PoreAmorphCylinder¶

class porems.system.PoreAmorphCylinder(diam, res=5, hydro=[0, 0])¶

This class carves a cylindrical pore system out of an amorph \(\beta\)-cristobalite block from Vink et al. with dimensions [9.605, 9.605, 9.605] (x, y, z).

Parameters:

diamfloat: Cylinder diameter
resfloat, optional: Reservoir size on each side
hydro: list, optional: Hydroxilation degree for interior and exterior of the pore in \(\frac{\mu\text{mol}}{\text{m}^2}\)

Examples

Following example generates a cylindrical pore with a diameter of 4nm, reservoirs of 5nm on each side and a surface functionalized with TMS

import porems as pms

pore = pms.PoreAmorphCylinder(4, 5)

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/")

Methods

`_normal_ex`(pos)	Normal function for the exterior surface
`_siloxane`(site_type[, slx_dist])	Attach siloxane bridges using function `porems.pore.Pore.siloxane()`.
`add_shape`(shape[, section, hydro])	Add shape to pore system for drilling.
`allocation`()	Calculate molecule allocation on the surface.
`attach`(mol, mount, axis, amount[, ...])	Attach molecule on the surface.
`attach_special`(mol, mount, axis, amount[, ...])	Special attachment of molecules on the surface.
`box`()	Return the box size of the pore block.
`build`([bonds])	Process provided structure to build connectivity matrix.
`centroid`()	Return pore centroid.
`diameter`()	Calculate true diameter after drilling and preparation.
`exterior`(res[, hydro])	Optionally create and adjust exterior surface.
`finalize`()	Finalize pore system.
`prepare`()	Prepare pore surface, add siloxane bridges, assign sites to sections, and assign a unique normal vector to each site by updating the original pore object site list.
`reservoir`()	Return the reservoir length.
`roughness`()	Calculate surface roughness.
`shape`()	Return the pore shape for analysis using PoreAna.
`shape_cone`(diam_1, diam_2[, length, ...])	Add cone shape
`shape_cylinder`(diam[, length, centroid, central])	Add cylindrical shape
`shape_slit`(height[, length, centroid, central])	Add slit shape
`shape_sphere`(diameter[, centroid, central])	Add sphere shape
`store`([link, sort_list])	Store pore system and all necessary files for simulation at given link.
`structure`(structure)	Add structure to the Pore builder.
`surface`([is_sum])	Calculate pore surface and exterior surface.
`table`([decimals])	Create properties as pandas table for easy viewing.
`volume`([is_sum])	Calculate pore volume.
`yml`([link])	Save yaml file with properties necessary for analysis.