def mx2(formula='MoS2',
kind='2H',
a=3.18,
thickness=3.19,
size=(1, 1, 1),
vacuum=7.5):
"""Create three-layer 2D materials with hexagonal structure.
For metal dichalcogenites, etc.
The kind argument accepts '2H', which gives a mirror plane symmetry
and '1T', which gives an inversion symmetry."""
if kind == '2H':
basis = [(0, 0, 0), (2 / 3, 1 / 3, 0.5 * thickness),
(2 / 3, 1 / 3, -0.5 * thickness)]
elif kind == '1T':
basis = [(0, 0, 0), (2 / 3, 1 / 3, 0.5 * thickness),
(1 / 3, 2 / 3, -0.5 * thickness)]
else:
raise ValueError('Structure not recognized')
cell = [[a, 0, 0], [-a / 2, a * 3**0.5 / 2, 0], [0, 0, 1]]
atoms = Atoms(formula, cell=cell, scaled_positions=basis, pbc=(1, 1, 0))
atoms = atoms.repeat(size)
atoms.center(vacuum=vacuum, axis=2)
return atoms
def build_system(self, name):
try:
# Known molecule or atom?
atoms = molecule(name)
if len(atoms) == 2 and self.bond_length is not None:
atoms.set_distance(0, 1, self.bond_length)
except NotImplementedError:
symbols = string2symbols(name)
if len(symbols) == 1:
magmom = ground_state_magnetic_moments[atomic_numbers[
symbols[0]]]
atoms = Atoms(name, magmoms=[magmom])
elif len(symbols) == 2:
# Dimer
if self.bond_length is None:
b = (covalent_radii[atomic_numbers[symbols[0]]] +
covalent_radii[atomic_numbers[symbols[1]]])
else:
b = self.bond_length
atoms = Atoms(name, positions=[(0, 0, 0), (b, 0, 0)])
else:
raise ValueError('Unknown molecule: ' + name)
if self.unit_cell is None:
atoms.center(vacuum=self.vacuum)
else:
atoms.cell = self.unit_cell
atoms.center()
return atoms
def get_structure(formula, prototype=None, base_dir="./", c=None, **filters):
db_file = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../c2db.db")
# Serial version, only on rank 0
candidates = {}
# if world.rank == 0:
db = ase.db.connect(db_file)
if prototype is None:
res = db.select(formula=formula, **filters)
else:
res = db.select(formula=formula, prototype=prototype)
for mol in res:
symbol = mol.formula
pos = mol.positions
cell = mol.cell
pbc = mol.pbc
# Change distance
if (c is not None) and (isinstance(c, (float, int))):
cell.setflags(write=True)
cell[-1][-1] = c
pbc = (True, True, True) # Use full periodic
name = "{}-{}".format(symbol, mol.prototype)
# name = os.path.join(os.path.abspath(base_dir),
# "{}-{}.traj".format(symbol, mol.prototype))
atoms = Atoms(symbol, positions=pos, cell=cell, pbc=pbc)
candidates[name] = atoms
if (c is not None) and (isinstance(c, (float, int))):
atoms.center() # center the atoms, although not really needed
return candidates
def mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19,
size=(1, 1, 1), vacuum=None):
"""Create three-layer 2D materials with hexagonal structure.
For metal dichalcogenites, etc.
The kind argument accepts '2H', which gives a mirror plane symmetry
and '1T', which gives an inversion symmetry."""
if kind == '2H':
basis = [(0, 0, 0),
(2 / 3, 1 / 3, 0.5 * thickness),
(2 / 3, 1 / 3, -0.5 * thickness)]
elif kind == '1T':
basis = [(0, 0, 0),
(2 / 3, 1 / 3, 0.5 * thickness),
(1 / 3, 2 / 3, -0.5 * thickness)]
else:
raise ValueError('Structure not recognized:', kind)
cell = [[a, 0, 0], [-a / 2, a * 3**0.5 / 2, 0], [0, 0, 0]]
atoms = Atoms(formula, cell=cell, pbc=(1, 1, 0))
atoms.set_scaled_positions(basis)
if vacuum is not None:
atoms.center(vacuum, axis=2)
atoms = atoms.repeat(size)
return atoms
def build_system(self, name):
try:
# Known molecule or atom?
atoms = molecule(name)
if len(atoms) == 2 and self.bond_length is not None:
atoms.set_distance(0, 1, self.bond_length)
except NotImplementedError:
symbols = string2symbols(name)
if len(symbols) == 1:
Z = atomic_numbers[symbols[0]]
magmom = ground_state_magnetic_moments[Z]
atoms = Atoms(name, magmoms=[magmom])
elif len(symbols) == 2:
# Dimer
if self.bond_length is None:
b = (covalent_radii[atomic_numbers[symbols[0]]] +
covalent_radii[atomic_numbers[symbols[1]]])
else:
b = self.bond_length
atoms = Atoms(name, positions=[(0, 0, 0),
(b, 0, 0)])
else:
raise ValueError('Unknown molecule: ' + name)
if self.unit_cell is None:
atoms.center(vacuum=self.vacuum)
else:
atoms.cell = self.unit_cell
atoms.center()
return atoms
def graphene(formula='C2', a=2.460, size=(1, 1, 1), vacuum=None):
"""Create a graphene monolayer structure."""
cell = [[a, 0, 0], [-a / 2, a * 3**0.5 / 2, 0], [0, 0, 0]]
basis = [[0, 0, 0], [2./3, 1./3, 0]]
atoms = Atoms(formula, cell=cell, pbc=(1, 1, 0))
atoms.set_scaled_positions(basis)
if vacuum is not None:
atoms.center(vacuum, axis=2)
atoms = atoms.repeat(size)
return atoms
def molecule(name, vacuum=None, **kwargs):
if name in extra:
kwargs.update(extra[name])
mol = Atoms(**kwargs)
else:
mol = g2[name]
if kwargs:
mol = Atoms(mol, **kwargs)
if vacuum is not None:
mol.center(vacuum=vacuum)
return mol
def build_molecule(self, name):
args = self.args
try:
# Known molecule or atom?
atoms = molecule(name)
except NotImplementedError:
symbols = string2symbols(name)
if len(symbols) == 1:
Z = atomic_numbers[symbols[0]]
magmom = ground_state_magnetic_moments[Z]
atoms = Atoms(name, magmoms=[magmom])
elif len(symbols) == 2:
# Dimer
if args.bond_length is None:
b = covalent_radii[atomic_numbers[symbols[0]]] + covalent_radii[atomic_numbers[symbols[1]]]
else:
b = args.bond_length
atoms = Atoms(name, positions=[(0, 0, 0), (b, 0, 0)])
else:
raise ValueError("Unknown molecule: " + name)
else:
if len(atoms) == 2 and args.bond_length is not None:
atoms.set_distance(0, 1, args.bond_length)
if args.unit_cell is None:
atoms.center(vacuum=args.vacuum)
else:
a = [float(x) for x in args.unit_cell.split(",")]
if len(a) == 1:
cell = [a[0], a[0], a[0]]
elif len(a) == 3:
cell = a
else:
a, b, c, alpha, beta, gamma = a
degree = np.pi / 180.0
cosa = np.cos(alpha * degree)
cosb = np.cos(beta * degree)
sinb = np.sin(beta * degree)
cosg = np.cos(gamma * degree)
sing = np.sin(gamma * degree)
cell = [
[a, 0, 0],
[b * cosg, b * sing, 0],
[
c * cosb,
c * (cosa - cosb * cosg) / sing,
c * np.sqrt(sinb ** 2 - ((cosa - cosb * cosg) / sing) ** 2),
],
]
atoms.cell = cell
atoms.center()
return atoms
def setup_atom(symbol, vac=3.0, t=0.0, odd=0.0):
from ase import Atoms
from ase.data import chemical_symbols, atomic_numbers, ground_state_magnetic_moments
assert symbol in chemical_symbols
Z = atomic_numbers[symbol]
m = ground_state_magnetic_moments[Z]
atoms = Atoms(symbol)
atoms.center(vacuum=vac)
atoms.translate([t,t,t])
atoms.cell[1][1] += odd
atoms.cell[2][2] += 2*odd
atoms.set_initial_magnetic_moments([m])
return atoms
def build_molecule(name, opts):
try:
# Known molecule or atom?
atoms = molecule(name)
except NotImplementedError:
symbols = string2symbols(name)
if len(symbols) == 1:
Z = atomic_numbers[symbols[0]]
magmom = ground_state_magnetic_moments[Z]
atoms = Atoms(name, magmoms=[magmom])
elif len(symbols) == 2:
# Dimer
if opts.bond_length is None:
b = (covalent_radii[atomic_numbers[symbols[0]]] +
covalent_radii[atomic_numbers[symbols[1]]])
else:
b = opts.bond_length
atoms = Atoms(name, positions=[(0, 0, 0),
(b, 0, 0)])
else:
raise ValueError('Unknown molecule: ' + name)
else:
if len(atoms) == 2 and opts.bond_length is not None:
atoms.set_distance(0, 1, opts.bond_length)
if opts.unit_cell is None:
atoms.center(vacuum=opts.vacuum)
else:
a = [float(x) for x in opts.unit_cell.split(',')]
if len(a) == 1:
cell = [a[0], a[0], a[0]]
elif len(a) == 3:
cell = a
else:
a, b, c, alpha, beta, gamma = a
degree = np.pi / 180.0
cosa = np.cos(alpha * degree)
cosb = np.cos(beta * degree)
sinb = np.sin(beta * degree)
cosg = np.cos(gamma * degree)
sing = np.sin(gamma * degree)
cell = [[a, 0, 0],
[b * cosg, b * sing, 0],
[c * cosb, c * (cosa - cosb * cosg) / sing,
c * np.sqrt(
sinb**2 - ((cosa - cosb * cosg) / sing)**2)]]
atoms.cell = cell
atoms.center()
return atoms
def test_md(cp2k_factory):
calc = cp2k_factory.calc(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
MaxwellBoltzmannDistribution(atoms, temperature_K=0.5 * 300,
force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
with VelocityVerlet(atoms, 0.5 * units.fs) as dyn:
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert abs(energy_start - energy_end) < 1e-4
def molecule(name, vacuum=None, **kwargs):
"""Create an atomic structure from a database.
This is a helper function to easily create molecules from the g2 and
extra databases.
Parameters
----------
name : str
Name of the molecule to build.
vacuum : float, optional
Amount of vacuum to pad the molecule with on all sides.
Additional keyword arguments (kwargs) can be supplied, which are passed
to ase.Atoms.
Returns
-------
ase.atoms.Atoms
An ASE Atoms object corresponding to the specified molecule.
Notes
-----
To see a list of allowed names, try:
>>> from ase.collections import g2
>>> print(g2.names)
>>> from ase.build.molecule import extra
>>> print(extra.keys())
Examples
--------
>>> from ase.build import molecule
>>> atoms = molecule('H2O')
"""
if name in extra:
kwargs.update(extra[name])
mol = Atoms(**kwargs)
else:
mol = g2[name]
if kwargs:
mol = Atoms(mol, **kwargs)
if vacuum is not None:
mol.center(vacuum=vacuum)
return mol
def test_md(cp2k_factory):
calc = cp2k_factory.calc(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def main():
if "ASE_CP2K_COMMAND" not in os.environ:
raise NotAvailable('$ASE_CP2K_COMMAND not defined')
calc = CP2K(label='test_H2_MD')
positions = [(0, 0, 0), (0, 0, 0.7245595)]
atoms = Atoms('HH', positions=positions, calculator=calc)
atoms.center(vacuum=2.0)
# Run MD
MaxwellBoltzmannDistribution(atoms, 0.5 * 300 * units.kB, force_temp=True)
energy_start = atoms.get_potential_energy() + atoms.get_kinetic_energy()
dyn = VelocityVerlet(atoms, 0.5 * units.fs)
#def print_md():
# energy = atoms.get_potential_energy() + atoms.get_kinetic_energy()
# print("MD total-energy: %.10feV" % energy)
#dyn.attach(print_md, interval=1)
dyn.run(20)
energy_end = atoms.get_potential_energy() + atoms.get_kinetic_energy()
assert energy_start - energy_end < 1e-4
print('passed test "H2_MD"')
def graphene_nanoribbon(n,
m,
type='zigzag',
saturated=False,
C_H=1.09,
C_C=1.42,
vacuum=None,
magnetic=False,
initial_mag=1.12,
sheet=False,
main_element='C',
saturate_element='H'):
"""Create a graphene nanoribbon.
Creates a graphene nanoribbon in the x-z plane, with the nanoribbon
running along the z axis.
Parameters:
n: int
The width of the nanoribbon. For armchair nanoribbons, this
n may be half-integer to repeat by half a cell.
m: int
The length of the nanoribbon.
type: str
The orientation of the ribbon. Must be either 'zigzag'
or 'armchair'.
saturated: bool
If true, hydrogen atoms are placed along the edge.
C_H: float
Carbon-hydrogen bond length. Default: 1.09 Angstrom.
C_C: float
Carbon-carbon bond length. Default: 1.42 Angstrom.
vacuum: None (default) or float
Amount of vacuum added to non-periodic directions, if present.
magnetic: bool
Make the edges magnetic.
initial_mag: float
Magnitude of magnetic moment if magnetic.
sheet: bool
If true, make an infinite sheet instead of a ribbon (default: False)
"""
if m % 1 != 0:
raise ValueError('m must be integer')
if type == 'zigzag' and n % 1 != 0:
raise ValueError('n must be an integer for zigzag ribbons')
b = sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + '4',
pbc=(1, 0, 1),
cell=[4 * b, 0, 3 * C_C])
arm_unit.positions = [[0, 0, 0], [b * 2, 0, C_C / 2.],
[b * 2, 0, 3 * C_C / 2.], [0, 0, 2 * C_C]]
arm_unit_half = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[2 * b, 0, 3 * C_C])
arm_unit_half.positions = [[b * 2, 0, C_C / 2.], [b * 2, 0, 3 * C_C / 2.]]
zz_unit = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[3 * C_C / 2.0, 0, b * 4])
zz_unit.positions = [[0, 0, 0], [C_C / 2.0, 0, b * 2]]
atoms = Atoms()
if type == 'zigzag':
edge_index0 = np.arange(m) * 2
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2 + 1
if magnetic:
mms = np.zeros(m * n * 2)
for i in edge_index0:
mms[i] = initial_mag
for i in edge_index1:
mms[i] = -initial_mag
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 0] += 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
xmin = atoms.positions[0, 0]
if magnetic:
atoms.set_initial_magnetic_moments(mms)
if saturated:
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 0] -= C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 0] += C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [n * 3 * C_C / 2, 0, m * 4 * b]
elif type == 'armchair':
n *= 2
n_int = int(round(n))
if abs(n_int - n) > 1e-10:
raise ValueError(
'The argument n has to be half-integer for armchair ribbons.')
n = n_int
for i in range(n // 2):
layer = arm_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * i
atoms += layer
if n % 2:
layer = arm_unit_half.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * (n // 2)
atoms += layer
xmin = atoms.positions[-1, 0]
if saturated:
if n % 2:
arm_right_saturation = Atoms(saturate_element + '2',
pbc=(1, 0, 1),
cell=[2 * b, 0, 3 * C_C])
arm_right_saturation.positions = [[
-sqrt(3) / 2 * C_H, 0, C_C / 2 - C_H * 0.5
], [-sqrt(3) / 2 * C_H, 0, 3 * C_C / 2.0 + C_H * 0.5]]
else:
arm_right_saturation = Atoms(saturate_element + '2',
pbc=(1, 0, 1),
cell=[4 * b, 0, 3 * C_C])
arm_right_saturation.positions = [[
-sqrt(3) / 2 * C_H, 0, C_H * 0.5
], [-sqrt(3) / 2 * C_H, 0, 2 * C_C - C_H * 0.5]]
arm_left_saturation = Atoms(saturate_element + '2',
pbc=(1, 0, 1),
cell=[4 * b, 0, 3 * C_C])
arm_left_saturation.positions = [[
b * 2 + sqrt(3) / 2 * C_H, 0, C_C / 2 - C_H * 0.5
], [b * 2 + sqrt(3) / 2 * C_H, 0, 3 * C_C / 2.0 + C_H * 0.5]]
arm_right_saturation.positions[:, 0] -= 4 * b * (n / 2.0 - 1)
atoms += arm_right_saturation.repeat((1, 1, m))
atoms += arm_left_saturation.repeat((1, 1, m))
atoms.cell = [b * 4 * n / 2.0, 0, 3 * C_C * m]
atoms.set_pbc([sheet, False, True])
# The ribbon was 'built' from x=0 towards negative x.
# Move the ribbon to positive x:
atoms.positions[:, 0] -= xmin
if not sheet:
atoms.cell[0] = 0.0
if vacuum is not None:
atoms.center(vacuum, axis=1)
if not sheet:
atoms.center(vacuum, axis=0)
return atoms
def graphene_nanoribbon(n,
m,
type='zigzag',
saturated=False,
C_H=1.09,
C_C=1.42,
vacuum=None,
magnetic=False,
initial_mag=1.12,
sheet=False,
main_element='C',
saturate_element='H'):
"""Create a graphene nanoribbon.
Creates a graphene nanoribbon in the x-z plane, with the nanoribbon
running along the z axis.
Parameters:
n: int
The width of the nanoribbon.
m: int
The length of the nanoribbon.
type: str
The orientation of the ribbon. Must be either 'zigzag'
or 'armchair'.
saturated: bool
If true, hydrogen atoms are placed along the edge.
C_H: float
Carbon-hydrogen bond length. Default: 1.09 Angstrom.
C_C: float
Carbon-carbon bond length. Default: 1.42 Angstrom.
vacuum: None (default) or float
Amount of vacuum added to non-periodic directions, if present.
magnetic: bool
Make the edges magnetic.
initial_mag: float
Magnitude of magnetic moment if magnetic.
sheet: bool
If true, make an infinite sheet instead of a ribbon (default: False)
"""
b = sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + '4',
pbc=(1, 0, 1),
cell=[4 * b, 0, 3 * C_C])
arm_unit.positions = [[0, 0, 0], [b * 2, 0, C_C / 2.],
[b * 2, 0, 3 * C_C / 2.], [0, 0, 2 * C_C]]
zz_unit = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[3 * C_C / 2.0, 0, b * 4])
zz_unit.positions = [[0, 0, 0], [C_C / 2.0, 0, b * 2]]
atoms = Atoms()
if type == 'zigzag':
edge_index0 = np.arange(m) * 2 + 1
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2
if magnetic:
mms = np.zeros(m * n * 2)
for i in edge_index0:
mms[i] = initial_mag
for i in edge_index1:
mms[i] = -initial_mag
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
if magnetic:
atoms.set_initial_magnetic_moments(mms)
if saturated:
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 0] += C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 0] -= C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [n * 3 * C_C / 2, 0, m * 4 * b]
elif type == 'armchair':
for i in range(n):
layer = arm_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * i
atoms += layer
if saturated:
arm_right_saturation = Atoms(saturate_element + '2',
pbc=(1, 0, 1),
cell=[4 * b, 0, 3 * C_C])
arm_right_saturation.positions = [[
-sqrt(3) / 2 * C_H, 0, C_H * 0.5
], [-sqrt(3) / 2 * C_H, 0, 2 * C_C - C_H * 0.5]]
arm_left_saturation = Atoms(saturate_element + '2',
pbc=(1, 0, 1),
cell=[4 * b, 0, 3 * C_C])
arm_left_saturation.positions = [[
b * 2 + sqrt(3) / 2 * C_H, 0, C_C / 2 - C_H * 0.5
], [b * 2 + sqrt(3) / 2 * C_H, 0, 3 * C_C / 2.0 + C_H * 0.5]]
arm_right_saturation.positions[:, 0] -= 4 * b * (n - 1)
atoms += arm_right_saturation.repeat((1, 1, m))
atoms += arm_left_saturation.repeat((1, 1, m))
atoms.cell = [b * 4 * n, 0, 3 * C_C * m]
atoms.set_pbc([sheet, False, True])
atoms.set_scaled_positions(atoms.get_scaled_positions() % 1.0)
if not sheet:
atoms.cell[0] = 0.0
if vacuum:
atoms.center(vacuum, axis=1)
if not sheet:
atoms.center(vacuum, axis=0)
return atoms
def surface(symbol, structure, face, size, a, c, vacuum, orthogonal=True):
"""Function to build often used surfaces.
Don't call this function directly - use fcc100, fcc110, bcc111, ..."""
Z = atomic_numbers[symbol]
if a is None:
sym = reference_states[Z]['symmetry'].lower()
if sym != structure:
raise ValueError("Can't guess lattice constant for %s-%s!" %
(structure, symbol))
a = reference_states[Z]['a']
if structure == 'hcp' and c is None:
if reference_states[Z]['symmetry'].lower() == 'hcp':
c = reference_states[Z]['c/a'] * a
else:
c = sqrt(8 / 3.0) * a
positions = np.empty((size[2], size[1], size[0], 3))
positions[..., 0] = np.arange(size[0]).reshape((1, 1, -1))
positions[..., 1] = np.arange(size[1]).reshape((1, -1, 1))
positions[..., 2] = np.arange(size[2]).reshape((-1, 1, 1))
numbers = np.ones(size[0] * size[1] * size[2], int) * Z
tags = np.empty((size[2], size[1], size[0]), int)
tags[:] = np.arange(size[2], 0, -1).reshape((-1, 1, 1))
slab = Atoms(numbers,
tags=tags.ravel(),
pbc=(True, True, False),
cell=size)
surface_cell = None
sites = {'ontop': (0, 0)}
surf = structure + face
if surf == 'fcc100':
cell = (sqrt(0.5), sqrt(0.5), 0.5)
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'bridge': (0.5, 0)})
elif surf == 'fcc110':
cell = (1.0, sqrt(0.5), sqrt(0.125))
positions[-2::-2, ..., :2] += 0.5
sites.update({
'hollow': (0.5, 0.5),
'longbridge': (0.5, 0),
'shortbridge': (0, 0.5)
})
elif surf == 'bcc100':
cell = (1.0, 1.0, 0.5)
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'bridge': (0.5, 0)})
else:
if orthogonal and size[1] % 2 == 1:
raise ValueError(("Can't make orthorhombic cell with size=%r. " %
(tuple(size), )) +
'Second number in size must be even.')
if surf == 'fcc111':
cell = (sqrt(0.5), sqrt(0.375), 1 / sqrt(3))
if orthogonal:
positions[-1::-3, 1::2, :, 0] += 0.5
positions[-2::-3, 1::2, :, 0] += 0.5
positions[-3::-3, 1::2, :, 0] -= 0.5
positions[-2::-3, ..., :2] += (0.0, 2.0 / 3)
positions[-3::-3, ..., :2] += (0.5, 1.0 / 3)
else:
positions[-2::-3, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-3::-3, ..., :2] += (1.0 / 3, 1.0 / 3)
sites.update({
'bridge': (0.5, 0),
'fcc': (1.0 / 3, 1.0 / 3),
'hcp': (2.0 / 3, 2.0 / 3)
})
elif surf == 'hcp0001':
cell = (1.0, sqrt(0.75), 0.5 * c / a)
if orthogonal:
positions[:, 1::2, :, 0] += 0.5
positions[-2::-2, ..., :2] += (0.0, 2.0 / 3)
else:
positions[-2::-2, ..., :2] += (-1.0 / 3, 2.0 / 3)
sites.update({
'bridge': (0.5, 0),
'fcc': (1.0 / 3, 1.0 / 3),
'hcp': (2.0 / 3, 2.0 / 3)
})
elif surf == 'bcc110':
cell = (1.0, sqrt(0.5), sqrt(0.5))
if orthogonal:
positions[:, 1::2, :, 0] += 0.5
positions[-2::-2, ..., :2] += (0.0, 1.0)
else:
positions[-2::-2, ..., :2] += (-0.5, 1.0)
sites.update({
'shortbridge': (0, 0.5),
'longbridge': (0.5, 0),
'hollow': (0.375, 0.25)
})
elif surf == 'bcc111':
cell = (sqrt(2), sqrt(1.5), sqrt(3) / 6)
if orthogonal:
positions[-1::-3, 1::2, :, 0] += 0.5
positions[-2::-3, 1::2, :, 0] += 0.5
positions[-3::-3, 1::2, :, 0] -= 0.5
positions[-2::-3, ..., :2] += (0.0, 2.0 / 3)
positions[-3::-3, ..., :2] += (0.5, 1.0 / 3)
else:
positions[-2::-3, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-3::-3, ..., :2] += (1.0 / 3, 1.0 / 3)
sites.update({'hollow': (1.0 / 3, 1.0 / 3)})
surface_cell = a * np.array([(cell[0], 0), (cell[0] / 2, cell[1])])
if not orthogonal:
cell = np.array([(cell[0], 0, 0), (cell[0] / 2, cell[1], 0),
(0, 0, cell[2])])
if surface_cell is None:
surface_cell = a * np.diag(cell[:2])
if isinstance(cell, tuple):
cell = np.diag(cell)
slab.set_positions(positions.reshape((-1, 3)))
slab.set_cell([a * v * n for v, n in zip(cell, size)], scale_atoms=True)
if vacuum is not None:
slab.center(vacuum=vacuum, axis=2)
slab.adsorbate_info['cell'] = surface_cell
slab.adsorbate_info['sites'] = sites
return slab
def nanotube(n,
m,
length=1,
bond=1.42,
symbol='C',
verbose=False,
vacuum=None):
"""Create an atomic structure.
Creates a single-walled nanotube whose structure is specified using the
standardized (n, m) notation.
Parameters
----------
n : int
n in the (n, m) notation.
m : int
m in the (n, m) notation.
length : int, optional
Length (axial repetitions) of the nanotube.
bond : float, optional
Bond length between neighboring atoms.
symbol : str, optional
Chemical element to construct the nanotube from.
verbose : bool, optional
If True, will display key geometric parameters.
Returns
-------
ase.atoms.Atoms
An ASE Atoms object corresponding to the specified molecule.
Examples
--------
>>> from ase.build import nanotube
>>> atoms1 = nanotube(6, 0, length=4)
>>> atoms2 = nanotube(3, 3, length=6, bond=1.4, symbol='Si')
"""
if n < m:
m, n = n, m
sign = -1
else:
sign = 1
nk = 6000
sq3 = sqrt(3.0)
a = sq3 * bond
l2 = n * n + m * m + n * m
l = sqrt(l2)
nd = gcd(n, m)
if (n - m) % (3 * nd) == 0:
ndr = 3 * nd
else:
ndr = nd
nr = (2 * m + n) // ndr
ns = -(2 * n + m) // ndr
nn = 2 * l2 // ndr
ichk = 0
if nr == 0:
n60 = 1
else:
n60 = nr * 4
absn = abs(n60)
nnp = []
nnq = []
for i in range(-absn, absn + 1):
for j in range(-absn, absn + 1):
j2 = nr * j - ns * i
if j2 == 1:
j1 = m * i - n * j
if j1 > 0 and j1 < nn:
ichk += 1
nnp.append(i)
nnq.append(j)
if ichk == 0:
raise RuntimeError('not found p, q strange!!')
if ichk >= 2:
raise RuntimeError('more than 1 pair p, q strange!!')
nnnp = nnp[0]
nnnq = nnq[0]
if verbose:
print('the symmetry vector is', nnnp, nnnq)
lp = nnnp * nnnp + nnnq * nnnq + nnnp * nnnq
r = a * sqrt(lp)
c = a * l
t = sq3 * c / ndr
if 2 * nn > nk:
raise RuntimeError('parameter nk is too small!')
rs = c / (2.0 * np.pi)
if verbose:
print('radius=', rs, t)
q1 = np.arctan((sq3 * m) / (2 * n + m))
q2 = np.arctan((sq3 * nnnq) / (2 * nnnp + nnnq))
q3 = q1 - q2
q4 = 2.0 * np.pi / nn
q5 = bond * np.cos((np.pi / 6.0) - q1) / c * 2.0 * np.pi
h1 = abs(t) / abs(np.sin(q3))
h2 = bond * np.sin((np.pi / 6.0) - q1)
ii = 0
x, y, z = [], [], []
for i in range(nn):
x1, y1, z1 = 0, 0, 0
k = np.floor(i * abs(r) / h1)
x1 = rs * np.cos(i * q4)
y1 = rs * np.sin(i * q4)
z1 = (i * abs(r) - k * h1) * np.sin(q3)
kk2 = abs(np.floor((z1 + 0.0001) / t))
if z1 >= t - 0.0001:
z1 -= t * kk2
elif z1 < 0:
z1 += t * kk2
ii += 1
x.append(x1)
y.append(y1)
z.append(z1)
z3 = (i * abs(r) - k * h1) * np.sin(q3) - h2
ii += 1
if z3 >= 0 and z3 < t:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - k * h1) * np.sin(q3) - h2
x.append(x2)
y.append(y2)
z.append(z2)
else:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - (k + 1) * h1) * np.sin(q3) - h2
kk = abs(np.floor(z2 / t))
if z2 >= t - 0.0001:
z2 -= t * kk
elif z2 < 0:
z2 += t * kk
x.append(x2)
y.append(y2)
z.append(z2)
ntotal = 2 * nn
X = []
for i in range(ntotal):
X.append([x[i], y[i], sign * z[i]])
if length > 1:
xx = X[:]
for mnp in range(2, length + 1):
for i in range(len(xx)):
X.append(xx[i][:2] + [xx[i][2] + (mnp - 1) * t])
transvec = t
numatom = ntotal * length
diameter = rs * 2
chiralangle = np.arctan((sq3 * n) / (2 * m + n)) / np.pi * 180
cell = [[0, 0, 0], [0, 0, 0], [0, 0, length * t]]
atoms = Atoms(symbol + str(numatom),
positions=X,
cell=cell,
pbc=[False, False, True])
if vacuum:
atoms.center(vacuum, axis=(0, 1))
if verbose:
print('translation vector =', transvec)
print('diameter = ', diameter)
print('chiral angle = ', chiralangle)
return atoms
def _surface(symbol, structure, face, size, a, c, vacuum, orthogonal=True):
"""Function to build often used surfaces.
Don't call this function directly - use fcc100, fcc110, bcc111, ..."""
Z = atomic_numbers[symbol]
if a is None:
sym = reference_states[Z]['symmetry']
if sym != structure:
raise ValueError("Can't guess lattice constant for %s-%s!" %
(structure, symbol))
a = reference_states[Z]['a']
if structure == 'hcp' and c is None:
if reference_states[Z]['symmetry'] == 'hcp':
c = reference_states[Z]['c/a'] * a
else:
c = sqrt(8 / 3.0) * a
positions = np.empty((size[2], size[1], size[0], 3))
positions[..., 0] = np.arange(size[0]).reshape((1, 1, -1))
positions[..., 1] = np.arange(size[1]).reshape((1, -1, 1))
positions[..., 2] = np.arange(size[2]).reshape((-1, 1, 1))
numbers = np.ones(size[0] * size[1] * size[2], int) * Z
tags = np.empty((size[2], size[1], size[0]), int)
tags[:] = np.arange(size[2], 0, -1).reshape((-1, 1, 1))
slab = Atoms(numbers,
tags=tags.ravel(),
pbc=(True, True, False),
cell=size)
surface_cell = None
sites = {'ontop': (0, 0)}
surf = structure + face
if surf == 'fcc100':
cell = (sqrt(0.5), sqrt(0.5), 0.5)
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'bridge': (0.5, 0)})
elif surf == 'diamond100':
cell = (sqrt(0.5), sqrt(0.5), 0.5 / 2)
positions[-4::-4, ..., :2] += (0.5, 0.5)
positions[-3::-4, ..., :2] += (0.0, 0.5)
positions[-2::-4, ..., :2] += (0.0, 0.0)
positions[-1::-4, ..., :2] += (0.5, 0.0)
elif surf == 'fcc110':
cell = (1.0, sqrt(0.5), sqrt(0.125))
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'longbridge': (0.5, 0),
'shortbridge': (0, 0.5)})
elif surf == 'bcc100':
cell = (1.0, 1.0, 0.5)
positions[-2::-2, ..., :2] += 0.5
sites.update({'hollow': (0.5, 0.5), 'bridge': (0.5, 0)})
else:
if orthogonal and size[1] % 2 == 1:
raise ValueError(("Can't make orthorhombic cell with size=%r. " %
(tuple(size),)) +
'Second number in size must be even.')
if surf == 'fcc111':
cell = (sqrt(0.5), sqrt(0.375), 1 / sqrt(3))
if orthogonal:
positions[-1::-3, 1::2, :, 0] += 0.5
positions[-2::-3, 1::2, :, 0] += 0.5
positions[-3::-3, 1::2, :, 0] -= 0.5
positions[-2::-3, ..., :2] += (0.0, 2.0 / 3)
positions[-3::-3, ..., :2] += (0.5, 1.0 / 3)
else:
positions[-2::-3, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-3::-3, ..., :2] += (1.0 / 3, 1.0 / 3)
sites.update({'bridge': (0.5, 0), 'fcc': (1.0 / 3, 1.0 / 3),
'hcp': (2.0 / 3, 2.0 / 3)})
elif surf == 'diamond111':
cell = (sqrt(0.5), sqrt(0.375), 1 / sqrt(3) / 2)
assert not orthogonal
positions[-1::-6, ..., :3] += (0.0, 0.0, 0.5)
positions[-2::-6, ..., :2] += (0.0, 0.0)
positions[-3::-6, ..., :3] += (-1.0 / 3, 2.0 / 3, 0.5)
positions[-4::-6, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-5::-6, ..., :3] += (1.0 / 3, 1.0 / 3, 0.5)
positions[-6::-6, ..., :2] += (1.0 / 3, 1.0 / 3)
elif surf == 'hcp0001':
cell = (1.0, sqrt(0.75), 0.5 * c / a)
if orthogonal:
positions[:, 1::2, :, 0] += 0.5
positions[-2::-2, ..., :2] += (0.0, 2.0 / 3)
else:
positions[-2::-2, ..., :2] += (-1.0 / 3, 2.0 / 3)
sites.update({'bridge': (0.5, 0), 'fcc': (1.0 / 3, 1.0 / 3),
'hcp': (2.0 / 3, 2.0 / 3)})
elif surf == 'hcp10m10':
cell = (1.0, 0.5 * c / a, sqrt(0.75))
assert orthogonal
positions[-2::-2, ..., 0] += 0.5
positions[:, ::2, :, 2] += 2.0 / 3
elif surf == 'bcc110':
cell = (1.0, sqrt(0.5), sqrt(0.5))
if orthogonal:
positions[:, 1::2, :, 0] += 0.5
positions[-2::-2, ..., :2] += (0.0, 1.0)
else:
positions[-2::-2, ..., :2] += (-0.5, 1.0)
sites.update({'shortbridge': (0, 0.5),
'longbridge': (0.5, 0),
'hollow': (0.375, 0.25)})
elif surf == 'bcc111':
cell = (sqrt(2), sqrt(1.5), sqrt(3) / 6)
if orthogonal:
positions[-1::-3, 1::2, :, 0] += 0.5
positions[-2::-3, 1::2, :, 0] += 0.5
positions[-3::-3, 1::2, :, 0] -= 0.5
positions[-2::-3, ..., :2] += (0.0, 2.0 / 3)
positions[-3::-3, ..., :2] += (0.5, 1.0 / 3)
else:
positions[-2::-3, ..., :2] += (-1.0 / 3, 2.0 / 3)
positions[-3::-3, ..., :2] += (1.0 / 3, 1.0 / 3)
sites.update({'hollow': (1.0 / 3, 1.0 / 3)})
else:
2 / 0
surface_cell = a * np.array([(cell[0], 0),
(cell[0] / 2, cell[1])])
if not orthogonal:
cell = np.array([(cell[0], 0, 0),
(cell[0] / 2, cell[1], 0),
(0, 0, cell[2])])
if surface_cell is None:
surface_cell = a * np.diag(cell[:2])
if isinstance(cell, tuple):
cell = np.diag(cell)
slab.set_positions(positions.reshape((-1, 3)))
slab.set_cell([a * v * n for v, n in zip(cell, size)], scale_atoms=True)
if vacuum is not None:
slab.center(vacuum=vacuum, axis=2)
slab.adsorbate_info['cell'] = surface_cell
slab.adsorbate_info['sites'] = sites
return slab
import numpy as np
debug = False
use_hdf5 = True
try:
import _gpaw_hdf5
restart_file = 'Al2_gs.hdf5'
except ImportError:
restart_file = 'Al2_gs.gpw'
d = 2.563
atoms = Atoms('Al2', positions=((0, 0, 0),
(0, 0, d))
)
atoms.center(4.0)
calc = GPAW(h=0.24, eigensolver='cg', basis='dzp',
occupations=FermiDirac(width=0.01),
convergence={'eigenstates': 4.0e-5, 'density' : 1.0e-2,
'bands' : 'all'},
nbands=20)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write(restart_file, mode='all')
# Try to run parallel over eh-pairs
if size % 2 == 0:
eh_size = 2
domain_size = size // eh_size
else:
eh_size = 1
def nanotube(n, m, length=1, bond=1.42, symbol='C', verbose=False):
if n < m:
m, n = n, m
sign = -1
else:
sign = 1
nk = 6000
sq3 = sqrt(3.0)
a = sq3 * bond
l2 = n * n + m * m + n * m
l = sqrt(l2)
nd = gcd(n, m)
if (n - m) % (3 * nd) == 0:
ndr = 3 * nd
else:
ndr = nd
nr = (2 * m + n) / ndr
ns = -(2 * n + m) / ndr
nn = 2 * l2 / ndr
ichk = 0
if nr == 0:
n60 = 1
else:
n60 = nr * 4
absn = abs(n60)
nnp = []
nnq = []
for i in range(-absn, absn + 1):
for j in range(-absn, absn + 1):
j2 = nr * j - ns * i
if j2 == 1:
j1 = m * i - n * j
if j1 > 0 and j1 < nn:
ichk += 1
nnp.append(i)
nnq.append(j)
if ichk == 0:
raise RuntimeError('not found p, q strange!!')
if ichk >= 2:
raise RuntimeError('more than 1 pair p, q strange!!')
nnnp = nnp[0]
nnnq = nnq[0]
if verbose:
print 'the symmetry vector is', nnnp, nnnq
lp = nnnp * nnnp + nnnq * nnnq + nnnp * nnnq
r = a * sqrt(lp)
c = a * l
t = sq3 * c / ndr
if 2 * nn > nk:
raise RuntimeError('parameter nk is too small!')
rs = c / (2.0 * np.pi)
if verbose:
print 'radius=', rs, t
q1 = np.arctan((sq3 * m) / (2 * n + m))
q2 = np.arctan((sq3 * nnnq) / (2 * nnnp + nnnq))
q3 = q1 - q2
q4 = 2.0 * np.pi / nn
q5 = bond * np.cos((np.pi / 6.0) - q1) / c * 2.0 * np.pi
h1 = abs(t) / abs(np.sin(q3))
h2 = bond * np.sin((np.pi / 6.0) - q1)
ii = 0
x, y, z = [], [], []
for i in range(nn):
x1, y1, z1 = 0, 0, 0
k = np.floor(i * abs(r) / h1)
x1 = rs * np.cos(i * q4)
y1 = rs * np.sin(i * q4)
z1 = (i * abs(r) - k * h1) * np.sin(q3)
kk2 = abs(np.floor((z1 + 0.0001) / t))
if z1 >= t - 0.0001:
z1 -= t * kk2
elif z1 < 0:
z1 += t * kk2
ii += 1
x.append(x1)
y.append(y1)
z.append(z1)
z3 = (i * abs(r) - k * h1) * np.sin(q3) - h2
ii += 1
if z3 >= 0 and z3 < t:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - k * h1) * np.sin(q3) - h2
x.append(x2)
y.append(y2)
z.append(z2)
else:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - (k + 1) * h1) * np.sin(q3) - h2
kk = abs(np.floor(z2 / t))
if z2 >= t - 0.0001:
z2 -= t * kk
elif z2 < 0:
z2 += t * kk
x.append(x2)
y.append(y2)
z.append(z2)
ntotal = 2 * nn
X = []
for i in range(ntotal):
X.append([x[i], y[i], sign * z[i]])
if length > 1:
xx = X[:]
for mnp in range(2, length + 1):
for i in range(len(xx)):
X.append(xx[i][:2] + [xx[i][2] + (mnp - 1) * t])
TransVec = t
NumAtom = ntotal * length
Diameter = rs * 2
ChiralAngle = np.arctan((sq3 * n) / (2 * m + n)) / (np.pi * 180)
cell = [Diameter * 2, Diameter * 2, length * t]
atoms = Atoms(symbol + str(NumAtom),
positions=X,
cell=cell,
pbc=[False, False, True])
atoms.center()
if verbose:
print 'translation vector =', TransVec
print 'diameter = ', Diameter
print 'chiral angle = ', ChiralAngle
return atoms
class execution(object):
def __init__(self, executionInput, xyz=None, stateFile='state.json'):
'''
Setup a new execution
Name: input file
xyz: xyz coordinates (for future automated execution)
stateFile: state file to use for tracking of executions
TODO:
- only ground state in non-periodic cell supported NOW, more to add!
- inputs from a dict to better handle automated executions
'''
if isinstance(executionInput, str):
self.inp = self.json(executionInput)
self.inputFileName = executionInput
if isinstance(executionInput, dict):
self.inp = executionInput
self.inputFileName = 'dict' # TODO: generate meaningful name here (how?)
self.setup()
def setup(self):
'''setup'''
self.functional = self.inp.get('functional') or 'LDA'
self.runtype = self.inp.get('runtype') or 'calc'
# this actually can't be none!
_xyz = self.inp.get('xyz')
if isinstance(_xyz, str):
self.inputXYZ = _xyz
self.atoms = read(self.inputXYZ)
else:
# support reading frm a dict (TODO: other type of objects - ?)
from ase.atoms import Atoms
from ase.atom import Atom
self.atoms = \
Atoms([Atom(a[0],(a[1],a[2],a[3])) for a in _xyz])
# TODO: support multiple cell types
self.atoms.cell = (self.inp['cell']['x'], self.inp['cell']['y'],
self.inp['cell']['z'])
# Mixer setup - only "broyden" supported
self.mixer = self.inp.get('mixer')
if self.mixer is None:
self.mixer = Mixer
else:
self.mixer = BroydenMixer
# Custom ID: allow to trace parameter set using a custom id
self.custom_id = self.inp.get('custom_id')
# Periodic Boundary Conditions
self.atoms.pbc = False
# This should not be done always
self.atoms.center()
self.nbands = self.inp.get('nbands')
self.gpts = None
self.setup_gpts()
self.max_iterations = self.inp.get('maxiter') or 333
# Name: to be set by __str__ first time it is run
self.name = None
#
self.logExtension = 'txt'
self.dataExtension = 'gpw'
# Timing / statistics
self.lastElapsed = None
#
def get_optimizer(self, name='QuasiNewton'):
from importlib import import_module
name = name.lower()
_optimMap = \
{
'mdmin': 'MDMin',
'hesslbfgs': 'HessLBFGS',
'linelbfgs': 'LineLBFGS',
'fire': 'FIRE',
'lbfgs': 'LBFGS',
'lbfgsls': 'LBFGSLineSearch',
'bfgsls': 'BFGSLineSearch',
'bfgs': 'BFGS',
'quasinewton': 'QuasiNewton'
}
_class = _optimMap[name]
_m = import_module('ase.optimize')
return getattr(_m, _class)
#
def setup_gpts(self):
self.gpts = h2gpts(self.inp.get('spacing') or 0.20,
self.atoms.get_cell(),
idiv=self.inp.get('idiv') or 8)
def filename(self, force_id=None, extension='txt'):
'''to correctly support this:
stateFile support must be completed
as it isn't just add "_0" to __str__() for now
'''
base = self.__str__()
if self.custom_id is not None:
base = base + '_' + self.custom_id
if force_id is None:
_fn = base + '_0.' + extension
else:
_fn = '{}_{}.{}'.format(base, force_id, extension)
return _fn
#
@property
def xyz(self):
return self.inp['xyz']
#
@property
def spacegroup(self):
'''international ID of determined spacegroup'''
sg = spglib.get_symmetry_dataset(spglib.refine_cell(
self.atoms))['international']
return sg.replace('/', ':')
#
def __str__(self):
'''get execution name - to be used for log filename
Components:
- Number atoms
- Volume
- Spacegroup number
- Functional name
'''
if self.name is None:
self.name = '{}_{}_{}_{}'.format(
len(self.atoms), int(self.atoms.get_volume() * 100),
self.spacegroup, self.functional)
_gpaw = os.environ['GPAW']
_pwd = os.environ['PWD']
self.procname = '{} ({})'.format(self.name,
_pwd.replace(_gpaw + '/', ''))
setproctitle(self.procname)
return self.name
##
def print(self, *args, **kwargs):
'''print wrapper - initial step before logger'''
r = print(*args, *kwargs)
return r
#
def pretty(self):
'''pretty print original parameters'''
_p = pformat(self.inp)
self.print(_p)
#
def json(self, filename):
'''load parameters from json'''
with open(filename, 'rb') as f:
s = f.read()
j = json.loads(s)
return j
#
def run(self, force_id=None, runtype=None):
'''
perform execution - only calc or optim supported now
'''
_lastStart = time.time()
if runtype is None and self.runtype is 'calc':
_f = self.calc
else:
_f = self.optim
# calculate
try:
result = _f(force_id)
finally:
_lastEnd = time.time()
self.lastElapsed = _lastEnd - _lastStart
return result
#
def calc(self, force_id=None, functional=None):
'''prepare and launch execution
force_id: use this id for filename generation
'''
# Allow to override the funtional
_fnl = functional or self.functional
# generate filenames
_fn = self.filename(force_id)
_dn = self.filename(force_id, extension=self.dataExtension)
self.print('Calculation with {} log and Input: {}.'.format(
_fn, self.inputFileName))
if self.nbands is None:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
else:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
nbands=self.nbands,
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
self.atoms.set_calculator(_calc)
self.atoms.get_potential_energy()
# write out wavefunctions
_calc.write(_dn, 'all')
return _calc
#####
def optim(self, force_id=None, functional=None):
'''prepare and launch execution
force_id: use this id for filename generation
'''
_optim_name = self.inp.get('optimizer') or 'QuasiNewton'
optimizer = self.get_optimizer(_optim_name)
# Allow to override the funtional
_fnl = functional or self.functional
# generate filenames
_fn = self.filename(force_id)
_dn = self.filename(force_id, extension=self.dataExtension)
self.print('Optimization with {} log and Input: {}.'.format(
_fn, self.inputFileName))
if self.nbands is None:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
else:
_calc = GPAW(xc=_fnl,
txt=self.filename(force_id),
nbands=self.nbands,
mixer=self.mixer(),
maxiter=self.max_iterations,
gpts=self.gpts)
self.atoms.set_calculator(_calc)
self.opt = optimizer(self.atoms,
trajectory=self.__str__() + '_emt.traj')
self.opt.run(fmax=0.05)
# write out wavefunctions
_calc.write(_dn, 'all')
return _calc
def graphene_nanoribbon(n,
m,
type='zigzag',
saturated=False,
C_H=1.09,
C_C=1.42,
vacuum=2.5,
magnetic=None,
initial_mag=1.12,
sheet=False,
main_element='C',
saturate_element='H',
vacc=None):
"""Create a graphene nanoribbon.
Creates a graphene nanoribbon in the x-z plane, with the nanoribbon
running along the z axis.
Parameters:
n: The width of the nanoribbon
m: The length of the nanoribbon.
type ('zigzag'): The orientation of the ribbon. Must be either 'zigzag'
or 'armchair'.
saturated (Falsi): If true, hydrogen atoms are placed along the edge.
C_H: Carbon-hydrogen bond length. Default: 1.09 Angstrom
C_C: Carbon-carbon bond length. Default: 1.42 Angstrom.
vacuum: Amount of vacuum added to both sides. Default 2.5 Angstrom.
magnetic: Make the edges magnetic.
initial_mag: Magnitude of magnetic moment if magnetic=True.
sheet: If true, make an infinite sheet instead of a ribbon.
"""
#This function creates the coordinates for a graphene nanoribbon,
#n is width, m is length
if vacc is not None:
warnings.warn('Use vacuum=%f' % (0.5 * vacc))
vacuum = 0.5 * vacc
assert vacuum > 0
b = sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + '4',
pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_unit.positions = [[0, 0, 0], [b * 2, 0, C_C / 2.],
[b * 2, 0, 3 * C_C / 2.], [0, 0, 2 * C_C]]
zz_unit = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[3 * C_C / 2., 2 * vacuum, b * 4])
zz_unit.positions = [[0, 0, 0], [C_C / 2., 0, b * 2]]
atoms = Atoms()
tol = 1e-4
if sheet:
vacuum2 = 0.0
else:
vacuum2 = vacuum
if type == 'zigzag':
edge_index0 = np.arange(m) * 2 + 1
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2
if magnetic:
mms = np.zeros(m * n * 2)
for i in edge_index0:
mms[i] = initial_mag
for i in edge_index1:
mms[i] = -initial_mag
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
if magnetic:
atoms.set_initial_magnetic_moments(mms)
if saturated:
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 0] += C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 0] -= C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [n * 3 * C_C / 2 + 2 * vacuum2, 2 * vacuum, m * 4 * b]
elif type == 'armchair':
for i in range(n):
layer = arm_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * i
atoms += layer
atoms.cell = [b * 4 * n + 2 * vacuum2, 2 * vacuum, 3 * C_C * m]
atoms.center()
atoms.set_pbc([sheet, False, True])
return atoms
def nanotube(n, m, length=1, bond=1.42, symbol="C", verbose=False):
if n < m:
m, n = n, m
sign = -1
else:
sign = 1
nk = 6000
sq3 = sqrt(3.0)
a = sq3 * bond
l2 = n * n + m * m + n * m
l = sqrt(l2)
dt = a * l / np.pi
nd = gcd(n, m)
if (n - m) % (3 * nd) == 0:
ndr = 3 * nd
else:
ndr = nd
nr = (2 * m + n) / ndr
ns = -(2 * n + m) / ndr
nt2 = 3 * l2 / ndr / ndr
nt = np.floor(sqrt(nt2))
nn = 2 * l2 / ndr
ichk = 0
if nr == 0:
n60 = 1
else:
n60 = nr * 4
absn = abs(n60)
nnp = []
nnq = []
for i in range(-absn, absn + 1):
for j in range(-absn, absn + 1):
j2 = nr * j - ns * i
if j2 == 1:
j1 = m * i - n * j
if j1 > 0 and j1 < nn:
ichk += 1
nnp.append(i)
nnq.append(j)
if ichk == 0:
raise RuntimeError("not found p, q strange!!")
if ichk >= 2:
raise RuntimeError("more than 1 pair p, q strange!!")
nnnp = nnp[0]
nnnq = nnq[0]
if verbose:
print "the symmetry vector is", nnnp, nnnq
lp = nnnp * nnnp + nnnq * nnnq + nnnp * nnnq
r = a * sqrt(lp)
c = a * l
t = sq3 * c / ndr
if 2 * nn > nk:
raise RuntimeError("parameter nk is too small!")
rs = c / (2.0 * np.pi)
if verbose:
print "radius=", rs, t
q1 = np.arctan((sq3 * m) / (2 * n + m))
q2 = np.arctan((sq3 * nnnq) / (2 * nnnp + nnnq))
q3 = q1 - q2
q4 = 2.0 * np.pi / nn
q5 = bond * np.cos((np.pi / 6.0) - q1) / c * 2.0 * np.pi
h1 = abs(t) / abs(np.sin(q3))
h2 = bond * np.sin((np.pi / 6.0) - q1)
ii = 0
x, y, z = [], [], []
for i in range(nn):
x1, y1, z1 = 0, 0, 0
k = np.floor(i * abs(r) / h1)
x1 = rs * np.cos(i * q4)
y1 = rs * np.sin(i * q4)
z1 = (i * abs(r) - k * h1) * np.sin(q3)
kk2 = abs(np.floor((z1 + 0.0001) / t))
if z1 >= t - 0.0001:
z1 -= t * kk2
elif z1 < 0:
z1 += t * kk2
ii += 1
x.append(x1)
y.append(y1)
z.append(z1)
z3 = (i * abs(r) - k * h1) * np.sin(q3) - h2
ii += 1
if z3 >= 0 and z3 < t:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - k * h1) * np.sin(q3) - h2
x.append(x2)
y.append(y2)
z.append(z2)
else:
x2 = rs * np.cos(i * q4 + q5)
y2 = rs * np.sin(i * q4 + q5)
z2 = (i * abs(r) - (k + 1) * h1) * np.sin(q3) - h2
kk = abs(np.floor(z2 / t))
if z2 >= t - 0.0001:
z2 -= t * kk
elif z2 < 0:
z2 += t * kk
x.append(x2)
y.append(y2)
z.append(z2)
ntotal = 2 * nn
X = []
for i in range(ntotal):
X.append([x[i], y[i], sign * z[i]])
if length > 1:
xx = X[:]
for mnp in range(2, length + 1):
for i in range(len(xx)):
X.append(xx[i][:2] + [xx[i][2] + (mnp - 1) * t])
TransVec = t
NumAtom = ntotal * length
Diameter = rs * 2
ChiralAngle = np.arctan((sq3 * n) / (2 * m + n)) / (np.pi * 180)
cell = [Diameter * 2, Diameter * 2, length * t]
atoms = Atoms(symbol + str(NumAtom), positions=X, cell=cell, pbc=[False, False, True])
atoms.center()
if verbose:
print "translation vector =", TransVec
print "diameter = ", Diameter
print "chiral angle = ", ChiralAngle
return atoms
def graphene_nanoribbon(
n,
m,
type="zigzag",
saturated=False,
C_H=1.09,
C_C=1.42,
vacuum=2.5,
magnetic=None,
initial_mag=1.12,
sheet=False,
main_element="C",
saturate_element="H",
vacc=None,
):
"""Create a graphene nanoribbon.
Creates a graphene nanoribbon in the x-z plane, with the nanoribbon
running along the z axis.
Parameters:
n: The width of the nanoribbon
m: The length of the nanoribbon.
type ('zigzag'): The orientation of the ribbon. Must be either 'zigzag'
or 'armchair'.
saturated (Falsi): If true, hydrogen atoms are placed along the edge.
C_H: Carbon-hydrogen bond length. Default: 1.09 Angstrom
C_C: Carbon-carbon bond length. Default: 1.42 Angstrom.
vacuum: Amount of vacuum added to both sides. Default 2.5 Angstrom.
magnetic: Make the edges magnetic.
initial_mag: Magnitude of magnetic moment if magnetic=True.
sheet: If true, make an infinite sheet instead of a ribbon.
"""
# This function creates the coordinates for a graphene nanoribbon,
# n is width, m is length
if vacc is not None:
warnings.warn("Use vacuum=%f" % (0.5 * vacc))
vacuum = 0.5 * vacc
assert vacuum > 0
b = sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + "4", pbc=(1, 0, 1), cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_unit.positions = [[0, 0, 0], [b * 2, 0, C_C / 2.0], [b * 2, 0, 3 * C_C / 2.0], [0, 0, 2 * C_C]]
zz_unit = Atoms(main_element + "2", pbc=(1, 0, 1), cell=[3 * C_C / 2.0, 2 * vacuum, b * 4])
zz_unit.positions = [[0, 0, 0], [C_C / 2.0, 0, b * 2]]
atoms = Atoms()
tol = 1e-4
if sheet:
vacuum2 = 0.0
else:
vacuum2 = vacuum
if type == "zigzag":
edge_index0 = np.arange(m) * 2 + 1
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2
if magnetic:
mms = np.zeros(m * n * 2)
for i in edge_index0:
mms[i] = initial_mag
for i in edge_index1:
mms[i] = -initial_mag
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
if magnetic:
atoms.set_initial_magnetic_moments(mms)
if saturated:
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 0] += C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 0] -= C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [n * 3 * C_C / 2 + 2 * vacuum2, 2 * vacuum, m * 4 * b]
elif type == "armchair":
for i in range(n):
layer = arm_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * i
atoms += layer
atoms.cell = [b * 4 * n + 2 * vacuum2, 2 * vacuum, 3 * C_C * m]
atoms.center()
atoms.set_pbc([sheet, False, True])
return atoms
def graphene_nanoribbon(n, m, type='zigzag', saturated=False, C_H=1.09,
C_C=1.42, vacuum=2.5, magnetic=None, initial_mag=1.12,
sheet=False, main_element='C', saturate_element='H',
vacc=None):
"""Create a graphene nanoribbon.
Creates a graphene nanoribbon in the x-z plane, with the nanoribbon
running along the z axis.
Parameters:
n: int
The width of the nanoribbon.
m: int
The length of the nanoribbon.
type: str
The orientation of the ribbon. Must be either 'zigzag'
or 'armchair'.
saturated: bool
If true, hydrogen atoms are placed along the edge.
C_H: float
Carbon-hydrogen bond length. Default: 1.09 Angstrom.
C_C: float
Carbon-carbon bond length. Default: 1.42 Angstrom.
vacuum: float
Amount of vacuum added to both sides. Default 2.5 Angstrom.
magnetic: bool
Make the edges magnetic.
initial_mag: float
Magnitude of magnetic moment if magnetic=True.
sheet: bool
If true, make an infinite sheet instead of a ribbon.
"""
if vacc is not None:
warnings.warn('Use vacuum=%f' % (0.5 * vacc))
vacuum = 0.5 * vacc
assert vacuum > 0
b = sqrt(3) * C_C / 4
arm_unit = Atoms(main_element + '4',
pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_unit.positions = [[0, 0, 0],
[b * 2, 0, C_C / 2.],
[b * 2, 0, 3 * C_C / 2.],
[0, 0, 2 * C_C]]
zz_unit = Atoms(main_element + '2',
pbc=(1, 0, 1),
cell=[3 * C_C / 2.0, 2 * vacuum, b * 4])
zz_unit.positions = [[0, 0, 0],
[C_C / 2.0, 0, b * 2]]
atoms = Atoms()
if sheet:
vacuum2 = 0.0
else:
vacuum2 = vacuum
if type == 'zigzag':
edge_index0 = np.arange(m) * 2 + 1
edge_index1 = (n - 1) * m * 2 + np.arange(m) * 2
if magnetic:
mms = np.zeros(m * n * 2)
for i in edge_index0:
mms[i] = initial_mag
for i in edge_index1:
mms[i] = -initial_mag
for i in range(n):
layer = zz_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 3 * C_C / 2 * i
if i % 2 == 1:
layer.positions[:, 2] += 2 * b
layer[-1].position[2] -= b * 4 * m
atoms += layer
if magnetic:
atoms.set_initial_magnetic_moments(mms)
if saturated:
H_atoms0 = Atoms(saturate_element + str(m))
H_atoms0.positions = atoms[edge_index0].positions
H_atoms0.positions[:, 0] += C_H
H_atoms1 = Atoms(saturate_element + str(m))
H_atoms1.positions = atoms[edge_index1].positions
H_atoms1.positions[:, 0] -= C_H
atoms += H_atoms0 + H_atoms1
atoms.cell = [n * 3 * C_C / 2 + 2 * vacuum2, 2 * vacuum, m * 4 * b]
elif type == 'armchair':
for i in range(n):
layer = arm_unit.repeat((1, 1, m))
layer.positions[:, 0] -= 4 * b * i
atoms += layer
if saturated:
arm_right_saturation = Atoms(saturate_element + '2', pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_right_saturation.positions = [
[- sqrt(3) / 2 * C_H, 0, C_H * 0.5],
[- sqrt(3) / 2 * C_H, 0, 2 * C_C - C_H * 0.5]]
arm_left_saturation = Atoms(saturate_element + '2', pbc=(1, 0, 1),
cell=[4 * b, 2 * vacuum, 3 * C_C])
arm_left_saturation.positions = [
[b * 2 + sqrt(3) / 2 * C_H, 0, C_C / 2 - C_H * 0.5],
[b * 2 + sqrt(3) / 2 * C_H, 0, 3 * C_C / 2.0 + C_H * 0.5]]
arm_right_saturation.positions[:, 0] -= 4 * b * (n - 1)
atoms += arm_right_saturation.repeat((1, 1, m))
atoms += arm_left_saturation.repeat((1, 1, m))
atoms.cell = [b * 4 * n + 2 * vacuum2, 2 * vacuum, 3 * C_C * m]
atoms.center()
atoms.set_pbc([sheet, False, True])
return atoms
from gpaw import GPAW, FermiDirac
from gpaw.mpi import world, size, rank
from gpaw.lrtddft2 import LrTDDFT2
from gpaw.lrtddft2.lr_communicators import LrCommunicators
from gpaw.test import equal
from ase.atoms import Atoms
debug = False
restart_file = 'Al2_gs.gpw'
d = 2.563
atoms = Atoms('Al2', positions=((0, 0, 0), (0, 0, d)))
atoms.center(4.0)
calc = GPAW(h=0.24,
eigensolver='cg',
basis='dzp',
occupations=FermiDirac(width=0.01),
convergence={
'eigenstates': 4.0e-5,
'density': 1.0e-2,
'bands': 'all'
},
nbands=20)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write(restart_file, mode='all')
# Try to run parallel over eh-pairs
if size % 2 == 0:
eh_size = 2
domain_size = size // eh_size
if os.path.exists(base_dir) is not True:
os.makedirs(base_dir)
os.chdir(base_dir)
calc = Vasp(restart=None,
xc="vdw-df2",
encut=800,
kpts={
"gamma": True,
"density": 5.0
},
setups="gw",
ismear=0,
sigma=0.001,
ediff=1e-7,
algo="Accurate")
atoms = Atoms(symbols=mol.formula,
positions=mol.positions,
cell=mol.cell,
pbc=[
True,
] * 3)
atoms.cell[-1, -1] = start_guess
atoms.center(axis=2) #center along z
calc.set_atoms(atoms)
calc.initialize(atoms)
calc.clean()
calc.write_input(atoms)
# Done with the input
os.chdir(curr_dir)
# +
import numpy as np
from ase.atoms import Atoms
from ase.calculators.vasp import Vasp
from ase.calculators.emt import EMT
from ase.optimize import LBFGS
from theforce.util.flake import generate_random_cluster
from theforce.calculator.active import ActiveCalculator, kcal_mol
# random cluster generation
ngold = 20
min_dist = 2.5
positions = generate_random_cluster(ngold, min_dist)
atoms = Atoms(numbers=ngold * [79], positions=positions)
atoms.center(vacuum=5.)
atoms.pbc = True
# Ab initio calculator; for now we just use EMT instead of vasp
# abinitio = Vasp(command="mpirun -n 16 vasp_std", directory='vasp')
abinitio = EMT()
# ML calculator
active_kwargs = {
'calculator': abinitio,
'ediff': 1.0 * kcal_mol, # decrease for more accuracy but lower speed
'fdiff': 1.0 * kcal_mol, # decrease for more accuracy but lower speed
'kernel_kw': {
'cutoff': 6.,
'lmax': 3,
'nmax': 3
},
from gpaw import GPAW
from ase.atoms import Atoms
atoms = Atoms("C", positions=[[0.0, 0.0, 0.0]])
atoms.center(vacuum=4.0)
print(atoms)
calc = GPAW(txt="-", hund=True)
from ase.units import Hartree
atoms.set_calculator(calc)
Etot = atoms.get_potential_energy()
# convert from eV to Ha
print("Etot = %18.10f Ha\n" % (Etot / Hartree))