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fix: Boltzmann Constant units

master
Daniel Kapla 3 months ago
parent
commit
1c024647ac
2 changed files with 7 additions and 6 deletions
  1. +5
    -5
      Exercise_02/molecular_dynamics.py
  2. +2
    -1
      Exercise_02/task02.py

+ 5
- 5
Exercise_02/molecular_dynamics.py View File

@@ -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

+ 2
- 1
Exercise_02/task02.py View File

@@ -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)

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