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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
2018-09-18	Mark Abraham	Separated partitioning and dlb code within domdec	commit \| commitdiff \| tree
2018-09-18	Pascal Merz	Introduce stop handler	commit \| commitdiff \| tree
2018-09-18	Pascal Merz	Introduce checkpoint handler	commit \| commitdiff \| tree
2018-09-18	Pascal Merz	Introduce reset handler	commit \| commitdiff \| tree
2018-09-18	Mark Abraham	Add not_null from GSL	commit \| commitdiff \| tree
2018-09-18	Roland Schulz	Fix bitmask printing	commit \| commitdiff \| tree
2018-09-17	M. Eric Irrgang	Framework in which to build gmxapi.	commit \| commitdiff \| tree
2018-09-17	Paul Bauer	Properly initialize idef in topologies	commit \| commitdiff \| tree
2018-09-17	Berk Hess	Move ifunc stuff from idef.h to ifunc.h	commit \| commitdiff \| tree
2018-09-17	Kevin Boyd	Added basic tests for gmx msd	commit \| commitdiff \| tree
2018-09-16	Joe Jordan	Move variables around in pdb2gmx	commit \| commitdiff \| tree
2018-09-14	M. Eric Irrgang	Rearrange mdrun/runner.h	commit \| commitdiff \| tree
2018-09-14	Paul Bauer	Introduce gmx report-methods	commit \| commitdiff \| tree
2018-09-13	Berk Hess	Add C++ version of t_ilist	commit \| commitdiff \| tree
2018-09-12	Berk Hess	Convert vsite structs to C++	commit \| commitdiff \| tree
2018-09-12	M. Eric Irrgang	Simplify add_suffix_to_output_names()	commit \| commitdiff \| tree
2018-09-12	Roland Schulz	Remove cpluscplus ifdefs	commit \| commitdiff \| tree
2018-09-12	Roland Schulz	Fix clang-tidy warnings for OCL	commit \| commitdiff \| tree
2018-09-12	Berk Hess	Convert DD gmx_reverse_top_t to C++	commit \| commitdiff \| tree
2018-09-11	Mark Abraham	Replace C-style library file handling with RAII approaches	commit \| commitdiff \| tree
2018-09-11	Mark Abraham	Improve DD logging	commit \| commitdiff \| tree
2018-09-11	Roland Schulz	Compile nonbonded kernels as C++	commit \| commitdiff \| tree
2018-09-11	David van der Spoel	Added option to gmx nmeig to print ZPE.	commit \| commitdiff \| tree
2018-09-11	Mark Abraham	Replace readConformation with TopologyInformation	commit \| commitdiff \| tree
2018-09-11	Pascal Merz	Added trivial const qualifiers	commit \| commitdiff \| tree
2018-09-11	Pascal Merz	Initialize total_vir and pres in init_md	commit \| commitdiff \| tree
2018-09-10	Roland Schulz	Replace rounding using int(x+0.5) with roundToInt	commit \| commitdiff \| tree
2018-09-10	Roland Schulz	Add roundToInt	commit \| commitdiff \| tree
2018-09-09	Mark Abraham	Change TopologyInformation implementation	commit \| commitdiff \| tree
2018-09-09	Paul Bauer	Remove macro for group type in topology	commit \| commitdiff \| tree
2018-09-07	Mark Abraham	Fix grompp memory leaks	commit \| commitdiff \| tree
2018-09-07	Roland Schulz	clang-tidy: override	commit \| commitdiff \| tree
2018-09-07	Magnus Lundborg	Check q perturbation when PME on GPU is tested	commit \| commitdiff \| tree
2018-09-06	Roland Schulz	HostAllocator: Remove unnecessary template	commit \| commitdiff \| tree
2018-09-06	Roland Schulz	Remove pin/unpin from HostAllocator	commit \| commitdiff \| tree
2018-09-05	Paul Bauer	Changes to documentation build script	commit \| commitdiff \| tree
2018-08-30	Paul Bauer	More fixes from clang-tidy-7	commit \| commitdiff \| tree
2018-08-30	Christian Blau	Store essential dynamics parameters as vectors instead...	commit \| commitdiff \| tree
2018-08-30	Mark Abraham	Update testing matrices for coverage and speed	commit \| commitdiff \| tree
2018-08-29	Mark Abraham	Merge branch release-2018	commit \| commitdiff \| tree
2018-08-29	Berk Hess	Refactor wall potential calculation	commit \| commitdiff \| tree
2018-08-29	Roland Schulz	Use more const in hardwaretopology	commit \| commitdiff \| tree
2018-08-29	Roland Schulz	Fix clang-tidy build with libstdc++ >= 7	commit \| commitdiff \| tree
2018-08-29	Mark Abraham	Move clang-tidy build	commit \| commitdiff \| tree
2018-08-28	Mark Abraham	Fix more clang-tidy issues	commit \| commitdiff \| tree
2018-08-28	Szilárd Páll	Quiet cmake about clFFT not found after first run	commit \| commitdiff \| tree
2018-08-28	boristim	Updates to gmx cluster	commit \| commitdiff \| tree
2018-08-28	Roland Schulz	Add hard limit for line length	commit \| commitdiff \| tree
2018-08-27	Mark Abraham	Fix use of nullptr	commit \| commitdiff \| tree
2018-08-27	Paul Bauer	Transfer information from old how-to section	commit \| commitdiff \| tree
2018-08-27	Roland Schulz	Enable more clang-tidy checks for new code	commit \| commitdiff \| tree
2018-08-24	Mark Abraham	Fix build without TNG	commit \| commitdiff \| tree
2018-08-24	Mark Abraham	Merge branch release-2018	commit \| commitdiff \| tree
2018-08-22	Paul Bauer	Fix trjconv when running without a structure file	commit \| commitdiff \| tree
2018-08-22	Mark Abraham	Fix handling of counter resets	commit \| commitdiff \| tree
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