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Replace all command line parsing with Options
2014-06-07 Teemu MurtolaReplace all command line parsing with Options
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2014-06-07 Teemu MurtolaMove residuetype handling to its own file.
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2014-06-07 Teemu MurtolaRemove support for "old" index file format
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2014-06-07 Teemu MurtolaMove index.* to topology/
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2014-06-02 Teemu MurtolaMove atomprop.* to topology/
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2014-05-31 Teemu MurtolaMove mtop_util.* and topsort.* to topology/
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2014-05-29 Teemu MurtolaRemove more uses of typedefs.h
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2014-05-25 Teemu MurtolaMove general functions out of typedefs.h
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2014-05-25 Teemu MurtolaRemove some typedefs.h dependencies
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2014-05-25 Teemu MurtolaMove types/topology.h to topology/
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2014-05-24 Teemu MurtolaMove types/idef.h to topology/
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2014-05-24 Teemu MurtolaMove types/atoms.h to topology/
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2014-05-24 Teemu MurtolaMove types/ishift.h to pbcutil/
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2014-05-24 Teemu MurtolaMove invblock.* to topology/
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2014-05-24 Teemu MurtolaMove types/block.h to topology/
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2014-05-24 Teemu MurtolaMove symtab.* to topology/
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2014-05-24 Teemu MurtolaMerge t_symtab into symtab.h
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2014-05-24 Teemu MurtolaMove pbc.* to pbcutil/
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2014-05-22 Teemu MurtolaMove cinvsqrtdata.c to math/ and remove Fortran remnants
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2014-05-22 Teemu MurtolaFix static group list indices in selection prompt
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2014-05-22 Teemu MurtolaMerge t_pbc definition into pbc.h
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2014-05-21 Teemu MurtolaMove mshift.* to pbcutil/
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2014-05-21 Teemu MurtolaMerge t_graph definition into mshift.h
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2014-05-20 Teemu MurtolaMove rmpbc.* to pbcutil/
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2014-05-18 Teemu MurtolaClean up matio.*
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2014-05-18 Teemu MurtolaMove 3dview.* to programs/view/
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2014-05-18 Teemu MurtolaClean up math/
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2014-05-17 Teemu MurtolaMore elaborate default handling for FileNameOption
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2014-05-17 Teemu MurtolaUnit tests for parse_common_args() file options
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2014-05-14 Teemu MurtolaMove physics.* to math/units.*
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2014-05-01 Teemu MurtolaFix incorrect limits in FloatOptionStorage
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2014-04-28 Teemu MurtolaMove mtxio.* to fileio/
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2014-04-27 Teemu MurtolaMove rvec and friends to math/vectypes.h
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2014-04-27 Teemu MurtolaMove 'real' definition to utility/real.h
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2014-04-17 Teemu MurtolaMove vec.h to math/
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2014-04-16 Teemu MurtolaRemove unused minvert.h
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2014-04-16 Teemu MurtolaFix typo in fatalerror.h
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2014-04-16 Teemu MurtolaMove xvgr.* to fileio/
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2014-04-16 Teemu MurtolaClean up xvgr.h and viewit.h usage
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2014-04-16 Teemu MurtolaRemove sysstuff.h
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2014-04-16 Teemu MurtolaRemove sysstuff.h includes from headers
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2014-04-16 Teemu MurtolaRefactor gmx_fatal()
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2014-04-13 Teemu MurtolaRemove unused shift.h
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2014-04-13 Teemu MurtolaRemove utility -> fileio dependencies
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2014-04-13 Teemu MurtolaClean up futil.*
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2014-04-10 Teemu MurtolaClean up and fix issues in doc-check scripts
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2014-04-10 Teemu MurtolaMove part of types/simple.h to utility/
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2014-04-10 Teemu MurtolaRemove utility/ dependencies on network.h and main.h
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2014-04-08 Teemu MurtolaRemove some utility -> legacyheaders dependencies
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2014-04-08 Teemu MurtolaVersion bump for post-5.0 development
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2014-04-08 Teemu MurtolaMove gmx_fatal.* to utility/fatalerror.*
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2014-04-07 Teemu MurtolaDoxygen documentation for version.h
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2014-04-04 Teemu MurtolaRemove ancient SGI-specific code
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2014-04-04 Teemu MurtolaClean up gmx_fatal.*
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2014-04-02 Teemu MurtolaMove string2.* to utility/cstringutil.*
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2014-04-01 Teemu MurtolaMove smalloc.h to utility/
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2014-03-31 Teemu MurtolaRemove #include <...> for local files in gmx-view
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2014-03-31 Teemu MurtolaClean up smalloc.h
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2014-03-31 Teemu MurtolaMove some math headers away from legacyheaders/
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2014-03-31 Teemu MurtolaRemove dependency on commandline/ from oenv.cpp
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2014-03-30 Teemu MurtolaClean up string2.h-related includes
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2014-03-29 Teemu MurtolaOptimize intermodule dependencies
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2014-03-29 Teemu MurtolaImprove version information handling
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2014-03-29 Teemu MurtolaBetter include dependency graph generator
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2014-03-27 Teemu MurtolaMove include dependency checks to doc-check
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2014-03-27 Teemu MurtolaBetter automated Doxygen documentation checker
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2014-03-27 Teemu MurtolaMisc. Doxygen fixes
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2014-03-27 Teemu MurtolaMove thread_mpi to src/external/
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2014-03-24 Teemu MurtolaRemove gmxpreprocess from include path
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2014-03-18 Teemu MurtolaRemove interactive help from core selection parser
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2014-03-18 Teemu MurtolaImprove interactive selection input
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2014-03-17 Teemu MurtolaUpdate manual analysis section
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2014-03-11 Teemu MurtolaFix misc. Doxygen issues
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2014-03-08 Teemu MurtolaRemove some unnecessary declarations
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2014-03-02 Teemu MurtolaFix incorrect grid cell size in g_sas -nopbc
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2014-03-01 Teemu MurtolaMove default library path search to program context
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2014-02-28 Teemu MurtolaResidual SIMD Doxygen improvements
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2014-02-28 Teemu MurtolaMisc. Doxygen configuration changes
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2014-02-28 Teemu MurtolaConvert gmx-sas to the C++ framework
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2014-02-28 Teemu MurtolaAdd support for non-uniform X axis in array data
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2014-02-27 Teemu MurtolaImprove support for data sets in C++ tools
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2014-02-27 Teemu MurtolaImprove floating point comparisons in unit tests
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2014-02-26 Teemu MurtolaMisc. Doxygen build system improvements
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2014-02-26 Teemu MurtolaFix GMX_PRIu32 and GMX_PRIu64 for MSVC
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2014-02-20 Teemu MurtolaAdd documentation for using Doxygen
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2014-02-16 Teemu MurtolaImprove man page formatting slightly
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2014-02-16 Teemu MurtolaFix default enum values in help output
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2014-02-15 Teemu MurtolaFix some broken links in HTML pages
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2014-02-09 Teemu MurtolaShell completions through Options
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2014-02-09 Teemu MurtolaMake 'gmx -h' invariant wrt. provided options
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2014-02-09 Teemu MurtolaRemove old help formatting code
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2014-02-09 Teemu MurtolaMake FileNameOption behave more like old filenm parser
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2014-02-09 Teemu MurtolaImplement synopsis for help output
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2014-02-09 Teemu MurtolaRefactor new help formatting implementation
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2014-02-08 Teemu MurtolaFix & update docs for GMX_TEST_OPTIONS
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2014-02-06 Teemu MurtolaFix build of share/template when installed
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2014-02-03 Teemu MurtolaMerge "Merge release-4-6 into master"
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2014-02-03 Teemu MurtolaOptimize Doxygen build
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2014-02-02 Teemu MurtolaFix segfault in 'gmx -h'
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2014-02-02 Teemu MurtolaGet rid of src/programs/gmx/
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