def calculate(name, system, **kwargs):
print('Calculate', name, system)
label = 'ink-%s' % name
kwargs0 = dict(stdout="'stdout.txt'",
FromScratch=True,
RestartWrite=False,
command='mpirun -np 4 octopus')
kwargs.update(**kwargs0)
calc = Octopus(label=label, **kwargs)
system.calc = calc
E = system.get_potential_energy()
eig = calc.get_eigenvalues()
check_interface(calc)
restartcalc = Octopus(label)
check_interface(restartcalc)
# Check reconstruction of Atoms object
new_atoms = restartcalc.get_atoms()
print('new')
print(new_atoms.positions)
calc2 = Octopus(label='ink-restart-%s' % name, **kwargs)
new_atoms.calc = calc2
E2 = new_atoms.get_potential_energy()
#print('energy', E, E2)
eig2 = calc2.get_eigenvalues()
eig_err = np.abs(eig - eig2).max()
e_err = abs(E - E2)
print('Restart E err', e_err)
print('Restart eig err', eig_err)
assert e_err < 5e-5
assert eig_err < 5e-5
return calc
def test_restart_octopus():
from ase.calculators.octopus import Octopus
from ase.calculators.interfacechecker import check_interface
from ase.build import molecule
system = molecule('H2')
system.center(vacuum=2.0)
directory = 'ink'
calc0 = Octopus(directory=directory,
check_keywords=False,
FromScratch=True,
stdout="'stdout.txt'",
stderr="'stderr.txt'",
Spacing='0.25 * Angstrom',
OutputFormat='cube + xcrysden')
system.set_calculator(calc0)
system.get_potential_energy()
# Must make one test with well-defined cell and one without.
calc1 = Octopus(directory)
system = calc1.get_atoms()
E = system.get_potential_energy()
print('energy', E)
check_interface(calc1)
# view(system)
atoms = Octopus.read_atoms(directory)
check_interface(atoms.calc)
changes = calc1.check_state(atoms)
print('changes', changes)
assert len(changes) == 0
label = 'ink'
calc0 = Octopus(label=label,
FromScratch=True,
stdout="'stdout.txt'",
stderr="'stderr.txt'",
Spacing='0.15 * Angstrom',
Output='density + wfs + potential',
OutputFormat='cube + xcrysden')
system.set_calculator(calc0)
system.get_potential_energy()
# Must make one test with well-defined cell and one without.
calc1 = Octopus(label)
system = calc1.get_atoms()
E = system.get_potential_energy()
print('energy', E)
errs = check_interface(calc1)
# view(system)
atoms = Octopus.read_atoms(label)
errs = check_interface(atoms.calc)
changes = calc1.check_state(atoms)
print('changes', changes)
assert len(changes) == 0
label = 'ink'
calc0 = Octopus(label=label,
FromScratch=True,
stdout="'stdout.txt'",
stderr="'stderr.txt'",
Spacing=0.15,
Output='density + wfs + potential',
OutputHow='cube + xcrysden')
system.set_calculator(calc0)
system.get_potential_energy()
# Must make one test with well-defined cell and one without.
calc1 = Octopus(label)
system = calc1.get_atoms()
E = system.get_potential_energy()
print('energy', E)
errs = check_interface(calc1)
#view(system)
atoms = Octopus.read_atoms(label)
errs = check_interface(atoms.calc)
changes = calc1.check_state(atoms)
print('changes', changes)
assert len(changes) == 0
