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test_bondcalculator.py
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#!/usr/bin/env python
"""Unit tests for diffpy.srreal.bondcalculator."""
import pickle
import unittest
import numpy
import pytest
from testutils import loadDiffPyStructure, loadObjCrystCrystal, pickle_with_attr
from diffpy.srreal.bondcalculator import BondCalculator
# ----------------------------------------------------------------------------
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))
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___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)))
self.assertEqual(0, len(bdc(self.niprim, rmax=2)))
self.assertRaises(TypeError, bdc, self.niprim, rmax=5, invalid=7)
self.assertEqual(2, bdc.rmax)
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(self.nickel)
spkl = pickle.dumps(bdc)
bdc1 = pickle.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.assertTrue(numpy.array_equal(bdc.distances, bdc1.distances))
self.assertRaises(RuntimeError, pickle_with_attr, bdc, foo="bar")
return
def test_pickling_derived_structure(self):
"""Check pickling of BondCalculator with DerivedStructureAdapter."""
from testutils import DerivedStructureAdapter
bdc = self.bdc
stru0 = DerivedStructureAdapter()
bdc.setStructure(stru0)
self.assertEqual(1, stru0.cpqcount)
spkl = pickle.dumps(bdc)
bdc1 = pickle.loads(spkl)
self.assertTrue(stru0 is bdc.getStructure())
stru1 = bdc1.getStructure()
self.assertTrue(type(stru1) is DerivedStructureAdapter)
self.assertFalse(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
# End of class TestBondCalculator
# ----------------------------------------------------------------------------
class TestBondCalculatorObjCryst(unittest.TestCase):
@pytest.fixture(autouse=True)
def _check_periodictable(self, has_pyobjcryst, _msg_nopyobjcryst):
if not has_pyobjcryst:
pytest.skip(_msg_nopyobjcryst)
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 tearDown(self):
return
def test___call__(self):
"""Check BondCalculator.__call__()"""
bdc = self.bdc
bdc.rmax = 0
self.assertEqual(0, len(bdc(self.rutile).tolist()))
bdc.rmax = 2.0
self.assertEqual(6 + 3, len(bdc(self.rutile)))
bdc.rmax = 2.5
self.assertEqual(12, len(bdc(self.nickel)))
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(1, numpy.max(bdc.sites0))
self.assertEqual(0, numpy.min(bdc.sites1))
self.assertEqual(1, 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(1, 1, True)
bdc(self.rutile)
self.assertTrue(len(bdc.sites0))
self.assertEqual(set([1]), 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.assertNotEqual(bdc.types0.tolist(), bdc.types1.tolist())
bdc.maskAllPairs(False)
bdc(self.rutile)
self.assertEqual(0, bdc.types0.size)
self.assertEqual(0, bdc.types1.size)
bdc.setPairMask(1, 1, 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
bdc.filterCone([+0.5, +0.5, 0], 1)
self.assertEqual(1, len(bdc(self.nickel)))
bdc.filterCone([-0.5, -0.5, 0], 1)
self.assertEqual(2, len(bdc(self.nickel)))
bdc.filterOff()
self.assertEqual(12, len(bdc(self.nickel)))
bdc.filterCone([+0.5, +0.5, 0.05], 6)
bdc(self.nickel)
self.assertEqual(1, len(bdc(self.nickel)))
bdc.filterCone([+0.5, +0.5, 0], 180)
self.assertEqual(12, len(bdc(self.nickel)))
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.nickel)))
bdc.filterOff()
self.assertEqual(12, len(bdc(self.nickel)))
return
# End of class TestBondCalculatorObjCryst
# ----------------------------------------------------------------------------
if __name__ == "__main__":
unittest.main()
# End of file