def alpha_N2(named_result='alpha_N2'):
"""
Simple cubic example
No charge transfer => Trivial to converge
"""
fname = '../' + cubic.cubic_cifs['alpha-N2'].file
crystal = cif_parser_wrapper(fname)
settings = collections.OrderedDict([('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
('ewald_real_cutoff', Set(40, 'bohr')),
('ewald_reciprocal_cutoff', Set(10)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([2, 2, 2])),
('symmetry_reduction', Set(True)),
('temperature', Set(0, 'kelvin'))])
xtb_potential = collections.OrderedDict([
('potential_type', Set('truncated')),
('smoothing_range', Set(1, 'bohr'))
])
sub_commands = collections.OrderedDict([('xtb_potential', xtb_potential)])
input_string = qcore_input.xtb_input_string(crystal,
settings=settings,
sub_commands=sub_commands,
named_result=named_result)
return input_string
def primitive_anatase(named_result='primitive_anatase'):
"""
Anatase primitive unit cell
SCC takes 26 iterations vs 11 SCF
:param named_result: named result
:return:
"""
crystal = tetragonal.tio2_anatase()
settings = collections.OrderedDict([('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
('ewald_real_cutoff', Set(40, 'bohr')),
('ewald_reciprocal_cutoff', Set(10)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([2, 2, 2])),
('symmetry_reduction', Set(False)),
('temperature', Set(0, 'kelvin'))])
xtb_potential = collections.OrderedDict([
('potential_type', Set('truncated')),
('smoothing_range', Set(1, 'bohr'))
])
sub_commands = collections.OrderedDict([('xtb_potential', xtb_potential)])
input_string = qcore_input.xtb_input_string(crystal,
settings=settings,
sub_commands=sub_commands,
named_result=named_result)
return input_string
def convention_sodium_chloride(named_result, ewald):
fname = '../' + cubic.conventional_fcc_cifs['sodium_chloride'].file
crystal = cif_parser_wrapper(fname, is_primitive_cell=False, fractional=True, bravais='cubic')
settings = collections.OrderedDict([
('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
('ewald_real_cutoff', Set(ewald['real'], 'bohr')),
('ewald_reciprocal_cutoff', Set(ewald['reciprocal'])),
('ewald_alpha', Set(ewald['alpha'])),
('monkhorst_pack', Set([4, 4, 4])),
('symmetry_reduction', Set(True)),
('temperature', Set(0, 'kelvin'))
])
input_string = qcore_input.xtb_input_string(crystal, settings, named_result=named_result)
return input_string
def magnesium_oxide():
file_name = '../' + cubic.conventional_fcc_cifs['magnesium_oxide'].file
crystal = cif_parser_wrapper(file_name,
fractional=True,
is_primitive_cell=False,
bravais='cubic')
unit = get_position_unit(crystal)
lattice_constant_factors = np.linspace(0.8, 1.2, 21, endpoint=True)
lattice_constants = cubic_lattice_constants(crystal,
lattice_constant_factors)
named_result = 'mgo_volume'
settings = collections.OrderedDict([
('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
# Ewald setting for hard-cutoff of potential at 30 bohr
('ewald_real_cutoff', Set(40, 'bohr')),
# Converged w.r.t. real-space value
('ewald_reciprocal_cutoff', Set(10)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([2, 2, 2])),
('symmetry_reduction', Set(True)),
('temperature', Set(0, 'kelvin')),
('solver', Set('SCC'))
])
total_energies = np.zeros(shape=(lattice_constant_factors.size))
for i, al in enumerate(lattice_constants):
lattice_factor = lattice_constant_factors[i]
crystal['lattice_parameters']['a'] = Set(al, unit)
input_string = qcore_input.xtb_input_string(crystal,
settings,
named_result=named_result)
output = run_qcore(input_string)
if not output:
print('No result:', lattice_factor)
else:
total_energies[i] = output[named_result]['energy']
# 4.19 ang is exp. See "Ab initio determination of the bulk properties of Mgo"
print(lattice_factor, al, output[named_result]['energy'])
return lattice_constant_factors, total_energies
def primitive_sodium_chloride():
named_result = 'primitive_nacl'
fname = '../' + cubic.fcc_cifs['sodium_chloride'].file
crystal = cif_parser_wrapper(fname, is_primitive_cell=True, fractional=True)
settings = collections.OrderedDict([
('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
('ewald_real_cutoff', Set(10, 'bohr')),
('ewald_reciprocal_cutoff', Set(1)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([4, 4, 4])),
('symmetry_reduction', Set(True)),
('temperature', Set(0, 'kelvin'))
])
input_string = qcore_input.xtb_input_string(crystal, settings, named_result=named_result)
return input_string
def primitive_potassium(named_result='primitive_potassium'):
"""
BCC Example
Notes:
Converges but with this warning
warning: solve(): system seems singular (rcond: 4.98607e-17);
attempting approx solution
13 7.217892848 -5.61e-12 5.55e-17 0.13
SCF takes ~ 35 iterations => SCC faster
symmetry reduction works
:param named_result: named result
:return:
"""
fname = '../' + cubic.bcc_cifs['potassium'].file
crystal = cif_parser_wrapper(fname)
settings = collections.OrderedDict([('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
('ewald_real_cutoff', Set(40, 'bohr')),
('ewald_reciprocal_cutoff', Set(10)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([2, 2, 2])),
('symmetry_reduction', Set(True)),
('temperature', Set(0, 'kelvin')),
('solver', Set('SCC'))])
xtb_potential = collections.OrderedDict([
('potential_type', Set('truncated')),
('smoothing_range', Set(1, 'bohr'))
])
sub_commands = collections.OrderedDict([('xtb_potential', xtb_potential)])
input_string = qcore_input.xtb_input_string(crystal,
settings=settings,
sub_commands=sub_commands,
named_result=named_result)
return input_string
def conventional_copper():
named_result = 'conventional_copper'
fname = '../' + cubic.conventional_fcc_cifs['copper'].file
crystal = cif_parser_wrapper(fname,
is_primitive_cell=False,
fractional=True,
bravais='cubic')
settings = OrderedDict([('h0_cutoff', Set(40, 'bohr')),
('overlap_cutoff', Set(40, 'bohr')),
('repulsive_cutoff', Set(40, 'bohr')),
('ewald_real_cutoff', Set(10, 'bohr')),
('ewald_reciprocal_cutoff', Set(1)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([4, 4, 4])),
('symmetry_reduction', Set(False)),
('temperature', Set(0, 'kelvin'))])
input_string = qcore_input.xtb_input_string(crystal,
settings,
named_result=named_result)
return input_string
