def test_vasp_co():
"""
Run some VASP tests to ensure that the VASP calculator works. This
is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test.vasp import installed
assert installed()
from ase import Atoms
from ase.io import write
from ase.calculators.vasp import Vasp
import numpy as np
def array_almost_equal(a1, a2, tol=np.finfo(type(1.0)).eps):
"""Replacement for old numpy.testing.utils.array_almost_equal."""
return (np.abs(a1 - a2) < tol).all()
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)], pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='PBE',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
co.calc = calc
en = co.get_potential_energy()
write('vasp_co.traj', co)
assert abs(en + 14.918933) < 5e-3
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
# Define the band structure calculation
calc_band = Vasp(system = "Band structure",
encut = 500.00,
gga = "PS",
kpts=kpts,
nsw = 0,
ismear = 0,
sigma = 0.01,
reciprocal = True)
zns.set_calculator(calc_band)
print "Band Calc"
bands = zns.get_potential_energy()
# Get the band energies across the Brillouin zone
e_kn = np.array([calc_band.get_eigenvalues(k) for k in range(len(kpts))])
# Get Fermi energy
ef = calc_band.get_fermi_level()
nbands = calc_band.get_number_of_bands()
# Plotting time
e_kn -= ef
emin = e_kn.min() - 1.0
emax = e_kn[:, nbands-1].max() + 1.0
# Plot the energy Vs k-point for each band
nelect = calc_band.get_number_of_electrons()
for n in range(nbands):
# Choose colour based on valence or conduction
for n in range(nbands):
if n < nelect/2:
algo = 'Fast',
ismear= 0,
sigma = 1.,
istart = 0,
lwave = False,
lcharg = False)
co.set_calculator(calc)
en = co.get_potential_energy()
assert abs(en + 14.918933) < 1e-4
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
algo='Fast',
ismear=0,
sigma=1.,
istart=0,
lwave=False,
lcharg=False)
co.set_calculator(calc)
en = co.get_potential_energy()
assert abs(en + 14.918933) < 1e-4
# Secondly, check that restart from the previously created VASP output works
calc2 = Vasp(restart=True)
co2 = calc2.get_atoms()
# Need tolerance of 1e-14 because VASP itself changes coordinates
# slightly between reading POSCAR and writing CONTCAR even if no ionic
# steps are made.
assert array_almost_equal(co.positions, co2.positions, 1e-14)
assert en - co2.get_potential_energy() == 0.
assert array_almost_equal(calc.get_stress(co), calc2.get_stress(co2))
assert array_almost_equal(calc.get_forces(co), calc2.get_forces(co2))
assert array_almost_equal(calc.get_eigenvalues(), calc2.get_eigenvalues())
assert calc.get_number_of_bands() == calc2.get_number_of_bands()
assert calc.get_xc_functional() == calc2.get_xc_functional()
# Cleanup
calc.clean()
# Define the band structure calculation
calc_band = Vasp(system="Band structure",
encut=500.00,
gga="PS",
kpts=kpts,
nsw=0,
ismear=0,
sigma=0.01,
reciprocal=True)
zns.set_calculator(calc_band)
print "Band Calc"
bands = zns.get_potential_energy()
# Get the band energies across the Brillouin zone
e_kn = np.array([calc_band.get_eigenvalues(k) for k in range(len(kpts))])
# Get Fermi energy
ef = calc_band.get_fermi_level()
nbands = calc_band.get_number_of_bands()
# Plotting time
e_kn -= ef
emin = e_kn.min() - 1.0
emax = e_kn[:, nbands - 1].max() + 1.0
# Plot the energy Vs k-point for each band
nelect = calc_band.get_number_of_electrons()
for n in range(nbands):
# Choose colour based on valence or conduction
for n in range(nbands):
if n < nelect / 2:
