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Created with Raphaël 2.2.04Aug130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614sPuReMD: fix issue with SMALL_BOX_SUPPORT incorrectly computing pairwise atomic distances for periodic self-images. Fix issue with integer vector sum function (used in bond order and torsion interactions).sPuReMD: remove global variable (array of function pointers for printing bonded interactions during debugging).sPuReMD: refactoring in geo_tools.cPuReMD: clean-up of heuristic for dynamically determining when to recompute the preconditioner for the charge solver.sPuReMD: improvements for building in debug mode (add assertion support for run-time checks). Fix issue with Verlet list recomputation logic being incorrect. Fixes to be string comparisons.sPuReMD: fix issue with certain preconditioners not being initialized for runs using restart files. Fix issue with part of simulation box struct not being initialized for runs using restart files (box->min). Other code clean-up from debugging issues with SMALL_BOX_SUPPORT.sPuReMD: add safety check for BGF input files (CRYSTX). Remove compiler warnings when enabling DEBUG_FOCUS.sPuReMD: fix issues with using sizeof with dynamically allocated pointers. Change OpenMP schedule policies for linear algebra code. PuReMD: correct discrepancy with charge matrix construction. Enable dual solver for charges by default.sPuReMD: refactoring to better align with PuReMD code. PuReMD: backport sPuReMD changes from validation efforts against Fortran ReaxFF code.sPuReMD: fixes to SAI preconditioner to correctly apply threshold to negative entries and to handle EE/ACKS2 cases when a threshold value of 1.0 is chosen.Tools: fix typo in job script creation.Tools: update tools/driver.py to be in sync with most recent version of sPuReMD.sPuReMD: fix FG_ICHOLT bugs.sPuReMD: fix bug with diagonal scaling during FG_ICHOL/FG_ILUT producing incorrect factorizations when diagonal entries were negative.sPuReMD: complete fine-grained Cholesky implementation. TODO: fix numeric breakdowns with water 6540 atom system.sPuReMD: remove unused code.sPuReMD: fix compiler warnings of uninitialized values.sPuReMD: backport list construction optimzations from PuReMD.sPuReMD: optimizations to fine-grain ILUT implementation.sPuReMD: workarounds for memory issues with ILUT factors. Implement ILU(0) and call when selecting ILUT with a droptol of 0.sPuReMD: corrections to ILUT preconditioner.Tools: small updates to run_sim.pyMerge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.sPuReMD: small correction to Jacobi preconditioner code.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMDPuReMD: added dynamic refactoringsPuReMD: small tweaks for Jacobi preconditioner code.sPuReMD: corrections to Coulomb forces to match reference Fortran ReaxFF code.sPuReMD: corrections to ACKS2 matrix to match reference Fortran ReaxFF code.sPuReMD: corrections to van der Waals calculations to match reference Fortran ReaxFF code.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.sPuReMD: fix issue with hbonds list indices not being reset correctly. Small algebraic rearrangements of valence angle calculations to match Fortran ReaxFF code (no numeric changes). Fix issue with rvec_isZero being incorrect. Fix issue with debugging arrays for TEST_FORCES not having indicies initialized. Other clean-up work.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMDsPuReMD: dynamic refactoring addedsPuReMD: revert force tabulation changes. Temporarily work around out-of-bound memory accesses in cubic spline interpolation routes (for force tabulation) by expanding array sizes. Revisit at a later date.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMDREADME: fix indentation.README: add pipeline status on Gitlab.com.Update .gitlab-ci.yml.sPuReMD: fix several more warning from Valgrind (out-of-bounds accesses in force tabulation lookup tables, sparse matrices with EE/ACKS2 with tabulation). Remove unused variables. Fixes to string handling. Other code clean-up.