Metadata-Version: 2.1
Name: lammps-step
Version: 2021.3.8
Summary: A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.
Home-page: https://github.com/molssi-seamm/lammps_step
Author: Paul Saxe
Author-email: psaxe@molssi.org
License: BSD-3-Clause
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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
        =======
        
        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.
        
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 :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/x-rst
