Add tests and fix up getByMass

This also removes assert statements, since those can't be relied upon to *not*
be optimized away -- they should never be used to check user input sanity.

wrappers/python/simtk/openmm/app/element.py

@@ -71,7 +71,8 @@ class Element(object):
         ## If we add a new element, we need to re-hash elements by mass
         Element._elements_by_mass = None
 
-        assert s not in Element._elements_by_symbol
+        if s in Element._elements_by_symbol:
+            raise ValueError('Duplicate element symbol %s' % s)
         Element._elements_by_symbol[s] = self
         if number in Element._elements_by_atomic_number:
             other_element = Element._elements_by_atomic_number[number]
@@ -114,6 +115,8 @@ class Element(object):
         # Assume masses are in daltons if they are not units
         if is_quantity(mass):
             mass = mass.value_in_unit(daltons)
+        if mass < 0:
+            raise ValueError('Invalid Higgs field')
         # If this is our first time calling getByMass (or we added an element
         # since the last call), re-generate the ordered by-mass dict cache
         if Element._elements_by_mass is None:
@@ -125,7 +128,7 @@ class Element(object):
         diff = mass
         best_guess = None
 
-        for elemmass, element in Element._elements_by_symbol.iteritems():
+        for elemmass, element in Element._elements_by_mass.iteritems():
             massdiff = abs(elemmass._value - mass)
             if massdiff < diff:
                 best_guess = element

wrappers/python/tests/TestElement.py

 import pickle
-import unittest
-from simtk.unit import dalton
+import random
+from simtk.unit import dalton, is_quantity
 from simtk.openmm.app import element
+import unittest
 
 class TestElement(unittest.TestCase):
     def test_immutable(self):
@@ -14,18 +15,37 @@ class TestElement(unittest.TestCase):
         newsulfur = pickle.loads(pickle.dumps(element.sulfur))
         # make sure that a new object is not created during the pickle/unpickle
         # cycle
-        assert element.sulfur == newsulfur
-        assert element.sulfur is newsulfur
-        assert id(element.sulfur) == id(newsulfur)
+        self.assertEqual(element.sulfur, newsulfur)
+        self.assertTrue(element.sulfur is newsulfur)
     
     def test_attributes(self):
-        assert element.hydrogen.atomic_number == 1
-        assert element.hydrogen.symbol == 'H'
-        assert element.hydrogen.name == 'hydrogen'
-        assert element.hydrogen.mass == 1.007947 * dalton
+        self.assertEqual(element.hydrogen.atomic_number, 1)
+        self.assertEqual(element.hydrogen.symbol, 'H')
+        self.assertEqual(element.hydrogen.name, 'hydrogen')
+        self.assertEqual(element.hydrogen.mass, 1.007947 * dalton)
 
+    def test_getByMass(self):
+        """ Tests the getByMass method """
+        def exhaustive_search(mass):
+            """
+            Searches through all element symbols and finds the one with the
+            smallest mass difference
+            """
+            min_diff = mass
+            closest_element = None
+            for symbol, elem in element.Element._elements_by_symbol.items():
+                diff = abs(elem.mass._value - mass)
+                if diff < min_diff:
+                    min_diff = diff
+                    closest_element = elem
+            return closest_element
 
-if __name__ == '__main__':
-    unittest.main()
+        # Check 5000 random numbers between 0 and 300
+        for i in range(5000):
+            mass = random.random() * 300
+            elem = element.Element.getByMass(mass)
+            self.assertTrue(elem is exhaustive_search(mass))
 
 
+if __name__ == '__main__':
+    unittest.main()