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Created with Raphaël 2.2.029Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614Merge remote-tracking branch 'origin/master' into new_setupsPuReMD: fix BGF parser to correctly remap atom coordinates to internal simulation box boundaries. Fix reax_list to handle case when total interactions is zero instead of terminating program.new setup/reset function that takes advantage of new soft reset functionalitysPuReMD: rework Fortran F90 interfaces for Amber specifics and declare this interface for such usage.sPuReMD: fix Coulomb energy calculations for QM/MM mode. Indicate QEq model not supported with QM/MM mode. Add Fortran interface for QM/MM mode.sPuReMD: add initial QM/MM support with work for integrating with Amber.sPuReMD: add extra QM/MM interfaces for getters and setters.sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.sPuReMD: reorganizaiton for multiple consecutive simulation codepath (cleanup only).Tools: update example Python driver.sPuReMD: fixes for multiple consecutive simulation codepath. Reorganization to this codepath (some data structure now carry a flag to designation their allocation state). Fix bug in force field parser (atom type not truncated correctly). Charge sparse_matrix structs to be non-pointers to jive with new allocation state flag. Other code clean-up.sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).PG-PuReMD: fix BGF parser for >1 process (correct atom counts within local simulation box boundaries).Fix template control file per BGF addition.PG-PuReMD: fixes to NVT with Berendsen thermostat. Use updated constants from sPuReMD. Add BGF geometry file parser. Other code clean-up.sPuReMD: fixes to Berendsen thermostat for NPT ensembles.sPuReMD: corrections to Berendsen thermostat with NVT (fix velocity scaling and thresholding).sPuReMD: fix memory leak with ICHOLT preconditioner (droptol for OpenMP only) for charge solver. Default to Jacobi preconditioner. Resolve several compiler warnings around C strings (snprintf, etc.). Other code clean-up.sPuReMD: add functionality to run multiple MD simulations (for usage via integration with external codebases).PG-PuReMD: in-progress implementation of CUDA-aware MPI for charge solver communications using OpenMPI (default off).sPuReMD: add checks for GNU scientific library (GSL) for use during energy minimization.sPuReMD: resolve OpenMP build errors with GCC v10 (behavior changes for function arguments). Suppress possibly unitialized variable warnings for BiCGStab.(incomplete) partially working CG with line search, increase mem. allocation to not get mem. errorPG-PuReMD: fix van der Waals and Coulomb force computations for 1 warp per atom implementation, and enable this implementation by default.PG-PuReMD: use registers for local arithmetic in CUDA nonbonded calculations and fix shared memory usage in 1 warp per atom implementation.PG-PuReMD: switch timers to use CUDA events and add additional timers for kernels to match MPI code. Other code cleanup.initial attempt to energy minimization and restraints (incomplete)PG-PuReMD: fix bitmask used for CSR matrix alignment.Revert "PG-PuReMD: remove unused members for structs involved in MPI comms for atom exchanges."PG-PuReMD: remove unused members for structs involved in MPI comms for atom exchanges.PG-PuReMD: align CSR sparse matrix data structure to 128-bit/256-bit segments for memory coalescing (for 1 warp per row SpMV implementation). Change default interaction list and sparse matrix allocations to be multiples of 32 for aforementioned memory coalescing.PG-PuReMD: switch from using strtok_r to strtok to avoid reliance on GNU extensions with building for the C11/C++11 standard.sPuReMD, PG-PuReMD: revert valence angle patch.PG-PuReMD: backport missing valence angle correction from sPuReMD.PG-PuReMD: only copy host generated grid to device on reneighboring steps (after rebinning atoms and regenerating the grid). Fix small NVE integration bug (reallocation checks before copying new atom info to device).PG-PuReMD: small clean-ups to QEq dual solver code.PG-PuReMD: change CUDA kernel error checking to only make calls to cudaDeviceSynchronize when in debugging mode (non-debug builds thus have better performance with kernel asynchronous launch behavior in single default stream). Change file I/O to only flush when in debugging mode (non-debug builds allow the I/O operations to be grouped for better performance).PG-PuReMD: add dual QEq BiCGStab solver.PG-PuReMD: add support for symmetric, half stored format (SYM_HALF_MATRIX) of the sparse matrix for the charge model (add initialization routines and fix-up solver).PG-PuReMD: rework custom reduction functions to use less shared memory and to have the correct thread and block counts. Fix bug in charge matrix initialization (under-allocated space previously). Split charge matrix and bonds/hydrogen bonds memory management routines to mirror the similar splitting of the initialization routines. Code clean-up related to half vs. full list and sparse matrix formats.