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.assertTrue(numpy.all(corepos[0] == sc.corepos[0]))
self.assertTrue(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.assertTrue(sc.coremap[0] == range(4))
self.assertTrue(sc.coremap[4] == range(4, 4 + 192))
return
def updateWidgets(self):
"""Update the widgets."""
# Update space group
sgname = self.sgComboBox.GetValue()
try:
self.spacegroup = self.structure.getSpaceGroup(sgname)
error = None
except ValueError:
error = "Space group %s does not exist." % sgname
# This changes list box value to the short_name of the new spacegroup
# or to the name of previous spacegroup when getSpaceGroup failed.
self.sgComboBox.SetValue(self.spacegroup.short_name)
# Update offset
for i in range(3):
textctrl = self.textCtrls[i]
val = textctrl.GetValue()
# make sure the value is meaningful
try:
val = float(eval("1.0*" + val, dict(math.__dict__)))
except (NameError, TypeError, SyntaxError):
val = 0.0
textctrl.SetValue("%s" % val)
self.offset[i] = val
# find how many new atoms would be generated
from diffpy.Structure.SymmetryUtilities import ExpandAsymmetricUnit
corepos = [self.structure[i].xyz for i in self.indices]
symposeps = self.structure.symposeps
eau = ExpandAsymmetricUnit(self.spacegroup,
corepos,
sgoffset=self.offset,
eps=symposeps)
newsize = sum(eau.multiplicity)
s = ""
if len(self.indices) != 1:
s = "s"
message = "%i atom%s selected. Expanding to %i positions." %\
(len(self.indices), s, newsize)
self.numConstrainedLabel.SetLabel(message)
# Raise an error if we had to change the space group
if error:
raise ControlValueError(error)
return
def test_UFormula_g186c_eqxyz(self):
'''Check rotated U formulas at the symmetry positions of c-site in 186.
'''
sg186 = GetSpaceGroup(186)
crules = [
{'U11': 'A', 'U22': 'A', 'U33': 'C',
'U12': 'D', 'U13': 'E', 'U23': '-E'},
{'U11': 'A', 'U22': '2*A-2*D', 'U33': 'C',
'U12': 'A-D', 'U13': 'E', 'U23': '2*E'},
{'U11': '2*A-2*D', 'U22': 'A', 'U33': 'C',
'U12': 'A-D', 'U13': '-2*E', 'U23': '-E'},
{'U11': 'A', 'U22': 'A', 'U33': 'C',
'U12': 'D', 'U13': '-E', 'U23': 'E'},
{'U11': 'A', 'U22': '2*A-2*D', 'U33': 'C',
'U12': 'A-D', 'U13': '-E', 'U23': '-2*E'},
{'U11': '2*A-2*D', 'U22': 'A', 'U33': 'C',
'U12': 'A-D', 'U13': '2*E', 'U23': 'E'},
]
self.assertEqual(6, len(self.g186c.eqxyz))
gc = self.g186c
for idx in range(6):
self.assertEqual(crules[idx], gc.UFormula(gc.eqxyz[idx], 'ABCDEF'))
uiso = numpy.array([[2, 1, 0], [1, 2, 0], [0, 0, 2]])
eau = ExpandAsymmetricUnit(sg186, [gc.xyz], [uiso])
for u in eau.expandedUijs:
du = numpy.linalg.norm((uiso - u).flatten())
self.assertAlmostEqual(0.0, du, 8)
symcon = SymmetryConstraints(sg186, sum(eau.expandedpos, []),
sum(eau.expandedUijs, []))
upd = dict(symcon.Upars)
self.assertEqual(2.0, upd['U110'])
self.assertEqual(2.0, upd['U330'])
self.assertEqual(1.0, upd['U120'])
self.assertEqual(0.0, upd['U130'])
uisod = {'U11' : 2.0, 'U22' : 2.0, 'U33' : 2.0,
'U12' : 1.0, 'U13' : 0.0, 'U23' : 0.0}
for ufms in symcon.UFormulas():
for n, fm in ufms.items():
self.assertEqual(uisod[n], eval(fm, upd))
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
from diffpy.Structure.SymmetryUtilities import ExpandAsymmetricUnit
positions = [[0.1, 0.2, 0.2]]
from diffpy.Structure.SpaceGroups import GetSpaceGroup
sg225 = GetSpaceGroup('Fm-3m')
eau = ExpandAsymmetricUnit(sg225, positions)
pos_expanded=eau.positions[0]