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2021-05-05	Joe Jordan	Remove mdatoms from coupling code and use more ArrayRef	commit \| commitdiff \| tree
2021-05-04	Joe Jordan	Apply clang-tidy11 to statistics	commit \| commitdiff \| tree
2021-05-03	Joe Jordan	ArrayRef in pme	commit \| commitdiff \| tree
2021-04-27	Joe Jordan	Apply clang-tidy11 to mdrun	commit \| commitdiff \| tree
2021-04-27	Joe Jordan	Unify constructor of nbnxn_atomdata_t	commit \| commitdiff \| tree
2021-04-27	Joe Jordan	Constructor for t_mde_delta_h_coll	commit \| commitdiff \| tree
2021-04-26	Joe Jordan	Remove inputrec from initialize_lambdas signature	commit \| commitdiff \| tree
2021-04-22	Joe Jordan	Vectors in history_t	commit \| commitdiff \| tree
2021-04-21	Joe Jordan	Mostly remove t_mdatoms from update signatures	commit \| commitdiff \| tree
2021-04-21	Joe Jordan	clang-tidy-11 fixes for gmxpreprocess	commit \| commitdiff \| tree
2021-04-21	Joe Jordan	Rename some enum names in ModuleMultiThread	commit \| commitdiff \| tree
2021-04-20	Joe Jordan	clang-tidy-11 fixes for topology, gpu_utils, and selection	commit \| commitdiff \| tree
2021-04-20	Joe Jordan	Use enum class for gmx_omp_nthreads	commit \| commitdiff \| tree
2021-04-20	Joe Jordan	clang-tidy-11 fixes for utils	commit \| commitdiff \| tree
2021-04-14	Joe Jordan	Pass forcerec arguments instead of forcerec to gmx_nb_free_e...	commit \| commitdiff \| tree
2021-04-13	Joe Jordan	Use array for term and foreign_term in gmx_enerdata_t	commit \| commitdiff \| tree
2021-04-12	Joe Jordan	Pass cFREEZE and cTC to update after DD partitioning	commit \| commitdiff \| tree
2021-04-12	Joe Jordan	Expose init_interaction_const and move to correct header...	commit \| commitdiff \| tree
2021-04-12	Joe Jordan	Replace defines with constexpr in ishift	commit \| commitdiff \| tree
2021-04-12	Joe Jordan	Add a fourth coordinate to virial tests	commit \| commitdiff \| tree
2021-04-11	Joe Jordan	Pass ref_t to initialize_lambdas	commit \| commitdiff \| tree
2021-03-31	Joe Jordan	ArrayRefs and const refs in global_stat	commit \| commitdiff \| tree
2021-03-31	Joe Jordan	Use more ArrayRefs in signatures of update impl class	commit \| commitdiff \| tree
2021-03-29	Joe Jordan	Add tests for calcvir	commit \| commitdiff \| tree
2021-03-29	Joe Jordan	Move nsgrid header/source from mdlib to domdec	commit \| commitdiff \| tree
2021-03-26	Joe Jordan	Use ArrayRefs instead of mdatoms in gmx_nb_free_energy_kerne...	commit \| commitdiff \| tree
2021-03-25	Joe Jordan	Use more vectors for EnergyOutput private members	commit \| commitdiff \| tree
2021-03-25	Joe Jordan	Constructor for t_tabledata	commit \| commitdiff \| tree
2021-03-25	Joe Jordan	Use ArrayRef in special forces	commit \| commitdiff \| tree
2021-03-25	Joe Jordan	Use ArrayRef in signatures of constraints and some...	commit \| commitdiff \| tree
2021-03-23	Joe Jordan	Modernize t_nrnb	commit \| commitdiff \| tree
2021-03-23	Joe Jordan	Use ArrayRef in calc_mu	commit \| commitdiff \| tree
2021-03-19	Joe Jordan	Use more arrayref in listed forces sigatures	commit \| commitdiff \| tree
2021-03-19	Joe Jordan	Use ArrayRef in ewald_LRcorrection	commit \| commitdiff \| tree
2021-03-19	Joe Jordan	Make non bonded energy terms enum class	commit \| commitdiff \| tree
2021-03-16	Joe Jordan	Use RVec and std::array in gmx_domdec_comm_t	commit \| commitdiff \| tree
2021-03-16	Joe Jordan	Remove conditional assignemnt of cell sizes from domdec...	commit \| commitdiff \| tree
2021-03-10	Joe Jordan	Remove param fillLocal, which was always false, from...	commit \| commitdiff \| tree
2021-03-09	Joe Jordan	Use constexpr for physical constants and move them...	commit \| commitdiff \| tree
2021-03-01	Joe Jordan	Use const ref for mtop and inputrec in EnergyOutput...	commit \| commitdiff \| tree
2021-02-28	Joe Jordan	Use more const ref in domdec API	commit \| commitdiff \| tree
2021-02-26	Joe Jordan	Only use const ref for mtop and inputrec in domdec	commit \| commitdiff \| tree
2021-02-23	Joe Jordan	Use verbose names in init_forcerec	commit \| commitdiff \| tree
2021-02-22	Joe Jordan	Hold unique_ptr to gmx_ewald_tab_t in forcerec	commit \| commitdiff \| tree
2021-02-22	Joe Jordan	Hold unique_ptr for interaction_const in forcerec	commit \| commitdiff \| tree
2021-02-20	Joe Jordan	Remove unsed structs from nblist and use vector in...	commit \| commitdiff \| tree
2021-02-19	Joe Jordan	Revome unused code from nsgrid	commit \| commitdiff \| tree
2021-02-19	Joe Jordan	Use const refs in init_nb_verlet	commit \| commitdiff \| tree
2021-02-19	Joe Jordan	Rename and add doxygen to reaction field params in...	commit \| commitdiff \| tree
2021-02-18	Joe Jordan	Use unique_ptr for forcerec in runner	commit \| commitdiff \| tree
2021-02-16	Joe Jordan	Use const ref to inputrec in do_force	commit \| commitdiff \| tree
2021-02-11	Joe Jordan	Use unique_ptr for tables	commit \| commitdiff \| tree
2021-02-05	Joe Jordan	Use raw strings instead of format in docker build script	commit \| commitdiff \| tree
2021-01-25	Joe Jordan	Check availability of compile flags at cmake time	commit \| commitdiff \| tree
2020-11-17	Joe Jordan	Remove some extraneous compiler flags from nblib	commit \| commitdiff \| tree
2020-11-09	Joe Jordan	Add backend for nblib listed forces API	commit \| commitdiff \| tree
2020-11-04	Joe Jordan	NBLIB listed forces API update	commit \| commitdiff \| tree
2020-10-30	Joe Jordan	Introduce nblib versioning	commit \| commitdiff \| tree
2020-10-13	Joe Jordan	Fix segfault in pull reading	commit \| commitdiff \| tree
2020-10-02	Joe Jordan	Add tests for setStringEntry	commit \| commitdiff \| tree
2020-09-30	Joe Jordan	Add nblib sample script	commit \| commitdiff \| tree
2020-09-29	Joe Jordan	Add nblib backend: Part 2 of 2	commit \| commitdiff \| tree
2020-09-28	Joe Jordan	Add nblib backend: Part 1 of 2	commit \| commitdiff \| tree
2020-09-28	Joe Jordan	Add initial nblib public API	commit \| commitdiff \| tree
2020-09-10	Joe Jordan	Replace GMX_ASSERT with assert in vectypes.h	commit \| commitdiff \| tree
2020-07-03	Joe Jordan	Use vector in atoms2md instead of pointer	commit \| commitdiff \| tree
2020-06-23	Joe Jordan	Remove some headers from install targets	commit \| commitdiff \| tree
2018-11-19	Joe Jordan	fix unused variable warning from gmxapi compilation	commit \| commitdiff \| tree
2018-11-12	Joe Jordan	Add coolquotes	commit \| commitdiff \| tree
2018-10-23	Joe Jordan	Properly attribute work and use correct dates for binaryinfo...	commit \| commitdiff \| tree
2018-09-17	Joe Jordan	Refactor pdb2gmx in c++ framework	commit \| commitdiff \| tree
2018-09-16	Joe Jordan	Move variables around in pdb2gmx	commit \| commitdiff \| tree
2018-08-24	Joe Jordan	change some char to string in gmxpreprocess	commit \| commitdiff \| tree
2018-08-22	Joe Jordan	Fix pdb2gmx -chainsep	commit \| commitdiff \| tree
2018-08-14	Joe Jordan	Add chainsep and merge tests for pdb2gmx	commit \| commitdiff \| tree
2018-07-30	Joe Jordan	remove most debug flags from gmxpreprocess	commit \| commitdiff \| tree
2018-07-17	Joe Jordan	change gmx_bool to bool in gmxpreprocess	commit \| commitdiff \| tree
2018-03-22	Joe Jordan	minor fix to flag strings for gmx potential	commit \| commitdiff \| tree

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