packmol-step 2024.7.25

A SEAMM plug-in for building periodic boxes of fluid using Packmol

SEAMM Packmol Plug-in

A SEAMM plug-in for building periodic boxes of fluid using Packmol

This plug-in takes the molecule in the current system and creates a periodic box containing many copies of the molecule in order to simulate a fluid.

• Free software: BSD license

• Documentation: https://molssi-seamm.github.io/packmol_step/index.html

• Code: https://github.com/molssi-seamm/packmol_step

Features

• Multiple ways to specify final cell:

  • Size of the cubic cell and density or number of molecules or number of atoms.

  • Volume and density or number of molecules or number of atoms.

  • density and size of the cubic cell or volume or number of molecules or of atoms.

Acknowledgements

This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under awards OAC-1547580 and CHE-2136142

History

2024.7.25 – Bugfix: initial setup of packmol.ini file

• The initial setup of the packmol.ini file did not add the information for Conda. This release fixes that problem.

2024.6.29 – Bugfix: bonding incorrect in some cases.

• The use of PDB with Packmol could in some cases lead to multiple bonds in the wrong place. This release fixes that problem.

2024.6.21.2 – Another internal release for Docker.

2024.6.21.1 – Internal release for Docker

• There was an internal issue creating the Docker image.

2024.6.21 – Switching to RDKit for SMILES

• Using RDKit for SMILES since we found some issues with OpenBabel, and also the atom typing uses RDKit, so this is more compatible.

2024.3.19 – Updated installer for new scheme

• packmol-step-installer now uses the new scheme, which supports both Conda and Docker installation.

• Added seamm-packmol Docker image

2024.1.16 – Adding support for containers

• Added the ability to work in Docker containers.

2023.9.6 – Using fractional coordinates for periodic systems.

• By convention, SEAMM is using fractional coordinates for periodic systems. The PACKMOL step was creating periodic structures with Cartesian coordinates, which can be a bit confusing, though it did not affect any reauls. This change fixes the issue.

2023.2.15 – Restructured documentation and moved to new theme.

2022.5.31 – Substantial enhancements

Added ability to solvate molecules and increased the options to include

• spherical regions

• cubic and rectangular regions

• cubic and rectangular unit cells for periodic systems

• input molecules from any combination of system/configurations and SMILES

• reworked GUI to be more intuitive.

2021.11.27 – Fixed bug with atom types.

2021.10.25 – Bugfix for problems with ideal gas approach.

2021.8.29 – Multiple different molecules available via SMILES

This release adds

• the ability to directly generate multiple different molecules from SMILES, giving the stoichiometry for packing into the fluid box.

• specifying the desired cell with the temperature and pressure, along with one of the volume, length of the box side, number of molecules or number of atoms. This uses the ideal gas law, so will only be reasonable at higher temperatures and lower densities.

Additionally, internally the release adds integration tests to check whether the module works properly in the SEAMM environment.

2021.6.3 – internal change for improvements in parsing the commandline

2021.5.25 – Added installer for Packmol executable.

2021.2.11 (11 February 2021)

• Updated the README file to give a better description.

• Updated the short description in setup.py to work with the new installer.

• Added keywords for better searchability.

2021.2.4 (4 February 2021)

• Updated for compatibility with the new system classes in MolSystem 2021.2.2 release.

2020.12.5 (5 December 2020)

• Internal: switching CI from TravisCI to GitHub Actions, and in the process moving documentation from ReadTheDocs to GitHub Pages where it is consolidated with the main SEAMM documentation.

2020.11.2 (2 November 2020)

• Updated to be compatible with the new command-line argument handling.

2020.10.7 (7 October 2020)

• Added citations to be printed and stored.

2020.9.29 (29 September 2020)

• Updated to be compatible with the new system classes in MolSystem.

2020.8.1 (1 August 2020)

• Fixed bugs in the edit dialog.

0.9 (15 April 2020)

• General bug fixing and code cleanup.

• Part of release of all modules.

0.7.0 (17 December 2019)

• General clean-up of code and output.

• Part of release of all modules.

v0.3.0 (27 August 2019)

• First running version with reasonable output.

0.2.0 (13 August 2019)

• First release on PyPI.