The sGFRD Method¶

The numpy-stl module is required for visualizations of a STL mesh.

[1]:

# !pip install numpy-stl
import stl

/home/kaizu/.local/share/virtualenvs/python-eSbFG-Wg/lib/python3.7/importlib/_bootstrap.py:219: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  return f(*args, **kwds)

Set Plotly as the default backend.

[2]:

from ecell4.prelude import *

[3]:

import ecell4.plotting
import ecell4.plotting._plotly
ecell4.plotting.BACKEND = ecell4.plotting._plotly
from ecell4.plotting._plotly import plot_stl

[4]:

f = sgfrd.Factory()

Diffusion on a Triangle Mesh¶

Here is a STL-format file named stanford_bunny.stl:

[5]:

plot_stl("stanford_bunny.stl")

[6]:

with species_attributes():
    A | {"radius": 0.005, "D": 1.0}

m = get_model()

[7]:

edge_lengths = Real3(90, 70, 90)
w = f.polygon("stanford_bunny.stl", STLFormat.Ascii).world(edge_lengths)

[8]:

w.bind_to(m)

[9]:

w.add_molecules(Species('A'), 50)

[10]:

plotting.plot_world(w, stl=["stanford_bunny.stl"])

[11]:

s = f.simulator(w, m)
obs = FixedIntervalTrajectoryObserver(1.0)
s.run(100.0, obs)

[12]:

plotting.plot_trajectory(obs, max_count=50, stl=["stanford_bunny.stl"], layout=dict(showlegend=False))

Reaction-Diffusion on a Planar Surface¶

[13]:

plot_stl("plane10x10.stl")

[14]:

with species_attributes():
    A | B | C | {"radius": 0.005, "D": 1.0}

with reaction_rules():
    A + B == C | (12.0, 60.0)

m = get_model()

[15]:

edge_lengths = Real3(10, 10, 2)
w = f.polygon("plane10x10.stl", STLFormat.Ascii).world(edge_lengths)

[16]:

w.bind_to(m)

[17]:

w.add_molecules(Species('A'), 1000)
w.add_molecules(Species('B'), 1000)

[18]:

s = f.simulator(w, m)
obs = FixedIntervalNumberObserver(0.001)
s.run(0.2, obs)

[19]:

show(obs)

[28]:

plotting.plot_world(w, stl=["plane10x10.stl"], max_count=50)

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