def test_UparSymbols(self):
"""check SymmetryConstraints.UparSymbols()
"""
sg1 = GetSpaceGroup(1)
sg225 = GetSpaceGroup(225)
pos = [[0, 0, 0]]
Uijs = numpy.zeros((1, 3, 3))
sc1 = SymmetryConstraints(sg1, pos, Uijs)
self.assertEqual(6, len(sc1.UparSymbols()))
sc225 = SymmetryConstraints(sg225, pos, Uijs)
self.assertEqual(['U110'], sc225.UparSymbols())
return
def test_UparValues(self):
"""check SymmetryConstraints.UparValues()
"""
places = 12
sg1 = GetSpaceGroup(1)
sg225 = GetSpaceGroup(225)
pos = [[0, 0, 0]]
Uijs = [[[0.1, 0.4, 0.5], [0.4, 0.2, 0.6], [0.5, 0.6, 0.3]]]
sc1 = SymmetryConstraints(sg1, pos, Uijs)
duv = 0.1 * numpy.arange(1, 7) - sc1.UparValues()
self.assertAlmostEqual(0, max(numpy.fabs(duv)), places)
sc225 = SymmetryConstraints(sg225, pos, Uijs)
self.assertEqual(1, len(sc225.UparValues()))
self.assertAlmostEqual(0.2, sc225.UparValues()[0], places)
return
def _set_spaceGroup(self, item):
from matter.SpaceGroups import SpaceGroup
if isinstance(item, SpaceGroup):
self._sg = item
self._sgid = item.number
else:
from matter.SpaceGroups import GetSpaceGroup
self._sg = GetSpaceGroup(item)
self._sgid = item
def setUp(self):
x, y, z = 0.07, 0.11, 0.13
self.x, self.y, self.z = x, y, z
if TestGeneratorSite.generators:
self.__dict__.update(TestGeneratorSite.generators)
return
sg117 = GetSpaceGroup(117)
sg143 = GetSpaceGroup(143)
sg164 = GetSpaceGroup(164)
sg227 = GetSpaceGroup(227)
g117c = GeneratorSite(sg117, [0, 0.5, 0])
g117h = GeneratorSite(sg117, [x, x + 0.5, 0.5])
g143a = GeneratorSite(sg143, [0, 0, z])
g143b = GeneratorSite(sg143, [1. / 3, 2. / 3, z])
g143c = GeneratorSite(sg143, [2. / 3, 1. / 3, z])
g143d = GeneratorSite(sg143, [x, y, z])
g164e = GeneratorSite(sg164, (0.5, 0, 0))
g164f = GeneratorSite(sg164, (0.5, 0, 0.5))
g164g = GeneratorSite(sg164, (x, 0, 0))
g164h = GeneratorSite(sg164, (x, 0, 0.5))
g227a = GeneratorSite(sg227, [0, 0, 0])
g227c = GeneratorSite(sg227, 3 * [1. / 8])
g227oa = GeneratorSite(sg227, 3 * [1. / 8], sgoffset=3 * [1. / 8])
g227oc = GeneratorSite(sg227, [0, 0, 0], sgoffset=3 * [1. / 8])
TestGeneratorSite.generators = {
'g117c': g117c,
'g117h': g117h,
'g143a': g143a,
'g143b': g143b,
'g143c': g143c,
'g143d': g143d,
'g164e': g164e,
'g164f': g164f,
'g164g': g164g,
'g164h': g164h,
'g227a': g227a,
'g227c': g227c,
'g227oa': g227oa,
'g227oc': g227oc
}
self.__dict__.update(TestGeneratorSite.generators)
return
def test_expandPosition(self):
"""check expandPosition()
"""
# ok again Ni example
fcc = GetSpaceGroup(225)
pos, pops, pmult = expandPosition(fcc, [0, 0, 0])
self.failUnless(numpy.all(pos[0] == 0.0))
self.assertEqual(4, len(pos))
self.assertEqual(192, sum([len(l) for l in pops]))
self.assertEqual(4, pmult)
return
def test_corepos(self):
"""test_corepos - find positions in the asymmetric unit.
"""
sg225 = GetSpaceGroup(225)
corepos = [[0, 0, 0], [0.1, 0.13, 0.17]]
eau = ExpandAsymmetricUnit(sg225, corepos)
sc = SymmetryConstraints(sg225, eau.expandedpos)
self.assertEqual(2, len(sc.corepos))
self.failUnless(numpy.all(corepos[0] == sc.corepos[0]))
self.failUnless(numpy.all(corepos[1] == sc.corepos[1]))
self.assertEqual(2, len(sc.coremap))
mapped_count = sum([len(idcs) for idcs in sc.coremap.values()])
self.assertEqual(len(sc.positions), mapped_count)
self.failUnless(sc.coremap[0] == range(4))
self.failUnless(sc.coremap[4] == range(4, 4 + 192))
return
def test__findUParameters(self):
"""check GeneratorSite._findUParameters()
"""
# by default all Uparameters equal zero, this would fail for NaNs
for gen in TestGeneratorSite.generators.values():
for usym, uval in gen.Uparameters:
self.assertEqual(0.0, uval)
# special test for g117h
Uij = numpy.array([[1, 3, 4], [3, 1, -4], [4, -4, 2]])
sg117 = GetSpaceGroup(117)
g117h = GeneratorSite(sg117, self.g117h.xyz, Uij)
upd = dict(g117h.Uparameters)
self.assertEqual(1, upd['U11'])
self.assertEqual(2, upd['U33'])
self.assertEqual(3, upd['U12'])
self.assertEqual(4, upd['U13'])
return
def test___init__(self):
"""check SymmetryConstraints.__init__()
"""
sg225 = GetSpaceGroup(225)
# initialize from nested lists and arrays from ExpandAsymmetricUnit
eau = ExpandAsymmetricUnit(sg225, [[0, 0, 0]])
sc0 = SymmetryConstraints(sg225, eau.expandedpos)
self.assertEqual(1, len(sc0.coremap))
# initialize from list of arrays of coordinates
poslistarrays = [xyz for xyz in sc0.positions]
sc1 = SymmetryConstraints(sg225, poslistarrays)
self.assertEqual(1, len(sc1.coremap))
# initialize from list of lists of coordinates
poslistlist = [list(xyz) for xyz in poslistarrays]
sc2 = SymmetryConstraints(sg225, poslistlist)
self.assertEqual(1, len(sc2.coremap))
# initialize from nx3 array
posarray = numpy.array(poslistlist)
sc3 = SymmetryConstraints(sg225, posarray)
self.assertEqual(1, len(sc3.coremap))
# finally initialize from a single coordinate
sc4 = SymmetryConstraints(sg225, [0, 0, 0])
self.assertEqual(1, len(sc4.coremap))
return
def test_isSpaceGroupLatPar(self):
"""check isSpaceGroupLatPar()
"""
triclinic = GetSpaceGroup("P1")
monoclinic = GetSpaceGroup("P2")
orthorhombic = GetSpaceGroup("P222")
tetragonal = GetSpaceGroup("P4")
trigonal = GetSpaceGroup("P3")
hexagonal = GetSpaceGroup("P6")
cubic = GetSpaceGroup("P23")
self.failUnless(isSpaceGroupLatPar(triclinic, 1, 2, 3, 40, 50, 60))
self.failIf(isSpaceGroupLatPar(monoclinic, 1, 2, 3, 40, 50, 60))
self.failUnless(isSpaceGroupLatPar(monoclinic, 1, 2, 3, 90, 50, 90))
self.failIf(isSpaceGroupLatPar(orthorhombic, 1, 2, 3, 90, 50, 90))
self.failUnless(isSpaceGroupLatPar(orthorhombic, 1, 2, 3, 90, 90, 90))
self.failIf(isSpaceGroupLatPar(tetragonal, 1, 2, 3, 90, 90, 90))
self.failUnless(isSpaceGroupLatPar(tetragonal, 2, 2, 3, 90, 90, 90))
self.failIf(isSpaceGroupLatPar(trigonal, 2, 2, 3, 90, 90, 90))
self.failUnless(isSpaceGroupLatPar(trigonal, 2, 2, 2, 80, 80, 80))
self.failIf(isSpaceGroupLatPar(hexagonal, 2, 2, 2, 80, 80, 80))
self.failUnless(isSpaceGroupLatPar(hexagonal, 2, 2, 3, 90, 90, 120))
self.failIf(isSpaceGroupLatPar(cubic, 2, 2, 3, 90, 90, 120))
self.failUnless(isSpaceGroupLatPar(cubic, 3, 3, 3, 90, 90, 90))
return
def _get_spaceGroup(self):
if not self._sg:
from matter.SpaceGroups import GetSpaceGroup
self._sg = GetSpaceGroup(self._sgid)
return self._sg