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Created with Raphaël 2.2.022Oct211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614Tools: 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.Tools: add Python file for running PuReMD code.PuReMD: small change on control.cPuReMD: monkey-patch new control file format for interfacing with tools/run_sim.py.PuReMD: cleand code and add timing performanceMerge branch 'master' of gitlab.msu.edu:SParTA/PuReMD.sPuReMD: fix ILUTP bug with order of permutation matrix application. Refactor dense vector permutation code (GC, ILUTP).Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.Tools: begin updating testing scripts.PuReMD: minor changesPuReMD: add sai_thres variablesPuReMD: fix control variable scoping in linear solvers.sPuReMD: fix permutation application when applying ILUTP preconditioner.PuReMD: add SAI preconditioner applicationPuReMD: fix build system to include autogenerated header config.h.PuReMD: add SAI setup and computation (LAPACKE is not linked)PuReMD: from half to full far neighbor list, etor and econj slightly differsPuReMD: small fix to print utils.sPuReMD: more ILUTP fixes.sPuReMD: more changes for ILUTP.sPuReMD: add ILUT and work-in-progress ILUTP.SAI corrected, allocated variable added to sparse_matrix structsPuReMD: remove defunct SuperLU code. Add boilerplate code for ILUT. Other cleanup work.sPuReMD: resolve issues with SMALL_BOX_SUPPORT.