Add fix style pimd/langevin

[Yi-FanLi]

Summary

This PR adds a new fix style pimd/langevin.
It renamed the fix style proposed in #3625

It is intended to add the following features:

stochastic thermostat
isotropic / anisotropic barostat (and triclinic in the future)
multi-processing for each bead
well-optimized inter-replica communication and synchronization scheme to guarantee speed
a set of post-processing code to calculate the quantum estimators

Author(s)

Yifan Li
Graduate Student
Department of Chemistry, Princeton University
yifanl0716@gmail.com

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Backward Compatibility

N/A

Implementation Notes

Post Submission Checklist

• The feature or features in this pull request is complete
• Licensing information is complete
• Corresponding author information is complete
• The source code follows the LAMMPS formatting guidelines
• Suitable new documentation files and/or updates to the existing docs are included
• The added/updated documentation is integrated and tested with the documentation build system
• The feature has been verified to work with the conventional build system
• The feature has been verified to work with the CMake based build system
• One or more example input decks are included

Further Information, Files, and Links

TODO list for making the pull request ready for review

• remove all dead code, unused keywords, unused class members, commented out code
• update the documentation:
• all supported keywords and features are documented
• there is no documentation for not yet implemented features
• add section that discusses the differences between fix pimd/nvt and fix pimd/langevin
• add a few small examples demonstrating the use of the command and some options
• remove all memory leaks:
• deallocate all allocated arrays in destructor
• delete all created classes in destructor
• delete all added communicators in destructor
• delete allocated storage before (re)allocating (requires initialization of pointers in with nullptr in constructor)
• there must be no uninitialized memory accesses (check with valgrind, same for memory leaks)

[Yi-FanLi]

Hi @akohlmey and @athomps , I have renamed the fix style pimd to pimd/langevin based on your suggestions.

[sjplimp]

I approved this - thanks for submitting and separating it into two commands. But I defer to @akohlmey on the implementation details.

[Yi-FanLi]

@akohlmey Hi Axel, could you please take a look at your convenience? Thanks a lot!

[akohlmey]

There are only some minor, cosmetic changes. Changing kBT is optional. Otherwise, this looks ready to merge.