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)
def test_lennard_jones():
atoms = Icosahedron("Ar", noshells=2, latticeconstant=3)
atoms.set_calculator(ase_LJ())
ase_forces = atoms.get_forces()
ase_energy = atoms.get_potential_energy()
coords = atoms.positions.flatten()
geom = Geometry(atoms.get_chemical_symbols(), coords / BOHR2ANG)
geom.set_calculator(LennardJones())
pysis_energy = geom.energy
assert pysis_energy == pytest.approx(ase_energy)
pysis_forces = geom.forces / BOHR2ANG
np.testing.assert_allclose(pysis_forces, ase_forces.flatten(), atol=1e-15)
def test_fake_ase():
# pysisyphus
pysis_calc = LennardJones()
ase_calc = FakeASE(pysis_calc)
# ASE atoms, pysisyphus calculator
atoms_pysis = Icosahedron("Ar", noshells=2, latticeconstant=3)
# ASE atoms, ASE calculator
atoms_ase = atoms_pysis.copy()
atoms_pysis.set_calculator(ase_calc)
atoms_ase.set_calculator(ase_LJ())
pysis_forces = atoms_pysis.get_forces()
ase_forces = atoms_ase.get_forces()
np.testing.assert_allclose(pysis_forces, ase_forces, atol=1e-15)
#!/usr/bin/env python
from ase import Atoms, Atom
from ase.calculators.aims import Aims, AimsCube
from ase.cluster.icosahedron import Icosahedron
from ase.io import write
import numpy as np
import os
np.set_printoptions(precision=3, suppress=True)
atoms = Icosahedron('Pt', noshells=2)
calc = Aims(label='cluster/pt-isosahedron-2-relax',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
sc_accuracy_rho=1e-4,
sc_accuracy_eev=1e-2,
sc_accuracy_etot=1e-5,
sc_iter_limit=100,
relax_geometry = 'bfgs 1.e-2')
atoms.set_calculator(calc)
print('energy = {0} eV'.format(atoms.get_potential_energy()))
print('Forces')
print('=======')
print(atoms.get_forces())
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)
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)
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['mass'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
calc = LAMMPS(specorder=['Ar'], parameters=params)
ar_nc.set_calculator(calc)
E = ar_nc.get_potential_energy()
F = ar_nc.get_forces()
assert abs(E - -0.47) < 1E-2
assert abs(norm(F) - 0.0574) < 1E-4
assert abs(norm(ar_nc.positions) - 23.588) < 1E-3
params['minimize'] = '1.0e-15 1.0e-6 2000 4000' # add minimize
calc.params = 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)
E = ar_nc.get_potential_energy()
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)
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(), calc.calculate_numerical_forces(ar_nc),
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)