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2020-06-24	Berk Hess	Add class ListedForces	commit \| commitdiff \| tree
2020-06-24	Berk Hess	Change grompp disres cost to linear	commit \| commitdiff \| tree
2020-06-23	Berk Hess	Add virtual site with one constructing atom	commit \| commitdiff \| tree
2020-06-22	Berk Hess	Move soft-core parameters to interaction_const_t	commit \| commitdiff \| tree
2020-06-18	Berk Hess	Convert t_forcetable to C++	commit \| commitdiff \| tree
2020-06-05	Berk Hess	Remove COM from SETTLE	commit \| commitdiff \| tree
2020-06-03	Berk Hess	Fix missing PBC in SHAKE	commit \| commitdiff \| tree
2020-06-03	Berk Hess	Turn SettleData into a class	commit \| commitdiff \| tree
2020-05-20	Berk Hess	Remove t_mdatoms from Nbnxm setAtomProperties()	commit \| commitdiff \| tree
2020-05-19	Berk Hess	Refactor print_missing_interactions()	commit \| commitdiff \| tree
2020-05-14	Berk Hess	Extract postProcessForceWithShiftForces()	commit \| commitdiff \| tree
2020-05-12	Berk Hess	Extract helper force buffers to a separate class	commit \| commitdiff \| tree
2020-05-12	Berk Hess	Refactor virtual site interface	commit \| commitdiff \| tree
2020-04-06	Berk Hess	Move force buffer resizing to mdsetup	commit \| commitdiff \| tree
2020-03-20	Berk Hess	Rename class Grid to BiasGrid in AWH module	commit \| commitdiff \| tree
2020-03-19	Berk Hess	Simplify finish_update()	commit \| commitdiff \| tree
2020-03-19	Berk Hess	Remove at_start from t_graph	commit \| commitdiff \| tree
2020-03-18	Berk Hess	Remove use of graph in do_force()	commit \| commitdiff \| tree
2020-03-18	Berk Hess	Use WholeMoleculeTransform for orires and epsilon-surface	commit \| commitdiff \| tree
2020-03-18	Berk Hess	Add WholeMoleculeTransform class	commit \| commitdiff \| tree
2020-03-17	Berk Hess	Convert t_graph to C++	commit \| commitdiff \| tree
2020-03-17	Berk Hess	Disable Ewald dipole correction without DD	commit \| commitdiff \| tree
2020-03-13	Berk Hess	Add tests for Ewald surface terms	commit \| commitdiff \| tree
2020-03-11	Berk Hess	Add tests for graph	commit \| commitdiff \| tree
2020-03-10	Berk Hess	Fix type in range and add tests	commit \| commitdiff \| tree
2020-03-07	Berk Hess	Make shake work without graph	commit \| commitdiff \| tree
2020-03-05	Berk Hess	Add InteractionDefinitions	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix center of mass motion removal with frozen atoms	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix grompp unbound atom check	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix nrdf with partial COMM removal	commit \| commitdiff \| tree
2020-03-02	Berk Hess	Fix too small pairlist buffer on Intel GPUs	commit \| commitdiff \| tree
2020-02-21	Berk Hess	Add fatal error when multisim runs sharing state have...	commit \| commitdiff \| tree
2020-02-15	Berk Hess	Remove 1 pulse DD request	commit \| commitdiff \| tree
2020-02-05	Berk Hess	Actually fix PME forces with FE without perturbed q/LJ	commit \| commitdiff \| tree
2020-02-04	Berk Hess	Actually fix PME forces with FE without perturbed q/LJ	commit \| commitdiff \| tree
2020-01-23	Berk Hess	Fix DD rank count prime check	commit \| commitdiff \| tree
2020-01-22	Berk Hess	Minor cleanup in constraint and shellfc code	commit \| commitdiff \| tree
2020-01-22	Berk Hess	Fix illegal memory access in PME communication	commit \| commitdiff \| tree
2020-01-22	Berk Hess	Clarify COMM/posres grompp note	commit \| commitdiff \| tree
2020-01-20	Berk Hess	Use ArrayRef(WithPadding) in constraint code	commit \| commitdiff \| tree
2020-01-20	Berk Hess	Use std::vector in shellfc	commit \| commitdiff \| tree
2020-01-17	Berk Hess	Add check for shells and GPU update	commit \| commitdiff \| tree
2020-01-16	Berk Hess	Correct fixed redmine issue id from 3297 to 3296	commit \| commitdiff \| tree
2020-01-15	Berk Hess	Fix multisim with parallel simulation	commit \| commitdiff \| tree
2020-01-13	Berk Hess	Avoid unnecessary exclusion generation in DD	commit \| commitdiff \| tree
2019-12-22	Berk Hess	Use ListOfLists for atom to constraint mapping	commit \| commitdiff \| tree
2019-12-22	Berk Hess	Move nr_nonperturbed out of t_ilist	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Expand ListOfLists pushBack() functionality	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Remove exclusions from t_topology	commit \| commitdiff \| tree
2019-12-19	Berk Hess	Fix mdrun appending invalidating energy files	commit \| commitdiff \| tree
2019-12-18	Berk Hess	Change grompp decoupling SD warning to note	commit \| commitdiff \| tree
2019-12-17	Berk Hess	Add note for COM removal with position restraints	commit \| commitdiff \| tree
2019-12-16	Berk Hess	Use ListOfLists in gmx_mtop_t and gmx_localtop_t	commit \| commitdiff \| tree
2019-12-16	Berk Hess	Fix issues in ListOfLists	commit \| commitdiff \| tree
2019-12-12	Berk Hess	Add class ListOfLists	commit \| commitdiff \| tree
2019-12-02	Berk Hess	Add check for coupled constraints for CUDA update	commit \| commitdiff \| tree
2019-12-02	Berk Hess	Extract LINCS CUDA helper functions	commit \| commitdiff \| tree
2019-11-29	Berk Hess	Merge "Merge branch release-2019 into release-2020...	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Update documenation for NPT GPU update	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Remove assertion failure in AWH without initial stage	commit \| commitdiff \| tree
2019-11-28	Berk Hess	Fix bug with GPU pressure scaling at non T-scaling...	commit \| commitdiff \| tree
2019-11-26	Berk Hess	Fix issues with AWH with periodic pulling	commit \| commitdiff \| tree
2019-11-20	Berk Hess	Quiet pdb2gmx and use gmx_fatal	commit \| commitdiff \| tree
2019-11-19	Berk Hess	Fix bonded atom communication performance	commit \| commitdiff \| tree
2019-11-18	Berk Hess	Fix intermolecular interactions with DD	commit \| commitdiff \| tree
2019-11-14	Berk Hess	Simplify t_forcerec destruction	commit \| commitdiff \| tree
2019-11-07	Berk Hess	Fix .gro large box writing	commit \| commitdiff \| tree
2019-11-06	Berk Hess	Deprecated sc-r-power=48	commit \| commitdiff \| tree
2019-11-01	Berk Hess	Add haveEwaldSurfaceContribution to SimulationWorkload	commit \| commitdiff \| tree
2019-10-31	Berk Hess	Update GPU update restrictions	commit \| commitdiff \| tree
2019-10-30	Berk Hess	Fix walls with GPU update	commit \| commitdiff \| tree
2019-10-29	Berk Hess	Add mdrun GPU update documentation	commit \| commitdiff \| tree
2019-10-29	Berk Hess	Fix Ewald dipole correction with GPU update	commit \| commitdiff \| tree
2019-10-29	Berk Hess	Disable pressure coupling with GPU update	commit \| commitdiff \| tree
2019-10-24	Berk Hess	Add bool useDomainDecomposition in mdrunner	commit \| commitdiff \| tree
2019-10-24	Berk Hess	Add gmx_mtop_interaction_count()	commit \| commitdiff \| tree
2019-10-24	Berk Hess	Fix initializers in locality.h	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Move locality.h from nbnxm to mdtypes	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Use gmx::Range in Nbnxm gridding functions	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Fix illegal memory access in FE calculations	commit \| commitdiff \| tree
2019-10-23	Berk Hess	Expand documentation for nbnxn_put_on_grid()	commit \| commitdiff \| tree
2019-10-22	Berk Hess	Require -ei for essential dynamics	commit \| commitdiff \| tree
2019-10-18	Berk Hess	Update grompp cutoff-scheme warnings	commit \| commitdiff \| tree
2019-10-15	Berk Hess	Const correctness for genhydro	commit \| commitdiff \| tree
2019-10-12	Berk Hess	Add class FixedCapacityVector	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Increase spc minimization test tolerance	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Fix harmless OpenMP write race	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Fix GPU atom data init timer issue	commit \| commitdiff \| tree
2019-10-09	Berk Hess	Fix random energy and virial with PME on GPU on a PME...	commit \| commitdiff \| tree
2019-10-08	Berk Hess	Make nbnxm a proper module	commit \| commitdiff \| tree
2019-10-08	Berk Hess	Simplify ewald_LRcorrection() call signature	commit \| commitdiff \| tree
2019-10-04	Berk Hess	Fix random energy and virial with PME on GPU on a PME...	commit \| commitdiff \| tree
2019-10-03	Berk Hess	Fix GPU atom data init timer issue	commit \| commitdiff \| tree
2019-10-03	Berk Hess	Use gmx::Range for iZones in pair search	commit \| commitdiff \| tree
2019-10-03	Berk Hess	Fix setting maxNumColumns in Nbnxm::GridSet	commit \| commitdiff \| tree
2019-10-02	Berk Hess	Fix harmless OpenMP write race	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Use gmx::Range in domdec	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Completely remove charge groups	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Simplify DD exclusion counting	commit \| commitdiff \| tree
2019-10-01	Berk Hess	Always output correct kinetic at last step	commit \| commitdiff \| tree
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