Skip to content

Commit b791c52

Browse files
sbillingesbillinge
committed
tests: diffpyparset
1 parent 9c825ec commit b791c52

File tree

1 file changed

+113
-114
lines changed

1 file changed

+113
-114
lines changed

‎tests/test_diffpyparset.py

Lines changed: 113 additions & 114 deletions
Original file line numberDiff line numberDiff line change
@@ -17,122 +17,121 @@
1717
import pickle
1818
import unittest
1919

20-
import numpy
21-
22-
from .utils import _msg_nostructure, has_structure
23-
24-
# Global variables to be assigned in setUp
25-
Atom = Lattice = Structure = DiffpyStructureParSet = None
26-
27-
# ----------------------------------------------------------------------------
28-
29-
30-
@unittest.skipUnless(has_structure, _msg_nostructure)
31-
class TestParameterAdapter(unittest.TestCase):
32-
33-
def setUp(self):
34-
global Atom, Lattice, Structure, DiffpyStructureParSet
35-
from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
36-
from diffpy.structure import Atom, Lattice, Structure
37-
38-
return
39-
40-
def testDiffpyStructureParSet(self):
41-
"""Test the structure conversion."""
42-
43-
a1 = Atom("Cu", xyz=numpy.array([0.0, 0.1, 0.2]), Uisoequiv=0.003)
44-
a2 = Atom("Ag", xyz=numpy.array([0.3, 0.4, 0.5]), Uisoequiv=0.002)
45-
l = Lattice(2.5, 2.5, 2.5, 90, 90, 90)
46-
47-
dsstru = Structure([a1, a2], l)
48-
# Structure makes copies
49-
a1 = dsstru[0]
50-
a2 = dsstru[1]
51-
52-
s = DiffpyStructureParSet("CuAg", dsstru)
53-
54-
self.assertEqual(s.name, "CuAg")
55-
56-
def _testAtoms():
57-
# Check the atoms thoroughly
58-
self.assertEqual(a1.element, s.Cu0.element)
59-
self.assertEqual(a2.element, s.Ag0.element)
60-
self.assertEqual(a1.Uisoequiv, s.Cu0.Uiso.getValue())
61-
self.assertEqual(a2.Uisoequiv, s.Ag0.Uiso.getValue())
62-
self.assertEqual(a1.Bisoequiv, s.Cu0.Biso.getValue())
63-
self.assertEqual(a2.Bisoequiv, s.Ag0.Biso.getValue())
64-
for i in range(1, 4):
65-
for j in range(i, 4):
66-
uijstru = getattr(a1, "U%i%i" % (i, j))
67-
uij = getattr(s.Cu0, "U%i%i" % (i, j)).getValue()
68-
uji = getattr(s.Cu0, "U%i%i" % (j, i)).getValue()
69-
self.assertEqual(uijstru, uij)
70-
self.assertEqual(uijstru, uji)
71-
bijstru = getattr(a1, "B%i%i" % (i, j))
72-
bij = getattr(s.Cu0, "B%i%i" % (i, j)).getValue()
73-
bji = getattr(s.Cu0, "B%i%i" % (j, i)).getValue()
74-
self.assertEqual(bijstru, bij)
75-
self.assertEqual(bijstru, bji)
76-
77-
self.assertEqual(a1.xyz[0], s.Cu0.x.getValue())
78-
self.assertEqual(a1.xyz[1], s.Cu0.y.getValue())
79-
self.assertEqual(a1.xyz[2], s.Cu0.z.getValue())
80-
return
81-
82-
def _testLattice():
83-
84-
# Test the lattice
85-
self.assertEqual(dsstru.lattice.a, s.lattice.a.getValue())
86-
self.assertEqual(dsstru.lattice.b, s.lattice.b.getValue())
87-
self.assertEqual(dsstru.lattice.c, s.lattice.c.getValue())
88-
self.assertEqual(dsstru.lattice.alpha, s.lattice.alpha.getValue())
89-
self.assertEqual(dsstru.lattice.beta, s.lattice.beta.getValue())
90-
self.assertEqual(dsstru.lattice.gamma, s.lattice.gamma.getValue())
91-
92-
_testAtoms()
93-
_testLattice()
94-
95-
# Now change some values from the diffpy Structure
96-
a1.xyz[1] = 0.123
97-
a1.U11 = 0.321
98-
a1.B32 = 0.111
99-
dsstru.lattice.setLatPar(a=3.0, gamma=121)
100-
_testAtoms()
101-
_testLattice()
102-
103-
# Now change values from the srfit DiffpyStructureParSet
104-
s.Cu0.x.setValue(0.456)
105-
s.Cu0.U22.setValue(0.441)
106-
s.Cu0.B13.setValue(0.550)
107-
d = dsstru.lattice.dist(a1.xyz, a2.xyz)
108-
s.lattice.b.setValue(4.6)
109-
s.lattice.alpha.setValue(91.3)
110-
_testAtoms()
111-
_testLattice()
112-
# Make sure the distance changed
113-
self.assertNotEqual(d, dsstru.lattice.dist(a1.xyz, a2.xyz))
20+
import numpy as np
21+
import pytest
22+
23+
from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
24+
25+
26+
def testDiffpyStructureParSet(diffpy_structure_available):
27+
"""Test the structure conversion."""
28+
if not diffpy_structure_available:
29+
pytest.skip("diffpy.structure package not available")
30+
from diffpy.structure import Atom, Lattice, Structure
31+
32+
a1 = Atom("Cu", xyz=np.array([0.0, 0.1, 0.2]), Uisoequiv=0.003)
33+
a2 = Atom("Ag", xyz=np.array([0.3, 0.4, 0.5]), Uisoequiv=0.002)
34+
lattice = Lattice(2.5, 2.5, 2.5, 90, 90, 90)
35+
36+
dsstru = Structure([a1, a2], lattice)
37+
# Structure makes copies
38+
a1 = dsstru[0]
39+
a2 = dsstru[1]
40+
41+
s = DiffpyStructureParSet("CuAg", dsstru)
42+
43+
assert s.name == "CuAg"
44+
45+
def _testAtoms():
46+
# Check the atoms thoroughly
47+
assert a1.element == s.Cu0.element
48+
assert a2.element == s.Ag0.element
49+
assert a1.Uisoequiv == s.Cu0.Uiso.getValue()
50+
assert a2.Uisoequiv == s.Ag0.Uiso.getValue()
51+
assert a1.Bisoequiv == s.Cu0.Biso.getValue()
52+
assert a2.Bisoequiv == s.Ag0.Biso.getValue()
53+
for i in range(1, 4):
54+
for j in range(i, 4):
55+
uijstru = getattr(a1, "U%i%i" % (i, j))
56+
uij = getattr(s.Cu0, "U%i%i" % (i, j)).getValue()
57+
uji = getattr(s.Cu0, "U%i%i" % (j, i)).getValue()
58+
assert uijstru == uij
59+
assert uijstru == uji
60+
bijstru = getattr(a1, "B%i%i" % (i, j))
61+
bij = getattr(s.Cu0, "B%i%i" % (i, j)).getValue()
62+
bji = getattr(s.Cu0, "B%i%i" % (j, i)).getValue()
63+
assert bijstru == bij
64+
assert bijstru == bji
65+
66+
assert a1.xyz[0] == s.Cu0.x.getValue()
67+
assert a1.xyz[1] == s.Cu0.y.getValue()
68+
assert a1.xyz[2] == s.Cu0.z.getValue()
11469
return
11570

116-
def test___repr__(self):
117-
"""Test representation of DiffpyStructureParSet objects."""
118-
lat = Lattice(3, 3, 2, 90, 90, 90)
119-
atom = Atom("C", [0, 0.2, 0.5])
120-
stru = Structure([atom], lattice=lat)
121-
dsps = DiffpyStructureParSet("dsps", stru)
122-
self.assertEqual(repr(stru), repr(dsps))
123-
self.assertEqual(repr(lat), repr(dsps.lattice))
124-
self.assertEqual(repr(atom), repr(dsps.atoms[0]))
125-
return
126-
127-
def test_pickling(self):
128-
"""Test pickling of DiffpyStructureParSet."""
129-
stru = Structure([Atom("C", [0, 0.2, 0.5])])
130-
dsps = DiffpyStructureParSet("dsps", stru)
131-
data = pickle.dumps(dsps)
132-
dsps2 = pickle.loads(data)
133-
self.assertEqual(1, len(dsps2.atoms))
134-
self.assertEqual(0.2, dsps2.atoms[0].y.value)
135-
return
71+
def _testLattice():
72+
73+
# Test the lattice
74+
assert dsstru.lattice.a == s.lattice.a.getValue()
75+
assert dsstru.lattice.b == s.lattice.b.getValue()
76+
assert dsstru.lattice.c == s.lattice.c.getValue()
77+
assert dsstru.lattice.alpha == s.lattice.alpha.getValue()
78+
assert dsstru.lattice.beta == s.lattice.beta.getValue()
79+
assert dsstru.lattice.gamma == s.lattice.gamma.getValue()
80+
81+
_testAtoms()
82+
_testLattice()
83+
84+
# Now change some values from the diffpy Structure
85+
a1.xyz[1] = 0.123
86+
a1.U11 = 0.321
87+
a1.B32 = 0.111
88+
dsstru.lattice.setLatPar(a=3.0, gamma=121)
89+
_testAtoms()
90+
_testLattice()
91+
92+
# Now change values from the srfit DiffpyStructureParSet
93+
s.Cu0.x.setValue(0.456)
94+
s.Cu0.U22.setValue(0.441)
95+
s.Cu0.B13.setValue(0.550)
96+
d = dsstru.lattice.dist(a1.xyz, a2.xyz)
97+
s.lattice.b.setValue(4.6)
98+
s.lattice.alpha.setValue(91.3)
99+
_testAtoms()
100+
_testLattice()
101+
# Make sure the distance changed
102+
assert d != dsstru.lattice.dist(a1.xyz, a2.xyz)
103+
return
104+
105+
106+
def test___repr__(diffpy_structure_available):
107+
"""Test representation of DiffpyStructureParSet objects."""
108+
if not diffpy_structure_available:
109+
pytest.skip("diffpy.structure package not available")
110+
from diffpy.structure import Atom, Lattice, Structure
111+
112+
lat = Lattice(3, 3, 2, 90, 90, 90)
113+
atom = Atom("C", [0, 0.2, 0.5])
114+
stru = Structure([atom], lattice=lat)
115+
dsps = DiffpyStructureParSet("dsps", stru)
116+
assert repr(stru) == repr(dsps)
117+
assert repr(lat) == repr(dsps.lattice)
118+
assert repr(atom) == repr(dsps.atoms[0])
119+
return
120+
121+
122+
def test_pickling(diffpy_structure_available):
123+
"""Test pickling of DiffpyStructureParSet."""
124+
if not diffpy_structure_available:
125+
pytest.skip("diffpy.structure package not available")
126+
from diffpy.structure import Atom, Structure
127+
128+
stru = Structure([Atom("C", [0, 0.2, 0.5])])
129+
dsps = DiffpyStructureParSet("dsps", stru)
130+
data = pickle.dumps(dsps)
131+
dsps2 = pickle.loads(data)
132+
assert 1 == len(dsps2.atoms)
133+
assert 0.2 == dsps2.atoms[0].y.value
134+
return
136135

137136

138137
# End of class TestParameterAdapter

0 commit comments

Comments
 (0)