GitLab

Fixed incorrect indexing in kernel

Replace nonstandard atom and residue names when loading PSF files

Implemented switchDistance option for GromacsTopFile

Fixed inconsistency between plaforms in constraints with CustomIntegrator

Catch exception when an OpenCL platform has no devices

Fixed error on CPU platform when forces disagree about whether the system is periodic

Windows tests on Azure

Updated simulation parameters in documentation and examples

Improved behavior of rigidWater option

Updates to documentation

Fixed error in BAOAB on CUDA and OpenCL

testInstallation: raise exception if large differences are observed

Update cl.hpp

Raise exception if large differences are observed so simtk.testInstallation can be used in CI testing reliably

Taken from:
https://github.com/KhronosGroup/OpenCL-CLHPP/commit/c5063c34675155fffc20185e74ba82a9dfd5dc84

Fixed incorrect formatting

Fixed errors in benchmark script

* Began creating common compute framework to unify code between CUDA and OpenCL

* Began OpenCL implementation of common compute framework

* Common implementation of CMMotionRemover

* CUDA implementation of common compute interface

* Converted HarmonicBondForce to common compute API

* Converted standard bonded forces to common compute API

* Converted ExpressionUtilities to common compute API

* Created ComputeParameterSet

* Converted custom bonded forces to common compute API

* Converted CustomCentroidBondForce to common compute API

* Converted CustomManyParticleForce to common compute API

* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext

* Converted GayBerneForce to common compute API

* Removed obsolete kernels

* Converted verlet integrators to common compute API

* Converted Langevin and Brownian integrators to common compute API

* Converted CustomIntegrator to common compute API

* Converted CustomNonbondedForce to common compute API

* Removed uses of a deprecated API

* Fixed failing test cases

* Converted GBSAOBCForce to common compute API

* Began converting CustomGBForce to common compute API

* Finished converting CustomGBForce to common compute API

* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities

* Converted RMSDForce and AndersenThermostat to common compute API

* Converted CustomHbondForce to common compute API

* Merged scripts for encoding kernel sources

* Converted Drude plugin to common compute API

* Fixed errors in CMake scripts

* Attempt at fixing errors on Windows

* Added discussion of common compute API to developer guide

* Added Windows export macro for common classes

* Fixed error in CMMotionRemover

* Ubdated travis to newer Ubuntu version

* Fixed errors on CPU OpenCL

* Fixed Windows linking errors

* Added missing pragma for 32 bit atomics

* Replaced long long with mm_long

* More fixes to Windows linking

* Bug fix

remove deprecated modules from project

Add support to ForceField for handling SMIRNOFF trefoil impropers