def test_vib():
import os
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from ase.thermochemistry import IdealGasThermo
n2 = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
QuasiNewton(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
freqs = vib.get_frequencies()
print(freqs)
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(n=None, nimages=20)
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=n2,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, atoms in vib.iterdisplace(inplace=True):
assert d[name] == atoms
vib = Vibrations(n2)
vib.run()
assert vib.combine() == 13
assert (freqs == vib.get_frequencies()).all()
vib = Vibrations(n2)
assert vib.split() == 1
assert (freqs == vib.get_frequencies()).all()
assert vib.combine() == 13
# Read the data from other working directory
dirname = os.path.basename(os.getcwd())
os.chdir('..') # Change working directory
vib = Vibrations(n2, name=os.path.join(dirname, 'vib'))
assert (freqs == vib.get_frequencies()).all()
assert vib.clean() == 1
def test_vibrations_methods(self, testdir, random_dimer):
vib = Vibrations(random_dimer)
vib.run()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=vib.atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
with open(self.logfile, 'w') as fd:
vib.summary(log=fd)
with open(self.logfile, 'rt') as fd:
log_txt = fd.read()
assert log_txt == '\n'.join(
VibrationsData._tabulate_from_energies(vib_energies)) + '\n'
last_mode = vib.get_mode(-1)
scale = 0.5
assert_array_almost_equal(
vib.show_as_force(-1, scale=scale, show=False).get_forces(),
last_mode * 3 * len(vib.atoms) * scale)
vib.write_mode(n=3, nimages=5)
for i in range(3):
assert not Path('vib.{}.traj'.format(i)).is_file()
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
random_dimer.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
random_dimer.get_all_distances())
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, image in vib.iterdisplace(inplace=True):
assert d[name] == random_dimer
from ase.vibrations import Vibrations
from ase.thermochemistry import IdealGasThermo
n2 = Atoms('N2',
positions=[(0, 0, 0), (0, 0, 1.1)],
calculator=EMT())
QuasiNewton(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
print(vib.get_frequencies())
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(n=None, nimages=20)
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=n2, symmetrynumber=2, spin=0)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, atoms in vib.iterdisplace(inplace=True):
assert d[name] == atoms
def test_vibrations(self, testdir, n2_emt, n2_optimized):
atoms = n2_emt
vib = Vibrations(atoms)
vib.run()
freqs = vib.get_frequencies()
vib.write_mode(n=None, nimages=5)
vib.write_jmol()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
vib.summary(log=self.logfile)
with open(self.logfile, 'rt') as f:
log_txt = f.read()
assert log_txt == vibrations_n2_log
mode1 = vib.get_mode(-1)
assert_array_almost_equal(mode1,
[[0., 0., -0.188935], [0., 0., 0.188935]])
assert_array_almost_equal(
vib.show_as_force(-1, show=False).get_forces(),
[[0., 0., -2.26722e-1], [0., 0., 2.26722e-1]])
for i in range(3):
assert not os.path.isfile('vib.{}.traj'.format(i))
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
atoms.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
atoms.get_all_distances())
with open('vib.xyz', 'rt') as f:
jmol_txt = f.read()
assert jmol_txt == jmol_txt_ref
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, image in vib.iterdisplace(inplace=True):
assert d[name] == atoms
atoms2 = n2_emt
vib2 = Vibrations(atoms2)
vib2.run()
assert_array_almost_equal(freqs, vib.get_frequencies())
# write/read the data from another working directory
atoms3 = n2_optimized.copy() # No calculator needed!
workdir = os.path.abspath(os.path.curdir)
try:
os.mkdir('run_from_here')
os.chdir('run_from_here')
vib = Vibrations(atoms3, name=os.path.join(os.pardir, 'vib'))
assert_array_almost_equal(freqs, vib.get_frequencies())
assert vib.clean() == 13
finally:
os.chdir(workdir)
if os.path.isdir('run_from_here'):
os.rmdir('run_from_here')