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Created with Raphaël 2.2.05Jun2112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614Tools: fix geo_format for run_md_custom (geo file is mandatory, so the file type extension should always happen).PG-PuReMD: add BiCGStab solver for GPU code. Corrections to CUDA block and thread sizes for some kernels. Fix some variables being used with uninitialized values.Build: default to -O2 optimization.PG-PuReMD: fix issue with charge solver preconditioner refactoring rate causes issues with reneighboring actions (preconditionering rate was previously coupled with reneighoring rate for SAI but this causes issues for Jacobi, etc.). Be more greedy with memory allocation sizes to decrease reallocation frequency (MPI buffers, etc.). More GPU code clean-up.PG-PuReMD: fix MPI buffer allocations sizes. Ensure that nonblocking MPI messages have completed for each dimension before continuing. Rework reallocation checks in integration routines. Temporarily disable CUDA-aware MPI code paths (need to perform packing/unpacking first on device before handing off pointers). Other code clean-up.PG-PuReMD: fix host-device transfers for charge solver code (SpMV data transfer sizes). Remove unused code. Other general code clean-up.PuReMD: fix compile errors with newer compilers due to function prototype mismatches.PG-PuReMD: re-write MPI code to dynamically allocate buffer sizes. Other general code refactoring.PG-PuReMD: fix issue with divergent MPI_Reduce calls by multiple MPI processes (timing logging code). Add run-time MPI routine error checking. Fix issue with upper limit of hydrogen atoms allowed being hard-coded in GPU code (use dynamic memory allocation instead). Other code clean-up.PG-PuReMD: clean-up MPI custom datatype initialization and error reporting. Avoid truncations in buffer size calculations. Other code clean-up.sPuReMD: finalize corrections for pressure calculations. Change output units from GPa to ATMs. Other formatting changes.PG-PuReMD: fix issues with MPI_Reduce calls using MPI_IN_PLACE for non-source processors.PG-PuReMD: improve memory management around temporary storage space on both the host and device (i.e., scratch space).PG-PuReMD: replace deprecated CUDA warp-level primitives with modern ones. Fix issue with modern GPU microarchitectures using incorrect code paths (post-Kepler). Other code clean-up.PG-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.