PoreKit¶

class porems.system.PoreKit¶

Pore construction kit.

Structure

`_normal_ex`(pos)	Normal function for the exterior surface
`_siloxane`(site_type[, slx_dist])	Attach siloxane bridges using function `porems.pore.Pore.siloxane()`.
`attach`(mol, mount, axis, amount[, ...])	Attach molecule on the surface.
`build`([bonds])	Process provided structure to build connectivity matrix.
`exterior`(res[, hydro])	Optionally create and adjust exterior surface.
`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.
`structure`(structure)	Add structure to the Pore builder.

Shape

`add_shape`(shape[, section, hydro])	Add shape to pore system for drilling.
`shape_cylinder`(diam[, length, centroid, central])	Add cylindrical shape
`shape_cone`(diam_1, diam_2[, length, ...])	Add cone shape
`shape_slit`(height[, length, centroid, central])	Add slit shape
`shape_sphere`(diameter[, centroid, central])	Add sphere shape

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.

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.