GitLab

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation

* Draft integration of the Alchemical Transfer Method (ATM) plugin

* Attempt to store and retrieve forces--does not compile

* Implement addForce()/getForce() methods

* Throw exception when specifying properties without a Platform (#4130)

* Fixed DOF calculation for NoseHooverIntegrator (#4128)

* Fix variance in documentation of VerletIntegrator (#4138)

* Python API for ATMForce

* Fixed compilation error

* Minor cleanup of formatting and documentation

* Files for ATMForce test cases

* More cleanup

* Removed variable groups

* Test ATMForce with two particles

* More tests for ATMForce plus fixes

* Added missing header

* Rework interface to pass displacements as vector of parameters

* Revert "Rework interface to pass displacements as vector of parameters"

This reverts commit 5e092031f31ded1137b677588f007add1c2d6f82.

* Test with nonbonded force

* Allow energy expression to be custom...

Platform specific header files get installed.  This allows plugins to be built with just an OpenMM installation, not a full source tree.

Moved SFMT into libraries folder, and restructured it to allow multiple independent random number generators

All platforms now handle nonbonded exceptions in a consistent way (they ignore cutoffs and periodic boundary conditions).  Also started OpenCL implementation of CustomHbondForce.

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

Implemented the Ewald summation method in the reference platform. Preliminary cuda prototype is included.