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Created with Raphaël 2.2.023Jan21181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PuReMD-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-matrixPuReMD: fix the allocation size of one of the arrays needed for SAI computationPuReMD-old: update tools/run_sim.py for fine-grained init timings.PuReMD: optimize atom enumeration for building dense matrix for SAIPuReMD: prevent possible enumeration problem for SAI dense matrixPuReMD: SAI computation optimizationsPuReMD: add conditional allocation to SAI computation arraysMerge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.PuReMD-old: change from array of structs to struct of arrays for far nbr list (far_neighbor_data).PuReMD: find SAi threshold among sampled entriesPuReMD-old: minor log file formatting tweaks. Default to full shell for now.PuReMD: split Init_Forces into 3 functions: Init_Distance, Init_CM and Init_Bond, and add timings for those functionssPuReMD: clean-up geometry file I/O code. Remove a few compiler warnings.PuReMD-old: fix timing issues. Remove fine-grained timing of Init_Forces due to high overhead. Disable SAI preconditioner optimization of changing far nbr list and matrix formats based on preconditioner refactoring step (not working). Tweak to not product numeric overflow when setting up SAI preconditioner (pivot sampling).sPuReMD: screen out non-periodic self-interactions when constructing far nbr list.sPuReMD: default to vlist_buffer of 2.5 angstroms. Fixes to cutoffs used in far neighbor list generation.PuReMD: fix qeq init timingPuReMD: fix the broken preconditioner setup