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import os
import numpy as np
from ase import Atom
from ase.build import bulk
from ase.calculators.checkpoint import Checkpoint, CheckpointCalculator
from ase.calculators.lj import LennardJones
from ase.lattice.cubic import Diamond
def op1(a, m):
a[1].position += m * np.array([0.1, 0.2, 0.3])
return a
def op2(a, m):
a += Atom('C', m * np.array([0.2, 0.3, 0.1]))
return a, a.positions[0]
def test_sqlite():
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
assert a == op1a
a, ra = CP(op2)(a, 2.0)
assert a == op2a
assert(np.abs(ra - op2ra).max() < 1e-5)
def rattle_calc(atoms, calc):
try:
os.remove('checkpoints.db')
except OSError:
pass
orig_atoms = atoms.copy()
# first do a couple of calculations
np.random.seed(0)
atoms.rattle()
cp_calc_1 = CheckpointCalculator(calc)
atoms.set_calculator(cp_calc_1)
e11 = atoms.get_potential_energy()
f11 = atoms.get_forces()
atoms.rattle()
e12 = atoms.get_potential_energy()
f12 = atoms.get_forces()
# then re-read them from checkpoint file
atoms = orig_atoms
np.random.seed(0)
atoms.rattle()
cp_calc_2 = CheckpointCalculator(calc)
atoms.set_calculator(cp_calc_2)
e21 = atoms.get_potential_energy()
f21 = atoms.get_forces()
atoms.rattle()
e22 = atoms.get_potential_energy()
f22 = atoms.get_forces()
assert e11 == e21
assert e12 == e22
assert(np.abs(f11 - f21).max() < 1e-5)
assert(np.abs(f12 - f22).max() < 1e-5)
def test_new_style_interface():
calc = LennardJones()
atoms = bulk('Cu')
rattle_calc(atoms, calc)
test_sqlite()
test_new_style_interface()
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