PoreMS 0.2
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        • PoreCapsule

    PoreCapsule¶

    class porems.system.PoreCapsule(size, diam, sep, res=5)¶

    This class carves a capsule pore system out of a \(\beta\)-cristobalite block.

    Parameters:
    size : list

    Size of the silicon-oxygen-grid

    diam : float

    Cylinder diameter

    sep : float

    Separation length between capsule

    res : float, optional

    Reservoir size on each side

    Examples

    Following example generates a capsule pore with a diameter of 4nm, a separation distance between the capsules of 2nm, reservoirs of 5nm on each side and a surface functionalized with TMS

    import porems as pms
    
    pore = pms.PoreCapsule([6, 6, 12], 4, 2)
    
    pore.attach(pms.gen.tms(), 0, [0, 1], 100, "in")
    pore.attach(pms.gen.tms(), 0, [0, 1], 20, "ex")
    
    pore.finalize()
    
    pore.store("output/")
    

    Attachement

    _normal_ex(self, pos) Normal function for the exterior surface
    _normal_in(self, pos) Normal function for the interior surface
    attach(self, mol, mount, axis, amount, site_type) Attach molecule on the surface.

    Analysis

    allocation(self) Calculate molecule allocation on the surface.
    box(self) Return the box size of the pore block.
    centroid(self) Return pore centroid.
    diameter(self) Calculate true cylinder diameter after drilling and preperation.
    reservoir(self) Return the reservoir length.
    roughness(self) Calculate surface roughness.
    surface(self) Calculate pore surface and exterior surface.
    table(self[, decimals]) Create properties as pandas table for easy viewing.
    volume(self) Calculate pore volume.

    Finalization

    finalize(self) Finalize pore system.
    store(self[, link, sort_list]) Store pore system and all necessary files for simulation at given link.

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    © Copyright 2021, Hamzeh Kraus.
    Created using Sphinx 1.6.6.