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import sys
import numpy as np
from ase.db import connect
from ase.build import bulk
from ase.io import read, write
from ase.visualize import view
from ase.build import molecule
from ase.atoms import Atoms
from ase.symbols import string2symbols
from ase.data import ground_state_magnetic_moments
from ase.data import atomic_numbers, covalent_radii
class CLICommand:
"""Build an atom, molecule or bulk structure.
Atom:
ase build <chemical symbol> ...
Molecule:
ase build <formula> ...
where <formula> must be one of the formulas known to ASE
(see here: https://wiki.fysik.dtu.dk/ase/ase/build/build.html#molecules).
Bulk:
ase build -x <crystal structure> <formula> ...
Examples:
ase build Li # lithium atom
ase build Li -M 1 # ... with a magnetic moment of 1
ase build Li -M 1 -V 3.5 # ... in a 7x7x7 Ang cell
ase build H2O # water molecule
ase build -x fcc Cu -a 3.6 # FCC copper
"""
@staticmethod
def add_arguments(parser):
add = parser.add_argument
add('name', metavar='formula/input-file',
help='Chemical formula or input filename.')
add('output', nargs='?', help='Output file.')
add('-M', '--magnetic-moment',
metavar='M1,M2,...',
help='Magnetic moments. '
'Use "-M 1" or "-M 2.3,-2.3"')
add('--modify', metavar='...',
help='Modify atoms with Python statement. '
'Example: --modify="atoms.positions[-1,2]+=0.1"')
add('-V', '--vacuum', type=float,
help='Amount of vacuum to add around isolated atoms '
'(in Angstrom)')
add('-v', '--vacuum0', type=float,
help='Deprecated. Use -V or --vacuum instead')
add('--unit-cell', metavar='CELL',
help='Unit cell in Angstrom. Examples: "10.0" or "9,10,11"')
add('--bond-length', type=float, metavar='LENGTH',
help='Bond length of dimer in Angstrom')
add('-x', '--crystal-structure',
help='Crystal structure',
choices=['sc', 'fcc', 'bcc', 'hcp', 'diamond',
'zincblende', 'rocksalt', 'cesiumchloride',
'fluorite', 'wurtzite'])
add('-a', '--lattice-constant', default='', metavar='LENGTH',
help='Lattice constant or comma-separated lattice constantes in '
'Angstrom')
add('--orthorhombic', action='store_true',
help='Use orthorhombic unit cell')
add('--cubic', action='store_true',
help='Use cubic unit cell')
add('-r', '--repeat',
help='Repeat unit cell. Use "-r 2" or "-r 2,3,1"')
add('-g', '--gui', action='store_true',
help='open ase gui')
add('--periodic', action='store_true',
help='make structure fully periodic')
@staticmethod
def run(args, parser):
if args.vacuum0:
parser.error('Please use -V or --vacuum instead!')
if '.' in args.name:
# Read from file:
atoms = read(args.name)
elif args.crystal_structure:
atoms = build_bulk(args)
else:
atoms = build_molecule(args)
if args.magnetic_moment:
magmoms = np.array(
[float(m) for m in args.magnetic_moment.split(',')])
atoms.set_initial_magnetic_moments(
np.tile(magmoms, len(atoms) // len(magmoms)))
if args.modify:
exec(args.modify, {'atoms': atoms})
if args.repeat is not None:
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
atoms = atoms.repeat([int(c) for c in r])
if args.gui:
view(atoms)
if args.output:
write(args.output, atoms)
elif sys.stdout.isatty():
write(args.name + '.json', atoms)
else:
con = connect(sys.stdout, type='json')
con.write(atoms, name=args.name)
def build_molecule(args):
try:
# Known molecule or atom?
atoms = molecule(args.name)
except (NotImplementedError, KeyError):
symbols = string2symbols(args.name)
if len(symbols) == 1:
Z = atomic_numbers[symbols[0]]
magmom = ground_state_magnetic_moments[Z]
atoms = Atoms(args.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(args.name, positions=[(0, 0, 0),
(b, 0, 0)])
else:
raise ValueError('Unknown molecule: ' + args.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:
if args.vacuum:
atoms.center(vacuum=args.vacuum)
else:
atoms.center(about=[0, 0, 0])
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()
atoms.pbc = args.periodic
return atoms
def build_bulk(args):
L = args.lattice_constant.replace(',', ' ').split()
d = dict([(key, float(x)) for key, x in zip('ac', L)])
atoms = bulk(args.name, crystalstructure=args.crystal_structure,
a=d.get('a'), c=d.get('c'),
orthorhombic=args.orthorhombic, cubic=args.cubic)
M, X = {'Fe': (2.3, 'bcc'),
'Co': (1.2, 'hcp'),
'Ni': (0.6, 'fcc')}.get(args.name, (None, None))
if M is not None and args.crystal_structure == X:
atoms.set_initial_magnetic_moments([M] * len(atoms))
return atoms
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