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2015-02-13	Teemu Murtola	Replace some [BR] in help texts with rst literals	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Move flow chart from old-html to Sphinx	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Make (most) HTML links to file formats work again	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Convert file format descriptions to rst	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Generate man pages through Sphinx	commit \| commitdiff \| tree
2015-02-13	Teemu Murtola	Replace tool HTML help with Sphinx-generated docs	commit \| commitdiff \| tree
2015-02-07	Teemu Murtola	Support more complex fixed position selections	commit \| commitdiff \| tree
2015-01-29	Teemu Murtola	Add input file options that accept missing files	commit \| commitdiff \| tree
2015-01-24	Teemu Murtola	Remove old selection parser error handling code	commit \| commitdiff \| tree
2015-01-24	Teemu Murtola	Improve selection error messages (use exceptions)	commit \| commitdiff \| tree
2015-01-23	Teemu Murtola	Ignore test-only dependency cycles	commit \| commitdiff \| tree
2015-01-20	Teemu Murtola	Make data file path search more reusable	commit \| commitdiff \| tree
2015-01-20	Teemu Murtola	Convert forcefield search to C++	commit \| commitdiff \| tree
2015-01-19	Teemu Murtola	Remove AnalysisNeighborhood::setUseBoundingBox()	commit \| commitdiff \| tree
2015-01-17	Teemu Murtola	Merge "Merge branch release-5-0"	commit \| commitdiff \| tree
2015-01-08	Teemu Murtola	Refactor logic for finding share/top/ files	commit \| commitdiff \| tree
2015-01-08	Teemu Murtola	Closed some .xvg files that were being left open	commit \| commitdiff \| tree
2015-01-07	Teemu Murtola	Custom program context for unit tests	commit \| commitdiff \| tree
2015-01-07	Teemu Murtola	Split unit test init from testoptions.cpp	commit \| commitdiff \| tree
2015-01-06	Teemu Murtola	Use analysis nbsearch for surface area calculation	commit \| commitdiff \| tree
2015-01-06	Teemu Murtola	Use xvgrclose() for files opened with xvgropen()	commit \| commitdiff \| tree
2015-01-05	Teemu Murtola	Support subset of rvec array as input for analysis...	commit \| commitdiff \| tree
2015-01-05	Teemu Murtola	Minimal C++ replacement for rvec	commit \| commitdiff \| tree
2015-01-05	Teemu Murtola	Clarify GMX_MPI management	commit \| commitdiff \| tree
2015-01-03	Teemu Murtola	Minor selection clarifications	commit \| commitdiff \| tree
2015-01-03	Teemu Murtola	Fix crash with 'z of ...' within an expression	commit \| commitdiff \| tree
2015-01-02	Teemu Murtola	Update copyright year in copyrite.cpp	commit \| commitdiff \| tree
2014-12-28	Teemu Murtola	Convert gmx-insert-molecules into proper C++ module	commit \| commitdiff \| tree
2014-12-28	Teemu Murtola	Add helper for generic C++ command-line modules	commit \| commitdiff \| tree
2014-12-18	Teemu Murtola	Rework gmx-solvate to use analysis nbsearch	commit \| commitdiff \| tree
2014-12-17	Teemu Murtola	Make 'gmx sasa' calculation thread-safe	commit \| commitdiff \| tree
2014-12-17	Teemu Murtola	Remove some backwards-compatibility glue for Jenkins	commit \| commitdiff \| tree
2014-12-16	Teemu Murtola	Make 'gmx sasa' volume computation translation-invariant	commit \| commitdiff \| tree
2014-12-15	Teemu Murtola	Use new XML format with cppcheck	commit \| commitdiff \| tree
2014-12-14	Teemu Murtola	C++ interface for surface area calculation	commit \| commitdiff \| tree
2014-12-11	Teemu Murtola	Convert gmx rdf to the C++ framework	commit \| commitdiff \| tree
2014-12-10	Teemu Murtola	Fix misc. analysis neighborhood search issues	commit \| commitdiff \| tree
2014-12-09	Teemu Murtola	Track locations for selection parsing products	commit \| commitdiff \| tree
2014-12-08	Teemu Murtola	Rectangular grid for analysis nbsearch	commit \| commitdiff \| tree
2014-12-06	Teemu Murtola	Simplify analysisdata parallelism model	commit \| commitdiff \| tree
2014-12-05	Teemu Murtola	Improve selection parsing error reporting	commit \| commitdiff \| tree
2014-12-05	Teemu Murtola	Non-periodic nbsearch with grid based on bounding box	commit \| commitdiff \| tree
2014-12-04	Teemu Murtola	Move/add uncrustify documentation to dev manual	commit \| commitdiff \| tree
2014-12-02	Teemu Murtola	Add 'gmx pairdist' tool as partial g_mindist replacement	commit \| commitdiff \| tree
2014-12-02	Teemu Murtola	Analysis grid nbsearch for more cases	commit \| commitdiff \| tree
2014-11-29	Teemu Murtola	Basic support for 'z of ...' selections	commit \| commitdiff \| tree
2014-11-28	Teemu Murtola	Clarify memory management for selection values	commit \| commitdiff \| tree
2014-11-28	Teemu Murtola	Helper function for grouping selection positions	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	Clean up gmx solvate	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	Port gmx-solvate tests to use CommandLineTestBase	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	More control over file backups	commit \| commitdiff \| tree
2014-11-27	Teemu Murtola	Further insert-molecules cleanup	commit \| commitdiff \| tree
2014-11-26	Teemu Murtola	Convert surface area calculation to C++	commit \| commitdiff \| tree
2014-11-26	Teemu Murtola	Add some unit tests for surface area calculation	commit \| commitdiff \| tree
2014-11-23	Teemu Murtola	Rename doc-* targets to be less generic	commit \| commitdiff \| tree
2014-11-21	Teemu Murtola	Describe doc-check in developer manual	commit \| commitdiff \| tree
2014-11-21	Teemu Murtola	Skeleton for a developer manual	commit \| commitdiff \| tree
2014-11-14	Teemu Murtola	Refactor position-evaluated selection keyword handling	commit \| commitdiff \| tree
2014-10-30	Teemu Murtola	Add more selection unit tests	commit \| commitdiff \| tree
2014-10-30	Teemu Murtola	Fix more memory leaks in default group creation	commit \| commitdiff \| tree
2014-10-30	Teemu Murtola	Fix memory leak in default index group creation	commit \| commitdiff \| tree
2014-10-29	Teemu Murtola	Merge release-5-0 into master	commit \| commitdiff \| tree
2014-10-29	Teemu Murtola	Improve analysis nbsearch grid mapping	commit \| commitdiff \| tree
2014-10-28	Teemu Murtola	Avoid common.h inclusion in CUDA code	commit \| commitdiff \| tree
2014-10-23	Teemu Murtola	Move truncate() wrapper to futil.h	commit \| commitdiff \| tree
2014-10-23	Teemu Murtola	Encapsulate use of nice()	commit \| commitdiff \| tree
2014-10-22	Teemu Murtola	Collect more platform-specific code to sysinfo.h	commit \| commitdiff \| tree
2014-10-22	Teemu Murtola	Rename common.h to classhelpers.h	commit \| commitdiff \| tree
2014-10-22	Teemu Murtola	Move basic macros from common.h to basedefinitions.h	commit \| commitdiff \| tree
2014-10-14	Teemu Murtola	Check config.h usage in doc-check	commit \| commitdiff \| tree
2014-10-14	Teemu Murtola	Use analysis nbsearch in insert-molecules	commit \| commitdiff \| tree
2014-10-11	Teemu Murtola	Clean up gmx insert-molecules	commit \| commitdiff \| tree
2014-10-11	Teemu Murtola	Make 'gmx insert-molecules' tests test output	commit \| commitdiff \| tree
2014-10-11	Teemu Murtola	Generalize command-line unit testing machinery	commit \| commitdiff \| tree
2014-10-03	Teemu Murtola	More robust handling for installed headers	commit \| commitdiff \| tree
2014-09-23	Teemu Murtola	Reorganize CPack management	commit \| commitdiff \| tree
2014-09-23	Teemu Murtola	Generate man pages and completions by default if possible	commit \| commitdiff \| tree
2014-09-22	Teemu Murtola	Merge "Merge release-5-0 into master"	commit \| commitdiff \| tree
2014-09-21	Teemu Murtola	Introduce a variable to identify in-source build	commit \| commitdiff \| tree
2014-09-21	Teemu Murtola	Skip man/html/completion generation if not needed	commit \| commitdiff \| tree
2014-09-20	Teemu Murtola	Remove duplication in version info target creation	commit \| commitdiff \| tree
2014-09-20	Teemu Murtola	Fix patterns for .gitattributes	commit \| commitdiff \| tree
2014-09-19	Teemu Murtola	Proper dependencies for Doxygen build rules	commit \| commitdiff \| tree
2014-09-19	Teemu Murtola	Fix histogram resampling output bin positions	commit \| commitdiff \| tree
2014-09-19	Teemu Murtola	Embed module dependency graph in Doxygen docs	commit \| commitdiff \| tree
2014-09-19	Teemu Murtola	Add support for cumulative histograms	commit \| commitdiff \| tree
2014-09-19	Teemu Murtola	More precise analysisdata histogram accumulation	commit \| commitdiff \| tree
2014-09-19	Teemu Murtola	Misc. Doxygen build system improvements	commit \| commitdiff \| tree
2014-09-13	Teemu Murtola	Extend support for float/double tolerances in testing	commit \| commitdiff \| tree
2014-09-13	Teemu Murtola	Declare __STDC_*_MACROS in gmxpre.h	commit \| commitdiff \| tree
2014-09-12	Teemu Murtola	Run include order check in doc-check	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Improve uncrustify.sh return code handling	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Include directive sorter	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Add gmx_getpid()	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Move _GNU_SOURCE to gmxpre.h	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Sort includes outside src/gromacs	commit \| commitdiff \| tree
2014-09-11	Teemu Murtola	Sort all includes in src/gromacs	commit \| commitdiff \| tree
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
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