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2021-06-07	ejjordan	Rename some paramters in nblib listed forces	commit \| commitdiff \| tree
2021-06-07	Joe Jordan	Miscellaneous updates from nblib	commit \| commitdiff \| tree
2021-06-06	Joe Jordan	Updates to nblib test infra and tests	commit \| commitdiff \| tree
2021-05-31	ejjordan	Increase const correctness in gmx_pme_send_parameters	commit \| commitdiff \| tree
2021-05-26	ejjordan	Remove foreign energy groups from gmx_enerdata_t	commit \| commitdiff \| tree
2021-05-26	Joe Jordan	Move t_forcetable and table enums to forcetable header	commit \| commitdiff \| tree
2021-05-25	Joe Jordan	Only Pass needed data to nonbonded param setup in forcerec	commit \| commitdiff \| tree
2021-05-24	Joe Jordan	Remove dead members from gmx_pme_t	commit \| commitdiff \| tree
2021-05-24	Joe Jordan	Remove forcerec from dispatchFreeEnergyKernel signature	commit \| commitdiff \| tree
2021-05-20	Joe Jordan	Localize variables in gmx_pme_do	commit \| commitdiff \| tree
2021-05-20	ejjordan	Remove inputrec from do_ewald	commit \| commitdiff \| tree
2021-05-20	Joe Jordan	Localize variables in ewald_LRcorrection	commit \| commitdiff \| tree
2021-05-19	ejjordan	Make TrotterSequence enum class	commit \| commitdiff \| tree
2021-05-19	Joe Jordan	Clean up some headers in mdlib	commit \| commitdiff \| tree
2021-05-19	ejjordan	Remove forcerec and inputrec from ewald_LRcorrection	commit \| commitdiff \| tree
2021-05-19	ejjordan	Remove forcerec from ewald_charge_correction	commit \| commitdiff \| tree
2021-05-18	Joe Jordan	Fix several doxygen errors	commit \| commitdiff \| tree
2021-05-10	Joe Jordan	Fix harmless bug in nonbonded FEP tests	commit \| commitdiff \| tree
2021-05-05	Joe Jordan	Apply clang-tidy11 to tools	commit \| commitdiff \| tree
2021-05-05	ejjordan	Remove dead functions from statistics module	commit \| commitdiff \| tree
2021-05-05	Joe Jordan	Pass ArrayRefs to dispatchNonbondedKernel	commit \| commitdiff \| tree
2021-05-05	Joe Jordan	Remove mdatoms from coupling code and use more ArrayRef	commit \| commitdiff \| tree
2021-05-04	ejjordan	Remove mdatoms from do_walls	commit \| commitdiff \| tree
2021-05-04	ejjordan	Remove mdatoms from vsite	commit \| commitdiff \| tree
2021-05-04	Joe Jordan	Apply clang-tidy11 to statistics	commit \| commitdiff \| tree
2021-05-04	ejjordan	Use enum : bool in commandline test	commit \| commitdiff \| tree
2021-05-04	ejjordan	Preven extension of DDBondedChecking	commit \| commitdiff \| tree
2021-05-03	ejjordan	Remove mdatoms from pairs in listed forces	commit \| commitdiff \| tree
2021-05-03	ejjordan	Remove mdatoms from expanded	commit \| commitdiff \| tree
2021-05-03	Joe Jordan	ArrayRef in pme	commit \| commitdiff \| tree
2021-04-27	ejjordan	Remove leftover function declaration from nbnxm atomdata	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
2021-04-27	ejjordan	Increase const correctness of t_mdatoms use in md.cpp	commit \| commitdiff \| tree
2021-04-26	Joe Jordan	Remove inputrec from initialize_lambdas signature	commit \| commitdiff \| tree
2021-04-26	ejjordan	Apply clang-tidy11 to correlationfunctions	commit \| commitdiff \| tree
2021-04-26	ejjordan	Apply clang-tidy11 to simd	commit \| commitdiff \| tree
2021-04-26	ejjordan	Apply clang-tidy11 to random	commit \| commitdiff \| tree
2021-04-26	ejjordan	Apply clang-tidy11 to commandline	commit \| commitdiff \| tree
2021-04-22	Joe Jordan	Vectors in history_t	commit \| commitdiff \| tree
2021-04-21	ejjordan	Finish removing t_mdatoms from update module	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	ejjordan	Use index instead of pointer in t_mde_delta_h_coll	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
2021-04-20	ejjordan	clang-tidy-11 fixes mdrun tests	commit \| commitdiff \| tree
2021-04-20	ejjordan	clang-tidy-11 fixes for listed_forces	commit \| commitdiff \| tree
2021-04-20	ejjordan	Apply clang-tidy11 to gmxana files with no dependencies	commit \| commitdiff \| tree
2021-04-19	ejjordan	clang-tidy-11 fixes for options	commit \| commitdiff \| tree
2021-04-19	ejjordan	clang-tidy-11 fixes for hardware	commit \| commitdiff \| tree
2021-04-19	ejjordan	clang-tidy-11 fixes for analysisdata	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	ejjordan	Constructor for gmx_ekindata_t	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
2021-04-10	ejjordan	Minor forcerec cleanup	commit \| commitdiff \| tree
2021-04-02	ejjordan	Move domdec/partition into gmx namespace; minor cleanup	commit \| commitdiff \| tree
2021-03-31	Joe Jordan	ArrayRefs and const refs in global_stat	commit \| commitdiff \| tree
2021-03-31	ejjordan	Fix doxygen for updateMDLeapfrogGeneral	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	ejjordan	ArrayRef and const ref in gmx_nb_free_energy_kernel	commit \| commitdiff \| tree
2021-03-25	Joe Jordan	Use ArrayRef in special forces	commit \| commitdiff \| tree
2021-03-25	ejjordan	Fix some doxygen errors	commit \| commitdiff \| tree
2021-03-25	Joe Jordan	Use ArrayRef in signatures of constraints and some...	commit \| commitdiff \| tree
2021-03-24	ejjordan	Remove nb_kernel_data_t	commit \| commitdiff \| tree
2021-03-24	ejjordan	Remove unneeded members from nb_kernel_data_t	commit \| commitdiff \| tree
2021-03-23	ejjordan	Forward declare ArrayRef more and inlcude basedefinitions...	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
2021-03-23	ejjordan	More const ref in shellfc	commit \| commitdiff \| tree
2021-03-22	ejjordan	Use ArrayRef in do_ewald	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
2021-03-19	ejjordan	Use ArrayRef in gmx_pme_send_parameters	commit \| commitdiff \| tree
2021-03-19	ejjordan	Use const refs in atoms2md signature	commit \| commitdiff \| tree
2021-03-17	ejjordan	Use ArrayRef<const real> in gmx_pme_do	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	ejjordan	Move radian-angle conversions to math/utility	commit \| commitdiff \| tree
2021-03-09	Joe Jordan	Use constexpr for physical constants and move them...	commit \| commitdiff \| tree
2021-03-08	ejjordan	Remove includes from math/utilities that are not needed...	commit \| commitdiff \| tree
2021-03-08	Joe Jordan	Correct the dependencies of nblib tests	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
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