Customization¶

---

BubbleBox contains a selection of "setters" and "getters" for setting and getting properties of the system. Here, we'll present the basic functions for setting system variables after initialization.

In [4]:

import bubblebox as bb
import numpy as np

b = bb.showcase.repulsive_gas()

import bubblebox as bb import numpy as np b = bb.showcase.repulsive_gas()

Positions¶

To set new positions, call the set_pos-method as follows:

In [8]:

new_positions = np.random.uniform(-1,1,b.pos.shape)

b.set_pos(new_positions)

new_positions = np.random.uniform(-1,1,b.pos.shape) b.set_pos(new_positions)

Velocities¶

To set new velocities, call the set_vel-method as follows:

In [9]:

new_velocities = np.random.uniform(-1,1,b.pos.shape)

b.set_vel(new_velocities)

new_velocities = np.random.uniform(-1,1,b.pos.shape) b.set_vel(new_velocities)

Note that the default time-integration technique is velocity-verlet (wikipedia), which operates on the half-step velocities. Thus, at any instance, the actual velocities are approximated from these half-step velocities, and setting the vel (instant) and vel_ (half-step) arrays must be done simultaneously.

Masses¶

BubbleBox stores both masses and their inverse separately, thus to properly update the masses you should call the set_masses method as follows:

In [7]:

new_masses = np.random.uniform(1,5,b.masses.shape)

b.set_masses(new_masses)

new_masses = np.random.uniform(1,5,b.masses.shape) b.set_masses(new_masses)

Forces¶

Forces in BubbleBox are explicitly defined for each pair of bubbles in a n_bubbles x n_bubbles x 3 matrix. On the one hand, this results in some performance issues for large systems, while on the other hand it makes it easy to implement heterogenous interactions such that Harmonic-, Coulomb-, Lennard-Jones- or custom forces simultaneously.

In order to set the forces between a set of bubbles, you may do the following:

In [10]:

from bubblebox.mdbox import lj_force, no_force, coulomb_force, hook_force

bubbles_a = [0,2,3] #indexed in same order as pos
bubbles_b = [1,4,5] #indexed in same order as pos

# set interaction potential to 10*(∆x - 2)**2 :
b.set_forces(hook_force, bubbles_a = bubbles_a, bubbles_b = bubbles_b, force_params = np.array([10.0,2]))

from bubblebox.mdbox import lj_force, no_force, coulomb_force, hook_force bubbles_a = [0,2,3] #indexed in same order as pos bubbles_b = [1,4,5] #indexed in same order as pos # set interaction potential to 10*(∆x - 2)**2 : b.set_forces(hook_force, bubbles_a = bubbles_a, bubbles_b = bubbles_b, force_params = np.array([10.0,2]))

In [ ]: