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2021-05-11	Andrey Alekseenko	Add SYCL implementation of GPU F buffer operations	commit \| commitdiff \| tree
2021-05-11	Mark Abraham	Rename pdb2gmx tests	commit \| commitdiff \| tree
2021-05-10	Joe Jordan	Fix harmless bug in nonbonded FEP tests	commit \| commitdiff \| tree
2021-05-10	Andrey Alekseenko	Add SYCL implementation of GPU X buffer operations	commit \| commitdiff \| tree
2021-05-10	Paul Bauer	Make clang-tidy check more aggressive	commit \| commitdiff \| tree
2021-05-10	Andrey Alekseenko	SYCL: Allow copying an uninitialized DeviceBuffer object	commit \| commitdiff \| tree
2021-05-04	ejjordan	Remove mdatoms from vsite	commit \| commitdiff \| tree
2021-05-03	ejjordan	Remove mdatoms from pairs in listed forces	commit \| commitdiff \| tree
2021-05-03	Artem Zhmurov	Fix copyright year	commit \| commitdiff \| tree
2021-05-03	Mark Abraham	Respect umask when creating temporary file	commit \| commitdiff \| tree
2021-05-03	ejjordan	Remove mdatoms from expanded	commit \| commitdiff \| tree
2021-05-03	Gilles Gouaillardet	densityfitting: add missing include file	commit \| commitdiff \| tree
2021-04-27	ejjordan	Increase const correctness of t_mdatoms use in md.cpp	commit \| commitdiff \| tree
2021-04-26	Paul Bauer	Fix incorrect handling of single residue chains	commit \| commitdiff \| tree
2021-04-21	Szilárd Páll	Remove isnormal() check around the atomic increment	commit \| commitdiff \| tree
2021-04-21	Joe Jordan	Mostly remove t_mdatoms from update signatures	commit \| commitdiff \| tree
2021-04-21	Szilárd Páll	Fix nbnxm hipSYCL kernels 64-wide exec on AMD	commit \| commitdiff \| tree
2021-04-21	Mark Abraham	Fix doxygen for MessageStringCollector	commit \| commitdiff \| tree
2021-04-20	Joe Jordan	clang-tidy-11 fixes for topology, gpu_utils, and selection	commit \| commitdiff \| tree
2021-04-19	ejjordan	clang-tidy-11 fixes for analysisdata	commit \| commitdiff \| tree
2021-04-19	Artem Zhmurov	Make Compartment, Channel, ChannelHistory and Domaint...	commit \| commitdiff \| tree
2021-04-19	Artem Zhmurov	Make XDR type into enum class	commit \| commitdiff \| tree
2021-04-14	Andrey Alekseenko	Use host buffer instead of host accessors in SYCL LeapFrog	commit \| commitdiff \| tree
2021-04-13	Pascal Merz	Fix check source	commit \| commitdiff \| tree
2021-04-12	Szilárd Páll	Workaround for compilation with hipSYCL 0.9.1	commit \| commitdiff \| tree
2021-04-11	Andrey Alekseenko	Add GpuEventSynchronizer::isMarked to SYCL verion	commit \| commitdiff \| tree
2021-04-11	Paul Bauer	Fix Apple OpenCL build and add to CI	commit \| commitdiff \| tree
2021-04-03	Artem Zhmurov	Rename NBAtomData into NBAtomDataGpu	commit \| commitdiff \| tree
2021-04-02	Paul Bauer	Replace gmx_mtop_ilistloop_all	commit \| commitdiff \| tree
2021-04-02	ejjordan	Move domdec/partition into gmx namespace; minor cleanup	commit \| commitdiff \| tree
2021-04-02	Andrey Alekseenko	Ensure coordinates are copied for dipole moment calculation	commit \| commitdiff \| tree
2021-04-02	Paul Bauer	Make FileOptionTypes enum class	commit \| commitdiff \| tree
2021-03-31	Mark Abraham	Make EnumerationArray::size() not static	commit \| commitdiff \| tree
2021-03-31	Paul Bauer	Move cluster methods to its own file	commit \| commitdiff \| tree
2021-03-30	Artem Zhmurov	Use default constructor for the device buffers that...	commit \| commitdiff \| tree
2021-03-30	Paul Bauer	Fix some include guards in gmx ana	commit \| commitdiff \| tree
2021-03-29	Joe Jordan	Add tests for calcvir	commit \| commitdiff \| tree
2021-03-29	Alan Gray	Avoid unnecessary CPU force buffer clearing	commit \| commitdiff \| tree
2021-03-29	Kevin Boyd	Remove unused LSAN suppressions	commit \| commitdiff \| tree
2021-03-27	Mark Abraham	Update developer guide on error handling	commit \| commitdiff \| tree
2021-03-27	Andrey Alekseenko	Avoid enqueueing the same event multiple times in nbnxn_atom...	commit \| commitdiff \| tree
2021-03-25	ejjordan	ArrayRef and const ref in gmx_nb_free_energy_kernel	commit \| commitdiff \| tree
2021-03-24	Andrey Alekseenko	Unify nbnxn_gpu_init_x_to_nbat_x	commit \| commitdiff \| tree
2021-03-24	Andrey Alekseenko	Add missing GMX_ASSERT(haveCopiedXFromGpu)	commit \| commitdiff \| tree
2021-03-23	Joe Jordan	Use ArrayRef in calc_mu	commit \| commitdiff \| tree
2021-03-22	Andrey Alekseenko	Remove incorrect assertion for GPU timing in SYCL	commit \| commitdiff \| tree
2021-03-22	Szilárd Páll	Remove a misplaced update cycle closing	commit \| commitdiff \| tree
2021-03-21	Artem Zhmurov	Move the atomToInteractionLocality(...) into locality.h	commit \| commitdiff \| tree
2021-03-18	Paul Bauer	Add wallcycle counting tests	commit \| commitdiff \| tree
2021-03-16	Joe Jordan	Use RVec and std::array in gmx_domdec_comm_t	commit \| commitdiff \| tree
2021-03-16	Artem Zhmurov	Unify gpu_launch_cpyback(...) function in NBNXM	commit \| commitdiff \| tree
2021-03-15	Artem Zhmurov	Move pmalloc(..)/pfree(...) to separate source files...	commit \| commitdiff \| tree
2021-03-15	Artem Zhmurov	Fix clang-format in topio.cpp	commit \| commitdiff \| tree
2021-03-13	Szilárd Páll	Rename launchReceiveCoordinatesFromPpCudaDirect	commit \| commitdiff \| tree
2021-03-13	Paul Bauer	Remove cyclic dependency check from check-source	commit \| commitdiff \| tree
2021-03-12	Andrey Alekseenko	Add DeviceAccessor<T,read> ctor from const DeviceBuffer<T>	commit \| commitdiff \| tree
2021-03-12	Alan Gray	Move responsibility for GPU force clearing to state...	commit \| commitdiff \| tree
2021-03-11	Artem Zhmurov	Unify insertNonLocalDependency(...) function in NBNXM	commit \| commitdiff \| tree
2021-03-11	Szilárd Páll	Simplify gmx_pme_send_force_vir_ener()	commit \| commitdiff \| tree
2021-03-11	Alan Gray	Fix unit test error due to GPU peer access already...	commit \| commitdiff \| tree
2021-03-11	Andrey Alekseenko	Properly check for frozen atoms when disabling GPU...	commit \| commitdiff \| tree
2021-03-10	Artem Zhmurov	Rename some variables in GPU task assignment and fix...	commit \| commitdiff \| tree
2021-03-10	Andrey Alekseenko	Convert PmeGpu->kernelParams->atoms.d_forces to RVec	commit \| commitdiff \| tree
2021-03-10	Andrey Alekseenko	Disable GPU update in the presence of frozen atoms	commit \| commitdiff \| tree
2021-03-10	Andrey Alekseenko	Wrap more device pointers in DeviceBuffer	commit \| commitdiff \| tree
2021-03-07	Andrey Alekseenko	Fix clang-tidy complaint failing our CI lint test	commit \| commitdiff \| tree
2021-02-26	Joe Jordan	Only use const ref for mtop and inputrec in domdec	commit \| commitdiff \| tree
2021-02-26	Artem Zhmurov	Add device-to-device copy function wrapper with tests...	commit \| commitdiff \| tree
2021-02-24	Artem Zhmurov	Use GpuTimers in CUDA and OpenCL versions of NBNXM...	commit \| commitdiff \| tree
2021-02-23	Artem Zhmurov	Fix doxygen in domdec	commit \| commitdiff \| tree
2021-02-22	Mark Abraham	Hide newly exposed domdec internals	commit \| commitdiff \| tree
2021-02-22	Mark Abraham	Fix code so clang-tidy no longer complains	commit \| commitdiff \| tree
2021-02-22	ejjordan	remove InteractionLocality from PairListSet constructor	commit \| commitdiff \| tree
2021-02-22	Artem Zhmurov	Add FloatN aliases to OpenCL and use them in NBNXM	commit \| commitdiff \| tree
2021-02-20	Joe Jordan	Remove unsed structs from nblist and use vector in...	commit \| commitdiff \| tree
2021-02-18	Andrey Alekseenko	Make the use of GpuEventSynchronizer in SYCL conformant...	commit \| commitdiff \| tree
2021-02-18	Szilárd Páll	Clean up box vector constants in do_force	commit \| commitdiff \| tree
2021-02-17	Artem Zhmurov	Use GpuEventSynchronizer in NBNXM	commit \| commitdiff \| tree
2021-02-13	Paul Bauer	Fix release docs build	commit \| commitdiff \| tree
2021-02-11	Joe Jordan	Use unique_ptr for tables	commit \| commitdiff \| tree
2021-02-09	Andrey Alekseenko	SYCL compilation and code compatibility changes	commit \| commitdiff \| tree
2021-02-09	Artem Zhmurov	Fix clang-format	commit \| commitdiff \| tree
2021-02-09	Paul Bauer	Fix range check bug in gmx covar	commit \| commitdiff \| tree
2021-02-08	Paul Bauer	Fix clang-tidy-11 for trajectoryanalysis	commit \| commitdiff \| tree
2021-02-07	Szilárd Páll	Fix clang-tidy 11 warning in nbnxm ocl kernels	commit \| commitdiff \| tree
2021-02-06	Mark Abraham	Add style code for function static variables	commit \| commitdiff \| tree
2021-02-05	Paul Bauer	Clang-tidy-11 fixes for utility	commit \| commitdiff \| tree
2021-02-05	Paul Bauer	Fix clang-tidy-11 for domdec and utility	commit \| commitdiff \| tree
2021-02-01	Paul Bauer	Fix clang-tidy	commit \| commitdiff \| tree
2021-01-29	Hubert Santuz	Allow MdModules to access the topology during simulation...	commit \| commitdiff \| tree
2021-01-29	Christian Blau	Update release note on QM/MM deprication	commit \| commitdiff \| tree
2021-01-27	Christian Blau	Clarify lambda vector usage with figure in manual	commit \| commitdiff \| tree
2021-01-26	Mark Abraham	Stop installing NB-LIB argon-forces-integration binary	commit \| commitdiff \| tree
2021-01-21	Mark Abraham	Ensure residue name used by pdb2gmx matches rtp name	commit \| commitdiff \| tree
2021-01-21	Mark Abraham	Suggest a workaround for pulling with -deffnm	commit \| commitdiff \| tree
2021-01-20	Mark Abraham	Describe the configured precision correctly for mdrun	commit \| commitdiff \| tree
2021-01-20	Paul Bauer	NBLIB: Remove preprocessor macros	commit \| commitdiff \| tree
2021-01-20	Paul Bauer	Fix TPR handling for older versions.	commit \| commitdiff \| tree
2021-01-20	Paul Bauer	Fix checksumming code	commit \| commitdiff \| tree
2021-01-20	Mark Abraham	Fix PaddedVector move constructor	commit \| commitdiff \| tree
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