def test_axis_layout():
system = Atoms('H')
a = 3.
system.cell = (a, a, a)
system.pbc = 1
for axis in range(3):
system.center()
system.positions[0, axis] = 0.0
calc = Octopus(**getkwargs(label='ink-%s' % 'xyz'[axis],
Output='density + potential + wfs'))
system.set_calculator(calc)
system.get_potential_energy()
rho = calc.get_pseudo_density(pad=False)
#for dim in rho.shape:
# assert dim % 2 == 1, rho.shape
maxpoint = np.unravel_index(rho.argmax(), rho.shape)
print('axis=%d: %s/%s' % (axis, maxpoint, rho.shape))
expected_max = [dim // 2 for dim in rho.shape]
expected_max[axis] = 0
assert maxpoint == tuple(expected_max), '%s vs %s' % (maxpoint,
expected_max)
errs = check_interface(calc)
for err in errs:
if err.code == 'not implemented':
continue
if err.methname == 'get_dipole_moment':
assert isinstance(err.error, OctopusIOError)
else:
raise AssertionError(err.error)
def test_axis_layout():
system = Atoms('H')
a = 3.
system.cell = (a, a, a)
system.pbc = 1
for axis in range(3):
system.center()
system.positions[0, axis] = 0.0
calc = Octopus(**getkwargs(label='ink-%s' % 'xyz'[axis],
Output='density + potential + wfs'))
system.set_calculator(calc)
system.get_potential_energy()
rho = calc.get_pseudo_density(pad=False)
#for dim in rho.shape:
# assert dim % 2 == 1, rho.shape
maxpoint = np.unravel_index(rho.argmax(), rho.shape)
print('axis=%d: %s/%s' % (axis, maxpoint, rho.shape))
expected_max = [dim // 2 for dim in rho.shape]
expected_max[axis] = 0
assert maxpoint == tuple(expected_max), '%s vs %s' % (maxpoint,
expected_max)
errs = check_interface(calc)
for err in errs:
if err.code == 'not implemented':
continue
if err.methname == 'get_dipole_moment':
assert isinstance(err.error, OctopusIOError)
else:
raise AssertionError(err.error)
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
from __future__ import print_function
from ase.calculators.octopus import Octopus
from ase.calculators.interfacechecker import check_interface
from ase.build import molecule
system = molecule('H2O')
system.center(vacuum=2.0)
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)
from ase.calculators.octopus import Octopus
from ase.build import bulk
system = bulk('Si', orthorhombic=True)
calc = Octopus(label='silicon',
Spacing=0.25,
KPointsGrid=[[4, 4, 4]],
KPointsUseSymmetries=True,
Output='dos + density + potential',
OutputHow='xcrysden',
DosGamma=0.1)
system.set_calculator(calc)
system.get_potential_energy()
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)
errs = check_interface(calc1)
# view(system)
def calc(self, **kwargs):
from ase.calculators.octopus import Octopus
command = f'{self.executable} > stdout.log'
return Octopus(command=command, **kwargs)
from ase.calculators.octopus import Octopus
from ase.build import molecule
from ase.optimize import QuasiNewton
# Ethanol molecule with somewhat randomized initial positions:
system = molecule('CH3CH2OH')
system.rattle(stdev=0.1, seed=42)
system.center(vacuum=3.0)
calc = Octopus(label='ethanol', Spacing=0.25, BoxShape='parallelepiped')
system.set_calculator(calc)
opt = QuasiNewton(system, logfile='opt.log', trajectory='opt.traj')
opt.run(fmax=0.05)
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
from __future__ import print_function
from ase.calculators.octopus import Octopus
from ase.calculators.interfacechecker import check_interface
from ase.build import molecule
system = molecule('H2O')
system.center(vacuum=2.0)
label = 'ink'
calc0 = Octopus(label=label,
FromScratch=True,
stdout="'stdout.txt'",
stderr="'stderr.txt'",
Spacing=0.15,
Output='density + wfs + potential',
OutputHow='cube + xcrysden',
_autofix_outputformats=True)
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)
def test_integrals(pbc=True):
system = molecule('H2O')
a = 2.6006 # So the spacing does not divide exactly
system.cell = (a, a, a)
system.center()
system.pbc = pbc
spacing = 0.2
calc = Octopus(**getkwargs(label='ink-integrals-pbc-%s' % pbc,
# Restart destroys normalization of output
# ...........sometimes.
RestartWrite=False,
Output='density + potential + wfs',
OutputHow='cube + xcrysden',
ExtraStates=0,
Spacing=spacing,
SCFCalculateDipole=True))
system.set_calculator(calc)
E = system.get_potential_energy()
if pbc:
Eref = -496.98663392
else:
Eref = -451.05348602
err = E - Eref
print('Energy=%f :: err=%e' % (E, err))
assert err < 1e-7
rho = calc.get_pseudo_density(pad=False)
v = calc.get_effective_potential(pad=False)
if pbc: # spacing adjusted but cell constant
dv = system.get_volume() / rho.size
else: # cell adjusted but spacing constant
dv = spacing**3
ne = rho.sum() * dv
err = abs(ne - 8.0)
print('nelectrons: %f, err: %e' % (ne, err))
assert err < 1e-12
for n in range(calc.get_number_of_bands()):
psi = calc.get_pseudo_wave_function(band=n, pad=True)
norm = (np.abs(psi)**2).sum() * dv
err = abs(norm - 1)
print('norm=%f :: err=%e' % (norm, err))
assert err < 1e-12
eps = calc.get_eigenvalues()
f = calc.get_occupation_numbers()
E_band = (eps * f).sum()
E_nv = (rho * v).sum() * dv
if pbc:
E_nl = -155.16024733 # Reference value from output.
E_kin_ref = 377.899824
else:
E_nl = -151.28372313 # Ref from output.
E_kin_ref = 396.66270596
E_kin_ours = E_band - E_nv - E_nl
err = abs(E_kin_ours - E_kin_ref)
print('E_band=%f :: E_nv=%f :: E_kin_ours=%f :: err=%e'
% (E_band, E_nv, E_kin_ours, err))
assert err < 5e-4 # Orig err: 6.8e-05 (pbc=False) and 3.47e-07 (pbc=True)
errs = check_interface(calc)
for err in errs:
if err.code == 'not implemented':
continue
else:
raise AssertionError(err.error)
def test_integrals(pbc=True):
system = molecule('H2O')
a = 2.6006 # So the spacing does not divide exactly
system.cell = (a, a, a)
system.center()
system.pbc = pbc
spacing = 0.2
calc = Octopus(**getkwargs(
label='ink-integrals-pbc-%s' % pbc,
# Restart destroys normalization of output
# ...........sometimes.
RestartWrite=False,
Output='density + potential + wfs',
OutputFormat='cube + xcrysden',
ExtraStates=0,
Spacing=spacing,
SCFCalculateDipole=True))
system.set_calculator(calc)
E = system.get_potential_energy()
if pbc:
Eref = -496.98663392
else:
Eref = -451.05348602
err = abs(E - Eref)
#print('Energy=%f :: err=%e' % (E, err))
# The reference has changed between version 5 and trunk,
# so we will not check the total energy.
# Checks of individual contributions that are physical and therefore
# trustworthy will have to be sufficient.
#assert err < 5e-3
rho = calc.get_pseudo_density(pad=False)
v = calc.get_effective_potential(pad=False)
if pbc: # spacing adjusted but cell constant
dv = system.get_volume() / rho.size
else: # cell adjusted but spacing constant
dv = spacing**3
ne = rho.sum() * dv
err = abs(ne - 8.0)
print('nelectrons: %f, err: %e' % (ne, err))
assert err < 1e-12
for n in range(calc.get_number_of_bands()):
psi = calc.get_pseudo_wave_function(band=n, pad=True)
norm = (np.abs(psi)**2).sum() * dv
err = abs(norm - 1)
print('norm=%f :: err=%e' % (norm, err))
assert err < 1e-12
eps = calc.get_eigenvalues()
f = calc.get_occupation_numbers()
E_band = (eps * f).sum()
E_nv = (rho * v).sum() * dv
if pbc:
E_nl = -155.16024733 # Reference value from output.
E_kin_ref = 377.899824
else:
E_nl = -151.28372313 # Ref from output.
E_kin_ref = 396.66270596
E_kin_ours = E_band - E_nv - E_nl
err = abs(E_kin_ours - E_kin_ref)
print('E_band=%f :: E_nv=%f :: E_kin_ours=%f :: err=%e' %
(E_band, E_nv, E_kin_ours, err))
assert err < 5e-3 # Orig err: 6.8e-05 (pbc=False) and 3.47e-07 (pbc=True)
errs = check_interface(calc)
for err in errs:
if err.code == 'not implemented':
continue
else:
raise AssertionError(err.error)