def test_socketio_espresso(factory):
name = factory.name
if name == 'abinit':
factory.require_version('9.4')
atoms = bulk('Si')
exe = factory.factory.executable
unixsocket = f'ase_test_socketio_{name}'
espresso = factory.calc(kpts=[2, 2, 2], )
template = commands[name]
command = template.format(exe=exe, unixsocket=unixsocket)
espresso.command = command
atoms.rattle(stdev=.2, seed=42)
opt = BFGS(ExpCellFilter(atoms))
with pytest.warns(UserWarning, match='Subprocess exited'):
with SocketIOCalculator(espresso, unixsocket=unixsocket) as calc:
atoms.calc = calc
for _ in opt.irun(fmax=0.05):
e = atoms.get_potential_energy()
fmax = max(np.linalg.norm(atoms.get_forces(), axis=0))
print(e, fmax)
def test_Pt_stress_cellopt(factory, pt_eam_potential_file):
params = {}
params['pair_style'] = 'eam'
params['pair_coeff'] = ['1 1 {}'.format(pt_eam_potential_file)]
# XXX Should it accept Path objects? Yes definitely for files.
with factory.calc(specorder=['Pt'], files=[str(pt_eam_potential_file)],
**params) as calc:
rng = np.random.RandomState(17)
atoms = bulk('Pt') * (2, 2, 2)
atoms.rattle(stdev=0.1)
atoms.cell += 2 * rng.rand(3, 3)
atoms.calc = calc
assert_allclose(atoms.get_stress(), calc.calculate_numerical_stress(atoms),
atol=1e-4, rtol=1e-4)
opt = BFGS(ExpCellFilter(atoms), trajectory='opt.traj')
for i, _ in enumerate(opt.irun(fmax=0.001)):
pass
cell1_ref = np.array(
[[0.16524, 3.8999, 3.92855],
[4.211015, 0.634928, 5.047811],
[4.429529, 3.293805, 0.447377]]
)
assert_allclose(np.asarray(atoms.cell), cell1_ref, atol=3e-4, rtol=3e-4)
assert_allclose(atoms.get_stress(), calc.calculate_numerical_stress(atoms),
atol=1e-4, rtol=1e-4)
assert i < 80, 'Expected 59 iterations, got many more: {}'.format(i)
def test_Pt_stress_cellopt():
import numpy as np
from numpy.testing import assert_allclose
from ase.calculators.lammpsrun import LAMMPS
from ase.build import bulk
from ase.test.eam_pot import Pt_u3
from ase.constraints import ExpCellFilter
from ase.optimize import BFGS
# (For now) reuse eam file stuff from other lammps test:
pot_fn = 'Pt_u3.eam'
f = open(pot_fn, 'w')
f.write(Pt_u3)
f.close()
params = {}
params['pair_style'] = 'eam'
params['pair_coeff'] = ['1 1 {}'.format(pot_fn)]
with LAMMPS(specorder=['Pt'], files=[pot_fn], **params) as calc:
rng = np.random.RandomState(17)
atoms = bulk('Pt') * (2, 2, 2)
atoms.rattle(stdev=0.1)
atoms.cell += 2 * rng.rand(3, 3)
atoms.calc = calc
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
opt = BFGS(ExpCellFilter(atoms), trajectory='opt.traj')
for i, _ in enumerate(opt.irun(fmax=0.001)):
pass
cell1_ref = np.array([[0.16524, 3.8999, 3.92855],
[4.211015, 0.634928, 5.047811],
[4.429529, 3.293805, 0.447377]])
assert_allclose(np.asarray(atoms.cell),
cell1_ref,
atol=3e-4,
rtol=3e-4)
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
assert i < 80, 'Expected 59 iterations, got many more: {}'.format(i)
params['pair_coeff'] = ['1 1 {}'.format(pot_fn)]
calc = LAMMPS(specorder=['Pt'], files=[pot_fn], **params)
rng = np.random.RandomState(17)
atoms = bulk('Pt') * (2, 2, 2)
atoms.rattle(stdev=0.1)
atoms.cell += 2 * rng.rand(3, 3)
atoms.calc = calc
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
opt = BFGS(ExpCellFilter(atoms), trajectory='opt.traj')
for i, _ in enumerate(opt.irun(fmax=0.05)):
pass
cell1_ref = np.array([[0.16298762, 3.89912471, 3.92825365],
[4.21007577, 0.63362427, 5.04668170],
[4.42895706, 3.29171414, 0.44623618]])
assert_allclose(np.asarray(atoms.cell), cell1_ref, atol=1e-4, rtol=1e-4)
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
assert i < 80, 'Expected 59 iterations, got many more: {}'.format(i)
