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Commit 4340498f authored by peastman's avatar peastman
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Merge pull request #750 from swails/fix_unit 

Fix small bug in `simtk.unit` related to mutable sequences.
parents 11e5dc73 f8a101d7
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Showing with 695 additions and 3 deletions
wrappers/python/simtk/unit/quantity.py
View file @ 4340498f
...@@ -356,7 +356,7 @@ class Quantity(object): ...@@ -356,7 +356,7 @@ class Quantity(object):
if unit.is_dimensionless(): if unit.is_dimensionless():
assert unit is dimensionless # should have been set earlier in this method assert unit is dimensionless # should have been set earlier in this method
if is_quantity(result): if is_quantity(result):
result = result._value result = copy.deepcopy(result._value)
return result return result
def __mul__(self, other): def __mul__(self, other):
...@@ -506,7 +506,7 @@ class Quantity(object): ...@@ -506,7 +506,7 @@ class Quantity(object):
except AttributeError: except AttributeError:
if args or kwargs: if args or kwargs:
raise TypeError('Unsupported arguments for Quantity.mean') raise TypeError('Unsupported arguments for Quantity.mean')
mean = self.sum() / len(self._value) mean = (self.sum() / len(self._value))._value
return Quantity(mean, self.unit) return Quantity(mean, self.unit)
def std(self, *args, **kwargs): def std(self, *args, **kwargs):
...@@ -526,7 +526,8 @@ class Quantity(object): ...@@ -526,7 +526,8 @@ class Quantity(object):
except AttributeError: except AttributeError:
if args or kwargs: if args or kwargs:
raise TypeError('Unsupported arguments for Quantity.std') raise TypeError('Unsupported arguments for Quantity.std')
mean = self.mean() mean = self.mean()._value
var = 0
for val in self._value: for val in self._value:
res = mean - val res = mean - val
var += res * res var += res * res
......
wrappers/python/tests/TestUnits.py 0 → 100644
View file @ 4340498f
"""
Tests the functionality in the simtk.unit package.
"""
from __future__ import division
from simtk import unit as u
import copy
import math
import unittest
try:
import numpy as np
except ImportError:
np = None
try:
from itertools import izip as zip
except ImportError:
pass # Python 3... zip _is_ izip
class QuantityTestCase(unittest.TestCase):
def assertAlmostEqualQuantities(self, item1, item2, places=6):
try:
val1 = item1.value_in_unit(item1.unit)
val2 = item2.value_in_unit(item1.unit)
except TypeError:
raise self.failureException('Incompatible units %s and %s' %
(item1.unit, item2.unit))
try:
if len(val1) != len(val2):
raise self.failureException('collections are different lengths')
for x, y in zip(val1, val2):
self.assertAlmostEqual(x, y, places=places)
except TypeError:
self.assertAlmostEqual(val1, val2, places=places)
class TestUnits(QuantityTestCase):
def testBaseUnit(self):
""" Tests the creation of a base unit furlong """
furlong = u.BaseUnit(u.length_dimension, "furlong", "fur")
furlong.define_conversion_factor_to(u.meter_base_unit, 201.168)
self.assertEqual(furlong.conversion_factor_to(u.angstrom_base_unit),
201.168e10)
def testIsUnit(self):
""" Tests the unit.is_unit introspective function """
self.assertTrue(u.is_unit(u.meters))
self.assertFalse(u.is_unit(None))
self.assertFalse(u.is_unit(10))
# Distinguish between "units" and "quantities"
self.assertFalse(u.is_unit(1*u.meters))
def testCalorieConversion(self):
""" Tests unit conversion with calories to joules """
c = 1.0 * u.calories
j = 1.0 * u.joules
j2c = j.in_units_of(u.calories)
self.assertNotEqual(c, 1.0) # Units do not equal scalars!
self.assertIs(c.unit, u.calories)
self.assertEqual(c._value, 1)
self.assertEqual(u.calorie.conversion_factor_to(u.joule), 4.184)
self.assertEqual(u.joule.conversion_factor_to(u.calorie), 1/4.184)
self.assertIs(j2c.unit, u.calories)
self.assertEqual(j2c._value, 1/4.184)
self.assertEqual(c / u.calories, 1.0) # Dimensionless now
self.assertEqual(j / u.calories, j2c._value)
c2 = c**2
cc = c * c
self.assertEqual(cc, c2)
self.assertTrue(c2.unit, u.calories**2)
self.assertEqual(c2.in_units_of(u.joules**2), (4.184*u.joules)**2)
def testScaledUnit(self):
""" Tests ScaledUnit class with kilokelvins """
kK = u.ScaledUnit(1000.0, u.kelvin, "kilokelvin", "kK")
self.assertIs(kK.master, u.kelvin)
self.assertEqual(kK.factor, 1000)
self.assertEqual(str(kK), 'kilokelvin')
self.assertEqual(kK.name, 'kilokelvin')
self.assertEqual(kK.symbol, 'kK')
def testComparisonOperators(self):
""" Tests unit comparison operators """
self.assertGreater(u.meters, u.centimeters)
self.assertLess(u.angstroms, u.centimeters)
def testUnitDivision(self):
""" Tests the division of units and is_dimensionless """
mps = u.meter / u.second
mpm = u.meter / u.meter
mpc = u.meter / u.centimeter
self.assertTrue(u.is_unit(mps))
self.assertTrue(u.is_unit(mpm))
self.assertTrue(u.is_unit(mpc))
self.assertFalse(mps.is_dimensionless())
self.assertTrue(mpm.is_dimensionless())
self.assertTrue(mpc.is_dimensionless())
def testCompositeUnits(self):
""" Tests the creation of a composite unit """
mps = u.Unit({u.meter_base_unit : 1.0, u.second_base_unit : -1.0})
self.assertTrue(u.is_unit(mps))
self.assertEqual(str(mps), 'meter/second')
def testUnitSystem(self):
""" Tests the creation of a UnitSystem and its behavior """
us = u.UnitSystem([u.ScaledUnit(1.0, u.coulomb/u.second, 'ampere', 'A'),
u.second_base_unit])
self.assertEqual(us.express_unit(u.second), u.second)
self.assertEqual(us.express_unit(u.hour), u.second)
self.assertNotEqual(u.hour, u.second)
self.assertEqual(us.express_unit(u.coulomb/u.second), u.ampere)
self.assertEqual(us.express_unit(u.meter/u.second), u.meter/u.second)
self.assertEqual(us.express_unit(u.kilometer/u.hour),
u.kilometer/u.second)
x = 100 * u.millimeters
self.assertEqual(x.value_in_unit_system(u.si_unit_system), 0.1)
self.assertEqual(x.value_in_unit_system(u.cgs_unit_system), 10.0)
self.assertAlmostEqual(x.value_in_unit_system(u.md_unit_system), 1e8)
y = 20 * u.millimeters / u.millisecond**2
self.assertAlmostEqual(y.value_in_unit_system(u.si_unit_system), 2e4)
self.assertAlmostEqual(y.value_in_unit_system(u.cgs_unit_system), 2e6)
self.assertAlmostEqual(y.value_in_unit_system(u.md_unit_system), 2e-11,
places=18)
kcal = 1 * u.md_kilocalorie / u.mole
self.assertEqual(kcal.value_in_unit_system(u.md_unit_system), 4.184)
def testUnitSqrt(self):
""" Tests taking the square root of units """
self.assertEqual((u.meter * u.meter).sqrt(), u.meter)
self.assertEqual((u.meter**4).sqrt(), u.meter**2)
def testQuantitySqrt(self):
""" Tests taking the square root of quantities """
self.assertEqual((9.0*u.meters**2).sqrt(), 3.0*u.meters)
self.assertEqual((9.0*u.meters**2/u.second**2).sqrt(),
3.0*u.meters/u.second)
def testUnitBadSqrt(self):
""" Tests that illegal sqrt calls on incompatible units fails """
mps2 = u.meters/u.second**2
self.assertRaises(ArithmeticError, lambda: u.meter.sqrt())
self.assertRaises(ArithmeticError, lambda: (u.meters**3).sqrt())
self.assertRaises(ArithmeticError, lambda: mps2.sqrt())
def testQuantityBadSqrt(self):
" Tests that taking sqrt of Quantities with incompatible units fails "
self.assertRaises(ArithmeticError, lambda: (9.0*u.meters).sqrt())
self.assertRaises(ArithmeticError, lambda: (9.0*u.meters**3).sqrt())
def testBaseScaleMix(self):
""" Test mixing of BaseUnit and ScaledUnit instances """
kgj = u.kilogram * u.joule
self.assertTrue(u.is_unit(kgj))
self.assertEqual(str(kgj.sqrt()), 'kilogram*meter/second')
def testGetUnitAttributes(self):
""" Tests the unit attribute `getters' """
self.assertEqual(u.newton.get_name(), 'newton')
self.assertEqual(u.newtons.get_name(), 'newton')
self.assertEqual(u.newton.get_symbol(), 'N')
self.assertEqual(u.ampere.get_symbol(), 'A')
self.assertEqual(u.meter.get_name(), 'meter')
self.assertEqual(u.meter.get_symbol(), 'm')
def testPresetUnitSystems(self):
""" Tests some of the pre-set UnitSystem's """
self.assertEqual(u.angstrom.in_unit_system(u.si_unit_system), u.meter)
self.assertEqual(u.angstrom.in_unit_system(u.cgs_unit_system),
u.centimeter)
self.assertEqual(u.angstrom.in_unit_system(u.md_unit_system),
u.nanometer)
mps = u.meter / u.second**2
self.assertEqual(str(mps), 'meter/(second**2)')
self.assertEqual(mps.in_unit_system(u.si_unit_system), mps)
self.assertEqual(mps.in_unit_system(u.cgs_unit_system),
u.centimeter/u.second**2)
self.assertEqual(mps.in_unit_system(u.md_unit_system),
u.nanometer/u.picosecond**2)
def testIsCompatible(self):
""" Tests the is_compatible attribute of units """
self.assertTrue(u.meter.is_compatible(u.centimeter))
self.assertTrue(u.centimeter.is_compatible(u.meter))
self.assertTrue(u.meter.is_compatible(u.meter))
self.assertTrue(u.joule.is_compatible(u.calorie))
self.assertFalse(u.meter.is_compatible(u.kelvin))
self.assertFalse(u.meter.is_compatible(u.meter/u.second))
self.assertFalse(u.meter.is_compatible(u.joule))
def testConversionFactorTo(self):
""" Tests the "conversion_factor_to" attribute of Units """
self.assertEqual(u.meter.conversion_factor_to(u.centimeter), 100)
self.assertEqual(u.kilocalorie.conversion_factor_to(u.joule), 4184)
self.assertEqual(u.calorie.conversion_factor_to(u.kilojoule), 4.184e-3)
self.assertEqual((u.kilocalorie/u.mole/u.angstrom).conversion_factor_to(
u.kilojoule/u.mole/u.nanometer), 41.84)
def testUnitString(self):
""" Test the Unit->str casting functionality """
# Always alphabetical order
self.assertEqual(str(u.meter * u.second * u.second * u.kilogram),
'kilogram*meter*second**2')
self.assertEqual(str(u.meter / u.second / u.second / u.kilogram),
'meter/(kilogram*second**2)')
self.assertEqual(str(u.meter**3), 'meter**3')
def testToBaseUnit(self):
""" Tests the "get_conversion_factor_to_base_units" method """
self.assertEqual(u.meter.get_conversion_factor_to_base_units(), 1)
self.assertEqual(u.calorie.get_conversion_factor_to_base_units(), 4.184)
kcpma = u.md_kilocalorie/u.mole/u.angstrom
self.assertEqual(kcpma.get_conversion_factor_to_base_units(), 4.184)
def testScalarQuantityMultiplyDivide(self):
""" Tests creating a scalar Quantity object by * or / by a Unit """
self.assertTrue(u.is_quantity(5 * u.centimeters))
self.assertTrue(u.is_quantity(1 / u.centimeters))
self.assertTrue(u.is_quantity(10 * u.centimeters))
self.assertTrue(u.is_quantity(9.81 * u.meters / u.second**2))
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 testValueInUnit(self):
""" Tests the value_in_unit functionality for Quantity """
i = 5 * u.centimeters
self.assertEqual(i.value_in_unit(u.millimeters), 50)
self.assertEqual(i / u.millimeters, 50)
def testCollectionQuantities(self):
""" Tests the use of collections as Quantity values """
s = [1, 2, 3] * u.centimeters
self.assertEqual(str(s), '[1, 2, 3] cm')
self.assertTrue(u.is_quantity(s))
s2 = s / u.millimeters
self.assertEqual(s2, [10.0, 20.0, 30.0])
self.assertEqual(s2, s.value_in_unit(u.millimeters))
# Test 2-D list
s = [[1, 2, 3], [4, 5, 6]]
s *= u.centimeters
self.assertTrue(u.is_quantity(s))
s2 = s / u.millimeters
self.assertEqual(s2, [[10.0, 20.0, 30.0], [40.0, 50.0, 60.0]])
self.assertEqual(s.value_in_unit(u.millimeters), s2)
# Test tuples
s = (1, 2, 3) * u.centimeters
self.assertTrue(u.is_quantity(s))
self.assertEqual(str(s), '(1, 2, 3) cm')
s2 = s / u.millimeters
self.assertEqual(s2, (10, 20, 30))
self.assertIsInstance(s2, tuple)
self.assertEqual(s.value_in_unit(u.millimeters), s2)
self.assertIsInstance(s.value_in_unit(u.millimeters), tuple)
x = [1, 2, 3] * u.centimeters
x *= u.meters
self.assertEqual(x, [100, 200, 300] * u.centimeters**2)
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 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 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])
self.assertEqual(s, u.Quantity([1, 2, 3, 4], u.angstroms))
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 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(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 testQuantityComplicatedMaths(self):
""" Tests a complicated set of mathematical operations on a Quantity """
s1 = 2.0
x1 = 2
x2 = 4.0 / 3.0
u1 = u.kilogram * u.meter / u.second**2
u2 = u1 * u.meter
q1 = 1.0 * u1
q2 = 2.0 * u2
self.assertEqual(s1, 2.0)
self.assertEqual(x1, 2)
self.assertAlmostEqual(x2, 1.33333333333333)
self.assertEqual(str(u1), 'kilogram*meter/(second**2)')
self.assertEqual(str(u2), 'kilogram*meter**2/(second**2)')
self.assertEqual(str(q1), '1.0 kg m/(s**2)')
self.assertEqual(str(q2), '2.0 kg m**2/(s**2)')
self.assertEqual(str(u1*s1), '2.0 kg m/(s**2)')
self.assertEqual(str(s1*u1), '2.0 kg m/(s**2)')
self.assertEqual(str(u1/s1), '0.5 kg m/(s**2)')
self.assertEqual(str(s1/u1), '2.0 s**2/(kg m)')
self.assertEqual(str(u1*u1), 'kilogram**2*meter**2/(second**4)')
self.assertEqual(u1/u1, u.dimensionless)
self.assertEqual(str(u1/u1), 'dimensionless')
self.assertEqual(str(u1*u2), 'kilogram**2*meter**3/(second**4)')
self.assertEqual(u1/u2, u.meters**-1)
self.assertEqual(str(u1/u2), '/meter')
self.assertEqual(u1**x1, u.kilogram**2*u.meter**2/(u.second**4))
self.assertEqual(u1**(1/x1), u.kilogram**0.5*u.meter**0.5/u.second)
self.assertEqual(u1**x2,
u.kilogram**(1+1/3)*u.meter**(1+1/3)/u.second**(2+2/3))
q = 1.0 * u.md_kilocalorie/u.mole/u.angstrom
self.assertEqual(str(q.in_units_of(u.md_kilojoule/u.mole/u.nanometer)),
'41.84 kJ/(nm mol)')
def testQuantityComparisons(self):
""" Tests binary comparison operators between Quantity """
l1 = 1.0 * u.meters
l2 = 2.0 * u.meters
l3 = 1.0 * u.meters
self.assertEqual(l1, l3)
self.assertNotEqual(l1, l2)
self.assertLessEqual(l1, l2)
self.assertLess(l1, l2)
self.assertGreater(l2, l1)
self.assertGreaterEqual(l2, l1)
self.assertLessEqual(l1, l3)
self.assertGreaterEqual(l1, l3)
self.assertGreater(1.2*u.meters, 72*u.centimeters)
self.assertLess(1*u.meters, 200*u.centimeters)
def testChemistryProblems(self):
""" Tests some gen-chem applications with Quantity's """
def work(f, dx):
return f * dx
F = 1.0 * u.kilogram * u.meter / u.second**2
dx = 1.0 * u.meter
self.assertEqual(work(F, dx), 1.0 * u.joule)
self.assertEqual(F, 1.0 * u.newton)
def ideal_gas_law(P, V, T):
R = u.MOLAR_GAS_CONSTANT_R
return (P * V / (R * T)).in_units_of(u.mole)
T = (273.0 + 37.0) * u.kelvin
P = (1.01325e5) * u.pascals
r = 0.5e-6 * u.meters
V = 4/3 * math.pi * r**3
n = ideal_gas_law(P, V, T)
val = 4/3*math.pi*0.5e-6**3*1
self.assertAlmostEqualQuantities(P*V, val * u.atmospheres*u.meters**3)
self.assertAlmostEqualQuantities(n, 2.05834818672e-17 * u.mole)
self.assertAlmostEqualQuantities(V, 5.2359833333333e-19 * u.meters**3)
self.assertEqual(str(T), '310.0 K')
self.assertEqual(str(u.MOLAR_GAS_CONSTANT_R), '8.31447247122 J/(K mol)')
self.assertTrue(u.is_quantity(V))
# Checks trouble with complicated unit conversion factors
p1 = 1.0 * u.atmospheres
p2 = p1.in_units_of(u.joules/u.nanometers**3)
V = 2.4 * u.nanometers**3
beta = 4.e-4 * u.mole/u.joule
x1 = beta * p1 * V
y1 = x1 * u.AVOGADRO_CONSTANT_NA
self.assertAlmostEqual(y1, 0.0585785776197)
x2 = beta * p2 * V
y2 = x2 * u.AVOGADRO_CONSTANT_NA
self.assertAlmostEqual(y1, y2)
def testAngleQuantities(self):
""" Tests angle measurements """
self.assertEqual(1.0*u.radians / u.degrees, 180 / math.pi)
self.assertTrue(u.is_quantity(1.0*u.radians))
self.assertTrue(u.is_quantity(1.0*u.degrees))
self.assertEqual((1.0*u.radians).in_units_of(u.degrees),
(180 / math.pi)*u.degrees)
self.assertEqual(90*u.degrees/u.radians, math.pi/2)
q = 90 * u.degrees + 0.3 * u.radians
self.assertEqual(q._value, 90 + 180*0.3/math.pi)
self.assertEqual(q.unit, u.degrees)
def testIsQuantity(self):
""" Tests if is_quantity can detect Quantities vs. scalars and units """
self.assertTrue(u.is_quantity(1/u.second))
self.assertFalse(u.is_quantity(u.second**-1))
self.assertTrue(u.is_quantity(10*u.meters))
self.assertFalse(u.is_quantity(10))
def testBadQuantityMaths(self):
""" Tests that Maths of incompatible units properly fails """
self.assertRaises(TypeError, lambda:1*u.meters + 1*u.liters)
self.assertRaises(AttributeError, lambda: 1*u.liters + 5)
def testBadQuantityComparisons(self):
""" Checks that comparisons of incompatible units fails """
self.assertRaises(TypeError, lambda: 1*u.meters > 1*u.liters)
self.assertRaises(TypeError, lambda: 1*u.nanometers > 1*u.degrees)
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 testTruthiness(self):
""" Tests the truthiness of units """
true = 2.3 * u.meters
false = 0.0 * u.meters
self.assertTrue(true)
self.assertFalse(false)
self.assertTrue(bool(true))
self.assertFalse(bool(false))
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))
def testUnitMathModule(self):
""" Tests the unit_math functions on Quantity objects """
self.assertEqual(u.sqrt(1.0*u.kilogram*u.joule),
1.0*u.kilogram*u.meter/u.second)
self.assertEqual(u.sqrt(1.0*u.kilogram*u.calorie),
math.sqrt(4.184)*u.kilogram*u.meter/u.second)
self.assertEqual(u.sqrt(9), 3) # Test on a scalar
self.assertEqual(u.sin(90*u.degrees), 1)
self.assertEqual(u.sin(math.pi/2*u.radians), 1)
self.assertEqual(u.sin(math.pi/2), 1)
self.assertEqual(u.cos(180*u.degrees), -1)
self.assertEqual(u.cos(math.pi*u.radians), -1)
self.assertEqual(u.cos(math.pi), -1)
self.assertAlmostEqual(u.tan(45*u.degrees), 1)
self.assertAlmostEqual(u.tan(math.pi/4*u.radians), 1)
self.assertAlmostEqual(u.tan(math.pi/4), 1)
acos = u.acos(1.0)
asin = u.asin(1.0)
atan = u.atan(1.0)
self.assertTrue(u.is_quantity(acos))
self.assertTrue(u.is_quantity(asin))
self.assertTrue(u.is_quantity(atan))
self.assertEqual(acos.unit, u.radians)
self.assertEqual(asin.unit, u.radians)
self.assertEqual(atan.unit, u.radians)
self.assertEqual(acos.value_in_unit(u.degrees), 0)
self.assertEqual(acos / u.radians, 0)
self.assertEqual(asin.value_in_unit(u.degrees), 90)
self.assertEqual(asin / u.radians, math.pi/2)
self.assertAlmostEqual(atan.value_in_unit(u.degrees), 45)
self.assertAlmostEqual(atan / u.radians, math.pi/4)
# Check some sequence maths
seq = [1, 2, 3, 4] * u.meters
self.assertEqual(u.sum(seq), 10*u.meters)
self.assertEqual(u.dot(seq, seq), (1+4+9+16)*u.meters**2)
self.assertEqual(u.norm(seq), math.sqrt(30)*u.meters)
def testUnitMathModuleBadInput(self):
""" Tests that bad units to unit_math fails appropriately """
self.assertRaises(ArithmeticError, lambda: u.sqrt(9*u.meters))
self.assertRaises(TypeError, lambda: u.sin(1*u.meters))
def testBadQuantityConversions(self):
""" Tests that conversions to incompatible units fails """
self.assertRaises(TypeError,
lambda: (1.0*u.meters).in_units_of(u.seconds))
self.assertRaises(TypeError,
lambda: (1.0*u.meters).value_in_unit(u.seconds))
def testCreateNewBaseUnit(self):
""" Tests creating a new base unit """
ms = u.milli * u.second_base_unit
self.assertIsInstance(ms, u.BaseUnit)
self.assertEqual(repr(ms),
'BaseUnit(base_dim=BaseDimension("time"), name="millisecond", '
'symbol="ms")')
self.assertEqual(ms.conversion_factor_to(u.second_base_unit), 0.001)
def testCreateNewScaledUnit(self):
""" Tests creating a new ScaledUnit """
mC = u.milli * u.ScaledUnit(4.184, u.joule, "calorie", "cal")
self.assertIsInstance(mC, u.ScaledUnit)
self.assertEqual(repr(mC),
"ScaledUnit(factor=0.004184, master=joule, name='millicalorie',"
" symbol='mcal')")
self.assertFalse(u.is_unit(mC))
def testCreateNewUnit(self):
""" Tests creating a new Unit """
ms = u.milli * u.second
self.assertTrue(u.is_unit(ms))
self.assertEqual(repr(ms),
'Unit({BaseUnit(base_dim=BaseDimension("time"), '
'name="millisecond", symbol="ms"): 1.0})')
def testIllegalQuantityOps(self):
""" Test that illegal operations on Quantity objects fails """
self.assertRaises(TypeError, lambda: u.milli * (1.0 * u.second))
def testQuantityFormat(self):
""" Tests the format method on Quantity instances """
x = 5.439999999 * u.picosecond
self.assertEqual(x.format("%.3f"), '5.440 ps')
def testQuantityCollectionMethods(self):
""" Tests some sequence methods on Quantity objects (no numpy) """
seq = [1, 2, 3, 4] * u.meters
self.assertEqual(seq.sum(), 10*u.meters)
self.assertEqual(seq.mean(), 2.5*u.meters)
self.assertEqual(seq.max(), 4*u.meters)
self.assertEqual(seq.min(), 1*u.meters)
self.assertAlmostEqual(seq.std(), 1.1180339887498949*u.meters)
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 testMisc(self):
""" Miscellaneous tests for the unit package """
self.assertTrue(u.meter is not None)
self.assertFalse(u.meter is None)
self.assertEqual(repr(1.2*u.meters), 'Quantity(value=1.2, unit=meter)')
class Foo(object):
def bar(self):
return 'bar'
x = Foo()
self.assertEqual(x.bar(), 'bar')
y = x * u.nanometers
self.assertEqual(y.bar(), 'bar')
self.assertEqual(str(u.meters*u.centimeters), 'centimeter*meter')
self.assertEqual(str(u.meters*u.meters), 'meter**2')
self.assertEqual(str(u.meter*u.meter), 'meter**2')
class TestNumpyUnits(QuantityTestCase):
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 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 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 testNumpyIsString(self):
""" Tests the internal _is_string method with numpy Quantities """
from simtk.unit.quantity import _is_string
a = np.array([[1, 2, 3], [4, 5, 6]])
self.assertIsInstance("", str)
self.assertTrue(_is_string(""))
self.assertTrue(_is_string("t"))
self.assertTrue(_is_string("test"))
self.assertFalse(_is_string(3))
self.assertFalse(_is_string(a))
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))
if np is None:
# Support lack of numpy
del TestNumpyUnits
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