def tio2_rutile() -> dict:
"""
TiO2 Rutile.
Notes
Space group P42/mnm (136)
Direct band gap: 1.781 eV
Ref: https://materialsproject.org/materials/mp-2657/
"""
positions = [[0.000000, 0.000000,
0.000000], [0.500000, 0.500000, 0.500000],
[0.695526, 0.695526,
0.000000], [0.304474, 0.304474, 0.000000],
[0.195526, 0.804474, 0.500000],
[0.804474, 0.195526, 0.500000]]
species = ['Ti', 'Ti', 'O', 'O', 'O', 'O']
bravais = 'tetragonal'
space_group = 136
lattice_parameters = {
'a': Set(4.6068, 'angstrom'),
'c': Set(2.9916, 'angstrom')
}
data = {
'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('', space_group),
'n_atoms': len(species)
}
return data
def tio2_anatase() -> dict:
"""
TiO2 Anatase. Space group: I4_1/amd (141)
Notes
Indirect band gap: 2.062 eV
Ref: https://materialsproject.org/materials/mp-390/#
SPGLib confirms that this is the primitive cell and is space group 141,
however, it looks body-centred cubic rather than body-centred tetragonal
from visual inspection of the lattice vectors and parameters.
"""
positions = [[0.500000, 0.500000,
0.000000], [0.250000, 0.750000, 0.500000],
[0.456413, 0.956413,
0.500000], [0.706413, 0.706413, 0.000000],
[0.043587, 0.543587, 0.500000],
[0.293587, 0.293587, 0.000000]]
species = ['Ti', 'Ti', 'O', 'O', 'O', 'O']
bravais = 'body_centred_tetragonal'
space_group = 141
lattice_parameters = {
'a': Set(5.55734663, 'angstrom'),
'c': Set(5.55734663, 'angstrom')
}
data = {
'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('', space_group),
'n_atoms': len(species)
}
return data
def boron_nitride():
"""
hexagonal boron nitride.
Notes
Space group: P63/mmc [194]
Primitive lattice vectors and atomic basis
Indirect and gap: 4.482 eV
https://materialsproject.org/materials/mp-984/
"""
positions = [[1 / 3, 2 / 3, 1 / 4], [2 / 3, 1 / 4, 3 / 4],
[1 / 3, 2 / 3, 3 / 4], [2 / 3, 1 / 3, 1 / 4]]
species = ['B', 'B', 'N', 'N']
bravais = 'hexagonal'
space_group = 194
lattice_parameters = {
'a': Set(2.51242804, 'angstrom'),
'c': Set(7.70726501, 'angstrom')
}
data = {
'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('', space_group),
'bravais': bravais,
'n_atoms': 4
}
return data
def xtb_symmetry_test_string(crystal: Optional[dict] = None,
sub_commands: Optional[dict] = None,
options: Optional[dict] = None,
assertions: Optional[dict] = None,
named_result: Optional[str] = None,
comments='') -> str:
#keys = [key for key in options.keys()]
options['symmetry_reduction'] = Set(False)
input_no_symmetry = qcore_input.xtb_input_string_cleaner(
crystal=crystal,
options=options,
assertions=assertions,
named_result=named_result + "_no_symmetry",
comments=comments)
options['symmetry_reduction'] = Set(True)
input_symmetry = qcore_input.xtb_input_string_cleaner(
crystal=crystal,
options=options,
assertions=assertions,
named_result=named_result + "_no_symmetry",
comments=comments)
return input_no_symmetry + input_symmetry
def boron_nitride_hex(named_result='boron_nitride') -> str:
"""
Hexagonal
:param named_result: named result string
:return: Input for testing symmetry reduction of MP grid
"""
crystal = hexagonal.boron_nitride()
assert crystal['bravais'] == 'hexagonal', "crystal not hexagonal"
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)
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 calcium_titanate():
"""
calcium titanate
Notes
Ref: https://materialsproject.org/materials/mp-4019/
Space group: Pnma [62]
"""
positions = [[0.991521, 0.044799,
0.750000], [0.491521, 0.455201, 0.250000],
[0.508479, 0.544799,
0.750000], [0.008479, 0.955201, 0.250000],
[0.500000, 0.000000,
0.500000], [0.000000, 0.500000, 0.500000],
[0.000000, 0.500000,
0.000000], [0.500000, 0.000000, 0.000000],
[0.921935, 0.520580,
0.250000], [0.421935, 0.979420, 0.750000],
[0.578065, 0.020580,
0.250000], [0.078065, 0.479420, 0.750000],
[0.707456, 0.291917,
0.959281], [0.207456, 0.208083, 0.040719],
[0.792544, 0.791917,
0.540719], [0.292544, 0.708083, 0.459281],
[0.707456, 0.291917,
0.540719], [0.207456, 0.208083, 0.459281],
[0.292544, 0.708083, 0.040719],
[0.792544, 0.791917, 0.959281]]
species = [
'Ca', 'Ca', 'Ca', 'Ca', 'Ti', 'Ti', 'Ti', 'Ti', 'O ', 'O ', 'O ', 'O ',
'O ', 'O ', 'O ', 'O ', 'O ', 'O ', 'O ', 'O '
]
bravais = 'orthorhombic'
space_group = 62
lattice_parameters = {
'a': Set(5.40444906, 'angstrom'),
'b': Set(5.51303112, 'angstrom'),
'c': Set(7.69713264, 'angstrom')
}
data = {
'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('', space_group),
'n_atoms': len(species)
}
return data
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 silicon():
"""
Silicon Crystal
Notes
Ref: https://doi.org/10.1103/PhysRevB.24.6121
Experimental value in Table I
"""
positions = [[0.00, 0.00, 0.00], [0.25, 0.25, 0.25]]
species = ['Si', 'Si']
bravais = 'fcc'
space_group = 227
lattice_parameters = {'a': Set(5.429, 'angstrom')}
data = {
'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('', space_group),
'bravais': bravais,
'n_atoms': 2
}
return data
def tio2_rutile_gamma(named_result='rutile') -> str:
"""
Simple tetragonal
:param named_result: named result string
:return: Input for testing translational invariance
"""
crystal = tetragonal.tio2_rutile()
arbitrary_shift = 0.24 #0.134
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)),
('potential_type', Set(xtb_potential_str(potential_type)))
])
assertions = {PotentialType.TRUNCATED: OrderedDict([("n_iter", SetAssert(12)),
("energy", SetAssert(-22.578519079, 1.e-6))]),
PotentialType.FULL: OrderedDict([("n_iter", SetAssert(0, 0)),
("energy", SetAssert(0, 0))])
}
return translation_string(crystal, options, assertions[potential_type],
arbitrary_shift, named_result)
def aluminum_hexathiohypodiphosphate():
"""
AlPS4.
Notes
Simple orthorhombic. Space group: P222 [16]
Indirect band gap: 2.634 eV
Ref: https://materialsproject.org/materials/mp-27462/
"""
positions = [[0.000000, 0.000000,
0.000000], [0.500000, 0.000000, 0.500000],
[0.000000, 0.500000,
0.000000], [0.000000, 0.000000, 0.500000],
[0.197847, 0.276435,
0.101916], [0.197847, 0.723565, 0.898084],
[0.802153, 0.276435,
0.898084], [0.802153, 0.723565, 0.101916],
[0.776404, 0.800507,
0.601208], [0.776404, 0.199493, 0.398792],
[0.223596, 0.800507, 0.398792],
[0.223596, 0.199493, 0.601208]]
species = ['Al', 'Al', 'P', 'P', 'S', 'S', 'S', 'S', 'S', 'S', 'S', 'S']
bravais = 'orthorhombic'
space_group = 16
lattice_parameters = {
'a': Set(5.71230345, 'angstrom'),
'b': Set(5.71644625, 'angstrom'),
'c': Set(11.46678755, 'angstrom')
}
data = {
'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('', space_group),
'n_atoms': len(species)
}
return data
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 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 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)
def MoS2():
"""
Molybdenum disulfide
Notes
Rhombohedral setting. Space group: 160
Indirect band gap: 1.228 eV
https://materialsproject.org/materials/mp-1434/
"""
positions = [[0.000000, 0.000000, 0.000000],
[0.254176, 0.254176, 0.254176],
[0.412458, 0.412458, 0.412458]]
species = ['Mo', 'S', 'S']
bravais = 'rhombohedral'
space_group = 160
lattice_parameters = {'a': Set(6.856, 'angstrom'), 'alpha': Set(26.94, 'degree')}
data = {'fractional': positions,
'species': species,
'lattice_parameters': lattice_parameters,
'space_group': ('',space_group),
'n_atoms': len(species)}
return data
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 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 lattice_parameters_from_cif(structure, length_unit='angstrom', angle_unit='degree') \
-> typing.Dict:
"""
Get lattice constants and angles from pymatgen structure object
and assign units to them.
Parameters
----------
structure : str
length_unit : str, optional,
Unit of lattice constants. Valid options = ['angstrom', 'bohr']
cif file lattice constants are angstrom by default (verify)
angle_unit : str : optional
Unit of lattice angles. Valid options = ['degree', 'radian']
cif file lattice angles are degrees by default (verify)
Returns
-------
lattice_parameters_with_units : dict
Valid keys = a, b, c, alpha, beta, gamma
Each dictionary value is an object with a float value and str unit.
"""
assert isinstance(structure, Structure)
assert length_unit in ['angstrom', 'bohr']
assert angle_unit in ['degree', 'radian']
lattice_parameters = structure.as_dict()['lattice']
lattice_parameters.pop('matrix')
lattice_parameters.pop('volume')
lattice_parameters_with_units = {}
for key, value in lattice_parameters.items():
if key in ['a', 'b', 'c']:
unit = length_unit
else:
unit = angle_unit
lattice_parameters_with_units[key] = Set(value, unit)
return lattice_parameters_with_units
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 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 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 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 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