Skip to content
Snippets Groups Projects
Select Git revision
  • dummy-atom-support
  • energy_minim
  • main default protected
  • new_setup
  • pg-puremd-charge-solver-opt-sdsc-hackaton
  • qeq-nonzero-net-charge
  • restraint_support
  • tensorflow_update
  • tensorflow_update_v2
  • v1.0-rc1
10 results
You can move around the graph by using the arrow keys.
Created with Raphaël 2.2.010Oct86324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PG-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.cPuReMD: clean-up of heuristic for dynamically determining when to recompute the preconditioner for the charge solver.sPuReMD: improvements for building in debug mode (add assertion support for run-time checks). Fix issue with Verlet list recomputation logic being incorrect. Fixes to be string comparisons.sPuReMD: fix issue with certain preconditioners not being initialized for runs using restart files. Fix issue with part of simulation box struct not being initialized for runs using restart files (box->min). Other code clean-up from debugging issues with SMALL_BOX_SUPPORT.sPuReMD: add safety check for BGF input files (CRYSTX). Remove compiler warnings when enabling DEBUG_FOCUS.sPuReMD: fix issues with using sizeof with dynamically allocated pointers. Change OpenMP schedule policies for linear algebra code. PuReMD: correct discrepancy with charge matrix construction. Enable dual solver for charges by default.sPuReMD: refactoring to better align with PuReMD code. PuReMD: backport sPuReMD changes from validation efforts against Fortran ReaxFF code.sPuReMD: fixes to SAI preconditioner to correctly apply threshold to negative entries and to handle EE/ACKS2 cases when a threshold value of 1.0 is chosen.Tools: fix typo in job script creation.Tools: update tools/driver.py to be in sync with most recent version of sPuReMD.sPuReMD: fix FG_ICHOLT bugs.sPuReMD: fix bug with diagonal scaling during FG_ICHOL/FG_ILUT producing incorrect factorizations when diagonal entries were negative.sPuReMD: complete fine-grained Cholesky implementation. TODO: fix numeric breakdowns with water 6540 atom system.sPuReMD: remove unused code.sPuReMD: fix compiler warnings of uninitialized values.sPuReMD: backport list construction optimzations from PuReMD.sPuReMD: optimizations to fine-grain ILUT implementation.