choderalab/openmmtools — pull request #18 by jchodera (2014-11-28 07:57:13+00:00)
Title: [WIP] Prepending scope identifiers for global parameters to limit namespace collisions

Since [OpenMM #717](https://github.com/pandegroup/openmm/issues/717) is under debate, this PR attempts to prepend scope-limiting identifiers to global context parameters to limit the potential for namespace collisions in test systems and integrators.

So far, I have just fixed up the test systems. I am still working on the integrators.

This solution is to be considered temporary at best. I have used the convention `testsystems_TestSystemName_parametername` for global context parameters previously named `parametername`. I have tried to avoid adding complexity to the energy expressions by introducing intermediate temporary variables in energy expression that should be compiled out by Lepton. I have also eliminated some context parameters that didn't need to be exposed as context parameters. Some others may still be eliminated.

Still a work in progress.