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2018-10-26	Mark Abraham	Merge "Merge branch release-2018 into release-2019...	commit \| commitdiff \| tree
2018-10-26	Mark Abraham	Merge branch release-2018 into release-2019	commit \| commitdiff \| tree
2018-10-26	Berk Hess	Add missing mass term to deltaH	commit \| commitdiff \| tree
2018-10-25	Mark Abraham	Introduce ArrayRefWithPadding	commit \| commitdiff \| tree
2018-10-25	Paul Bauer	Change doc build without image conversion	commit \| commitdiff \| tree
2018-10-24	Paul Bauer	Fix MPI w/o MPI_IN_PLACE	commit \| commitdiff \| tree
2018-10-21	Berk Hess	Fix mdrun start/end time print	commit \| commitdiff \| tree
2018-10-19	M. Eric Irrgang	Documentation bug in gmxapi/context.h	commit \| commitdiff \| tree
2018-10-18	Berk Hess	Add env.var. to disable update groups	commit \| commitdiff \| tree
2018-10-16	Mark Abraham	Eliminated t_ifunc from t_interaction_function	commit \| commitdiff \| tree
2018-10-16	Magnus Lundborg	Move gmx_ffparams_t to forcefieldparameters	commit \| commitdiff \| tree
2018-10-16	Mark Abraham	Task assignment for bonded interactions on CUDA GPUs	commit \| commitdiff \| tree
2018-10-16	Mark Abraham	Fix compiler issues	commit \| commitdiff \| tree
2018-10-16	Mark Abraham	Removed support for NVIDIA CC 2.x devices (codename...	commit \| commitdiff \| tree
2018-10-15	Mark Abraham	Create ExclusionBlocks	commit \| commitdiff \| tree
2018-10-15	Mark Abraham	De-duplicating mdrun setup	commit \| commitdiff \| tree
2018-10-15	Magnus Lundborg	Enable output of average pull force and positions.	commit \| commitdiff \| tree
2018-10-14	M. Eric Irrgang	Resolve some linter warnings.	commit \| commitdiff \| tree
2018-10-14	M. Eric Irrgang	Test signaling facility through session resources.	commit \| commitdiff \| tree
2018-10-14	Szilárd Páll	Modernize OpenCL memory allocation flags	commit \| commitdiff \| tree
2018-10-14	M. Eric Irrgang	Clean up gmxapi testsupport output.	commit \| commitdiff \| tree
2018-10-14	M. Eric Irrgang	gmxapi::UsageError	commit \| commitdiff \| tree
2018-10-14	M. Eric Irrgang	Allow API access to simulation signals.	commit \| commitdiff \| tree
2018-10-13	Aleksei Iupinov	Add and enable PME OpenCL	commit \| commitdiff \| tree
2018-10-12	M. Eric Irrgang	Add API for adding MDModules / Restraints.	commit \| commitdiff \| tree
2018-10-12	Berk Hess	Implement assigning bondeds to the GPU	commit \| commitdiff \| tree
2018-10-12	M. Eric Irrgang	Add restraints framework.	commit \| commitdiff \| tree
2018-10-12	Viacheslav Bolnykh	Implemented QM/MM workflow inside core GROMACS	commit \| commitdiff \| tree
2018-10-12	Mark Abraham	Exclude gmxapi source files from include sorting	commit \| commitdiff \| tree
2018-10-11	David van der Spoel	Reinstated quasiharmonic entropy calculation in gmx...	commit \| commitdiff \| tree
2018-10-11	M. Eric Irrgang	Add gmxapi::Session.	commit \| commitdiff \| tree
2018-10-11	Mark Abraham	Fix PaddedVector issues	commit \| commitdiff \| tree
2018-10-11	Paul Bauer	Add short security notice	commit \| commitdiff \| tree
2018-10-10	Paul Bauer	Include doi strings from zenodo during release	commit \| commitdiff \| tree
2018-10-10	M. Eric Irrgang	gmxapi expects position independent code.	commit \| commitdiff \| tree
2018-10-10	Szilárd Páll	Swap custom OpenCL memset kernel for clEnqueueFillBuffer	commit \| commitdiff \| tree
2018-10-09	Szilárd Páll	Update regressiontest ref to download	commit \| commitdiff \| tree
2018-10-09	Viacheslav Bolnykh	Implemented changes to preprocessor to work with MiMiC...	commit \| commitdiff \| tree
2018-10-09	Mark Abraham	Fix DomdecOptions default	commit \| commitdiff \| tree
2018-10-09	Roland Schulz	Fix MSAN errors	commit \| commitdiff \| tree
2018-10-08	Berk Hess	Enable update groups	commit \| commitdiff \| tree
2018-10-08	Szilárd Páll	Tweak FindFFTW API checks	commit \| commitdiff \| tree
2018-10-08	Szilárd Páll	Fix clang-6 warnings	commit \| commitdiff \| tree
2018-10-08	Roland Schulz	OCL: Add const to function arguments	commit \| commitdiff \| tree
2018-10-08	Roland Schulz	Add OCL kernel target	commit \| commitdiff \| tree
2018-10-08	Mark Abraham	Disable FPE explicitly for TPI force calculation	commit \| commitdiff \| tree
2018-10-08	Szilárd Páll	Replace some NULL with nullptr in CUDA code	commit \| commitdiff \| tree
2018-10-08	Mark Abraham	Implement PaddedVector	commit \| commitdiff \| tree
2018-10-08	Paul Bauer	Workaround for ICC postsubmit bug	commit \| commitdiff \| tree
2018-10-08	Mark Abraham	More updates to test matrix	commit \| commitdiff \| tree
2018-10-08	Mark Abraham	Fix make test	commit \| commitdiff \| tree
2018-10-07	Mark Abraham	Test with gcc 8 and cuda 10	commit \| commitdiff \| tree
2018-10-05	Mark Abraham	Check log and other files differently during appending...	commit \| commitdiff \| tree
2018-10-05	Berk Hess	Add update groups to DD atom displacement	commit \| commitdiff \| tree
2018-10-05	Mark Abraham	Change to test TSAN with clang and libomp	commit \| commitdiff \| tree
2018-10-05	Roland Schulz	OCL: Make variables const	commit \| commitdiff \| tree
2018-10-05	M. Eric Irrgang	Add gmxapi::System.	commit \| commitdiff \| tree
2018-10-05	Szilárd Páll	Update test matrices with new GPU specifiers	commit \| commitdiff \| tree
2018-10-04	Berk Hess	Make AVX2 pass TSAN	commit \| commitdiff \| tree
2018-10-04	Mark Abraham	Extract helper functions for preparing for appending	commit \| commitdiff \| tree
2018-10-04	Mark Abraham	Simplify EM usage of mdebin	commit \| commitdiff \| tree
2018-10-03	Mark Abraham	Use fast returns in md5 computation	commit \| commitdiff \| tree
2018-10-03	Magnus Lundborg	Allow using COM of previous step as PBC reference	commit \| commitdiff \| tree
2018-10-03	Mark Abraham	Add end-to-end tests of energy minimization	commit \| commitdiff \| tree
2018-10-03	Paul Bauer	Disable GMXAPI when only building mdrun	commit \| commitdiff \| tree
2018-10-03	M. Eric Irrgang	Add gmxapi::Context.	commit \| commitdiff \| tree
2018-10-03	M. Eric Irrgang	Move mdrun mainFunction to client code.	commit \| commitdiff \| tree
2018-10-03	M. Eric Irrgang	Add test data for gmxapi.	commit \| commitdiff \| tree
2018-10-03	M. Eric Irrgang	Add gmxapi exceptions.	commit \| commitdiff \| tree
2018-10-02	Paul Bauer	Fix include formatting in gmxapi	commit \| commitdiff \| tree
2018-10-02	Roland Schulz	Use subgroup shuffle for reduction	commit \| commitdiff \| tree
2018-10-02	Berk Hess	Update DD cutoffs for update groups	commit \| commitdiff \| tree
2018-10-02	Mark Abraham	Reduce mdrun tests using group scheme	commit \| commitdiff \| tree
2018-10-01	Mark Abraham	Fix gcc-8 warnings about strings	commit \| commitdiff \| tree
2018-10-01	Paul Bauer	Change get_atom_index to return int	commit \| commitdiff \| tree
2018-10-01	Mark Abraham	Add release notes for removing non-reproducible aspects	commit \| commitdiff \| tree
2018-10-01	Mark Abraham	Tests for md5 computation on open files	commit \| commitdiff \| tree
2018-09-29	Mark Abraham	Stop ICC ICE	commit \| commitdiff \| tree
2018-09-29	Berk Hess	Add UpdateGroupsCog to DD	commit \| commitdiff \| tree
2018-09-28	Mark Abraham	Use more default initialization of mdrun structs	commit \| commitdiff \| tree
2018-09-28	Mark Abraham	Make some symbols in gmxpre-config.h always defined	commit \| commitdiff \| tree
2018-09-27	Kevin Boyd	Reduce preprocessor dependency in resourcedivision.cpp	commit \| commitdiff \| tree
2018-09-26	Berk Hess	Extract settle test water coordinates	commit \| commitdiff \| tree
2018-09-26	Magnus Lundborg	Added pullCheckPbcWithinGroup() to check one group	commit \| commitdiff \| tree
2018-09-26	Mark Abraham	Clarify distinct paths for mdrun log file handling	commit \| commitdiff \| tree
2018-09-25	Berk Hess	Add UpdateGroupsCog class	commit \| commitdiff \| tree
2018-09-25	Pascal Merz	Remove obsolete braces in do_md()	commit \| commitdiff \| tree
2018-09-25	Pascal Merz	Remove rerun from do_md	commit \| commitdiff \| tree
2018-09-24	M. Eric Irrgang	Fix gmxapi::Version test regression.	commit \| commitdiff \| tree
2018-09-24	Berk Hess	Fix performance report when init_step!=0	commit \| commitdiff \| tree
2018-09-24	Mark Abraham	Fix Doxygen links	commit \| commitdiff \| tree
2018-09-23	Mark Abraham	Leak less from gromppp with cmap	commit \| commitdiff \| tree
2018-09-22	Berk Hess	Add update groups boolean to DD	commit \| commitdiff \| tree
2018-09-22	Berk Hess	Rename DD constraint booleans	commit \| commitdiff \| tree
2018-09-22	Berk Hess	Add update groups	commit \| commitdiff \| tree
2018-09-21	Szilárd Páll	Bump test timeout only for OpenCL integration tests	commit \| commitdiff \| tree
2018-09-21	Roland Schulz	Fix clang-tidy warnings for clang 7	commit \| commitdiff \| tree
2018-09-20	Mark Abraham	Update to test with clang-7	commit \| commitdiff \| tree
2018-09-20	Berk Hess	Change pull buffers to std::vector	commit \| commitdiff \| tree
2018-09-18	Berk Hess	Introduce extractILists helper function	commit \| commitdiff \| tree
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