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Created with Raphaël 2.2.015Apr1318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PuReMD: 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.Update .gitlab-ci.yml.Update .gitlab-ci.yml.sPuReMD: fix several issues with strings not being null-terminated. Fix use of uninitialized values reported by Valgrind (heap memory). Other general clean-ups.sPuReMD: fix issue with list for debugging forces not having indices initialized (dDelta, dBO). Fix interaction counting in OpenMP code (greater than 1 thread). Other general clean-up.sPuReMD: fix small differences in valence angle energy term with Fortran ReaxFF code. Other minor code updates.Update .gitlab-ci.yml.PuReMD-old: add missing NT macro definitiontools/run_sim.py: begin adding validation code starting with basic log file comparisons.sPuReMD: change log file column headers to be contigious strings of non-whitespace characters to facilitate post-processing.Fix build issue where config.h.in is only generated once (for sPuReMD) => common file across all versions.Merge branch full-far-nbrs-list-charge-matrix.Enable full shell communications by default. Remove extraneous editor file.PuReMD-old: implementation of dual-PIPECGsPuReMD: fix issue with incorrect cutoff being applied for periodic neighbors in small simulation boxes (nonb_cut -> vlist_cut). Other clean-up and debug I/O updates.PuReMD-old: change dual_Sparse_MatVec function to enable NT techniquePuReMD-old: change dual_CG with respect to SAI preconditioner and Neutral TerritoryAdd CI script.Build toos: refactor to remove recurisve Makefiles. Fix issue with OpenMP flags being overridden when user supplied value for CFLAGS variable.PuReMD-old: fix average solver iteration calculation to be correct when energy_update_freq > 1.PuReMD-old: add missing header in summary file for tools/run_sim.py.PuReMD-old: fix issue where nonbonded time was incorrect when energy_update_freq > 1. Update tools/run_sim.py to include both total simulation time and mean time per step.PuReMD-old: fix scaling issue with log file parsing.PuReMD-old: update tools/run_sim.py to get correct value for total simulation time.PuReMD-old: update tools/run_sim.py to get correct value for total simulation time.PuReMD-old: update tools/run_sim.py for non-unit logging freqeuncy.