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Created with Raphaël 2.2.026Mar181615543126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17change 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.set q_init in reset_qmmmAll: remove errant use of 38th ReaxFF global parameter.Update README.QMMM interface related: ignore QM-MM bonds while forming bond lists, update charge matrix so that the total charge constraint only applies to QM atomssPuReMD: rework QMMM interface to use string representations of atom element types.sPuReMD: fix geo_tools parsers not recognizing element types with 2 character names.sPuReMD: fix type mismatch for SAI preconditioner computation.Test: Remove unnecessary target keyword for QMMM test.Test: add README for QMMM.Test: updates to QMMM to match Fortran interface used with Amber.PG-PuReMD: handle a few missed reductions in nonbonded interactions more efficiently. Clean-up bonded interactions functions and do not export kernels via header files. Increase C++ standard to c++14 for CUB (Thrust dependency). Continue with bundled CUB version and transition to version included with CUDA SDK in the future.PG-PuReMD: fix warp-per-atom kernel for atomic distance calculations. Resolve compiler warnings.PG-PuReMD: fix warp-per-atom kernel for atomic distance calculations. Resolve compiler warnings.PG-PuReMD: fix atomic force reductions and reduce the number of atomic operations.PG-PuReMD: use atomics for both partial energy and force accumulation (small reworks to reduce number of atomic operations). Remove several unneccesary cudaMemset calls. Other code clean-up.Revert accidentially committed files from previous commit (WIP).Test: fix Python wrapper for QM/MM (interfaces out-of-date). Fix Fortran tester bugs. Add test artifacts.Tests: add missing Makefile to Amber QM/MM.Tests: refactor QMMM Fortran tester for Amber integration.sPuReMD: standardize QM/MM interface. Add test codes for QM/MM interface for AVE dataset in Python and Fortran.sPuReMD: enable multiple simulations to be run with a single invocation of the stand-alone code.sPuReMD: merge changes from branch 'new_setup'. Rework interface for geometry initialization without file I/O. Other code clean-up.sPuReMD: fixes for non-file I/O setup / reset functions (qmmm, etc.).new_setupnew_setupPG-PuReMD: add atomic operations for partial force accumulation.