def test_water():
from ase.calculators.gaussian import Gaussian
from ase.atoms import Atoms
from ase.optimize.lbfgs import LBFGS
from ase.io import read
# First test to make sure Gaussian works
calc = Gaussian(xc='pbe', chk='water.chk', label='water')
calc.clean()
water = Atoms('OHH',
positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0)],
calculator=calc)
opt = LBFGS(water)
opt.run(fmax=0.05)
forces = water.get_forces()
energy = water.get_potential_energy()
positions = water.get_positions()
# Then test the IO routines
water2 = read('water.log')
forces2 = water2.get_forces()
energy2 = water2.get_potential_energy()
positions2 = water2.get_positions()
# Compare distances since positions are different in standard orientation.
dist = water.get_all_distances()
dist2 = read('water.log', index=-1).get_all_distances()
assert abs(energy - energy2) < 1e-7
assert abs(forces - forces2).max() < 1e-9
assert abs(positions - positions2).max() < 1e-6
assert abs(dist - dist2).max() < 1e-6
from ase.calculators.gaussian import Gaussian
from ase.atoms import Atoms
from ase.optimize.lbfgs import LBFGS
# First test to make sure Gaussian works
calc = Gaussian(method='pbepbe',
basis='sto-3g',
force='force',
nproc=1,
chk='water.chk',
label='water')
calc.clean()
water = Atoms('OHH',
positions=[(0, 0, 0), (1, 0, 0), (0, 1, 0)],
calculator=calc)
opt = LBFGS(water)
opt.run(fmax=0.05)
forces = water.get_forces()
energy = water.get_potential_energy()
positions = water.get_positions()
# Then test the IO routines
from ase.io import read
water2 = read('water.log')
forces2 = water2.get_forces()
energy2 = water2.get_potential_energy()
positions2 = water2.get_positions()
#compare distances since positions are different in standard orientation
from ase.test import NotAvailable
from ase.calculators.gaussian import Gaussian
if Gaussian().get_command() is None:
raise NotAvailable('Gaussian required')
from ase.atoms import Atoms
from ase.optimize.lbfgs import LBFGS
# First test to make sure Gaussian works
calc = Gaussian(method='pbepbe', basis='sto-3g', force='force',
nproc=1, chk='water.chk', label='water')
calc.clean()
water = Atoms('OHH',
positions=[(0., 0. ,0. ), (1. ,0. ,0. ), (0. ,1. ,0. )],
calculator=calc)
opt = LBFGS(water)
opt.run(fmax=0.05)
forces = water.get_forces()
energy = water.get_potential_energy()
positions = water.get_positions()
# Then test the IO routines
from ase.io import read
water2 = read('water/water.log')
forces2 = water2.get_forces()
energy2 = water2.get_potential_energy()