PoreCylinder¶

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

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

Parameters:

sizelist: Size of the silicon-oxygen-grid
diamfloat: Cylinder diameter
resfloat, optional: Reservoir size on each side
hydrolist, 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.PoreCylinder([6, 6, 6], 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/")

Attachement

`attach`(mol, mount, axis, amount[, ...])	Attach molecule on the surface.
`attach_special`(mol, mount, axis, amount[, ...])	Special attachment of molecules on the surface.

Analysis

`allocation`()	Calculate molecule allocation on the surface.
`box`()	Return the box size of the pore block.
`centroid`()	Return pore centroid.
`diameter`()	Calculate true diameter after drilling and preparation.
`reservoir`()	Return the reservoir length.
`roughness`()	Calculate surface roughness.
`shape`()	Return the pore shape for analysis using PoreAna.
`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.

Finalization

`finalize`()	Finalize pore system.
`store`([link, sort_list])	Store pore system and all necessary files for simulation at given link.
`yml`([link])	Save yaml file with properties necessary for analysis.