Interactivity

In [1]:

import bubblebox as bb
help(bb.showcase.double_harmonic_chain)

import bubblebox as bb help(bb.showcase.double_harmonic_chain)

Help on function double_harmonic_chain in module bubblebox.showcase:

double_harmonic_chain(n_bubbles=200, size=(10, 10, 10), charge=20.0, force_params=array([4., 1.]))
    # Harmonic Chain
    
    Generates a double-layered structure of n_bubbles connected to their neighbors with 
    harmonic potentials, and repelling all others with a coulomb potential
    Auhor: Audun Skau Hansen 2022
    
    ## Keyword arguuments
    
    | Argument      | Description | Default |
    | ----------- | ----------- | --- |
    | n_bubbles   | number of bubbles         | 120   |
    | size   | size of simulation box         | (10,10,10)  |
    | charge  | repulsive charge         | 20.0  |

In [2]:

m = bb.showcase.double_harmonic_chain(80)

m.view()

m = bb.showcase.double_harmonic_chain(80) m.view()

Out[2]:

MDView(bg_color=[1.0, 1.0, 1.0], box=[10, 10, 10], colors=[[0.4993901038167592, 0.5549452882456589, 0.91639324…

In [3]:

# relax geometry interactively
for i in range(1000):
    for j in range(5):
        m.advance()
    m.vel_ *= 0.99
    m.update_view()

# relax geometry interactively for i in range(1000): for j in range(5): m.advance() m.vel_ *= 0.99 m.update_view()

In [8]:

import evince as ev

m.pos *= 2
bonds = ev.spotlight.extract_bonds(m)
mv = ev.SpotlightView(m, realism = False, bonds = bonds, dof = True, focus = 5, aperture = 0.001, max_blur = 0.001)

mv

import evince as ev m.pos *= 2 bonds = ev.spotlight.extract_bonds(m) mv = ev.SpotlightView(m, realism = False, bonds = bonds, dof = True, focus = 5, aperture = 0.001, max_blur = 0.001) mv

Out[8]:

SpotlightView(aperture=0.001, bg_color=[1.0, 1.0, 1.0], bonds=[[0, 1], [0, 40], [1, 2], [1, 41], [2, 3], [2, 4…

Manual update¶

What happens here is that the mdbox-instance above (that is m) has a model and a view. The view is rendered to screen in the line m.view(), which explicitly returns the view to the cell-output in Jupyter.

In the cell below, we manually change the list of positions m.view().pos-list and observe that the view updates the positions:

In [9]:

mv.save("harmonic_chain.html")

mv.save("harmonic_chain.html")

In [ ]: