GitLab

I finally got nvidia-docker2 installed and actually working on my Gentoo
machine (I had to disable their restriction of using GPU devices to
users in the 'video' group, since the nvidia container runtime hook
didn't run as a user with those privileges, and I can't figure out what
user it was running as).

The other GPU-enabled node I added to the Jenkins array runs Ubuntu, and
that one already has nvidia-docker2 installed and running correctly on
it.

Avoid repeated matching of duplicate impropers

Has a much smaller effect compared to caching the improper search, but non-negligible and easy to do.

Fixed bug in vector operations in CustomIntegrator on CUDA

Sync with official repository

simple optimization to ForceField class

Ensuring opened files are properly closed

This reverts commit 5ef91d22.

Fixed inconsistency in computing Ewald self energy

Improved behavior of energy minimizer

Fixed error using tabulated functions with a CustomGBForce

Properly define GBSAOBC alpha beta gamma constants to be doubles.

Fixed bug involving nested cross products

Fixed an error in parsing PSF files with multiple segments

Fixed error using 2D tabulated function with CustomHbondForce

* Improve vec3

* Added a ``__neg__`` operator overload so that -Vec3(1, 2, 3) returns
  the same thing as Vec3(-1, -2, -3)
* Derived Vec3 from namedtuple instead of tuple. This allows you to
  access the 3 elements of the vector by name. i.e., vec.x, vec.y, vec.z

* Make sure we use floating point division all the time.

Eliminated use of a deprecated shuffle function

* Implementation of OPLS through DMS reader

* Improved Implementation of OPLS through DMS reader

* raise errors for invalid implicit solvent settings