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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	Only use fshift when needed	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
2019-06-19	Berk Hess	Removed unused code paths in the NB FE kernel	commit \| commitdiff \| tree
2019-06-18	Berk Hess	Make forcerec const in dispatchNonbondedKernel()	commit \| commitdiff \| tree
2019-06-17	Berk Hess	Simplify GPU nbnxm x conversion	commit \| commitdiff \| tree
2019-06-17	Berk Hess	Remove unused nbnxm include files	commit \| commitdiff \| tree
2019-06-11	Berk Hess	Allow AWH geometry 'direction' to be periodic	commit \| commitdiff \| tree
2019-06-10	Berk Hess	Fix gmx wham with angle geometries	commit \| commitdiff \| tree
2019-06-05	Berk Hess	Fix reference SIMD memory alignment	commit \| commitdiff \| tree
2019-05-29	Berk Hess	Fix missing intermolecular interactions with DD	commit \| commitdiff \| tree
2019-05-27	Berk Hess	Work around gcc 7 avx512 bug	commit \| commitdiff \| tree
2019-05-23	Berk Hess	Fix SHAKE dH/dlambda contributions	commit \| commitdiff \| tree
2019-05-14	Berk Hess	Make all do_force_lowlevel() input const	commit \| commitdiff \| tree
2019-05-14	Berk Hess	Correct user guide postion restraint virial	commit \| commitdiff \| tree
2019-05-04	Berk Hess	Remove PME exclusion correction	commit \| commitdiff \| tree
2019-05-03	Berk Hess	Removed non-existent AWH mdp option	commit \| commitdiff \| tree
2019-05-03	Berk Hess	Convert manage_threading_t and gmx_enerdata_t to C++	commit \| commitdiff \| tree
2019-05-02	Berk Hess	Change nbnxm FEP pointer to unique_ptr	commit \| commitdiff \| tree
2019-04-30	Berk Hess	Add con/destructor for t_forcetable	commit \| commitdiff \| tree
2019-04-30	Berk Hess	Convert DispersionCorrection to a class	commit \| commitdiff \| tree
2019-04-18	Berk Hess	Remove nbnxm kernel type from pairlist generation	commit \| commitdiff \| tree
2019-04-18	Berk Hess	Remove charge groups from domdec and localtop	commit \| commitdiff \| tree
2019-04-18	Berk Hess	Fix pdb-related issues	commit \| commitdiff \| tree
2019-04-17	Berk Hess	Remove group scheme search code	commit \| commitdiff \| tree
2019-04-17	Berk Hess	Simplify vsite PBC handling	commit \| commitdiff \| tree
2019-04-17	Berk Hess	Reduce nbnxm CPU kernel arguments	commit \| commitdiff \| tree
2019-04-17	Berk Hess	Simplify nbnxm shift force handling	commit \| commitdiff \| tree
2019-04-16	Berk Hess	Simplify nbnxm buffer clearing	commit \| commitdiff \| tree
2019-04-16	Berk Hess	Remove RF_excl_correction()	commit \| commitdiff \| tree
2019-04-16	Berk Hess	Make mdrun -nsteps work again.	commit \| commitdiff \| tree
2019-04-15	Berk Hess	Update 2019 release notes for issue 2845	commit \| commitdiff \| tree
2019-04-15	Berk Hess	Fix pdb-related issues	commit \| commitdiff \| tree
2019-04-15	Berk Hess	Disallow pull geometry direction-periodic with AWH	commit \| commitdiff \| tree
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