def testCollectionQuantityOperations(self):
""" Tests that Quantity collections behave correctly """
# Tests that __getitem__ returns a unit
s = [1, 2, 3, 4] * u.angstroms
self.assertTrue(u.is_quantity(s[0]))
for i, val in enumerate(s):
self.assertTrue(u.is_quantity(val))
self.assertEqual(val, (i+1) * u.angstroms)
# Tests that __setitem__ fails when an incompatible type is added
def fail(s): s[0] = 5
self.assertRaises(AttributeError, lambda: fail(s))
def fail(s): s[0] = 5 * u.joules
self.assertRaises(TypeError, lambda: fail(s))
def fail(s): s[0] /= 10 * u.meters
self.assertRaises(AttributeError, lambda: fail(s))
# Tests that __setitem__ converts to the unit of the container
s[0] = 1 * u.nanometers
self.assertEqual(s[0]._value, 10)
# Tests standard unit conversions
x = [1, 2, 3] * u.centimeters
self.assertEqual(x / u.millimeters, [10, 20, 30])
# Test the construction of a container in which each element is a
# Quantity, passed to the Quantity constructor
x = u.Quantity([1*u.angstrom, 2*u.nanometer, 3*u.angstrom])
self.assertEqual(x._value, [1, 20, 3])
self.assertEqual(x.unit, u.angstrom)
x = u.Quantity((1, 2, 3))
self.assertTrue(u.is_quantity(x))
self.assertTrue(x.unit.is_dimensionless())
x = u.Quantity(([1*u.angstrom, 2*u.nanometer, 3*u.angstrom],
[1*u.angstrom, 4*u.nanometer, 3*u.angstrom]))
self.assertEqual(x._value, ([1, 20, 3], [1, 40, 3]))
self.assertEqual(x.unit, u.angstrom)
self.assertTrue(u.is_quantity(u.Quantity([])))
def testScalarQuantityConstructor(self):
""" Tests creating a Quantity using the Quantity constructor """
self.assertTrue(u.is_quantity(u.Quantity(5, u.centimeters)))
self.assertTrue(u.is_quantity(u.Quantity(5, u.centimeters**-1)))
x = u.Quantity(value=5.0, unit=100.0*u.meters)
self.assertTrue(u.is_quantity(x))
self.assertEqual(x, 500*u.meters)
def testNumpyDivision(self):
""" Tests that division of numpy Quantities works correctly """
x = u.Quantity(np.asarray([1., 2.]), u.nanometers)
y = u.Quantity(np.asarray([3., 4.]), u.picoseconds)
xy = x / y
self.assertTrue(u.is_quantity(xy))
self.assertEqual(xy.unit, u.nanometers/u.picoseconds)
self.assertEqual(xy[0].value_in_unit(u.nanometers/u.picoseconds), 1/3)
self.assertEqual(xy[1].value_in_unit(u.nanometers/u.picoseconds), 0.5)
def testNumpyDeepCopy(self):
""" Check that deepcopy on numpy array does not strip units """
x = u.Quantity(np.zeros((2, 3)), u.nanometer)
y = copy.deepcopy(x)
self.assertTrue(np.all(x == y))
self.assertTrue(u.is_quantity(x))
self.assertTrue(u.is_quantity(y))
def testDimensionless(self):
""" Tests the properties of unit.dimensionless """
x = 5 * u.dimensionless
y = u.Quantity(5, u.dimensionless)
self.assertTrue(u.is_quantity(x))
self.assertTrue(u.is_quantity(y))
self.assertNotEqual(x, 5)
self.assertNotEqual(y, 5)
self.assertEqual(x, y)
self.assertEqual(x.value_in_unit_system(u.si_unit_system), 5)
self.assertEqual(x.value_in_unit_system(u.cgs_unit_system), 5)
self.assertEqual(x.value_in_unit_system(u.md_unit_system), 5)
x = u.Quantity(1.0, u.dimensionless)
y = u.Quantity(1.0, u.dimensionless)
self.assertIsNot(x, y)
self.assertEqual(x, y)
def testReduceUnit(self):
""" Tests the reduce_unit functionality """
x = u.nanometer**2 / u.angstrom**2
self.assertEqual(str(x), 'nanometer**2/(angstrom**2)')
self.assertTrue(x.is_dimensionless())
q = u.Quantity(2.0, x)
self.assertEqual(str(q), '2.0 nm**2/(A**2)')
self.assertEqual(q.reduce_unit(), 200)
def testMutableQuantityOperations(self):
" Tests that mutable Quantity objects do not get unexpectedly changed "
# This used to be a bug -- t and s._value were the same object, so
# changing t would also change s silently
s = [1, 2, 3, 4] * u.angstroms
t = s / u.angstroms
self.assertEqual(t, [1, 2, 3, 4])
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.angstroms))
t[0] = 2
self.assertEqual(t, [2, 2, 3, 4])
if not utils.openmm_version or utils.openmm_version > (6, 2):
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.angstroms))
else:
t[0] = 1
t = s.value_in_unit(u.angstroms)
self.assertEqual(t, [1, 2, 3, 4])
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.angstroms))
t[0] = 2
self.assertEqual(t, [2, 2, 3, 4])
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.angstroms))
s = [1, 2, 3, 4] * u.nanometers
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.nanometers))
t = s.in_units_of(u.nanometers)
self.assertEqual(s, t)
t[0] = 1 * u.meters
self.assertAlmostEqualQuantities(t,
u.Quantity([1e9, 2, 3, 4], u.nanometers))
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.nanometers))
def testNumpyFunctions(self):
""" Tests various numpy attributes that they result in Quantities """
a = u.Quantity(np.arange(10), u.seconds)
self.assertEqual(a.max(), 9*u.seconds)
self.assertEqual(a.min(), 0*u.seconds)
self.assertEqual(a.mean(), 4.5*u.seconds)
self.assertAlmostEqualQuantities(a.std(), 2.8722813232690143*u.seconds)
b = a.reshape((5, 2))
self.assertTrue(u.is_quantity(b))
def testQuantityMaths(self):
""" Tests dimensional analysis & maths on and b/w Quantity objects """
x = 1.3 * u.meters
y = 75.2 * u.centimeters
self.assertEqual((x + y) / u.meters, 2.052)
self.assertEqual((x - y) / u.meters, 0.548)
self.assertEqual(x / y, 1.3 / 0.752)
self.assertEqual(x * y, 1.3*0.752*u.meters**2)
d1 = 2.0*u.meters
d2 = 2.0*u.nanometers
self.assertEqual(d1 + d2, (2+2e-9)*u.meters)
self.assertAlmostEqual((d2+d1-(2e9+2)*u.nanometers)._value, 0, places=6)
self.assertEqual(d1 + d1, 4.0*u.meters)
self.assertEqual(d1 - d1, 0.0*u.meters)
self.assertEqual(d1 / d1, 1.0)
self.assertEqual(d1 * u.meters, 2.0*u.meters**2)
self.assertEqual(u.kilograms*(d1/u.seconds)*(d1/u.seconds),
4*u.kilograms*u.meters**2/u.seconds**2)
self.assertEqual(u.kilograms*(d1/u.seconds)**2,
4*u.kilograms*u.meters**2/u.seconds**2)
self.assertEqual(d1**3, 8.0*u.meters**3)
x = d1**(3/2)
self.assertAlmostEqual(x._value, math.sqrt(2)**3)
self.assertEqual(x.unit, u.meters**(3/2))
self.assertAlmostEqual((d1**0.5)._value, math.sqrt(2))
self.assertEqual((d1**0.5).unit, u.meters**0.5)
comp = (3.0 + 4.0j) * u.meters
self.assertTrue(u.is_quantity(comp))
self.assertEqual(comp.unit, u.meters)
self.assertEqual(str(comp), '(3+4j) m')
self.assertEqual(comp + comp, (6.0 + 8.0j)*u.meters)
self.assertEqual(comp - comp, 0*u.meters)
self.assertEqual(comp * comp, (3.0 + 4.0j)**2 * u.meters**2)
self.assertAlmostEqual(abs(comp / comp), 1)
self.assertAlmostEqual(1.5*u.nanometers / u.meters, 1.5e-9, places=15)
self.assertEqual((2.3*u.meters)**2, 2.3**2*u.meters**2)
x = 4.3 * u.meters
self.assertEqual(x / u.centimeters, 430)
self.assertEqual(str(x / u.seconds), '4.3 m/s')
self.assertEqual(str(8.4 / (4.2*u.centimeters)), '2.0 /cm')
x = 1.2 * u.meters
self.assertEqual(x * 5, u.Quantity(6.0, u.meters))
def testNumpyQuantity(self):
""" Tests that numpy arrays can form Quantity values """
q = u.Quantity(np.array([1, 2, 3]), u.centimeters)
self.assertTrue(u.is_quantity(q))
self.assertIsInstance(q._value, np.ndarray)
self.assertTrue(np.all(q / u.millimeters == np.array([1, 2, 3])*10))
def testString(self):
""" Tests unit handling with strings, which should be dimensionless """
s = u.Quantity("string")
self.assertEqual(s.value_in_unit_system(u.md_unit_system), "string")
def testUnaryOperators(self):
""" Tests unary operators on units """
self.assertEqual(-(2.3*u.meters), u.Quantity(-2.3, u.meters))
self.assertEqual(-(2.3*u.meters), -u.Quantity(2.3, u.meters))
self.assertEqual(+(2.3*u.meters), u.Quantity(2.3, u.meters))
self.assertEqual(2.3*u.meters, +u.Quantity(2.3, u.meters))