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2019-09-24	Mark Abraham	Merge "Merge branch release-2019 into master"	commit \| commitdiff \| tree
2019-09-24	Mark Abraham	Fix clang unused-function warnings	commit \| commitdiff \| tree
2019-09-24	Paul Bauer	Add release notes for modular simulator	commit \| commitdiff \| tree
2019-09-23	Paul Bauer	Fix issues when PME rank request becomes negative	commit \| commitdiff \| tree
2019-09-23	Paul Bauer	Change MPI setup to communicate TPR as buffer	commit \| commitdiff \| tree
2019-09-23	Pascal Merz	Zero pressure and virial tensors at beginning of step	commit \| commitdiff \| tree
2019-09-23	Pascal Merz	Introduce FEP into modular simulator	commit \| commitdiff \| tree
2019-09-22	Christoph Junghans	workaround for rhel bug #1749463, cmake bug #18349	commit \| commitdiff \| tree
2019-09-22	Paul Bauer	Remove update flag again	commit \| commitdiff \| tree
2019-09-22	Berk Hess	Remove cgs_gl from gmx_domdec_comm_t	commit \| commitdiff \| tree
2019-09-20	Mark Abraham	Refactor to create a GpuTaskAssignments object	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Remove bLocalCG from DD code	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Remove obsolete make_exclusions_zone_cg()	commit \| commitdiff \| tree
2019-09-19	Christian Blau	Check input record also in tests	commit \| commitdiff \| tree
2019-09-19	Mark Abraham	Use GPU halo exchange only when compatible DD is available	commit \| commitdiff \| tree
2019-09-19	Mark Abraham	Further improve getDDGridSetup	commit \| commitdiff \| tree
2019-09-19	Paul Bauer	Add basic interface to run update on GPU	commit \| commitdiff \| tree
2019-09-19	Berk Hess	Add haveFreeEnergyWork to DomainLifetimeWorkload flags	commit \| commitdiff \| tree
2019-09-19	Christian Blau	Consistently change densityfitting spreading weight...	commit \| commitdiff \| tree
2019-09-18	Berk Hess	Added free-energy kernel performance note	commit \| commitdiff \| tree
2019-09-18	Berk Hess	Fix incorrect DD ndim assertion	commit \| commitdiff \| tree
2019-09-18	Pascal Merz	v-rescale thermostat for modular simulator	commit \| commitdiff \| tree
2019-09-18	Paul Bauer	Read TPR file body in buffer	commit \| commitdiff \| tree
2019-09-18	Alan Gray	GPU Force Halo Exchange	commit \| commitdiff \| tree
2019-09-17	Pascal Merz	Fix position pinning for modular simulator	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Remove obsolete mdp option ns-type	commit \| commitdiff \| tree
2019-09-16	ejjordan	Add some cool quotes	commit \| commitdiff \| tree
2019-09-16	Paul Bauer	Formatting fixes for reference manual	commit \| commitdiff \| tree
2019-09-16	M. Eric Irrgang	Add gmxapi release notes.	commit \| commitdiff \| tree
2019-09-16	Alan Gray	GPU halo exchange	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Add virtual site type 2FD	commit \| commitdiff \| tree
2019-09-16	Mark Abraham	Avoid short-range GPU operations with no work	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Remove cut-off schemes from manual	commit \| commitdiff \| tree
2019-09-16	Szilárd Páll	Eliminate unnecessary GPU stream dependency call	commit \| commitdiff \| tree
2019-09-16	Berk Hess	Add option request 1D DD with 1 pulse	commit \| commitdiff \| tree
2019-09-16	Kevin Boyd	Remove group scheme from deprecated release notes	commit \| commitdiff \| tree
2019-09-15	Pascal Merz	Introduce the modular simulator	commit \| commitdiff \| tree
2019-09-15	Peter Kasson	Patch gmxapi for Python 3.7	commit \| commitdiff \| tree
2019-09-13	M. Eric Irrgang	Normalize usage of GMXTOOLCHAINDIR in gmxapi setup.py	commit \| commitdiff \| tree
2019-09-13	M. Eric Irrgang	Do not use gromacs-toolchain in darwin gmxapi builds.	commit \| commitdiff \| tree
2019-09-13	M. Eric Irrgang	Update gmxapi setup.py	commit \| commitdiff \| tree
2019-09-12	Mark Abraham	Disable report-methods end-to-end test	commit \| commitdiff \| tree
2019-09-12	Szilárd Páll	Reorganize on-GPU PME force reduction flag handling	commit \| commitdiff \| tree
2019-09-12	Artem Zhmurov	Change PaddedVector to PaddedHostVector for force CPU...	commit \| commitdiff \| tree
2019-09-12	Christian Blau	Add release note for density fitting.	commit \| commitdiff \| tree
2019-09-12	Pascal Merz	Update modular simulator tests	commit \| commitdiff \| tree
2019-09-12	Erik Lindahl	Added SIMD log2 and pow math functions	commit \| commitdiff \| tree
2019-09-12	Erik Lindahl	Update SIMD math tests and improve accuracy	commit \| commitdiff \| tree
2019-09-11	Paul Bauer	Remove -sub option from trjconv	commit \| commitdiff \| tree
2019-09-11	Artem Zhmurov	Fix for the post-submit failure	commit \| commitdiff \| tree
2019-09-11	Artem Zhmurov	Decouple GPU force buffer management from buffer ops...	commit \| commitdiff \| tree
2019-09-11	M. Eric Irrgang	Use GROMACS CMake toolchain file for gmxapi Python...	commit \| commitdiff \| tree
2019-09-11	Paul Bauer	Basic toolchain to facilitate GMXAPI build	commit \| commitdiff \| tree
2019-09-11	M. Eric Irrgang	Add gmxapi.modify_input operation.	commit \| commitdiff \| tree
2019-09-11	M. Eric Irrgang	Provide a gmxapi.read_tpr operation.	commit \| commitdiff \| tree
2019-09-11	M. Eric Irrgang	Update gmxapi.simulation.context details.	commit \| commitdiff \| tree
2019-09-11	M. Eric Irrgang	Update gmxapi Python package infrastructure for new...	commit \| commitdiff \| tree
2019-09-11	M. Eric Irrgang	Normalize some testing resources for the Python packages.	commit \| commitdiff \| tree
2019-09-11	Magnus Lundborg	Tidy up the FE kernel	commit \| commitdiff \| tree
2019-09-10	Paul Bauer	Fix nightly build	commit \| commitdiff \| tree
2019-09-10	Szilárd Páll	Use thread-MPI in the gpucomm matrix	commit \| commitdiff \| tree
2019-09-10	Pascal Merz	Coordinate Propagators	commit \| commitdiff \| tree
2019-09-10	Pascal Merz	StatePropagatorData: Introduced const box accessor...	commit \| commitdiff \| tree
2019-09-10	Pascal Merz	Add trivial const qualifiers to shellfc and EnergyOutput	commit \| commitdiff \| tree
2019-09-10	Pascal Merz	Constraint element for the modular simulator	commit \| commitdiff \| tree
2019-09-09	Szilárd Páll	Pass gmx::ForceFlags to CPU nbnxm dispatch code	commit \| commitdiff \| tree
2019-09-09	Szilárd Páll	Pass the new gmx::ForceFlags to the nbnxm module	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Remove incorrect check with rf-zero	commit \| commitdiff \| tree
2019-09-09	Pascal Merz	Domain decomposition and PME load balancing for modular...	commit \| commitdiff \| tree
2019-09-09	Christian Blau	Relative entropy as density similarity measure	commit \| commitdiff \| tree
2019-09-09	Paul Bauer	Add gmx convert-trj	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Rename DDSetup to DDGridSetup	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Clean up PME rank variables	commit \| commitdiff \| tree
2019-09-09	Berk Hess	Refactor init_domain_decomposition()	commit \| commitdiff \| tree
2019-09-07	Pascal Merz	Make pme_loadbal_do() independent of t_state	commit \| commitdiff \| tree
2019-09-07	Pascal Merz	ForceElement and ShellFCElement for the modular simulator	commit \| commitdiff \| tree
2019-09-06	Szilárd Páll	Add gpuupdate and gpucomm OnDemand tokens	commit \| commitdiff \| tree
2019-09-06	Berk Hess	Extract getting of DDRankSetup	commit \| commitdiff \| tree
2019-09-06	Berk Hess	Add PP grid info to DDRankSetup	commit \| commitdiff \| tree
2019-09-05	Mark Abraham	Update mdrun test comparison infrastructure	commit \| commitdiff \| tree
2019-09-05	Pascal Merz	Rename MicroState to StatePropagatorData for modular...	commit \| commitdiff \| tree
2019-09-05	Christian Blau	Add reference density file option to densityfitting	commit \| commitdiff \| tree
2019-09-05	Berk Hess	Split off getting of the DD setup	commit \| commitdiff \| tree
2019-09-04	Szilárd Páll	Bump ARM HPC toolchain in post-submit to v19.3	commit \| commitdiff \| tree
2019-09-04	Szilárd Páll	Add back a clang-tidy exception	commit \| commitdiff \| tree
2019-09-04	Christian Blau	Read mrc file using file name	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Move update grouping to DDSystemInfo	commit \| commitdiff \| tree
2019-09-04	Magnus Lundborg	Inline functions of calculations of FE interaction...	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Change DD pme force buffer to std::vector	commit \| commitdiff \| tree
2019-09-04	Berk Hess	Initialize all members of gmx_domdec_t	commit \| commitdiff \| tree
2019-09-03	M. Eric Irrgang	Python wrapping code for gmxapi mdrun bindings.	commit \| commitdiff \| tree
2019-09-03	Pascal Merz	Introduce energy element for modular simulator	commit \| commitdiff \| tree
2019-09-03	Mark Abraham	Simplify energy-file comparisons in tests	commit \| commitdiff \| tree
2019-09-03	Artem Zhmurov	Add Parrinello-Rahman pressure coupling to CUDA Leap...	commit \| commitdiff \| tree
2019-09-02	Berk Hess	Only use fshift when needed	commit \| commitdiff \| tree
2019-09-01	Christian Blau	Add checkpointing for MdModules	commit \| commitdiff \| tree
2019-08-30	Christian Blau	LocalAtomSet construction with vectors of gmx::index	commit \| commitdiff \| tree
2019-08-30	M. Eric Irrgang	Import base code for Python-driven simulation from...	commit \| commitdiff \| tree
2019-08-30	Magnus Lundborg	Changed some variables from SCReal to real in FE kernel.	commit \| commitdiff \| tree
2019-08-30	Christian Blau	Implementing the density fitting force provider	commit \| commitdiff \| tree
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