def test_parallel_bonds(self):
"""check parallel BondCalculator
"""
from diffpy.srreal.bondcalculator import BondCalculator
nickel = self.nickel
bc = BondCalculator()
d0 = bc(nickel)
pbc1 = createParallelCalculator(BondCalculator(), 3, map)
d1 = pbc1(nickel)
self.failUnless(numpy.array_equal(d0, d1))
pbc2 = createParallelCalculator(BondCalculator(), self.ncpu,
self.pool.imap_unordered)
d2 = pbc2(nickel)
self.failUnless(numpy.array_equal(d0, d2))
bc.rmax = pbc1.rmax = pbc2.rmax = 2.5
for bci in (bc, pbc1, pbc2):
bci.maskAllPairs(False)
bci.setPairMask(0, 'all', True)
bci.filterCone([1, 0, 0], 48)
d0a = bc(nickel)
self.assertEqual(8, len(d0a))
d1a = pbc1(nickel)
self.failUnless(numpy.array_equal(d0a, d1a))
d2a = pbc2(nickel)
self.failUnless(numpy.array_equal(d0a, d2a))
return
def setUp(self):
self.bdc = BondCalculator()
if not hasattr(self, 'rutile'):
type(self).rutile = loadDiffPyStructure('rutile.cif')
if not hasattr(self, 'nickel'):
type(self).nickel = loadDiffPyStructure('Ni.stru')
if not hasattr(self, 'niprim'):
type(self).niprim = loadDiffPyStructure('Ni_primitive.stru')
return
def setUp(self):
self.bdc = BondCalculator()
if not hasattr(self, 'rutile'):
type(self).rutile = loadObjCrystCrystal('rutile.cif')
if not hasattr(self, 'nickel'):
type(self).nickel = loadObjCrystCrystal('Ni.cif')
return
def setUp(self):
self.bdc = BondCalculator()
if not hasattr(self, 'rutile'):
type(self).rutile = loadDiffPyStructure('rutile.cif')
if not hasattr(self, 'nickel'):
type(self).nickel = loadDiffPyStructure('Ni.stru')
if not hasattr(self, 'niprim'):
type(self).niprim = loadDiffPyStructure('Ni_primitive.stru')
return
def test___init__(self):
"""check BondCalculator.__init__()
"""
self.assertEqual(0, self.bdc.rmin)
self.assertEqual(5, self.bdc.rmax)
self.assertEqual(0, len(self.bdc.distances))
bdc1 = BondCalculator(rmin=2, rmax=7)
self.assertEqual(2, bdc1.rmin)
self.assertEqual(7, bdc1.rmax)
self.assertRaises(TypeError, BondCalculator, invalid=55)
return
def test_distances(self):
"""check BondCalculator.distances
"""
self.bdc.eval(self.nickel)
dst = self.bdc.distances
self.assertTrue(numpy.array_equal(dst, BondCalculator()(self.nickel)))
self.assertTrue(numpy.array_equal(dst, numpy.sort(dst)))
self.bdc.maskAllPairs(False)
for i in range(4):
self.bdc.setPairMask(0, i, True)
dst0a = self.bdc(self.nickel)
idx0a = (self.bdc.sites0 == 0)
self.bdc.maskAllPairs(False)
for i in range(4):
self.bdc.setPairMask(3, i, True)
dst3a = self.bdc(self.nickel)
self.bdc.maskAllPairs(True)
dstp = self.bdc(self.niprim)
self.assertTrue(numpy.allclose(dst0a, dst3a))
self.assertTrue(numpy.allclose(dst0a[idx0a], dstp))
return
class TestBondCalculator(unittest.TestCase):
def setUp(self):
self.bdc = BondCalculator()
if not hasattr(self, 'rutile'):
type(self).rutile = loadDiffPyStructure('rutile.cif')
if not hasattr(self, 'nickel'):
type(self).nickel = loadDiffPyStructure('Ni.stru')
if not hasattr(self, 'niprim'):
type(self).niprim = loadDiffPyStructure('Ni_primitive.stru')
return
def tearDown(self):
return
def test___init__(self):
"""check BondCalculator.__init__()
"""
self.assertEqual(0, self.bdc.rmin)
self.assertEqual(5, self.bdc.rmax)
self.assertEqual(0, len(self.bdc.distances))
return
def test___call__(self):
"""check BondCalculator.__call__()
"""
bdc = self.bdc
bdc.rmax = 0
self.assertEqual(0, len(bdc(self.rutile)))
bdc.rmax = 2.0
self.assertEqual(24, len(bdc(self.rutile)))
self.assertEqual(0, len(bdc(self.niprim)))
bdc.rmax = 2.5
self.assertEqual(12, len(bdc(self.niprim)))
return
def test_pickling(self):
'''check pickling and unpickling of BondCalculator.
'''
bdc = self.bdc
bdc.rmin = 0.1
bdc.rmax = 12.3
bdc.setPairMask(1, 2, False)
bdc.foobar = 'asdf'
bdc(self.nickel)
spkl = cPickle.dumps(bdc)
bdc1 = cPickle.loads(spkl)
self.assertFalse(bdc is bdc1)
for a in bdc._namesOfDoubleAttributes():
self.assertEqual(getattr(bdc, a), getattr(bdc1, a))
self.assertFalse(bdc1.getPairMask(1, 2))
self.assertTrue(bdc1.getPairMask(0, 0))
self.assertEqual('asdf', bdc1.foobar)
self.assertTrue(numpy.array_equal(bdc.distances, bdc1.distances))
return
def test_distances(self):
"""check BondCalculator.distances
"""
self.bdc.eval(self.nickel)
dst = self.bdc.distances
self.assertTrue(numpy.array_equal(dst,
BondCalculator()(self.nickel)))
self.assertTrue(numpy.array_equal(dst, numpy.sort(dst)))
self.bdc.maskAllPairs(False)
for i in range(4):
self.bdc.setPairMask(0, i, True)
dst0a = self.bdc(self.nickel)
idx0a = (self.bdc.sites0 == 0)
self.bdc.maskAllPairs(False)
for i in range(4):
self.bdc.setPairMask(3, i, True)
dst3a = self.bdc(self.nickel)
self.bdc.maskAllPairs(True)
dstp = self.bdc(self.niprim)
self.assertTrue(numpy.allclose(dst0a, dst3a))
self.assertTrue(numpy.allclose(dst0a[idx0a], dstp))
return
def test_directions(self):
"""check BondCalculator.directions
"""
dst = self.bdc(self.rutile)
drs = self.bdc.directions
nms = numpy.sqrt(numpy.sum(numpy.power(drs, 2), axis=1))
self.assertTrue(numpy.allclose(dst, nms))
return
def test_sites(self):
"""check BondCalculator.sites
"""
bdc = self.bdc
dst = bdc(self.rutile)
self.assertEqual(len(dst), len(bdc.sites0))
self.assertEqual(len(dst), len(bdc.sites1))
self.assertEqual(0, numpy.min(bdc.sites0))
self.assertEqual(5, numpy.max(bdc.sites0))
self.assertEqual(0, numpy.min(bdc.sites1))
self.assertEqual(5, numpy.max(bdc.sites1))
dij = [(tuple(d) + (i0, i1)) for d, i0, i1 in zip(
bdc.directions, bdc.sites0, bdc.sites1)]
self.assertEqual(len(dij), len(set(dij)))
bdc.maskAllPairs(False)
bdc(self.rutile)
self.assertEqual(0, len(bdc.sites0))
bdc.setPairMask(3, 3, True)
bdc(self.rutile)
self.assertTrue(len(bdc.sites0))
self.assertEqual(set([3]), set(bdc.sites0).union(bdc.sites1))
return
def test_types(self):
"""check BondCalculator.types
"""
bdc = self.bdc
dst = bdc(self.rutile)
self.assertEqual(len(dst), len(bdc.types0))
self.assertEqual(len(dst), len(bdc.types1))
self.assertEqual(set(('Ti', 'O')), set(bdc.types0))
self.assertEqual(set(('Ti', 'O')), set(bdc.types1))
self.assertFalse((bdc.types0 == bdc.types1).all())
bdc.maskAllPairs(False)
bdc(self.rutile)
self.assertEqual(0, bdc.types0.size)
self.assertEqual(0, bdc.types1.size)
bdc.setPairMask(3, 3, True)
bdc(self.rutile)
self.assertTrue(len(bdc.types0))
self.assertEqual(set(['O']), set(bdc.types0).union(set(bdc.types1)))
return
def test_filterCone(self):
"""check BondCalculator.filterCone()
"""
bdc = self.bdc
bdc.rmax = 2.5
self.assertEqual(12, len(bdc(self.niprim)))
bdc.filterCone([0, 0, +1], 1)
self.assertEqual(1, len(bdc(self.niprim)))
bdc.filterCone([0, 0, -1], 1)
self.assertEqual(2, len(bdc(self.niprim)))
bdc.filterOff()
self.assertEqual(12, len(bdc(self.niprim)))
bdc.filterCone([0, 0.1, +1], 6)
bdc(self.niprim)
self.assertEqual(1, len(bdc(self.niprim)))
bdc.filterCone([0, 0, +1], 180)
self.assertEqual(12, len(bdc(self.niprim)))
return
def test_filterOff(self):
"""check BondCalculator.filterOff()
"""
bdc = self.bdc
bdc.rmax = 2.5
bdc.filterCone([1, 2, 3], -1)
self.assertEqual(0, len(bdc(self.niprim).tolist()))
bdc.filterOff()
self.assertEqual(12, len(bdc(self.niprim)))
return
def test_setPairMask(self):
'''check different setPairMask arguments.
'''
bdc = self.bdc
dall = bdc(self.nickel)
bdc.maskAllPairs(False)
self.assertEqual(0, len(bdc(self.nickel)))
for i in range(4):
bdc.setPairMask(0, i, True)
dst0a = bdc(self.nickel)
bdc.setPairMask(range(4), 0, True, others=False)
dst0b = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dst0a, dst0b))
bdc.maskAllPairs(False)
bdc.setPairMask(0, -7, True)
dst0c = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dst0a, dst0c))
bdc.maskAllPairs(False)
bdc.setPairMask(0, 'all', True)
dst0d = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dst0a, dst0d))
bdc.setPairMask('all', 'all', False)
self.assertEqual(0, len(bdc(self.nickel)))
bdc.setPairMask('all', range(4), True)
dall2 = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dall, dall2))
self.assertRaises(ValueError, bdc.setPairMask, 'fooo', 2, True)
self.assertRaises(ValueError, bdc.setPairMask, 'aLL', 2, True)
return
def test_setTypeMask(self):
'''check different setTypeMask arguments.
'''
bdc = self.bdc
dall = bdc(self.rutile)
bdc.setTypeMask('all', 'All', False)
self.assertTrue(numpy.array_equal(dall, bdc(self.rutile)))
bdc.setTypeMask('all', 'ALL', False)
self.assertEqual(0, len(bdc(self.rutile)))
bdc.maskAllPairs(True)
bdc.setTypeMask('Ti', ['O'], True, others=False)
bdc()
tps = set(zip(bdc.types0, bdc.types1))
self.assertEqual(2, len(tps))
self.assertTrue(('Ti', 'O') in tps)
self.assertTrue(('O', 'Ti') in tps)
bdc.setTypeMask(['Ti'], self.rutile.element, 0, others=1)
bdc()
tps = set(zip(bdc.types0, bdc.types1))
self.assertEqual(set([('O', 'O')]), tps)
return
class TestBondCalculator(unittest.TestCase):
def setUp(self):
self.bdc = BondCalculator()
if not hasattr(self, 'rutile'):
type(self).rutile = loadDiffPyStructure('rutile.cif')
if not hasattr(self, 'nickel'):
type(self).nickel = loadDiffPyStructure('Ni.stru')
if not hasattr(self, 'niprim'):
type(self).niprim = loadDiffPyStructure('Ni_primitive.stru')
return
def tearDown(self):
return
def test___init__(self):
"""check BondCalculator.__init__()
"""
self.assertEqual(0, self.bdc.rmin)
self.assertEqual(5, self.bdc.rmax)
self.assertEqual(0, len(self.bdc.distances))
return
def test___call__(self):
"""check BondCalculator.__call__()
"""
bdc = self.bdc
bdc.rmax = 0
self.assertEqual(0, len(bdc(self.rutile)))
bdc.rmax = 2.0
self.assertEqual(24, len(bdc(self.rutile)))
self.assertEqual(0, len(bdc(self.niprim)))
bdc.rmax = 2.5
self.assertEqual(12, len(bdc(self.niprim)))
return
def test_pickling(self):
'''check pickling and unpickling of BondCalculator.
'''
bdc = self.bdc
bdc.rmin = 0.1
bdc.rmax = 12.3
bdc.setPairMask(1, 2, False)
bdc.foobar = 'asdf'
bdc(self.nickel)
spkl = cPickle.dumps(bdc)
bdc1 = cPickle.loads(spkl)
self.assertFalse(bdc is bdc1)
for a in bdc._namesOfDoubleAttributes():
self.assertEqual(getattr(bdc, a), getattr(bdc1, a))
self.assertFalse(bdc1.getPairMask(1, 2))
self.assertTrue(bdc1.getPairMask(0, 0))
self.assertEqual('asdf', bdc1.foobar)
self.assertTrue(numpy.array_equal(bdc.distances, bdc1.distances))
return
def test_pickling_derived_structure(self):
'''check pickling of BondCalculator with DerivedStructureAdapter.
'''
from diffpy.srreal.tests.testutils import DerivedStructureAdapter
bdc = self.bdc
stru0 = DerivedStructureAdapter()
bdc.setStructure(stru0)
self.assertEqual(1, stru0.cpqcount)
spkl = cPickle.dumps(bdc)
bdc1 = cPickle.loads(spkl)
self.failUnless(stru0 is bdc.getStructure())
stru1 = bdc1.getStructure()
self.failUnless(type(stru1) is DerivedStructureAdapter)
self.failIf(stru1 is stru0)
self.assertEqual(1, stru1.cpqcount)
return
def test_distances(self):
"""check BondCalculator.distances
"""
self.bdc.eval(self.nickel)
dst = self.bdc.distances
self.assertTrue(numpy.array_equal(dst,
BondCalculator()(self.nickel)))
self.assertTrue(numpy.array_equal(dst, numpy.sort(dst)))
self.bdc.maskAllPairs(False)
for i in range(4):
self.bdc.setPairMask(0, i, True)
dst0a = self.bdc(self.nickel)
idx0a = (self.bdc.sites0 == 0)
self.bdc.maskAllPairs(False)
for i in range(4):
self.bdc.setPairMask(3, i, True)
dst3a = self.bdc(self.nickel)
self.bdc.maskAllPairs(True)
dstp = self.bdc(self.niprim)
self.assertTrue(numpy.allclose(dst0a, dst3a))
self.assertTrue(numpy.allclose(dst0a[idx0a], dstp))
return
def test_directions(self):
"""check BondCalculator.directions
"""
dst = self.bdc(self.rutile)
drs = self.bdc.directions
nms = numpy.sqrt(numpy.sum(numpy.power(drs, 2), axis=1))
self.assertTrue(numpy.allclose(dst, nms))
return
def test_sites(self):
"""check BondCalculator.sites
"""
bdc = self.bdc
dst = bdc(self.rutile)
self.assertEqual(len(dst), len(bdc.sites0))
self.assertEqual(len(dst), len(bdc.sites1))
self.assertEqual(0, numpy.min(bdc.sites0))
self.assertEqual(5, numpy.max(bdc.sites0))
self.assertEqual(0, numpy.min(bdc.sites1))
self.assertEqual(5, numpy.max(bdc.sites1))
dij = [(tuple(d) + (i0, i1)) for d, i0, i1 in zip(
bdc.directions, bdc.sites0, bdc.sites1)]
self.assertEqual(len(dij), len(set(dij)))
bdc.maskAllPairs(False)
bdc(self.rutile)
self.assertEqual(0, len(bdc.sites0))
bdc.setPairMask(3, 3, True)
bdc(self.rutile)
self.assertTrue(len(bdc.sites0))
self.assertEqual(set([3]), set(bdc.sites0).union(bdc.sites1))
return
def test_types(self):
"""check BondCalculator.types
"""
bdc = self.bdc
dst = bdc(self.rutile)
self.assertEqual(len(dst), len(bdc.types0))
self.assertEqual(len(dst), len(bdc.types1))
self.assertEqual(set(('Ti', 'O')), set(bdc.types0))
self.assertEqual(set(('Ti', 'O')), set(bdc.types1))
self.assertFalse((bdc.types0 == bdc.types1).all())
bdc.maskAllPairs(False)
bdc(self.rutile)
self.assertEqual(0, bdc.types0.size)
self.assertEqual(0, bdc.types1.size)
bdc.setPairMask(3, 3, True)
bdc(self.rutile)
self.assertTrue(len(bdc.types0))
self.assertEqual(set(['O']), set(bdc.types0).union(set(bdc.types1)))
return
def test_filterCone(self):
"""check BondCalculator.filterCone()
"""
bdc = self.bdc
bdc.rmax = 2.5
self.assertEqual(12, len(bdc(self.niprim)))
bdc.filterCone([0, 0, +1], 1)
self.assertEqual(1, len(bdc(self.niprim)))
bdc.filterCone([0, 0, -1], 1)
self.assertEqual(2, len(bdc(self.niprim)))
bdc.filterOff()
self.assertEqual(12, len(bdc(self.niprim)))
bdc.filterCone([0, 0.1, +1], 6)
bdc(self.niprim)
self.assertEqual(1, len(bdc(self.niprim)))
bdc.filterCone([0, 0, +1], 180)
self.assertEqual(12, len(bdc(self.niprim)))
return
def test_filterOff(self):
"""check BondCalculator.filterOff()
"""
bdc = self.bdc
bdc.rmax = 2.5
bdc.filterCone([1, 2, 3], -1)
self.assertEqual(0, len(bdc(self.niprim).tolist()))
bdc.filterOff()
self.assertEqual(12, len(bdc(self.niprim)))
return
def test_setPairMask(self):
'''check different setPairMask arguments.
'''
bdc = self.bdc
dall = bdc(self.nickel)
bdc.maskAllPairs(False)
self.assertEqual(0, len(bdc(self.nickel)))
for i in range(4):
bdc.setPairMask(0, i, True)
dst0a = bdc(self.nickel)
bdc.setPairMask(range(4), 0, True, others=False)
dst0b = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dst0a, dst0b))
bdc.maskAllPairs(False)
bdc.setPairMask(0, -7, True)
dst0c = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dst0a, dst0c))
bdc.maskAllPairs(False)
bdc.setPairMask(0, 'all', True)
dst0d = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dst0a, dst0d))
bdc.setPairMask('all', 'all', False)
self.assertEqual(0, len(bdc(self.nickel)))
bdc.setPairMask('all', range(4), True)
dall2 = bdc(self.nickel)
self.assertTrue(numpy.array_equal(dall, dall2))
self.assertRaises(ValueError, bdc.setPairMask, 'fooo', 2, True)
self.assertRaises(ValueError, bdc.setPairMask, 'aLL', 2, True)
return
def test_setTypeMask(self):
'''check different setTypeMask arguments.
'''
bdc = self.bdc
dall = bdc(self.rutile)
bdc.setTypeMask('all', 'All', False)
self.assertTrue(numpy.array_equal(dall, bdc(self.rutile)))
bdc.setTypeMask('all', 'ALL', False)
self.assertEqual(0, len(bdc(self.rutile)))
bdc.maskAllPairs(True)
bdc.setTypeMask('Ti', ['O'], True, others=False)
bdc()
tps = set(zip(bdc.types0, bdc.types1))
self.assertEqual(2, len(tps))
self.assertTrue(('Ti', 'O') in tps)
self.assertTrue(('O', 'Ti') in tps)
bdc.setTypeMask(['Ti'], self.rutile.element, 0, others=1)
bdc()
tps = set(zip(bdc.types0, bdc.types1))
self.assertEqual(set([('O', 'O')]), tps)
return