GitLab

* Initial implementation of PythonForce

* Continuing implementation of PythonForce

* Tests for PythonForce

* Fix memory leaks

* Documentation for PythonForce

* Fixed incorrect return type

* Fix compilation error on Python older than 3.12

* Handle all dtypes

* Optimizations to PythonForce

* Optimized getPositions()

* Test all platforms

* Fix test failures

* Ensure that neighbor list is valid before solving for charges

* Add test with neighbor list that needs to be resized

* Try another approach to skip interactions for neighbor list generation only

* Increase CG error tolerance for test

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* Initial implementation of C++ API

* Add kernel interface and information for API generation

* API updates for updating electrode parameters

* Add serialization proxy for ConstantPotentialForce

* Update file headers

* Add CG error tolerance and fix units on getCharges() return value

* Initial implementation of matrix solver

* Fixes and conjugate gradient solver

* Try to fix Linux and Windows builds

* Make sure charge constraint target is on total charge

* Restore handling of exceptions like NonbondedForce since they won't involve electrode atoms

* Ameliorate numerical instability in constrained conjugate gradient

* Fix uninitialized pointers, memory leak, and style

* Set CG tolerance units in Python API

* Test ConstantPotentialForce serialization

* Read/write ExceptionsUsePeriodicBoundaryConditions as bool

* Improve constrained conjugate gradient robustness to roundoff error accumulation

* Recompute matrix if electrode atoms move due to setPositions()

* Tolerance is now in gradient (potential) units again

* Add neutralizing background correction

* Add Python API tests

* Fixes for CG and nonbonded exceptions

* Add initial tests checking against existing NonbondedForce behavior

* Expand test suite and fix some implementation issues

* Add additional tests using larger reference system

* Add Gaussian test

* Finish test against reference computation

* CPU platform implementation

* Fixes for compilation on some platforms

* Fixes for constant potential with AVX/AVX2

* Test linking CPU PME library to constant potential test directly

* Older SWIG versions don't support Python set to C++ set conversion

* Add user guide entry

* Increase speed of reference test

* Conditional building constant potential CPU test is unreliable

* Debugging

* Miscellaneous fixes and improvements for CI

* Cache charges so solver will not run if system and coordinates have not changed

* Preconditioner flag, stability, and automatic detection improvements

* Add GPU platform-specific constant potential kernel classes

* PME and device-host I/O changes to support constant potential

* Initial common constant potential implementation

* Constant potential fixes:

* Fix preconditioner PME position/charge save/restore logic

* Fix reduction synchronization in constant potential solver kernels

* Add double-float accumulation for conjugate gradient solver when
  double unsupported by hardware

* Improve conditioning of a test system, and make sure particles are in or
out of cutoff for consistency and ease of comparing between platforms

* Reorder guess charges for CG when atom reordering changes positions

* Remove PME queue for now

* Trying to debug optimized direct space derivative kernel

* Remove extraneous debugging lines

* Style updates; just make CPU preconditioner double precision

* Debugging updated optimized direct derivatives kernel for all but OpenCL CPU

* OpenCL CPU implementation of direct space derivatives, and cleanup

* Try to make test even shorter to not time out on CI

* Temporary - Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Remove debugging code and fix reduction synchronization

* Fix other reductions

* Debugging - are tests hanging or just slow on CI?

* Debugging

* Debugging

* Fix macro for case when double precision is available on hardware

* Remove changes for debugging again

* Try to improve matrix solver cache locality by uploading transpose

* Fixes for atom ordering and periodic images

* Can't rely on reorder listener for cell offset updates

* Test reducing number of contexts and timing for CI

* Debugging

* Remove timing code and revert debugging changes

* Matrix solver and plasma term optimizations

* Reduce CG solver kernel calls and downloads

* Don't read back convergence flag from global memory

* Update PME due to refactoring in master branch

* Faster matrix solver (1st step)

* Faster matrix solver for CUDA

* Faster matrix solver compatibility with non-CUDA platforms

* Matrix solver fixes

* Use warp shuffle reductions when possible

* Attempt to work around intermittent compiler crash in Intel CPU OpenCL

* Optimize CG solver kernel 1

* Rework CG solver so some kernels can use more than 1 block

* Don't run out of shared memory

* Asynchronously download convergence flag while clearing buffers

---------
Co-authored-by: Evan Pretti <pretti@sh03-17n15.int>

* Created OrientationRestraintForce

* Python API

* Documentation

* Serialization

* GPU implementation of OrientationRestraintForce

* Bug fix

* Remove unused code

* Reference implementation of RGForce

* GPU implementation of RGForce

* Serialization

* Documentation

* Fix compilation error

* Fixed error building API docs

* Began implementing QTBIntegrator

* Adaptation and deconvolution

* Continuing reference implementation

* Continuing to implement QTBIntegrator

* Use common thread pool

* More tests, documentation, and threading

* Fix segfault

* Serialize adapted friction when creating a State

* Beginning of GPU implementation

* Added missing files

* Bug fixes

* Fixed inverse FFT

* Continuing GPU implementation

* Checkpointing

* Bug fixes

* Test cases run faster

* Changes needed for latest main branch

* Minor optimizations

* Documentation

* Fixed atom reordering

* Added parahydrogen test case

* Workaround for bug in Microsoft's compiler

* Added a Python test

* Normalize kernel in deconvolution

* Minor documentation improvements

* Unified storage of global parameters

* Fixes to CUDA and HIP

* Store global parameters as real instead of float

* Use common API for kernels

* More code uses common interface

* Bug fixes

* Unified interface for sorting

* Simplified interface for FFT

* Use common event API for synchronization

* Minor changes to make code more consistent between platforms

* Common implementation of NonbondedForce

* Bug fixes

* Flag to enable list of single pairs

* CUDA and OpenCL use common implementation of NonbondedForce

* Fixed compilation error

* HIP uses common implementation of NonbondedForce

* Added computeCurrentPressure() to MonteCarloBarostat

* Use instantaneous temperature to compute pressure

* Added computeCurrentPressure() to MonteCarloAnisotropicBarostat

* Added computeCurrentPressure() to MonteCarloMembraneBarostat

* Fixed compilation error

* Fixed error in typemap

* Added documentation on computing pressure

* Fixed CUDA compilation errors

* Made test case more robust

* Made a test case more robust

* Added computeCurrentPressure() to MonteCarloFlexibleBarostat

* Fixed compilation error

* More documentation on computing pressure

* Created DPDIntegrator class

* Reference implementation of DPDIntegrator

* Build neighbor list for DPDIntegrator

* Minor fixes

* Documentation for DPDIntegrator

* Python API for DPDIntegrator

* Preliminary OpenCL implementation of DPDIntegrator

* Enable USE_PERIODIC

* Use updated positions in DPD thermostat

* Working on neighbor list for OpenCL DPDIntegrator

* ReorderListener for particle types

* Serialization for DPDIntegrator

* CUDA implementation of DPDIntegrator

* HIP implementation of DPDIntegrator

* Fixed compile error in Python wrapper

* Fixed compile error in wrappers

* Fixed uninitialized memory in reference neighbor list

* Added DPDIntegrator to C++ API docs

* Fixed incorrect launch size

* Fixed nan in DPD random number generator

* Minor optimizations

* Improved load balancing

* Fixed an indexing error

* Neighbor list uses the maximum cutoff of any force

* Fixed HIP compilation error

* Fixed access to invalid memory

* Added test case for diffusion coefficient

* Try to debug segfaults on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Possible fix

* Debugging

* Debugging

* Debugging

* Use correct block size on CPU OpenCL

* Workaround for bug in Intel's OpenCL for CPUs

* Removed an unnecessary define

* Removed debugging code

* Include Dart

* More Intel workarounds

* Workaround for error in NVIDIA OpenCL

* Use Intel OpenCL for CI

* Set environment variables

* Try to get CI to run

* Debugging

* Debugging

* Fixes for Intel OpenCL

* Unified lots of parallel computation code between platforms

* Unified test code between platforms

* Eliminated duplicated timing code

* Optimize CustomNonbondedForce.updateParametersInContext()

* Optimized uploading changed values to GPU

* Optimized updateParametersInContext() for lots of bonded forces

* Optimized updateParametersInContext() for CustomExternalForce

* Optimized updateParametersInContext() for NonbondedForce

* Code changes for HIP platform

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation

* 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 customized

* Optional displacements at the initial state

* Fixed compilation error build C wrapper

* Address edge case of default energy expression

* Consistent naming of the variables of the displacement states

* Test of soft core function of the default energy expression

* Mark addForce() as taking ownership

* initial python test for ATMForce

* Test custom expressions

* Expanded C++ API documentation for ATMForce

* Energy parameter derivatives

* Serialization for ATMForce

* Documentation, cleanup, and fixes

* Fixed typos

* getPerturbationEnergy() computes energy

* Another test case

* Minor edits

---------
Co-authored-by: Peter Eastman <peastman@stanford.edu>
Co-authored-by: Michael Plainer <plainer@ymail.com>

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

* Optimized CudaSort for non-uniformly distributed data

* Optimized OpenCLSort for non-uniformly distributed data

* Further tuned distributing elements between buckets

* Copied optimizations over to OpenCL

* 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

4*(1<<30) evaluates to 0 so the check returns true on 2GB cards. Test runs fine on 2GB cards but requires over 4GB of system memory.

* Fixed range overflow with very large numbers of atoms

* More fixes to overflow with large numbers of atoms

* Fix test failures

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default