# # ChangeLog for src/Actions/Makefile.am # # Generated by Trac 1.6 # May 24, 2025, 10:01:15 AM Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [c015b3] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * tests/Makefile.am (modified) * tests/Python/AllActions/getPossibleOptions.sh (moved) * tests/Python/AllActions/listcmds.py (moved) * tests/Python/AllActions/missing.dat (moved) * tests/Python/AllActions/moltest.py (moved) * tests/Python/AllActions/moltest_check.py (moved) * tests/Python/AllActions/options.dat (moved) * tests/Python/AllActions/testsuite-python-allactions.at (added) * tests/Python/AllActions/testsuite-python-options_dat.at (added) * tests/Python/BoxMaker/post/out.data (moved) * tests/Python/BoxMaker/post/out.xyz (moved) * tests/Python/BoxMaker/pre/argon.data (moved) * tests/Python/BoxMaker/pre/argon.potentials (moved) * tests/Python/BoxMaker/pre/argon.tremolo (moved) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (added) * tests/Python/CommandHelp/testsuite-python-commandhelp.at (moved) * tests/Python/Makefile.am (added) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (moved) * tests/Python/atlocal.in (added) * tests/Python/run.in (moved) * tests/Python/testsuite.at (added) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (deleted) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (deleted) * tests/regression/Python/BoxMaker/testsuite-python-boxmaker.at (deleted) * tests/regression/Python/testsuite-python.at (deleted) * tests/regression/testsuite.at (modified) * utils/Makefile.am (modified) Added enable-switches for Qt-based GUI and python module and scripts. ... 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 [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 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 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 12:24:02 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 10:46:25 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 ... 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: ... Mon, 31 Oct 2011 11:16:17 GMT Frederik Heber [41d023] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (deleted) * src/Actions/ParserAction/SetParserParametersAction.cpp (added) * src/Actions/ParserAction/SetParserParametersAction.def (moved) * src/Actions/ParserAction/SetParserParametersAction.hpp (moved) * src/Parser/FormatParser_Parameters.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (moved) * tests/regression/Parser/SetParameters/Mpqc/pre/test.xyz (moved) * tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-theory.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (moved) * tests/regression/Parser/SetParameters/Psi3/pre/test.xyz (added) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-wavefunction.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Renamed SetMpqcParametersAction to SetParserParametersAction and ... Tue, 25 Oct 2011 15:28:06 GMT Frederik Heber [208237b] * 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) Renamed DipoleAngularCorrelation(Action) -> DipoleCorrelation(Action) ... Thu, 06 Oct 2011 09:15:04 GMT Frederik Heber [81c980b] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (added) * src/Actions/ParserAction/SetTremoloAtomdataAction.def (added) * src/Actions/ParserAction/SetTremoloAtomdataAction.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/pre/argon.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Added new action to set the ATOMDATA in tremolo's .data output file. ... Wed, 05 Oct 2011 09:18:20 GMT Frederik Heber [807c0e] * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (moved) * src/Actions/MoleculeAction/CreateMicelleAction.def (added) * src/Actions/MoleculeAction/CreateMicelleAction.hpp (added) * src/Makefile.am (modified) Daniel has recently changed his mizelledata to work as an action ... Wed, 21 Sep 2011 20:04:30 GMT Frederik Heber [e69c87] * src/Actions/Action.cpp (modified) * src/Actions/ActionExceptions.hpp (added) * src/Actions/ActionHistory.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/boundary.cpp (modified) * src/builder_init.cpp (modified) * tests/regression/Analysis/AngularDipoleCorrelation-Empty/testsuite-analysis-angular-dipole-correlation-empty.at (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) * tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified) * tests/regression/Atoms/RemoveCuboid/post/test-cuboid.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/post/test.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/pre/test.xyz (moved) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (moved) * tests/regression/Atoms/RemoveSphere/post/test-sphere.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/post/test.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/pre/test.xyz (moved) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (moved) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (added) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (deleted) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (added) * tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (added) * tests/regression/Molecules/Copy/post/tensid-undo.data (added) * tests/regression/Molecules/Copy/post/test-undo.xyz (added) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) * tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/Translation-Periodic/post/test-undo.conf (added) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/post/test-undo.conf (added) * tests/regression/Molecules/Translation/post/test2-undo.conf (added) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified) * tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-basis.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-maxiterations.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-theory.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc.at (modified) * tests/regression/Parser/Pcp/post/empty.conf (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp.at (modified) * tests/regression/Parser/Pdb/post/empty.pdb (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb.at (modified) * tests/regression/Parser/Tremolo/post/empty.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo.at (modified) * tests/regression/Parser/Xyz/post/empty.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz.at (modified) * tests/regression/Parser/testsuite-parser.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) Splitted off Undo and Redo parts into own tests (3-step rule). - ... Thu, 21 Apr 2011 16:26:04 GMT Frederik Heber [dd8990] * src/Actions/Makefile.am (modified) FIX: .def files of Actions have not been present in Makefile.am, ... Thu, 21 Apr 2011 16:25:23 GMT Frederik Heber [3001c9] * src/Actions/Makefile.am (modified) FIX: LoadAction.cpp and RemoveAction.cpp were doubly included instead ... Thu, 21 Apr 2011 16:23:50 GMT Frederik Heber [7159ed] * src/Actions/Makefile.am (modified) DISTFIX: Missing header files in Actions/Makefile.am - missing: ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [455573] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Large Commit: SUBDIRS in src/Makefile.am replaced by include. - ... Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber [bf4b9f] * LinearAlgebra/.gitignore (added) * LinearAlgebra/AUTHORS (added) * LinearAlgebra/COPYING (added) * LinearAlgebra/ChangeLog (added) * LinearAlgebra/INSTALL (added) * LinearAlgebra/LinearAlgebra-debug.pc.in (added) * LinearAlgebra/LinearAlgebra.pc.in (moved) * LinearAlgebra/Makefile.am (added) * LinearAlgebra/NEWS (added) * LinearAlgebra/README (added) * LinearAlgebra/bootstrap (added) * LinearAlgebra/build-aux/README (added) * LinearAlgebra/configure.ac (added) * LinearAlgebra/doc/Doxyfile (added) * LinearAlgebra/doc/Makefile.am (added) * LinearAlgebra/libLinearAlgebra_config.h.in (added) * LinearAlgebra/m4 (added) * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * LinearAlgebra/src/unittests/Makefile.am (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (added) * LinearAlgebra/src/unittests/UnitTestMain.cpp (added) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * LinearAlgebra/tests/CodeChecks/Makefile.am (added) * LinearAlgebra/tests/CodeChecks/atlocal.in (added) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added) * LinearAlgebra/tests/CodeChecks/testsuite.at (added) * Makefile.am (modified) * bootstrap (modified) * build-aux/README (added) * config/depcomp (deleted) * config/install-sh (deleted) * config/ltmain.sh (deleted) * config/missing (deleted) * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra from folder src/ into distinct sub-package. - ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [d09093] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (moved) * src/Actions/GraphAction/CreateAdjacencyAction.def (moved) * src/Actions/GraphAction/CreateAdjacencyAction.hpp (moved) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (moved) * src/Actions/GraphAction/DepthFirstSearchAction.def (moved) * src/Actions/GraphAction/DepthFirstSearchAction.hpp (moved) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (moved) * src/Actions/GraphAction/SubgraphDissectionAction.def (moved) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) Moved all graph-related Actions into own folder Actions/GraphAction/. ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [e73ad9a] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Graph/CyclicStructureAnalysis.cpp (added) * src/Graph/CyclicStructureAnalysis.hpp (added) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Moved CyclicStructureAnalysis from molecule_graph.cpp into own ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [fe6f20] * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (added) * src/Actions/AtomAction/SaveSelectedAtomsAction.def (added) * src/Actions/AtomAction/SaveSelectedAtomsAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (moved) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.def (moved) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.hpp (added) * tests/regression/Atoms/SaveSelectedAtoms/post/testsave.xyz (added) * tests/regression/Atoms/SaveSelectedAtoms/pre/test.xyz (added) * tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/SaveSelectedMolecules/post/testsave.xyz (added) * tests/regression/Molecules/SaveSelectedMolecules/pre/test.xyz (added) * tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) New Action SaveSelectedAtoms and renamed SaveAction -> ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [d4a44c] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (moved) * src/Actions/FragmentationAction/CreateAdjacencyAction.def (moved) * src/Actions/FragmentationAction/CreateAdjacencyAction.hpp (moved) * src/Actions/Makefile.am (modified) * tests/regression/Graph/1/pre/test2.conf (deleted) Renamed ConstructBondGraphAction -> CreateAdjacencyAction. Thu, 24 Feb 2011 16:01:50 GMT Frederik Heber [aa04ae] * src/Actions/Makefile.am (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (added) * src/Actions/WorldAction/SetWorldTimeAction.def (added) * src/Actions/WorldAction/SetWorldTimeAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (added) * tests/regression/Options/testsuite-options.at (modified) Implemented SetWorldTimeAction and regression test on that. - ... Thu, 10 Feb 2011 19:09:30 GMT Frederik Heber [528b3e] * src/Actions/Makefile.am (modified) * src/Actions/Values.cpp (added) * src/Actions/Values.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) Added conversion functions to VectorValue and BoxValue and changed ... Wed, 09 Feb 2011 17:25:13 GMT Frederik Heber [4d4d33] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (added) * src/Actions/ParserAction/ParseTremoloPotentialsAction.def (added) * src/Actions/ParserAction/ParseTremoloPotentialsAction.hpp (added) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloAtomInfoContainer.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) Added tremolo's potential file parsing, reported by Daniel Dueck. ... Mon, 07 Feb 2011 10:43:50 GMT Frederik Heber [963321a] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetGaussianBasisAction.cpp (deleted) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (added) * src/Actions/ParserAction/SetMpqcParametersAction.def (moved) * src/Actions/ParserAction/SetMpqcParametersAction.hpp (moved) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Mpqc-SetBasis/testsuite-parser-mpqc-set-basis.at (deleted) * tests/regression/Parser/Mpqc-SetParameters/pre/test.xyz (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Converted SetGaussianBasisAction into SetMpqcParametersAction. - ... Mon, 07 Feb 2011 10:43:27 GMT Frederik Heber [9cff8b] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetGaussianBasisAction.cpp (moved) * src/Actions/ParserAction/SetGaussianBasisAction.def (moved) * src/Actions/ParserAction/SetGaussianBasisAction.hpp (moved) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (moved) * src/Actions/ParserAction/SetOutputFormatsAction.def (moved) * src/Actions/ParserAction/SetOutputFormatsAction.hpp (moved) Moved SetGaussianBasisAction and SetOutputFormatsAction from World to ... Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber [3f9eba] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (added) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.def (added) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.hpp (added) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (added) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.def (added) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.hpp (added) * src/Makefile.am (modified) * src/RandomNumbers/RandomNumberDistribution.hpp (added) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (added) * src/RandomNumbers/RandomNumberEngine.hpp (added) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (added) * src/RandomNumbers/RandomNumberGenerator.cpp (added) * src/RandomNumbers/RandomNumberGenerator.hpp (added) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (added) * src/RandomNumbers/RandomNumberGeneratorFactory.def (added) * src/RandomNumbers/RandomNumberGeneratorFactory.hpp (added) * src/RandomNumbers/RandomNumberGeneratorFactory.undef (added) * src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (added) * src/RandomNumbers/TemplatePowerSetGenerator.hpp (added) * src/RandomNumbers/unittests/Makefile.am (added) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (added) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp (added) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (added) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (added) * tests/regression/RandomNumbers/testsuite-randomnumbers.at (added) * tests/regression/testsuite.at (modified) New classes for random number generation. - we use boost::random as ... Thu, 03 Feb 2011 09:51:18 GMT Frederik Heber [be945c] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) New DipoleAngularCorrelationAction that calculates angular ... Thu, 03 Feb 2011 09:51:14 GMT Frederik Heber [e5bf2b] * src/Actions/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) removed CPPUNIT_LIBS/FLAGS from most Makefile.am and LIBS/libs -> ... Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber [acbe1b] * MoleCuilder.pc.in (added) * configure.ac (modified) * molecuilder.pc.in (deleted) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) All libraries don't have version in name anymore. - we used gained ... Thu, 23 Dec 2010 17:40:04 GMT Frederik Heber [a0064e] * configure.ac (modified) * m4/ax_codepatterns.m4 (added) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/Formula.hpp (modified) * src/Helpers/Assert.cpp (deleted) * src/Helpers/Assert.hpp (deleted) * src/Helpers/Info.cpp (deleted) * src/Helpers/Info.hpp (deleted) * src/Helpers/Log.cpp (deleted) * src/Helpers/Log.hpp (deleted) * src/Helpers/Makefile.am (deleted) * src/Helpers/MemDebug.cpp (deleted) * src/Helpers/MemDebug.hpp (deleted) * src/Helpers/Range.hpp (deleted) * src/Helpers/Verbose.cpp (deleted) * src/Helpers/Verbose.hpp (deleted) * src/Helpers/errorlogger.cpp (deleted) * src/Helpers/errorlogger.hpp (deleted) * src/Helpers/fast_functions.hpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/Helpers/logger.cpp (deleted) * src/Helpers/logger.hpp (deleted) * src/Helpers/toString.hpp (deleted) * src/Helpers/unittests/InfoUnitTest.cpp (deleted) * src/Helpers/unittests/InfoUnitTest.hpp (deleted) * src/Helpers/unittests/LogUnitTest.cpp (deleted) * src/Helpers/unittests/LogUnitTest.hpp (deleted) * src/Helpers/unittests/Makefile.am (deleted) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Patterns/Cacheable.hpp (deleted) * src/Patterns/ObservedContainer.hpp (deleted) * src/Patterns/ObservedContainer_impl.hpp (deleted) * src/Patterns/ObservedIterator.hpp (deleted) * src/Patterns/Observer.cpp (deleted) * src/Patterns/Observer.hpp (deleted) * src/Patterns/Registry.hpp (deleted) * src/Patterns/Registry_impl.hpp (deleted) * src/Patterns/Singleton.hpp (deleted) * src/Patterns/Singleton_impl.hpp (deleted) * src/Patterns/unittests/CacheableUnitTest.cpp (deleted) * src/Patterns/unittests/CacheableUnitTest.hpp (deleted) * src/Patterns/unittests/Makefile.am (deleted) * src/Patterns/unittests/ObserverUnitTest.cpp (deleted) * src/Patterns/unittests/ObserverUnitTest.hpp (deleted) * src/Patterns/unittests/RegistryUnitTest.cpp (deleted) * src/Patterns/unittests/RegistryUnitTest.hpp (deleted) * src/Patterns/unittests/SingletonUnitTest.cpp (deleted) * src/Patterns/unittests/SingletonUnitTest.hpp (deleted) * src/Shapes/unittests/Makefile.am (modified) * src/SubspaceFactorizer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/SubspaceFactorizerUnitTest.cpp (modified) Moved stuff in src/Helpers and src/Patterns out to stand-alone ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [125002] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AtomByElementAction.def (moved) * src/Actions/SelectionAction/Atoms/AtomByElementAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AtomByIdAction.def (moved) * src/Actions/SelectionAction/Atoms/AtomByIdAction.hpp (moved) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (moved) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.def (moved) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp (moved) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (moved) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.def (moved) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.hpp (moved) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (moved) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.def (moved) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.def (moved) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp (moved) Splitted SelectionAction modules into two groups - atoms, molecules - ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [92d756] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByNameAction.cpp (added) * src/Actions/SelectionAction/MoleculeByNameAction.def (added) * src/Actions/SelectionAction/MoleculeByNameAction.hpp (added) * src/Actions/SelectionAction/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByNameAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByNameAction.def (added) * src/Actions/SelectionAction/NotMoleculeByNameAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByOrderAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByOrderAction.def (added) * src/Actions/SelectionAction/NotMoleculeByOrderAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (added) * src/Descriptors/MoleculeOrderDescriptor.hpp (added) * src/Descriptors/MoleculeOrderDescriptor_impl.hpp (added) * src/Makefile.am (modified) Larger update of selections. - new selections: - ... Sun, 05 Dec 2010 00:20:42 GMT Frederik Heber [ca03c7] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/MoleculeByOrderAction.cpp (added) * src/Actions/SelectionAction/MoleculeByOrderAction.def (added) * src/Actions/SelectionAction/MoleculeByOrderAction.hpp (added) Added select-molecule-by-order Action. Sun, 05 Dec 2010 00:20:07 GMT Frederik Heber [cabb46] * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/LoadAction.cpp (added) * src/Actions/MoleculeAction/LoadAction.def (moved) * src/Actions/MoleculeAction/LoadAction.hpp (moved) * src/Actions/MoleculeAction/SaveAction.cpp (moved) * src/Actions/MoleculeAction/SaveAction.def (moved) * src/Actions/MoleculeAction/SaveAction.hpp (moved) * src/Actions/ParserAction/LoadXyzAction.cpp (deleted) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/unittests/ParserCommonUnitTest.cpp (modified) * tests/regression/Simple_configuration/2/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.pdb (modified) * tests/regression/Simple_configuration/2/pre/test.conf (added) * tests/regression/Simple_configuration/2/pre/test.pdb (added) * tests/regression/Simple_configuration/2/pre/test.xyz (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Extended LoadXyz and SaveXyz to any format. - renamed ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [d5240d] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/Helpers/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Linking to non-system boost is working now. - FIX: ... Sat, 30 Oct 2010 20:42:44 GMT Frederik Heber [e4afb4] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (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/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.def (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpAction.def (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.def (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.def (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.def (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (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/MapOfActions.cpp (deleted) * src/Actions/MapOfActions.hpp (deleted) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.def (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/OptionRegistry.cpp (added) * src/Actions/OptionRegistry.hpp (added) * src/Actions/OptionTrait.cpp (added) * src/Actions/OptionTrait.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RedoAction.cpp (added) * src/Actions/RedoAction.def (added) * src/Actions/RedoAction.hpp (added) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (modified) * src/Actions/UndoAction.cpp (added) * src/Actions/UndoAction.def (moved) * src/Actions/UndoAction.hpp (added) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (modified) * src/Actions/convert5.sh (added) * src/CommandLineParser.cpp (deleted) * src/Makefile.am (modified) * src/Patterns/Registry.hpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (added) * src/UIElements/CommandLineUI/CommandLineParser.hpp (moved) * 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/EmptyCommandLineQuery.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/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (added) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MenuDescriptionUnitTest.cpp (modified) * src/unittests/MenuDescriptionUnitTest.hpp (modified) * src/unittests/RegistryUnitTest.cpp (added) * src/unittests/RegistryUnitTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Huge refactoring: Introduction of Traits to Actions. This change is ... Sat, 30 Oct 2010 18:44:28 GMT Frederik Heber [df32ee] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionTraits.cpp (added) * src/Actions/ActionTraits.hpp (added) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Makefile.am (modified) New class ActionTrait(s). - ActionTrait is the template class that ... Thu, 14 Oct 2010 10:00:28 GMT Frederik Heber [7230be] * src/Actions/CommandAction/WarrantyAction.cpp (added) * src/Actions/CommandAction/WarrantyAction.def (added) * src/Actions/CommandAction/WarrantyAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-standard_options.at (modified) Added WarrantyAction. This closed ticket #117. Sat, 28 Aug 2010 06:08:52 GMT Frederik Heber [eee966] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (added) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (added) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (added) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * tests/regression/Filling/3/post/tensid.data (added) * tests/regression/Filling/3/post/test.conf (added) * tests/regression/Filling/3/post/test.xyz (added) * tests/regression/Filling/3/pre/tensid.data (added) * tests/regression/Filling/3/pre/test.conf (added) * tests/regression/Filling/3/pre/water.data (added) * tests/regression/testsuite-filling.at (modified) New Action FillVoidWithMoleculeAction. - in contrast to ... Sat, 28 Aug 2010 00:58:44 GMT Frederik Heber [1a7fd2] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (added) * src/Actions/MoleculeAction/CopyAction.def (added) * src/Actions/MoleculeAction/CopyAction.hpp (added) * tests/regression/Molecules/11/post/test-copy.xyz (added) * tests/regression/Molecules/11/pre/test.xyz (added) * tests/regression/testsuite-molecules.at (modified) New Action MoleculeAction/CopyAction. Sat, 28 Aug 2010 00:57:57 GMT Frederik Heber [c449d9] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) Added new Action ConstructBondGraphAction. Sat, 28 Aug 2010 00:57:56 GMT Frederik Heber [53d01c] * src/Actions/CommandAction/BondLengthTableAction.cpp (moved) * src/Actions/CommandAction/BondLengthTableAction.hpp (moved) * src/Actions/CommandAction/ElementDbAction.cpp (moved) * src/Actions/CommandAction/ElementDbAction.hpp (moved) * src/Actions/CommandAction/FastParsingAction.cpp (moved) * src/Actions/CommandAction/FastParsingAction.hpp (moved) * src/Actions/CommandAction/HelpAction.cpp (moved) * src/Actions/CommandAction/HelpAction.hpp (moved) * src/Actions/CommandAction/VerboseAction.cpp (moved) * src/Actions/CommandAction/VerboseAction.hpp (moved) * src/Actions/CommandAction/VersionAction.cpp (moved) * src/Actions/CommandAction/VersionAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified) Renamed dir Actions/CmdAction -> Actions/CommandAction, renamed class ... Sat, 28 Aug 2010 00:52:58 GMT Frederik Heber [9ee38b] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_post.hpp (deleted) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/unittests/Makefile.am (modified) Extended macro framework. Extensions: - all central definitions ... Thu, 12 Aug 2010 15:08:47 GMT Frederik Heber [51769f] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (added) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (added) Added (un)select-molecule-by-formula/..-atom-by-element actions.. Mon, 09 Aug 2010 17:57:50 GMT Frederik Heber [1cc87e] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (deleted) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (deleted) * src/Makefile.am (modified) * tests/regression/Simple_configuration/8/post/test-cuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-sphere.xyz-sorted (moved) * tests/regression/Simple_configuration/8/post/test-withoutcuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-withoutsphere.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test.xyz-sorted (modified) * tests/regression/Simple_configuration/8/pre/test.conf (deleted) * tests/regression/Simple_configuration/8/pre/test.xyz (added) * tests/regression/testsuite-simple_configuration.at (modified) Added select-atoms-inside-sphere/cuboid and unselect-.. - new ... Mon, 09 Aug 2010 15:03:05 GMT Frederik Heber [22c44bf] * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (moved) * src/Actions/AtomAction/TranslateAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (deleted) * tests/regression/testsuite-molecules.at (modified) Changed RotateAroundOriginByAngleAction from acting on molecules to ... Mon, 09 Aug 2010 14:13:27 GMT Frederik Heber [34c338] * src/Actions/AtomAction/TranslateAction.cpp (added) * src/Actions/AtomAction/TranslateAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (deleted) * tests/regression/testsuite-molecules.at (modified) Changed TranslateAction from acting on molecules to acting on ... Mon, 09 Aug 2010 13:21:21 GMT Frederik Heber [75a80f] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (added) New selection: unselect-molecule-of-atom. Mon, 09 Aug 2010 13:21:21 GMT Frederik Heber [381c5f] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (added) New selection: unselect-molecules-atoms. Mon, 09 Aug 2010 13:21:12 GMT Frederik Heber [481e92] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (added) New selection: select-molecule-of-atom. Mon, 09 Aug 2010 12:57:20 GMT Frederik Heber [770287] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (added) new selection: select-molecules-atoms. Mon, 09 Aug 2010 12:49:19 GMT Frederik Heber [2218d94] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (added) New selection: clear-molecule-selection. Mon, 09 Aug 2010 12:46:00 GMT Frederik Heber [e212ff] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (added) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (added) New selection: clear-atom-selection. Fri, 06 Aug 2010 13:32:19 GMT Frederik Heber [eaf4ae] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.hpp (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (added) Added two new actions. - RotateAroundOriginByAngle: Rotates around ... Fri, 06 Aug 2010 09:34:59 GMT Frederik Heber [d223d5] * Makefile.am (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * config/ltmain.sh (added) * configure.ac (modified) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (moved) * src/Actions/ValueStorage.hpp (moved) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Exceptions/Makefile.am (added) * src/Formula.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/MemDebug.hpp (modified) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Merge branch 'SharedLibraries' into stable - BUGFIX: MemDebug.cpp ... Thu, 05 Aug 2010 15:48:55 GMT Frederik Heber [861874] * Makefile.am (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * config/ltmain.sh (added) * configure.ac (modified) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.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/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (moved) * src/Actions/ValueStorage.hpp (moved) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/unittests/Makefile.am (modified) libMolecuilderAction is now a shared lib via libtool. This is all ... Wed, 04 Aug 2010 13:25:25 GMT Tillmann Crueger [796aa6] * Makefile.am (modified) * src/Actions/Makefile.am (modified) * src/Helpers/Assert.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Added faster unity build target to makefiles - unity build means a ... Mon, 26 Jul 2010 18:06:18 GMT Frederik Heber [e076cd] * src/Actions/ActionCalls.hpp (deleted) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) * src/Actions/CmdAction/VersionAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) Moved each action call function definition into the header file of ... Mon, 26 Jul 2010 13:37:29 GMT Frederik Heber [aa3d7a] * src/Actions/ActionCalls.hpp (added) * src/Actions/Makefile.am (modified) ActionCalls.hpp header added that contains concise function calls of ... Sun, 25 Jul 2010 21:41:34 GMT Frederik Heber [e472eab] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) Added new all/none selection actions for atoms and molecules. - new ... Sun, 25 Jul 2010 19:07:06 GMT Frederik Heber [533838] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Merge branch 'SelectionActions' into ... Thu, 22 Jul 2010 19:11:35 GMT Frederik Heber [d02e07] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) Split PairCorrelation into Pair, Point and SurfaceCorrelation. - ... Thu, 22 Jul 2010 16:11:07 GMT Frederik Heber [e2009b] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) Added a number of SelectionActions. - (un)select atom/molecule. - ... Mon, 05 Jul 2010 17:03:53 GMT Frederik Heber [361ba7] * src/Actions/Makefile.am (modified) Trailing whitespace in src/Actions/Makefile.am Fri, 02 Jul 2010 13:44:23 GMT Frederik Heber [b9c847] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) New SetOutputFormatsAction introduced. Fixes: - World::setDomain() ... Fri, 25 Jun 2010 08:11:20 GMT Frederik Heber [4f7f34e] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) ParseCommandLineOptions() is not used anymore. - new Actions ... Wed, 09 Jun 2010 14:04:54 GMT Frederik Heber [104524] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToPointAction.hpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp (deleted) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Legacy/oldmenu.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) Changed PairCorrelationAction to incorporate all three cases and ... Mon, 07 Jun 2010 23:53:44 GMT Frederik Heber [0286bc] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/Values.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) BUGFIX: ListOfDoubles changed to Box and Vector. - ListOfDoubles is ... Tue, 18 May 2010 15:18:24 GMT Frederik Heber [5079a0] * Makefile.am (modified) * configure.ac (modified) * src/Actions/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (moved) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (moved) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (moved) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (moved) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (moved) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (moved) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Makefile.am (added) * src/UIElements/Menu/ActionMenuItem.cpp (moved) * src/UIElements/Menu/ActionMenuItem.hpp (moved) * src/UIElements/Menu/DisplayMenuItem.cpp (moved) * src/UIElements/Menu/DisplayMenuItem.hpp (moved) * src/UIElements/Menu/Menu.cpp (moved) * src/UIElements/Menu/Menu.hpp (moved) * src/UIElements/Menu/MenuItem.cpp (moved) * src/UIElements/Menu/MenuItem.hpp (moved) * src/UIElements/Menu/SeperatorItem.cpp (moved) * src/UIElements/Menu/SeperatorItem.hpp (moved) * src/UIElements/Menu/SubMenuItem.cpp (moved) * src/UIElements/Menu/SubMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu.cpp (moved) * src/UIElements/Menu/TextMenu.hpp (moved) * src/UIElements/TextUI/TextDialog.cpp (moved) * src/UIElements/TextUI/TextDialog.hpp (moved) * src/UIElements/TextUI/TextStatusIndicator.cpp (moved) * src/UIElements/TextUI/TextStatusIndicator.hpp (moved) * src/UIElements/TextUI/TextUIFactory.cpp (moved) * src/UIElements/TextUI/TextUIFactory.hpp (moved) * src/UIElements/TextUI/TextWindow.cpp (moved) * src/UIElements/TextUI/TextWindow.hpp (moved) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (moved) * src/UIElements/Views/MethodStringView.hpp (moved) * src/UIElements/Views/StreamStringView.cpp (moved) * src/UIElements/Views/StreamStringView.hpp (moved) * src/UIElements/Views/StringView.cpp (moved) * src/UIElements/Views/StringView.hpp (moved) * src/UIElements/Views/View.cpp (moved) * src/UIElements/Views/View.hpp (moved) Actions put into libMolecuilderActions, UIElements into ...