GitLab

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* Added computeCurrentPressure() to MonteCarloBarostat

* Use instantaneous temperature to compute pressure

* Added computeCurrentPressure() to MonteCarloAnisotropicBarostat

* Added computeCurrentPressure() to MonteCarloMembraneBarostat

* Fixed compilation error

* Fixed error in typemap

* Added documentation on computing pressure

* Fixed CUDA compilation errors

* Made test case more robust

* Made a test case more robust

* Added computeCurrentPressure() to MonteCarloFlexibleBarostat

* Fixed compilation error

* More documentation on computing pressure

* Created MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

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

Using a const Vec3& instead of three doubles for the AnisotropicBarostat API.  Still figuring out SWIG issues.

Fixed same pressure unit conversion error in MonteCarloBarostatImpl.cpp that occurs in tests.  Tests now pass.

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

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

Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.

Changed how kernels get initialized.  StandardMMForceField now has you set the 1-4 interactions explicitly.  CMMotionRemover allows the removal frequency to be set.

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.