Package: packmol-step
SEAMM Packmol Plug-inA SEAMM plug-in for building periodic boxes of fluid usingPackmolThis 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 licenseDocumentation:https://molssi-seamm.github.io/packmol_step/index.htmlCode:https://github.com/molssi-seamm/packmol_stepFeaturesMultiple ways to specify final cell:Size of the cubic cellanddensityornumber of moleculesornumber of atoms.Volumeanddensityornumber of moleculesornumber of atoms.densityandsize of the cubic cellorvolumeornumber of
moleculesorof atoms.AcknowledgementsThis package was created withCookiecutterand themolssi-seamm/cookiecutter-seamm-pluginproject template.Developed by the Molecular Sciences Software Institute (MolSSI),
which receives funding from theNational Science Foundationunder
awards OAC-1547580 and CHE-2136142History2024.1.16 – Adding support for containersAdded 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 enhancementsAdded ability to solvate molecules and increased the options to includespherical regionscubic and rectangular regionscubic and rectangular unit cells for periodic systemsinput molecules from any combination of system/configurations and SMILESreworked 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 SMILESThis release addsthe 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 commandline2021.5.25 – 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.