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Created with Raphaël 2.2.017Dec16151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PuReMD: fix qeq init timingPuReMD: fix the broken preconditioner setupPuReMD: change timing functions with MPI_Wtime()PuReMD-old: tools update in run_sim_mpi.py for larger silica and water systems.PuReMD: include charge matrix fill in timing for performance comparisonPuReMD-old: revert debugging code.PuReMD-old: note barrier removal for later.PuReMD: SAFE_ZONE change for NTsPuReMD: remove unused code.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.sPuReMD: re-enable SMALL_BOX_SUPPORT. Fix issue with far nbrs list being incorrectly generated for small boxes (missing nbr ID). Fix issue with ACKS2 matrix being incorrect for small boxes due to multiple non-zeros being added for each perioidic image of an atom (accumulate instead). Add missing ACKS2-specific energy and forces term. Clean-up far nbr list estimation and generation code for small boxes. Do not add far list struct entries unless the atom is below the specified cutoff.PuReMD-old: fix typo (malloc -> smalloc).PuReMD-old: more clean-up of linear algebra code. Remove or conditionally enable debugging code (DEBUG preprocessor). Fix memory leak in SAI setup. Better memory allocation checks.PuReMD: fix charge matrix reallocation bugPuReMD: fix a minor bug regarding Init_ForcesPuReMD-old: remove non-source junk files. Clean-up to remove debugging code for neutral territory. Conditionally toggle SpMV implementation (Sparse_MatVec) debugging on if neutral territory is selected.PuReMD: enable NT for half matrixPuReMD: fix the communication bug for NTPuReMD-old: more control file format changes.PuReMD: fix allocation problem regarding NT buffersPuReMD: continue NT for Jacobi debuggingTools: fix short jobs script typo. Set default HBond cutoff to 7.5 angstroms in run_sim.py.PuReMD-old: backport control file format changes.PuReMD: fix errors regarding matrix formatPuReMD: minor change: remove output statements for debuggingPuReMD: add preprocessors for Neutral TerritoryFix compilation errors (MAX_NT_NBRS -> REAX_MAX_NT_NBRS).Merge branch 'full-far-nbrs-list-charge-matrix' into full-far-nbrs-list-charge-matrix-half-full-refactor.Merge branch 'full-far-nbrs-list-charge-matrix-half-full-refactor' into full-far-nbrs-list-charge-matrix-half-full-refactor2.Fix issue with bonds list ordering leading to different torsion and conjugation energies due to changing the far neighbors list to a full list.Merge commit 'cc6d9994' into full-far-nbrs-list-charge-matrix-half-full-refactor.Merge with branch full-far-nbrs-list-charge-matrix at commit 1134d3bf.Merge with branch full-far-nbrs-list-charge-matrix at commit 65d820.Build systems updates for sPuReMD, PuReMD-GPU, and PG-PuReMD (use safer optimization level defaults).PuReMD: NT debugging continuesPuReMD: backport build system updates from branch full-far-nbrs-list-charge-matrix.PuReMD: move headers to SOURCES Automake variable. Fix duplication of flags. Other build clean-up.Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.PuReMD: fix compilation error. Use safer default optimization levels for compilation.PuReMD: first draft of Neutral Territory