1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
|
#!/usr/bin/env python
""" Tests of Larch Scripts """
import os
import time
import shutil
import pytest
import numpy as np
from numpy.testing import assert_allclose
from xraydb import (chemparse, validate_formula, material_mu,
material_mu_components, find_material, get_materials,
get_material, add_material)
from xraydb.materials import get_user_materialsfile
def test_chemparse():
examples = {'H2O': {'H':2, 'O':1},
'Mn(SO4)2(H2O)7': {'H': 14.0, 'S': 2.0, 'Mn': 1, 'O': 15.0},
'Mg(SO4)2': {'Mg': 1, 'S': 2, 'O':8},
'Mg0.5Fe0.5' : {'Mg': 0.5, 'Fe': 0.5},
'Mg.3Fe.7' : {'Mg': 0.3, 'Fe': 0.7},
'CO': {'C': 1, 'O': 1} }
for formula, cert in examples.items():
ret = chemparse(formula)
for elem, quant in cert.items():
v = ret.pop(elem)
assert_allclose(v, quant, rtol=1.e3)
assert len(ret)==0
def test_validate_formula():
examples = {'H2O': True,
'Mn(SO4)2(H2O)7': True,
'Mn(SO42(H2O)7': False,
'Z': False}
for formula, cert in examples.items():
ret = validate_formula(formula)
assert (ret == cert)
def test_get_materials():
examples = {'water': True, 'lead': True, 'acetone': True,
'kapton': True, 'sapphire': True,
'cheese': False, 'spice': False, 'bicycle': False}
known_materials = get_materials()
for name, found in examples.items():
if found:
assert (name in known_materials)
else:
assert (name not in known_materials)
def test_material_mu1():
en = np.linspace(8500, 9500, 21)
known_mu = np.array([236.2, 232.4, 228.7, 225.1, 221.5, 218.1, 214.7,
211.4, 208.1, 204.9, 1403.6, 1385.6, 1367.9, 1350.6,
1333.5, 1316.7, 1300.3, 1284.0, 1268.1, 1252.4,
1237.0])
mu = material_mu('CuO', en, density=6.3)
assert_allclose(mu, known_mu, rtol=0.005)
def test_material_mu2():
en = np.linspace(5000, 10000, 21)
known_mu = np.array([0.04934, 0.04267, 0.03715, 0.03254, 0.02866,
0.02538, 0.02257, 0.02016, 0.01809, 0.01629,
0.01472, 0.01334, 0.01214, 0.01108, 0.01014,
0.00930, 0.00856, 0.00789, 0.00729, 0.00675,
0.00626])
mu = material_mu('air', en)
assert_allclose(mu, known_mu, rtol=0.05)
air_formula, air_density = get_material('air')
air_comps = chemparse(air_formula)
assert air_comps['Ar'] < 0.013
assert air_comps['Ar'] > 0.007
mu = material_mu('air', en, density=2.0*air_density)
assert_allclose(mu, 2.0*known_mu, rtol=0.05)
def test_material_mu3():
en = np.linspace(5000, 10000, 21)
known_mu = np.array([42.592, 36.801, 32.006, 28.005, 24.641, 21.794,
19.367, 17.288, 15.496, 13.943, 12.592, 11.411,
10.373, 9.458, 8.649, 7.931, 7.291, 6.719, 6.206,
5.745, 5.330])
mu = material_mu('H2O', en)
assert_allclose(mu, known_mu, rtol=0.05)
def test_material_mu4():
en = np.linspace(5000, 10000, 21)
known_mu = np.array([42.592, 36.801, 32.006, 28.005, 24.641, 21.794,
19.367, 17.288, 15.496, 13.943, 12.592, 11.411,
10.373, 9.458, 8.649, 7.931, 7.291, 6.719, 6.206,
5.745, 5.330])
with pytest.raises(Warning):
out = material_mu('H2SO4', en)
def test_material_mu_components1():
mu = material_mu('quartz', 10000)
assert_allclose(mu, 50.368, rtol=0.001)
comps = material_mu_components('quartz', 10000)
known_comps = {'mass': 60.08, 'density': 2.65, 'elements': ['Si', 'O'],
'Si': (1, 28.1, 33.879), 'O': (2.0, 16.0, 5.953)}
assert 'Si'in comps['elements']
assert 'O'in comps['elements']
for attr in ('mass', 'density'):
assert_allclose(comps[attr], known_comps[attr], rtol=0.01)
for attr in ('Si', 'O'):
assert_allclose(comps[attr][0], known_comps[attr][0], rtol=0.01)
assert_allclose(comps[attr][1], known_comps[attr][1], rtol=0.01)
assert_allclose(comps[attr][2], known_comps[attr][2], rtol=0.01)
def test_material_mu_components2():
mu = material_mu('TiO2', 10000, density=4.23)
assert_allclose(mu, 290.7, rtol=0.001)
mu = material_mu('TiO2', 10000)
assert_allclose(mu, 290.7, rtol=0.001)
mu = material_mu('TiO2', 10000, density=4.5)
assert_allclose(mu, 309.26, rtol=0.001)
comps = material_mu_components('TiO2', 10000, density=4.23)
known_comps = {'mass': 79.88, 'density': 4.23, 'elements': ['Ti', 'O'],
'Ti': (1, 47.88, 110.676), 'O': (2.0, 15.9994, 5.953)}
assert 'Ti'in comps['elements']
assert 'O'in comps['elements']
for attr in ('mass', 'density'):
assert_allclose(comps[attr], known_comps[attr], rtol=0.01)
for attr in ('Ti', 'O'):
assert_allclose(comps[attr][0], known_comps[attr][0], rtol=0.01)
assert_allclose(comps[attr][1], known_comps[attr][1], rtol=0.01)
assert_allclose(comps[attr][2], known_comps[attr][2], rtol=0.01)
with pytest.raises(Warning):
c = material_mu_components('TiO2', 10000)
def test_material_find():
mat_ = {'kapton': ('C22H10N2O5', 1.43, 'polymer'),
'lead': ('Pb', 11.34, 'metal'),
'aluminum': ('Al', 2.72, 'metal'),
'water': ('H2O', 1.0, 'solvent')}
for mname, mdat in mat_.items():
mat = find_material(mname)
f1 = chemparse(mat.formula)
f2 = chemparse(mdat[0])
for k, v in f2.items():
assert v == f1[k]
assert_allclose(mat.density, mdat[1], rtol=0.1)
assert(mdat[2] in mat.categories)
for formula in ('WSO3', 'CdAs140CO3', 'KAs'):
out = find_material(formula)
assert out == None
def test_material_get():
mat_ = {'kapton': ('C22H10N2O5', 1.43),
'lead': ('Pb', 11.34),
'aluminum': ('Al', 2.72),
'water': ('H2O', 1.0)}
for mname in mat_.keys():
formula, density = get_material(mname)
f1 = chemparse(formula)
f2 = chemparse(mat_[mname][0])
for k, v in f2.items():
assert v == f1[k]
assert_allclose(density, mat_[mname][1], rtol=0.1)
for formula, density in mat_.values():
_f, _d = get_material(formula)
assert _f == formula
assert_allclose(density, _d, rtol=0.1)
for formula in ('WSO3', 'CdAs140CO3', 'KAs'):
out = get_material(formula)
assert out == None
@pytest.mark.skip("Unsafe test directory location.")
def test_material_add():
matfile = get_user_materialsfile()
savefile = matfile + '_Save'
if os.path.exists(matfile):
had_matfile = True
shutil.move(matfile, savefile)
time.sleep(2.0)
add_material('caffeine', 'C8H10N4O2', density=1.23)
assert get_material('caffeine') is not None
time.sleep(2.0)
add_material('rutile', 'TiO2', density=4.23)
with open(matfile, 'r') as fh:
text = fh.read()
assert 'caffeine' in text
assert 'rutile' in text
os.unlink(matfile)
if os.path.exists(savefile):
shutil.move(savefile, matfile)
|
