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from ase.units import Ry
from ase.io import read
from ase.calculators.siesta.parameters import Species, PAOBasisBlock
from ase.calculators.siesta.siesta import Siesta
from ase.optimize import QuasiNewton
from ase import Atoms
import numpy as np
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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