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Created with Raphaël 2.2.03Mar126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614sPuReMD: fix geo_tools parsers not recognizing element types with 2 character names.sPuReMD: fix type mismatch for SAI preconditioner computation.Test: Remove unnecessary target keyword for QMMM test.Test: add README for QMMM.Test: updates to QMMM to match Fortran interface used with Amber.PG-PuReMD: handle a few missed reductions in nonbonded interactions more efficiently. Clean-up bonded interactions functions and do not export kernels via header files. Increase C++ standard to c++14 for CUB (Thrust dependency). Continue with bundled CUB version and transition to version included with CUDA SDK in the future.PG-PuReMD: fix warp-per-atom kernel for atomic distance calculations. Resolve compiler warnings.PG-PuReMD: fix warp-per-atom kernel for atomic distance calculations. Resolve compiler warnings.PG-PuReMD: fix atomic force reductions and reduce the number of atomic operations.PG-PuReMD: use atomics for both partial energy and force accumulation (small reworks to reduce number of atomic operations). Remove several unneccesary cudaMemset calls. Other code clean-up.Revert accidentially committed files from previous commit (WIP).Test: fix Python wrapper for QM/MM (interfaces out-of-date). Fix Fortran tester bugs. Add test artifacts.Tests: add missing Makefile to Amber QM/MM.Tests: refactor QMMM Fortran tester for Amber integration.sPuReMD: standardize QM/MM interface. Add test codes for QM/MM interface for AVE dataset in Python and Fortran.sPuReMD: enable multiple simulations to be run with a single invocation of the stand-alone code.sPuReMD: merge changes from branch 'new_setup'. Rework interface for geometry initialization without file I/O. Other code clean-up.sPuReMD: fixes for non-file I/O setup / reset functions (qmmm, etc.).new_setupnew_setupPG-PuReMD: add atomic operations for partial force accumulation.Merge remote-tracking branch 'origin/master' into new_setupsPuReMD: fix BGF parser to correctly remap atom coordinates to internal simulation box boundaries. Fix reax_list to handle case when total interactions is zero instead of terminating program.new setup/reset function that takes advantage of new soft reset functionalitysPuReMD: rework Fortran F90 interfaces for Amber specifics and declare this interface for such usage.sPuReMD: fix Coulomb energy calculations for QM/MM mode. Indicate QEq model not supported with QM/MM mode. Add Fortran interface for QM/MM mode.sPuReMD: add initial QM/MM support with work for integrating with Amber.sPuReMD: add extra QM/MM interfaces for getters and setters.sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.sPuReMD: reorganizaiton for multiple consecutive simulation codepath (cleanup only).Tools: update example Python driver.sPuReMD: fixes for multiple consecutive simulation codepath. Reorganization to this codepath (some data structure now carry a flag to designation their allocation state). Fix bug in force field parser (atom type not truncated correctly). Charge sparse_matrix structs to be non-pointers to jive with new allocation state flag. Other code clean-up.sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).PG-PuReMD: fix BGF parser for >1 process (correct atom counts within local simulation box boundaries).Fix template control file per BGF addition.PG-PuReMD: fixes to NVT with Berendsen thermostat. Use updated constants from sPuReMD. Add BGF geometry file parser. Other code clean-up.sPuReMD: fixes to Berendsen thermostat for NPT ensembles.sPuReMD: corrections to Berendsen thermostat with NVT (fix velocity scaling and thresholding).sPuReMD: fix memory leak with ICHOLT preconditioner (droptol for OpenMP only) for charge solver. Default to Jacobi preconditioner. Resolve several compiler warnings around C strings (snprintf, etc.). Other code clean-up.sPuReMD: add functionality to run multiple MD simulations (for usage via integration with external codebases).PG-PuReMD: in-progress implementation of CUDA-aware MPI for charge solver communications using OpenMPI (default off).sPuReMD: add checks for GNU scientific library (GSL) for use during energy minimization.