GitLab

Adding alternative names of terminal nucleic acids (5' and 3' as DG5 and DG3). Adding alternative names of atoms H2', H2'', H5' and H5'' for nucleic acids.

* Created API for HIPPO force field

* Beginning of reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Continuing reference implementation of HIPPO

* Completed reference of HIPPO with no cutoff

* Beginning cutoffs/PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Continuing PME for reference implementation of HIPPO

* Completed reference implementation of HIPPO

* Cleanup and optimization to HIPPO reference

* Further cleanup to HIPPO

* Combined direct space interactions into a single loop

* Compute direct space interactions in quasi-internal frame

* Beginning of CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Continuing CUDA implementation of HIPPO

* Finished CUDA implementation of HIPPO

* More features and test cases for HippoNonbondedForce

* Serialization and Python API for HippoNonbondedForce

* Fixed sign error in computing forces

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

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

This reverts commit 5ef91d22.

* 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.

* Implementation of OPLS through DMS reader

* Improved Implementation of OPLS through DMS reader

* raise errors for invalid implicit solvent settings

* 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 -- fix Jenkinsfile syntax.

* Test CPU and Reference together.

* Avoid stashing -- not necessary really.

* Print env (Debug).

* try a new way to get env vars set up.

* More test shuffling.

* Load conda module.

* Fix docker build and test script.

* Fix up install.

* More tweaks to the build.

* Do python tests in Docker container

* Separate CUDA and OpenCL platforms and install make in the docker
container

* reorder arguments to ctest so the retesting only does the failed tests (and can't get overwritten by anything else)

* Add LD_LIBRARY_PATH to find OpenMM libs (it should be found :(...)

* Trying this...

* Seems that some stuff runs inside docker and some doesn't??

* Move all execution to a shell script for the dockerfile install

* Add fixes for Python 3.7

* Revert "Add fixes for Python 3.7"

This reverts commit ef826edbba52f6388fe2b4c483ed1afb337c7d8f.

* Python 3.7 turned StopIteration into RuntimeError, as per PEP 479.

A quick-fix for the PDBx library is to catch both StopIteration *and*
RuntimeError to preserve the old behavior.

* Make sure we clean first.

* More thorough cleaning

* Stop trying to do it in a container. >:o

* Consolidate, and go back to docker.

This is irritating.

* Add some debugging commands and temporarily stop testing GPU platforms.

* Oops :-[]

* whoami doesn't work in the docker container :(

* Stop trying to find libdl

* Need to install cython.

* whoami fails -- try id instead.

* Clean up install script now that I have the basics working

Also restrict CPU runs to nodes with the "docker" label.  This allows
exclusion from nodes where docker isn't creating a suitable environment
(most likely due to irritating permission issues).