def main():
supported_elements = 'Ni, C, Pt, Ag, H, Al, O, N, Au, Pd, Cu'.split(', ')
formulas = [
formula for formula in g1 if np.all([
symbol in supported_elements
for symbol in molecule(formula).get_chemical_symbols()
])
]
atoms = [symbol for symbol in g2_atoms if symbol in supported_elements]
dimers = [formula for formula in formulas if len(molecule(formula)) == 2]
name1 = 'testfiles/energy'
name2 = 'testfiles/bond'
test1 = BatchTest(EMTEnergyTest(name1, vacuum=3.0))
test2 = BatchTest(EMTBondLengthTest(name2, vacuum=3.0))
print('Energy test')
print('-----------')
test1.run(formulas + atoms)
print()
print('Bond length test')
print('----------------')
test2.run(dimers)
print()
print('Atomization energies')
print('--------------------')
atomic_energies = dict(test1.collect(atoms))
molecular_energies = dict(test1.collect(formulas))
atomization_energies = {}
for formula, energy in molecular_energies.items():
system = molecule(formula)
atomic = [atomic_energies[s] for s in system.get_chemical_symbols()]
atomization_energy = energy - sum(atomic)
atomization_energies[formula] = atomization_energy
print(formula.rjust(10), '%.02f' % atomization_energy)
print()
print('Bond lengths')
print('------------')
for formula, (d_i, e_i, d0, e0, poly) in test2.collect(dimers):
system = molecule(formula)
bref = np.linalg.norm(system.positions[1] - system.positions[0])
print(formula.rjust(10), '%6.3f' % d0, ' g2ref =', '%2.3f' % bref)
def setup_system(self, formula):
"""Create an Atoms object from the given formula.
By default this will be loaded from the g2 database, setting
the cell size by means of the molecule test's vacuum parameter."""
system = molecule(formula)
system.center(vacuum=self.vacuum)
return system
def calculate_atomization_energies(self, molecular_energies,
atomic_energies):
atomic_energy_dict = dict(atomic_energies)
for formula, molecular_energy in molecular_energies:
try:
system = molecule(formula)
atomic = [
atomic_energy_dict[s]
for s in system.get_chemical_symbols()
]
atomization_energy = molecular_energy - sum(atomic)
yield formula, atomization_energy
except KeyError:
pass
def build():
p = OptionParser(usage='%prog [options] [ads@]surf [output file]',
version='%prog 0.1',
description='Example ads/surf: CO@2x2Ru0001')
p.add_option('-l',
'--layers',
type='int',
default=4,
help='Number of layers.')
p.add_option('-v', '--vacuum', type='float', default=5.0, help='Vacuum.')
p.add_option('-x',
'--crystal-structure',
help='Crystal structure.',
choices=['sc', 'fcc', 'bcc', 'hcp'])
p.add_option('-a',
'--lattice-constant',
type='float',
help='Lattice constant in Angstrom.')
p.add_option('--c-over-a', type='float', help='c/a ratio.')
p.add_option('--height',
type='float',
help='Height of adsorbate over surface.')
p.add_option('--distance',
type='float',
help='Distance between adsorbate and nearest surface atoms.')
p.add_option('--site',
help='Adsorption site.',
choices=['fcc', 'hcc', 'hollow', 'bridge'])
p.add_option('-M',
'--magnetic-moment',
type='float',
default=0.0,
help='Magnetic moment.')
p.add_option('-G', '--gui', action='store_true', help="Pop up ASE's GUI.")
opt, args = p.parse_args()
if not 1 <= len(args) <= 2:
p.error("incorrect number of arguments")
if '@' in args[0]:
ads, surf = args[0].split('@')
else:
ads = None
surf = args[0]
if surf[0].isdigit():
i1 = surf.index('x')
n = int(surf[:i1])
i2 = i1 + 1
while surf[i2].isdigit():
i2 += 1
m = int(surf[i1 + 1:i2])
surf = surf[i2:]
else:
n = 1
m = 1
if surf[-1].isdigit():
if surf[1].isdigit():
face = surf[1:]
surf = surf[0]
else:
face = surf[2:]
surf = surf[:2]
else:
face = None
Z = atomic_numbers[surf]
state = reference_states[Z]
if opt.crystal_structure:
x = opt.crystal_structure
else:
x = state['symmetry'].lower()
if opt.lattice_constant:
a = opt.lattice_constant
else:
a = estimate_lattice_constant(surf, x, opt.c_over_a)
if x == 'fcc':
if face is None:
face = '111'
slab = fcc111(surf, (n, m, opt.layers), a, opt.vacuum)
r = a / np.sqrt(2) / 2
elif x == 'bcc':
if face is None:
face = '110'
slab = bcc110(surf, (n, m, opt.layers), a, opt.vacuum)
r = a * np.sqrt(3) / 4
elif x == 'hcp':
if face is None:
face = '0001'
slab = hcp0001(surf, (n, m, opt.layers), a, a * opt.c_over_a,
opt.vacuum)
r = a / 2
else:
raise NotImplementedError
magmom = opt.magnetic_moment
if magmom is None:
magmom = {'Ni': 0.6, 'Co': 1.2, 'Fe': 2.3}.get(surf, 0.0)
slab.set_initial_magnetic_moments([magmom] * len(slab))
slab.pbc = 1
name = '%dx%d%s%s' % (n, m, surf, face)
if ads:
site = 'ontop'
if '-' in ads:
site, ads = ads.split('-')
name = site + '-' + ads + '@' + name
symbols = string2symbols(ads)
nads = len(symbols)
if nads == 1:
ads = Atoms(ads)
else:
ads = molecule(ads)
add_adsorbate(slab, ads, 0.0, site)
d = opt.distance
if d is None:
d = r + covalent_radii[ads[0].number] / 2
h = opt.height
if h is None:
R = slab.positions
y = ((R[:-nads] - R[-nads])**2).sum(1).min()**0.5
print(y)
h = (d**2 - y**2)**0.5
print(h)
else:
assert opt.distance is None
slab.positions[-nads:, 2] += h
if len(args) == 2:
write(args[1], slab)
elif not opt.gui:
write(name + '.traj', slab)
if opt.gui:
view(slab)
import os
from ase_ext.data.molecules import molecule
from ase_ext.io.bader import attach_charges
fname = 'ACF.dat'
f = open(fname, 'w')
print("""
# X Y Z CHARGE MIN DIST
----------------------------------------------------------------
1 7.0865 8.5038 9.0672 9.0852 1.3250
2 7.0865 9.9461 7.9403 0.4574 0.3159
3 7.0865 7.0615 7.9403 0.4574 0.3159
----------------------------------------------------------------
NUMBER OF ELECTRONS: 9.99999
""",
file=f)
f.close()
atoms = molecule('H2O')
atoms.set_cell([7.5, 9, 9])
atoms.center()
attach_charges(atoms)
attach_charges(atoms, fname)
os.remove(fname)
for atom in atoms:
print('Atom', atom.symbol, 'Bader charge', atom.charge)