def test_createStructureAdapter(self):
"""check createStructureAdapter() routine.
"""
adpt = createStructureAdapter(self.nickel)
self.assertEqual(4, adpt.countSites())
self.assertTrue(False is adpt.siteAnisotropy(0))
self.assertTrue(isinstance(adpt, StructureAdapter))
adpt1 = createStructureAdapter(adpt)
self.assertTrue(adpt is adpt1)
self.assertRaises(TypeError, createStructureAdapter, 77)
self.assertRaises(TypeError, createStructureAdapter, range(8))
self.assertRaises(TypeError, createStructureAdapter, None)
self.assertRaises(TypeError, createStructureAdapter, {})
return
def test_createStructureAdapter(self):
"""check createStructureAdapter() routine.
"""
adpt = createStructureAdapter(self.nickel)
self.assertEqual(4, adpt.countSites())
self.assertTrue(False is adpt.siteAnisotropy(0))
self.assertTrue(isinstance(adpt, StructureAdapter))
adpt1 = createStructureAdapter(adpt)
self.assertTrue(adpt is adpt1)
self.assertRaises(TypeError, createStructureAdapter, 77)
self.assertRaises(TypeError, createStructureAdapter, list(range(8)))
self.assertRaises(TypeError, createStructureAdapter, None)
self.assertRaises(TypeError, createStructureAdapter, {})
return
def eval(self, stru=None):
'''Perform parallel calculation and return internal value array.
stru -- object that can be converted to StructureAdapter,
e.g., example diffpy Structure or pyobjcryst Crystal.
Use the last structure when None.
Return numpy array.
'''
# use StructureAdapter for faster pickles
from diffpy.srreal.structureadapter import createStructureAdapter
if stru is None:
struadpt = self.pqobj.getStructure()
else:
struadpt = createStructureAdapter(stru)
self.pqobj.setStructure(struadpt)
kwd = {
'cpuindex': None,
'ncpu': self.ncpu,
'pqobj': copy.copy(self.pqobj),
}
# shallow copies of kwd dictionary each with a unique cpuindex
arglist = [kwd.copy() for kwd['cpuindex'] in range(self.ncpu)]
for pdata in self.pmap(_parallelData, arglist):
self.pqobj._mergeParallelData(pdata, self.ncpu)
return self.pqobj.value
def test_nometa(self):
'''check NoMetaStructureAdapter.
'''
r0, g0 = PDFCalculator()(self.nickel)
ni1 = self.nickel.copy()
ni1.pdffit['scale'] = 2.0
r1, g1 = PDFCalculator()(ni1)
self.assertTrue(numpy.array_equal(r0, r1))
self.assertTrue(numpy.allclose(2 * g0, g1))
ni1nm = nometa(ni1)
self.assertTrue(ni1nm is nometa(ni1nm))
r1nm, g1nm = PDFCalculator()(ni1nm)
self.assertTrue(numpy.array_equal(r0, r1nm))
self.assertTrue(numpy.allclose(g0, g1nm))
ni2 = self.nickel.copy()
ni2.pdffit['delta2'] = 4
r2, g2 = PDFCalculator()(ni2)
r2, g2nm = PDFCalculator()(nometa(ni2))
self.assertFalse(numpy.allclose(g0, g2))
self.assertTrue(numpy.allclose(g0, g2nm))
adpt2 = createStructureAdapter(ni2)
ra2, ga2 = PDFCalculator()(adpt2)
ra2, ga2nm = PDFCalculator()(nometa(adpt2))
self.assertTrue(numpy.allclose(g2, ga2))
self.assertTrue(numpy.allclose(g0, ga2nm))
return
def setUp(self):
self.pwconst = PeakWidthModel.createByType('constant')
self.pwconst.width = 2
if self.tio2stru is None:
self.tio2stru = loadDiffPyStructure('rutile.cif')
self.tio2adpt = createStructureAdapter(self.tio2stru)
return
def test_nometa(self):
'''check NoMetaStructureAdapter.
'''
r0, g0 = PDFCalculator()(self.nickel)
ni1 = Structure(self.nickel)
ni1.pdffit['scale'] = 2.0
r1, g1 = PDFCalculator()(ni1)
self.assertTrue(numpy.array_equal(r0, r1))
self.assertTrue(numpy.allclose(2 * g0, g1))
ni1nm = nometa(ni1)
self.assertTrue(ni1nm is nometa(ni1nm))
r1nm, g1nm = PDFCalculator()(ni1nm)
self.assertTrue(numpy.array_equal(r0, r1nm))
self.assertTrue(numpy.allclose(g0, g1nm))
ni2 = Structure(self.nickel)
ni2.pdffit['delta2'] = 4
r2, g2 = PDFCalculator()(ni2)
r2, g2nm = PDFCalculator()(nometa(ni2))
self.assertFalse(numpy.allclose(g0, g2))
self.assertTrue(numpy.allclose(g0, g2nm))
adpt2 = createStructureAdapter(ni2)
ra2, ga2 = PDFCalculator()(adpt2)
ra2, ga2nm = PDFCalculator()(nometa(adpt2))
self.assertTrue(numpy.allclose(g2, ga2))
self.assertTrue(numpy.allclose(g0, ga2nm))
return
def setUp(self):
self.pwconst = PeakWidthModel.createByType('constant')
self.pwconst.width = 2
if self.tio2stru is None:
self.tio2stru = loadDiffPyStructure('rutile.cif')
self.tio2adpt = createStructureAdapter(self.tio2stru)
return
def eval(self, stru=None):
'''Perform parallel calculation and return internal value array.
stru -- object that can be converted to StructureAdapter,
e.g., example diffpy Structure or pyobjcryst Crystal.
Use the last structure when None.
Return numpy array.
'''
# use StructureAdapter for faster pickles
from diffpy.srreal.structureadapter import createStructureAdapter
if stru is None:
struadpt = self.pqobj.getStructure()
else:
struadpt = createStructureAdapter(stru)
self.pqobj.setStructure(struadpt)
kwd = { 'cpuindex' : None,
'ncpu' : self.ncpu,
'pqobj' : copy.copy(self.pqobj),
}
# shallow copies of kwd dictionary each with a unique cpuindex
arglist = [kwd.copy() for kwd['cpuindex'] in range(self.ncpu)]
for pdata in self.pmap(_parallelData, arglist):
self.pqobj._mergeParallelData(pdata, self.ncpu)
return self.pqobj.value
def test_createStructureAdapterTypes(self):
'''Check types returned by conversion from diffpy.structure.
'''
from diffpy.srreal.structureconverters import (
DiffPyStructureAtomicAdapter, DiffPyStructurePeriodicAdapter)
adpt = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt) is DiffPyStructurePeriodicAdapter)
self.nickel.pdffit = None
adpt1 = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt1) is PeriodicStructureAdapter)
self.nickel.lattice.setLatPar(1, 1, 1, 90, 90, 90)
adpt2 = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt2) is AtomicStructureAdapter)
self.nickel.pdffit = dict(scale=1)
adpt3 = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt3) is DiffPyStructureAtomicAdapter)
return
def test_createStructureAdapter_int64_occupancy(self):
"""Check Structure conversion when occupany is of numpy.int64 type.
"""
self.nickel[0].occupancy = numpy.int64(0)
self.nickel[1].occupancy = numpy.int64(1)
adpt = createStructureAdapter(self.nickel)
self.assertEqual(0.0, adpt.siteOccupancy(0))
self.assertEqual(1.0, adpt.siteOccupancy(1))
return
def test_createStructureAdapter_int64_occupancy(self):
"""Check Structure conversion when occupany is of numpy.int64 type.
"""
self.nickel[0].occupancy = numpy.int64(0)
self.nickel[1].occupancy = numpy.int64(1)
adpt = createStructureAdapter(self.nickel)
self.assertEqual(0.0, adpt.siteOccupancy(0))
self.assertEqual(1.0, adpt.siteOccupancy(1))
return
def test_createStructureAdapterTypes(self):
'''Check types returned by conversion from diffpy.Structure.
'''
from diffpy.srreal.structureconverters import (
DiffPyStructureAtomicAdapter,
DiffPyStructurePeriodicAdapter)
adpt = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt) is DiffPyStructurePeriodicAdapter)
self.nickel.pdffit = None
adpt1 = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt1) is PeriodicStructureAdapter)
self.nickel.lattice.setLatPar(1, 1, 1, 90, 90, 90)
adpt2 = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt2) is AtomicStructureAdapter)
self.nickel.pdffit = dict(scale=1)
adpt3 = createStructureAdapter(self.nickel)
self.assertTrue(type(adpt3) is DiffPyStructureAtomicAdapter)
return
def test_pickling(self):
'''check pickling of StructureAdapter instances.
'''
adpt = createStructureAdapter(self.nickel)
adpt1 = cPickle.loads(cPickle.dumps(adpt))
self.assertFalse(adpt is adpt1)
self.assertEqual(adpt.countSites(), adpt1.countSites())
self.assertEqual(adpt.totalOccupancy(), adpt1.totalOccupancy())
self.assertEqual(adpt.siteAtomType(1), adpt1.siteAtomType(1))
self.assertTrue(numpy.array_equal(
adpt.siteCartesianPosition(1), adpt1.siteCartesianPosition(1)))
self.assertEqual(adpt.siteMultiplicity(1), adpt1.siteMultiplicity(1))
self.assertEqual(adpt.siteOccupancy(1), adpt1.siteOccupancy(1))
self.assertTrue(adpt.siteAnisotropy(1) is adpt1.siteAnisotropy(1))
self.assertTrue(numpy.array_equal(
adpt.siteCartesianUij(1), adpt1.siteCartesianUij(1)))
return
def test_pickling(self):
'''check pickling of StructureAdapter instances.
'''
adpt = createStructureAdapter(self.nickel)
adpt1 = pickle.loads(pickle.dumps(adpt))
self.assertFalse(adpt is adpt1)
self.assertEqual(adpt.countSites(), adpt1.countSites())
self.assertEqual(adpt.totalOccupancy(), adpt1.totalOccupancy())
self.assertEqual(adpt.siteAtomType(1), adpt1.siteAtomType(1))
self.assertTrue(
numpy.array_equal(adpt.siteCartesianPosition(1),
adpt1.siteCartesianPosition(1)))
self.assertEqual(adpt.siteMultiplicity(1), adpt1.siteMultiplicity(1))
self.assertEqual(adpt.siteOccupancy(1), adpt1.siteOccupancy(1))
self.assertTrue(adpt.siteAnisotropy(1) is adpt1.siteAnisotropy(1))
self.assertTrue(
numpy.array_equal(adpt.siteCartesianUij(1),
adpt1.siteCartesianUij(1)))
return
def fromStructure(cls, stru, sftb, q=0):
"""\
Calculate average scattering factors from a structure object.
Parameters
----------
stru : diffpy Structure or pyobjcryst Crystal or StructureAdapter
The structure object that stores the atom species and their
occupancies. Can be any type with a registered conversion
to the StructureAdapter class.
sftb : ScatteringFactorTable or str
The ScatteringFactorTable object for looking up the values.
When string use `ScatteringFactorTable.createByType` to create
a new lookup table of the specified type.
q : float or NumPy array (optional)
The Q value in inverse Angstroms for which to lookup
the scattering factor values.
See also
--------
RegisterStructureAdapter : to add support for more structure types.
Returns
-------
SFAverage
The calculated scattering factor averages.
"""
# a bit of duck-typing for faster handling of diffpy.structure
if hasattr(type(stru), 'composition'):
composition = stru.composition
if isinstance(composition, dict):
return cls.fromComposition(composition, sftb, q)
# otherwise let's convert to a known structure type
from diffpy.srreal.structureadapter import createStructureAdapter
adpt = createStructureAdapter(stru)
composition = {}
for i in range(adpt.countSites()):
smbl = adpt.siteAtomType(i)
cnt = adpt.siteOccupancy(i) * adpt.siteMultiplicity(i)
composition[smbl] = composition.get(smbl, 0) + cnt
return cls.fromComposition(composition, sftb, q)
def fromStructure(cls, sftb, stru, q=0):
"""\
Calculate average scattering factors from a structure object.
Parameters
----------
sftb : ScatteringFactorTable
The ScatteringFactorTable object for looking up the values.
stru : diffpy Structure or pyobjcryst Crystal or StructureAdapter
The structure object that stores the atom species and their
occupancies. Can be any type with a registered conversion
to the StructureAdapter class.
q : float or NumPy array (optional)
The Q value in inverse Angstroms for which to lookup
the scattering factor values.
See also
--------
RegisterStructureAdapter : to add support for more structure types.
Returns
-------
SFAverage
The calculated scattering factor averages.
"""
# a bit of duck-typing for faster handling of diffpy.Structure
if hasattr(type(stru), 'composition'):
composition = stru.composition
if isinstance(composition, dict):
return cls.fromComposition(sftb, composition, q)
# otherwise let's convert to a known structure type
from diffpy.srreal.structureadapter import createStructureAdapter
adpt = createStructureAdapter(stru)
composition = {}
for i in range(adpt.countSites()):
smbl = adpt.siteAtomType(i)
cnt = adpt.siteOccupancy(i) * adpt.siteMultiplicity(i)
composition[smbl] = composition.get(smbl, 0) + cnt
return cls.fromComposition(sftb, composition, q)
def test_nosymmetry(self):
'''check NoSymmetryStructureAdapter.
'''
pdfc0 = PDFCalculator()
r0, g0 = pdfc0(self.nickel)
rdf0 = pdfc0.rdf
niuc = nosymmetry(self.nickel)
self.assertTrue(niuc is nosymmetry(niuc))
pdfc1 = PDFCalculator()
r1, g1 = pdfc1(niuc)
self.assertTrue(numpy.array_equal(r0, r1))
self.assertFalse(numpy.allclose(g0, g1))
tail = (r0 > 5.0)
self.assertTrue(numpy.allclose(0.0 * g1[tail], g1[tail]))
rdf0 = pdfc0.rdf
rdf1 = pdfc1.rdf
head = r0 < 3.0
self.assertAlmostEqual(12.0, numpy.sum(rdf0[head] * pdfc0.rstep), 5)
self.assertAlmostEqual(3.0, numpy.sum(rdf1[head] * pdfc1.rstep), 5)
adpt0 = createStructureAdapter(self.nickel)
ra2, ga2 = PDFCalculator()(nosymmetry(adpt0))
self.assertTrue(numpy.array_equal(r0, ra2))
self.assertTrue(numpy.allclose(g1, ga2))
return
def test_nosymmetry(self):
'''check NoSymmetryStructureAdapter.
'''
pdfc0 = PDFCalculator()
r0, g0 = pdfc0(self.nickel)
rdf0 = pdfc0.rdf
niuc = nosymmetry(self.nickel)
self.assertTrue(niuc is nosymmetry(niuc))
pdfc1 = PDFCalculator()
r1, g1 = pdfc1(niuc)
self.assertTrue(numpy.array_equal(r0, r1))
self.assertFalse(numpy.allclose(g0, g1))
tail = (r0 > 5.0)
self.assertTrue(numpy.allclose(0.0 * g1[tail], g1[tail]))
rdf0 = pdfc0.rdf
rdf1 = pdfc1.rdf
head = r0 < 3.0
self.assertAlmostEqual(12.0, numpy.sum(rdf0[head] * pdfc0.rstep), 5)
self.assertAlmostEqual(3.0, numpy.sum(rdf1[head] * pdfc1.rstep), 5)
adpt0 = createStructureAdapter(self.nickel)
ra2, ga2 = PDFCalculator()(nosymmetry(adpt0))
self.assertTrue(numpy.array_equal(r0, ra2))
self.assertTrue(numpy.allclose(g1, ga2))
return
def setUp(self):
rutile_crystal = loadObjCrystCrystal('TiO2_rutile-fit.cif')
self.rutile = createStructureAdapter(rutile_crystal)
return
def setUp(self):
rutile_crystal = loadObjCrystCrystal(rutile_cif)
self.rutile = createStructureAdapter(rutile_crystal)
return
def setUp(self):
rutile_crystal = loadObjCrystCrystal(rutile_cif)
self.rutile = createStructureAdapter(rutile_crystal)
return
def setUp(self):
rutile_crystal = loadObjCrystCrystal('TiO2_rutile-fit.cif')
self.rutile = createStructureAdapter(rutile_crystal)
return
