forcefield-step

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======================== SEAMM Forcefield Plug-in

A SEAMM plug-in for setting up a forcefield or EAM potentials for subsequent simulations.

This plug-in provides a graphical user interface (GUI) for choosing the forcefield or EAM potentials use by subsequent simulation steps.

• Free software: BSD license
• Documentation: https://molssi-seamm.github.io/forcefield_step/index.html

Features

• Support for PCFF class II forcefield.
• Support for OpenKIM and the potentials it supports.
• For OpenKIM potentials choice is managed through a periodic table interface, making it simple to find the right potentials.

Acknowledgements

This package was created with Cookiecutter_ and the molssi-seamm/cookiecutter-seamm-plugin_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter .. _molssi-seamm/cookiecutter-seamm-plugin: https://github.com/molssi-seamm/cookiecutter-seamm-plugin

Developed by the Molecular Sciences Software Institute (MolSSI_), which receives funding from the National Science Foundation_ under award ACI-1547580

.. _MolSSI: https://www.molssi.org .. _National Science Foundation: https://www.nsf.gov

======= History

2024.6.30 -- Bugfix: Error submitting jobs with local forcefield files.

2024.6.29 -- Bugfix: factor of 2 for dihedrals and impropers in ligpargen

• The ligpargen tool was missing a factor of 2 in the dihedral and improper parameters.
• Corrected the search paths for forcefields.
• Improved the documentation.

2024.6.28 -- Added customizable local forcefields and LigParGen interface.

• Added the machinery to handle local forcefield files in either ~/.seamm.d/data/Forcefields (personal) or ~/SEAMM/data/Forcefields (site).
• Added 'ligpargen' command to access custom parameters from the LigParGen service at Yale University, ading them to the 'ligpargen.frc' personal forcefield, which is automatically included in 'oplsaa.frc' if it exists.

2024.1.10 -- Fixed PF6- issue in CL&P forcefield

• The angle parameters for PF6- in the CL&P forcefield only work if the 180º F-P-F angles are not included in the calculation. Replacing them with an equivalent periodic SHAPES-like potential almost works; however, since 0º is a valid angle and there are no 1-3 nonbonds, nothing keeps the F atoms apart. This is solved using a tabulated potential based on the SHAPES potential but with an added 1-3 repulsion large enough that the gradient is always pusing small angles apart, but not large enough to affect the minimum at 90º.

2023.9.14 -- Fixed errors! And added C2mim to test.

• The units of the torsions were incorrect in the last implementation.
• Added parameters for 1-alkyl-3-methylimidazolium cations from JCP 108, 2038 (2004)
• Tested much more thoroughly.

2023.9.13 -- Added parameters for TFSI to CL&P/OPLSAA

• Parameters for TFSI - bis[(trifluoromethyl)sulfonyl]imide

2023.9.8 -- Added more typing for OPLS-AA

• cyclopropane -CH2-, -CHR-, and -CR2-
• hexafluorobenzene
• difluorobenzene
• bromobenzene
• iodobenzene
• thiophenol
• alkyl nitriles
• nitroalkanes
• nitrobenzene
• methylene in phenylacetonitrile
• corrections to methylene nitrile anion

2023.9.7 -- Added typing in OPLS_AA for fluorobenzene

2023.9.6 -- Fixed issue with PF6- geometry

• The Lennard-Jones repulsive term added to the F-P-F angle was too weak, allowing the structure to get trapped in a symmetric state with ~40º angles.

2023.8.27 -- Fixed issue with angle in octahedral systems

• The SHAPES-type simple fourier potential used for octahedral complexes has a fals minimim at 0º. Added a LJ 1/R^12 repulsive term between the two end atoms of the angle to prevent small angles. This required using tabulated potentials in LAMMPS.

2023.5.1 -- Fixed bug in Lithium battery forcefield

• Fixed a typo in the angle type unit line which caused a crash

2023.4.6 -- Added Lithium battery forcefield

• An initial set of parameters for cathode materials, specifically LiCoO2.

2023.2.13 -- Added OPLS-AA forcefield

• Added parameters for OPLS-AA along with some extra parameters for ionic liquids
  • PF6-
  • ethylene carbonate (EC) and fluoronated EC (FEC)
• Added atom-typing templates for most of OPLS-AA. Still missing a few and amino acids and DNA not yet tested.
• Added extensive, almost-complete testing, for OPLS-AA

2021.2.10 (10 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.

2020.8.1 (1 August 2020)

• Added support for OpenKIM potentials in LAMMPS

0.9.1 (24 May 2020)

• Added the specialized NaCl_water forcefield for testing the MolSSI Driver Interface (MDI) metadynamics driver.

0.9 (15 April 2020)

• Internal changes for compatibility

0.1.0 (24 December 2017)

• First release on PyPI.