:orphan:

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Diffusion Analysis in a Pore (Bin Method)
=========================================

The bin diffusion analysis needs the sampled object file using the bin
diffusion routine

.. code-block:: python

    import porems as pms
    import poreana as pa

    mol = pms.Molecule(inp="data/benzene.gro")

    sample = pa.Sample("data/pore_system_cylinder.obj", "data/traj_cylinder.xtc", mol, [])
    sample.init_diffusion_bin("output/diff.h5")
    sample.sample()

``Finished frame 2001/2001...``


The diffusion can be calculated through the entire pore

.. code-block:: python

    pa.diffusion.cui("output/diff.h5")

``Diffusion axial:  0.741 10^-9 m^2s^-1``

``Diffusion radial: 648.838 10^-9 m^2 s^-1; Number of zeros: 41; Radius:  0.17``

.. figure::  /pics/diffusion_bins_01.svg
  :align: center
  :width: 50%
  :name: fig1


or binwise

.. code-block:: python

    pa.diffusion.bins("output/diff.h5")


.. figure::  /pics/diffusion_bins_02.svg
  :align: center
  :width: 50%
  :name: fig2


By weighting the diffusion profile with the density profile, one can
calculate an axial mean value

.. code-block:: python

    pa.diffusion.mean("output/diff.h5", "output/dens.h5")


``Mean Diffusion axial: 1.131 10^-9 m^2s^-1``


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