def test_Ar_minimize_multistep(factory, ar_nc, params):
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
with factory.calc(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
F1_numer = calc.calculate_numerical_forces(ar_nc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(), F1_numer, atol=1e-4, rtol=1e-4)
params['minimize'] = '1.0e-15 1.0e-6 2000 4000' # add minimize
calc.parameters = params
# set_atoms=True to read final coordinates after minimization
calc.run(set_atoms=True)
# get final coordinates after minimization
ar_nc.set_positions(calc.atoms.positions)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815887032201,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
def test_Ar_minimize_multistep():
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
with LAMMPS(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
F1_numer = calc.calculate_numerical_forces(ar_nc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(), F1_numer, atol=1e-4, rtol=1e-4)
params['minimize'] = '1.0e-15 1.0e-6 2000 4000' # add minimize
calc.parameters = params
# set_atoms=True to read final coordinates after minimization
calc.run(set_atoms=True)
# get final coordinates after minimization
ar_nc.set_positions(calc.atoms.positions)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815887032201,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
def test_Ar_minimize():
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
from ase.optimize import LBFGS
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
with LAMMPS(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815886953914,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
from ase.optimize import LBFGS
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
calc = LAMMPS(specorder=['Ar'], **params)
ar_nc.set_calculator(calc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
def ar_nc():
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
return ar_nc