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2014-09-11	Teemu Murtola	Use absolute include paths in nbnxn kernels	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Manually sort some includes in src/gromacs	commit \| commitdiff \| tree
2014-09-08	Teemu Murtola	Support custom default extension for FileNameOption	commit \| commitdiff \| tree
2014-09-08	Teemu Murtola	Remove unnecessary extensions in t_filenm defaults	commit \| commitdiff \| tree
2014-09-07	Teemu Murtola	More consistent default handling for StringOption	commit \| commitdiff \| tree
2014-09-07	Teemu Murtola	Update template/README	commit \| commitdiff \| tree
2014-09-05	Teemu Murtola	Remove unnecessary config.h includes	commit \| commitdiff \| tree
2014-09-05	Teemu Murtola	Move some defines to gmxpre.h for thread-MPI	commit \| commitdiff \| tree
2014-09-05	Teemu Murtola	Another batch of added config.h	commit \| commitdiff \| tree
2014-09-05	Teemu Murtola	Make doc-check fail the build on warnings	commit \| commitdiff \| tree
2014-09-05	Teemu Murtola	Merge "Merge release-5-0 into master"	commit \| commitdiff \| tree
2014-09-04	Teemu Murtola	Include config.h directly if used	commit \| commitdiff \| tree
2014-09-04	Teemu Murtola	Make doc-check silent for in-source build	commit \| commitdiff \| tree
2014-09-04	Teemu Murtola	Merge "Merge release-5-0 into master"	commit \| commitdiff \| tree
2014-08-24	Teemu Murtola	Precalculate pbc shift for analysis nbsearch	commit \| commitdiff \| tree
2014-08-24	Teemu Murtola	Improve analysis nbsearch grid mapping	commit \| commitdiff \| tree
2014-08-23	Teemu Murtola	Backport of 'Remove unused figures from share/html/'	commit \| commitdiff \| tree
2014-08-22	Teemu Murtola	Move -nice handling to CommandLineModuleManager	commit \| commitdiff \| tree
2014-08-20	Teemu Murtola	Misc. gmxpre.h-related changes	commit \| commitdiff \| tree
2014-08-20	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2014-08-20	Teemu Murtola	Remove unused config.h defines	commit \| commitdiff \| tree
2014-08-19	Teemu Murtola	Introduce gmxpre.h for truly global definitions	commit \| commitdiff \| tree
2014-08-16	Teemu Murtola	Disable analysisdata generic tests if not compilable	commit \| commitdiff \| tree
2014-08-14	Teemu Murtola	Fix CMake package config after recent version changes	commit \| commitdiff \| tree
2014-08-13	Teemu Murtola	Use native CMake mechanism for find_package(GROMACS)	commit \| commitdiff \| tree
2014-08-13	Teemu Murtola	Reorganize CMake version information management	commit \| commitdiff \| tree
2014-08-10	Teemu Murtola	Improve initAfterFirstFrame() usability	commit \| commitdiff \| tree
2014-08-10	Teemu Murtola	Make vec.h const-correct with both C and C++	commit \| commitdiff \| tree
2014-08-10	Teemu Murtola	Basic exclusion support for analysis nbsearch	commit \| commitdiff \| tree
2014-08-09	Teemu Murtola	Add Selection::hasOnlyAtoms()	commit \| commitdiff \| tree
2014-08-07	Teemu Murtola	Basic support for 2D neighborhood search for analysis	commit \| commitdiff \| tree
2014-08-04	Teemu Murtola	Verify MD5 sum for FFTW download	commit \| commitdiff \| tree
2014-08-03	Teemu Murtola	Check frame atom count before evaluating selections	commit \| commitdiff \| tree
2014-07-31	Teemu Murtola	Merge "Merge release-5-0 into master"	commit \| commitdiff \| tree
2014-07-24	Teemu Murtola	Do not actually install uniqueptr.h	commit \| commitdiff \| tree
2014-07-16	Teemu Murtola	Fix HTML help and man pages for commands with dashes	commit \| commitdiff \| tree
2014-07-12	Teemu Murtola	Make gmx_node_num/rank safer	commit \| commitdiff \| tree
2014-07-11	Teemu Murtola	Fix HTML links that contain file extensions	commit \| commitdiff \| tree
2014-07-10	Teemu Murtola	Bump SOVERSION	commit \| commitdiff \| tree
2014-07-09	Teemu Murtola	Clean up gmx_header_config	commit \| commitdiff \| tree
2014-07-09	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2014-07-09	Teemu Murtola	Improve module dependency graph layout	commit \| commitdiff \| tree
2014-07-09	Teemu Murtola	Module dependency cycle checker for 'doc-check'	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Remove PCA_QUIET	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Additional index group checks for selections	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Clean up program name handling in oenv	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Improve FileNameOption error handling	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Move GMX_CXX11 to config.h	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Remove gmx_unique_ptr from options public headers	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Make selections ignore \r in input	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Remove selection help from SelectionCollection	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Change some gmx_unique_ptr to shared_ptr in public...	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Move -debug to cmdlinemodulemanager.cpp	commit \| commitdiff \| tree
2014-07-08	Teemu Murtola	Make doc-check pass again without warnings	commit \| commitdiff \| tree
2014-07-05	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2014-07-05	Teemu Murtola	Reinstantiate unsorted index group check	commit \| commitdiff \| tree
2014-07-05	Teemu Murtola	Update some installation-related docs	commit \| commitdiff \| tree
2014-07-01	Teemu Murtola	Adjust include directory order for some corner cases	commit \| commitdiff \| tree
2014-06-30	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2014-06-29	Teemu Murtola	Remove some hardcoded selection string buffers	commit \| commitdiff \| tree
2014-06-28	Teemu Murtola	Remove overeager selection index group check	commit \| commitdiff \| tree
2014-06-21	Teemu Murtola	Convert checkpoint.c to C++ compilation	commit \| commitdiff \| tree
2014-06-15	Teemu Murtola	Convert gmx_residuetype_t to a non-pointer	commit \| commitdiff \| tree
2014-06-15	Teemu Murtola	Remove unused figures from share/html/	commit \| commitdiff \| tree
2014-06-07	Teemu Murtola	Clean up FileNameOptionStorage implementation	commit \| commitdiff \| tree
2014-06-07	Teemu Murtola	Improve (Selection\|FileName)OptionManager handling	commit \| commitdiff \| tree
2014-06-07	Teemu Murtola	Replace all command line parsing with Options	commit \| commitdiff \| tree
2014-06-07	Teemu Murtola	Move residuetype handling to its own file.	commit \| commitdiff \| tree
2014-06-07	Teemu Murtola	Remove support for "old" index file format	commit \| commitdiff \| tree
2014-06-07	Teemu Murtola	Move index.* to topology/	commit \| commitdiff \| tree
2014-06-02	Teemu Murtola	Move atomprop.* to topology/	commit \| commitdiff \| tree
2014-05-31	Teemu Murtola	Move mtop_util.* and topsort.* to topology/	commit \| commitdiff \| tree
2014-05-29	Teemu Murtola	Remove more uses of typedefs.h	commit \| commitdiff \| tree
2014-05-25	Teemu Murtola	Move general functions out of typedefs.h	commit \| commitdiff \| tree
2014-05-25	Teemu Murtola	Remove some typedefs.h dependencies	commit \| commitdiff \| tree
2014-05-25	Teemu Murtola	Move types/topology.h to topology/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move types/idef.h to topology/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move types/atoms.h to topology/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move types/ishift.h to pbcutil/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move invblock.* to topology/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move types/block.h to topology/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move symtab.* to topology/	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Merge t_symtab into symtab.h	commit \| commitdiff \| tree
2014-05-24	Teemu Murtola	Move pbc.* to pbcutil/	commit \| commitdiff \| tree
2014-05-22	Teemu Murtola	Move cinvsqrtdata.c to math/ and remove Fortran remnants	commit \| commitdiff \| tree
2014-05-22	Teemu Murtola	Fix static group list indices in selection prompt	commit \| commitdiff \| tree
2014-05-22	Teemu Murtola	Merge t_pbc definition into pbc.h	commit \| commitdiff \| tree
2014-05-21	Teemu Murtola	Move mshift.* to pbcutil/	commit \| commitdiff \| tree
2014-05-21	Teemu Murtola	Merge t_graph definition into mshift.h	commit \| commitdiff \| tree
2014-05-20	Teemu Murtola	Move rmpbc.* to pbcutil/	commit \| commitdiff \| tree
2014-05-18	Teemu Murtola	Clean up matio.*	commit \| commitdiff \| tree
2014-05-18	Teemu Murtola	Move 3dview.* to programs/view/	commit \| commitdiff \| tree
2014-05-18	Teemu Murtola	Clean up math/	commit \| commitdiff \| tree
2014-05-17	Teemu Murtola	More elaborate default handling for FileNameOption	commit \| commitdiff \| tree
2014-05-17	Teemu Murtola	Unit tests for parse_common_args() file options	commit \| commitdiff \| tree
2014-05-14	Teemu Murtola	Move physics.* to math/units.*	commit \| commitdiff \| tree
2014-05-01	Teemu Murtola	Fix incorrect limits in FloatOptionStorage	commit \| commitdiff \| tree
2014-04-28	Teemu Murtola	Move mtxio.* to fileio/	commit \| commitdiff \| tree
2014-04-27	Teemu Murtola	Move rvec and friends to math/vectypes.h	commit \| commitdiff \| tree
2014-04-27	Teemu Murtola	Move 'real' definition to utility/real.h	commit \| commitdiff \| tree
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