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Created with Raphaël 2.2.09Nov8765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PuReMD: 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.Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.PuReMD-old: improve file I/O checks.PuReMD: add Neutral Territory functions (not finished)Tools: update run_sim.py to work with absolute paths (by refereing supplied executable path). Begin updating testing scripts.Tools: work around pathing issues with run_sim.py for running testing benchmarks.Tools: fix results parsing when restricting MD simulations to a specific range of steps.Tools: heavily refactor run_sim.py. Add job submission action.sPuReMD: revert change on evolving atoms (Verlet method) for NVE ensemble.sPuReMD: refactoring to align code with PuReMD. Disable SMALL_BOX_SUPPORT. Refactor to remove union-based polymorphic behavior for reax_list. Other general code clean-ups.PuReMD: fix issue with force tabulation when using full nbr list / charge matrix.Tools: fix MPI command. Change control file generation to be in running directory (for temporary directories and files) => necessary for running with MPI (shared filesystem needed across nodes).Tools: update for usage with Slurm.PuReMD: fix read option for python scriptMerge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrixTest: add MPI+GPU control files.Test: add serial control files. Update MPI control files.Testing: add script for submitting short jobs.PuReMD: fix a small bugPuReMD: fix a small bugTools: reformat proc_by_dim and fix an issue with subprocess command building.Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.