ajax23 / porems

Pore generator for molecular simulations.

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Documentation

Online documentation is available at ajax23.github.io/PoreMS.

The docs include an example for generating molecules and pores, and an API reference. Visit process for an overview of the programs operating principle.

An examplary workflow has been provided for using the PoreMS package to create a pore system and run molecular dynamics simulation using Gromacs.

Dependencies

PoreMS supports Python 3.5+.

Installation requires numpy, pandas and matplotlib.

Installation

The latest stable release (and older versions) can be installed from PyPI:

pip install porems

You may instead want to use the development version from Github:

pip install git+https://github.com/ajax23/porems.git#egg=porems

pip install git+https://github.com/ajax23/porems.git@develop#egg=porems

Or download the repository and install in the top directory via:

pip install .

Testing

To test porems, run the test in the test directory.

Development

PoreMS development takes place on Github: www.github.com/Ajax23/PoreMS

Please submit any reproducible bugs you encounter to the issue tracker.

How to Cite PoreMS

When citing PoreMS please use the following: Kraus et al., Molecular Simulation, 2021, DOI: 10.1080/08927022.2020.1871478

Additionaly, to assure reproducability of the generated pore systems, please cite the Zenodo DOI corresponding to the used PoreMS version. (Current DOI is listed in the badges.)

Published Work

• Kraus et al., 2023. Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models. The Journal of Physical Chemistry C, doi:10.1021/acs.jpcc.3c01974.
  • Data-Repository: doi:10.18419/darus-3067
• Kraus and Hansen, 2022. An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica. Adsorption, doi:10.1007/s10450-022-00356-w.
  • Data-Repository: doi:10.18419/darus-2154
• Kraus et al., 2021. PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions. Molecular Simulation, 47(4), pp.306-316, doi:10.1080/08927022.2020.1871478.
  • Data-Repository: doi:10.18419/darus-1170
• Ziegler et al., 2021. Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N-Heterocyclic Carbene Complexes. ACS Catalysis, 11(18), pp. 11570-11578, doi:10.1021/acscatal.1c03057
  • Data-Repository: doi:10.18419/darus-1752
• Kobayashi et al., 2021. Confined Ru-catalysts in a Two-phase Heptane/Ionic Liquid Solution: Modeling Aspects. ChemCatChem, 13(2), pp.739-746, doi:10.1002/cctc.202001596.
  • Data-Repository: doi:10.18419/darus-1138
• Ziegler et al., 2019. Olefin Metathesis in Confined Geometries: A Biomimetic Approach toward Selective Macrocyclization. Journal of the American Chemical Society, 141(48), pp.19014-19022, doi:10.1021/jacs.9b08776.
  • Data-Repository: doi:10.18419/darus-477

porems's Issues

Readable properties output

Request

Readable output format for calculated properties.

Soluation

Use pandas tables to show the different properties.

how to change the shape from cubic to spherical?

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

generate non_silica pores

Hi,

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

Thanks in advance

Different Crystal Structures

Request

Generate different crystal structures like Alpha-Quartz.

Solution

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

Amorphous surface

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.

cannot use pos_list keyword argument in Pore.attach

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.

Wrong centroid for aligning

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

Pore.store() isn't generating the required .itp files.

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.

Arbitrary pore shape

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.

Additional Materials

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

Hydroxilation degree

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

Don't use nbsphinx_prompt_width to hide prompts

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.