- Jun 17, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix out-of-bounds mmeory accesses and unitialized data usage in energy and force tabulation routines for van der Waals and Coulomb interactions.
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- Jun 12, 2020
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with some interaction lists not being initialized on first step of simulations from restarted runs. Fix typos in C++ code for utilizing C code (__cplusplus). Clean up C code for utilizing C++ code (unconditional extern's for unmangled member naming). Ensure that CUDA thread and block sizes are correctly set. Tweaks to memory transfers and allocation logic in integration code (GPU). Fix logic error with charge matrix allocation in GPU code. Other code clean-up.
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- Jun 05, 2020
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Kurt A. O'Hearn authored
Tools: fix geo_format for run_md_custom (geo file is mandatory, so the file type extension should always happen).
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Kurt A. O'Hearn authored
PG-PuReMD: add BiCGStab solver for GPU code. Corrections to CUDA block and thread sizes for some kernels. Fix some variables being used with uninitialized values.
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- Jun 02, 2020
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with charge solver preconditioner refactoring rate causes issues with reneighboring actions (preconditionering rate was previously coupled with reneighoring rate for SAI but this causes issues for Jacobi, etc.). Be more greedy with memory allocation sizes to decrease reallocation frequency (MPI buffers, etc.). More GPU code clean-up.
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- Jun 01, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix MPI buffer allocations sizes. Ensure that nonblocking MPI messages have completed for each dimension before continuing. Rework reallocation checks in integration routines. Temporarily disable CUDA-aware MPI code paths (need to perform packing/unpacking first on device before handing off pointers). Other code clean-up.
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- May 12, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix host-device transfers for charge solver code (SpMV data transfer sizes). Remove unused code. Other general code clean-up.
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- May 10, 2020
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Kurt A. O'Hearn authored
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- May 07, 2020
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Kurt A. O'Hearn authored
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- May 04, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with divergent MPI_Reduce calls by multiple MPI processes (timing logging code). Add run-time MPI routine error checking. Fix issue with upper limit of hydrogen atoms allowed being hard-coded in GPU code (use dynamic memory allocation instead). Other code clean-up.
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- Apr 30, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: clean-up MPI custom datatype initialization and error reporting. Avoid truncations in buffer size calculations. Other code clean-up.
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- Apr 20, 2020
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Kurt A. O'Hearn authored
sPuReMD: finalize corrections for pressure calculations. Change output units from GPa to ATMs. Other formatting changes.
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- Apr 15, 2020
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Kurt A. O'Hearn authored
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- Apr 13, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: improve memory management around temporary storage space on both the host and device (i.e., scratch space).
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Kurt A. O'Hearn authored
PG-PuReMD: replace deprecated CUDA warp-level primitives with modern ones. Fix issue with modern GPU microarchitectures using incorrect code paths (post-Kepler). Other code clean-up.
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- Apr 06, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: include missing header file in Automake make file (includes file in distribution tarball).
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- Mar 10, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: revert to 1 thread per atom implementation in nonbonded energy and force calculations in order to correct issue with forces being incorrectly calculated (revisit 1 warp per atom implementation later). Disable charge matrix row-wise sorting. Other general code clean-up.
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- Mar 05, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: corrections to van der Waals and Coulomb energies calculations (far neighbor list in full format, not half). Fix QEq charge matrix initialization (full format). Other refactoring and code clean-up.
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- Mar 03, 2020
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Kurt A. O'Hearn authored
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- Mar 02, 2020
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Kurt A. O'Hearn authored
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- Feb 26, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: fix issue with SpMVs operations using incorrect row-wise bounds (end pointer incorrect in light of sparse_matrix struct changes).
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Feb 19, 2020
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Kurt A. O'Hearn authored
PG-PuReMD: merge changes from sPuReMD and PuReMD for validation work for simulation accuracy. Small correction to lone pair energy calculation. PuReMD: code formatting changes to better align with sPuReMD. sPuReMD: fix issue with valence angle calculations not setting list indices under certain sitations (taking previous continue statement missed index assignment).
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- Feb 10, 2020
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PuReMD: backport changes for interaction function calculations. sPuReMD: alignment with PuReMD code.
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Kurt A. O'Hearn authored
PuReMD: begin EE and ACKS2 charge model implementation. Refactor charge solvers in order to enable optimizated communication for sparse matrix structure (specifically around SpMV operations). Other general refactoring.
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- Jan 16, 2020
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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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- Jan 08, 2020
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Kurt A. O'Hearn authored
Tools: add function to apply Gaussian noise to atomic positions in order to generate a new structure file.
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- Jan 07, 2020
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Kurt A. O'Hearn authored
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- Jan 06, 2020
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Kurt A. O'Hearn authored
sPuReMD: output PDB files according to write_freq value in control file in addition to outputting to the trajectory file. Small tweak to PDB output format to be in compliance with specification.
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- Dec 18, 2019
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Kurt A. O'Hearn authored
sPuReMD: fix issue with runs using restart files overwriting velocities to zero. Change behavor to warn if conflicting conditions exist for generating initial atom velocities. Revert formatting change of pressure logs. Enable pressure file logging when compute_pressure = 1.
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- Dec 11, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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