More Programmer Guide and Library Interface updates for next release

[akohlmey]

Summary

This contains various updates to the Programmer Guide, the library interfaces, the python module, CMake scripts, and the LAMMPS shell in preparation for the stable release.

Author(s)

Axel Kohlmeyer, Temple U

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

The -DLAMMPS_LIB_NO_MPI has been replaced with -DLAMMPS_LIB_MPI and the meaning is now reversed.

Implementation Notes

Individual changes are:

• the LAMMPS shell prints now OS/Compiler information when starting and has a new "mem" command.
• various minor reorganizations and corrections in the documentation of the C-library interface
• add and document missing C-library functions in the Python module
• consolidate two redundant sections documenting the building of the manual.
• various minor tweaks to the documentation
• improve formatting of the description of the reax/c control file
• Move tools and LAMMPS shell build target code to separate Tools.cmake file
• Add a few more useful outputs to the CMake configuration summary
• Print warning when reading positions from a data file with non-zero image flags to non-periodic dimensions

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
• Suitable tests have been added to the unittest tree.
• A package specific README file has been included or updated

[rbberger]

We should think about updating this to the venv module that is part of Python 3. That way we avoid having to install virtualenv.

[akohlmey]

won't be able to do this in this PR. too many ripples.

[rbberger]

Should this be here?

[akohlmey]

yes