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2018-09-17	Berk Hess	Move ifunc stuff from idef.h to ifunc.h	commit \| commitdiff \| tree
2018-09-17	Berk Hess	Change pointers to InteractionList to references	commit \| commitdiff \| tree
2018-09-16	Berk Hess	Refactoring in DD redistribute	commit \| commitdiff \| tree
2018-09-14	Berk Hess	Refactor getAtomGroupDistribution()	commit \| commitdiff \| tree
2018-09-14	Berk Hess	Change gmx_moltype_t.ilist to InteractionLists	commit \| commitdiff \| tree
2018-09-13	Berk Hess	Add C++ version of t_ilist	commit \| commitdiff \| tree
2018-09-12	Berk Hess	Convert vsite structs to C++	commit \| commitdiff \| tree
2018-09-12	Berk Hess	Convert DD gmx_reverse_top_t to C++	commit \| commitdiff \| tree
2018-08-29	Berk Hess	Refactor wall potential calculation	commit \| commitdiff \| tree
2018-08-24	Berk Hess	Replace gmx_hash_t by HashedMap	commit \| commitdiff \| tree
2018-08-24	Berk Hess	Merge "Merge branch release-2018"	commit \| commitdiff \| tree
2018-08-24	Berk Hess	Add size optimization to HashedMap	commit \| commitdiff \| tree
2018-08-24	Berk Hess	Add tests for HashedMap	commit \| commitdiff \| tree
2018-08-22	Berk Hess	Fix missing interactions with GPU and DD	commit \| commitdiff \| tree
2018-08-21	Berk Hess	Ensure domains are large enough for atom motion	commit \| commitdiff \| tree
2018-08-21	Berk Hess	Fixed mdrun segv with QM/MM ONIOM scheme	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Refactor calc_verlet_buffer_size()	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Remove compacting from DD redistribute	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Fix Verlet buffer estimate with BD	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Fix clang namespace comment warning	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Fix assertion failure in CG	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Really fix CG with multiple domains	commit \| commitdiff \| tree
2018-08-20	Berk Hess	Make gmx_ga2la_t a proper class	commit \| commitdiff \| tree
2018-08-18	Berk Hess	Add check for pull group PBC to grompp	commit \| commitdiff \| tree
2018-08-17	Berk Hess	Make pull pbc atom use LocalAtomSet	commit \| commitdiff \| tree
2018-07-18	Berk Hess	Apply local atom sets in pull code	commit \| commitdiff \| tree
2018-07-03	Berk Hess	Convert gmx_hash_t to C++	commit \| commitdiff \| tree
2018-07-03	Berk Hess	Localize variables in dd_redistribute_cg()	commit \| commitdiff \| tree
2018-07-02	Berk Hess	Convert DD DLB cell size handling to C++	commit \| commitdiff \| tree
2018-07-02	Berk Hess	Fix recent bug with 2D/3D DLB	commit \| commitdiff \| tree
2018-07-01	Berk Hess	Removed smalloc.h from many DD files	commit \| commitdiff \| tree
2018-06-29	Berk Hess	Convert gmx_domdec_constraints_t to C++	commit \| commitdiff \| tree
2018-06-29	Berk Hess	Convert gmx_domdec_specat_comm_t to C++	commit \| commitdiff \| tree
2018-06-29	Berk Hess	Initialize DD DLB variable	commit \| commitdiff \| tree
2018-06-29	Berk Hess	New quote from a referee	commit \| commitdiff \| tree
2018-06-28	Berk Hess	Rename atomGroups in gmx_domdec_t to atomGrouping	commit \| commitdiff \| tree
2018-06-28	Berk Hess	Clean up dd_move_cellx()	commit \| commitdiff \| tree
2018-06-28	Berk Hess	Convert gmx_domdec_sort_t to C++	commit \| commitdiff \| tree
2018-06-28	Berk Hess	Change BlockRanges to class RangePartitioning	commit \| commitdiff \| tree
2018-06-27	Berk Hess	Fix bug with 2D/3D triclinic DD	commit \| commitdiff \| tree
2018-06-27	Berk Hess	Base vacuum DD on atom coordinates	commit \| commitdiff \| tree
2018-06-27	Berk Hess	Add consistency check to DDAtomRanges	commit \| commitdiff \| tree
2018-06-27	Berk Hess	Partial conversion of gmx_domdec_comm_t to C++	commit \| commitdiff \| tree
2018-06-27	Berk Hess	Template and overload dd_sendrecv functions	commit \| commitdiff \| tree
2018-06-27	Berk Hess	Correct DD zone size loop bound	commit \| commitdiff \| tree
2018-06-14	Berk Hess	Minimization now detects infinite forces	commit \| commitdiff \| tree
2018-06-14	Berk Hess	Introduced DDAtomRanges class	commit \| commitdiff \| tree
2018-06-13	Berk Hess	Remove LINCS prints to log file	commit \| commitdiff \| tree
2018-06-13	Berk Hess	Partial conversion of gmx_domdec_t to C++	commit \| commitdiff \| tree
2018-06-12	Berk Hess	Add AWH continuation consistency checking	commit \| commitdiff \| tree
2018-06-12	Berk Hess	Add fatal error for inconsistent graph	commit \| commitdiff \| tree
2018-06-12	Berk Hess	Avoid COM removal moving frozen atoms	commit \| commitdiff \| tree
2018-06-12	Berk Hess	Remove constraint v correction for frozen atoms	commit \| commitdiff \| tree
2018-06-06	Berk Hess	Clean up make_at2con	commit \| commitdiff \| tree
2018-06-06	Berk Hess	Fix MPI inconsistency in EM after constraint failure	commit \| commitdiff \| tree
2018-06-05	Berk Hess	Make nbnxn_grid_t counts and sizes arrays	commit \| commitdiff \| tree
2018-06-04	Berk Hess	Fix segv in AWH error message	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Fix grompp bug with blocks of same molecules	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Simplify idef_fe in calc_listed_lambda	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Change nbs in nbv to std::unique	commit \| commitdiff \| tree
2018-05-24	Berk Hess	Convert gmx_domdec_master_t to C++	commit \| commitdiff \| tree
2018-05-23	Berk Hess	Split off collect.cpp from domdec.cpp	commit \| commitdiff \| tree
2018-05-23	Berk Hess	Convert nbnxn_search to C++	commit \| commitdiff \| tree
2018-05-22	Berk Hess	Change nbnxn grid reallocation	commit \| commitdiff \| tree
2018-05-22	Berk Hess	Use std::vector in nbnxn_search_t	commit \| commitdiff \| tree
2018-05-22	Berk Hess	Use std::vector in nbnxn_grid_t	commit \| commitdiff \| tree
2018-05-18	Berk Hess	Clean up in nbnxn_grid.cpp	commit \| commitdiff \| tree
2018-05-17	Berk Hess	Split off domdec distribution and cellsizes	commit \| commitdiff \| tree
2018-05-17	Berk Hess	Split atom redistribution off from domdec.cpp	commit \| commitdiff \| tree
2018-05-17	Berk Hess	Remove commrec from set_ddbox()	commit \| commitdiff \| tree
2018-05-15	Berk Hess	Clean up PME domain count passing	commit \| commitdiff \| tree
2018-05-03	Berk Hess	Enable SIMD version of update	commit \| commitdiff \| tree
2018-04-27	Berk Hess	Remove pull MPI code duplication	commit \| commitdiff \| tree
2018-04-24	Berk Hess	Fix indexing issue in the pull code	commit \| commitdiff \| tree
2018-04-16	Berk Hess	Move natoms_mol out of gmx_molblock_t	commit \| commitdiff \| tree
2018-04-09	Berk Hess	Convert gmx_molblock_t to C++	commit \| commitdiff \| tree
2018-04-03	Berk Hess	Convert gmx_mtop_t to C++	commit \| commitdiff \| tree
2018-04-03	Berk Hess	Change warninp filenm to std::string	commit \| commitdiff \| tree
2018-04-03	Berk Hess	Do not calculate COM for pull group 0	commit \| commitdiff \| tree
2018-03-29	Berk Hess	Move file opening out of init_pull()	commit \| commitdiff \| tree
2018-03-29	Berk Hess	Modularize pull_coord_work_t	commit \| commitdiff \| tree
2018-03-28	Berk Hess	Remove mols from gmx_mtop_t	commit \| commitdiff \| tree
2018-03-20	Berk Hess	Fix gmx dump AWH formatting issue	commit \| commitdiff \| tree
2018-03-20	Berk Hess	Disallow single simulation with multisim	commit \| commitdiff \| tree
2018-03-16	Berk Hess	Correct PMF sign error in AWH bias sharing	commit \| commitdiff \| tree
2018-03-16	Berk Hess	Fix recent mdrun signaling bug	commit \| commitdiff \| tree
2018-03-15	Berk Hess	Fix virial with external pull potential and MPI	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Improve inter-simulation signaling	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Fix mdrun signalling with AWH bias sharing	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Fix COM pulling with external potential with #ranks>32	commit \| commitdiff \| tree
2018-03-14	Berk Hess	Fix pull bug with geometry=direction-periodic	commit \| commitdiff \| tree
2018-03-13	Berk Hess	Add AWH fixes to release notes	commit \| commitdiff \| tree
2018-03-13	Berk Hess	Fix AWH ensemble checkpointing	commit \| commitdiff \| tree
2018-03-13	Berk Hess	Fix AWH deconvolution when sharing a bias	commit \| commitdiff \| tree
2018-03-09	Berk Hess	Correct pdb2gmx -missing option	commit \| commitdiff \| tree
2018-03-07	Berk Hess	Fix memory leak in PME	commit \| commitdiff \| tree
2018-03-06	Berk Hess	Convert t_filenm to C++	commit \| commitdiff \| tree
2018-03-06	Berk Hess	Make multi-atom TPI reproducible	commit \| commitdiff \| tree
2018-03-05	Berk Hess	Work around gcc bug with group kernel tables	commit \| commitdiff \| tree
2018-03-05	Berk Hess	Leave nullptr opt in t_filenm	commit \| commitdiff \| tree
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