Merge pull request #48 from arm61/sansona-master

Building on #47

docs/source/conf.py

@@ -60,7 +60,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.3.2'
+version = '1.3.3'
 # The full version, including alpha/beta/rc tags.
 release = version
 

pylj/forcefields.py

@@ -100,13 +100,13 @@ def buckingham(dr, constants, force=False):
     float: array_like
         The potential energy or force between the particles.
     """
-
     if force:
         return constants[0] * constants[1] * np.exp(
-            -constants[1] * dr) - 6 * constants[2] / np.power(dr, 7)
+            - np.multiply(constants[1], dr)) - 6 * constants[2] / np.power(
+            dr, 7)
     else:
         return constants[0] * np.exp(
-            -constants[1] * dr) - constants[2] / np.power(dr, 6)
+            - np.multiply(constants[1], dr)) - constants[2] / np.power(dr, 6)
 
 
 def square_well(dr, constants, max_val=np.inf, force=False):

pylj/tests/test_forcefields.py

@@ -55,10 +55,21 @@ def test_lennard_jones_sigma_epsilon_force(self):
     def test_buckingham_energy(self):
         a = forcefields.buckingham(2.0, [1.0, 1.0, 1.0])
         assert_almost_equal(a, 0.1197103832)
+        b = forcefields.buckingham([2.0], [1.0, 1.0, 1.0])
+        assert_almost_equal(b, 0.1197103832)
+        c = forcefields.buckingham([2.0, 4.0], [1.0, 1.0, 1.0])
+        assert_almost_equal(c, [0.1197103832, 0.0180715])
+        d = forcefields.buckingham([2.0, 4.0, 5.0], [0.01, 0.01, 0.01])
+        assert_almost_equal(d, [0.0096457, 0.0096055, 0.0095117])
 
     def test_buckingham_force(self):
         a = forcefields.buckingham(2.0, [1.0, 1.0, 1.0], force=True)
         assert_almost_equal(a, 0.08846028324)
+        b = forcefields.buckingham([2.0], [1.0, 1.0, 1.0], force=True)
+        assert_almost_equal(b, 0.08846028324)
+        c = forcefields.buckingham(
+            [2.0, 1.0, 4.0], [1.5, 0.1, 2.0], force=True)
+        assert_almost_equal(c, [0.0290596, -11.8642744, 0.0998156])
 
     def test_square_well_energy(self):
         a = forcefields.square_well(2.0, [1.0, 1.5, 2.0])

pylj/util.py

@@ -246,7 +246,7 @@ def __version__():  # pragma: no cover
     """This will print the number of the pylj version currently in use."""
     major = 1
     minor = 3
-    micro = 2
+    micro = 3
     print("pylj-{:d}.{:d}.{:d}".format(major, minor, micro))
 
 

requirements.txt

@@ -1,6 +1,6 @@
 jupyter
 cython
-numpy
+numpy>=1.16
 matplotlib==2.2.3
 numba
 coverage

setup.py

@@ -17,7 +17,7 @@
 # versioning
 MAJOR = 1
 MINOR = 3
-MICRO = 2
+MICRO = 3
 ISRELEASED = True
 VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)