porems.system.
PoreAmorphCylinder
(diam, res=5, hydro=[0, 0])¶This class carves a cylindric 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: |
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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/")
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[, …]) |
Attach molecule on the surface. |
attach_special (self, mol, mount, axis, amount) |
Special attachment of molecules on the surface. |
Analysis
_table_base (self, props[, decimals]) |
Base functino for converting properties to pandas table for easy viewing. |
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. |
shape (self) |
Return the pore shape for analysis using PoreAna. |
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. |
yml (self[, link]) |
Save yaml file with properties necessary for analysis. |