Storing data during simulation

Example of how to store data during a simulation.

/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/zipfile/__init__.py:1642: UserWarning: Duplicate name: 'trajectory/.zattrs'
  return self._open_to_write(zinfo, force_zip64=force_zip64)
/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/zipfile/__init__.py:1642: UserWarning: Duplicate name: 'trajectory/.zattrs'
  return self._open_to_write(zinfo, force_zip64=force_zip64)
/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/zipfile/__init__.py:1642: UserWarning: Duplicate name: 'trajectory/data/.zarray'
  return self._open_to_write(zinfo, force_zip64=force_zip64)
/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/zipfile/__init__.py:1642: UserWarning: Duplicate name: 'trajectory/time/.zarray'
  return self._open_to_write(zinfo, force_zip64=force_zip64)
/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/zipfile/__init__.py:1642: UserWarning: Duplicate name: 'trajectory/data/.zarray'
  return self._open_to_write(zinfo, force_zip64=force_zip64)
/home/docs/.asdf/installs/python/3.13.9/lib/python3.13/zipfile/__init__.py:1642: UserWarning: Duplicate name: 'trajectory/time/.zarray'
  return self._open_to_write(zinfo, force_zip64=force_zip64)
{'actors': [{'class': 'DiffusionActor', 'parameters': {'boundary_conditions': 'auto_periodic_neumann', 'diffusivity': 1.0}, 'pde': {'class': 'DiffusionPDE'}, 'element_names': ['background']}, {'class': 'SphericalDropletActor', 'parameters': {'background_correction': False, 'diffusivity': 1.0, 'drift_enabled': True, 'equilibrium_concentration': '1e-5 / radius', 'mean_reaction_inside': 'automatic', 'num_threads': 1, 'reaction_outside': '0', 'shell_sector_count': 6, 'shell_sector_method': 'size', 'shell_sector_size': 'dx', 'shell_thickness': 'dx'}, 'element_names': ['droplets', 'background']}], 'controller': {'mpi_run': False, 't_start': 0, 't_end': 10.0, 'profiler': {'solver': 0.0, 'tracker': 0.0}}, 'item_type': 'object', 'package_version': '0.56.1', 'solver': {'class': 'SimulationSolver'}, 'state': {'parameters': {'bounds': None, 'invisible_elements': set(), 'plot_args': {}}}}

from droplets import SphericalDroplet
from pde import ScalarField, UnitGrid

import emulsim

# set up state
grid = UnitGrid([32, 32], periodic=True)
background = emulsim.ScalarFieldElement.from_field(ScalarField(grid, 0.1))
droplet_data = [SphericalDroplet(grid.get_random_point(), 1) for _ in range(3)]
droplets = emulsim.SphericalDropletsElement.from_droplets(droplet_data)
state = emulsim.State({"background": background, "droplets": droplets})

# set up simulation
simulation = emulsim.Simulation(state)
simulation.add_actor("background", emulsim.DiffusionActor())
simulation.add_actor(("droplets", "background"), emulsim.SphericalDropletActor())

# run simulation and store data periodically
tracker = emulsim.TrajectoryTracker(
    "trajectory.zip", interrupts=2, mode="truncate", info=simulation.info
)
simulation.run(t_range=10, tracker=tracker)

# retrieve data and plot last state
stored_data = emulsim.Trajectory("trajectory.zip")
print(stored_data.info)  # recover the auxillary information
stored_data[-1].plot()  # plot the last time point of the stored data