print_exc(file=self.logfile)
else:
tstop = time.time()
data['time'] = tstop - tstart
self.write(name, data)
from ase.data.g2_1_ref import ex_atomization, atomization
from ase.tasks.io import read_json
from ase.atoms import string2symbols
from ase.units import kcal, mol
data = read_json('molecule-pw.json')
maepbe = 0.0
maeexx = 0.0
print(' PBE EXX')
print('-' * 48)
for name in ex_atomization:
epberef = atomization[name][2] * kcal / mol
epbe = (sum(data[atom]['energy'] for atom in string2symbols(name)) -
data[name]['energy'])
eexxref = ex_atomization[name][0] * kcal / mol
eexx = (sum(data[atom]['energy'] + data[atom]['EXX']
for atom in string2symbols(name)) -
data[name]['energy'] - data[name]['EXX'])
maepbe += abs(epbe - epberef) / len(ex_atomization)
maeexx += abs(eexx - eexxref) / len(ex_atomization)
print('%-4s %10.3f %10.3f %10.3f %10.3f' %
(name, epbe, epbe - epberef, eexx, eexx - eexxref))
print('-' * 48)
print('MAE %10.3f %10.3f %10.3f %10.3f' % (0, maepbe, 0, maeexx))
assert maepbe < 0.025
assert maeexx < 0.05
def read(self, skipempty=True):
self.data = read_json(self.get_filename(ext='json'))
if skipempty:
self.data = dict((key.encode('ascii'), value)
for key, value in self.data.items()
if value)
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 run(self, names=None):
"""Run task for all names.
The task will be one of these four:
* Open ASE's GUI
* Write configuration to file
* Write summary
* Do the actual calculation
"""
if self.lock is None:
# Create lock object:
self.lock = Lock(self.get_filename(ext='lock'))
if self.clean:
self.clean_json_file(names)
return
if names is None or len(names) == 0:
names = self.collection.keys()
names = self.expand(names)
names = names[self.slice]
names = self.exclude(names)
if self.gui:
for name in names:
view(self.create_system(name))
return
if self.write_to_file:
if self.write_to_file[0] == '.':
for name in names:
filename = self.get_filename(name, self.write_to_file)
write(filename, self.create_system(name))
else:
assert len(names) == 1
write(self.write_to_file, self.create_system(names[0]))
return
if self.write_summary:
self.read()
self.analyse()
self.summarize(names)
return
atoms = None
for name in names:
if self.use_lock_files:
try:
filename = self.get_filename(ext='json')
self.lock.acquire()
if os.path.isfile(filename):
data = read_json(filename)
if name not in data:
data[name] = {}
write_json(filename, data)
else:
self.log('Skipping', name)
continue
else:
write_json(filename, {name: {}})
finally:
self.lock.release()
if atoms is not None:
del atoms.calc
atoms = self.run_single(name)
return atoms
def read(self, skipempty=True):
self.data = read_json(self.get_filename(ext='json'))
if skipempty:
self.data = dict((key.encode('ascii'), value)
for key, value in self.data.items() if value)
def read(self):
filename = self.get_filename(ext="json")
return read_json(filename)
def run(self, names=None):
"""Run task for all names.
The task will be one of these four:
* Open ASE's GUI
* Write configuration to file
* Write summary
* Do the actual calculation
"""
if self.lock is None:
# Create lock object:
self.lock = Lock(self.get_filename(ext='lock'))
if self.clean:
self.clean_json_file(names)
return
if names is None or len(names) == 0:
names = self.collection.keys()
names = self.expand(names)
names = names[self.slice]
names = self.exclude(names)
if self.gui:
for name in names:
view(self.create_system(name))
return
if self.write_to_file:
if self.write_to_file[0] == '.':
for name in names:
filename = self.get_filename(name, self.write_to_file)
write(filename, self.create_system(name))
else:
assert len(names) == 1
write(self.write_to_file, self.create_system(names[0]))
return
if self.write_summary:
self.read()
self.analyse()
self.summarize(names)
return
atoms = None
for name in names:
if self.use_lock_files:
try:
filename = self.get_filename(ext='json')
self.lock.acquire()
if os.path.isfile(filename):
data = read_json(filename)
if name not in data:
data[name] = {}
write_json(filename, data)
else:
self.log('Skipping', name)
continue
else:
write_json(filename, {name: {}})
finally:
self.lock.release()
if atoms is not None:
del atoms.calc
atoms = self.run_single(name)
return atoms