porems 0.3.0

Pore Generator for Molecular Simulations.

---

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

• Nguyen et al., 2024. Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru–H Complex: Insights from Molecular Simulation and Neutron Scattering. ACS Catalysis, doi:doi.org/10.1021/acscatal.4c02626
  • Data-Repository: doi:
• 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