def test_qchem_calculator():
import numpy as np
from ase.build import molecule
from ase.calculators.qchem import QChem
from ase.optimize import LBFGS
mol = molecule('C2H6')
calc = QChem(label='calc/ethane', method='B3LYP', basis='6-31+G*')
mol.set_calculator(calc)
# Check energy and forces
np.testing.assert_allclose(mol.get_potential_energy(),
-2172.379183703419,
atol=10.)
np.testing.assert_allclose(mol.get_forces(),
np.array(
[[0., 0.00240141, 0.04992568],
[-0., -0.00240141, -0.04992568],
[-0., 0.11626015, 0.07267481],
[-0.10132204, -0.05804009, 0.07538475],
[0.10132204, -0.05804009, 0.07538475],
[-0., -0.11626015, -0.07267481],
[-0.10132204, 0.05804009, -0.07538475],
[0.10132204, 0.05804009, -0.07538475]]),
atol=0.05)
opt = LBFGS(mol)
opt.run()
assert opt.converged()
def SurfaceEnergy(images, natoms, calc, fmax=0.01, debug=False):
"""Calculate the surface energy from a list of slab images.
Parameters
----------
images: List of slab images which the calculation is based on. The x and
y dimensions of the images unit cell must be conserved.
natoms: Number of atoms in a atomic layer in the slabs.
calc: Calculator object that can be attached to the images.
"""
ucell = images[0].get_cell()
layers = np.zeros(len(images))
energies = np.zeros(len(images))
if debug:
print "Layers Energy LBFGS steps"
for i, atoms in enumerate(images):
cell = atoms.get_cell()
if (ucell[0] != cell[0]).any() or (ucell[1] != cell[1]).any():
raise ValueError(
"The x and y dimensions of the unit cell must be conserved.")
atoms.set_calculator(calc)
dyn = LBFGS(atoms, logfile=None, trajectory=None)
dyn.run(fmax=fmax, steps=1000)
assert dyn.converged(), "LBFGS not converged in 100 steps!"
layers[i] = len(atoms) / natoms
energies[i] = atoms.get_potential_energy()
if debug:
print "%4i%12.3f%10i" % (layers[i], energies[i],
dyn.get_number_of_steps())
p = polyfit(layers.reshape((-1, 1)), energies, 1)
surface_energy = p.c[0] / (2 * natoms)
assert surface_energy > 0.0
return surface_energy
def SurfaceEnergy(images, natoms, calc, fmax=0.01, debug=False):
"""Calculate the surface energy from a list of slab images.
Parameters
----------
images: List of slab images which the calculation is based on. The x and
y dimensions of the images unit cell must be conserved.
natoms: Number of atoms in a atomic layer in the slabs.
calc: Calculator object that can be attached to the images.
"""
ucell = images[0].get_cell()
layers = np.zeros(len(images))
energies = np.zeros(len(images))
if debug:
print "Layers Energy LBFGS steps"
for i, atoms in enumerate(images):
cell = atoms.get_cell()
if (ucell[0] != cell[0]).any() or (ucell[1] != cell[1]).any():
raise ValueError("The x and y dimensions of the unit cell must be conserved.")
atoms.set_calculator(calc)
dyn = LBFGS(atoms, logfile=None, trajectory=None)
dyn.run(fmax=fmax, steps=1000)
assert dyn.converged(), "LBFGS not converged in 100 steps!"
layers[i] = len(atoms) / natoms
energies[i] = atoms.get_potential_energy()
if debug:
print "%4i%12.3f%10i" % (layers[i], energies[i], dyn.get_number_of_steps())
p = polyfit(layers.reshape((-1,1)), energies, 1)
surface_energy = p.c[0] / (2 * natoms)
assert surface_energy > 0.0
return surface_energy
import numpy as np
from ase.build import molecule
from ase.calculators.qchem import QChem
from ase.optimize import LBFGS
mol = molecule('C2H6')
calc = QChem(label='calc/ethane', method='B3LYP', basis='6-31+G*')
mol.set_calculator(calc)
# Check energy and forces
np.testing.assert_allclose(mol.get_potential_energy(),
-2172.379183703419,
atol=10.)
np.testing.assert_allclose(mol.get_forces(),
np.array([[0., 0.00240141, 0.04992568],
[-0., -0.00240141, -0.04992568],
[-0., 0.11626015, 0.07267481],
[-0.10132204, -0.05804009, 0.07538475],
[0.10132204, -0.05804009, 0.07538475],
[-0., -0.11626015, -0.07267481],
[-0.10132204, 0.05804009, -0.07538475],
[0.10132204, 0.05804009, -0.07538475]]),
atol=0.05)
opt = LBFGS(mol)
opt.run()
assert opt.converged()
