Best Practices for Simulation Software Validation / Physical Validation

Best Practices articles treating simulation software validation and physical validation, to be submitted to LiveCoMS (Living Journal of Computational Molecular Science, www.livecomsjournal.org). We plan to divide the topic into two largely independent documents:

1. Best practices for simulation software verification (developer best practices)
2. Best practices for physical validation of simulation results (user best practices)

The groundwork for these articles was laid during the Best Practices workshop organized by Michael Shirts on behalf of MolSSI, held at NIST on Aug 24-25, 2017, by Justin Gilmer, David Kofke, Pascal Merz, Conor Parks, Julia Rice, Matthew Spellings, Terry Stouch, and William Swope (authors in alphabetical order). Please contact Pascal Merz if you would like to contribute but have not been invited to do so.

Best practices for simulation software verification

Scope: The authors are experts on simulation software, not necessarily on general software engineering. Consequently, the scope of the article will not be general software engineering best practices (version control, continuous integration, unit/system/regression testing, ...), but the testing of simulation software. We will propose a hierarchically organized set of tests intended to help developers to detect and localize errors in simulation software.

Best practices for physical validation of simulation results

Scope: A checklist of methods to analyze whether simulation results fulfill basic physical validity, including checks of the sampled ensemble, the equipartition principle, conservation / drift of constants, correlation times (to be extended).

Author guidelines

A few suggestions to simplify collaboration on a LaTeX document:

• Use issues and pull requests to keep track of to-dos, discuss issues and review and comment text.

• We are using the template of LiveCoMS. Have a look at their sample files [1, 2] for examples on how to use the different environments.

• If you need to put text-related comments or to-dos directly in the LaTeX files, please use

  \comm{Your initials}{Your comment here}
  

  and

  \todo{Your todo here}
  

  These commands will be compiled into the document and highlighted in color. They are easy to find and filter out for release versions.

• Make ample use of additional files included into main.tex via

  \include{file.tex}
  

  Please use at least one file per section (or even subsection, if sections get very large). This should help keeping the main file tidy and will make merging significantly easier.

• Use the siunitx package included in the LiveCoMS template to typeset units.

License

The content of this repository is licensed under a Creative Commons Attribution 4.0 International License.