GitLab

Implemented private _addIons method that improves placement of ions in solvated box, specially for membrane systems

Fixed bug in vector operations in CustomIntegrator on CUDA

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

Improved logic for matching multi-residue patches

Completed CPU implementation of LJPME

Improvements to testInstallation script

* Add a Jenkinsfile to drive a pipeline

* Also tweaks the installation script for Jenkins to be more amenable to
running other variants in parallel
* Restrict packaging script to only accept Python 2.7, since I think
that's long been the minimum supported Python version
* Allow run-ctest.py to run tests in parallel (and take advantage of
that in the Jenkins tests).

* CUDA -> CUDA_VERSION

* Jenkins will automatically post result back to GitHub.

Not need to have a separate step do that explicitly.

* Run as a login shell.

* Force looking for CUDA node.

* Make sure we load conda module.

* Start building in a docker slave -- much nicer!

* Try to fix up the installation a little.

* Fix more build issues.

* More build debugging.

* Oops -- recursive :-o

* Put opencl lib in library path

* Try 9.2

* Fix library path

* More updates to Jenkins build recipes.

* Try a new (simpler?) approach with building

* Oops...