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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
2019-05-14	Berk Hess	Make all do_force_lowlevel() input const	commit \| commitdiff \| tree
2019-05-04	Berk Hess	Remove PME exclusion correction	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
2019-03-28	Berk Hess	Simplify nbnxm final force reduction	commit \| commitdiff \| tree
2019-03-28	Berk Hess	Move early return for nbnxm force reduction	commit \| commitdiff \| tree
2019-03-28	Berk Hess	Move PairlistSet declaration	commit \| commitdiff \| tree
2019-03-28	Berk Hess	Move nbnxm domainSetup to GridSet	commit \| commitdiff \| tree
2019-03-28	Berk Hess	Extract nbnxm PairlistSets	commit \| commitdiff \| tree
2019-03-27	Berk Hess	Fix nbnxm OpenCL with cluster size 4	commit \| commitdiff \| tree
2019-03-25	Berk Hess	Convert nbnxn_pairlist_set_t to class PairlistSet	commit \| commitdiff \| tree
2019-03-20	Berk Hess	Move around PairSearch code	commit \| commitdiff \| tree
2019-03-19	Berk Hess	Reduce dependencies of nbnxn_atomdata_t	commit \| commitdiff \| tree
2019-03-15	Berk Hess	Change nbnxn_search to class PairSearch	commit \| commitdiff \| tree
2019-03-15	Berk Hess	Extract DomainSetup from nbnxn_search	commit \| commitdiff \| tree
2019-03-14	Berk Hess	Change nbnxm macros to constexpr	commit \| commitdiff \| tree
2019-03-14	Berk Hess	Move functions to gridset.cpp	commit \| commitdiff \| tree
2019-03-14	Berk Hess	Add nbnxm GridSet class	commit \| commitdiff \| tree
2019-03-14	Berk Hess	Fix compilation issue	commit \| commitdiff \| tree
2019-03-12	Berk Hess	Move nbnxm atom macros to atomdata.h	commit \| commitdiff \| tree
2019-03-08	Berk Hess	Clean up calc_verlet_buffer_size()	commit \| commitdiff \| tree
2019-03-06	Berk Hess	Clean up nbnxm bounding box functions	commit \| commitdiff \| tree
2019-03-06	Berk Hess	Clean up nbnxm bounding boxes	commit \| commitdiff \| tree
2019-03-06	Berk Hess	Convert nbnxm bounding box to a struct	commit \| commitdiff \| tree
2019-03-05	Berk Hess	Fix post-submit warnings	commit \| commitdiff \| tree
2019-03-05	Berk Hess	Move nbnxm atomdata types to atomdata.h	commit \| commitdiff \| tree
2019-03-05	Berk Hess	Turn nbnxn_grid_t into a class	commit \| commitdiff \| tree
2019-02-28	Berk Hess	Use unique_ptr in nonbonded_verlet_t	commit \| commitdiff \| tree
2019-02-27	Berk Hess	Use new/delete for t_forcerec	commit \| commitdiff \| tree
2019-02-27	Berk Hess	Clean up dispersioncorrection.cpp	commit \| commitdiff \| tree
2019-02-27	Berk Hess	Fix 4 compilers warnings	commit \| commitdiff \| tree
2019-02-27	Berk Hess	Collect dispersion correction code	commit \| commitdiff \| tree
2019-02-26	Berk Hess	Correct grompp index file error message	commit \| commitdiff \| tree
2019-02-26	Berk Hess	Clean up mtop pbc functions	commit \| commitdiff \| tree
2019-02-23	Berk Hess	Move all nbnxm pruning details into module	commit \| commitdiff \| tree
2019-02-23	Berk Hess	Hide internals of nbnxm parlist	commit \| commitdiff \| tree
2019-02-22	Berk Hess	Formalize dynamic pruning with GPU emulation	commit \| commitdiff \| tree
2019-02-21	Berk Hess	Move free-energy kernel dispatch into nbnxm module	commit \| commitdiff \| tree
2019-02-21	Berk Hess	Minor nbnxm cleanup	commit \| commitdiff \| tree
2019-02-21	Berk Hess	Clean up nbnxm enums	commit \| commitdiff \| tree
2019-02-21	Berk Hess	Simplify make_pairlist() call signature	commit \| commitdiff \| tree
2019-02-20	Berk Hess	Add havePPDomainDecomposition()	commit \| commitdiff \| tree
2019-02-20	Berk Hess	Refactor DLB region handling	commit \| commitdiff \| tree
2019-02-17	Berk Hess	Use enum class for nbnxm locality	commit \| commitdiff \| tree
2019-02-17	Berk Hess	Extract nbnxm grid.h and pairlistwork.h	commit \| commitdiff \| tree
2019-02-17	Berk Hess	Fix compiler warnings	commit \| commitdiff \| tree
2019-02-17	Berk Hess	Move nbnxm details from sim_util.cpp to module	commit \| commitdiff \| tree
2019-02-16	Berk Hess	Move nbnxn files to nbnxm directory	commit \| commitdiff \| tree
2019-02-15	Berk Hess	Fix mass Delta H double counting	commit \| commitdiff \| tree
2019-02-09	Berk Hess	Disallow rerun with perturbed masses or constraints	commit \| commitdiff \| tree
2019-02-06	Berk Hess	Fix segfault with EM, DD and group scheme	commit \| commitdiff \| tree
2019-02-01	Berk Hess	Fix incorrect LJ repulsion force switching on GPUs	commit \| commitdiff \| tree
2019-01-25	Berk Hess	Fix LINCS bug from recent commit 211039fc	commit \| commitdiff \| tree
2019-01-23	Berk Hess	Fix error with 2D/3D DLB	commit \| commitdiff \| tree
2019-01-22	Berk Hess	Add utility method to NbnxnPairlistGpu	commit \| commitdiff \| tree
2019-01-22	Berk Hess	Remove now usused GPU alloc/free functions	commit \| commitdiff \| tree
2019-01-22	Berk Hess	Convert NbnxnPairlistGpu to C++	commit \| commitdiff \| tree
2019-01-21	Berk Hess	Convert nbnxn_atomdata_t to C++	commit \| commitdiff \| tree
2019-01-16	Berk Hess	Rename HostVector to PaddedHostVector	commit \| commitdiff \| tree
2019-01-10	Berk Hess	Split nbnxn_atomdata_init()	commit \| commitdiff \| tree
2019-01-10	Berk Hess	Change grid pointers in nbnxn search to references	commit \| commitdiff \| tree
2019-01-10	Berk Hess	Split nbnxn_list_work_t and change to C++	commit \| commitdiff \| tree
2019-01-10	Berk Hess	Use std::vector in NbnxnPairlistCpu	commit \| commitdiff \| tree
2019-01-09	Berk Hess	Fix gcc-8 release warnings in tng_io	commit \| commitdiff \| tree
2019-01-09	Berk Hess	Added DefaultInitializationAllocator	commit \| commitdiff \| tree
2019-01-04	Berk Hess	Split nbnxn pairlist types for CPU and GPU	commit \| commitdiff \| tree
2019-01-04	Berk Hess	Replace NBNXN_CPU_CLUSTER_I_SIZE by c_nbnxnCpuIClusterSize	commit \| commitdiff \| tree
2019-01-03	Berk Hess	Fix segmentation fault in DD code	commit \| commitdiff \| tree
2018-12-27	Berk Hess	Use AtomPair for LINCS indexing	commit \| commitdiff \| tree
2018-12-27	Berk Hess	Use arrayref in LINCS	commit \| commitdiff \| tree
2018-12-21	Berk Hess	Improve nbnxn cjFromCi() function	commit \| commitdiff \| tree
2018-12-18	Berk Hess	Use std::vector in LINCS	commit \| commitdiff \| tree
2018-12-14	Berk Hess	Fix LINCS triangle constraining with OpenMP	commit \| commitdiff \| tree
2018-12-14	Berk Hess	Fixed nullptr derefence in LINCS error	commit \| commitdiff \| tree
2018-12-14	Berk Hess	Fix LINCS triangle constraining with OpenMP	commit \| commitdiff \| tree
2018-12-12	Berk Hess	Temporary fix for OpenCL PME gather	commit \| commitdiff \| tree
2018-12-11	Berk Hess	Fix update groups with 2D/3D DLB	commit \| commitdiff \| tree
2018-12-11	Berk Hess	Make large PME grids work on GPU	commit \| commitdiff \| tree
2018-12-11	Berk Hess	Document mdrun mdp option modification	commit \| commitdiff \| tree
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