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Created with Raphaël 2.2.03Dec25Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614sPuReMD: 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.PuReMD: add BiCGStab solver.sPuReMD: fix box initialization for custom geometry file format.Increase boundary spacing for PETN LAMMPS benchmark.Increase boundary spacing for PETN LAMMPS benchmark.Update PETN LAMMPS benchmark. Add PDB replication support to geo_tools.py.PG-PuReMD: remove outdated debugging and validation code (was performing host-only simulation with host+device simulation and comparing results).PG-PuReMD: finish removing global variables.PG-PuReMD: refactoring to unify CUDA code naming conventions and to simply code in cuda_system_props.cu.PG-PuReMD: fix compilation errors.PG-PuReMD: begin refactoring to remove global variables.PuReMD: fixes to PIPECR. Reorganize charge solver code to better seperate solver setup.PG-PuReMD: remove compilation warnings. Remove debug prints in MPI codepath. Other code clean-up.PG-PuReMD: update CUB to commit c3cceac1 (on v1.8.0 branch).PG-PuReMD: fix issue with portions of interaction lists not being initialized for Cuda_Init_Forces. Utilize more targeted debugging prints (DEBUG -> DEBUG_FOCUS). Other general code cleanup.sPuReMD: fix issue with configure script nuking Tensorflow link variables when LAPACK link variables are set.sPuReMD: refine BiCGStab implementation to not falsely report numeric breakdown. TODO: decide on correct checks for level of precision in numeric breakdown checks.sPuReMD: add build system support for Tensorflow. Fix compilation errors for Tensorflow wrappers.sPuReMD: add support for using the Tensorflow machine learning library to prediction initial guesses for the charge solver using the long short-term memory model (LSTM) via frozen models in GraphDef files.sPuReMD: fix deadlock condition in BiCGStab (global shared variables in Norm and Dot functions could overwritten in some multi-threaded runs). Remove debugging prints.sPuReMD: modify BiCGStab implementation to utilize preconditioning.sPuReMD: fix small formatting issue with writing out PDB formatted files. Fix issue with bond restrictions when running with BGF formatted geometry files. Respect buffer size of snprintf calls.sPuReMD: fix formatting in writing PDB files (extra newline).sPuReMD: small fixes around BGF geometry file format parsing and memory management.sPuReMD: small updates to Python wrapper (data structure changes). Fix issue with system energies not being computed for step 0 with the wrapper.sPuReMD: fix issue with far neighbor list being incorrectly generated on MD steps where the list was not being computed (issue with atomic distances being incorrectly computed for peroidic neighbors). Disable several debugging print statements (DEBUG -> DEBUG_FOCUS). Other code clean-up.sPuReMD: add sanity checks on file parsing.PuReMD: code refactoring to remove global variables (similar to sPuReMD). sPuReMD: minor refactoring to match naming conventions of PuReMD.sPuReMD: fix compilation error.v1.0-rc1v1.0-rc1sPuReMD: minor code clean-up.sPuReMD: fix issue with SMALL_BOX_SUPPORT incorrectly computing pairwise atomic distances for periodic self-images. Fix issue with integer vector sum function (used in bond order and torsion interactions).sPuReMD: remove global variable (array of function pointers for printing bonded interactions during debugging).sPuReMD: refactoring in geo_tools.c