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2019-10-08	Berk Hess	Make nbnxm a proper module	commit \| commitdiff \| tree
2019-10-08	Berk Hess	Simplify ewald_LRcorrection() call signature	commit \| commitdiff \| tree
2019-10-04	Berk Hess	Fix random energy and virial with PME on GPU on a PME...	commit \| commitdiff \| tree
2019-10-03	Berk Hess	Fix GPU atom data init timer issue	commit \| commitdiff \| tree
2019-10-03	Berk Hess	Use gmx::Range for iZones in pair search	commit \| commitdiff \| tree
2019-10-03	Berk Hess	Fix setting maxNumColumns in Nbnxm::GridSet	commit \| commitdiff \| tree
2019-10-02	Berk Hess	Fix harmless OpenMP write race	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Use gmx::Range in domdec	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Completely remove charge groups	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Simplify DD exclusion counting	commit \| commitdiff \| tree
2019-09-30	Berk Hess	Remove charge group code from forcerec	commit \| commitdiff \| tree
2019-09-29	Berk Hess	Increase ti3p5 minimization test tolerance	commit \| commitdiff \| tree
2019-09-28	Berk Hess	Fix CG minimization with DD	commit \| commitdiff \| tree
2019-09-27	Berk Hess	Extract gmx::Range	commit \| commitdiff \| tree
2019-09-27	Berk Hess	Fix location of angle in vsite figure	commit \| commitdiff \| tree
2019-09-26	Berk Hess	Made mdrun appending work again	commit \| commitdiff \| tree
2019-09-24	Berk Hess	Remove obsolete dd_get_ns_ranges()	commit \| commitdiff \| tree
2019-09-23	Berk Hess	Limit Zen nbnxm kernel choice to Zen 1	commit \| commitdiff \| tree
2019-09-22	Berk Hess	Remove cgs_gl from gmx_domdec_comm_t	commit \| commitdiff \| tree
2019-09-21	Berk Hess	Fix incorrect shift forces for CMAP	commit \| commitdiff \| tree
2019-09-20	Berk Hess	Fix DD 1 pulse checks without DLB	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Remove bLocalCG from DD code	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Remove obsolete make_exclusions_zone_cg()	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Remove charge group data from t_forcerec	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Add haveFreeEnergyWork to DomainLifetimeWorkload flags	commit \| commitdiff \| tree
2019-09-18	Berk Hess	Added free-energy kernel performance note	commit \| commitdiff \| tree
2019-09-18	Berk Hess	Fix incorrect DD ndim assertion	commit \| commitdiff \| tree
2019-09-17	Berk Hess	Remove spurious newline from log file	commit \| commitdiff \| tree
2019-09-17	Berk Hess	Fix todos for update groups	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Remove obsolete mdp option ns-type	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Add virtual site type 2FD	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Remove cut-off schemes from manual	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Add option request 1D DD with 1 pulse	commit \| commitdiff \| tree
2019-09-13	Berk Hess	Fix nonbonded-bench compilation issue	commit \| commitdiff \| tree
2019-09-13	Berk Hess	Add nbnxm kernel benchmark tool	commit \| commitdiff \| tree
2019-09-12	Berk Hess	Updated mdp documentation for group scheme removal	commit \| commitdiff \| tree
2019-09-12	Berk Hess	Fix master not compiling	commit \| commitdiff \| tree
2019-09-12	Berk Hess	Enable TPI with the Verlet cut-off scheme	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Remove incorrect check with rf-zero	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Extract Cartesian data from DDRankSetup	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Rename DDSetup to DDGridSetup	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Clean up PME rank variables	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Refactor init_domain_decomposition()	commit \| commitdiff \| tree
2019-09-06	Berk Hess	Extract getting of DDRankSetup	commit \| commitdiff \| tree
2019-09-06	Berk Hess	Add PP grid info to DDRankSetup	commit \| commitdiff \| tree
2019-09-05	Berk Hess	Extract DDRankSetup from gmx_domdec_comm_t	commit \| commitdiff \| tree
2019-09-05	Berk Hess	Split off getting of the DD setup	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Collect settings for DD in DDSettings	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Extract getting of DDSystemInfo	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Simplify handling of DD bonded distances	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Move constraint and bonded filtering info into DDSystemInfo	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Move update grouping to DDSystemInfo	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Change DD pme force buffer to std::vector	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Initialize all members of gmx_domdec_t	commit \| commitdiff \| tree
2019-09-03	Berk Hess	Extract DDSystemInfo from gmx_domdec_comm_t	commit \| commitdiff \| tree
2019-09-03	Berk Hess	Unify manual and auto DD grid choices	commit \| commitdiff \| tree
2019-09-03	Berk Hess	Remove gmx_domdec_t from dd_choose_grid()	commit \| commitdiff \| tree
2019-09-03	Berk Hess	Extact UnitCellInfo from gmx_domdec_t	commit \| commitdiff \| tree
2019-09-02	Berk Hess	Fix incorrect rvdw on GPU with rvdw<rcoulomb	commit \| commitdiff \| tree
2019-09-02	Berk Hess	Only use fshift when needed	commit \| commitdiff \| tree
2019-08-26	Berk Hess	Fix grompp constraints=all-angles with constraints	commit \| commitdiff \| tree
2019-08-22	Berk Hess	Fix perturbed bonded bug	commit \| commitdiff \| tree
2019-08-20	Berk Hess	Merge two dihedral functions	commit \| commitdiff \| tree
2019-08-20	Berk Hess	Use shiftForces in ForceOuputs	commit \| commitdiff \| tree
2019-08-20	Berk Hess	Make bonded virial computation conditional	commit \| commitdiff \| tree
2019-08-20	Berk Hess	Fix missing bonded forces with CUDA GPUs and DD	commit \| commitdiff \| tree
2019-08-15	Berk Hess	Template bonded interactions on kernel flavor	commit \| commitdiff \| tree
2019-08-09	Berk Hess	Move bonded function table into bonded.cpp	commit \| commitdiff \| tree
2019-08-09	Berk Hess	SIMD acceleration for F_FOURDIHS and F_PIDIHS	commit \| commitdiff \| tree
2019-08-06	Berk Hess	Add ForceWithShiftForces class	commit \| commitdiff \| tree
2019-08-06	Berk Hess	Fix latex formula in reference manual	commit \| commitdiff \| tree
2019-08-05	Berk Hess	Make box const in do_force()	commit \| commitdiff \| tree
2019-08-05	Berk Hess	Change ForceOutputs to a class	commit \| commitdiff \| tree
2019-08-03	Berk Hess	Remove semicolon from GPU TERM macros	commit \| commitdiff \| tree
2019-08-02	Berk Hess	Made gmx disre work with non-consecutively labeled...	commit \| commitdiff \| tree
2019-08-01	Berk Hess	Remove a pointer in t_forcerec	commit \| commitdiff \| tree
2019-08-01	Berk Hess	Fix nbnxm GPU memory reservation issue	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Remove unused CGLO_INITIALIZATION	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Remove vcm removal from compute_globals()	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Add grompp warning with use of GROMOS FF	commit \| commitdiff \| tree
2019-07-31	Berk Hess	Remove need for GROMOS FF in test	commit \| commitdiff \| tree
2019-07-30	Berk Hess	Use invsqrt and cbrt in free energy kernel	commit \| commitdiff \| tree
2019-07-29	Berk Hess	Remove LJ Ewald correction tables	commit \| commitdiff \| tree
2019-07-29	Berk Hess	Add initialization to t_nrnb	commit \| commitdiff \| tree
2019-07-29	Berk Hess	Fix segmentation fault with cosine pulling	commit \| commitdiff \| tree
2019-07-28	Berk Hess	Removed generalized reaction-field	commit \| commitdiff \| tree
2019-07-28	Berk Hess	Convert Ewald correction tables to C++	commit \| commitdiff \| tree
2019-07-26	Berk Hess	Add default initialization to interaction_const_t	commit \| commitdiff \| tree
2019-07-26	Berk Hess	Remove sh_invrc6 from interaction_const_t	commit \| commitdiff \| tree
2019-07-25	Berk Hess	Split canDetectGpus()	commit \| commitdiff \| tree
2019-07-08	Berk Hess	Store nbnxm gridSet data in GridSetData	commit \| commitdiff \| tree
2019-07-05	Berk Hess	Change affinity enum to enum class	commit \| commitdiff \| tree
2019-07-02	Berk Hess	Refactor thread affinity checking	commit \| commitdiff \| tree
2019-07-02	Berk Hess	Re-enable affinity diagonostics with MPI	commit \| commitdiff \| tree
2019-07-01	Berk Hess	Fix MPI deadlock in affinity setting	commit \| commitdiff \| tree
2019-07-01	Berk Hess	Template free-energy kernel on differing coul/vdw soft...	commit \| commitdiff \| tree
2019-06-26	Berk Hess	Remove tabulation from free-energy kernel	commit \| commitdiff \| tree
2019-06-20	Berk Hess	Remove unnecessary #if GMX_MPI in pme code	commit \| commitdiff \| tree
2019-06-20	Berk Hess	Template free-energy kernel on soft-core	commit \| commitdiff \| tree
2019-06-19	Berk Hess	Refactor PME atom handling	commit \| commitdiff \| tree
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