def set_calculator(self, atoms, name):
cls = get_calculator(self.calculator_name)
parameters = str2dict(self.args.parameters)
if getattr(cls, 'nolabel', False):
atoms.calc = cls(**parameters)
else:
atoms.calc = cls(label=self.get_filename(name), **parameters)
def dict2atoms(dct, attach_calculator=False):
constraint_dicts = dct.get('constraints')
if constraint_dicts:
constraints = [dict2constraint(c) for c in constraint_dicts]
else:
constraints = None
atoms = Atoms(dct['numbers'],
dct['positions'],
cell=dct['cell'],
pbc=dct['pbc'],
magmoms=dct.get('initial_magmoms'),
charges=dct.get('initial_charges'),
tags=dct.get('tags'),
masses=dct.get('masses'),
momenta=dct.get('momenta'),
constraint=constraints)
if attach_calculator:
atoms.calc = get_calculator(
dct['calculator'])(**dct['calculator_parameters'])
else:
results = {}
for prop in all_properties:
if prop in dct:
results[prop] = dct[prop]
if results:
atoms.calc = SinglePointCalculator(atoms, **results)
return atoms
def run(name):
Calculator = get_calculator(name)
par = required.get(name, {})
calc = Calculator(label=name + '_bandgap', xc='PBE',
# abinit, aims, elk - do not recognize the syntax below:
# https://trac.fysik.dtu.dk/projects/ase/ticket/98
# kpts={'size': kpts, 'gamma': True}, **par)
kpts=kpts, **par)
si = bulk('Si', crystalstructure='diamond', a=5.43)
si.calc = calc
si.get_potential_energy()
print(name, bandgap(si.calc))
del si.calc
# test spin-polarization
calc = Calculator(label=name + '_bandgap_spinpol', xc='PBE',
# abinit, aims, elk - do not recognize the syntax below:
# https://trac.fysik.dtu.dk/projects/ase/ticket/98
# kpts={'size': kpts, 'gamma': True}, **par)
kpts=kpts, **par)
si.set_initial_magnetic_moments([-0.1, 0.1])
# this should not be necessary in the new ase interface standard ...
if si.get_initial_magnetic_moments().any(): # spin-polarization
if name == 'aims':
calc.set(spin='collinear')
if name == 'elk':
calc.set(spinpol=True)
si.set_calculator(calc)
si.get_potential_energy()
print(name, bandgap(si.calc))
def h2dft(name):
Calculator = get_calculator(name)
par = required.get(name, {})
calc = Calculator(label=name, xc='LDA', **par)
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
e2 = h2.get_potential_energy()
calc.set(xc='PBE')
e2pbe = h2.get_potential_energy()
h1 = h2.copy()
del h1[1]
h1.set_initial_magnetic_moments([1])
h1.calc = calc
e1pbe = h1.get_potential_energy()
calc.set(xc='LDA')
e1 = h1.get_potential_energy()
try:
m1 = h1.get_magnetic_moment()
except NotImplementedError:
pass
else:
print m1
print(2 * e1 - e2)
print(2 * e1pbe - e2pbe)
print e1, e2, e1pbe, e2pbe
calc = Calculator(name)
print calc.parameters, calc.results, calc.atoms
assert not calc.calculation_required(h1, ['energy'])
h1 = calc.get_atoms()
print h1.get_potential_energy()
label = 'dir/' + name + '-h1'
calc = Calculator(label=label, atoms=h1, xc='LDA', **par)
print h1.get_potential_energy()
print Calculator.read_atoms(label).get_potential_energy()
def dict2atoms(dct, attach_calculator=False):
constraint_dicts = dct.get('constraints')
if constraint_dicts:
constraints = [dict2constraint(c) for c in constraint_dicts]
else:
constraints = None
atoms = Atoms(dct['numbers'],
dct['positions'],
cell=dct['cell'],
pbc=dct['pbc'],
magmoms=dct.get('initial_magmoms'),
charges=dct.get('initial_charges'),
tags=dct.get('tags'),
masses=dct.get('masses'),
momenta=dct.get('momenta'),
constraint=constraints)
if attach_calculator:
atoms.calc = get_calculator(dct['calculator'])(
**dct['calculator_parameters'])
else:
results = {}
for prop in all_properties:
if prop in dct:
results[prop] = dct[prop]
if results:
atoms.calc = SinglePointCalculator(atoms, **results)
return atoms
def dict2atoms(dct, attach_calculator=False):
constraint_dicts = dct.get('constraints')
if constraint_dicts:
constraints = []
for c in constraint_dicts:
assert c.pop('__name__') == 'ase.constraints.FixAtoms'
constraints.append(FixAtoms(**c))
else:
constraints = None
atoms = Atoms(dct['numbers'],
dct['positions'],
cell=dct['cell'],
pbc=dct['pbc'],
magmoms=dct.get('magmoms'),
charges=dct.get('charges'),
tags=dct.get('tags'),
masses=dct.get('masses'),
momenta=dct.get('momenta'),
constraint=constraints)
results = dct.get('results')
if attach_calculator:
atoms.calc = get_calculator(
dct['calculator_name'])(**dct['calculator_parameters'])
elif results:
atoms.calc = SinglePointCalculator(atoms, **results)
return atoms
def h2dft(name):
Calculator = get_calculator(name)
par = required.get(name, {})
calc = Calculator(label=name, xc='LDA', **par)
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
e2 = h2.get_potential_energy()
calc.set(xc='PBE')
e2pbe = h2.get_potential_energy()
h1 = h2.copy()
del h1[1]
h1.set_initial_magnetic_moments([1])
h1.calc = calc
e1pbe = h1.get_potential_energy()
calc.set(xc='LDA')
e1 = h1.get_potential_energy()
try:
m1 = h1.get_magnetic_moment()
except NotImplementedError:
pass
else:
print(m1)
print(2 * e1 - e2)
print(2 * e1pbe - e2pbe)
print(e1, e2, e1pbe, e2pbe)
calc = Calculator(name)
print(calc.parameters, calc.results, calc.atoms)
assert not calc.calculation_required(h1, ['energy'])
h1 = calc.get_atoms()
print(h1.get_potential_energy())
label = 'dir/' + name + '-h1'
calc = Calculator(label=label, atoms=h1, xc='LDA', **par)
print(h1.get_potential_energy())
print(Calculator.read_atoms(label).get_potential_energy())
def dict2atoms(dct, attach_calculator=False):
constraint_dicts = dct.get("constraints")
if constraint_dicts:
constraints = [dict2constraint(c) for c in constraint_dicts]
else:
constraints = None
atoms = Atoms(
dct["numbers"],
dct["positions"],
cell=dct["cell"],
pbc=dct["pbc"],
magmoms=dct.get("initial_magmoms"),
charges=dct.get("initial_charges"),
tags=dct.get("tags"),
masses=dct.get("masses"),
momenta=dct.get("momenta"),
constraint=constraints,
)
if attach_calculator:
atoms.calc = get_calculator(dct["calculator"])(**dct["calculator_parameters"])
else:
results = {}
for prop in all_properties:
if prop in dct:
results[prop] = dct[prop]
if results:
atoms.calc = SinglePointCalculator(atoms, **results)
return atoms
def dict2atoms(dct, attach_calculator=False):
constraint_dicts = dct.get('constraints')
if constraint_dicts:
constraints = []
for c in constraint_dicts:
assert c.pop('__name__') == 'ase.constraints.FixAtoms'
constraints.append(FixAtoms(**c))
else:
constraints = None
atoms = Atoms(dct['numbers'],
dct['positions'],
cell=dct['cell'],
pbc=dct['pbc'],
magmoms=dct.get('magmoms'),
charges=dct.get('charges'),
tags=dct.get('tags'),
masses=dct.get('masses'),
momenta=dct.get('momenta'),
constraint=constraints)
results = dct.get('results')
if attach_calculator:
atoms.calc = get_calculator(dct['calculator_name'])(
**dct['calculator_parameters'])
elif results:
atoms.calc = SinglePointCalculator(atoms, **results)
return atoms
def set_calculator(self, atoms, name):
cls = get_calculator(self.calculator_name)
parameters = str2dict(self.args.parameters)
if getattr(cls, 'nolabel', False):
atoms.calc = cls(**parameters)
else:
atoms.calc = cls(label=self.get_filename(name), **parameters)
def run(name):
Calculator = get_calculator(name)
par = required.get(name, {})
calc = Calculator(
label=name + '_bandgap',
xc='PBE',
# abinit, aims, elk - do not recognize the syntax below:
# https://trac.fysik.dtu.dk/projects/ase/ticket/98
# kpts={'size': kpts, 'gamma': True}, **par)
kpts=kpts,
**par)
si = bulk('Si', crystalstructure='diamond', a=5.43)
si.calc = calc
si.get_potential_energy()
print(name, bandgap(si.calc))
del si.calc
# test spin-polarization
calc = Calculator(
label=name + '_bandgap_spinpol',
xc='PBE',
# abinit, aims, elk - do not recognize the syntax below:
# https://trac.fysik.dtu.dk/projects/ase/ticket/98
# kpts={'size': kpts, 'gamma': True}, **par)
kpts=kpts,
**par)
si.set_initial_magnetic_moments([-0.1, 0.1])
# this should not be necessary in the new ase interface standard ...
if si.get_initial_magnetic_moments().any(): # spin-polarization
if name == 'aims':
calc.set(spin='collinear')
if name == 'elk':
calc.set(spinpol=True)
si.set_calculator(calc)
si.get_potential_energy()
print(name, bandgap(si.calc))
def main(args=None):
parser = optparse.OptionParser(usage='%prog [options] filename',
description=description)
add = parser.add_option
add('-n', '--band-index', type=int, metavar='INDEX',
help='Band index counting from zero.')
add('-s', '--spin-index', type=int, metavar='SPIN',
help='Spin index: zero or one.')
add('-c', '--contours', default='4',
help='Use "-c 3" for 3 contours or "-c -0.5,0.5" for specific ' +
'values. Default is four contours.')
add('-r', '--repeat', help='Example: "-r 2,2,2".')
add('-C', '--calculator-name', metavar='NAME', help='Name of calculator.')
opts, args = parser.parse_args(args)
if len(args) != 1:
parser.error('Incorrect number of arguments')
arg = args[0]
if arg.endswith('.cube'):
data, atoms = read_cube_data(arg)
else:
calc = get_calculator(opts.calculator_name)(arg, txt=None)
atoms = calc.get_atoms()
if opts.band_index is None:
data = calc.get_pseudo_density(opts.spin_index)
else:
data = calc.get_pseudo_wave_function(opts.band_index,
opts.spin_index or 0)
if data.dtype == complex:
data = abs(data)
mn = data.min()
mx = data.max()
print('Min: %16.6f' % mn)
print('Max: %16.6f' % mx)
if opts.contours.isdigit():
n = int(opts.contours)
d = (mx - mn) / n
contours = np.linspace(mn + d / 2, mx - d / 2, n).tolist()
else:
contours = [float(x) for x in opts.contours.split(',')]
if len(contours) == 1:
print('1 contour:', contours[0])
else:
print('%d contours: %.6f, ..., %.6f' %
(len(contours), contours[0], contours[-1]))
if opts.repeat:
repeat = [int(r) for r in opts.repeat.split(',')]
data = np.tile(data, repeat)
atoms *= repeat
plot(atoms, data, contours)
def h2(name, par):
h2 = molecule('H2', pbc=par.pop('pbc', False))
h2.center(vacuum=2.0)
h2.calc = get_calculator(name)(**par)
e = h2.get_potential_energy()
f = h2.get_forces()
assert not h2.calc.calculation_required(h2, ['energy', 'forces'])
write('h2.traj', h2)
h2 = read('h2.traj')
assert abs(e - h2.get_potential_energy()) < 1e-12
assert abs(f - h2.get_forces()).max() < 1e-12
def h2(name, par):
h2 = molecule('H2', pbc=par.pop('pbc', False))
h2.center(vacuum=2.0)
h2.calc = get_calculator(name)(**par)
e = h2.get_potential_energy()
f = h2.get_forces()
assert not h2.calc.calculation_required(h2, ['energy', 'forces'])
write('h2.traj', h2)
h2 = read('h2.traj')
assert abs(e - h2.get_potential_energy()) < 1e-12
assert abs(f - h2.get_forces()).max() < 1e-12
def set_calculator(self, atoms, name):
args = self.args
cls = get_calculator(args.calculator)
if self._calculator is None:
namespace = {}
else:
namespace = self._calculator.namespace
parameters = str2dict(args.parameters, namespace)
if getattr(cls, 'nolabel', False):
atoms.calc = cls(**parameters)
else:
atoms.calc = cls(label=self.get_filename(name), **parameters)
def disable_calculators(names):
def __init__(self, *args, **kwargs):
raise NotAvailable
for name in names:
if name in ['emt', 'lj', 'eam', 'morse']:
continue
try:
cls = get_calculator(name)
except ImportError:
pass
else:
cls.__init__ = __init__
def disable_calculators(names):
def __init__(self, *args, **kwargs):
raise NotAvailable
for name in names:
if name in ['emt', 'lj', 'eam', 'morse']:
continue
try:
cls = get_calculator(name)
except ImportError:
pass
else:
cls.__init__ = __init__
def run(name):
Calculator = get_calculator(name)
par = required.get(name, {})
calc = Calculator(label=name, xc='LDA', kpts=1.0, **par)
al = bulk('AlO', crystalstructure='rocksalt', a=4.5)
al.calc = calc
e = al.get_potential_energy()
calc.set(xc='PBE', kpts=(2, 2, 2))
epbe = al.get_potential_energy()
print(e, epbe)
calc = Calculator(name)
print calc.parameters, calc.results, calc.atoms
assert not calc.calculation_required(al, ['energy'])
al = calc.get_atoms()
print al.get_potential_energy()
label = 'dir/' + name + '-2'
calc = Calculator(label=label, atoms=al, xc='LDA', kpts=1.0, **par)
print al.get_potential_energy()
print Calculator.read_atoms(label).get_potential_energy()
def disable_calculators(names):
for name in names:
if name in ['emt', 'lj', 'eam', 'morse', 'tip3p']:
continue
try:
cls = get_calculator(name)
except ImportError:
pass
else:
def get_mock_init(name):
def mock_init(obj, *args, **kwargs):
raise NotAvailable('use --calculators={0} to enable'
.format(name))
return mock_init
def mock_del(obj):
pass
cls.__init__ = get_mock_init(name)
cls.__del__ = mock_del
def run(name):
Calculator = get_calculator(name)
par = required.get(name, {})
calc = Calculator(label=name, xc='LDA', kpts=1.0, **par)
al = bulk('AlO', crystalstructure='rocksalt', a=4.5)
al.calc = calc
e = al.get_potential_energy()
calc.set(xc='PBE', kpts=(2, 2, 2))
epbe = al.get_potential_energy()
print(e, epbe)
calc = Calculator(name)
print(calc.parameters, calc.results, calc.atoms)
assert not calc.calculation_required(al, ['energy'])
al = calc.get_atoms()
print(al.get_potential_energy())
label = 'dir/' + name + '-2'
calc = Calculator(label=label, atoms=al, xc='LDA', kpts=1.0, **par)
print(al.get_potential_energy())
print(Calculator.read_atoms(label).get_potential_energy())
def disable_calculators(names):
for name in names:
if name in ['emt', 'lj', 'eam', 'morse', 'tip3p']:
continue
try:
cls = get_calculator(name)
except ImportError:
pass
else:
def get_mock_init(name):
def mock_init(obj, *args, **kwargs):
raise NotAvailable('use --calculators={0} to enable'
.format(name))
return mock_init
def mock_del(obj):
pass
cls.__init__ = get_mock_init(name)
cls.__del__ = mock_del
def toatoms(self,
attach_calculator=False,
add_additional_information=False):
"""Create Atoms object."""
atoms = Atoms(self.numbers,
self.positions,
cell=self.cell,
pbc=self.pbc,
magmoms=self.get('initial_magmoms'),
charges=self.get('initial_charges'),
tags=self.get('tags'),
masses=self.get('masses'),
momenta=self.get('momenta'),
constraint=self.constraints)
if attach_calculator:
params = self.get('calculator_parameters', {})
atoms.calc = get_calculator(self.calculator)(**params)
else:
results = {}
for prop in all_properties:
if prop in self:
results[prop] = self[prop]
if results:
atoms.calc = SinglePointCalculator(atoms, **results)
atoms.calc.name = self.calculator
if add_additional_information:
atoms.info = {}
atoms.info['unique_id'] = self.unique_id
if self._keys:
atoms.info['key_value_pairs'] = self.key_value_pairs
data = self.get('data')
if data:
atoms.info['data'] = data
return atoms
def toatoms(self, attach_calculator=False,
add_additional_information=False):
"""Create Atoms object."""
atoms = Atoms(self.numbers,
self.positions,
cell=self.cell,
pbc=self.pbc,
magmoms=self.get('initial_magmoms'),
charges=self.get('initial_charges'),
tags=self.get('tags'),
masses=self.get('masses'),
momenta=self.get('momenta'),
constraint=self.constraints)
if attach_calculator:
params = decode(self.get('calculator_parameters', '{}'))
atoms.calc = get_calculator(self.calculator)(**params)
else:
results = {}
for prop in all_properties:
if prop in self:
results[prop] = self[prop]
if results:
atoms.calc = SinglePointCalculator(atoms, **results)
atoms.calc.name = self.calculator
if add_additional_information:
atoms.info = {}
atoms.info['unique_id'] = self.unique_id
if self._keys:
atoms.info['key_value_pairs'] = self.key_value_pairs
data = self.get('data')
if data:
atoms.info['data'] = data
return atoms
def run(opts, args, verbosity):
filename = args.pop(0)
query = ','.join(args)
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_int_float_or_str(value)
if opts.delete_keys:
delete_keys = opts.delete_keys.split(',')
else:
delete_keys = []
con = connect(filename, use_lock_file=not opts.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if opts.analyse:
con.analyse()
return
if opts.add_from_file:
filename = opts.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if opts.count:
n = con.count(query)
print('%s' % plural(n, 'row'))
return
if opts.explain:
for row in con.select(query, explain=True,
verbosity=verbosity,
limit=opts.limit, offset=opts.offset):
print(row['explain'])
return
if opts.insert_into:
nkvp = 0
nrows = 0
with connect(opts.insert_into,
use_lock_file=not opts.no_lock_file) as con2:
for row in con.select(query):
kvp = row.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if opts.unique:
row['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
con2.write(row, data=row.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [row['id'] for row in con.select(query)]
m, n = con.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if opts.delete:
ids = [row['id'] for row in con.select(query)]
if ids and not opts.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
con.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if opts.plot_data:
from ase.db.plot import dct2plot
dct2plot(con.get(query).data, opts.plot_data)
return
if opts.plot:
if ':' in opts.plot:
tags, keys = opts.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = opts.plot
keys = keys.split(',')
plots = collections.defaultdict(list)
X = {}
labels = []
for row in con.select(query, sort=opts.sort):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if opts.long:
row = con.get(query)
summary = Summary(row)
summary.write()
elif opts.json:
row = con.get(query)
con2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = row.get('key_value_pairs', {})
con2.write(row, data=row.get('data'), **kvp)
else:
if opts.open_web_browser:
import ase.db.app as app
app.db = con
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c and c.startswith('++'):
keys = set()
for row in con.select(query,
limit=opts.limit, offset=opts.offset):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit, opts.offset)
if opts.csv:
table.write_csv()
else:
table.write(query)
def run(opts, args, verbosity):
filename = args.pop(0)
query = ','.join(args)
if query.isdigit():
query = int(query)
if opts.add_keywords:
add_keywords = opts.add_keywords.split(',')
else:
add_keywords = []
if opts.delete_keywords:
delete_keywords = opts.delete_keywords.split(',')
else:
delete_keywords = []
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(','):
key, value = pair.split('=')
for type in [int, float]:
try:
value = type(value)
except ValueError:
pass
else:
break
add_key_value_pairs[key] = value
if opts.delete_key_value_pairs:
delete_key_value_pairs = opts.delete_key_value_pairs.split(',')
else:
delete_key_value_pairs = []
con = connect(filename)
def out(*args):
if verbosity > 0:
print(*args)
if opts.add_from_file:
filename = opts.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, add_keywords, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if opts.count:
n = 0
for dct in con.select(query):
n += 1
print('%s' % plural(n, 'row'))
return
if opts.explain:
for dct in con.select(query, explain=True,
verbosity=verbosity, limit=opts.limit):
print(dct['explain'])
return
if opts.insert_into:
con2 = connect(opts.insert_into)
nkw = 0
nkvp = 0
nrows = 0
for dct in con.select(query):
keywords = dct.get('keywords', [])
for keyword in add_keywords:
if keyword not in keywords:
keywords.append(keyword)
nkw += 1
kvp = dct.get('key_value_pairs', {})
nkvp = -len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
con2.write(dct, keywords, data=dct.get('data'), **kvp)
nrows += 1
out('Added %s and %s (%s updated)' %
(plural(nkw, 'keyword'),
plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_keywords or add_key_value_pairs:
ids = [dct['id'] for dct in con.select(query)]
nkw, nkv = con.update(ids, add_keywords, **add_key_value_pairs)
out('Added %s and %s (%s updated)' %
(plural(nkw, 'keyword'),
plural(nkv, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - nkv, 'pair')))
return
if opts.delete:
ids = [dct['id'] for dct in con.select(query)]
if ids and not opts.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if raw_input(msg).lower() != 'yes':
return
con.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if delete_keywords or delete_key_value_pairs:
ids = [dct['id'] for dct in con.select(query)]
nkw, nkv = con.delete_keywords_and_key_value_pairs(
ids, delete_keywords, delete_key_value_pairs)
print('Removed %s and %s' %
(plural(nkw, 'keyword'),
plural(nkv, 'key-value pair')))
return
if opts.python_expression:
for dct in con.select(query):
row = eval(opts.python_expression, dct)
if not isinstance(row, (list, tuple, np.ndarray)):
row = [row]
print(', '.join(str(x) for x in row))
return
if opts.long:
dct = con.get(query)
summary = Summary(dct)
summary.write()
else:
if opts.open_web_browser:
import ase.db.app as app
app.connection = con
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit)
if opts.csv:
table.write_csv()
else:
table.write()
def run(opts, args, verbosity):
filename = args.pop(0)
query = ','.join(args)
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_float_or_str(value)
if opts.delete_keys:
delete_keys = opts.delete_keys.split(',')
else:
delete_keys = []
con = connect(filename, use_lock_file=not opts.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if opts.analyse:
con.analyse()
return
if opts.add_from_file:
filename = opts.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if opts.count:
n = con.count(query)
print('%s' % plural(n, 'row'))
return
if opts.explain:
for dct in con.select(query,
explain=True,
verbosity=verbosity,
limit=opts.limit,
offset=opts.offset):
print(dct['explain'])
return
if opts.insert_into:
nkvp = 0
nrows = 0
with connect(opts.insert_into,
use_lock_file=not opts.no_lock_file) as con2:
for dct in con.select(query):
kvp = dct.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if opts.unique:
dct['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
con2.write(dct, data=dct.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [dct['id'] for dct in con.select(query)]
m, n = con.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if opts.delete:
ids = [dct['id'] for dct in con.select(query)]
if ids and not opts.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
con.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if opts.plot_data:
from ase.db.plot import dct2plot
dct2plot(con.get(query).data, opts.plot_data)
return
if opts.plot:
if ':' in opts.plot:
tags, keys = opts.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = opts.plot
keys = keys.split(',')
plots = collections.defaultdict(list)
X = {}
labels = []
for row in con.select(query, sort=opts.sort):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if opts.long:
dct = con.get(query)
summary = Summary(dct)
summary.write()
elif opts.json:
dct = con.get(query)
con2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = dct.get('key_value_pairs', {})
con2.write(dct, data=dct.get('data'), **kvp)
else:
if opts.open_web_browser:
import ase.db.app as app
app.db = con
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c and c.startswith('++'):
keys = set()
for row in con.select(query,
limit=opts.limit,
offset=opts.offset):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit, opts.offset)
if opts.csv:
table.write_csv()
else:
table.write(query)
def run(opts, args, verbosity):
filename = args.pop(0)
query = ','.join(args)
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(','):
key, value = pair.split('=')
for type in [int, float]:
try:
value = type(value)
except ValueError:
pass
else:
break
add_key_value_pairs[key] = value
if opts.delete_keys:
delete_keys = opts.delete_keys.split(',')
else:
delete_keys = []
con = connect(filename, use_lock_file=not opts.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if opts.add_from_file:
filename = opts.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if opts.count:
n = con.count(query)
print('%s' % plural(n, 'row'))
return
if opts.explain:
for dct in con.select(query,
explain=True,
verbosity=verbosity,
limit=opts.limit,
offset=opts.offset):
print(dct['explain'])
return
if opts.insert_into:
nkvp = 0
nrows = 0
with connect(opts.insert_into,
use_lock_file=not opts.no_lock_file) as con2:
for dct in con.select(query):
kvp = dct.get('key_value_pairs', {})
nkvp = -len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
con2.write(dct, data=dct.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [dct['id'] for dct in con.select(query)]
m, n = con.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if opts.delete:
ids = [dct['id'] for dct in con.select(query)]
if ids and not opts.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if raw_input(msg).lower() != 'yes':
return
con.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if opts.python_expression:
for dct in con.select(query):
row = eval(opts.python_expression, dct)
if not isinstance(row, (list, tuple, np.ndarray)):
row = [row]
print(', '.join(str(x) for x in row))
return
if opts.long:
dct = con.get(query)
summary = Summary(dct)
summary.write()
else:
if opts.open_web_browser:
import ase.db.app as app
app.db = con
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit, opts.offset)
if opts.csv:
table.write_csv()
else:
table.write()
"""
Test if we can find vasp2 using get_calculator()
"""
from ase.test.vasp import installed2 as installed
from ase.calculators.calculator import get_calculator
assert installed()
get_calculator('vasp2')
def run(opts, args, verbosity):
filename = args.pop(0)
query = ",".join(args)
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(","):
key, value = pair.split("=")
add_key_value_pairs[key] = convert_str_to_float_or_str(value)
if opts.delete_keys:
delete_keys = opts.delete_keys.split(",")
else:
delete_keys = []
con = connect(filename, use_lock_file=not opts.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if opts.analyse:
con.analyse()
return
if opts.add_from_file:
filename = opts.add_from_file
if ":" in filename:
calculator_name, filename = filename.split(":")
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, key_value_pairs=add_key_value_pairs)
out("Added {0} from {1}".format(atoms.get_chemical_formula(), filename))
return
if opts.count:
n = con.count(query)
print("%s" % plural(n, "row"))
return
if opts.explain:
for dct in con.select(query, explain=True, verbosity=verbosity, limit=opts.limit, offset=opts.offset):
print(dct["explain"])
return
if opts.insert_into:
nkvp = 0
nrows = 0
with connect(opts.insert_into, use_lock_file=not opts.no_lock_file) as con2:
for dct in con.select(query):
kvp = dct.get("key_value_pairs", {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if opts.unique:
dct["unique_id"] = "%x" % randint(16 ** 31, 16 ** 32 - 1)
con2.write(dct, data=dct.get("data"), **kvp)
nrows += 1
out(
"Added %s (%s updated)"
% (plural(nkvp, "key-value pair"), plural(len(add_key_value_pairs) * nrows - nkvp, "pair"))
)
out("Inserted %s" % plural(nrows, "row"))
return
if add_key_value_pairs or delete_keys:
ids = [dct["id"] for dct in con.select(query)]
m, n = con.update(ids, delete_keys, **add_key_value_pairs)
out(
"Added %s (%s updated)"
% (plural(m, "key-value pair"), plural(len(add_key_value_pairs) * len(ids) - m, "pair"))
)
out("Removed", plural(n, "key-value pair"))
return
if opts.delete:
ids = [dct["id"] for dct in con.select(query)]
if ids and not opts.yes:
msg = "Delete %s? (yes/No): " % plural(len(ids), "row")
if input(msg).lower() != "yes":
return
con.delete(ids)
out("Deleted %s" % plural(len(ids), "row"))
return
if opts.plot:
if ":" in opts.plot:
tags, keys = opts.plot.split(":")
tags = tags.split(",")
else:
tags = []
keys = opts.plot
keys = keys.split(",")
plots = collections.defaultdict(list)
X = {}
labels = []
for row in con.select(query, sort=opts.sort):
name = ",".join(row[tag] for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, (unicode, str)):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if opts.long:
dct = con.get(query)
summary = Summary(dct)
summary.write()
elif opts.json:
dct = con.get(query)
con2 = connect(sys.stdout, "json", use_lock_file=False)
kvp = dct.get("key_value_pairs", {})
con2.write(dct, data=dct.get("data"), **kvp)
else:
if opts.open_web_browser:
import ase.db.app as app
app.db = con
app.app.run(host="0.0.0.0", debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c and c.startswith("++"):
keys = set()
for row in con.select(query, limit=opts.limit, offset=opts.offset):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ",":
c = c[3:]
else:
c = ""
if c:
if c[0] == "+":
c = c[1:]
elif c[0] != "-":
columns = []
for col in c.split(","):
if col[0] == "-":
columns.remove(col[1:])
else:
columns.append(col.lstrip("+"))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit, opts.offset)
if opts.csv:
table.write_csv()
else:
table.write(query)
def main(args):
verbosity = 1 - args.quiet + args.verbose
query = ','.join(args.query)
if args.sort.endswith('-'):
args.sort = '-' + args.sort[:-1]
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if args.add_key_value_pairs:
for pair in args.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_int_float_or_str(value)
if args.delete_keys:
delete_keys = args.delete_keys.split(',')
else:
delete_keys = []
db = connect(args.database, use_lock_file=not args.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if args.analyse:
db.analyse()
return
if args.add_from_file:
filename = args.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
db.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if args.count:
n = db.count(query)
print('%s' % plural(n, 'row'))
return
if args.explain:
for row in db.select(query,
explain=True,
verbosity=verbosity,
limit=args.limit,
offset=args.offset):
print(row['explain'])
return
if args.show_metadata:
print(json.dumps(db.metadata, sort_keys=True, indent=4))
return
if args.set_metadata:
with open(args.set_metadata) as fd:
db.metadata = json.load(fd)
return
if args.insert_into:
nkvp = 0
nrows = 0
with connect(args.insert_into,
use_lock_file=not args.no_lock_file) as db2:
for row in db.select(query, sort=args.sort):
kvp = row.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if args.unique:
row['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
db2.write(row, data=row.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [row['id'] for row in db.select(query)]
m, n = db.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if args.delete:
ids = [row['id'] for row in db.select(query)]
if ids and not args.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
db.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if args.plot_data:
from ase.db.plot import dct2plot
dct2plot(db.get(query).data, args.plot_data)
return
if args.plot:
if ':' in args.plot:
tags, keys = args.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = args.plot
keys = keys.split(',')
plots = collections.defaultdict(list)
X = {}
labels = []
for row in db.select(query, sort=args.sort, include_data=False):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if args.json:
row = db.get(query)
db2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = row.get('key_value_pairs', {})
db2.write(row, data=row.get('data'), **kvp)
return
db.python = args.metadata_from_python_script
db.meta = process_metadata(db, html=args.open_web_browser)
if args.long:
# Remove .png files so that new ones will be created.
for func, filenames in db.meta.get('functions', []):
for filename in filenames:
try:
os.remove(filename)
except OSError: # Python 3 only: FileNotFoundError
pass
row = db.get(query)
summary = Summary(row, db.meta)
summary.write()
else:
if args.open_web_browser:
import ase.db.app as app
app.databases['default'] = db
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = args.columns
if c and c.startswith('++'):
keys = set()
for row in db.select(query,
limit=args.limit,
offset=args.offset,
include_data=False):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(db, verbosity, args.cut)
table.select(query, columns, args.sort, args.limit, args.offset)
if args.csv:
table.write_csv()
else:
table.write(query)
def main(args=None):
parser = optparse.OptionParser(usage='%prog [options] filename',
description=description)
add = parser.add_option
add('-n',
'--band-index',
type=int,
metavar='INDEX',
help='Band index counting from zero.')
add('-s',
'--spin-index',
type=int,
metavar='SPIN',
help='Spin index: zero or one.')
add('-c',
'--contours',
default='4',
help='Use "-c 3" for 3 contours or "-c -0.5,0.5" for specific ' +
'values. Default is four contours.')
add('-r', '--repeat', help='Example: "-r 2,2,2".')
add('-C', '--calculator-name', metavar='NAME', help='Name of calculator.')
opts, args = parser.parse_args(args)
if len(args) != 1:
parser.error('Incorrect number of arguments')
arg = args[0]
if arg.endswith('.cube'):
data, atoms = read_cube_data(arg)
else:
calc = get_calculator(opts.calculator_name)(arg, txt=None)
atoms = calc.get_atoms()
if opts.band_index is None:
data = calc.get_pseudo_density(opts.spin_index)
else:
data = calc.get_pseudo_wave_function(opts.band_index,
opts.spin_index or 0)
if data.dtype == complex:
data = abs(data)
mn = data.min()
mx = data.max()
print('Min: %16.6f' % mn)
print('Max: %16.6f' % mx)
if opts.contours.isdigit():
n = int(opts.contours)
d = (mx - mn) / n
contours = np.linspace(mn + d / 2, mx - d / 2, n).tolist()
else:
contours = [float(x) for x in opts.contours.split(',')]
if len(contours) == 1:
print('1 contour:', contours[0])
else:
print('%d contours: %.6f, ..., %.6f' %
(len(contours), contours[0], contours[-1]))
if opts.repeat:
repeat = [int(r) for r in opts.repeat.split(',')]
data = np.tile(data, repeat)
atoms *= repeat
plot(atoms, data, contours)