Metadata-Version: 2.1
Name: lammps_step
Version: 2023.4.6
Summary: A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.
Home-page: https://github.com/molssi-seamm/lammps_step
Author: MolSSI @ Virginia Tech
Author-email: seamm@molssi.org
License: BSD-3-Clause
Keywords: SEAMM,plug-in,flowchart,forcefield,EAM,OpenKIM,molecular dynamics,atomistic,MD
Platform: Linux
Platform: Mac OS-X
Platform: Unix
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS.rst

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====================
SEAMM LAMMPS Plug-in
====================

A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.

This plug-in provides a graphical user interface (GUI) for setting up
complex simulations using LAMMPS. It uses a sub-flowchart that
provides steps such as constant pressure and temperature (NPT)
dynamics which give access to the functionality in LAMMPS in a more
consistent and understandable way than the inscrutable fixes that
LAMMPS uses.

These sub-flowcharts mirror the main flowchart in form and function
and can use the same variables such as temperature and pressure that
are accessible anywhere in the flowcharts. This allows "programming" a
LAMMPS workflow in the same familiar way that SEAMM uses to represent
the overall workflow.

* Free software: BSD license
* Documentation: https://molssi-seamm.github.io/lammps_step/index.html
* Code: https://github.com/molssi-seamm/lammps_step


Features
--------

* Use of any forcefield supported by the forcefield plug-in:

  - PCFF
  - OpenKIM: EAM, MEAM, LJ, ReaxFF

* Molecular statics: minimization
* Molecular dynamics: NVE, NVT, and NPT with any of the approaches
  supported in LAMMPS
* Automatic statistical analysis of averages from MD

  - Detection of equilibration
  - Mean and standard error of the mean for the sampling after
    equilibration
  - Autocorrelation function and time
  - Statistical inefficiency
  - Plotting of results in the Dashboard

* Using property values to drive MD. Rather than running MD for a
  length of time, automatically run long enough to determine a set of
  properties within given error bars.

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
=======
2023.4.6 -- Better forcefield handling.
   * Added correct molecule numbers for valence forcefields.
   * Correctly handle ReaxFF from OpenKim
   * Updated for some minor changes in OpenKim

2023.2.6 -- Added handling of OPLS-AA forcefield
   * Added handling of the OPLS-AA forcefield
   * Moved documentation to new MolSSI theme and diátaxis layout
   * Cleaned up internale dependencies and workflows for GitHub

2022.10.31 -- Bugfix: properties with commas
  Properties with commas in their name in data/properties.csv need to have quotes to
  protect the property name!

2022.10.27 -- Added properties
  * Added properties to be saved in the database.
  * Updated calls to `pymbar` because the names of methods were changed.
  * Add the missing references for `pymbar`

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.

2021.2.4.1 (4 February 2021)
  Internal patch to fix CI; no changes for users.

2021.2.4 (4 February 2021)
  Updated for compatibility with the new system classes in MolSystem
  2021.2.2 release.

2020.12.4 (4 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.

2020.10.13 (13 October 2020)
  Added capability to run MD until a set of user-selected properties
  are converged to requested accuracy.

2020.9.25 (25 September 2020)
  Updated to be compatible with the new system classes in MolSystem.

2020.8.2.1 (2 August 2020)
  Bugfix: Fixed problem with nonbonds and charges just introduced.

2020.8.2 (2 August 2020)
  Bugfix: Corrected the time units when using `metal` units with
  e.g. EAM potentials.

2020.8.1 (1 August 2020)
  Added support for OpenKIM potentials.

0.9.4 (29 May 2020)
  Cleaned up the output for the statistical analysis.

0.9.3 (29 May 2020)
  Fixed issue with settings for bins in LAMMPS for small nonperiodic
  systems with just a few atoms.

0.9.2 (25 May 2020)
  Switched to using PYMBAR for detecting covergence to equilibrium for
  MD runs. This is a more robust solution than the previous approach.

0.9.1 (24 May 2020)
  Support for rigid water models, such as TIP-3P.

0.9 (15 April 2020)
  Support for plots in the dashboard of properties from MD.
  Added option to produce local HTML for the above plots.

0.8.2 (2020-01-25)
  * No significant changes in functionality.
  * Incorporating changes to the SEAMM infrastructure, which simplify
    the code for plug-ins.
  * Updating the Travis CI to handle incompatible changes in Travis, and
    to use Conda environments in all steps.

0.7.1 (18 December 2019)
  Fixed problem with assigning charges to the system.

0.7.0 (17 December 2019)
  General clean-up of code and output.

0.6 (8 September 2019)
  * Switched to ConfigArgParse for handling command-line arguments.
  * Added the locations of LAMMPS executables to a configuration file
    for easier access.

0.5.2 (31 August 2019)
  Defined the correct requirements for installation.

0.5.1 (30 August 2019)
  Bugfix: corrected the name of the LAMMPS executable.
  
0.5.0 (30 August 2019)
  Added ability to use serial or parallel versions of LAMMPS based on
  an environment variable.

0.3.1 (27 August 2019)
  Added initial, fairly reasonable output.
  
0.2.1 (29 July 2019)
  First release on PyPI.
