- May 23, 2018
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PG-PuReMD: add deallocation routines at simulation termination for aiding with validating memory management.
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- May 22, 2018
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Kurt A. O'Hearn authored
PG-PuReMD: fix CUDA compilation error. Revert library building via libtool due to issues with recognizing custom suffix rules for building CUDA source files and revisit at a later date.
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Kurt A. O'Hearn authored
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- May 21, 2018
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Kurt A. O'Hearn authored
Change MPI build target to use newer MPI-only code by default, and add option to build older MPI code (to be removed in the future).
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with MPI outgoinging buffer size. Refactor MPI communication code for better encapsulation. Continue cleaning up linear solver code.
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Kurt A. O'Hearn authored
PG-PuReMD: fix charge matrix allocation issue. Update CUDA code to reflect data structure changes. Begin removing global variables. Seperate struct declarations and definitions to avoid circular data dependencies when refactoring data structures. Small I/O updates.
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- May 18, 2018
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Kurt A. O'Hearn authored
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- May 16, 2018
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Kurt A. O'Hearn authored
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- May 15, 2018
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Kurt A. O'Hearn authored
PG-PuReMD: begin merging preconditioner code from sPuReMD. Make data structures between sPuReMD and PG-PuReMD consistent. Update control file parsing.
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- May 14, 2018
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Kurt A. O'Hearn authored
PG-PuReMD: merge memory management and step retry logic from MPI+GPU code into MPI-only code. Fix and backport numerous bugs (void pointer arithmetic and dereferences, etc.). Update code to match new data structures. Begin merging changes from OpenMP code (sPuReMD) for preconditioning work.
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Kurt A. O'Hearn authored
sPuReMD: make CoM logic consistent with PuReMD. Other build system updates for debugging and newer versions of MPICH.
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- Apr 30, 2018
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Kurt A. O'Hearn authored
sPuReMD: add checks on string and file handling. Rewrite PDB writing to be line-by-line. Other refactoring.
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- Apr 19, 2018
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Kurt A. O'Hearn authored
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- Apr 17, 2018
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Kurt A. O'Hearn authored
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- Apr 15, 2018
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Kurt A. O'Hearn authored
sPuReMD: remove debug prints. Default to no good initial guess for out of range values for spline extrapolation.
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- Apr 11, 2018
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Kurt A. O'Hearn authored
sPuReMD: move NaN checks on system energy to after logging. This allows better diagnostics for, e.g., the potential logging.
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- Apr 03, 2018
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Kurt A. O'Hearn authored
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- Apr 02, 2018
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Kurt A. O'Hearn authored
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- Mar 27, 2018
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Mar 26, 2018
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Kurt A. O'Hearn authored
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- Mar 22, 2018
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Kurt A. O'Hearn authored
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- Mar 21, 2018
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Mar 13, 2018
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Kurt A. O'Hearn authored
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- Mar 12, 2018
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Kurt A. O'Hearn authored
All: fix issue with pi bonds being incorrectly computed in bond orders. Patch originally submitted to LAMMPS mailing list by Tomas Trnka, SCM (refer to Issue #837 on Github).
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Kurt A. O'Hearn authored
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- Mar 01, 2018
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Kurt A. O'Hearn authored
sPuReMD: separate total energy computation and fix Python driver bug with structure definition for ctypes. Allow disabling file logging during simulation.
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- Feb 26, 2018
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Kurt A. O'Hearn authored
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- Feb 23, 2018
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Kurt A. O'Hearn authored
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- Feb 20, 2018
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
sPuReMD: refactor and clean up preconditioner application code (level scheduling, graph coloring, Jacobi iteration). Conditionally change charge matrix for setting up preconditioner for ICHOLT and ILU(T).
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Alperen, Abdullah authored
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- Feb 19, 2018
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Kurt A. O'Hearn authored
sPuReMD: fix issue with graph coloring causing sporadic failures in solver convergence for EE and ACKS2. Conditionally change the charge matrix for ICHOLT and ILU(T) preconditioning. Refactor graph coloring code.
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- Feb 18, 2018
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Kurt A. O'Hearn authored
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- Feb 15, 2018
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Alperen, Abdullah authored
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Kurt A. O'Hearn authored
sPuReMD: remove force tabulation for charge matrices. Revise list references to mirror MPI code. Revert GMRES iteration counter.
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