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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
2014-02-02	Teemu Murtola	Get rid of src/programs/gmx/	commit \| commitdiff \| tree
2014-02-02	Teemu Murtola	Simplify Options::setDescription() usage	commit \| commitdiff \| tree
2014-02-02	Teemu Murtola	Extend valgrind suppressions for OpenMPI	commit \| commitdiff \| tree
2014-02-01	Teemu Murtola	Fix some issues reported by 'make depcheck doccheck'	commit \| commitdiff \| tree
2014-01-31	Teemu Murtola	Overview docs for unit testing	commit \| commitdiff \| tree
2014-01-30	Teemu Murtola	Fix shell completions of ffMULT options	commit \| commitdiff \| tree
2014-01-30	Teemu Murtola	Overview docs for wrapper binary implementation	commit \| commitdiff \| tree
2014-01-30	Teemu Murtola	Overview docs for using Gromacs as a library	commit \| commitdiff \| tree
2014-01-30	Teemu Murtola	Rename ProgramInfo to CommandLineProgramContext	commit \| commitdiff \| tree
2014-01-30	Teemu Murtola	Refactor ProgramInfo use	commit \| commitdiff \| tree
2014-01-30	Teemu Murtola	Move command listing to 'gmx help commands'	commit \| commitdiff \| tree
2014-01-29	Teemu Murtola	Fixes to filename shell completions	commit \| commitdiff \| tree
2014-01-29	Teemu Murtola	Print common options to 'gmx -h'	commit \| commitdiff \| tree
2014-01-29	Teemu Murtola	Merge "Merge branch 'release-4-6'"	commit \| commitdiff \| tree
2014-01-28	Teemu Murtola	Shell completion export from the wrapper binary	commit \| commitdiff \| tree
2014-01-28	Teemu Murtola	Extend version information output	commit \| commitdiff \| tree
2014-01-27	Teemu Murtola	Simplify ProgramInfo	commit \| commitdiff \| tree
2014-01-22	Teemu Murtola	Use local ProgramInfo in CommandLineModuleManager	commit \| commitdiff \| tree
2014-01-21	Teemu Murtola	Remove unused split.h	commit \| commitdiff \| tree
2014-01-21	Teemu Murtola	Improve file name option help	commit \| commitdiff \| tree
2014-01-20	Teemu Murtola	Fix test reference data	commit \| commitdiff \| tree
2014-01-20	Teemu Murtola	Rewrite help output from Options	commit \| commitdiff \| tree
2014-01-19	Teemu Murtola	Fix installed headers	commit \| commitdiff \| tree
2014-01-19	Teemu Murtola	Move md5.* to fileio/	commit \| commitdiff \| tree
2014-01-19	Teemu Murtola	Move strdb.* to src/gromacs/fileio/	commit \| commitdiff \| tree
2014-01-16	Teemu Murtola	Fix build with GMX_BUILD_UNITTESTS=OFF	commit \| commitdiff \| tree
2014-01-15	Teemu Murtola	Support for 64-bit int and real valued Options	commit \| commitdiff \| tree
2014-01-15	Teemu Murtola	Remove unused PCA_KEEP_ARGS	commit \| commitdiff \| tree
2014-01-15	Teemu Murtola	Unit tests for parse_common_args()	commit \| commitdiff \| tree
2014-01-15	Teemu Murtola	Simplify C array handling in C++ code	commit \| commitdiff \| tree
2014-01-15	Teemu Murtola	Reorganize shared unit test code	commit \| commitdiff \| tree
2014-01-14	Teemu Murtola	Don't install links.dat	commit \| commitdiff \| tree
2014-01-14	Teemu Murtola	Split CommandLineHelpModule into a separate file	commit \| commitdiff \| tree
2014-01-14	Teemu Murtola	Fix line wrapping for long options	commit \| commitdiff \| tree
2014-01-13	Teemu Murtola	Move writeps.* into fileio/	commit \| commitdiff \| tree
2014-01-13	Teemu Murtola	Move gmxcomplex.h to gromacs/math/	commit \| commitdiff \| tree
2014-01-13	Teemu Murtola	Fix installation of HTML manual	commit \| commitdiff \| tree
2014-01-09	Teemu Murtola	Add messages for skipped tests in make check	commit \| commitdiff \| tree
2014-01-09	Teemu Murtola	Fix copyright check in admin/uncrustify.sh	commit \| commitdiff \| tree
2014-01-08	Teemu Murtola	Move gmx_sort.* to src/gromacs/utility/	commit \| commitdiff \| tree
2014-01-07	Teemu Murtola	Move gstat.h to gmxana/	commit \| commitdiff \| tree
2014-01-07	Teemu Murtola	Improve include dependency script	commit \| commitdiff \| tree
2014-01-05	Teemu Murtola	Support for default values for SelectionOption	commit \| commitdiff \| tree
2014-01-04	Teemu Murtola	Fix #include style issues	commit \| commitdiff \| tree
2014-01-04	Teemu Murtola	Don't print quotes on gmx_fatal()	commit \| commitdiff \| tree
2014-01-01	Teemu Murtola	Add copyright year 2013 to files modified this year	commit \| commitdiff \| tree
2014-01-01	Teemu Murtola	Include CUDA and latex files in copyright check	commit \| commitdiff \| tree
2014-01-01	Teemu Murtola	Suppress remaining errors from copyright script	commit \| commitdiff \| tree
2014-01-01	Teemu Murtola	Fix remaining copyright headers	commit \| commitdiff \| tree
2014-01-01	Teemu Murtola	More copyright header updates	commit \| commitdiff \| tree
2014-01-01	Teemu Murtola	Remove obsolete large file support info	commit \| commitdiff \| tree
2013-12-30	Teemu Murtola	More robust shell detection in GMXRC	commit \| commitdiff \| tree
2013-12-30	Teemu Murtola	Initialize default index groups for C++ tools	commit \| commitdiff \| tree
2013-12-29	Teemu Murtola	Minor vec.h cleanup	commit \| commitdiff \| tree
2013-12-29	Teemu Murtola	Fix pkgconfig flags with internal Boost	commit \| commitdiff \| tree
2013-12-29	Teemu Murtola	Reset SOVERSION for libgromacs	commit \| commitdiff \| tree
2013-12-28	Teemu Murtola	Change use of compiler flags with GPU + C++11	commit \| commitdiff \| tree
2013-12-28	Teemu Murtola	Move bin/lib suffix management into separate file.	commit \| commitdiff \| tree
2013-12-24	Teemu Murtola	Move shell completion things into a separate file	commit \| commitdiff \| tree
2013-12-24	Teemu Murtola	Get rid of set_default_file_name()	commit \| commitdiff \| tree
2013-12-21	Teemu Murtola	Move parse_common_args() into commandline/pargs.*	commit \| commitdiff \| tree
2013-12-21	Teemu Murtola	Move pargs.cpp into src/gromacs/commandline/	commit \| commitdiff \| tree
2013-12-20	Teemu Murtola	Move Program() and ShortProgram() into copyrite.h	commit \| commitdiff \| tree
2013-12-20	Teemu Murtola	Clean up trajectory time control	commit \| commitdiff \| tree
2013-12-18	Teemu Murtola	Clean up old command line parsing	commit \| commitdiff \| tree
2013-12-08	Teemu Murtola	Don't create symlinks in the build tree	commit \| commitdiff \| tree
2013-12-04	Teemu Murtola	Fix test build with GMX_BUILD_MDRUN_ONLY	commit \| commitdiff \| tree
2013-12-02	Teemu Murtola	Remove remaining uses of programs.txt	commit \| commitdiff \| tree
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