class TestDebyePDFCalculator(unittest.TestCase):
bucky = None
tio2rutile = None
def setUp(self):
self.dpdfc = DebyePDFCalculator()
if not TestDebyePDFCalculator.bucky:
TestDebyePDFCalculator.bucky = (
loadDiffPyStructure('C60bucky.stru'))
if not TestDebyePDFCalculator.tio2rutile:
TestDebyePDFCalculator.tio2rutile = (
loadDiffPyStructure('TiO2_rutile-fit.stru'))
return
# def tearDown(self):
# return
#
# def test___call__(self):
# """check DebyePDFCalculator.__call__()
# """
# return
#
# def test___init__(self):
# """check DebyePDFCalculator.__init__()
# """
# return
def test___getattr__(self):
"""check DebyePDFCalculator.__getattr__()
"""
self.assertEqual(0.0, self.dpdfc.qmin)
self.dpdfc._setDoubleAttr('qmin', 1.23)
self.assertEqual(1.23, self.dpdfc.qmin)
return
def test___setattr__(self):
"""check DebyePDFCalculator.__setattr__()
"""
self.assertNotEqual(1.23, self.dpdfc._getDoubleAttr('rmin'))
self.dpdfc.rmin = 1.23
self.assertEqual(1.23, self.dpdfc._getDoubleAttr('rmin'))
return
def test__getDoubleAttr(self):
"""check DebyePDFCalculator._getDoubleAttr()
"""
gdba = self.dpdfc._getDoubleAttr
self.assertEqual(1.0, gdba('scale'))
self.assertEqual(0.0, gdba('qdamp'))
self.assertRaises(Exception, gdba, 'notanattribute')
return
def test__hasDoubleAttr(self):
"""check DebyePDFCalculator._hasDoubleAttr()
"""
self.assertTrue(self.dpdfc._hasDoubleAttr('scale'))
self.assertFalse(self.dpdfc._hasDoubleAttr('notanattribute'))
return
def test__namesOfDoubleAttributes(self):
"""check DebyePDFCalculator._namesOfDoubleAttributes()
"""
self.assertTrue(type(self.dpdfc._namesOfDoubleAttributes()) is set)
self.assertTrue('qmax' in self.dpdfc._namesOfDoubleAttributes())
return
def test__setDoubleAttr(self):
"""check DebyePDFCalculator._setDoubleAttr()
"""
gdba = self.dpdfc._getDoubleAttr
sdba = self.dpdfc._setDoubleAttr
self.assertEqual(0.0, gdba('rmin'))
sdba('rmin', 3.0)
self.assertEqual(3.0, gdba('rmin'))
return
def test_PDF_C60bucky(self):
"""check DebyePDFCalculator.pdf for C60 Bucky ball.
"""
qmax = self.dpdfc.qmax
r0, g0 = PDFCalculator(qmax=qmax)(self.bucky)
r1, g1 = self.dpdfc(self.bucky)
mxnd = _maxNormDiff(g0, g1)
self.assertTrue(mxnd < 0.0006)
return
def test_partial_pdfs(self):
"""Check calculation of partial PDFs.
"""
dpdfc = self.dpdfc
dpdfc.qmin = 1.0
rutile = self.tio2rutile
r0, g0 = dpdfc(rutile)
# Ti-Ti
dpdfc.maskAllPairs(False)
dpdfc.setTypeMask("Ti", "Ti", True)
r1, g1 = dpdfc(rutile)
self.assertTrue(numpy.array_equal(r0, r1))
dpdfc.invertMask()
r1i, g1i = dpdfc(rutile)
self.assertTrue(numpy.array_equal(r0, r1i))
self.assertTrue(numpy.allclose(g0, g1 + g1i))
# Ti-O
dpdfc.maskAllPairs(False)
dpdfc.setTypeMask('all', 'ALL', True)
dpdfc.setTypeMask('Ti', 'Ti', False)
dpdfc.setTypeMask('O', 'O', False)
r2, g2 = dpdfc(rutile)
self.assertTrue(numpy.array_equal(r0, r2))
dpdfc.invertMask()
r2i, g2i = dpdfc(rutile)
self.assertTrue(numpy.allclose(g0, g2 + g2i))
# Ti-O from type mask
dpdfc.maskAllPairs(True)
dpdfc.setTypeMask("Ti", "Ti", False)
dpdfc.setTypeMask("O", "O", False)
r2t, g2t = dpdfc(rutile)
self.assertTrue(numpy.array_equal(r0, r2t))
self.assertTrue(numpy.array_equal(g2, g2t))
dpdfc.invertMask()
r2ti, g2ti = dpdfc(rutile)
self.assertTrue(numpy.array_equal(g2i, g2ti))
# O-O
dpdfc.maskAllPairs(False)
dpdfc.setTypeMask('O', 'O', True)
r3, g3 = dpdfc(rutile)
dpdfc.invertMask()
r3i, g3i = dpdfc(rutile)
self.assertTrue(numpy.allclose(g0, g3 + g3i))
# check the sum of all partials
self.assertTrue(numpy.allclose(g0, g1 + g2 + g3))
return
def test_pickling(self):
'''check pickling and unpickling of PDFCalculator.
'''
dpdfc = self.dpdfc
dpdfc.setScatteringFactorTableByType('N')
dpdfc.scatteringfactortable.setCustomAs('Na', 'Na', 7)
dpdfc.addEnvelope('sphericalshape')
dpdfc.debyeprecision = 0.001
dpdfc.delta1 = 0.2
dpdfc.delta2 = 0.3
dpdfc.maxextension = 10.1
dpdfc.qbroad = 0.01
dpdfc.qdamp = 0.05
dpdfc.qmax = 10
dpdfc.qmin = 0.5
dpdfc.rmax = 10.0
dpdfc.rmin = 0.02
dpdfc.rstep = 0.02
dpdfc.scale = 1.1
dpdfc.spdiameter = 13.3
dpdfc.foobar = 'asdf'
spkl = pickle.dumps(dpdfc)
dpdfc1 = pickle.loads(spkl)
self.assertFalse(dpdfc is dpdfc1)
sft = dpdfc.scatteringfactortable
sft1 = dpdfc1.scatteringfactortable
self.assertEqual(sft.type(), sft1.type())
self.assertEqual(7.0, sft1.lookup('Na'))
for a in dpdfc._namesOfDoubleAttributes():
self.assertEqual(getattr(dpdfc, a), getattr(dpdfc1, a))
self.assertEqual(13.3, dpdfc1.getEnvelope('sphericalshape').spdiameter)
self.assertEqual(dpdfc._namesOfDoubleAttributes(),
dpdfc1._namesOfDoubleAttributes())
self.assertEqual(dpdfc.usedenvelopetypes, dpdfc1.usedenvelopetypes)
self.assertEqual('asdf', dpdfc1.foobar)
return
def test_mask_pickling(self):
'''Check if mask gets properly pickled and restored.
'''
self.dpdfc.maskAllPairs(False)
self.dpdfc.setPairMask(0, 1, True)
self.dpdfc.setTypeMask("Na", "Cl", True)
self.assertTrue(False is self.dpdfc.getPairMask(0, 0))
self.assertTrue(True is self.dpdfc.getPairMask(0, 1))
self.assertTrue(True is self.dpdfc.getTypeMask("Cl", "Na"))
dpdfc1 = pickle.loads(pickle.dumps(self.dpdfc))
self.assertTrue(False is dpdfc1.getPairMask(0, 0))
self.assertTrue(True is dpdfc1.getPairMask(0, 1))
self.assertTrue(True is self.dpdfc.getTypeMask("Cl", "Na"))
return
def test_pickling_derived_structure(self):
'''check pickling of DebyePDFCalculator with DerivedStructureAdapter.
'''
from diffpy.srreal.tests.testutils import DerivedStructureAdapter
dpdfc = self.dpdfc
stru0 = DerivedStructureAdapter()
dpdfc.setStructure(stru0)
self.assertEqual(1, stru0.cpqcount)
spkl = pickle.dumps(dpdfc)
dpdfc1 = pickle.loads(spkl)
self.assertTrue(stru0 is dpdfc.getStructure())
stru1 = dpdfc1.getStructure()
self.assertTrue(type(stru1) is DerivedStructureAdapter)
self.assertFalse(stru1 is stru0)
self.assertEqual(1, stru1.cpqcount)
return
class TestDebyePDFCalculator(unittest.TestCase):
bucky = None
tio2rutile = None
def setUp(self):
self.dpdfc = DebyePDFCalculator()
if not TestDebyePDFCalculator.bucky:
TestDebyePDFCalculator.bucky = (
loadDiffPyStructure('C60bucky.stru'))
if not TestDebyePDFCalculator.tio2rutile:
TestDebyePDFCalculator.tio2rutile = (
loadDiffPyStructure('TiO2_rutile-fit.stru'))
return
# def tearDown(self):
# return
#
# def test___call__(self):
# """check DebyePDFCalculator.__call__()
# """
# return
#
# def test___init__(self):
# """check DebyePDFCalculator.__init__()
# """
# return
def test___getattr__(self):
"""check DebyePDFCalculator.__getattr__()
"""
self.assertEqual(0.0, self.dpdfc.qmin)
self.dpdfc._setDoubleAttr('qmin', 1.23)
self.assertEqual(1.23, self.dpdfc.qmin)
return
def test___setattr__(self):
"""check DebyePDFCalculator.__setattr__()
"""
self.assertNotEquals(1.23, self.dpdfc._getDoubleAttr('rmin'))
self.dpdfc.rmin = 1.23
self.assertEqual(1.23, self.dpdfc._getDoubleAttr('rmin'))
return
def test__getDoubleAttr(self):
"""check DebyePDFCalculator._getDoubleAttr()
"""
gdba = self.dpdfc._getDoubleAttr
self.assertEqual(1.0, gdba('scale'))
self.assertEqual(0.0, gdba('qdamp'))
self.assertRaises(Exception, gdba, 'notanattribute')
return
def test__hasDoubleAttr(self):
"""check DebyePDFCalculator._hasDoubleAttr()
"""
self.failUnless(self.dpdfc._hasDoubleAttr('scale'))
self.failIf(self.dpdfc._hasDoubleAttr('notanattribute'))
return
def test__namesOfDoubleAttributes(self):
"""check DebyePDFCalculator._namesOfDoubleAttributes()
"""
self.failUnless(type(self.dpdfc._namesOfDoubleAttributes()) is set)
self.failUnless('qmax' in self.dpdfc._namesOfDoubleAttributes())
return
def test__setDoubleAttr(self):
"""check DebyePDFCalculator._setDoubleAttr()
"""
gdba = self.dpdfc._getDoubleAttr
sdba = self.dpdfc._setDoubleAttr
self.assertEqual(0.0, gdba('rmin'))
sdba('rmin', 3.0)
self.assertEqual(3.0, gdba('rmin'))
return
def test_PDF_C60bucky(self):
"""check DebyePDFCalculator.pdf for C60 Bucky ball.
"""
qmax = self.dpdfc.qmax
r0, g0 = PDFCalculator(qmax=qmax)(self.bucky)
r1, g1 = self.dpdfc(self.bucky)
mxnd = _maxNormDiff(g0, g1)
self.failUnless(mxnd < 0.0006)
return
def test_partial_pdfs(self):
"""Check calculation of partial PDFs.
"""
dpdfc = self.dpdfc
dpdfc.qmin = 1.0
rutile = self.tio2rutile
atomtypes = [a.element for a in rutile]
r0, g0 = dpdfc(rutile)
# Ti-Ti
dpdfc.maskAllPairs(False)
dpdfc.setTypeMask("Ti", "Ti", True)
r1, g1 = dpdfc(rutile)
self.failUnless(numpy.array_equal(r0, r1))
dpdfc.invertMask()
r1i, g1i = dpdfc(rutile)
self.failUnless(numpy.array_equal(r0, r1i))
self.failUnless(numpy.allclose(g0, g1 + g1i))
# Ti-O
dpdfc.maskAllPairs(False)
dpdfc.setTypeMask('all', 'ALL', True)
dpdfc.setTypeMask('Ti', 'Ti', False)
dpdfc.setTypeMask('O', 'O', False)
r2, g2 = dpdfc(rutile)
self.failUnless(numpy.array_equal(r0, r2))
dpdfc.invertMask()
r2i, g2i = dpdfc(rutile)
self.failUnless(numpy.allclose(g0, g2 + g2i))
# Ti-O from type mask
dpdfc.maskAllPairs(True)
dpdfc.setTypeMask("Ti", "Ti", False)
dpdfc.setTypeMask("O", "O", False)
r2t, g2t = dpdfc(rutile)
self.failUnless(numpy.array_equal(r0, r2t))
self.failUnless(numpy.array_equal(g2, g2t))
dpdfc.invertMask()
r2ti, g2ti = dpdfc(rutile)
self.failUnless(numpy.array_equal(g2i, g2ti))
# O-O
dpdfc.maskAllPairs(False)
dpdfc.setTypeMask('O', 'O', True)
r3, g3 = dpdfc(rutile)
dpdfc.invertMask()
r3i, g3i = dpdfc(rutile)
self.failUnless(numpy.allclose(g0, g3 + g3i))
# check the sum of all partials
self.failUnless(numpy.allclose(g0, g1 + g2 + g3))
return
def test_pickling(self):
'''check pickling and unpickling of PDFCalculator.
'''
dpdfc = self.dpdfc
dpdfc.setScatteringFactorTableByType('N')
dpdfc.scatteringfactortable.setCustomAs('Na', 'Na', 7)
dpdfc.addEnvelopeByType('sphericalshape')
dpdfc.debyeprecision = 0.001
dpdfc.delta1 = 0.2
dpdfc.delta2 = 0.3
dpdfc.maxextension = 10.1
dpdfc.qbroad = 0.01
dpdfc.qdamp = 0.05
dpdfc.qmax = 10
dpdfc.qmin = 0.5
dpdfc.rmax = 10.0
dpdfc.rmin = 0.02
dpdfc.rstep = 0.02
dpdfc.scale = 1.1
dpdfc.spdiameter = 13.3
dpdfc.foobar = 'asdf'
spkl = cPickle.dumps(dpdfc)
dpdfc1 = cPickle.loads(spkl)
self.failIf(dpdfc is dpdfc1)
sft = dpdfc.scatteringfactortable
sft1 = dpdfc1.scatteringfactortable
self.assertEqual(sft.type(), sft1.type())
self.assertEqual(7.0, sft1.lookup('Na'))
for a in dpdfc._namesOfDoubleAttributes():
self.assertEqual(getattr(dpdfc, a), getattr(dpdfc1, a))
self.assertEqual(13.3,
dpdfc1.getEnvelopeByType('sphericalshape').spdiameter)
self.assertEqual(dpdfc._namesOfDoubleAttributes(),
dpdfc1._namesOfDoubleAttributes())
self.assertEqual(dpdfc.usedenvelopetypes, dpdfc1.usedenvelopetypes)
self.assertEqual('asdf', dpdfc1.foobar)
return
def test_mask_pickling(self):
'''Check if mask gets properly pickled and restored.
'''
self.dpdfc.maskAllPairs(False)
self.dpdfc.setPairMask(0, 1, True)
self.dpdfc.setTypeMask("Na", "Cl", True)
self.failUnless(False is self.dpdfc.getPairMask(0, 0))
self.failUnless(True is self.dpdfc.getPairMask(0, 1))
self.failUnless(True is self.dpdfc.getTypeMask("Cl", "Na"))
dpdfc1 = cPickle.loads(cPickle.dumps(self.dpdfc))
self.failUnless(False is dpdfc1.getPairMask(0, 0))
self.failUnless(True is dpdfc1.getPairMask(0, 1))
self.failUnless(True is self.dpdfc.getTypeMask("Cl", "Na"))
return
