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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
2018-12-05	Berk Hess	Add update groups to parallelization docs	commit \| commitdiff \| tree
2018-12-05	Berk Hess	Make large PME grids work on GPU	commit \| commitdiff \| tree
2018-11-26	Berk Hess	Fix FP exception in pull code	commit \| commitdiff \| tree
2018-11-16	Berk Hess	grompp now checks tau-p>=2*tau-t with NH+PR	commit \| commitdiff \| tree
2018-11-08	Berk Hess	Fix bug with DD for dims without PBC	commit \| commitdiff \| tree
2018-11-01	Berk Hess	Fix broken update groups	commit \| commitdiff \| tree
2018-10-31	Berk Hess	Limit auto assignment of bondeds to GPUs	commit \| commitdiff \| tree
2018-10-31	Berk Hess	Pin important buffers in CUDA bondeds	commit \| commitdiff \| tree
2018-10-31	Berk Hess	Work around expanded ensemble issues	commit \| commitdiff \| tree
2018-10-31	Berk Hess	Fix FP exception in energy reduction	commit \| commitdiff \| tree
2018-10-31	Berk Hess	Correct VV integrator nstcalcenergy use	commit \| commitdiff \| tree
2018-10-31	Berk Hess	Correct grompp nstexpanded/nstcalcenergy check	commit \| commitdiff \| tree
2018-10-26	Berk Hess	Add missing mass term to deltaH	commit \| commitdiff \| tree
2018-10-23	Berk Hess	Add missing constraint term to deltaH	commit \| commitdiff \| tree
2018-10-21	Berk Hess	Fix mdrun start/end time print	commit \| commitdiff \| tree
2018-10-18	Berk Hess	Add env.var. to disable update groups	commit \| commitdiff \| tree
2018-10-12	Berk Hess	Implement assigning bondeds to the GPU	commit \| commitdiff \| tree
2018-10-10	Berk Hess	Move pull output functions to output.cpp	commit \| commitdiff \| tree
2018-10-10	Berk Hess	Minor refactoring in bonded threading	commit \| commitdiff \| tree
2018-10-09	Berk Hess	Fix compiler warning	commit \| commitdiff \| tree
2018-10-08	Berk Hess	Enable update groups	commit \| commitdiff \| tree
2018-10-05	Berk Hess	Add update groups to DD atom displacement	commit \| commitdiff \| tree
2018-10-04	Berk Hess	Make AVX2 pass TSAN	commit \| commitdiff \| tree
2018-10-04	Berk Hess	Add note to avoid constraints=all-bonds	commit \| commitdiff \| tree
2018-10-03	Berk Hess	Remove unnecessary clearing in gmxcpp	commit \| commitdiff \| tree
2018-10-03	Berk Hess	Convert gmx_cpp to C++	commit \| commitdiff \| tree
2018-10-02	Berk Hess	Update DD cutoffs for update groups	commit \| commitdiff \| tree
2018-09-30	Berk Hess	Correct update group angle param type	commit \| commitdiff \| tree
2018-09-29	Berk Hess	Refactoring in calc_verletbuf.cpp	commit \| commitdiff \| tree
2018-09-29	Berk Hess	Add UpdateGroupsCog to DD	commit \| commitdiff \| tree
2018-09-27	Berk Hess	Move maxReferenceTemperature() to inputrec	commit \| commitdiff \| tree
2018-09-27	Berk Hess	Improve update group radii	commit \| commitdiff \| tree
2018-09-27	Berk Hess	Reorganize RVec scaling functions	commit \| commitdiff \| tree
2018-09-26	Berk Hess	Extract settle test water coordinates	commit \| commitdiff \| tree
2018-09-26	Berk Hess	Support atom groups in nbnxn_search	commit \| commitdiff \| tree
2018-09-25	Berk Hess	Add UpdateGroupsCog class	commit \| commitdiff \| tree
2018-09-24	Berk Hess	Fix performance report when init_step!=0	commit \| commitdiff \| tree
2018-09-22	Berk Hess	Add update groups boolean to DD	commit \| commitdiff \| tree
2018-09-22	Berk Hess	Rename DD constraint booleans	commit \| commitdiff \| tree
2018-09-22	Berk Hess	Add update groups	commit \| commitdiff \| tree
2018-09-20	Berk Hess	Change pull buffers to std::vector	commit \| commitdiff \| tree
2018-09-20	Berk Hess	Fix type bug in trilinic DD code	commit \| commitdiff \| tree
2018-09-19	Berk Hess	Convert gmx_cmap_t to C++	commit \| commitdiff \| tree
2018-09-19	Berk Hess	Convert gmx_ffparams_t to C++	commit \| commitdiff \| tree
2018-09-18	Berk Hess	Introduce extractILists helper function	commit \| commitdiff \| tree
2018-09-18	Berk Hess	Refactor ddbox handling	commit \| commitdiff \| tree
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