- Sep 12, 2019
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Kurt A. O'Hearn authored
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.
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- Sep 10, 2019
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Kurt A. O'Hearn authored
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- Sep 09, 2019
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Kurt A. O'Hearn authored
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- Sep 05, 2019
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Kurt A. O'Hearn authored
sPuReMD: small updates to Python wrapper (data structure changes). Fix issue with system energies not being computed for step 0 with the wrapper.
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- Aug 29, 2019
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Kurt A. O'Hearn authored
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.
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- Aug 17, 2019
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Kurt A. O'Hearn authored
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- Aug 06, 2019
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Kurt A. O'Hearn authored
PuReMD: code refactoring to remove global variables (similar to sPuReMD). sPuReMD: minor refactoring to match naming conventions of PuReMD.
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- Aug 04, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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).
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- Aug 01, 2019
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Kurt A. O'Hearn authored
sPuReMD: remove global variable (array of function pointers for printing bonded interactions during debugging).
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Kurt A. O'Hearn authored
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- Jul 30, 2019
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Kurt A. O'Hearn authored
PuReMD: clean-up of heuristic for dynamically determining when to recompute the preconditioner for the charge solver.
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- Jul 27, 2019
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Kurt A. O'Hearn authored
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.
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- Jul 12, 2019
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Kurt A. O'Hearn authored
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.
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- Jun 21, 2019
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Kurt A. O'Hearn authored
sPuReMD: add safety check for BGF input files (CRYSTX). Remove compiler warnings when enabling DEBUG_FOCUS.
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- Jun 12, 2019
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Kurt A. O'Hearn authored
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.
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- Jun 10, 2019
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Kurt A. O'Hearn authored
sPuReMD: refactoring to better align with PuReMD code. PuReMD: backport sPuReMD changes from validation efforts against Fortran ReaxFF code.
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- Jun 03, 2019
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Kurt A. O'Hearn authored
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.
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- May 30, 2019
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Kurt A. O'Hearn authored
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- May 29, 2019
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Kurt A. O'Hearn authored
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- May 28, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
sPuReMD: fix bug with diagonal scaling during FG_ICHOL/FG_ILUT producing incorrect factorizations when diagonal entries were negative.
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- May 27, 2019
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Kurt A. O'Hearn authored
sPuReMD: complete fine-grained Cholesky implementation. TODO: fix numeric breakdowns with water 6540 atom system.
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- May 24, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- May 23, 2019
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Kurt A. O'Hearn authored
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- May 05, 2019
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Kurt A. O'Hearn authored
sPuReMD: workarounds for memory issues with ILUT factors. Implement ILU(0) and call when selecting ILUT with a droptol of 0.
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- May 04, 2019
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Kurt A. O'Hearn authored
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- Apr 30, 2019
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Kurt A. O'Hearn authored
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- Apr 18, 2019
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Kurt A. O'Hearn authored
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- Apr 15, 2019
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Alperen, Abdullah authored
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- Apr 13, 2019
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Kurt A. O'Hearn authored
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- Mar 18, 2019
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Kurt A. O'Hearn authored
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- Mar 17, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Mar 14, 2019
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