GitLab

Fix hardcode SYSROOT on mac.

Various bug fixes and code cleanup

Avoid writing malformed PDBs when the positions are too large.

Converted the array containing atom block indices for the neighbor list from ushort2 to int.  This removes the hard limit of 2 million atoms.

Bug fix to Modeller

Improved error checking

Implemented RPMD ring polymer contraction

Add support for long long shuffle

Improved infrastructure for integrators

Integrators control when atom reordering gets done, instead of having it happen automatically when forces are evaluated.  This simplifies some code, and also improves unintuitive behavior with CustomIntegrator.

Bug fixes to use of shuffle

Completed implementation of DrudeSCFIntegrator.  Also cleaned up other details of Drude plugin.

Nonbonded.cu now uses shuffle intrinsic