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2020-01-20	Berk Hess	Use ArrayRef(WithPadding) in constraint code	commit \| commitdiff \| tree
2020-01-20	Berk Hess	Use std::vector in shellfc	commit \| commitdiff \| tree
2020-01-13	Berk Hess	Avoid unnecessary exclusion generation in DD	commit \| commitdiff \| tree
2019-12-22	Berk Hess	Use ListOfLists for atom to constraint mapping	commit \| commitdiff \| tree
2019-12-22	Berk Hess	Move nr_nonperturbed out of t_ilist	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Expand ListOfLists pushBack() functionality	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Remove exclusions from t_topology	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Fix mdrun appending invalidating energy files	commit \| commitdiff \| tree
2019-12-18	Berk Hess	Change grompp decoupling SD warning to note	commit \| commitdiff \| tree
2019-12-17	Berk Hess	Add note for COM removal with position restraints	commit \| commitdiff \| tree
2019-12-16	Berk Hess	Use ListOfLists in gmx_mtop_t and gmx_localtop_t	commit \| commitdiff \| tree
2019-12-16	Berk Hess	Fix issues in ListOfLists	commit \| commitdiff \| tree
2019-12-12	Berk Hess	Add class ListOfLists	commit \| commitdiff \| tree
2019-12-02	Berk Hess	Add check for coupled constraints for CUDA update	commit \| commitdiff \| tree
2019-12-02	Berk Hess	Extract LINCS CUDA helper functions	commit \| commitdiff \| tree
2019-11-29	Berk Hess	Merge "Merge branch release-2019 into release-2020...	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Update documenation for NPT GPU update	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Remove assertion failure in AWH without initial stage	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Fix bug with GPU pressure scaling at non T-scaling...	commit \| commitdiff \| tree
2019-11-26	Berk Hess	Fix issues with AWH with periodic pulling	commit \| commitdiff \| tree
2019-11-20	Berk Hess	Quiet pdb2gmx and use gmx_fatal	commit \| commitdiff \| tree
2019-11-19	Berk Hess	Fix bonded atom communication performance	commit \| commitdiff \| tree
2019-11-18	Berk Hess	Fix intermolecular interactions with DD	commit \| commitdiff \| tree
2019-11-14	Berk Hess	Simplify t_forcerec destruction	commit \| commitdiff \| tree
2019-11-07	Berk Hess	Fix .gro large box writing	commit \| commitdiff \| tree
2019-11-06	Berk Hess	Deprecated sc-r-power=48	commit \| commitdiff \| tree
2019-11-01	Berk Hess	Add haveEwaldSurfaceContribution to SimulationWorkload	commit \| commitdiff \| tree
2019-10-31	Berk Hess	Update GPU update restrictions	commit \| commitdiff \| tree
2019-10-30	Berk Hess	Fix walls with GPU update	commit \| commitdiff \| tree
2019-10-29	Berk Hess	Add mdrun GPU update documentation	commit \| commitdiff \| tree
2019-10-29	Berk Hess	Fix Ewald dipole correction with GPU update	commit \| commitdiff \| tree
2019-10-29	Berk Hess	Disable pressure coupling with GPU update	commit \| commitdiff \| tree
2019-10-24	Berk Hess	Add bool useDomainDecomposition in mdrunner	commit \| commitdiff \| tree
2019-10-24	Berk Hess	Add gmx_mtop_interaction_count()	commit \| commitdiff \| tree
2019-10-24	Berk Hess	Fix initializers in locality.h	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Move locality.h from nbnxm to mdtypes	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Use gmx::Range in Nbnxm gridding functions	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Fix illegal memory access in FE calculations	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Expand documentation for nbnxn_put_on_grid()	commit \| commitdiff \| tree
2019-10-22	Berk Hess	Require -ei for essential dynamics	commit \| commitdiff \| tree
2019-10-18	Berk Hess	Update grompp cutoff-scheme warnings	commit \| commitdiff \| tree
2019-10-15	Berk Hess	Const correctness for genhydro	commit \| commitdiff \| tree
2019-10-12	Berk Hess	Add class FixedCapacityVector	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Increase spc minimization test tolerance	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Fix harmless OpenMP write race	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Fix GPU atom data init timer issue	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Fix random energy and virial with PME on GPU on a PME...	commit \| commitdiff \| tree
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
2019-10-01	Berk Hess	Always output correct kinetic at last step	commit \| commitdiff \| tree
2019-09-30	Berk Hess	Remove charge group code from forcerec	commit \| commitdiff \| tree
2019-09-30	Berk Hess	Actually fix gmx wham with angle geometries	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
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