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Created with Raphaël 2.2.01Nov25Oct228716Aug1210526Jul2320142129Jun2824232221982124May131211107429Apr28262019161514930Mar26181615543126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug26PG-PuReMD: fix queue usage in SAI preconditioner (memory leak, previously fixed size).Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.Merge branch 'fix-issue-9' into 'master'Fix memory allocation issues related to API usage (setup => cleanup but no simulate) as detailed in Issue #9.PG-PuReMD: port memory allocation checks. Begin fixing SAI code.sPuReMD: fix hbond list initialization when empty.sPuReMD: fix another reallocation issue. Fix list index initialization issue. Other code clean-up.sPuReMD: fix reallocation issue.sPuReMD: rework memory management logic to better match PG-PuReMD code. Adapt new memory management logic for multiple simulation logic (as motivated by memory issues observed with QM/MM code for AMBER integration work). Other code clean-up.PG-PuReMD: fix bugs in the SAI preconditioner for the charge solver (memory leak, incorrect row numbers).PG-PuReMD: adjust energy conversion constant to match sPuReMD code.PG-PuReMD: port SAI preconditioner from MPI codebase. Rework charge solver preconditioner code. Other code clean-up.sPuReMD: change dummy atom behavior to participate only in Coulomb interactions (exclude from van der Waal interactions in this changeset).PG-PuReMD: fix compilation issue with MPI code (from SDSC hackathon branch merge).Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.PG-PuReMD: fix cross-stream race conditions on intermediary force calculation variables (CdDelta, Cdbo, etc.). Rework valency and torsion calculations to minmize the number of atomic operations performed. Split lone pair and over-/under-coordination kernels. Fix small size mismatch in allocation routines (over-allocation). Other code clean-up.pg-puremd-charg…pg-puremd-charge-solver-opt-sdsc-hackatonPG-PuReMD: fix adding keyword for polarization energy.sPuReMD, PG-PuReMD: add control file keyword (include_polarization_energy) to toggle polarization energy calcuation in ReaxFF.Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.sPuReMD: ensure matrix rows are sorted.sPuReMD: fix charge matrix storage estimate for molecular charge constraints.sPuReMD: rework charge solver for QMMM to not require explicit masking (MM atom fixed charges are not respected). Other code clean-up.PG-PuReMD: add missing dual QEq solver implementations for MPI.PG-PuReMD: refactor MPI charge solver code to better align with shared-memory and MPI+CUDA codes.sPuReMD: fix dummy atoms for QMMM simulations.sPuReMD: fix masking charge constraints for QMMM interface.sPuReMD: ensure reallocation for multi-simulation runs happens correctly for the charge solver codepath.sPuReMD: ensure matrix reallocation correctly occurs in multiple simulation cases where the linear system size increases.sPuReMD: correctly detect dummy atoms for non-standalone simulations.sPuReMD: add dummy atom support for other geometry file formats (PDB, custom). Rework interal logging during debugging for memory management. Other code clean-up.dummy-atom-supp…dummy-atom-supportassign FALSE explicitly for non-dummy atomsadd support for dummy atom (only in BGF format with 'X' keyword for dummy atoms')sPuReMD: fix charge matrix initialize for charge constraints for QMMM.sPuReMD: simplify QMMM masking code for charge matrix.sPuReMD: update QMMM interface for specifying molecular charge constraints for charge model (EEM only currently).Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.sPuReMD: fix issue with atoms exactly on the upper boundary of the simulation box not being correctly binned into grid cells for the cell method. Refine conversion constants for kinetic energy and temperature calculations to obtain better agreement with the Fortran ReaxFF codebase.Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.sPuReMD: backport most recent QMMM changes for simulations with AmberMD.sPuReMD: fix code to remove several compiler warnings. Remove unused code. Disable compilation of several debug routines. Other code clean-up.