def test_h2o_xas_xes():
import ase.calculators.demon as demon
from ase import Atoms
#from ase.optimize import BFGS
import numpy as np
# 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'}
auxis = {'all': 'GEN-A2*'}
# XAS hch
input_arguments = {
'GRID': 'FINE',
'MOMODIFY': [[1, 0], [1, 0.5]],
'CHARGE': 0,
'XRAY': 'XAS'
}
calc = demon.Demon(basis=basis,
auxis=auxis,
scftype='UKS TOL=1.0E-6 CDF=1.0E-5',
guess='TB',
xc=['BLYP', 'BASIS'],
input_arguments=input_arguments)
atoms.calc = calc
# energy
print('XAS hch')
print('energy')
energy = atoms.get_potential_energy()
print(energy)
ref = -1815.44708987 # -469.604737006
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# check xas
results = calc.results
print('xray, first transition, energy')
value = results['xray']['E_trans'][0]
print(value)
ref = 539.410015646
error = np.sqrt(np.sum((value - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
print('xray, first transition, transition dipole moments')
value = results['xray']['trans_dip'][0]
print(value)
ref = np.array([1.11921906e-02, 1.61393975e-02, 1.70983631e-07])
error = np.sqrt(np.sum((value - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# XES
input_arguments = {'GRID': 'FINE', 'CHARGE': 0, 'XRAY': 'XES ALPHA=1-1'}
calc = demon.Demon(basis=basis,
auxis=auxis,
scftype='UKS TOL=1.0E-6 CDF=1.0E-5',
guess='TB',
xc=['BLYP', 'BASIS'],
input_arguments=input_arguments)
atoms.calc = calc
# energy
print('')
print('XES')
print('energy')
energy = atoms.get_potential_energy()
print(energy)
ref = -2079.6635944
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# check xes
results = calc.results
print('xray, first transition, energy')
value = results['xray']['E_trans'][0]
print(value)
ref = 486.862715888 # 539.410015646
error = np.sqrt(np.sum((value - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
print('xray, first transition, transition dipole moments')
value = results['xray']['trans_dip'][0]
print(value)
ref = np.array([6.50528073e-03, 9.37895253e-03, 6.99433480e-09])
error = np.sqrt(np.sum((value - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# and XPS
input_arguments = {
'GRID': 'FINE',
'MOMODIFY': [[1, 0], [1, 0.0]],
'CHARGE': 0,
'XRAY': 'XAS'
}
calc = demon.Demon(basis=basis,
auxis=auxis,
scftype='UKS TOL=1.0E-6 CDF=1.0E-5',
guess='TB',
xc=['BLYP', 'BASIS'],
input_arguments=input_arguments)
atoms.calc = calc
# energy
print('')
print('XPS')
print('energy')
energy = atoms.get_potential_energy()
print(energy)
ref = -1536.9295935
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
# First excited state
input_arguments = {
'GRID': 'FINE',
'MOMODIFY': [[1, 0], [1, 0.0]],
'CHARGE': -1
}
calc = demon.Demon(basis=basis,
auxis=auxis,
scftype='UKS TOL=1.0E-6 CDF=1.0E-5',
guess='TB',
xc=['BLYP', 'BASIS'],
input_arguments=input_arguments)
atoms.calc = calc
# energy
print('')
print('EXC')
print('energy')
energy = atoms.get_potential_energy()
print(energy)
ref = -1543.18092135
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)
tol = 1.0e-4
assert (error < tol)
print('tests passed')
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')
# set up deMon calculator
basis = {'all': 'aug-cc-pvdz'}
auxis = {'all': 'GEN-A2*'}
# XAS hch
input_arguments = {
'GRID': 'FINE',
'MOMODIFY': [[1, 0], [1, 0.5]],
'CHARGE': 0,
'XRAY': 'XAS'
}
calc = demon.Demon(basis=basis,
auxis=auxis,
scftype='UKS TOL=1.0E-6 CDF=1.0E-5',
guess='TB',
xc=['BLYP', 'BASIS'],
input_arguments=input_arguments)
atoms.set_calculator(calc)
# energy
print('XAS hch')
print('energy')
energy = atoms.get_potential_energy()
print(energy)
ref = -1815.44708987 #-469.604737006
error = np.sqrt(np.sum((energy - ref)**2))
print('diff from reference:')
print(error)