GitLab

* ATMForce reorders inner contexts for better performance

* Fixed obsolete comments

* Improved performance of CustomHbondForce on large systems

* Fixed CUDA compilation errors

* Made LangevinIntegrator identical to LangevinMiddleIntegrator

* Removed unused code

* VariableLangevinIntegrator uses LFMiddle

* Common implementation of BondedUtilities

* Common implementation of UpdateStateDataKernel

WIP - looking for a way to optimise performance of creating contexts by removing temporary arrays (and their associated mallocs/frees) (#4261)

* Suggesting a "haveSameParameters" function for CustomNonbondedForce which could be
used to avoid creating temporary copies of arrays when testing if particles are
the same.

Also updating "getParticleParameters" so that it re-uses the memory of the
passed vector argument, rather than deallocating and reallocating it
via a copy.

* Revert "Suggesting a "haveSameParameters" function for CustomNonbondedForce which could be"

This reverts commit e80ec2d2e9981abb90711636bf3a78d0c49e43fc.

* Moved to `thread_local static` as suggested to prevent new vector allocations on each function call.

Updated `getParameters` and `getBondParameters` to re-use the memory from the argument rather
than re-allocating via the copy.

* Forgot to reuse the memory for the groups...

* Reverted back the manual copies via memcpy as they aren't needed. Looking at the header
file and benchmarking shows that std::vector does the right thing.

* Confined `thread_local static` only to ForceInfo methods, and have also put declarations
for multiple variables back onto a single line

* Removed `thread_local static` from the constructor

* Moved constructor declarations back into the for loop

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation

* Amoeba minor cleanup

- Fix variable name in string
- Remove odd space between variable and period that is inconsistently styled

* Replaces random tabs with spaces in ATM Force

* Draft integration of the Alchemical Transfer Method (ATM) plugin

* Attempt to store and retrieve forces--does not compile

* Implement addForce()/getForce() methods

* Throw exception when specifying properties without a Platform (#4130)

* Fixed DOF calculation for NoseHooverIntegrator (#4128)

* Fix variance in documentation of VerletIntegrator (#4138)

* Python API for ATMForce

* Fixed compilation error

* Minor cleanup of formatting and documentation

* Files for ATMForce test cases

* More cleanup

* Removed variable groups

* Test ATMForce with two particles

* More tests for ATMForce plus fixes

* Added missing header

* Rework interface to pass displacements as vector of parameters

* Revert "Rework interface to pass displacements as vector of parameters"

This reverts commit 5e092031f31ded1137b677588f007add1c2d6f82.

* Test with nonbonded force

* Allow energy expression to be custom...

* save atomIndex order in MCBarostat kernel

* Update device indices

* Only setAtomIndex if there was a reorder

* Attempt at fixing errors with barostat

* Missing ContextSelector

* Skip neighbor list for very small systems

* Fixed typos

* Don't skip box size check when not using neighbor list

* Made test larger to ensure it uses neighbor list

* Faster implementation of CustomHbondForce

* Minor optimization

* Optimized writing forces, which are often zero

* Fix test failure on CPU OpenCL

* Bug fix

It allows to use a faster float-to-int64 in the HIP platform.

* Reference implementation of computed values for CustomNonbondedForce

* CPU implementation of computed values for CustomNonbondedForce

* Common implementation of computed values for CustomNonbondedForce

* Serialization of computed values

* ForceField supports computed values

* Fixed potential invalid memory access

* Fixed exception

* updateParametersInContext() can change tabulated functions

* Fixed error in building C wrappers

* updateParametersInContext() can change tabulated functions for CustomCentroidBondForce

* CustomNonbondedForce can update tabulated functions

* CustomGBForce can update tabulated functions

* CustomManyParticleForce can update tabulated functions

* CustomHbondForce can update tabulated functions

* Created MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

* Further optimization to updating long range correction

* Bug fix

* Use cuCtxPushCurrent() and cuCtxPopCurrent() for selecting CUDA context

* Fixed errors in amoeba coda

* Fixed more errors in context selection