GitLab

* Variable displacements based on particle positions

* set variable displacements when adding particles

* update documentation

* address compilation error in OpenMMFortranWrapper

* update python API tests

* fix stray 'and'

* addParticle() without arguments add a particle that is not displaced

* pack displacement particles into int4

* put back default displacement removed in error

* ATMForce interface with coordinate transformation objects

* revise variable displacement API

* documentation, formatting, serialization

* Fixed C and Fortran wrappers

* Fixed Python wrappers

* Fixed factory

* Sort files to ensure classes are listed in the correct order

* Converted APIUnits test to new ATMForce API

* write class name

* skip the documentation for forward declarations

* undo 9e91d0b since it does not fix the doc build

* remove temporary doc files for nested classes

* Clean away tabs

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Co-authored-by: Peter Eastman <peastman@stanford.edu>

* 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>

Continuing to implement ReferencePlatform (implemented kinetic energy calculation and LangevinIntegrator)

Created a test case for StandardMMForceFieldImpl's findExclusions() method.  Fixed some bugs that it found.  Created a CMake script and configured it for building and running test cases.