.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples_gallery/bulk_boundary_coupling.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_gallery_bulk_boundary_coupling.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_gallery_bulk_boundary_coupling.py:


Bulk-boundary coupling
======================

Demonstrates coupling of bulk and boundary fields.

.. GENERATED FROM PYTHON SOURCE LINES 8-36



.. image-sg:: /examples_gallery/images/sphx_glr_bulk_boundary_coupling_001.png
   :alt: bulk boundary coupling
   :srcset: /examples_gallery/images/sphx_glr_bulk_boundary_coupling_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


      0%|          | 0/100.0 [00:00<?, ?it/s]
    Initializing:   0%|          | 0/100.0 [00:00<?, ?it/s]
      0%|          | 0/100.0 [00:10<?, ?it/s]              
      0%|          | 0.1/100.0 [00:13<3:44:04, 134.58s/it]
      0%|          | 0.2/100.0 [00:13<1:51:55, 67.29s/it] 
      0%|          | 0.3/100.0 [00:13<1:14:32, 44.86s/it]
     13%|█▎        | 12.7/100.0 [00:13<01:32,  1.06s/it] 
     13%|█▎        | 12.7/100.0 [00:13<01:32,  1.06s/it]
    100%|██████████| 100.0/100.0 [00:13<00:00,  7.43it/s]
    100%|██████████| 100.0/100.0 [00:13<00:00,  7.43it/s]






|

.. code-block:: Python


    import numpy as np

    import pde

    import emulsim

    # set up a 2d cytosol with a 1d boundary membrane
    grid = pde.UnitGrid([32, 8], periodic=[True, False])
    cytosol = emulsim.ScalarFieldElement.from_field(pde.ScalarField(grid, 0.001))
    membrane = emulsim.ScalarBoundaryFieldElement.from_bulk_grid(
        grid, axis=1, upper=True, data=np.random.uniform(-1, 1, 32)
    )
    state = emulsim.State({"cytosol": cytosol, "membrane": membrane})

    # set up simulation of phase separation in membrane and diffusion in cytosol
    simulation = emulsim.Simulation(state)
    simulation.add_actor("cytosol", emulsim.DiffusionActor())
    simulation.add_actor("membrane", emulsim.ScalarPDEActor(pde.CahnHilliardPDE()))
    # couple both domains using an exchange flux
    boundary_coupling = emulsim.FieldBoundaryExchangeActor(
        {"exchange_flux": "0.1 * (bulk - boundary)"}
    )
    simulation.add_actor(("cytosol", "membrane"), boundary_coupling)

    # run the simulation
    result = simulation.run(t_range=100)
    result.plot(vmin=-0.2, vmax=0.2)


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 13.556 seconds)


.. _sphx_glr_download_examples_gallery_bulk_boundary_coupling.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: bulk_boundary_coupling.ipynb <bulk_boundary_coupling.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: bulk_boundary_coupling.py <bulk_boundary_coupling.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: bulk_boundary_coupling.zip <bulk_boundary_coupling.zip>`