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# Note:
# Try to avoid module level import statements here to reduce
# import time during CLI execution
import sys
import numpy as np
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):
from ase.db import connect
from ase.io import read, write
from ase.visualize import view
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):
from ase.atoms import Atoms
from ase.build import molecule
from ase.data import (
atomic_numbers,
covalent_radii,
ground_state_magnetic_moments,
)
from ase.symbols import string2symbols
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):
from ase.build import bulk
L = args.lattice_constant.replace(',', ' ').split()
d = {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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