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# fmt: off
import numpy as np
from ase import Atoms
from ase.calculators.siesta.parameters import PAOBasisBlock, Species
from ase.calculators.siesta.siesta import Siesta
from ase.io import read
from ase.optimize import QuasiNewton
from ase.units import Ry
traj = 'bud.traj'
try:
bud = read(traj)
assert not isinstance(bud, list)
except FileNotFoundError:
bud = Atoms('CH4', np.array([
[0.000000, 0.000000, 0.100000],
[0.682793, 0.682793, 0.682793],
[-0.682793, -0.682793, 0.68279],
[-0.682793, 0.682793, -0.682793],
[0.682793, -0.682793, -0.682793]]),
cell=[10, 10, 10])
c_basis = """2 nodes 1.00
0 1 S 0.20 P 1 0.20 6.00
5.00
1.00
1 2 S 0.20 P 1 E 0.20 6.00
6.00 5.00
1.00 0.95"""
species = Species(symbol='C', basis_set=PAOBasisBlock(c_basis))
calc = Siesta(
label='ch4',
basis_set='SZ',
xc='LYP',
mesh_cutoff=300 * Ry,
species=[species],
restart='ch4.XV',
fdf_arguments={'DM.Tolerance': 1E-5,
'DM.MixingWeight': 0.15,
'DM.NumberPulay': 3,
'MaxSCFIterations': 200,
'ElectronicTemperature': (0.02585, 'eV'), # 300 K
'SaveElectrostaticPotential': True})
bud.calc = calc
dyn = QuasiNewton(bud, trajectory=traj)
dyn.run(fmax=0.02)
e = bud.get_potential_energy()
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