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https://github.com/openmm/openmm
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* 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>