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# Universe tests
#
# Written by Konrad Hinsen
#
import unittest
from MMTK import *
from MMTK.Random import randomPointInBox
from Scientific import N
class PeriodicUniverseTest:
def test_basisVectors(self):
e1, e2, e3 = self.universe.basisVectors()
self.assertEqual(e1, self.a)
self.assertEqual(e2, self.b)
self.assertEqual(e3, self.c)
def test_reciprocalBasisVectors(self):
r1, r2, r3 = self.universe.reciprocalBasisVectors()
self.assertAlmostEqual(r1*self.a, 1., 14)
self.assertAlmostEqual(r2*self.b, 1., 14)
self.assertAlmostEqual(r3*self.c, 1., 14)
self.assert_(abs(r1*self.b) < 1.e-15)
self.assert_(abs(r1*self.c) < 1.e-15)
self.assert_(abs(r2*self.a) < 1.e-15)
self.assert_(abs(r2*self.c) < 1.e-15)
self.assert_(abs(r3*self.a) < 1.e-15)
self.assert_(abs(r3*self.b) < 1.e-15)
def test_volume(self):
volume = self.universe.cellVolume()
self.assertAlmostEqual(volume, self.a*(self.b.cross(self.c)), 14)
def test_boxCoordinates1(self):
for i in range(500):
p = randomPointInBox(5.)
pt = self.universe.realToBoxCoordinates(p)
self.assert_((self.universe.boxToRealCoordinates(pt)-p).length()
< 1.e-14)
pt = self.universe.boxToRealCoordinates(p)
self.assert_((self.universe.realToBoxCoordinates(pt)-p).length()
< 1.e-14)
def test_boxCoordinates2(self):
configuration = self.universe.copyConfiguration()
configuration.convertToBoxCoordinates()
for atom in self.universe.atomList():
rb = self.universe.realToBoxCoordinates(atom.position())
self.assert_((configuration[atom]-rb).length() < 1.e-15)
configuration.convertFromBoxCoordinates()
self.assert_(N.maximum.reduce(N.ravel(N.fabs(
configuration.array-self.universe.configuration().array))) < 1.e-15)
def test_coordinateFold(self):
for i in range(500):
self.universe.translateBy(randomPointInBox(0.5))
self.universe.foldCoordinatesIntoBox()
for atom in self.universe.atomList():
rb = self.universe.realToBoxCoordinates(atom.position())
self.assert_(rb[0] >= -0.5)
self.assert_(rb[1] >= -0.5)
self.assert_(rb[2] >= -0.5)
self.assert_(rb[0] <= 0.5)
self.assert_(rb[1] <= 0.5)
self.assert_(rb[2] <= 0.5)
cconf = self.universe.contiguousObjectConfiguration(
self.universe.objectList())
for o in self.universe:
for bu in o.bondedUnits():
for bond in bu.bonds:
l = (bond.a1.position(cconf)
- bond.a2.position(cconf)).length()
self.assert_(l < 0.16)
class ParallelepipedicPeriodicUniverseTest(unittest.TestCase,
PeriodicUniverseTest):
def setUp(self):
self.a = Vector(1.5, 0.3, 0.)
self.b = Vector(-0.1, 0.8, 0.2)
self.c = Vector(0., -0.2, 1.1)
self.universe = ParallelepipedicPeriodicUniverse((self.a,
self.b,
self.c))
self.universe.addObject(Molecule('water'))
class OrthorhombicPeriodicUniverseTest(unittest.TestCase,
PeriodicUniverseTest):
def setUp(self):
self.a = Vector(0.7, 0., 0.)
self.b = Vector(0., 1., 0.)
self.c = Vector(0., 0., 0.8)
self.universe = OrthorhombicPeriodicUniverse((self.a.length(),
self.b.length(),
self.c.length()))
self.universe.addObject(Molecule('water'))
def suite():
loader = unittest.TestLoader()
s = unittest.TestSuite()
s.addTest(loader.loadTestsFromTestCase(ParallelepipedicPeriodicUniverseTest))
s.addTest(loader.loadTestsFromTestCase(OrthorhombicPeriodicUniverseTest))
return s
if __name__ == '__main__':
unittest.main()
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