def calc_NDreflWeights(npy_materialDef, hkls):
if isinstance(npy_materialDef, dict):
mat = Material(npy_materialDef)
str_fac = {}
for fi, fam in enumerate(hkls):
str_fac[fi] = []
for h in fam:
str_fac[fi].append(_np.abs(mat.calc_nuc_str_fac(h))**2)
str_fac[fi] = _np.average(str_fac[fi])
#normalize
norm = 1 / _np.max(list(str_fac.values()))
for fi, fam in enumerate(hkls):
str_fac[fi] *= norm
if abs(str_fac[fi] - 1) < 1E-3: str_fac[fi] = 1
return str_fac
else:
raise ValueError('supplied mat def not valid')
def test_case():
"""Test formulaUnits
"""
input_test = input
del input_test['formulaUnits']
structure = Material(input_test)
del structure
def test_dynamic_susceptibility():
"""Test dynamic susceptibility
"""
from neutronpy import Material
input_mat = {'name': 'FeTe',
'composition': [{'ion': 'Fe', 'pos': [0.75, 0.25, 0.]},
{'ion': 'Fe', 'pos': [1. - 0.75, 1. - 0.25, 0.0]},
{'ion': 'Te', 'pos': [0.25, 0.25, 1. - 0.2839]},
{'ion': 'Te', 'pos': [1. - 0.25, 1. - 0.25, 1. - (1. - 0.2839)]}],
'debye-waller': True,
'massNorm': True,
'formulaUnits': 1.,
'lattice': dict(abc=[3.81, 3.81, 6.25], abg=[90, 90, 90])}
data = build_data()
material = Material(input_mat)
ki = Energy(energy=14.7).wavevector
kf = Energy(energy=14.7 - data.e).wavevector
assert (np.all(data.dynamic_susceptibility(material, 14.7) == 4 * np.pi / (
material.total_scattering_cross_section) * ki / kf * data.detector * data.detailed_balance_factor))
def test_optimal_thickness():
"""Test optimal thickness calculation
"""
structure = Material(input)
assert (structure.calc_optimal_thickness() == 1.9552936422413782)
def test_plot(mock_show):
"""Test unitcell plot
"""
structure = Material(input)
structure.plot_unit_cell()
def test_str_fac():
"""Tests various positions for structure factor
"""
structure = Material(input)
assert (np.abs(structure.calc_nuc_str_fac((2., 0., 0.))) ** 2 - 1702170.4663405998 < 1e-6)
assert (np.abs(structure.calc_nuc_str_fac((2, 0, 0))) ** 2 - 1702170.4663405998 < 1e-6)
assert (np.abs(structure.calc_nuc_str_fac((0, 2., 0))) ** 2 - 1702170.4663405998 < 1e-6)
assert (np.abs(structure.calc_nuc_str_fac((0, 2, 0))) ** 2 - 1702170.4663405998 < 1e-6)
ndarray_example = np.linspace(0.5, 1.5, 21)
assert (np.sum(abs(structure.calc_nuc_str_fac((ndarray_example, 0, 0))) ** 2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac((0, ndarray_example, 0))) ** 2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac((0, 0, ndarray_example))) ** 2) - 16831011.814390473 < 1e-6)
assert (
np.sum(abs(structure.calc_nuc_str_fac((ndarray_example, ndarray_example, 0))) ** 2) - 10616602.544519115 < 1e-6)
list_example = list(ndarray_example)
assert (np.sum(abs(structure.calc_nuc_str_fac((list_example, 0, 0))) ** 2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac((0, list_example, 0))) ** 2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac((0, 0, list_example))) ** 2) - 16831011.814390473 < 1e-6)
tuple_example = tuple(ndarray_example)
assert (np.sum(abs(structure.calc_nuc_str_fac((tuple_example, 0, 0))) ** 2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac((0, tuple_example, 0))) ** 2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac((0, 0, tuple_example))) ** 2) - 16831011.814390473 < 1e-6)
from neutronpy import Material
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
h, k = np.meshgrid(np.linspace(0, 2, 81), np.linspace(0, 2, 81))
def_FeTe = {'name': 'Fe1.1Te',
'composition': [{'ion': 'Fe', 'pos': [0.75, 0.25, 0.0]},
{'ion': 'Fe', 'pos': [0.25, 0.75, 0.0]},
{'ion': 'Te', 'pos': [0.25, 0.25, 0.2839]},
{'ion': 'Te', 'pos': [0.75, 0.75, -0.2839]},
{'ion': 'Fe', 'pos': [0.25, 0.25, 0.721], 'occupancy': 0.1},
{'ion': 'Fe', 'pos': [0.75, 0.75, -0.721], 'occupancy': 0.1}],
'debye-waller': False,
'massNorm': False,
'lattice': {'abc': [3.81, 3.81, 6.25],
'abg': [90, 90, 90]}}
FeTe = Material(def_FeTe)
str_fac = 0.25 * (np.abs(FeTe.calc_nuc_str_fac((h, k, 0))) ** 2 +
np.abs(FeTe.calc_nuc_str_fac((-h, k, 0))) ** 2 +
np.abs(FeTe.calc_nuc_str_fac((h, -k, 0))) ** 2 +
np.abs(FeTe.calc_nuc_str_fac((-h, -k, 0))) ** 2)
plt.pcolormesh(h, k, str_fac, cmap=cm.jet)
plt.xlabel('h (r.l.u.)')
plt.ylabel('k (r.l.u.)')
plt.show()
from neutronpy import Material
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
h, k = np.meshgrid(np.linspace(0, 2, 81), np.linspace(0, 2, 81))
def_FeTe = {'name': 'Fe1.1Te',
'composition': [{'ion': 'Fe', 'pos': [0.75, 0.25, 0.0]},
{'ion': 'Fe', 'pos': [0.25, 0.75, 0.0]},
{'ion': 'Te', 'pos': [0.25, 0.25, 0.2839]},
{'ion': 'Te', 'pos': [0.75, 0.75, -0.2839]},
{'ion': 'Fe', 'pos': [0.25, 0.25, 0.721], 'occupancy': 0.1},
{'ion': 'Fe', 'pos': [0.75, 0.75, -0.721], 'occupancy': 0.1}],
'debye-waller': False,
'massNorm': False,
'lattice': {'abc': [3.81, 3.81, 6.25],
'abg': [90, 90, 90]},
'space_group': 'P4/nmm'}
FeTe = Material(def_FeTe)
str_fac = np.abs(FeTe.calc_nuc_str_fac((h, k, 0))) ** 2
plt.pcolormesh(h, k, str_fac, cmap=cm.jet)
plt.xlabel('h (r.l.u.)')
plt.ylabel('k (r.l.u.)')
plt.show()
def test_volume():
"""Tests volume of unitcell
"""
structure = Material(input)
assert (structure.volume == 90.725624999999965)
def test_N_atoms():
"""Tests number of atoms in X g of material
"""
structure = Material(input)
assert (structure.N_atoms(22) == 36110850351331465494528)
def test_str_fac():
"""Tests various positions for structure factor
"""
structure = Material(input)
assert (np.abs(structure.calc_nuc_str_fac(
(2., 0., 0.)))**2 - 1702170.4663405998 < 1e-6)
assert (np.abs(structure.calc_nuc_str_fac(
(2, 0, 0)))**2 - 1702170.4663405998 < 1e-6)
assert (np.abs(structure.calc_nuc_str_fac(
(0, 2., 0)))**2 - 1702170.4663405998 < 1e-6)
assert (np.abs(structure.calc_nuc_str_fac(
(0, 2, 0)))**2 - 1702170.4663405998 < 1e-6)
ndarray_example = np.linspace(0.5, 1.5, 21)
assert (
np.sum(abs(structure.calc_nuc_str_fac(
(ndarray_example, 0, 0)))**2) - 7058726.6759794801 < 1e-6)
assert (
np.sum(abs(structure.calc_nuc_str_fac(
(0, ndarray_example, 0)))**2) - 7058726.6759794801 < 1e-6)
assert (
np.sum(abs(structure.calc_nuc_str_fac(
(0, 0, ndarray_example)))**2) - 16831011.814390473 < 1e-6)
assert (np.sum(
abs(structure.calc_nuc_str_fac(
(ndarray_example, ndarray_example, 0)))**2) - 10616602.544519115 <
1e-6)
list_example = list(ndarray_example)
assert (np.sum(abs(structure.calc_nuc_str_fac(
(list_example, 0, 0)))**2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac(
(0, list_example, 0)))**2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac(
(0, 0, list_example)))**2) - 16831011.814390473 < 1e-6)
tuple_example = tuple(ndarray_example)
assert (np.sum(abs(structure.calc_nuc_str_fac(
(tuple_example, 0, 0)))**2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac(
(0, tuple_example, 0)))**2) - 7058726.6759794801 < 1e-6)
assert (np.sum(abs(structure.calc_nuc_str_fac(
(0, 0, tuple_example)))**2) - 16831011.814390473 < 1e-6)
def test_optimal_thickness():
"""Test optimal thickness calculation
"""
structure = Material(input)
assert (structure.calc_optimal_thickness() == 1.9552936422413782)
def test_plot(mock_show):
"""Test unitcell plot
"""
structure = Material(input)
structure.plot_unit_cell()
def test_total_scattering_cross_section():
"""Tests scattering cross section
"""
structure = Material(input)
assert (structure.total_scattering_cross_section == 31.880000000000003)
'Al',
'composition': [
dict(ion='Al', pos=[0, 0, 0]),
dict(ion='Al', pos=[0.5, 0, 0.5]),
dict(ion='Al', pos=[0.5, 0.5, 0]),
dict(ion='Al', pos=[0, 0.5, 0.5])
],
'lattice':
dict(abc=[4.0495, 4.0495, 4.0495], abg=[90, 90, 90]),
'debye-waller':
False,
'massNorm':
False
}
al = Material(def_al)
str_fac = {}
for fi, fam in enumerate(symHKL):
str_fac[hkls[fi]] = []
for h in fam:
str_fac[hkls[fi]].append(np.abs(al.calc_nuc_str_fac(h))**2)
str_fac[hkls[fi]] = np.average(str_fac[hkls[fi]])
#normalize
norm = 1 / np.max(list(str_fac.values()))