BioD PNPI Git Repos - alexxy/gromacs.git/search

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2014-09-29	Berk Hess	Avoid PME tuning decreasing rcoulomb	commit \| commitdiff \| tree
2014-09-29	Berk Hess	Fix calc_grid avoiding PME grid factor 84	commit \| commitdiff \| tree
2014-09-09	Berk Hess	Fixed DD state collection issue	commit \| commitdiff \| tree
2014-09-08	Berk Hess	Check for implicit solvent + Verlet scheme	commit \| commitdiff \| tree
2014-08-28	Berk Hess	Fixed two PME issues with MPI+OpenMP	commit \| commitdiff \| tree
2014-08-25	Berk Hess	Fixed bugs in vsiteN with OpenMP	commit \| commitdiff \| tree
2014-08-24	Berk Hess	Initialize unused velocity constraint components	commit \| commitdiff \| tree
2014-08-17	Berk Hess	Halved the cost of the pull communication	commit \| commitdiff \| tree
2014-08-14	Berk Hess	Corrected SIMD math overflow documentation	commit \| commitdiff \| tree
2014-08-10	Berk Hess	Added checks for TPI + Verlet scheme	commit \| commitdiff \| tree
2014-08-05	Berk Hess	Fix hang with LJ-PME and empty domains	commit \| commitdiff \| tree
2014-08-02	Berk Hess	Fixed PME bug with high OpenMP thread count	commit \| commitdiff \| tree
2014-07-31	Berk Hess	Avoid division by 0 in nbnxn_search	commit \| commitdiff \| tree
2014-06-29	Berk Hess	Take LJ-PME into account for table spacing	commit \| commitdiff \| tree
2014-06-29	Berk Hess	Updated LJ-PME documentation	commit \| commitdiff \| tree
2014-06-24	Berk Hess	Fixed the sign of mass perturbed contribution	commit \| commitdiff \| tree
2014-06-20	Berk Hess	Fix g_mindist with pbc=XY	commit \| commitdiff \| tree
2014-06-20	Berk Hess	Fixed shells with particle decomposition	commit \| commitdiff \| tree
2014-06-18	Berk Hess	Fixed sign error in posres dvdl	commit \| commitdiff \| tree
2014-06-17	Berk Hess	Updated mdrun -npme documentation	commit \| commitdiff \| tree
2014-06-17	Berk Hess	Removed rounding issue in nbnxn Ewald table	commit \| commitdiff \| tree
2014-06-14	Berk Hess	Fixed PME bug with #OpenMP-threads a large prime	commit \| commitdiff \| tree
2014-06-13	Berk Hess	Changed appending file name error message	commit \| commitdiff \| tree
2014-06-13	Berk Hess	Made shells work with the Verlet scheme	commit \| commitdiff \| tree
2014-06-12	Berk Hess	Fixed perturbed wall interactions	commit \| commitdiff \| tree
2014-06-12	Berk Hess	Made gmxcheck -rmsd work again with forces	commit \| commitdiff \| tree
2014-06-11	Berk Hess	Decoupled repl_ex_nst from nstcalcenergy	commit \| commitdiff \| tree
2014-06-11	Berk Hess	Made repl_ex time step more readable	commit \| commitdiff \| tree
2014-06-10	Berk Hess	Replaced gmx_hostname_num by gmx_physicalnode_id_hash	commit \| commitdiff \| tree
2014-06-09	Berk Hess	Set make_ndx max name length and count to 1024	commit \| commitdiff \| tree
2014-06-05	Berk Hess	Fixed shift and switch modifiers, particularly for...	commit \| commitdiff \| tree
2014-06-05	Berk Hess	Fix constraint virial with multiple time stepping	commit \| commitdiff \| tree
2014-06-02	Berk Hess	Fixed g_energy Einstein viscosity	commit \| commitdiff \| tree
2014-05-22	Berk Hess	Avoid energy drift with verlet-buffer-tolerance	commit \| commitdiff \| tree
2014-05-09	Berk Hess	Minor tweaks to the DD setup	commit \| commitdiff \| tree
2014-04-29	Berk Hess	Removed truncation of nrdf in v-rescale thermostat	commit \| commitdiff \| tree
2014-04-23	Berk Hess	Fixed nbnxn FE list allocation issue	commit \| commitdiff \| tree
2014-04-02	Berk Hess	Added LJ-PME and LJ Pot-switch to PME load estimate	commit \| commitdiff \| tree
2014-03-24	Berk Hess	Adds cut-off checks for triclinic domain decomposition	commit \| commitdiff \| tree
2014-03-23	Berk Hess	Fixed bug in parallel v/f constraining	commit \| commitdiff \| tree
2014-03-23	Berk Hess	CUDA cut-off kernels now shift exclusion energies	commit \| commitdiff \| tree
2014-03-11	Berk Hess	PME load balancing now works with LJ-PME	commit \| commitdiff \| tree
2014-03-06	Berk Hess	Fixed exit with FEP with PME nodes without LJ-PME	commit \| commitdiff \| tree
2014-03-05	Berk Hess	Buffer estimate now works with rvd-switch=0	commit \| commitdiff \| tree
2014-02-26	Berk Hess	Free-energy now works with the Verlet scheme	commit \| commitdiff \| tree
2014-02-25	Berk Hess	Fixes seperate PME nodes without LJ-PME	commit \| commitdiff \| tree
2014-02-24	Berk Hess	Implemented LJ-PME nbnxn kernels	commit \| commitdiff \| tree
2014-02-24	Berk Hess	Fixed bug with LJ pot-switch in 4xN kernels	commit \| commitdiff \| tree
2014-02-19	Berk Hess	Implemented nbnxn LJ switch functions	commit \| commitdiff \| tree
2014-01-30	Berk Hess	Made reference SIMD work again	commit \| commitdiff \| tree
2014-01-29	Berk Hess	Automated Verlet rlist for NVE simulations	commit \| commitdiff \| tree
2013-12-03	Berk Hess	Removed restriction of one reference pull group	commit \| commitdiff \| tree
2013-12-02	Berk Hess	Made cutoff-scheme=Verlet the default	commit \| commitdiff \| tree
2013-12-02	Berk Hess	Renamed verlet-buffer-drift to verlet-buffer-tolerance	commit \| commitdiff \| tree
2013-12-01	Berk Hess	Fixed zero hardware thread count	commit \| commitdiff \| tree
2013-11-29	Berk Hess	Created SIMD module	commit \| commitdiff \| tree
2013-11-26	Berk Hess	Fixed return value of gmx_mtop_bondeds_free_energy	commit \| commitdiff \| tree
2013-11-15	Berk Hess	corrected potential nbnxn SIMD memory issue	commit \| commitdiff \| tree
2013-11-08	Berk Hess	fix nbnxn atom sorting with distant bondeds	commit \| commitdiff \| tree
2013-11-07	Berk Hess	corrected dynamic load balancing when sharing GPUs	commit \| commitdiff \| tree
2013-11-05	Berk Hess	GPU detection is done once per physical node	commit \| commitdiff \| tree
2013-11-05	Berk Hess	removed (harmless) left-over in nbnxn SIMD kernels	commit \| commitdiff \| tree
2013-10-31	Berk Hess	reorganized GPU detection and selection	commit \| commitdiff \| tree
2013-10-29	Berk Hess	corrected volume with serial NPT replica exchange	commit \| commitdiff \| tree
2013-10-28	Berk Hess	improved the nbnxn buffer size estimate with GPUs	commit \| commitdiff \| tree
2013-10-22	Berk Hess	fixed recent bug with CUDA texture objects	commit \| commitdiff \| tree
2013-10-22	Berk Hess	fixed OpenMP threads being pinned to the same cores	commit \| commitdiff \| tree
2013-10-16	Berk Hess	avoid division by zero in SIMD angles and dihedrals	commit \| commitdiff \| tree
2013-10-16	Berk Hess	fixed a half bin misalignment in gmx_vanhove -or	commit \| commitdiff \| tree
2013-10-11	Berk Hess	introduced general 4-wide SIMD support	commit \| commitdiff \| tree
2013-10-10	Berk Hess	fixed nbnxn 4x8 pair search without AVX	commit \| commitdiff \| tree
2013-10-02	Berk Hess	Fixes reaction field free energy bug	commit \| commitdiff \| tree
2013-09-24	Berk Hess	optimized generic SIMD invsqrt	commit \| commitdiff \| tree
2013-09-21	Berk Hess	fixed multiple distance restraints with OpenMP	commit \| commitdiff \| tree
2013-09-18	Berk Hess	made free energy PME kernel 40% faster	commit \| commitdiff \| tree
2013-09-16	Berk Hess	mdrun without OpenMP with thread-MPI now uses all cores	commit \| commitdiff \| tree
2013-09-13	Berk Hess	corrected grompp constraint/DOF warning with vsites	commit \| commitdiff \| tree
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
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