fix: Boltzmann Constant units

Exercise_02/molecular_dynamics.py

@@ -88,7 +88,7 @@ def energy(position, box_size):
     # enforce expected shape
     # (`scipy.optimize.minimize` drops shape information)
     if len(position.shape) == 1:
-        position = position.reshape((position.shape[0] // 3, 3))
+        position = position.reshape((-1, 3))
     # compute all pairwise position differences (all!)
     diff = position[:, jnp.newaxis, :] - position
     # extract only one of two distance combinations of non-equal particles
@@ -122,16 +122,16 @@ def kinetic(velocity):
     return (mass / 2.0) * (velocity**2).sum()
 
 @jit
-def step(position, velocity, acceleration, box_size, step_size):
+def step(position, velocity, acceleration, box_size, delta_t):
     """
-    Performs a single Newton time step with `step_size` given system state
+    Performs a single Newton time step with `delta_t` given system state
     through the current particle `position`, `velocity` and `acceleration`.
     """
     # update position with a second order Taylor expantion
-    position += step_size * velocity + (0.5 * step_size**2) * acceleration
+    position += delta_t * velocity + (0.5 * delta_t**2) * acceleration
     # compute new particle acceleration through Newton’s second law of motion
     acceleration_next = force(position, box_size) / mass
     # update velocity with a finite mean approximation
-    velocity += (0.5 * step_size) * (acceleration + acceleration_next)
+    velocity += (0.5 * delta_t) * (acceleration + acceleration_next)
     # updated state
     return position, velocity, acceleration_next

Exercise_02/task02.py

@@ -59,7 +59,8 @@ from molecular_dynamics import dump, energy, force, mass
 position = np.random.uniform(0.0, config.box_size, (config.nr_particles, 3))
 
 # Sample particle velocities
-sd = np.sqrt(scipy.constants.Boltzmann * config.temperature / mass)
+K_b = scipy.constants.Boltzmann / scipy.constants.eV # [eV / K]
+sd = np.sqrt(K_b * config.temperature / mass)
 velocity = np.random.normal(0.0, sd, (config.nr_particles, 3))
 # center velocities
 velocity -= velocity.mean(axis = 0)