getting the examples running and ensuring backwords compatibiilty

arm61 · Aug 26, 2018 · 78234a7 · 78234a7
1 parent 936f2ce
commit 78234a7
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diff --git a/pylj/comp.cpython-36m-x86_64-linux-gnu.so b/pylj/comp.cpython-36m-x86_64-linux-gnu.so
diff --git a/pylj/md.py b/pylj/md.py
@@ -124,7 +124,7 @@ def sample(particles, box_length, initial_particles, system):
                                           temperature_new)
     pressure_new = heavy.calculate_pressure(particles, box_length,
                                             temperature_new, system.cut_off,
-                                            system.a, system.b)
+                                            system.constants)
     msd_new = calculate_msd(particles, initial_particles, box_length)
     system.pressure_sample = np.append(system.pressure_sample, pressure_new)
     system.force_sample = np.append(system.force_sample,
@@ -272,18 +272,23 @@ def calculate_temperature(particles):
     return k
 
 
-def compute_force(particles, box_length, cut_off, a=1.363e-134, b=9.273e-78,
-                  mass=39.948, forcefield=ff.lennard_jones):
+def compute_force(particles, box_length, cut_off,
+                  constants=[1.363e-134, 9.273e-78], mass=39.948,
+                  forcefield=ff.lennard_jones):
     part, dist, forces, energies = heavy.compute_force(particles, box_length,
-                                                       cut_off, a=a, b=b,
-                                                       mass=mass)
+                                                       cut_off,
+                                                       constants=constants,
+                                                       mass=mass,
+                                                       forcefield=forcefield)
     return part, dist, forces, energies
 
 
-def compute_energy(particles, box_length, cut_off, a=1.363e-134, b=9.273e-78,
+def compute_energy(particles, box_length, cut_off,
+                   constants=[1.363e-134, 9.273e-78],
                    forcefield=ff.lennard_jones):
-    dist, energies = heavy.compute_energy(particles, box_length, cut_off, a=a,
-                                          b=b)
+    dist, energies = heavy.compute_energy(particles, box_length, cut_off,
+                                          constants=constants,
+                                          forcefield=forcefield)
     return dist, energies
 
 

diff --git a/pylj/util.py b/pylj/util.py
@@ -29,11 +29,10 @@ class System:
     """
     def __init__(self, number_of_particles, temperature, box_length,
                  init_conf='square', timestep_length=1e-14,
-                 cut_off=15, a=1.363e-134, b=9.273e-78, mass=39.948):
+                 cut_off=15, constants=[1.363e-134, 9.273e-78], mass=39.948):
         self.number_of_particles = number_of_particles
         self.init_temp = temperature
-        self.a = a
-        self.b = b
+        self.constants = constants
         self.mass = mass
         if box_length <= 600:
             self.box_length = box_length * 1e-10
@@ -119,12 +118,12 @@ def compute_force(self):
         """Maps to the compute_force function in either the comp (if Cython is
         installed) or the pairwise module and allows for a cleaner interface.
         """
-        a = self.a
-        b = self.b
+        constants = self.constants
         mass = self.mass
         part, dist, forces, energies = md.compute_force(self.particles,
                                                         self.box_length,
-                                                        self.cut_off, a=a, b=b,
+                                                        self.cut_off,
+                                                        constants = constants,
                                                         mass=mass)
         self.particles = part
         self.distances = dist
@@ -136,12 +135,11 @@ def compute_energy(self):
         is installed) or the pairwise module and allows for a cleaner
         interface.
         """
-        a = self.a
-        b = self.b
+        constants = self.constants
         self.distances, self.energies = md.compute_energy(self.particles,
                                                           self.box_length,
-                                                          self.cut_off, a=a,
-                                                          b=b)
+                                                          self.cut_off,
+                                                          constants=constants)
 
     def integrate(self, method):
         """Maps the chosen integration method.