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Created with Raphaël 2.2.013Dec12107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PuReMD-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 TerritoryTools: update testing short job script.Tools: add functionality to run different code version (serial, OpenMP, MPI, MPI+GPU). Update sPuReMD control file parser to ignore non-shared memory parameters.PuReMD: refactor to allow selection of far range interaction Verlet list format at runtime (half or full). Similar change for symmetric charge matrix format (half or full). For SAI, toggle between half and full depending on whether it is a refactoring step.