def convention_sodium_chloride(supercell_coefficients, named_result):
fname = '../' + cubic.conventional_fcc_cifs['sodium_chloride'].file
crystal = cif_parser_wrapper(
fname,
is_primitive_cell=False,
fractional=True,
bravais=get_supercell_bravais(supercell_coefficients),
supercell_coefficients=supercell_coefficients)
options = 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')),
('potential_type',
Set(xtb_potential_str(potential_type)))])
assertions = {
PotentialType.TRUNCATED:
OrderedDict([("n_iter", SetAssert(0)), ("energy", SetAssert(0, 0))]),
PotentialType.FULL:
OrderedDict([("n_iter", SetAssert(0, 0)), ("energy", SetAssert(0, 0))])
}
return xtb_input_string_cleaner(crystal=crystal,
options=options,
assertions=assertions[potential_type],
named_result=named_result)
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 sio2_zeolite_gamma_point(named_result='SiO2') -> str:
"""
BCC structure
:param named_result: named result string
:return: Input for testing translational invariance
"""
fname = '../' + cubic.bcc_cifs['sio2'].file
crystal = cif_parser_wrapper(fname)
assert crystal['bravais'] == 'bcc', "crystal not simple cubic"
arbitrary_shifts = [0., 0.1, 0.2, 0.24, 0.25]
options = OrderedDict([
('h0_cutoff', Set(60, 'bohr')),
('overlap_cutoff', Set(60, 'bohr')),
('repulsive_cutoff', Set(60, 'bohr')),
('dispersion_cutoff', Set(60, 'bohr')),
('ewald_real_cutoff', Set(60, 'bohr')),
('ewald_reciprocal_cutoff', Set(1)),
('ewald_alpha', Set(0.5)),
('potential_type', Set(xtb_potential_str(potential_type))),
])
assertions = {
PotentialType.TRUNCATED: OrderedDict([("n_iter", SetAssert(14)),
("energy", SetAssert(-69.074350228, 5.e-6))]),
PotentialType.FULL: OrderedDict([("n_iter", SetAssert(0, 0)),
("energy", SetAssert(0, 0))])
}
comments = ['! Fractional shift of '] * len(arbitrary_shifts)
return translation_string(crystal, options, assertions[potential_type],
arbitrary_shifts, named_result,
comments=[x + str(arbitrary_shifts[i]) for i, x in enumerate(comments)])
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_silicon(named_result='primitive_cell_si') -> str:
"""
Primitive silicon
Note, this will likely give slightly difference results to using
cubic.silicon, which (probably) has a slightly different lattice
parameter
:param named_result: named_result
:return: input string
"""
fname = '../' + cubic.conventional_fcc_cifs['silicon'].file
crystal = cif_parser_wrapper(fname,
is_primitive_cell=True,
fractional=True,
bravais='fcc')
assert crystal['n_atoms'] == 2, "Expect 2-atom basis for primitive si"
options = 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([2, 2, 2])),
('potential_type',
Set(xtb_potential_str(potential_type)))])
assertions = {
PotentialType.TRUNCATED:
OrderedDict([("n_iter", SetAssert(0)), ("energy", SetAssert(0,
1.e-6))]),
PotentialType.FULL:
OrderedDict([("n_iter", SetAssert(0)), ("energy", SetAssert(0, 0))])
}
return qcore_input.xtb_input_string_cleaner(
crystal=crystal,
options=options,
assertions=assertions[potential_type],
named_result=named_result)
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_silicon(named_result='conventional_cell_si'):
fname = '../' + cubic.conventional_fcc_cifs['silicon'].file
crystal = cif_parser_wrapper(fname,
is_primitive_cell=False,
fractional=True,
bravais='cubic')
assert crystal['n_atoms'] == 8, "Expect 8-atom basis for primitive si"
options = 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([2, 2, 2])),
('potential_type',
Set(xtb_potential_str(potential_type)))])
return qcore_input.xtb_input_string_cleaner(crystal=crystal,
options=options,
named_result=named_result)
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
def sio2_zeolite(named_result='SiO2') -> str:
"""
BCC structure
:param named_result: named result string
:return: Input for testing translational invariance
"""
fname = '../' + cubic.bcc_cifs['sio2'].file
crystal = cif_parser_wrapper(fname)
assert crystal['bravais'] == 'bcc', "crystal not simple cubic"
arbitrary_shift = 0.1
options = 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(1)),
('ewald_alpha', Set(0.5)),
('monkhorst_pack', Set([2, 2, 2])),
('potential_type', Set(xtb_potential_str(potential_type))),
])
assertions = {
PotentialType.TRUNCATED:
OrderedDict([("n_iter", SetAssert(14)),
("energy", SetAssert(-69.074163659, 1.e-6))]),
PotentialType.FULL:
OrderedDict([("n_iter", SetAssert(0, 0)), ("energy", SetAssert(0, 0))])
}
comments = '! Fractional shift of 0.1'
return translation_string(crystal,
options,
assertions[potential_type],
arbitrary_shift,
named_result,
comments=comments)
def nickel_triphosphide(named_result='nickel_triphosphide') -> str:
"""
BCC
Won't converge with these settings
:param named_result: named result string
:return: Input for testing symmetry reduction of MP grid
"""
fname = '../' + cubic.bcc_cifs[named_result].file
crystal = cif_parser_wrapper(fname)
assert crystal['bravais'] == 'bcc', "crystal not bcc"
options = 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([2, 2, 2])),
('symmetry_reduction', Set(True)),
('temperature', Set(0, 'kelvin')),
('potential_type',
Set(xtb_potential_str(potential_type)))])
assertions = {
PotentialType.TRUNCATED:
OrderedDict([("n_iter", SetAssert(0)), ("energy", SetAssert(0,
1.e-6))]),
PotentialType.FULL:
OrderedDict([("n_iter", SetAssert(0)), ("energy", SetAssert(0, 0))])
}
return xtb_symmetry_test_string(
crystal=crystal,
options=options,
assertions=assertions[PotentialType.TRUNCATED],
named_result=named_result)