ajax23 / porems Goto Github PK

Ability to generate pores from other materials than silica such as quartz pores or carbon nanotubes.

When saving a pore object with pore.store(), the resulting pore.top file requires .itp files for all the attached molecules; however, these .itp files aren't being generated.

Request

Create amorphous surfaces.

Solution

After determining the binding sites, use a gaussian distribution to randomly translate binding site atoms. Add an acceptance condition similar to MC.

Request

Readable output format for calculated properties.

Soluation

Use pandas tables to show the different properties.

Issue
Sphere centroid, or rather all shape centroids have to align towards their own chape centroid, not silica block centroid.

Example
Wrong surface group alignment in capsule pore

Todo

• Adjust normal vectors in shape class
• Adjust property calculations in system class

I'm creating this issue because your repo contains a conf.py file with

nbsphinx_prompt_width = 0

... presumably in an attempt to remove the prompts from code cells.

I just want to give you a heads-up that this will stop working once spatialaudio/nbsphinx#439 is merged.

For more reliable alternatives, see https://nbsphinx.readthedocs.io/en/latest/custom-css.html.

Hello, I am using your program to generate a pore on a spherical surface but the program generates it cubic. As it changed the form, I reviewed that the Shape class exists but as it will implement it by generating the pore. Thanks

Hi,

Is it possible to create nanopores with a different molecule to silica?

Thanks in advance

Request

Ability to generate arbitrary pore shapes.

Solution

Create new class containing for defining pore shape, and setting rules for properties calculation like surface and volume.

The calculation does not consider the double amount of OH on the geminal silanol.

Request

Generate different crystal structures like Alpha-Quartz.

Solution

Create individual class for generating structures which are then processed via verlet and bonding logic.

whenever i try to use the pos_list keyword, i get the error:

TypeError: attach() got an unexpected keyword argument 'pos_list'

as if this keyword is not actually implemented in the package.