class PreyClass(BaseFishModel):
def add_geometry(self, **kwargs):
prey = Circle((3, 2), 0.5)
self.model_geometry.add_domain("prey", prey, sigma=1)
model = PreyClass()
parameters = {"fish_x": [-15, 15], "fish_y": [0, 0]}
model.compile(**parameters)
model.solve(**parameters)
"""
Extract the solution object
Plot the "FEM solution"
Mask only the water (outside fish)
"""
model_solution = model.solution # pull solution
mask = plotting.generate_mask(model.solution, include_domains=("water", ))
plotting.mesh_plot_2d(model_solution, "solution",
mask=mask) # plot the result named solution
# For convenience you can also exclude a domain by setting include=False
plt.figure()
mask = plotting.generate_mask(model.solution,
include_domains=("water", ),
include=False)
plotting.mesh_plot_2d(model_solution, "solution",
mask=mask) # plot the result named solution
"""Example where we show how to set eod phase."""
from fish2eod import BaseFishModel, plotting
"""
Define model parameters.
Here we draw a normal 20cm fish but set its phase to 0.5 in the EOD cycle
"""
parameters = {"fish_x": [0, 20], "fish_y": [0, 0], "phase": 0.5}
"""
Create the model and compile it
Plot the subdomains afterwards
"""
model = BaseFishModel()
model.compile(**parameters)
model.solve(**parameters)
plotting.mesh_plot_2d(model.solution, "solution")
plotting.plot_outline(model.solution)
"""Example with Neumann conditions (current sources)."""
from fish2eod import BaseFishModel, Circle, BoundaryCondition, plotting
class ExampleCurrentSource(BaseFishModel):
"""Example model with an additional voltage source."""
def add_geometry(self, **kwargs):
"""Add a circular object to carry the current."""
source = Circle([0, 3], 1)
self.model_geometry.add_domain("fg", source, sigma=1)
def add_current_sources(self, **kwargs):
"""Add a voltage source to the circle"""
# We can pull the domain id of the "fg" domain from the model geometry
# value=-3e-6 means that the Neurmann condition is as -3uA/cm^2 source
return (BoundaryCondition(value=-3e-6, label=self.model_geometry["fg"]),)
"""
Compile and solve the model
Plot the result with a color bar
"""
model = ExampleCurrentSource()
model.compile(fish_x=[0, 20], fish_y=[0, 0])
model.solve(fish_x=[0, 20], fish_y=[0, 0])
plotting.plot_outline(model.solution, color="k")
plotting.mesh_plot_2d(model.solution, "solution", colorbar=True)
prey_x = ParameterSet("prey_x", prey_x=[3, 6], rebuild_mesh=True)
prey_y = ParameterSet("prey_y", prey_y=[2, 4], rebuild_mesh=True)
parameter_sweep = ParameterSweep(prey_x, prey_y)
it = IterativeSolver("temp",
d.name,
PreyClass,
parameter_sweep,
fish_x=[-15, 15],
fish_y=[0, 0])
it.run()
"""
Extract the solution object
Plot the "FEM solution"
"""
loaded_solution = load_from_file(d.name + "/temp")
prey_x_values = loaded_solution.parameter_levels["prey_x"]
prey_y_values = loaded_solution.parameter_levels["prey_y"]
for prey_x, prey_y in product(prey_x_values, prey_y_values):
plt.figure()
# pass the solution parameters in an additional dictionary.
# all other arguments can be used as normal
plotting.mesh_plot_2d(loaded_solution,
"solution",
prey_x=prey_x,
prey_y=prey_y)
plotting.plot_outline(loaded_solution, prey_x=prey_x, prey_y=prey_y)
class PreyClass(BaseFishModel):
def add_geometry(self, prey_cond, **kwargs):
prey = Circle((3, 2), 0.5)
self.model_geometry.add_domain("prey", prey, sigma=prey_cond)
parameter_set = ParameterSet("sigma", prey_cond=[0.00023 / 10, 0.00023, 0.00023 * 10])
parameter_sweep = ParameterSweep(parameter_set)
d = TemporaryDirectory() # VERY IMPORTANT - do not do this!
# you want to use a proper save directiory. This directory created as is WILL BE DELETED when python closes.
EIP = ElectricImageParameters(domains=("prey",), value=BaseFishModel.WATER_CONDUCTIVITY)
solver = IterativeSolver(
"Example",
d.name,
PreyClass,
parameter_sweep,
fish_x=[-15, 15],
fish_y=[0, 0],
image=EIP,
)
solver.run()
loaded_solution = load_from_file(d.name + "/Example")
for ix in range(3):
plt.figure()
plotting.mesh_plot_2d(loaded_solution, "solution", sigma=ix)
plotting.plot_outline(loaded_solution, sigma=ix)
model = PreyClass()
parameters = {"fish_x": [-15, 15], "fish_y": [0, 0]}
model.compile(**parameters)
model.solve(**parameters)
"""
Plot showing effect of color_style and flags
The colorbar flag turns the colorbar on or off
The mask flag sets the mask (requires valid mask)
"""
model_solution = model.solution # pull solution
plt.figure()
plotting.mesh_plot_2d(model_solution,
"solution",
colorbar=True,
mask=None,
color_style="Full") # plot the result named solution
plt.figure()
plotting.mesh_plot_2d(model_solution,
"solution",
colorbar=True,
mask=None,
color_style="Equal") # plot the result named solution
plt.figure()
plotting.mesh_plot_2d(model_solution,
"solution",
colorbar=True,
mask=None,
color_style=None) # plot the result named solution
plt.figure()
