- Feb 10, 2020
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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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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Dec 10, 2019
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Kurt A. O'Hearn authored
sPuReMD: add control file parameter to compute atomic system pressure for non-NPT ensembles. Fix issues with isotropic NPT ensemble (incorrect pressure and temperature scalers). Change atomic position remapping behavior to include upper boundaries of the simulation box (shared memory code only). Other code clean-up.
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- Dec 06, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Dec 04, 2019
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Kurt A. O'Hearn authored
sPuReMD: replace OpenMP critical sections on ext_press with thread-local storage and subsequent reduction (ext_press_local). Other code clean-up.
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- Dec 03, 2019
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Kurt A. O'Hearn authored
sPuReMD: corrections to external pressure calculations for NPT-type ensemble simulations (use correct periodic images between reneighboring steps). Other code clean-up.
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- Nov 25, 2019
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Kurt A. O'Hearn authored
sPuReMD: fix issue with torsion & conjugation forces being incorrect due to rel_box arithmetic being wrong (incorrect directions for position vectors). Redesign atomic distance and position update functions to support both periodic boundary conditions and non-periodic boundary conditions. Behavior change: let random_velocity parameter in control file take precedent over specifying a non-zero initial temperature value. Other code clean-up.
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- Nov 08, 2019
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Kurt A. O'Hearn authored
Build: work around Autoconf bug in AC_SEARCH_LIBS preventing both LAPACK and Tensorflow from being used together for sPuReMD.
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- Nov 04, 2019
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Kurt A. O'Hearn authored
sPuReMD: disable debug prints (DEBUG -> DEBUG_FOCUS). Small tweaks to valence angle code to better match reference. Other code clean-up.
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- Oct 29, 2019
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
PG-PuReMD: backport fixes from sPuReMD to control file parsing. Tools: formatting tweaks for MPI-GPU code.
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- Oct 25, 2019
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Kurt A. O'Hearn authored
PuReMD: disable debug prints during basic debugging (DEBUG -> DEBUG_FOCUS). Re-enable DUAL_SOLVER. Small buffer reworking around trajectory file (REG_TRAJ). Other code clean-up.
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Kurt A. O'Hearn authored
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- Oct 24, 2019
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Kurt A. O'Hearn authored
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- Oct 20, 2019
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Kurt A. O'Hearn authored
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- Oct 17, 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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- Oct 11, 2019
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Kurt A. O'Hearn authored
PG-PuReMD: remove outdated debugging and validation code (was performing host-only simulation with host+device simulation and comparing results).
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Kurt A. O'Hearn authored
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- Oct 10, 2019
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Kurt A. O'Hearn authored
PG-PuReMD: refactoring to unify CUDA code naming conventions and to simply code in cuda_system_props.cu.
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Kurt A. O'Hearn authored
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Kurt A. O'Hearn authored
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- Oct 08, 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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- Oct 06, 2019
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Kurt A. O'Hearn authored
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.
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