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Created with Raphaël 2.2.029Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614Tools: add functionality to run different code version (serial, OpenMP, MPI, MPI+GPU). Update sPuReMD control file parser to ignore non-shared memory parameters.PuReMD: refactor to allow selection of far range interaction Verlet list format at runtime (half or full). Similar change for symmetric charge matrix format (half or full). For SAI, toggle between half and full depending on whether it is a refactoring step.Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.PuReMD-old: improve file I/O checks.PuReMD: add Neutral Territory functions (not finished)Tools: update run_sim.py to work with absolute paths (by refereing supplied executable path). Begin updating testing scripts.Tools: work around pathing issues with run_sim.py for running testing benchmarks.Tools: fix results parsing when restricting MD simulations to a specific range of steps.Tools: heavily refactor run_sim.py. Add job submission action.sPuReMD: revert change on evolving atoms (Verlet method) for NVE ensemble.sPuReMD: refactoring to align code with PuReMD. Disable SMALL_BOX_SUPPORT. Refactor to remove union-based polymorphic behavior for reax_list. Other general code clean-ups.PuReMD: fix issue with force tabulation when using full nbr list / charge matrix.Tools: fix MPI command. Change control file generation to be in running directory (for temporary directories and files) => necessary for running with MPI (shared filesystem needed across nodes).Tools: update for usage with Slurm.PuReMD: fix read option for python scriptMerge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrixTest: add MPI+GPU control files.Test: add serial control files. Update MPI control files.Testing: add script for submitting short jobs.PuReMD: fix a small bugPuReMD: fix a small bugTools: reformat proc_by_dim and fix an issue with subprocess command building.Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.Tools: add Python file for running PuReMD code.PuReMD: small change on control.cPuReMD: monkey-patch new control file format for interfacing with tools/run_sim.py.PuReMD: cleand code and add timing performanceMerge branch 'master' of gitlab.msu.edu:SParTA/PuReMD.sPuReMD: fix ILUTP bug with order of permutation matrix application. Refactor dense vector permutation code (GC, ILUTP).Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.Tools: begin updating testing scripts.PuReMD: minor changesPuReMD: add sai_thres variablesPuReMD: fix control variable scoping in linear solvers.sPuReMD: fix permutation application when applying ILUTP preconditioner.PuReMD: add SAI preconditioner applicationPuReMD: fix build system to include autogenerated header config.h.PuReMD: add SAI setup and computation (LAPACKE is not linked)PuReMD: from half to full far neighbor list, etor and econj slightly differsPuReMD: small fix to print utils.