- Jan 23, 2019
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Kurt A. O'Hearn authored
PuReMD-old: fix communications to only use full shell pattern for non-charge methods (bug only present using neutral territory communication method). TODO: revisit code structure at a later date.
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Kurt A. O'Hearn authored
PuReMD-old: fix convergence checks for PIPECG and PIPECR. Update CG to used preconditioned residual in it's check.
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- Jan 21, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Jan 18, 2019
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Kurt A. O'Hearn authored
PuReMD-old: protect against buffer overflows for traj_title. NOTE: strcpy IS NOT SAFE, DO NOT USE EVER. USE strncpy INSTEAD.
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Kurt A. O'Hearn authored
PuReMD-old: back-port run_sim.py from master branch. Update control file parsing to ignore sPuReMD/PG-PuReMD options.
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- Jan 10, 2019
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Kurt A. O'Hearn authored
PuReMD-old: optimizations in Init_Bond_Full for fusing hbond and bond list computation and removing unnecessary sorting and sym_index updating.
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Kurt A. O'Hearn authored
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Alperen, Abdullah authored
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- Jan 09, 2019
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Kurt A. O'Hearn authored
PuReMD-old: clean-up and comment initialization optimizations. WIP: remove redundant computation of bonds list (not working for full far nbrs list). Improve hbond list computation for full far nbr list case.
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- Jan 08, 2019
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Alperen, Abdullah authored
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- Jan 06, 2019
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Kurt A. O'Hearn authored
PuReMD-old: complete PIPECG and PIPECR implementations. Fix dense linear algebra code to loop beginning with lowest address in memory (vector.c -> level 1 BLAS-like operations).
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- Jan 05, 2019
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Kurt A. O'Hearn authored
Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.
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Kurt A. O'Hearn authored
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- Jan 04, 2019
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Alperen, Abdullah authored
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- Jan 03, 2019
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Kurt A. O'Hearn authored
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- Jan 02, 2019
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Kurt A. O'Hearn authored
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- Dec 31, 2018
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Alperen, Abdullah authored
Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix
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Alperen, Abdullah authored
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Kurt A. O'Hearn authored
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- Dec 28, 2018
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Alperen, Abdullah authored
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- Dec 27, 2018
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Alperen, Abdullah authored
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Alperen, Abdullah authored
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Alperen, Abdullah authored
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- Dec 23, 2018
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Kurt A. O'Hearn authored
Merge branch 'full-far-nbrs-list-charge-matrix' of https://gitlab.msu.edu/SParTA/PuReMD into full-far-nbrs-list-charge-matrix.
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Kurt A. O'Hearn authored
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- Dec 22, 2018
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Alperen, Abdullah authored
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Kurt A. O'Hearn authored
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- Dec 21, 2018
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Alperen, Abdullah authored
PuReMD: split Init_Forces into 3 functions: Init_Distance, Init_CM and Init_Bond, and add timings for those functions
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- Dec 19, 2018
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Kurt A. O'Hearn authored
PuReMD-old: fix timing issues. Remove fine-grained timing of Init_Forces due to high overhead. Disable SAI preconditioner optimization of changing far nbr list and matrix formats based on preconditioner refactoring step (not working). Tweak to not product numeric overflow when setting up SAI preconditioner (pivot sampling).
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- Dec 17, 2018
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Alperen, Abdullah authored
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- Dec 16, 2018
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Alperen, Abdullah authored
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- Dec 15, 2018
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Alperen, Abdullah authored
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- Dec 13, 2018
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Kurt A. O'Hearn authored
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Alperen, Abdullah authored
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- Dec 12, 2018
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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Alperen, Abdullah authored
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- Dec 04, 2018
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PuReMD-old: more clean-up of linear algebra code. Remove or conditionally enable debugging code (DEBUG preprocessor). Fix memory leak in SAI setup. Better memory allocation checks.
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