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Created with Raphaël 2.2.021Feb25Jan19622Dec1716718Nov9125Oct228716Aug1210526Jul2320142129Jun2824232221982124May131211107429Apr28262019161514930Mar26181615543126Feb23191817151143129Jan282218116416Dec15141020Nov22Oct22Sep2016920Aug1714121110765129Jul226129Jun252423171252112May107430Apr201513610Mar53226Feb191017Jan1687618Dec111064325Nov8429Oct25242017111086324Sep2312109529Aug1764130Jul271221Jun1210330May29282724235430Apr18151318Mar17141264128Feb27252120191814137629Jan282726252321181510986543231Dec282723222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep876sPuReMD: fix issue with API functions (setup2 / reset2 -> cleanup) regarding new contiguous and custom charge constraint implementation (identified and suggested fix by Cagri Kaymak).sPuReMD: fixes for custom charge constraint specification for QM/MM simulations.sPuReMD: fix uninitialized variable compilation warning.sPuReMD: do not compute hydrogen bond interactions when there are no valid force field parameters available for the given triplet of atom types. Allow arbitrary numbers of H-bond interactions per atom.sPuReMD: fix issue with sparse charge matrix (for preconditioning) not being reallocated upon out-of-memory condition. Fix issues where charge matrix and bond/H-bond list entries were reading from and potentially writing to invalid memory locations. Remove unused code for grid. Other code clean-up.sPuReMD: fix uninitialized variable issue with API functions (charge constraints => setup2, reset2).sPuReMD: add support for custom charge constraints with EEM for QM/MM simulations.sPuReMD: add support for setting charge computation frequency (charge_freq).sPuReMD: add error checks around I/O routines to silence warnings regarding disregarded return values.PG-PuReMD: fix potential MPI message collision issue in SAI preconditioner (same tags to same source rank => use different tags). Reorder communications to allow message size detection and buffer reallocation if needed.PG-PuReMD: fix queue usage in SAI preconditioner (memory leak, previously fixed size).Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.Merge branch 'fix-issue-9' into 'master'Fix memory allocation issues related to API usage (setup => cleanup but no simulate) as detailed in Issue #9.PG-PuReMD: port memory allocation checks. Begin fixing SAI code.sPuReMD: fix hbond list initialization when empty.sPuReMD: fix another reallocation issue. Fix list index initialization issue. Other code clean-up.sPuReMD: fix reallocation issue.sPuReMD: rework memory management logic to better match PG-PuReMD code. Adapt new memory management logic for multiple simulation logic (as motivated by memory issues observed with QM/MM code for AMBER integration work). Other code clean-up.PG-PuReMD: fix bugs in the SAI preconditioner for the charge solver (memory leak, incorrect row numbers).PG-PuReMD: adjust energy conversion constant to match sPuReMD code.PG-PuReMD: port SAI preconditioner from MPI codebase. Rework charge solver preconditioner code. Other code clean-up.sPuReMD: change dummy atom behavior to participate only in Coulomb interactions (exclude from van der Waal interactions in this changeset).PG-PuReMD: fix compilation issue with MPI code (from SDSC hackathon branch merge).Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.PG-PuReMD: fix cross-stream race conditions on intermediary force calculation variables (CdDelta, Cdbo, etc.). Rework valency and torsion calculations to minmize the number of atomic operations performed. Split lone pair and over-/under-coordination kernels. Fix small size mismatch in allocation routines (over-allocation). Other code clean-up.pg-puremd-charg…pg-puremd-charge-solver-opt-sdsc-hackatonPG-PuReMD: fix adding keyword for polarization energy.sPuReMD, PG-PuReMD: add control file keyword (include_polarization_energy) to toggle polarization energy calcuation in ReaxFF.Merge branch 'master' into pg-puremd-charge-solver-opt-sdsc-hackaton.sPuReMD: ensure matrix rows are sorted.sPuReMD: fix charge matrix storage estimate for molecular charge constraints.sPuReMD: rework charge solver for QMMM to not require explicit masking (MM atom fixed charges are not respected). Other code clean-up.PG-PuReMD: add missing dual QEq solver implementations for MPI.PG-PuReMD: refactor MPI charge solver code to better align with shared-memory and MPI+CUDA codes.sPuReMD: fix dummy atoms for QMMM simulations.sPuReMD: fix masking charge constraints for QMMM interface.sPuReMD: ensure reallocation for multi-simulation runs happens correctly for the charge solver codepath.sPuReMD: ensure matrix reallocation correctly occurs in multiple simulation cases where the linear system size increases.sPuReMD: correctly detect dummy atoms for non-standalone simulations.sPuReMD: add dummy atom support for other geometry file formats (PDB, custom). Rework interal logging during debugging for memory management. Other code clean-up.dummy-atom-supp…dummy-atom-support