GitLab

* 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 customized

* Optional displacements at the initial state

* Fixed compilation error build C wrapper

* Address edge case of default energy expression

* Consistent naming of the variables of the displacement states

* Test of soft core function of the default energy expression

* Mark addForce() as taking ownership

* initial python test for ATMForce

* Test custom expressions

* Expanded C++ API documentation for ATMForce

* Energy parameter derivatives

* Serialization for ATMForce

* Documentation, cleanup, and fixes

* Fixed typos

* getPerturbationEnergy() computes energy

* Another test case

* Minor edits

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Co-authored-by: Peter Eastman <peastman@stanford.edu>
Co-authored-by: Michael Plainer <plainer@ymail.com>

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default

Restructured how force and energy computations are done to make it easier to write plugins for the CUDA platform

Optimization: introduced a kernel to clear forces at the start of each time step rather than relying on the stream

1) Added DLL export macros to many classes; enough to get tests to compile
2) Cosmetic changes to reduce warnings in Visual Studio:
   a) change many "for (int i ="... to "for (size_t i ="... to avoid unsigned mismatch warnings
   b) included many explicit static_cast<OpenMMReal>() casts to document places where double->float conversion warnings occur