def test_BaseClass():
b = Base(1, 's')
base_checker(b)
assert b['header'] == 'Undefined'
assert b['tooltip'] == ''
assert b['url'] == ''
assert b['mapping'] is None
def fromPars(cls,
atom_site_label: str,
type_symbol: str,
scat_length_neutron: complex,
fract_x: float,
fract_y: float,
fract_z: float,
occupancy: float,
adp_type: str,
U_iso_or_equiv: float,
ADp: list = None,
MSp: list = None) -> 'Atom':
"""
Atom constructor from parameters
:param atom_site_label: The unique name of the atom in the phase
:param type_symbol: The type of atom
:param scat_length_neutron: Neutron scattering length
:param fract_x: X position
:param fract_y: Y position
:param fract_z: Z position
:param occupancy: Site occupancy
:param adp_type: ADP type code
:param U_iso_or_equiv: Isotropic atomic displacement parameter
:return: Fully formed atom data store
"""
type_symbol = Base(type_symbol,
ATOM_DETAILS['type_symbol']['default'][1])
scat_length_neutron = Base(
scat_length_neutron,
ATOM_DETAILS['scat_length_neutron']['default'][1])
occupancy = Base(occupancy, ATOM_DETAILS['occupancy']['default'][1])
adp_type = Base(adp_type, ATOM_DETAILS['adp_type']['default'][1])
U_iso_or_equiv = Base(U_iso_or_equiv,
ATOM_DETAILS['U_iso_or_equiv']['default'][1])
fract_x = Base(fract_x, ATOM_DETAILS['fract']['default'][1])
fract_y = Base(fract_y, ATOM_DETAILS['fract']['default'][1])
fract_z = Base(fract_z, ATOM_DETAILS['fract']['default'][1])
if not isinstance(ADp, ADP):
if ADp is not None:
ADp = ADP.fromPars(*ADp)
else:
ADp = ADP.default()
if not isinstance(MSp, MSP):
if MSp is not None:
MSp = MSP.fromPars(*MSp)
else:
MSp = MSP.default()
return cls(atom_site_label, type_symbol, scat_length_neutron, fract_x,
fract_y, fract_z, occupancy, adp_type, U_iso_or_equiv, ADp,
MSp)
def default(cls) -> 'MSP':
MSPtype = Base(None, '')
chi_11 = Base(*ATOM_DETAILS['MSP']['default'])
chi_12 = Base(*ATOM_DETAILS['MSP']['default'])
chi_13 = Base(*ATOM_DETAILS['MSP']['default'])
chi_22 = Base(*ATOM_DETAILS['MSP']['default'])
chi_23 = Base(*ATOM_DETAILS['MSP']['default'])
chi_33 = Base(*ATOM_DETAILS['MSP']['default'])
return cls(MSPtype, chi_11, chi_22, chi_33, chi_12, chi_13, chi_23)
def default(cls) -> 'ADP':
u_11 = Base(*ATOM_DETAILS['ADP']['default'])
u_12 = Base(*ATOM_DETAILS['ADP']['default'])
u_13 = Base(*ATOM_DETAILS['ADP']['default'])
u_22 = Base(*ATOM_DETAILS['ADP']['default'])
u_23 = Base(*ATOM_DETAILS['ADP']['default'])
u_33 = Base(*ATOM_DETAILS['ADP']['default'])
return cls(u_11, u_22, u_33, u_12, u_13, u_23)
def fromPars(cls, MSPtype: str, chi_11: float, chi_22: float,
chi_33: float, chi_12: float, chi_13: float,
chi_23: float) -> 'MSP':
MSPtype = Base(MSPtype, '')
chi_11 = Base(chi_11, ATOM_DETAILS['MSP']['default'][1])
chi_12 = Base(chi_12, ATOM_DETAILS['MSP']['default'][1])
chi_13 = Base(chi_13, ATOM_DETAILS['MSP']['default'][1])
chi_22 = Base(chi_22, ATOM_DETAILS['MSP']['default'][1])
chi_23 = Base(chi_23, ATOM_DETAILS['MSP']['default'][1])
chi_33 = Base(chi_33, ATOM_DETAILS['MSP']['default'][1])
return cls(MSPtype, chi_11, chi_22, chi_33, chi_12, chi_13, chi_23)
def fromPars(cls, u_11: float, u_12: float, u_13: float, u_22: float,
u_23: float, u_33: float) -> 'ADP':
u_11 = Base(u_11, ATOM_DETAILS['ADP']['default'][1])
u_12 = Base(u_12, ATOM_DETAILS['ADP']['default'][1])
u_13 = Base(u_13, ATOM_DETAILS['ADP']['default'][1])
u_22 = Base(u_22, ATOM_DETAILS['ADP']['default'][1])
u_23 = Base(u_23, ATOM_DETAILS['ADP']['default'][1])
u_33 = Base(u_33, ATOM_DETAILS['ADP']['default'][1])
return cls(u_11, u_22, u_33, u_12, u_13, u_23)
def default(cls, atom_site_label: str) -> 'Atom':
"""
Default constructor for an atom given a unique name in the phase
:param atom_site_label: The atoms unique name in the phase
:return: Default atom with a given name
"""
type_symbol = Base(*ATOM_DETAILS['type_symbol']['default'])
scat_length_neutron = Base(
*ATOM_DETAILS['scat_length_neutron']['default'])
fract_x = Base(*ATOM_DETAILS['fract']['default'])
fract_y = Base(*ATOM_DETAILS['fract']['default'])
fract_z = Base(*ATOM_DETAILS['fract']['default'])
occupancy = Base(*ATOM_DETAILS['occupancy']['default'])
adp_type = Base(*ATOM_DETAILS['adp_type']['default'])
U_iso_or_equiv = Base(*ATOM_DETAILS['U_iso_or_equiv']['default'])
ADp = ADP.default()
MSp = MSP.default()
return cls(atom_site_label, type_symbol, scat_length_neutron, fract_x,
fract_y, fract_z, occupancy, adp_type, U_iso_or_equiv, ADp,
MSp)
def test_Base_set_max():
b = Base(1, 's')
b.max = 10
assert b.max == 10
assert b['store']['max'] == 10
def test_Base_set_min():
b = Base(1, 's')
b.min = -10
assert b.min == -10
assert b['store']['min'] == -10
def test_Base_set_refine():
b = Base(1, 's')
b.refine = True
assert b.refine is True
assert b['store']['refine'] is True
def test_Base_get_value():
b = Base(1, 's')
assert b.value == 1
assert b['store']['value'] == 1
def test_Base_value_in_unit():
b = Base(1, 's')
val = b.valueInUnit('h')
assert val == 1 / 3600
def test_Base_convert_units():
b = Base(1, 's')
b.convertUnits('h')
base_checker(b)
assert b.value == 1 / 3600
assert str(b['store']['unit']) == 'h'
def test_Base_unit_conversion_factor():
b = Base(1, 's')
fac = b.unitConversionFactor('h')
assert fac == 1 / 3600
def test_Base_set():
b = Base(1, 's')
b.set('hide', False)
assert b.get('hide') is False
def test_Base_get():
b = Base(1, 's')
assert b.get('hide') is True
def test_Base_set_value():
b = Base(1, 's')
b.value = 2
assert b.value == 2
assert b['store']['value'] == 2
def test_Base_get_refine():
b = Base(1, 's')
assert b.refine is False
assert b['store']['refine'] is False