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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
2014-04-17	Teemu Murtola	Move vec.h to math/	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Remove unused minvert.h	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Fix typo in fatalerror.h	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Move xvgr.* to fileio/	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Clean up xvgr.h and viewit.h usage	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Remove sysstuff.h	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Remove sysstuff.h includes from headers	commit \| commitdiff \| tree
2014-04-16	Teemu Murtola	Refactor gmx_fatal()	commit \| commitdiff \| tree
2014-04-13	Teemu Murtola	Remove unused shift.h	commit \| commitdiff \| tree
2014-04-13	Teemu Murtola	Remove utility -> fileio dependencies	commit \| commitdiff \| tree
2014-04-13	Teemu Murtola	Clean up futil.*	commit \| commitdiff \| tree
2014-04-10	Teemu Murtola	Clean up and fix issues in doc-check scripts	commit \| commitdiff \| tree
2014-04-10	Teemu Murtola	Move part of types/simple.h to utility/	commit \| commitdiff \| tree
2014-04-10	Teemu Murtola	Remove utility/ dependencies on network.h and main.h	commit \| commitdiff \| tree
2014-04-08	Teemu Murtola	Remove some utility -> legacyheaders dependencies	commit \| commitdiff \| tree
2014-04-08	Teemu Murtola	Version bump for post-5.0 development	commit \| commitdiff \| tree
2014-04-08	Teemu Murtola	Move gmx_fatal.* to utility/fatalerror.*	commit \| commitdiff \| tree
2014-04-07	Teemu Murtola	Doxygen documentation for version.h	commit \| commitdiff \| tree
2014-04-04	Teemu Murtola	Remove ancient SGI-specific code	commit \| commitdiff \| tree
2014-04-04	Teemu Murtola	Clean up gmx_fatal.*	commit \| commitdiff \| tree
2014-04-02	Teemu Murtola	Move string2.* to utility/cstringutil.*	commit \| commitdiff \| tree
2014-04-01	Teemu Murtola	Move smalloc.h to utility/	commit \| commitdiff \| tree
2014-03-31	Teemu Murtola	Remove #include <...> for local files in gmx-view	commit \| commitdiff \| tree
2014-03-31	Teemu Murtola	Clean up smalloc.h	commit \| commitdiff \| tree
2014-03-31	Teemu Murtola	Move some math headers away from legacyheaders/	commit \| commitdiff \| tree
2014-03-31	Teemu Murtola	Remove dependency on commandline/ from oenv.cpp	commit \| commitdiff \| tree
2014-03-30	Teemu Murtola	Clean up string2.h-related includes	commit \| commitdiff \| tree
2014-03-29	Teemu Murtola	Optimize intermodule dependencies	commit \| commitdiff \| tree
2014-03-29	Teemu Murtola	Improve version information handling	commit \| commitdiff \| tree
2014-03-29	Teemu Murtola	Better include dependency graph generator	commit \| commitdiff \| tree
2014-03-27	Teemu Murtola	Move include dependency checks to doc-check	commit \| commitdiff \| tree
2014-03-27	Teemu Murtola	Better automated Doxygen documentation checker	commit \| commitdiff \| tree
2014-03-27	Teemu Murtola	Misc. Doxygen fixes	commit \| commitdiff \| tree
2014-03-27	Teemu Murtola	Move thread_mpi to src/external/	commit \| commitdiff \| tree
2014-03-24	Teemu Murtola	Remove gmxpreprocess from include path	commit \| commitdiff \| tree
2014-03-18	Teemu Murtola	Remove interactive help from core selection parser	commit \| commitdiff \| tree
2014-03-18	Teemu Murtola	Improve interactive selection input	commit \| commitdiff \| tree
2014-03-17	Teemu Murtola	Update manual analysis section	commit \| commitdiff \| tree
2014-03-11	Teemu Murtola	Fix misc. Doxygen issues	commit \| commitdiff \| tree
2014-03-08	Teemu Murtola	Remove some unnecessary declarations	commit \| commitdiff \| tree
2014-03-02	Teemu Murtola	Fix incorrect grid cell size in g_sas -nopbc	commit \| commitdiff \| tree
2014-03-01	Teemu Murtola	Move default library path search to program context	commit \| commitdiff \| tree
2014-02-28	Teemu Murtola	Residual SIMD Doxygen improvements	commit \| commitdiff \| tree
2014-02-28	Teemu Murtola	Misc. Doxygen configuration changes	commit \| commitdiff \| tree
2014-02-28	Teemu Murtola	Convert gmx-sas to the C++ framework	commit \| commitdiff \| tree
2014-02-28	Teemu Murtola	Add support for non-uniform X axis in array data	commit \| commitdiff \| tree
2014-02-27	Teemu Murtola	Improve support for data sets in C++ tools	commit \| commitdiff \| tree
2014-02-27	Teemu Murtola	Improve floating point comparisons in unit tests	commit \| commitdiff \| tree
2014-02-26	Teemu Murtola	Misc. Doxygen build system improvements	commit \| commitdiff \| tree
2014-02-26	Teemu Murtola	Fix GMX_PRIu32 and GMX_PRIu64 for MSVC	commit \| commitdiff \| tree
2014-02-20	Teemu Murtola	Add documentation for using Doxygen	commit \| commitdiff \| tree
2014-02-16	Teemu Murtola	Improve man page formatting slightly	commit \| commitdiff \| tree
2014-02-16	Teemu Murtola	Fix default enum values in help output	commit \| commitdiff \| tree
2014-02-15	Teemu Murtola	Fix some broken links in HTML pages	commit \| commitdiff \| tree
2014-02-09	Teemu Murtola	Shell completions through Options	commit \| commitdiff \| tree
2014-02-09	Teemu Murtola	Make 'gmx -h' invariant wrt. provided options	commit \| commitdiff \| tree
2014-02-09	Teemu Murtola	Remove old help formatting code	commit \| commitdiff \| tree
2014-02-09	Teemu Murtola	Make FileNameOption behave more like old filenm parser	commit \| commitdiff \| tree
2014-02-09	Teemu Murtola	Implement synopsis for help output	commit \| commitdiff \| tree
2014-02-09	Teemu Murtola	Refactor new help formatting implementation	commit \| commitdiff \| tree
2014-02-08	Teemu Murtola	Fix & update docs for GMX_TEST_OPTIONS	commit \| commitdiff \| tree
2014-02-06	Teemu Murtola	Fix build of share/template when installed	commit \| commitdiff \| tree
2014-02-03	Teemu Murtola	Merge "Merge release-4-6 into master"	commit \| commitdiff \| tree
2014-02-03	Teemu Murtola	Optimize Doxygen build	commit \| commitdiff \| tree
2014-02-02	Teemu Murtola	Fix segfault in 'gmx -h'	commit \| commitdiff \| tree
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