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Created with Raphaël 2.2.020Feb191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614Merge branch full-far-nbrs-list-charge-matrix.Enable full shell communications by default. Remove extraneous editor file.PuReMD-old: implementation of dual-PIPECGsPuReMD: fix issue with incorrect cutoff being applied for periodic neighbors in small simulation boxes (nonb_cut -> vlist_cut). Other clean-up and debug I/O updates.PuReMD-old: change dual_Sparse_MatVec function to enable NT techniquePuReMD-old: change dual_CG with respect to SAI preconditioner and Neutral TerritoryAdd CI script.Build toos: refactor to remove recurisve Makefiles. Fix issue with OpenMP flags being overridden when user supplied value for CFLAGS variable.PuReMD-old: fix average solver iteration calculation to be correct when energy_update_freq > 1.PuReMD-old: add missing header in summary file for tools/run_sim.py.PuReMD-old: fix issue where nonbonded time was incorrect when energy_update_freq > 1. Update tools/run_sim.py to include both total simulation time and mean time per step.PuReMD-old: fix scaling issue with log file parsing.PuReMD-old: update tools/run_sim.py to get correct value for total simulation time.PuReMD-old: update tools/run_sim.py to get correct value for total simulation time.PuReMD-old: update tools/run_sim.py for non-unit logging freqeuncy.PuReMD-old: increase precision in log file to 4 decimal places for select fields. Merge MPI log parsing logic.PuReMD-old: fix communications to only use full shell pattern for non-charge methods (bug only present using neutral territory communication method). TODO: revisit code structure at a later date.PuReMD-old: fix convergence checks for PIPECG and PIPECR. Update CG to used preconditioned residual in it's check.PuReMD-old: add parameters for restarts.PuReMD-old: update neutral territory functions to make other communication function changes.Tools: fix typo in parameter name in run_sim.py (energy_update_freq).PuReMD-old: protect against buffer overflows for traj_title. NOTE: strcpy IS NOT SAFE, DO NOT USE EVER. USE strncpy INSTEAD.PuReMD-old: back-port run_sim.py from master branch. Update control file parsing to ignore sPuReMD/PG-PuReMD options.Change sample control file name.sPuReMD: add ACKS2 geometry-dependent forces to tabulated computation of van der Waals and Coulomb terms. Replace double precision equality check with difference comparison.sPuReMD: add missing header files when distributing (make dist). Fix OpenMP bug with ACKS2 geometry-dependent force contribution. Fix small OpenMP compilation issue. Update tools/run_sim.py to respect geo_format parameter and infer if not present for md_run_custom.PuReMD-old: optimizations in Init_Bond_Full for fusing hbond and bond list computation and removing unnecessary sorting and sym_index updating.PuReMD-old: fix cutoffs in bond initialization optimizations.PuReMD: fix bond_listsPuReMD: update tools/run_sim.py for running user-specified (custom) MD simulations.PuReMD-old: clean-up and comment initialization optimizations. WIP: remove redundant computation of bonds list (not working for full far nbrs list). Improve hbond list computation for full far nbr list case.PuReMD: pruning bonded interactions list through hop numbersPuReMD: minor correction to ACKS2-specific force contribution (no cut-off check).PuReMD-old: complete PIPECG and PIPECR implementations. Fix dense linear algebra code to loop beginning with lowest address in memory (vector.c -> level 1 BLAS-like operations).Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.PuReMD-old: add preconditioned pipelined CG (PIPECG) (WIP).PuReMD: fix the calculation of bond_mark and move it to Init_Distance funcPuReMD-old: fix issue with using wrong cutoffs in (h)bond list initialization.PuReMD-old: initialization optimizations for (h)bonds lists and charge matrix.Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix