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Created with Raphaël 2.2.06Apr10Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PG-PuReMD: include missing header file in Automake make file (includes file in distribution tarball).PG-PuReMD: revert to 1 thread per atom implementation in nonbonded energy and force calculations in order to correct issue with forces being incorrectly calculated (revisit 1 warp per atom implementation later). Disable charge matrix row-wise sorting. Other general code clean-up.PG-PuReMD: corrections to van der Waals and Coulomb energies calculations (far neighbor list in full format, not half). Fix QEq charge matrix initialization (full format). Other refactoring and code clean-up.sPuReMD: more fixes for pressure calculations.sPuReMD: corrections to pressure calculations.PG-PuReMD: fix issue with SpMVs operations using incorrect row-wise bounds (end pointer incorrect in light of sparse_matrix struct changes).Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.sPuReMD: corrections for pressure calculations (virial).PG-PuReMD: refactor linear solver code. Increase MPI buffers sizes.PG-PuReMD: merge changes from sPuReMD and PuReMD for validation work for simulation accuracy. Small correction to lone pair energy calculation. PuReMD: code formatting changes to better align with sPuReMD. sPuReMD: fix issue with valence angle calculations not setting list indices under certain sitations (taking previous continue statement missed index assignment).sPuReMD: fix merge issue.PuReMD: backport changes for interaction function calculations. sPuReMD: alignment with PuReMD code.PuReMD: begin EE and ACKS2 charge model implementation. Refactor charge solvers in order to enable optimizated communication for sparse matrix structure (specifically around SpMV operations). Other general refactoring.Merge branch 'master' into tensorflow_updatetensorflow_updatetensorflow_updatenew control params, 2 model support for predictionsPuReMD: ensure three body list indices are reset before construction.sPuReMD: report conflicting control file parameters regarding atom initial velocities.sPuReMD: optimizations for memory allocation in SAI preconditioner computation.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.Tools: add function to apply Gaussian noise to atomic positions in order to generate a new structure file.Build: add missing linkage to LAPACKE library (C bindings to Fortran LAPACK library).tensorflow updatessPuReMD: output PDB files according to write_freq value in control file in addition to outputting to the trajectory file. Small tweak to PDB output format to be in compliance with specification.sPuReMD: fix issue with runs using restart files overwriting velocities to zero. Change behavor to warn if conflicting conditions exist for generating initial atom velocities. Revert formatting change of pressure logs. Enable pressure file logging when compute_pressure = 1.sPuReMD: update temperature scaler for semi-isotropic NPT ensemble.sPuReMD: more clean-up to thermostat code.sPuReMD: corrections to velocity scalings in NVT ensemble with Berendsen thermostat.sPuReMD: correction to NPT code to conditionally set thread-local storage.sPuReMD: add control file parameter to compute atomic system pressure for non-NPT ensembles. Fix issues with isotropic NPT ensemble (incorrect pressure and temperature scalers). Change atomic position remapping behavior to include upper boundaries of the simulation box (shared memory code only). Other code clean-up.Tools: add option to submit_jobs to specify versions of software modules to load.Tools: fix error in submit_jobs when using the MPI run type.sPuReMD: replace OpenMP critical sections on ext_press with thread-local storage and subsequent reduction (ext_press_local). Other code clean-up.sPuReMD: corrections to external pressure calculations for NPT-type ensemble simulations (use correct periodic images between reneighboring steps). Other code clean-up.sPuReMD: fix issue with torsion & conjugation forces being incorrect due to rel_box arithmetic being wrong (incorrect directions for position vectors). Redesign atomic distance and position update functions to support both periodic boundary conditions and non-periodic boundary conditions. Behavior change: let random_velocity parameter in control file take precedent over specifying a non-zero initial temperature value. Other code clean-up.Build: work around Autoconf bug in AC_SEARCH_LIBS preventing both LAPACK and Tensorflow from being used together for sPuReMD.sPuReMD: disable debug prints (DEBUG -> DEBUG_FOCUS). Small tweaks to valence angle code to better match reference. Other code clean-up.Tools: modify compare_logs to enable comparison across different run types.PG-PuReMD: backport fixes from sPuReMD to control file parsing. Tools: formatting tweaks for MPI-GPU code.PuReMD: disable debug prints during basic debugging (DEBUG -> DEBUG_FOCUS). Re-enable DUAL_SOLVER. Small buffer reworking around trajectory file (REG_TRAJ). Other code clean-up.PuReMD: add SDM solver.