def run_mio_test(test=None):
database_folder = os.getenv('MIO')
if database_folder is None:
raise RuntimeError('Please use environment variable MIO to specify path to mio Slater-Koster tables.')
calc = Atomistica(
[ native.TightBinding(
database_folder = database_folder,
SolverLAPACK = dict(electronic_T=0.001),
SCC = dict(dq_crit = 1e-4,
mixing = 0.2, # 0.2
andersen_memory = 3, # 3
maximum_iterations = 100,
log = True)
),
native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0) ],
avgn = 1000
)
check_db(calc, db2, test=test)
a = molecule('H2O')
a.center(vacuum=10.0)
###
database_folder = os.getenv('MIO')
if database_folder is None:
raise RuntimeError(
'Please use environment variable MIO to specify path to mio Slater-Koster tables.'
)
tb = native.TightBinding(
database_folder=database_folder,
SolverLAPACK=dict(electronic_T=0.001),
SCC=dict(
dq_crit=1e-4,
mixing=0.2, # 0.2
andersen_memory=3, # 3
maximum_iterations=100,
log=True))
calc = Atomistica(
[tb, native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0)], avgn=1000)
a.set_calculator(calc)
print('potential energy =', a.get_potential_energy())
print('eigenvalues:')
for ev, occ in zip(tb.eigenvalues, tb.occupation):
print(ev, occ)
def run_dftb3_test(test=None, tol=0.05):
mio_database_folder = os.getenv('MIO')
if mio_database_folder is None:
raise RuntimeError(
'Please use environment variable MIO to specify path to mio Slater-Koster tables.'
)
dftb3_database_folder = os.getenv('DFTB3')
if dftb3_database_folder is None:
raise RuntimeError(
'Please use environment variable DFTB3 to specify path to 3ob Slater-Koster tables.'
)
dftb2_calc = Atomistica(
[
native.TightBinding(
database_folder=mio_database_folder,
SolverLAPACK=dict(electronic_T=0.001),
SCC=dict(
dq_crit=1e-6,
mixing=0.05, # 0.2
andersen_memory=15, # 3
maximum_iterations=100,
log=True)),
native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0)
],
avgn=1000)
dftb2_XH_calc = Atomistica(
[
native.TightBinding(
database_folder=mio_database_folder,
SolverLAPACK=dict(electronic_T=0.001),
SCC=dict(
dq_crit=1e-6,
mixing=0.05, # 0.2
andersen_memory=15, # 3
maximum_iterations=100,
log=True)),
native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0, damp_gamma=True, zeta=3.70)
],
avgn=1000)
dftb3_calc = Atomistica(
[
native.TightBinding(
database_folder=mio_database_folder,
SolverLAPACK=dict(electronic_T=0.001),
SCC=dict(
dq_crit=1e-6,
mixing=0.05, # 0.2
andersen_memory=15, # 3
maximum_iterations=100,
log=True)),
native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0,
dftb3=True,
HubbardDerivatives=dict(H=-0.1857, O=-0.1575))
],
avgn=1000)
dftb3_XH_calc = Atomistica(
[
native.TightBinding(
database_folder=mio_database_folder,
SolverLAPACK=dict(electronic_T=0.001),
SCC=dict(
dq_crit=1e-6,
mixing=0.05, # 0.2
andersen_memory=15, # 3
maximum_iterations=100,
log=True)),
native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0,
dftb3=True,
damp_gamma=True,
zeta=4.05,
HubbardDerivatives=dict(H=-0.1857, O=-0.1575))
],
avgn=1000)
dftb3_XH_3ob_calc = Atomistica(
[
native.TightBinding(
database_folder=dftb3_database_folder,
SolverLAPACK=dict(electronic_T=0.001),
SCC=dict(
dq_crit=1e-6,
mixing=0.05, # 0.2
andersen_memory=15, # 3
maximum_iterations=100,
log=True)),
native.DirectCoulomb(),
native.SlaterCharges(cutoff=10.0,
dftb3=True,
damp_gamma=True,
zeta=4.00,
HubbardDerivatives=dict(H=-0.1857, O=-0.1575))
],
avgn=1000)
if test is None:
print(
' nH2O| G3B3| DFTB2 (MIO) | DFTB2+XH (MIO) | DFTB3 (MIO) | DFTB3+XH (MIO) | DFTB3+XH (3OB) |'
)
print(
' | | me ref. | me ref. | me ref. | me ref. | me ref. |'
)
print(
' | |-----------------|-----------------|-----------------|-----------------|-----------------|'
)
for name, data in table5_data.items():
e0_DFTB2 = 0.0
e0_DFTB3 = 0.0
e0_DFTB2_XH = 0.0
e0_DFTB3_XH = 0.0
e0_DFTB3_3ob_XH = 0.0
for structure in data['reference_structures']:
if os.path.exists(structure):
a = read(structure)
else:
a = molecule(structure)
a.center(vacuum=10.0)
a.set_calculator(dftb2_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e0_DFTB2 += a.get_potential_energy()
a.set_calculator(dftb2_XH_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e0_DFTB2_XH += a.get_potential_energy()
a.set_calculator(dftb3_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e0_DFTB3 += a.get_potential_energy()
a.set_calculator(dftb3_XH_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e0_DFTB3_XH += a.get_potential_energy()
a.set_calculator(dftb3_XH_3ob_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e0_DFTB3_3ob_XH += a.get_potential_energy()
eref_G3B3 = data['G3B3']
eref_DFTB2 = data['DFTB2']
eref_DFTB2_XH = data['DFTB2+XH']
eref_DFTB3 = data['DFTB3']
eref_DFTB3_XH = data['DFTB3+XH']
eref_DFTB3_3ob_XH = data['DFTB3+XH_3ob']
a = read(data['structure'])
a.center(vacuum=10.0)
a.set_calculator(dftb2_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e_DFTB2 = a.get_potential_energy()
e_DFTB2 = (e_DFTB2 - e0_DFTB2) / (ase.units.kcal / ase.units.mol)
a.set_calculator(dftb2_XH_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e_DFTB2_XH = a.get_potential_energy()
e_DFTB2_XH = (e_DFTB2_XH - e0_DFTB2_XH) / (ase.units.kcal /
ase.units.mol)
a.set_calculator(dftb3_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e_DFTB3 = a.get_potential_energy()
e_DFTB3 = (e_DFTB3 - e0_DFTB3) / (ase.units.kcal / ase.units.mol)
a.set_calculator(dftb3_XH_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e_DFTB3_XH = a.get_potential_energy()
e_DFTB3_XH = (e_DFTB3_XH - e0_DFTB3_XH) / (ase.units.kcal /
ase.units.mol)
a.set_calculator(dftb3_XH_3ob_calc)
FIRE(a, logfile=None).run(fmax=0.001)
e_DFTB3_3ob_XH = a.get_potential_energy()
e_DFTB3_3ob_XH = (e_DFTB3_3ob_XH - e0_DFTB3_3ob_XH) / (ase.units.kcal /
ase.units.mol)
success_DFTB2 = abs(e_DFTB2 - eref_G3B3 - eref_DFTB2) < tol
success_DFTB2_XH = abs(e_DFTB2_XH - eref_G3B3 - eref_DFTB2_XH) < tol
success_DFTB3 = abs(e_DFTB3 - eref_G3B3 - eref_DFTB3) < tol
success_DFTB3_XH = abs(e_DFTB3_XH - eref_G3B3 - eref_DFTB3_XH) < tol
success_DFTB3_3ob_XH = abs(e_DFTB3_3ob_XH - eref_G3B3 -
eref_DFTB3_3ob_XH) < tol
success_str = {True: ' ', False: 'X'}
if test is None:
print(
'{0:>8}| {1:>7.3f}|{2:>7.3f} {3:>7.3f} {4}|{5:>7.3f} {6:>7.3f} {7}|{8:>7.3f} {9:>7.3f} {10}|{11:>7.3f} {12:>7.3f} {13}|{14:>7.3f} {15:>7.3f} {16}|'
.format(name, eref_G3B3, e_DFTB2 - eref_G3B3, eref_DFTB2,
success_str[success_DFTB2], e_DFTB2_XH - eref_G3B3,
eref_DFTB2_XH, success_str[success_DFTB2_XH],
e_DFTB3 - eref_G3B3, eref_DFTB3,
success_str[success_DFTB3], e_DFTB3_XH - eref_G3B3,
eref_DFTB3_XH, success_str[success_DFTB3_XH],
e_DFTB3_3ob_XH - eref_G3B3, eref_DFTB3_3ob_XH,
success_str[success_DFTB3_3ob_XH]))
else:
test.assertTrue(success_DFTB2)
test.assertTrue(success_DFTB2_XH)
test.assertTrue(success_DFTB3)
test.assertTrue(success_DFTB3_XH)
test.assertTrue(success_DFTB3_3ob_XH)