def test_write_and_read_trivial_trajectories(self):
"""Ensure write and read trajectory files with single structures."""
# An open-shell single point calculation.
data = ccopen("data/ORCA/basicORCA4.2/dvb_sp_un.out").parse()
cclib2ase.write_trajectory("dvb_sp_un.traj", data)
trajdata = cclib2ase.read_trajectory("dvb_sp_un.traj")
assert np.allclose(trajdata.atomcoords, data.atomcoords)
assert np.allclose(trajdata.scfenergies, data.scfenergies)
# No grads here.
assert np.allclose(trajdata.atomnos, data.atomnos)
assert np.allclose(trajdata.atommasses, data.atommasses)
assert np.allclose(trajdata.natom, data.natom)
assert np.allclose(trajdata.charge, data.charge)
assert np.allclose(trajdata.mult, data.mult)
assert np.allclose(trajdata.moments, data.moments)
# No temperature here.
# No freeenergy here.
assert np.allclose(trajdata.atomcharges["mulliken"],
data.atomcharges["mulliken"])
assert np.allclose(trajdata.atomspins["mulliken"],
data.atomspins["mulliken"])
# A closed-shell single structure frequency calculation.
data = ccopen("data/ORCA/basicORCA4.2/dvb_ir.out").parse()
cclib2ase.write_trajectory("dvb_ir.traj", data)
trajdata = cclib2ase.read_trajectory("dvb_ir.traj")
assert np.allclose(trajdata.atomcoords, data.atomcoords)
assert np.allclose(trajdata.scfenergies, data.scfenergies)
# No grads here.
assert np.allclose(trajdata.atomnos, data.atomnos)
assert np.allclose(trajdata.atommasses, data.atommasses)
assert np.allclose(trajdata.natom, data.natom)
assert np.allclose(trajdata.charge, data.charge, atol=1e-5)
assert np.allclose(trajdata.mult, data.mult)
assert np.allclose(trajdata.moments, data.moments)
# No temperature here.
# No freeenergy here.
assert np.allclose(trajdata.atomcharges["mulliken"],
data.atomcharges["mulliken"])
def test_read_ase_native_trajectory(self):
"""Ensure we can read ASE native trajectory files."""
trajdata = cclib2ase.read_trajectory("test/bridge/h2o.traj")
assert np.allclose(len(trajdata.atomcoords), 7)
assert np.allclose( # initial structure
trajdata.atomcoords[0], [[0, 0, 0], [1, 0, 0], [0, 1, 0]])
assert np.allclose(trajdata.scfenergies[0], -324.61300863874163)
assert np.allclose( # final structure
trajdata.atomcoords[-1],
[
[0.06884815, 0.06884815, -0.00000000],
[1.00852115, -0.07736930, 0.00000000],
[-0.07736930, 1.00852115, 0.00000000],
],
)
assert np.allclose(trajdata.scfenergies[-1], -324.9073873170798)
assert np.allclose(trajdata.atomnos, [8, 1, 1])
assert np.allclose(trajdata.atommasses, [15.999, 1.008, 1.008])
assert np.allclose(trajdata.natom, 3)
assert np.allclose(trajdata.charge, 0)
assert np.allclose(trajdata.mult, 1)
def test_write_and_read_opt_trajectories(self):
"""Ensure write and read trajectory files with optimizations."""
# Geometry optimization.
data = ccopen("data/ORCA/basicORCA4.2/dvb_gopt.out").parse()
cclib2ase.write_trajectory("dvb_gopt.traj", data)
trajdata = cclib2ase.read_trajectory("dvb_gopt.traj")
assert np.allclose(trajdata.atomcoords, data.atomcoords)
assert np.allclose(trajdata.scfenergies, data.scfenergies)
assert np.allclose(trajdata.grads, data.grads)
assert np.allclose(trajdata.atomnos, data.atomnos)
assert np.allclose(trajdata.atommasses, data.atommasses)
assert np.allclose(trajdata.natom, data.natom)
assert np.allclose(trajdata.charge, data.charge)
assert np.allclose(trajdata.mult, data.mult)
assert np.allclose(trajdata.moments, data.moments, atol=1e-5)
# No temperature here.
# No freeenergy here.
assert np.allclose(trajdata.atomcharges["mulliken"],
data.atomcharges["mulliken"])