def main():
assert installed()
# simple test calculation of CO molecule
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,
ldipol=True)
co.set_calculator(calc)
energy = co.get_potential_energy()
forces = co.get_forces()
dipole_moment = co.get_dipole_moment()
# check that parsing of vasprun.xml file works
conf = read('vasprun.xml')
assert conf.calc.parameters['kpoints_generation']
assert conf.calc.parameters['sigma'] == 1.0
assert conf.calc.parameters['ialgo'] == 68
assert energy - conf.get_potential_energy() == 0.0
assert np.allclose(conf.get_forces(), forces)
assert np.allclose(conf.get_dipole_moment(), dipole_moment, atol=1e-6)
# Cleanup
calc.clean()
def main():
if sys.version_info < (2, 7):
raise NotAvailable('read_xml requires Python version 2.7 or greater')
assert installed()
# simple test calculation of CO molecule
d = 1.14
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)],
pbc=True)
co.center(vacuum=5.)
calc = Vasp(xc='LDA',
prec='Low',
algo='Fast',
ismear=0,
sigma=1.,
nbands=12,
istart=0,
nelm=3,
lwave=False,
lcharg=False,
ldipol=True)
co.set_calculator(calc)
energy = co.get_potential_energy()
forces = co.get_forces()
dipole_moment = co.get_dipole_moment()
# check that parsing of vasprun.xml file works
conf = read('vasprun.xml')
assert conf.calc.parameters['kpoints_generation']
assert conf.calc.parameters['sigma'] == 1.0
assert conf.calc.parameters['ialgo'] == 68
assert energy - conf.get_potential_energy() == 0.0
# Check some arrays
assert np.allclose(conf.get_forces(), forces)
assert np.allclose(conf.get_dipole_moment(), dipole_moment, atol=1e-6)
# Check k-point-dependent properties
assert len(conf.calc.get_eigenvalues(spin=0)) >= 12
assert conf.calc.get_occupation_numbers()[2] == 2
assert conf.calc.get_eigenvalues(spin=1) is None
kpt = conf.calc.get_kpt(0)
assert kpt.weight == 1.
# Perform a spin-polarised calculation
co.calc.set(ispin=2, ibrion=-1)
co.get_potential_energy()
conf = read('vasprun.xml')
assert len(conf.calc.get_eigenvalues(spin=1)) >= 12
assert conf.calc.get_occupation_numbers(spin=1)[0] == 1.
# Cleanup
calc.clean()
def test_h2o():
import ase.calculators.demon as demon
from ase import Atoms
from ase.optimize import BFGS
import numpy as np
tol = 1.0e-6
# d = 0.9575
d = 0.9775
# t = np.pi / 180 * 104.51
t = np.pi / 180 * 110.51
atoms = Atoms('H2O',
positions=[(d, 0, 0), (d * np.cos(t), d * np.sin(t), 0),
(0, 0, 0)])
# set up deMon calculator
basis = {'all': 'aug-cc-pvdz', 'O': 'RECP6|SD'}
auxis = {'all': 'GEN-A2*'}
input_arguments = {'GRID': 'FINE'}
calc = demon.Demon(basis=basis,
auxis=auxis,
scftype='RKS TOL=1.0E-6 CDF=1.0E-5',
guess='TB',
xc=['BLYP', 'BASIS'],
input_arguments=input_arguments)
atoms.calc = calc
# energy
energy = atoms.get_potential_energy()
ref = -469.604737006
print('energy')
print(energy)
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-6
assert (error < tol)
# dipole
dipole = atoms.get_dipole_moment()
ref = np.array([0.19228183, 0.27726241, 0.0])
error = np.sqrt(np.sum((dipole - ref)**2))
print('dipole')
print(dipole)
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# numerical forces
forces_num = calc.calculate_numerical_forces(atoms, d=0.001)
ref = np.array([[-1.26056746e-01, 4.10007559e-01, 2.85719551e-04],
[4.28062314e-01, 2.56059142e-02, 2.17691110e-04],
[-3.02019173e-01, -4.35613473e-01, -5.03410632e-04]])
error = np.sqrt(np.sum((forces_num - ref)**2))
print('forces_num')
print(forces_num)
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# analytical forces
forces_an = atoms.get_forces()
ref = np.array([[-1.26446863e-01, 4.09628186e-01, -0.00000000e+00],
[4.27934442e-01, 2.50425467e-02, -5.14220671e-05],
[-2.99225008e-01, -4.31533987e-01, -5.14220671e-05]])
error = np.sqrt(np.sum((forces_an - ref)**2))
print('forces_an')
print(forces_an)
print('diff from reference:')
print(error)
tol = 1.0e-3
assert (error < tol)
# optimize geometry
dyn = BFGS(atoms)
dyn.run(fmax=0.01)
positions = atoms.get_positions()
ref = np.array([[9.61364579e-01, 2.81689367e-02, -1.58730770e-06],
[-3.10444398e-01, 9.10289261e-01, -5.66399075e-06],
[-1.56957763e-02, -2.26044053e-02, -2.34155615e-06]])
error = np.sqrt(np.sum((positions - ref)**2))
print('positions')
print(positions)
print('diff from reference:')
print(error)
tol = 1.0e-3
assert (error < tol)
print('tests passed')
atoms.set_calculator(calc)
# energy
energy = atoms.get_potential_energy()
ref = -469.604737006
print('energy')
print(energy)
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
assert(error < tol)
# dipole
dipole = atoms.get_dipole_moment()
ref = np.array([0.19228183, 0.27726241, 0.0])
error = np.sqrt(np.sum((dipole - ref)**2))
print('dipole')
print(dipole)
print('diff from reference:')
print(error)
assert(error < tol)
# numerical forces
forces_num = calc.calculate_numerical_forces(atoms, d=0.001)
ref = np.array([[-1.26056746e-01, 4.10007559e-01, 2.85719551e-04],
atoms.set_calculator(calc)
# energy
energy = atoms.get_potential_energy()
ref = -469.604737006
print('energy')
print(energy)
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
assert (error < tol)
# dipole
dipole = atoms.get_dipole_moment()
ref = np.array([0.19228183, 0.27726241, 0.0])
error = np.sqrt(np.sum((dipole - ref)**2))
print('dipole')
print(dipole)
print('diff from reference:')
print(error)
assert (error < tol)
# numerical forces
forces_num = calc.calculate_numerical_forces(atoms, d=0.001)
ref = np.array([[-1.26056746e-01, 4.10007559e-01, 2.85719551e-04],
[4.28062314e-01, 2.56059142e-02, 2.17691110e-04],
# Initial structural parameters
d = 0.974
theta = 104.4 * np.pi/180.
# Positions of the H2O atoms (in that order)
pos = [[d*np.cos(theta/2.), d*np.sin(theta/2.), 0.],
[d*np.cos(theta/2.), -d*np.sin(theta/2.), 0.],
[0., 0., 0.]]
# Let us instantiate an Atoms object and add some vacuum around the molecule
atoms = Atoms("H2O", positions=pos, pbc=False)
atoms.center(vacuum=4.)
# Let's view the molecule
view(atoms)
# We create a GPAW calculator object and assign it to atoms
if print_to_screen:
calc = GPAW(xc="PBE")
else:
calc = GPAW(xc="PBE", txt="gpaw.out")
atoms.set_calculator(calc)
# Let us run a GPAW calculation to get the cohesive energy of this configuration
e_water = atoms.get_potential_energy()
dip_water = atoms.get_dipole_moment()
print("Dipole of a H2O monomer: (%f, %f, %f) electrons/Angstrom" % \
(dip_water[0], dip_water[1], dip_water[2]))
bond_lengths = [1.1, 1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18]
energies = []
dipoles = []
for d in bond_lengths: # possible bond lengths
co = Atoms('CO', [(0, 0, 0), (0, 0, d)])
calc = Aims(label='molecules/co-{0}'.format(d), # output dir
xc='PBE',
output=['dipole', 'mulliken'],
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-3)
co.set_calculator(calc)
try:
e = co.get_potential_energy()
dip = co.get_dipole_moment()
print(dip)
energies.append(e)
dipoles.append(dip[2]) # only in z direction
print('d = {0:1.2f} ang'.format(d))
print('energy = {0:1.3f} eV'.format(e))
print('dipole = {0:1.3f} eV'.format(dip[2]))
print('forces = (eV/ang)\n {0}'.format(co.get_forces()))
print('') # blank line
except:
energies.append(None)
dipoles.append(None)
print('bond lengths {0:1.3f} fhi-aims fails'.format(d))
pass
if None not in energies:
import matplotlib.pyplot as plt
