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2015-10-03	Teemu Murtola	Use more std::vector for solvate/insert-molecules	commit \| commitdiff \| tree
2015-10-03	Teemu Murtola	Use std::vector for makeExclusionDistances()	commit \| commitdiff \| tree
2015-10-03	Teemu Murtola	Remove SelectionOptionBehavior::useDefaultGroups	commit \| commitdiff \| tree
2015-10-03	Teemu Murtola	Move reusable code into SelectionOptionBehavior	commit \| commitdiff \| tree
2015-10-03	Teemu Murtola	Add --ref-data update-changed	commit \| commitdiff \| tree
2015-10-03	Teemu Murtola	Make cmdlinerunner.cpp use ICommandLineOptionsModule	commit \| commitdiff \| tree
2015-10-02	Teemu Murtola	More flexible API for xvg testing	commit \| commitdiff \| tree
2015-10-02	Teemu Murtola	More headers out of legacyheaders	commit \| commitdiff \| tree
2015-10-01	Teemu Murtola	Enable time unit and selections in ICommandLineOptionsModule	commit \| commitdiff \| tree
2015-10-01	Teemu Murtola	Convert nb_free_energy.c to C++	commit \| commitdiff \| tree
2015-10-01	Teemu Murtola	Move mdoutf and trajectory_writing to mdlib	commit \| commitdiff \| tree
2015-09-27	Teemu Murtola	Remove unnecessary includes from legacyheaders/	commit \| commitdiff \| tree
2015-09-27	Teemu Murtola	Move viewit.* to commandline/	commit \| commitdiff \| tree
2015-09-27	Teemu Murtola	More headers out of legacyheaders	commit \| commitdiff \| tree
2015-09-26	Teemu Murtola	Remove types/membedt.h	commit \| commitdiff \| tree
2015-09-25	Teemu Murtola	More legacyheaders to gmxlib/mdlib	commit \| commitdiff \| tree
2015-09-25	Teemu Murtola	Move some headers from legacyheaders to mdlib/gmxlib	commit \| commitdiff \| tree
2015-09-25	Teemu Murtola	Remove types/shellfc.h	commit \| commitdiff \| tree
2015-09-25	Teemu Murtola	Remove some extern "C" declarations	commit \| commitdiff \| tree
2015-09-22	Teemu Murtola	Move oenv.* to fileio/	commit \| commitdiff \| tree
2015-09-22	Teemu Murtola	Reduce use of output_env_t from types/oenv.h	commit \| commitdiff \| tree
2015-09-19	Teemu Murtola	Convert calc_verletbuf.c to C++	commit \| commitdiff \| tree
2015-09-18	Teemu Murtola	Remove unused macros.h includes (fix build)	commit \| commitdiff \| tree
2015-09-18	Teemu Murtola	Move asize() from macros.h and reduce use of macros.h	commit \| commitdiff \| tree
2015-09-18	Teemu Murtola	Create topology/atom_id.h	commit \| commitdiff \| tree
2015-09-11	Teemu Murtola	Build script for coverage	commit \| commitdiff \| tree
2015-09-10	Teemu Murtola	Run clang analysis for test code	commit \| commitdiff \| tree
2015-09-08	Teemu Murtola	Improve gmx sasa error message	commit \| commitdiff \| tree
2015-09-08	Teemu Murtola	Refactor reference data checking	commit \| commitdiff \| tree
2015-09-08	Teemu Murtola	Minor build script improvements	commit \| commitdiff \| tree
2015-09-08	Teemu Murtola	Reduce coupling between refdata and libxml2	commit \| commitdiff \| tree
2015-09-08	Teemu Murtola	Refactor TestReferenceData lifetime management	commit \| commitdiff \| tree
2015-09-01	Teemu Murtola	Build scripts for new releng	commit \| commitdiff \| tree
2015-08-29	Teemu Murtola	Remove separate title parameter for read_tps_conf()	commit \| commitdiff \| tree
2015-08-29	Teemu Murtola	Fix memory leaks in read_tps_conf() and some callers	commit \| commitdiff \| tree
2015-08-28	Teemu Murtola	Remove read_stx_conf() and get_stx_coordnum() uses	commit \| commitdiff \| tree
2015-08-15	Teemu Murtola	Merge "Merge branch release-5-1 into master"	commit \| commitdiff \| tree
2015-07-25	Teemu Murtola	Remove Options::isSet()	commit \| commitdiff \| tree
2015-07-25	Teemu Murtola	Add basic grouping to Options	commit \| commitdiff \| tree
2015-07-25	Teemu Murtola	Extract IOptionsContainer from Options	commit \| commitdiff \| tree
2015-07-24	Teemu Murtola	Rename trnio routines	commit \| commitdiff \| tree
2015-07-24	Teemu Murtola	Rename trnio.* to trrio.*	commit \| commitdiff \| tree
2015-07-23	Teemu Murtola	Split espresso I/O routines from confio.cpp	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Split gro I/O routines from confio.cpp	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Split g96 I/O routines from confio.cpp	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Move read_tps_conf() to confio.h	commit \| commitdiff \| tree
2015-07-22	Teemu Murtola	Add basic tests for reading/writing structure files	commit \| commitdiff \| tree
2015-07-20	Teemu Murtola	Merge release-5-0 into release-5-1	commit \| commitdiff \| tree
2015-07-18	Teemu Murtola	Move Options::setDescription() elsewhere	commit \| commitdiff \| tree
2015-07-18	Teemu Murtola	Change naming convention for C++ interfaces	commit \| commitdiff \| tree
2015-07-10	Teemu Murtola	More gmxfio simplification	commit \| commitdiff \| tree
2015-07-09	Teemu Murtola	Fix -deffnm -multi[dir]	commit \| commitdiff \| tree
2015-07-07	Teemu Murtola	Wrap uses of thread_mpi/mutex.h	commit \| commitdiff \| tree
2015-07-05	Teemu Murtola	Improve gmx help -export Sphinx rebuild behavior	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Fix error wrapping in interactive selection input	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Tests for interactive selection input	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Fix copy-paste bug in gmx distance	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Refactor for testing interactive selection input	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Remove gmx::File (except for File::exists())	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Replace direct uses of gmx::File with streams	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Bump various version numbers	commit \| commitdiff \| tree
2015-07-04	Teemu Murtola	Make some unit tests use mock file output	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Convert gmxfio to C++	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Remove status messages about Sphinx detection	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Clean up gmxfio includes	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Reorder code within gmxfio	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Further gmxfio cleanup related to xdr handling	commit \| commitdiff \| tree
2015-07-02	Teemu Murtola	Minor include sorting changes	commit \| commitdiff \| tree
2015-07-01	Teemu Murtola	Clean up unused code from gmxfio	commit \| commitdiff \| tree
2015-06-29	Teemu Murtola	Only accept exact matches for selection keywords	commit \| commitdiff \| tree
2015-06-29	Teemu Murtola	Make some unit tests skip file system access	commit \| commitdiff \| tree
2015-06-27	Teemu Murtola	Document tool changes in 5.1	commit \| commitdiff \| tree
2015-06-25	Teemu Murtola	Move documentation on tool changes from wiki	commit \| commitdiff \| tree
2015-06-17	Teemu Murtola	Minor clean up for refdata.*	commit \| commitdiff \| tree
2015-06-17	Teemu Murtola	Improve logic for automatic selection names	commit \| commitdiff \| tree
2015-06-16	Teemu Murtola	Fix broken links from the old flow chart	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Update help output	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Improve uncrustify Jenkins builds	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Initial docs for Jenkins integration	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Initial build system documentation in dev guide	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Improve Jenkins docs build	commit \| commitdiff \| tree
2015-06-12	Teemu Murtola	Extend source layout description in dev guide	commit \| commitdiff \| tree
2015-06-11	Teemu Murtola	Script for Jenkins documentation build	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Misc. improvements to docs build system	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Add description of relocatable binaries	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Resolve one TODO for command line help tests	commit \| commitdiff \| tree
2015-06-09	Teemu Murtola	Improve user guide text for command line interface	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Fix potential FPE in selection tests	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Refactor rst parsing for console output	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Replace gromacs.7 man page with gmx.1	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Document current help formatting	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Basic support for titles within tool help	commit \| commitdiff \| tree
2015-06-04	Teemu Murtola	Support rst tables in tool help texts	commit \| commitdiff \| tree
2015-05-28	Teemu Murtola	Improve lists in user guide for selections	commit \| commitdiff \| tree
2015-05-28	Teemu Murtola	Additional selection examples	commit \| commitdiff \| tree
2015-05-25	Teemu Murtola	Overview docs for analysis nbsearch	commit \| commitdiff \| tree
2015-05-24	Teemu Murtola	Include selection keyword details in user guide	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Allow any order for sections in 'gmx help -export'	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Base to get all 'gmx help' contents to user guide	commit \| commitdiff \| tree
2015-05-22	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
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