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Created with Raphaël 2.2.04May29Apr28262019161514930Mar26181615543126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun2827212018171614129WIP: finish the explicit single stream port by using cudaMemcpyAsync and cudaStreamSynchronize calls.WIP: changes to support multiple CUDA streams. This commit contains porting of all kernels from the default stream to a single non-default stream. This commit has bugs regarding cudaMemcpy's still being in the default stream (and synchronous).Tools: add support for jobs using LSF (on OLCF at ONL).sPuReMD: add MKL support for ELM methodtensorflow_upda…tensorflow_update_v2PG-PuReMD: refactor CUDA memory management routines.PG-PuReMD: update CUDA library checks. Assume lib64 for new CUDA library locations.PG-PuReMD: use a warp of threads for hydrogen bonds.PG-PuReMD: use a warp of threads for lone pair/over/under interactions.PG-PuReMD: implement MPI+CUDA versions of SDM, PIPECG, PIPECR for charge solver methods (along with missing dual QEq versions).PG-PuReMD: use a warp of threads for addtional bonded interaction computations (bond orders, bonds, lone pair/over/under).add a new model (ELM), accelerate predictionPG-PuReMD: use a warp of threads for apply bond derivatives to forces and simplify these code paths.improve init. and allocation logic for restraintsrestraint_supportrestraint_supportadd restraint energy to the total energyreset restraint energiesadd deallocation for restraintsAdd bond and angle restraint supportUpdate restraint related functionsenergy_minimenergy_minimPG-PuReMD: use a warp of threads for torsion computations.PG-PuReMD: fix incorrect summations in kinetic energy and temperature calculation functions. Replace several hand-coded device-wide reduction kernels with CUB libary reduction.PG-PuReMD: use a warp of threads for valence angle computations.PG-PuReMD: use a warp of threads to initialize the bonds and hydrogen bonds lists.PG-PuReMD: split bond and hbond initialization kernels for future optimizations. Cleanup CUDA code related to far neighbor list being in full format (remove unnecessary conditionals and arithmetic).PG-PuReMD: use a warp of threads to initialize each row of the charge matrix.change the callback function related linesallocate larger memory for s and t arrays to store data for finetuning the modellog TF timing dataadd TF related new parameters(for timing and control), update the callback function to better callect solver dataadd TF related control variablescreate a new file for all TF related functionssPuReMD: correctly set the number of OpenMP threads.sPuReMD: fix OpenMP compilation issues with LAPACKE routines (see note in commit 8c276ea4).sPuReMD: enable setting the number of OpenMP threads via control file keyword or OpenMP environment variable (OMP_NUM_THREADS).sPuReMD: fix atom element name setting in QMMM code path (reset_qmmm).sPuReMD: make zlib dependency optional (trajectory file compression). PG-PuReMD: remove erroneous zlib header file inclusion.Fix typo in README.Fix typo in README. Fix issue with CI run script (wrong output file names).sPuReMD: fix OpenMP compilation issue with specifications prior to 4.0 (behavior change regarding implicit shared attribute assignment to const variables).sPuReMD: small formatting fixes.Merge branch 'master' into QMMM_force_update.