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2013-08-25	Berk Hess	introduced nbnxn data structure for bounding boxes	commit \| commitdiff \| tree
2013-08-20	Berk Hess	fixed parallel normal modes with PME	commit \| commitdiff \| tree
2013-07-24	Berk Hess	implemented plain-C SIMD macros for reference	commit \| commitdiff \| tree
2013-06-20	Berk Hess	fixed SD and BD integrator OpenMP performance	commit \| commitdiff \| tree
2013-06-20	Berk Hess	flops table now reports CUDA analytical Ewald	commit \| commitdiff \| tree
2013-06-14	Berk Hess	fixed minor g_bar output issues	commit \| commitdiff \| tree
2013-06-05	Berk Hess	fixed DD internal state corruption with energy minimization	commit \| commitdiff \| tree
2013-06-03	Berk Hess	fixed deadlock with replica exchange and -maxh	commit \| commitdiff \| tree
2013-05-08	Berk Hess	fixed incorrect scaling of cos-acceleration viscosity	commit \| commitdiff \| tree
2013-04-29	Berk Hess	general SIMD acceleration for angles+dihedrals	commit \| commitdiff \| tree
2013-04-26	Berk Hess	PME load balancing now checks for PME grid restrictions	commit \| commitdiff \| tree
2013-04-18	Berk Hess	changed mdrun -nsteps to gmx_large_int_t	commit \| commitdiff \| tree
2013-04-12	Berk Hess	improved load balancing with Verlet cut-off scheme	commit \| commitdiff \| tree
2013-03-27	Berk Hess	removed x86 specifics from nbnxn SIMD kernels	commit \| commitdiff \| tree
2013-03-27	Berk Hess	corrected log file wall time breakdown	commit \| commitdiff \| tree
2013-03-21	Berk Hess	made PME work with a mix of 1 and more threads	commit \| commitdiff \| tree
2013-03-14	Berk Hess	corrected grompp rvdw charge-group radii check	commit \| commitdiff \| tree
2013-03-05	Berk Hess	fixed bug with DD cut-off check and PME DLB	commit \| commitdiff \| tree
2013-03-05	Berk Hess	fixed recent bug with sorting atoms for GPUs	commit \| commitdiff \| tree
2013-02-26	Berk Hess	fixed PME time print with -ntomp_pme != -ntomp	commit \| commitdiff \| tree
2013-02-20	Berk Hess	added mdrun check for Verlet+perturbed atoms	commit \| commitdiff \| tree
2013-02-20	Berk Hess	fixed issues with FEP soft-core and cut-off's	commit \| commitdiff \| tree
2013-02-18	Berk Hess	fixed GPU particle gridding performance issue	commit \| commitdiff \| tree
2013-02-15	Berk Hess	improved PME load balancing reporting	commit \| commitdiff \| tree
2013-02-06	Berk Hess	fixed bug with sd integrator and OpenMP threading	commit \| commitdiff \| tree
2013-02-05	Berk Hess	improved load balancing on the GPU	commit \| commitdiff \| tree
2013-02-04	Berk Hess	fixed segv in init_forcerec with fr->hwinfo=NULL	commit \| commitdiff \| tree
2013-02-01	Berk Hess	PME-only counters are now reset with -maxh -resethway	commit \| commitdiff \| tree
2013-01-18	Berk Hess	thread affinity now uses some topology information	commit \| commitdiff \| tree
2013-01-17	Berk Hess	fixed SD+BD integration slowing down with OpenMP threads	commit \| commitdiff \| tree
2013-01-17	Berk Hess	improved CUDA kernel performance by pre-loading cj	commit \| commitdiff \| tree
2013-01-17	Berk Hess	fixed nbnxn hybrid mode with OpenMP	commit \| commitdiff \| tree
2013-01-17	Berk Hess	made PME load balancing + DD DLB more efficient	commit \| commitdiff \| tree
2013-01-16	Berk Hess	split off pick_nbnxn_resource from nbnxn_pick_nbnxn	commit \| commitdiff \| tree
2013-01-13	Berk Hess	fixed resetting states with parallel Verlet scheme	commit \| commitdiff \| tree
2013-01-12	Berk Hess	prepared the nbnxn code for non-x86 SIMD	commit \| commitdiff \| tree
2013-01-11	Berk Hess	made SHAKE work again with particle decompostion	commit \| commitdiff \| tree
2013-01-10	Berk Hess	fixed nbnxn no LJ comb.rule AVX256 PME kernel	commit \| commitdiff \| tree
2013-01-10	Berk Hess	fixed bug with Verlet + DD + bonded atom communication	commit \| commitdiff \| tree
2013-01-07	Berk Hess	fixed nbnxn AVX-256 Ewald table pointer alignment	commit \| commitdiff \| tree
2013-01-02	Berk Hess	minor speed-up and code clean-up in nbnxn kernels	commit \| commitdiff \| tree
2012-12-20	Berk Hess	fixed recent bugs in LINCS for derivatives	commit \| commitdiff \| tree
2012-12-18	Berk Hess	renamed gmx_x86_simd_macros.h to gmx_simd_macros.h	commit \| commitdiff \| tree
2012-12-18	Berk Hess	implemented nbnxn AVX-256 2x(N+N) kernels	commit \| commitdiff \| tree
2012-12-11	Berk Hess	reduced PLINCS communication with H-bond constraints	commit \| commitdiff \| tree
2012-12-07	Berk Hess	fixed GPU pair-search with GMX_CPU_ACCELERATION=None	commit \| commitdiff \| tree
2012-12-06	Berk Hess	removed last OpenMP O(nthreads) bottleneck	commit \| commitdiff \| tree
2012-12-05	Berk Hess	fixed incorrect virial with virtual sites and OpenMP	commit \| commitdiff \| tree
2012-12-05	Berk Hess	fixed segv in Verlet pair-search with trilinic DD	commit \| commitdiff \| tree
2012-11-30	Berk Hess	fixed issue with -multi and GPUs	commit \| commitdiff \| tree
2012-11-28	Berk Hess	fixed thread pinning with mdrun -multi	commit \| commitdiff \| tree
2012-11-28	Berk Hess	extended nbnxn x86 SIMD kernel blendv support	commit \| commitdiff \| tree
2012-11-27	Berk Hess	fixed bug in nbnxn OpenMP non-bonded force reduction	commit \| commitdiff \| tree
2012-11-26	Berk Hess	made nbnxn analytical Ewald consistent	commit \| commitdiff \| tree
2012-11-26	Berk Hess	added nbnxn analytical Ewald correction kernels	commit \| commitdiff \| tree
2012-11-16	Berk Hess	reduced the cost of the nbnxn OpenMP nb-force reduction	commit \| commitdiff \| tree
2012-11-15	Berk Hess	fixed incorrect 1-4 energies with OpenMP + energy groups	commit \| commitdiff \| tree
2012-11-14	Berk Hess	fixed nbnxn x86 SIMD non-bonded performance regression	commit \| commitdiff \| tree
2012-11-12	Berk Hess	nbnxn CPU force buffer reduction now uses SIMD	commit \| commitdiff \| tree
2012-11-06	Berk Hess	Merge "Add option to install libcudart" into release-4-6	commit \| commitdiff \| tree
2012-11-06	Berk Hess	Merge "don't execute any mpi_info/mpiname in the path...	commit \| commitdiff \| tree
2012-11-05	Berk Hess	Merge "updated several things related with OpenMP thread...	commit \| commitdiff \| tree
2012-11-05	Berk Hess	updated several things related with OpenMP thread count	commit \| commitdiff \| tree
2012-10-26	Berk Hess	fixed incorrect PME load balancing limitation	commit \| commitdiff \| tree
2012-10-26	Berk Hess	set the default for nstdhdl to 100	commit \| commitdiff \| tree
2012-10-26	Berk Hess	fixed incorrect group energies with nbnxn CPU kernels	commit \| commitdiff \| tree
2012-10-23	Berk Hess	fixed bondfree.c thread safety with free energy	commit \| commitdiff \| tree
2012-10-23	Berk Hess	moved part of nbnxn_search.c to nbnxn_atomdata.c	commit \| commitdiff \| tree
2012-10-23	Berk Hess	fixed incorrect LJ energy with GPU and PME load balancing	commit \| commitdiff \| tree
2012-10-22	Berk Hess	added OpenMP parallelization for virtual sites	commit \| commitdiff \| tree
2012-10-18	Berk Hess	renamed constraint variables rmdr to vir_r_m_dr	commit \| commitdiff \| tree
2012-10-18	Berk Hess	added OpenMP parallelization to LINCS projection	commit \| commitdiff \| tree
2012-10-17	Berk Hess	renamed pme_switch... to pme_loadbal...	commit \| commitdiff \| tree
2012-10-16	Berk Hess	made pair-search with GPU 20% faster	commit \| commitdiff \| tree
2012-10-12	Berk Hess	Merge "Fix illegal barrier in worksharing" into release-4-6	commit \| commitdiff \| tree
2012-10-08	Berk Hess	made non-bonded potential shifts mdp options	commit \| commitdiff \| tree
2012-10-04	Berk Hess	fixed backward compatibility of tpr files with dihres	commit \| commitdiff \| tree
2012-10-03	Berk Hess	improved the energy conservation with SETTLE	commit \| commitdiff \| tree
2012-09-13	Berk Hess	fixed recent bug with grompp check for P-R P-coupling	commit \| commitdiff \| tree
2012-08-29	Berk Hess	bug fix for pme.c MPI_COMM_NULL fix dcf8b67e	commit \| commitdiff \| tree
2012-08-09	Berk Hess	fixed trjconv not writing velocities with cpt input	commit \| commitdiff \| tree
2012-08-06	Berk Hess	fixed incorrect TPI results with dynamic box	commit \| commitdiff \| tree
2012-07-18	Berk Hess	fixed DD charge group displacement error check	commit \| commitdiff \| tree
2012-07-17	Berk Hess	fix a segfault in sse_mask_init	commit \| commitdiff \| tree
2012-07-04	Berk Hess	set default for rcoulomb, rvdw and rlist to -1	commit \| commitdiff \| tree
2012-06-25	Berk Hess	fixed segv/hang with EM and foreign lambda values	commit \| commitdiff \| tree
2012-06-25	Berk Hess	added check for log fp!=NULL when disabling acceleration	commit \| commitdiff \| tree
2012-05-24	Berk Hess	now mdrun always initializes MPI	commit \| commitdiff \| tree
2012-05-21	Berk Hess	grompp now retains the order of bonds converted to...	commit \| commitdiff \| tree
2012-05-21	Berk Hess	re-introduced fix for real/double issue in gmx_density	commit \| commitdiff \| tree
2012-05-08	Berk Hess	fixed mdrun -cpi SD and pcoupl initialization	commit \| commitdiff \| tree
2012-04-28	Berk Hess	fixed PME forces with FE, fixes #929 introduced in...	commit \| commitdiff \| tree
2012-04-27	Berk Hess	fixed segv in TPI with PME, fixes #927	commit \| commitdiff \| tree
2012-04-27	Berk Hess	changed PME MPI_Comm comparisions to MPI_COMM_NULL...	commit \| commitdiff \| tree
2012-04-27	Berk Hess	changed number of iatoms for F_SETTLE from 1 to 3	commit \| commitdiff \| tree
2012-04-26	Berk Hess	added support for graphs not starting at 0	commit \| commitdiff \| tree
2012-04-26	Berk Hess	Merge "Merge release-4-5-patches into release-4-6"...	commit \| commitdiff \| tree
2012-04-26	Berk Hess	Merge release-4-5-patches into release-4-6	commit \| commitdiff \| tree
2012-04-26	Berk Hess	fixed the reported temperature with Brownian dynamics	commit \| commitdiff \| tree
2012-04-26	Berk Hess	fixed dispersion correction with parallel EM	commit \| commitdiff \| tree
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