# # ChangeLog for / # # Generated by Trac 1.6 # Jun 1, 2025, 5:12:19 PM Wed, 28 Dec 2011 15:24:24 GMT Frederik Heber [68c923] * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/IPointCloud.hpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) Lots of small compiler warning fixes. Issues: - non-virtual ... Wed, 28 Dec 2011 15:24:23 GMT Frederik Heber [de29ad6] * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) Some optimization to speed up Subgraph dissections. - Replaced ... Thu, 10 Nov 2011 16:05:43 GMT Frederik Heber [bde4a6] * configure.ac (modified) Set version to 1.2.0 - Molecuilder library is now 6:0:0. - ... Thu, 10 Nov 2011 16:05:39 GMT Frederik Heber [936a02] * data/bondtables/bondtable.dat (added) * data/databases/Hbondangle.db (moved) * data/databases/Hbonddistance.db (moved) * data/databases/elements.db (moved) * data/databases/orbitals.db (moved) * data/databases/valence.db (moved) * data/molecules/ATPase.pdb (added) * data/molecules/AntifreezeProtein.pdb (added) * data/molecules/bpti.pdb (added) * data/molecules/oxirane.pdb (added) * data/molecules/portlandite.pdb (added) * data/molecules/propene.pdb (added) * data/molecules/testosterone.pdb (added) * data/molecules/tmv_periodic_segment.pdb (added) * data/molecules/tmv_periodic_tube.pdb (added) * data/molecules/water.pdb (added) * src/Makefile.am (modified) * src/documentation/data.dox (added) * src/documentation/mainpage.dox (modified) Creating data dir for bondtables, databases, and molecules. - Moved ... Thu, 10 Nov 2011 11:23:54 GMT Frederik Heber [1a041f] * src/documentation/debug.dox (added) DOCU: added documentation on how to debug the code. Thu, 10 Nov 2011 11:23:49 GMT Frederik Heber [04e1fb] * configure.ac (modified) * utils/Makefile.am (modified) * utils/python_wrapper.in (added) Added rules to utils/Makefile.am such that python script can be ... Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [938ffd] * Makefile.am (modified) * configure.ac (modified) * utils/Makefile.am (added) Added Makefile to utils to install python scripts. Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [0d571d7] * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) DISTCHECKFIX: Forgot to set write permissions for new ec.data test ... Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [a55be1] * tests/regression/Makefile.am (modified) DISTCHECKFIX: testsuite does not depends on run scripts. - ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [12facf] * src/Actions/hello.cpp (deleted) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/Pythontest/testsuite-python-pythontest.at (deleted) * tests/regression/Python/testsuite-python.at (modified) Removed now obsolete Pythontest including regression test. - as ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [dd0f1b] * tests/CodeChecks/testsuite-config_h.at (modified) DISTCHECKFIX: Added AllActionPython.hpp and AllActionHeaders.hpp to ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [48d3c0] * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) DISTCHECKFIX: Added some missing header files in src/Actions. - ... Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [4269ca] * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) FIX: Some Qt includes were not style-consistent. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [5dfeeb] * LinearAlgebra/doc/Makefile.am (modified) * doc/Makefile.am (modified) DISTCHECKFIX: Added forgotten Doxyfile to EXTRA_DIST. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [24da48] * src/Actions/Makefile.am (modified) DISTCHECKFIX: Added missing ActionTraits.hpp to src/Actions/Makefile.am. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [c1ab1f] * src/Actions/Makefile.am (modified) DISTCHECKFIX: Added all Reaction...hpp to src/Actions/Makefile.am. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [ed3000] * Makefile.am (modified) DISTCHECKFIX: Removed bnv_have_qt.m4 from EXTRA_DIST. Mon, 07 Nov 2011 18:34:05 GMT Frederik Heber [e85bf2] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-globallistofactions_hpp.at (added) * tests/CodeChecks/testsuite.at (modified) Added code check test whether every .def's Action is listed in ... Mon, 07 Nov 2011 18:33:50 GMT Frederik Heber [5ab796] * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/moltest_check.py (added) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (added) * tests/regression/Python/testsuite-python.at (modified) Added regression test on whether all options in the python module are ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [f894fe] * utils/boxmaker.py.in (modified) Changed GetSourceMolareMass() and GetSourceBBabs() of boxmaker.py. ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [f89b45] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/listcmds.py (added) * tests/regression/Python/AllActions/moltest.py (modified) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) Added Reaction CalculateBoundingBoxAction. - calculate bounding box ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [55f299] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateMolarMass/pre/argon.xyz (added) * tests/regression/Analysis/CalculateMolarMass/pre/water.xyz (added) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/options.dat (modified) Added Reaction CalculateMolarMassAction. - calculate molar mass ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [6c61a9] * tests/regression/Makefile.am (modified) * tests/regression/Python/BoxMaker/post/out.data (added) * tests/regression/Python/BoxMaker/post/out.xyz (added) * tests/regression/Python/BoxMaker/pre/argon.data (added) * tests/regression/Python/BoxMaker/pre/argon.potentials (added) * tests/regression/Python/BoxMaker/pre/argon.tremolo (added) * tests/regression/Python/BoxMaker/testsuite-python-boxmaker.at (added) * tests/regression/Python/testsuite-python.at (modified) Added regression test for boxmaker.py. Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [2aa9ef] * utils/boxmaker.py.in (modified) UpdateSource function of boxmaker.py is not an external call to ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [dfef3f] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/cleanUp.cpp (modified) FIX: empty states Action::success and ::failure are now managed by ... Mon, 07 Nov 2011 16:13:17 GMT Frederik Heber [d628da] * src/Actions/Action_impl_python.hpp (modified) Added docstring also to python exported functions without any ... Mon, 07 Nov 2011 16:13:17 GMT Frederik Heber [567357] * src/Actions/pyMoleCuilder.cpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) FIX: cleanUp() replaced by module_reinit() and .._exit() in ... Mon, 07 Nov 2011 16:13:01 GMT Frederik Heber [b5d38d] * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) Moved dumpMemory() and saveAll() from module builder_init to cleanUp. Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [bcfb77] * configure.ac (modified) * utils/boxmaker.py.in (moved) Added correct shebang to boxmaker.py. - also configure fills in ... Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [239cc5] * utils/boxmaker.py (modified) Didn't save the file -.-" Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [bfbb62] * utils/boxmaker.py (modified) Final version 1.0 - Added shebang line - Added short file ... Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [c0c85f] * utils/boxmaker.py (modified) Restructured Code - temp_source.xyz is created only once - boolean ... Mon, 07 Nov 2011 16:12:25 GMT Frederik Heber [b82ede] * utils/HOWTO-boxmaker (added) Very basic documentation on how to use boxmaker Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [0ad49c] * utils/boxmaker.py (modified) Update: Automatic mass calculation Also: - Shortcut for every option Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [39cbae] * utils/boxmaker.py (modified) Update: Unit handling - temp might have a dimension now - Leading ... Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [751d7f1] * utils/boxmaker.py (modified) Update: Shortcuts for common Parameters Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [32bc47] * utils/boxmaker.py (modified) Update: autorotate Not tested yet, but it seems like it does ... Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [0c83d8] * utils/boxmaker.py (modified) Less ugly advanced version - Class (struct) based global options - ... Mon, 07 Nov 2011 16:12:24 GMT Frederik Heber [5735ba] * utils/boxmaker.py (added) Ugly base version of boxmaker.py TODO: - stability fixes - ... Mon, 07 Nov 2011 12:24:07 GMT Frederik Heber [54088a] * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (added) * tests/regression/Python/testsuite-python.at (modified) Added first Reaction named CalculateCellVolumeAction. - this sets ... Mon, 07 Nov 2011 12:24:06 GMT Frederik Heber [6aa485] * src/Actions/Action_impl_python.hpp (modified) * src/Actions/Action_impl_undef.hpp (modified) Actions exported to Python may contain a returntype. - returntype ... Mon, 07 Nov 2011 12:24:06 GMT Frederik Heber [1540859] * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (added) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (added) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (added) * src/Actions/Reaction.hpp (added) * src/Actions/Reaction_impl.hpp (added) * src/Actions/Reaction_impl_header.hpp (added) * src/Actions/Reaction_impl_pre.hpp (added) Added Reaction as Action with a return value. - this is derived ... Mon, 07 Nov 2011 12:24:05 GMT Frederik Heber [874597] * src/Actions/Action_impl_python.hpp (modified) FIX: some defines were forgotten to be undefined in ... Mon, 07 Nov 2011 12:24:05 GMT Frederik Heber [9d613f] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * tests/regression/Domain/RepeatBox/post/ec.data (added) * tests/regression/Domain/RepeatBox/pre/ec.data (added) * tests/regression/Domain/RepeatBox/pre/ec.potentials (added) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) FIX: RepeatBoxAction did not use CopyMolecule() but copied by hand. ... Mon, 07 Nov 2011 12:24:05 GMT Frederik Heber [f27fa7] * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) TESTFIX: Added test whether calling not present command truely fails. ... Mon, 07 Nov 2011 12:24:04 GMT Frederik Heber [cbb32d] * tests/regression/Python/AllActions/moltest.py (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) Small cosmetical changes to moltest.py. - We now use Popen to call ... Mon, 07 Nov 2011 12:24:03 GMT Frederik Heber [3493da] * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/getPossibleOptions.sh (added) * tests/regression/Python/AllActions/missing.dat (added) * tests/regression/Python/AllActions/options.dat (added) * tests/regression/Python/AllActions/testsuite-python-allactions.at (added) * tests/regression/Python/testsuite-python.at (modified) Gathered default values for each action and wrote regression test ... Mon, 07 Nov 2011 12:24:03 GMT Frederik Heber [6ca7b9] * tests/regression/Python/AllActions/moltest.py (added) Wrote python script to gather all functions in a pyMoleCuilder module ... Mon, 07 Nov 2011 12:24:02 GMT Frederik Heber [3139b2] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionTrait.cpp (moved) * src/Actions/ActionTrait.hpp (added) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) Renamed ActionTrait and ActionTraits. - the specialized Trait ... Mon, 07 Nov 2011 12:24:00 GMT Frederik Heber [c20b35] * src/Actions/Makefile.am (modified) Added commented-out stuff for a extra libMolecuilderActionPython.la. ... Mon, 07 Nov 2011 12:23:52 GMT Frederik Heber [949953] * src/Actions/Action_impl_python.hpp (added) * src/Actions/Action_impl_undef.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Makefile.am (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (added) * src/cleanUp.hpp (added) pyMoleCuilder now has full functionality. - For each header file ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [071243] * src/Actions/hello.cpp (modified) * src/Makefile.am (modified) Enhanced tiny example to resemble action structure. - Pythontest ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [88ba1f] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/ValueStorage.hpp (modified) Added Action's COMMAND_stringargs() function call. - also added ... Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [ddde10] * src/Actions/Action_impl_pre.hpp (modified) FIX: In Action's COMMAND() we don't need a params instance. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [6a2dae] * src/Actions/Action_impl_header.hpp (modified) Corrected indenting in ActionTrait<>s cstor. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [05736a] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) Simplified Action's COMMAND() definition a bit. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [d41313] * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) Added output operators for both ActionTraits and OptionTrait. Mon, 07 Nov 2011 10:46:37 GMT Frederik Heber [dad802] * src/Actions/ActionTraits.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) Modified ActionTraits' and OptionTrait's cstor and dstor slightly. ... Mon, 07 Nov 2011 10:46:25 GMT Frederik Heber [83e90c] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GlobalListOfActions.hpp (added) * src/Actions/Makefile.am (modified) New function ActionRegistry::fillRegistry() fills instead of static ... Fri, 04 Nov 2011 15:20:41 GMT Frederik Heber [aee2da] * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Added BUILT_SOURCES as appendable variable in various Makefile.am's. Fri, 04 Nov 2011 15:20:41 GMT Frederik Heber [cb85f24] * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) Removed using namespace MoleCuilder from TxMenuLeaveAction. - due ... Fri, 04 Nov 2011 15:20:41 GMT Frederik Heber [693a80] * src/Actions/pyMoleCuilder.cpp (added) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/CommandHelp/testsuite-python-commandhelp.at (added) * tests/regression/Python/testsuite-python.at (modified) Added pyMoleCuilder as python module with single exported function ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [a02f78] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) FIX: Undefined preprocessor macro functions in Action_impl_....hpp. ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [d470a6] * tests/regression/Makefile.am (modified) * tests/regression/Python/Pythontest/testsuite-python-pythontest.at (added) * tests/regression/Python/testsuite-python.at (modified) Moved regression test on little test module Pythontest into ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [b4e6b4] * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (modified) Added note that we really may use the address of a type_info object. ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [807d91] * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/OptionTrait.hpp (modified) MEMFIX: Virtualized destructors of OptionTrait, ActionTraits and ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [b22179] * src/Actions/ActionTraits.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) FIX: Removed OptionTrait's copy constructor as there are no pointers ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [d44d7b] * src/Actions/Action.cpp (modified) Dstor of Action now unregisters itself and its Options in Action- and ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [2d31e1] * configure.ac (modified) * src/Actions/hello.cpp (modified) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/run.in (added) * tests/regression/Python/testsuite-python.at (modified) Python tests are now launched via small script run.in. - this is ... Fri, 04 Nov 2011 15:20:40 GMT Frederik Heber [715085] * configure.ac (modified) * m4/ax_python.m4 (added) * src/Actions/hello.cpp (added) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/testsuite-python.at (added) * tests/regression/testsuite.at (modified) Simple boost::python test program added. - we have a function ... Fri, 04 Nov 2011 15:20:22 GMT Frederik Heber [46bba0] * src/Analysis/Makefile.am (modified) * src/Element/Makefile.am (modified) * src/Helpers/Makefile.am (modified) FIX: Removed versioning info from some convenience libraries. Fri, 04 Nov 2011 15:20:22 GMT Frederik Heber [42c9e2] * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.hpp (modified) FIX: getKeys() and getValues() are now simply internal functions of ... Fri, 04 Nov 2011 15:20:21 GMT Frederik Heber [13c969] * src/atom_atominfo.cpp (modified) FIX: atominfo::getType() does not care whether element exists. - ... Fri, 04 Nov 2011 15:20:21 GMT Frederik Heber [e5cec4] * configure.ac (modified) * m4/bnv_have_qt.m4 (deleted) * src/UIElements/Makefile.am (modified) Removed macro bnv_have_qt, replaced by pkg-config info. - ... Fri, 04 Nov 2011 15:20:21 GMT Frederik Heber [22db89] * configure.ac (modified) * m4/ax_codepatterns.m4 (modified) Using new version of CodePatterns 1.1.7. - m4 macro ... Fri, 04 Nov 2011 15:20:06 GMT Frederik Heber [bf3379] * configure.ac (modified) Set version to 1.1.6 - Molecuilder library is now 5:2:0. - ... Fri, 04 Nov 2011 15:19:53 GMT Frederik Heber [4faa30] * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) FIX: EmptyQtQuery forgot to initialise thisLayout. Fri, 04 Nov 2011 15:19:32 GMT Frederik Heber [3b5fca] * src/Makefile.am (modified) FIX: joiner, analzer and units lacked appropriate ..._LDFLAGS. - ... Fri, 04 Nov 2011 15:19:31 GMT Frederik Heber [3995764] * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite.at (modified) DISTCHECKFIX: LinearAlgebra CodeChecks testsuite fails due to doubly ... Fri, 04 Nov 2011 15:19:31 GMT Frederik Heber [6bdba0] * LinearAlgebra/doc/Makefile.am (modified) * LinearAlgebra/src/documentation/Makefile.am (added) * doc/Makefile.am (modified) * src/documentation/Makefile.am (added) DISTCHECKFIX: all .dox files are now given as EXTRA_DIST. - ... Fri, 04 Nov 2011 15:19:11 GMT Frederik Heber [d24953] * src/Makefile.am (modified) * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) DISTCHECKFIX: target unity.cpp has no MemDebug.hpp or config.h. - ... Fri, 04 Nov 2011 08:07:54 GMT Frederik Heber [262ecc] * m4/boost.m4 (modified) * src/Fragmentation/Makefile.am (modified) * src/Makefile.am (modified) DISTCHECKFIX: Forgotten .hpp files included. Thu, 03 Nov 2011 19:44:02 GMT Frederik Heber [c2808e] * src/Parser/ChangeTracker.cpp (modified) * src/Parser/XyzParser.cpp (modified) FormatParser< xyz >::save() now uses numeric_limits. Thu, 03 Nov 2011 19:44:02 GMT Frederik Heber [ab26c3] * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (moved) * src/Thermostats/ThermoStatContainer.hpp (moved) * src/Thermostats/Woodcock.cpp (modified) * src/World.cpp (modified) Moved ThermoStatContainer to folder src/Thermostats. Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [41a467] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Makefile.am (modified) * src/Parser/ConfigFileBuffer.cpp (moved) * src/Parser/ConfigFileBuffer.hpp (moved) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (added) * src/Parser/PcpParser_helper.hpp (added) * src/Parser/Psi3Parser.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) LARGE: config class is now just a tiny container. - this was ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [47d041] * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Element/periodentafel.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) HUGE: Removed all calls to Log(), eLog(), replaced by LOG() and ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [50e4e5] * tests/Fragmentations/Makefile.am (modified) * tests/Tesselations/Makefile.am (modified) * tests/regression/Makefile.am (modified) Test target installcheck-local now also runs parallel with up to 4 ... Thu, 03 Nov 2011 19:44:01 GMT Frederik Heber [862b6a] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/builder_init.cpp (modified) All Actions are timed now, timings are given on exit. - Chronos is ... Thu, 03 Nov 2011 19:21:42 GMT Frederik Heber [004ae7] * m4/bnv_have_qt.m4 (modified) * m4/boost.m4 (modified) FIX: Changes to bnv_have_qt.m4 and boost.m4. - moved search in /opt ... Thu, 03 Nov 2011 10:38:31 GMT Frederik Heber [bbff92] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/doc/Doxyfile (modified) * LinearAlgebra/src/documentation/groups.dox (added) * LinearAlgebra/src/documentation/mainpage.dox (added) * LinearAlgebra/tests/CodeChecks/Makefile.am (modified) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite-date_in_dox.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite.at (modified) * Makefile.am (modified) * configure.ac (modified) * doc/Doxyfile (modified) * doc/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/builder.cpp (modified) * src/documentation/code.dox (added) * src/documentation/constructs/actions.dox (added) * src/documentation/constructs/atoms.dox (added) * src/documentation/constructs/bondgraph.dox (added) * src/documentation/constructs/constructs.dox (added) * src/documentation/constructs/descriptors.dox (added) * src/documentation/constructs/fragmentation.dox (added) * src/documentation/constructs/linearalgebra.dox (added) * src/documentation/constructs/logger.dox (added) * src/documentation/constructs/molecules.dox (added) * src/documentation/constructs/observers_observables.dox (added) * src/documentation/constructs/parsers.dox (added) * src/documentation/constructs/randomnumbers.dox (added) * src/documentation/constructs/serialization.dox (added) * src/documentation/constructs/shapes.dox (added) * src/documentation/constructs/tesselation.dox (added) * src/documentation/constructs/world.dox (added) * src/documentation/copyright.dox (added) * src/documentation/faq.dox (added) * src/documentation/fileformats.dox (added) * src/documentation/future.dox (added) * src/documentation/howtos/action.dox (added) * src/documentation/howtos/howtos.dox (added) * src/documentation/install.dox (added) * src/documentation/launch.dox (added) * src/documentation/mainpage.dox (added) * src/documentation/tests/code-tests.dox (added) * src/documentation/tests/regression-tests.dox (added) * src/documentation/tests/tests.dox (added) * src/documentation/tests/unit-tests.dox (added) * src/documentation/userinterfaces/commandline.dox (added) * src/documentation/userinterfaces/graphical.dox (added) * src/documentation/userinterfaces/python.dox (added) * src/documentation/userinterfaces/textmenu.dox (added) * src/documentation/userinterfaces/userinterfaces.dox (added) * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-date_in_dox.at (added) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/CodeChecks/testsuite.at (modified) Merge branch 'Doxygen_Documentation_Enhancement' into mergeMaster Thu, 03 Nov 2011 10:35:53 GMT Frederik Heber [f11c23] * src/documentation/code.dox (modified) * src/documentation/future.dox (added) Added documentation on how to understand the code and its (maybe) ... Thu, 03 Nov 2011 10:01:03 GMT Frederik Heber [1e3265] * doc/userguide.xml (modified) Changed userguide a bit. Thu, 03 Nov 2011 09:52:29 GMT Frederik Heber [7ba268] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0012.dat (added) * 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tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (added) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox-mirrored_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/pre/water.xyz (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/emptybox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/hydrogenbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (moved) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'DipoleAngularCorrelation' into mergeMaster Conflicts: ... Wed, 02 Nov 2011 22:47:00 GMT Frederik Heber [f281c5] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/documentation/groups.dox (modified) * LinearAlgebra/src/documentation/mainpage.dox (modified) * LinearAlgebra/tests/CodeChecks/Makefile.am (modified) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite-date_in_dox.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * LinearAlgebra/tests/CodeChecks/testsuite.at (modified) Added .dox check to LinearAlgebra as well and various other test ... Wed, 02 Nov 2011 01:29:40 GMT Frederik Heber [5837dd] * src/Analysis/analysis_correlation.cpp (modified) Cosmetical fix to PairCorrelation(). Wed, 02 Nov 2011 01:29:33 GMT Frederik Heber [c3a70d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) Added time-step-zero option to dipole-angular-correlation. - this ... Wed, 02 Nov 2011 01:28:20 GMT Frederik Heber [870b4b] * src/Analysis/analysis_correlation.cpp (modified) Added rejected molecule counting to DipoleAngularCorrelation(). Tue, 01 Nov 2011 20:45:48 GMT Frederik Heber [a28cc4] * src/documentation/userinterfaces/python.dox (added) * src/documentation/userinterfaces/userinterfaces.dox (modified) DOCU: Added python as fourth user interface. Tue, 01 Nov 2011 20:45:14 GMT Frederik Heber [35a889] * src/documentation/userinterfaces/commandline.dox (modified) * src/documentation/userinterfaces/graphical.dox (modified) * src/documentation/userinterfaces/textmenu.dox (modified) * src/documentation/userinterfaces/userinterfaces.dox (modified) DOCUFIX: Prefixes all three userinterface labels with userinterfaces-. Tue, 01 Nov 2011 19:56:15 GMT Frederik Heber [bc3411] * src/documentation/constructs/serialization.dox (modified) DOCU: Added some important notes in usual mistakes to serialization.dox.