# # ChangeLog for / # # Generated by Trac 1.4.4 # Jan 18, 2025, 1:30:45 PM Mon, 31 Oct 2011 11:49:19 GMT Frederik Heber <heber@…> [e65878] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Selection is now done inside DipoleAngularCorrelation. - as ... Mon, 31 Oct 2011 11:48:46 GMT Frederik Heber <heber@…> [505d05] * src/Analysis/analysis_correlation.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) DipoleAngularCorrelation: output now contains name _and position_ of ... Mon, 31 Oct 2011 11:48:46 GMT Frederik Heber <heber@…> [72105a] * src/Analysis/analysis_correlation.cpp (modified) Verbosity fix: DipoleAngularCorrelation() - info given when ... Mon, 31 Oct 2011 11:48:45 GMT Frederik Heber <heber@…> [99b87a] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) DipoleAngularCorrelation() can be told not to reset time to old ... Mon, 31 Oct 2011 11:48:38 GMT Frederik Heber <heber@…> [a860a1] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (modified) * 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) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0032.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0033.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0034.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0035.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.dat (deleted) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (added) * 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/testsuite-analysis-dipole-angular-correlation.at (modified) TESTFIX: Regression test Analysis/DipoleAngularCorrelation now also ... Thu, 27 Oct 2011 16:46:20 GMT Frederik Heber <heber@…> [a2b0ce] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) FIX: Filenames are appended with step with fixed width of 4 digits, ... Thu, 27 Oct 2011 16:45:47 GMT Frederik Heber <heber@…> [cda81d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) DipoleAngularCorrelation is now calculated per time step not over all ... Thu, 27 Oct 2011 11:07:20 GMT Frederik Heber <heber@…> [9e1709] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) AnalysisDipoleAngularCorrelationAction now calculates zero ... Thu, 27 Oct 2011 11:07:20 GMT Frederik Heber <heber@…> [bef3b9] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) Restructured code in ... Thu, 27 Oct 2011 11:06:42 GMT Frederik Heber <heber@…> [325687] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) DipoleAngularCorrelation() - External zero orientation vector may be ... Tue, 25 Oct 2011 15:33:14 GMT Frederik Heber <heber@…> [0a7fad] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Refactored part of code in DipoleAngularCorrelation into new method ... Tue, 25 Oct 2011 15:33:14 GMT Frederik Heber <heber@…> [1cc661] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Refactored part of DipoleAngularCorrelation into method ... Tue, 25 Oct 2011 15:33:14 GMT Frederik Heber <heber@…> [be0c61] * src/Analysis/analysis_correlation.cpp (modified) FIX: DipoleAngularCorrelation() - ZeroVector is now map over atoms, ... Tue, 25 Oct 2011 15:31:54 GMT Frederik Heber <heber@…> [4b8630] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) World::setTime() now updates bond structure of system and related ... Tue, 25 Oct 2011 15:28:27 GMT Frederik Heber <heber@…> [4fc828] * src/Analysis/analysis_correlation.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb (added) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) DipoleAngularCorrelation working with multi-timestep PDBs with CONECT ... Tue, 25 Oct 2011 15:28:27 GMT Frederik Heber <heber@…> [df8759] * 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) Renamed test dirs Analysis/AngularDipoleCorrelation-... ... Tue, 25 Oct 2011 15:28:06 GMT Frederik Heber <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) ... Tue, 25 Oct 2011 09:48:21 GMT Frederik Heber <heber@…> [5fd0f4] * configure.ac (modified) Set version to 1.1.5 - Molecuilder library is now 5:1:0. - ... Tue, 25 Oct 2011 09:47:01 GMT Frederik Heber <heber@…> [f94953] * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (modified) DISTCHECKFIX: regression test Fragmentations/Joining required ... Thu, 20 Oct 2011 22:42:16 GMT Frederik Heber <heber@…> [360c8b] * configure.ac (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserInterface.hpp (added) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParserTrait.hpp (added) * src/Parser/FormatParserTrait_specializations_header.hpp (added) * src/Parser/FormatParser_Parameters.cpp (added) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/FormatParser_common.cpp (moved) * src/Parser/FormatParser_common.hpp (added) * src/Parser/FormatParser_specializations_header.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Parameters/ContinuousParameter.hpp (added) * src/Parser/Parameters/ContinuousParameter_impl.hpp (added) * src/Parser/Parameters/ContinuousValue.hpp (added) * src/Parser/Parameters/ContinuousValue_impl.hpp (added) * src/Parser/Parameters/DiscreteParameter.hpp (added) * src/Parser/Parameters/DiscreteParameter_impl.hpp (added) * src/Parser/Parameters/DiscreteValue.hpp (added) * src/Parser/Parameters/DiscreteValue_impl.hpp (added) * src/Parser/Parameters/Parameter.hpp (added) * src/Parser/Parameters/ParameterStorage.cpp (added) * src/Parser/Parameters/ParameterStorage.hpp (added) * src/Parser/Parameters/StringParameter.cpp (added) * src/Parser/Parameters/StringParameter.hpp (added) * src/Parser/Parameters/ValueInterface.hpp (added) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.hpp (added) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (added) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.hpp (added) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.hpp (added) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (added) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (added) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (added) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.hpp (added) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/StringParameterUnitTest.hpp (added) * src/Parser/ParserTypes.cpp (added) * src/Parser/ParserTypes.def (added) * src/Parser/ParserTypes.hpp (added) * src/Parser/ParserTypes.undef (added) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbAtomInfoContainer.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/Psi3Parser.cpp (added) * src/Parser/Psi3Parser.hpp (added) * src/Parser/Psi3Parser_Parameters.cpp (added) * src/Parser/Psi3Parser_Parameters.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (added) * src/Parser/unittests/ParserPsi3UnitTest.hpp (added) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Psi3/post/empty.psi (added) * tests/regression/Parser/Psi3/post/test.psi (added) * tests/regression/Parser/Psi3/pre/empty.psi (added) * tests/regression/Parser/Psi3/pre/test.xyz (added) * tests/regression/Parser/Psi3/pre/testrhf.psi (added) * tests/regression/Parser/Psi3/pre/testrohf.psi (added) * tests/regression/Parser/Psi3/pre/testtwocon.psi (added) * tests/regression/Parser/Psi3/pre/testuhf.psi (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Merge branch 'Adding_Psi3Parser' into stable Conflicts: ... Thu, 20 Oct 2011 21:29:24 GMT Frederik Heber <heber@…> [fa9d1d] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) FIX: CreateAdjacencyAction now uses BondGraph::CreateAdjacency. Thu, 20 Oct 2011 13:20:09 GMT Frederik Heber <heber@…> [539f32] * src/Graph/BondGraph.cpp (modified) Enhanced BondGraph::CreateAdjacency() a bit. Thu, 20 Oct 2011 13:20:03 GMT Frederik Heber <heber@…> [9317be] * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) Replaced molecule::atomVector by World::AtomComposite everywhere. Thu, 20 Oct 2011 12:39:01 GMT Frederik Heber <heber@…> [025048] * src/Box.cpp (modified) * src/Box.hpp (modified) Enhanced Box::periodicDistanceSquared() by an internal_explode(). - ... Thu, 20 Oct 2011 08:49:51 GMT Frederik Heber <heber@…> [93d78e8] * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) TEST: Added missing atom keyword to regression tests on selection of ... Thu, 20 Oct 2011 08:21:40 GMT Frederik Heber <heber@…> [a8b9136] * tests/Fragmentations/testsuite.at (modified) Merge branch 'Fix_Test-Fragmentation_Header' into stable Thu, 20 Oct 2011 08:20:53 GMT Frederik Heber <heber@…> [6a5108] * tests/Fragmentations/testsuite.at (modified) FIX: Header name of Fragmentations test was wrong. Thu, 20 Oct 2011 07:04:50 GMT Frederik Heber <heber@…> [9c27b0] * configure.ac (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * 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/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/Makefile.am (added) * src/Analysis/analysis_bonds.cpp (moved) * src/Analysis/analysis_bonds.hpp (moved) * src/Analysis/analysis_correlation.cpp (moved) * src/Analysis/analysis_correlation.hpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (moved) * src/Analysis/unittests/CountBondsUnitTest.cpp (moved) * src/Analysis/unittests/CountBondsUnitTest.hpp (moved) * src/Analysis/unittests/Makefile.am (added) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Element/Hbondangle.db (moved) * src/Element/Hbonddistance.db (moved) * src/Element/Makefile.am (added) * src/Element/element.cpp (moved) * src/Element/element.hpp (moved) * src/Element/elements.db (moved) * src/Element/elements_db.cpp (moved) * src/Element/elements_db.hpp (moved) * src/Element/orbitals.db (moved) * src/Element/periodentafel.cpp (moved) * src/Element/periodentafel.hpp (moved) * src/Element/unittests/ElementUnitTest.cpp (moved) * src/Element/unittests/ElementUnitTest.hpp (moved) * src/Element/unittests/Makefile.am (added) * src/Element/unittests/PeriodentafelUnitTest.cpp (moved) * src/Element/unittests/PeriodentafelUnitTest.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (added) * src/Fragmentation/EnergyMatrix.hpp (added) * src/Fragmentation/ForceMatrix.cpp (added) * src/Fragmentation/ForceMatrix.hpp (added) * src/Fragmentation/HessianMatrix.cpp (added) * src/Fragmentation/HessianMatrix.hpp (added) * src/Fragmentation/KeySetsContainer.cpp (added) * src/Fragmentation/KeySetsContainer.hpp (added) * src/Fragmentation/Makefile.am (added) * src/Fragmentation/MatrixContainer.cpp (added) * src/Fragmentation/MatrixContainer.hpp (added) * src/Fragmentation/analyzer.cpp (moved) * src/Fragmentation/datacreator.cpp (moved) * src/Fragmentation/datacreator.hpp (moved) * src/Fragmentation/defs.hpp (added) * src/Fragmentation/helpers.cpp (added) * src/Fragmentation/helpers.hpp (added) * src/Fragmentation/joiner.cpp (moved) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (added) * src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (added) * src/Fragmentation/unittests/Makefile.am (added) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (added) * src/Fragmentation/unittests/MatrixContainerUnitTest.hpp (added) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (moved) * src/Graph/unittests/BondGraphUnitTest.hpp (moved) * src/Graph/unittests/Makefile.am (added) * src/Helpers/Makefile.am (added) * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/PointCloudAdaptor.hpp (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Tesselation/BoundaryLineSet.cpp (moved) * src/Tesselation/BoundaryLineSet.hpp (moved) * src/Tesselation/BoundaryMaps.hpp (moved) * src/Tesselation/BoundaryPointSet.cpp (moved) * src/Tesselation/BoundaryPointSet.hpp (moved) * src/Tesselation/BoundaryPolygonSet.cpp (moved) * src/Tesselation/BoundaryPolygonSet.hpp (moved) * src/Tesselation/BoundaryTriangleSet.cpp (moved) * src/Tesselation/BoundaryTriangleSet.hpp (moved) * src/Tesselation/CandidateForTesselation.cpp (moved) * src/Tesselation/CandidateForTesselation.hpp (moved) * src/Tesselation/TesselPoint.cpp (moved) * src/Tesselation/TesselPoint.hpp (moved) * src/Tesselation/boundary.cpp (moved) * src/Tesselation/boundary.hpp (moved) * src/Tesselation/ellipsoid.cpp (moved) * src/Tesselation/ellipsoid.hpp (moved) * src/Tesselation/tesselation.cpp (moved) * src/Tesselation/tesselation.hpp (moved) * src/Tesselation/tesselationhelpers.cpp (moved) * src/Tesselation/tesselationhelpers.hpp (moved) * src/Tesselation/triangleintersectionlist.cpp (moved) * src/Tesselation/triangleintersectionlist.hpp (moved) * src/Tesselation/unittests/Makefile.am (added) * src/Tesselation/unittests/TesselationUnitTest.cpp (moved) * src/Tesselation/unittests/TesselationUnitTest.hpp (moved) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (moved) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (moved) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (moved) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (moved) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (deleted) * src/parser.hpp (deleted) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinMeanMaxTotalForce-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaSimTime-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Forces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Makefile (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinMeanMaxTotalForce-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/energy-forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentForces-Factors.dat (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentKeySets.dat (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.speed (added) * tests/Fragmentations/Analyzing/heptan/testsuite-analyzing-heptan.at (added) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (moved) * tests/Fragmentations/Fragmenting/benzene/pre/benzene.xyz (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/pre/cholesterol.xyz (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/pre/cycloheptane.xyz (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (moved) * tests/Fragmentations/Fragmenting/glucose/pre/glucose.xyz (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (moved) * tests/Fragmentations/Fragmenting/heptan/pre/heptan.xyz (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/pre/isoleucine.xyz (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (moved) * tests/Fragmentations/Fragmenting/neohexane/pre/neohexane.xyz (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (moved) * tests/Fragmentations/Fragmenting/proline/pre/proline.xyz (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (moved) * tests/Fragmentations/Fragmenting/putrescine/pre/putrescine.xyz (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/pre/tartaric_acid.xyz (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (moved) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragmentForces-Factors.dat (added) * tests/Fragmentations/Joining/heptan/pre/BondFragmentKeySets.dat (added) * tests/Fragmentations/Joining/heptan/pre/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/pcp.speed (added) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (added) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/analyzer.in (added) * tests/Fragmentations/joiner.in (added) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) Merge branch 'MatrixContainer_Serialization_rewrite' into stable Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber <heber@…> [b1ac7a] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) Added Undo/Redo capabilities to BondLengthTableAction. - thanks to ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber <heber@…> [829761] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) New function BondGraph::CleanupBondLengthTable(). - allows for ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber <heber@…> [1ac24b] * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.hpp (modified) Added unit test function SerializationTest to BondGraphUnitTest. Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber <heber@…> [f007a1] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) Added serialization capability to class BondGraph. - note that we ... Tue, 18 Oct 2011 15:48:58 GMT Frederik Heber <heber@…> [9b6663] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.hpp (modified) Added operator==() to BondGraph. - also added new unit test ... Tue, 18 Oct 2011 15:48:57 GMT Frederik Heber <heber@…> [2d5fee] * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) Added unit test functions SerializationTest for KeySetsContainer and ... Tue, 18 Oct 2011 15:42:54 GMT Frederik Heber <heber@…> [942906] * configure.ac (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) Added serialize() template functions to MatrixContainer and ... Tue, 18 Oct 2011 08:32:28 GMT Frederik Heber <heber@…> [752bb4] * src/Parser/Psi3Parser.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Psi3/post/empty.psi (added) * tests/regression/Parser/Psi3/post/test.psi (added) * tests/regression/Parser/Psi3/pre/empty.psi (added) * tests/regression/Parser/Psi3/pre/test.xyz (added) * tests/regression/Parser/Psi3/pre/testrhf.psi (added) * tests/regression/Parser/Psi3/pre/testrohf.psi (added) * tests/regression/Parser/Psi3/pre/testtwocon.psi (added) * tests/regression/Parser/Psi3/pre/testuhf.psi (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Added regression test Parser/Psi3. - this is heavily inspired from ... Tue, 18 Oct 2011 08:23:11 GMT Frederik Heber <heber@…> [d640ea] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Implemented Psi3Parser::save(). - also we now have working unit ... Tue, 18 Oct 2011 08:23:11 GMT Frederik Heber <heber@…> [9011c1] * src/atom.cpp (modified) * src/atom.hpp (modified) Added atom::OutputPsi3Line() to output a Psi3 conforming geometry line. Tue, 18 Oct 2011 08:22:49 GMT Frederik Heber <heber@…> [120a86] * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) TESTFIX: Added check whether streams are empty to ... Tue, 18 Oct 2011 08:07:56 GMT Frederik Heber <heber@…> [1b145f] * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.hpp (modified) Added operator==() to KeySetsContainer and MatrixContainer. - also ... Tue, 18 Oct 2011 08:07:37 GMT Frederik Heber <heber@…> [9758f7] * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/KeySetsContainer.hpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) Removed C arrays in KeySetsContainer and MatrixContainer. - ... Mon, 17 Oct 2011 20:17:51 GMT Frederik Heber <heber@…> [a9b86d] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/EnergyMatrix.cpp (added) * src/Fragmentation/EnergyMatrix.hpp (added) * src/Fragmentation/ForceMatrix.cpp (added) * src/Fragmentation/ForceMatrix.hpp (added) * src/Fragmentation/HessianMatrix.cpp (added) * src/Fragmentation/HessianMatrix.hpp (added) * src/Fragmentation/KeySetsContainer.cpp (added) * src/Fragmentation/KeySetsContainer.hpp (added) * src/Fragmentation/Makefile.am (added) * src/Fragmentation/MatrixContainer.cpp (added) * src/Fragmentation/MatrixContainer.hpp (added) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/defs.hpp (added) * src/Fragmentation/helpers.cpp (added) * src/Fragmentation/helpers.hpp (added) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/parser.cpp (deleted) * src/Fragmentation/parser.hpp (deleted) * src/Graph/BondGraph.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) Split up modules parser.[ch]pp into one module per class. - fixed ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber <heber@…> [c17091] * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) Added convenience function Psi3Parser_Parameters::getReferenceName(). Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber <heber@…> [a67cf0] * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Renamed Psi3Parser_Parameters::multipParam to ::multiplicityParam. Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber <heber@…> [032f31] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) Implemented Psi3Parser::load(). - also we now have working unit ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber <heber@…> [7f570c] * configure.ac (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/Psi3Parser_Parameters.hpp (modified) Moved operator<<() and operator>>() from Mpqc/Psi3Parser_Parameters ... Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber <heber@…> [f758dd] * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) ParserPsi3UnitTest::ParameterSetterTest() is working. Mon, 17 Oct 2011 16:56:37 GMT Frederik Heber <heber@…> [154a45] * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.hpp (modified) ParserPsi3UnitTest::ParameterCloneTest() is working. Mon, 17 Oct 2011 16:56:36 GMT Frederik Heber <heber@…> [1bef07] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/ParserTypes.def (modified) * src/Parser/Psi3Parser.cpp (added) * src/Parser/Psi3Parser.hpp (added) * src/Parser/Psi3Parser_Parameters.cpp (added) * src/Parser/Psi3Parser_Parameters.hpp (added) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (added) * src/Parser/unittests/ParserPsi3UnitTest.hpp (added) Added first working version of a Psi3Parser. - is so far mostly ... Mon, 17 Oct 2011 16:56:36 GMT Frederik Heber <heber@…> [ee50c1] * src/Parser/FormatParser_Parameters.cpp (added) * src/Parser/FormatParser_Parameters.hpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) Complete rewrite of MpqcParser_Parameters to incorporate new ... Mon, 17 Oct 2011 16:56:31 GMT Frederik Heber <heber@…> [89a67f] * src/Parser/Parameters/StringParameter.cpp (added) * src/Parser/Parameters/StringParameter.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/StringParameterUnitTest.hpp (added) Added StringParameter as ContinuousParameter<string> as string do not ... Mon, 17 Oct 2011 16:52:28 GMT Frederik Heber <heber@…> [c0da07] * src/Parser/Parameters/ContinuousParameter.hpp (modified) * src/Parser/Parameters/ContinuousParameter_impl.hpp (modified) * src/Parser/Parameters/DiscreteParameter.hpp (modified) * src/Parser/Parameters/DiscreteParameter_impl.hpp (modified) Added constructor that set value to ContinuousParameter and ... Mon, 17 Oct 2011 16:52:28 GMT Frederik Heber <heber@…> [ec0acc] * src/Parser/Parameters/ParameterStorage.cpp (added) * src/Parser/Parameters/ParameterStorage.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (added) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.hpp (added) Added ParameterStorage which is a Registry for Parameter instances. ... Mon, 17 Oct 2011 16:52:28 GMT Frederik Heber <heber@…> [6b5228] * src/Parser/Parameters/ContinuousParameter.hpp (modified) * src/Parser/Parameters/ContinuousParameter_impl.hpp (modified) * src/Parser/Parameters/DiscreteParameter.hpp (modified) * src/Parser/Parameters/DiscreteParameter_impl.hpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.hpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.hpp (modified) Added operator==() to Continuous- and DiscreteParameter classes. - ... Mon, 17 Oct 2011 16:52:27 GMT Frederik Heber <heber@…> [39fa96] * src/Parser/Parameters/ContinuousParameter.hpp (modified) * src/Parser/Parameters/ContinuousParameter_impl.hpp (modified) * src/Parser/Parameters/DiscreteParameter.hpp (modified) * src/Parser/Parameters/DiscreteParameter_impl.hpp (modified) * src/Parser/Parameters/Parameter.hpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) Added variable name and function getName() to interface Parameter. ... Mon, 17 Oct 2011 16:52:20 GMT Frederik Heber <heber@…> [c4afd1] * src/Parser/Parameters/ContinuousParameter.hpp (added) * src/Parser/Parameters/ContinuousParameter_impl.hpp (added) * src/Parser/Parameters/DiscreteParameter.hpp (added) * src/Parser/Parameters/DiscreteParameter_impl.hpp (added) * src/Parser/Parameters/Parameter.hpp (added) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.hpp (added) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (added) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.hpp (added) * src/Parser/Parameters/unittests/Makefile.am (modified) Added Continuous- and DiscreteParameter classes. - new interface ... Mon, 17 Oct 2011 16:18:56 GMT Frederik Heber <heber@…> [5f61dde] * src/Fragmentation/parser.cpp (modified) * src/Fragmentation/parser.hpp (modified) Removed usage of namespace std in module parser.[ch]pp. Mon, 17 Oct 2011 16:18:56 GMT Frederik Heber <heber@…> [3613a2] * src/Element/periodentafel.cpp (modified) FIX: periodentafel::LoadPeriodentafel() did not load color db from path. Mon, 17 Oct 2011 16:18:55 GMT Frederik Heber <heber@…> [4ae823] * src/Element/periodentafel.cpp (modified) * src/Element/periodentafel.hpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/World.cpp (modified) periodentafel may or may not Load internal databases in its cstor. ... Mon, 17 Oct 2011 16:18:55 GMT Frederik Heber <heber@…> [9d4ff35] * src/RandomNumbers/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Reduced library dependencies of RandomNumbers and BoxUnitTest. Mon, 17 Oct 2011 16:18:55 GMT Frederik Heber <heber@…> [592be9] * src/Element/unittests/ElementUnitTest.cpp (moved) * src/Element/unittests/ElementUnitTest.hpp (moved) * src/Element/unittests/Makefile.am (added) * src/Element/unittests/PeriodentafelUnitTest.cpp (moved) * src/Element/unittests/PeriodentafelUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved unitests on Element... into subfolder src/Element/unittests. ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber <heber@…> [3bdb6d] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.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/CommandAction/ElementDbAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/Hbondangle.db (moved) * src/Element/Hbonddistance.db (moved) * src/Element/Makefile.am (added) * src/Element/element.cpp (moved) * src/Element/element.hpp (moved) * src/Element/elements.db (moved) * src/Element/elements_db.cpp (moved) * src/Element/elements_db.hpp (moved) * src/Element/orbitals.db (moved) * src/Element/periodentafel.cpp (moved) * src/Element/periodentafel.hpp (moved) * src/Element/valence.db (moved) * src/Formula.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/ElementUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PeriodentafelUnitTest.cpp (modified) Moved all stuff related to elements into own subfolder and has its ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber <heber@…> [2fadb6f] * src/Helpers/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Helpers now reside in own convenience library. - this allows for ... Mon, 17 Oct 2011 16:18:54 GMT Frederik Heber <heber@…> [dd9d69] * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.hpp (modified) Prefixed double inclusion-preventing defines in header files in ... Mon, 17 Oct 2011 16:18:42 GMT Frederik Heber <heber@…> [9b5a2c] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Analysis/Makefile.am (added) * src/Analysis/analysis_bonds.cpp (moved) * src/Analysis/analysis_bonds.hpp (moved) * src/Analysis/analysis_correlation.cpp (moved) * src/Analysis/analysis_correlation.hpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisBondsUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (moved) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (moved) * src/Analysis/unittests/CountBondsUnitTest.cpp (moved) * src/Analysis/unittests/CountBondsUnitTest.hpp (moved) * src/Analysis/unittests/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved analysis modules into subfolder Analysis along with its unit ... Mon, 17 Oct 2011 14:45:04 GMT Frederik Heber <heber@…> [498ddd] * src/Parser/Parameters/ContinuousValue.hpp (modified) * src/Parser/Parameters/ContinuousValue_impl.hpp (modified) * src/Parser/Parameters/DiscreteValue.hpp (modified) * src/Parser/Parameters/DiscreteValue_impl.hpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.hpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.hpp (modified) Added operator==() and operator!=() to Continuous- and DiscreteValue. ... Mon, 17 Oct 2011 14:36:56 GMT Frederik Heber <heber@…> [84e752] * src/Parser/Makefile.am (modified) * src/Parser/Parameters/ContinuousValue.hpp (moved) * src/Parser/Parameters/ContinuousValue_impl.hpp (moved) * src/Parser/Parameters/DiscreteValue.hpp (moved) * src/Parser/Parameters/DiscreteValue_impl.hpp (moved) * src/Parser/Parameters/ValueInterface.hpp (moved) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (moved) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.hpp (moved) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (moved) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.hpp (moved) * src/Parser/Parameters/unittests/Makefile.am (added) * src/Parser/unittests/Makefile.am (modified) Moved Continuous- and DiscreteValue into subfolder Parameters. - ... Mon, 17 Oct 2011 14:36:47 GMT Frederik Heber <heber@…> [a7d753] * src/Parser/ContinuousValue.hpp (added) * src/Parser/ContinuousValue_impl.hpp (added) * src/Parser/DiscreteValue.hpp (modified) * src/Parser/DiscreteValue_impl.hpp (modified) * src/Parser/ValueInterface.hpp (added) * src/Parser/unittests/ContinuousValueUnitTest.cpp (added) * src/Parser/unittests/ContinuousValueUnitTest.hpp (added) * src/Parser/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/unittests/DiscreteValueUnitTest.hpp (modified) * src/Parser/unittests/Makefile.am (modified) Extended DiscreteValue to ContinuousValue and added ValueInterface ... Mon, 17 Oct 2011 14:31:00 GMT Frederik Heber <heber@…> [3308b6] * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) FIX: 3 out of 4 unit tests have not been told to throw ... Mon, 17 Oct 2011 14:30:55 GMT Frederik Heber <heber@…> [e09d67] * src/Parser/DiscreteValue.hpp (added) * src/Parser/DiscreteValue_impl.hpp (added) * src/Parser/unittests/DiscreteValueUnitTest.cpp (added) * src/Parser/unittests/DiscreteValueUnitTest.hpp (added) * src/Parser/unittests/Makefile.am (modified) Added class DiscreteValue that contains enums. - class has ... Fri, 14 Oct 2011 15:15:32 GMT Frederik Heber <heber@…> [d3d6c6] * src/Parser/MpqcParser_Parameters.cpp (modified) Added templated InvertMap function to ease MpqcParser_Parameters::Init(). Fri, 14 Oct 2011 15:15:30 GMT Frederik Heber <heber@…> [765f16] * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserInterface.hpp (added) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/FormatParserTrait.hpp (added) * src/Parser/FormatParserTrait_specializations_header.hpp (added) * src/Parser/FormatParser_common.cpp (moved) * src/Parser/FormatParser_common.hpp (added) * src/Parser/FormatParser_specializations_header.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/ParserTypes.cpp (added) * src/Parser/ParserTypes.def (added) * src/Parser/ParserTypes.hpp (modified) * src/Parser/ParserTypes.undef (added) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbAtomInfoContainer.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.hpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.hpp (modified) * src/moleculelist.cpp (modified) Huge Refactoring of FormatParserStorage and all FormatParser's. ... Fri, 14 Oct 2011 15:12:06 GMT Frederik Heber <heber@…> [9a6b76e] * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/ParserTypes.hpp (added) Refactored enumeration ParserTypes into extra module. Fri, 14 Oct 2011 15:11:19 GMT Frederik Heber <heber@…> [ebb87c] * src/Actions/MoleculeAction/LoadAction.cpp (modified) FIX: Added check whether suffix belongs to well-defined parser type. Fri, 14 Oct 2011 15:09:53 GMT Frederik Heber <heber@…> [6d0f058] * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/moleculelist.cpp (modified) Removed all FormatParserStorage::get() and ::set(). - we now call ... Fri, 14 Oct 2011 15:09:46 GMT Frederik Heber <heber@…> [e114e3] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) FormatParserStorage::add...() and ::get...() now use internally the ... Fri, 14 Oct 2011 14:10:54 GMT Frederik Heber <heber@…> [db67ea] * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) Added template getParser/setParser to FormatParserStorage. - ... Fri, 14 Oct 2011 14:08:41 GMT Frederik Heber <heber@…> [629e43] * src/Graph/unittests/BondGraphUnitTest.cpp (moved) * src/Graph/unittests/BondGraphUnitTest.hpp (moved) * src/Graph/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Moved unitests on BondGraph into subfolder src/Graph/unittests. - ... Fri, 14 Oct 2011 12:10:02 GMT Frederik Heber <heber@…> [45f835] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * tests/regression/Domain/RepeatBox/post/test-undo.xyz (added) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) Added Undo/Redo capabilities to RepeatBoxAction. - adapted ... Fri, 14 Oct 2011 12:09:30 GMT Frederik Heber <heber@…> [34fbb3] * src/Actions/MoleculeAction/CopyAction.cpp (modified) FIX: CopyAction did not simply use removeAtomsinMolecule(). Fri, 14 Oct 2011 10:48:21 GMT Frederik Heber <heber@…> [cbfb9a] * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * tests/regression/Domain/ScaleBox/post/test-undo.conf (added) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) Added Undo/Redo capabilities to ScaleBoxAction. - adapted ... Fri, 14 Oct 2011 10:46:54 GMT Frederik Heber <heber@…> [7b4a29] * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified) Added Undo/Redo capabilities to ChangeBoxAction. - removed XFAIL ... Fri, 14 Oct 2011 10:44:10 GMT Frederik Heber <heber@…> [de7d1d] * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * tests/regression/Domain/CenterOnEdge/post/test-undo.conf (added) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) Added Undo/Redo capabilities to CenterOnEdgeAction. - adapted ... Fri, 14 Oct 2011 10:41:09 GMT Frederik Heber <heber@…> [23526c] * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * tests/regression/Domain/CenterInBox/post/test-undo.conf (added) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) Added Undo/Redo capabilities to CenterInBoxAction. - adapted ... Fri, 14 Oct 2011 10:37:32 GMT Frederik Heber <heber@…> [e670e4] * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * tests/regression/Domain/BoundInBox/post/test-undo.conf (added) * tests/regression/Domain/BoundInBox/post/test.conf (added) * tests/regression/Domain/BoundInBox/pre/test.conf (added) * tests/regression/Domain/BoundInBox/testsuite-domain-bound-in-box.at (added) * tests/regression/Domain/testsuite-domain.at (modified) * tests/regression/Makefile.am (modified) Added Undo/Redo capabilities to BoundInBoxAction. - also added ... Fri, 14 Oct 2011 09:43:40 GMT Frederik Heber <heber@…> [9cd6bf] * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * tests/regression/Domain/AddEmptyBoundary/post/test-undo.conf (added) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) Added Undo/Redo capabilities to AddEmptyBoundaryAction. - adapted ... Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [0b004b] * src/Tesselation/unittests/Makefile.am (added) * src/Tesselation/unittests/TesselationUnitTest.cpp (moved) * src/Tesselation/unittests/TesselationUnitTest.hpp (moved) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (moved) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (moved) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (moved) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved all unittests on Tesselation into subfolder ... Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [d127c8] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Makefile.am (modified) * src/PointCloudAdaptor.hpp (modified) * src/Tesselation/BoundaryLineSet.cpp (moved) * src/Tesselation/BoundaryLineSet.hpp (moved) * src/Tesselation/BoundaryMaps.hpp (moved) * src/Tesselation/BoundaryPointSet.cpp (moved) * src/Tesselation/BoundaryPointSet.hpp (moved) * src/Tesselation/BoundaryPolygonSet.cpp (moved) * src/Tesselation/BoundaryPolygonSet.hpp (moved) * src/Tesselation/BoundaryTriangleSet.cpp (moved) * src/Tesselation/BoundaryTriangleSet.hpp (moved) * src/Tesselation/CandidateForTesselation.cpp (moved) * src/Tesselation/CandidateForTesselation.hpp (moved) * src/Tesselation/TesselPoint.cpp (moved) * src/Tesselation/TesselPoint.hpp (moved) * src/Tesselation/boundary.cpp (moved) * src/Tesselation/boundary.hpp (moved) * src/Tesselation/ellipsoid.cpp (moved) * src/Tesselation/ellipsoid.hpp (moved) * src/Tesselation/tesselation.cpp (moved) * src/Tesselation/tesselation.hpp (moved) * src/Tesselation/tesselationhelpers.cpp (moved) * src/Tesselation/tesselationhelpers.hpp (moved) * src/Tesselation/triangleintersectionlist.cpp (moved) * src/Tesselation/triangleintersectionlist.hpp (moved) * src/analysis_correlation.cpp (modified) * src/atom.hpp (modified) * src/builder_init.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.hpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) Moved modules related to Tesselation into own source subfolder. - ... Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [feb7df] * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (added) * src/Fragmentation/unittests/KeySetsContainerUnitTest.hpp (added) * src/Fragmentation/unittests/Makefile.am (added) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (added) * src/Fragmentation/unittests/MatrixContainerUnitTest.hpp (added) * src/unittests/Makefile.am (modified) Added unittests to Fragmentation subfolder. - added empty tests for ... Thu, 13 Oct 2011 19:00:47 GMT Frederik Heber <heber@…> [bc28b0] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Fragmentation/analyzer.cpp (moved) * src/Fragmentation/datacreator.cpp (moved) * src/Fragmentation/datacreator.hpp (moved) * src/Fragmentation/joiner.cpp (moved) * src/Fragmentation/parser.cpp (moved) * src/Fragmentation/parser.hpp (moved) * src/Graph/BondGraph.cpp (modified) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) Moved modules associated with fragmentation into source subfolder ... Thu, 13 Oct 2011 19:00:40 GMT Frederik Heber <heber@…> [878044] * configure.ac (modified) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaEnergies-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMaxForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMeanForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaMinMeanMaxTotalForce-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/DeltaSimTime-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Energies-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Forces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/Makefile (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxEnergies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MaxForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MeanForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinEnergies-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Fragment.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-FragmentOrder.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinForces-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/MinMeanMaxTotalForce-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/SimTime-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.dat (added) * tests/Fragmentations/Analyzing/heptan/post/plots/VectorSum-Order.pyx (added) * tests/Fragmentations/Analyzing/heptan/post/plots/energy-forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment00/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment01/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment02/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment03/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment04/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment05/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment06/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment07/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment08/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment09/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment10/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment11/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment12/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment13/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment14/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment15/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment16/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment17/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment18/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment19/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment20/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragment21/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentForces-Factors.dat (moved) * tests/Fragmentations/Analyzing/heptan/pre/BondFragmentKeySets.dat (moved) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order1.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order2.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order3.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.energy.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.Order4.forces.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energy.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/pcp.energyfragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forcefragment.all (added) * tests/Fragmentations/Analyzing/heptan/pre/pcp.forces.all (moved) * tests/Fragmentations/Analyzing/heptan/pre/pcp.speed (moved) * tests/Fragmentations/Analyzing/heptan/testsuite-analyzing-heptan.at (added) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (moved) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (moved) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (moved) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (moved) * tests/Fragmentations/Fragmenting/benzene/pre/benzene.xyz (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (moved) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/pre/cholesterol.xyz (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (moved) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/pre/cycloheptane.xyz (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (moved) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (moved) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (moved) * tests/Fragmentations/Fragmenting/glucose/pre/glucose.xyz (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (moved) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (moved) * tests/Fragmentations/Fragmenting/heptan/pre/heptan.xyz (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (moved) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/pre/isoleucine.xyz (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (moved) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (moved) * tests/Fragmentations/Fragmenting/neohexane/pre/neohexane.xyz (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (moved) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (moved) * tests/Fragmentations/Fragmenting/proline/pre/proline.xyz (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (moved) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (moved) * tests/Fragmentations/Fragmenting/putrescine/pre/putrescine.xyz (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (moved) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/pre/tartaric_acid.xyz (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (moved) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (moved) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment00/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment01/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment02/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment03/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment04/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment05/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment06/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment07/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment08/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment09/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment10/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment11/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment12/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment13/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment14/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment15/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment16/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment17/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment18/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment19/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment20/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/BondFragment21/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order1.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order2.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order3.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.energy.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.Order4.forces.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.energyfragment.all (added) * tests/Fragmentations/Joining/heptan/post/pcp.forcefragment.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment00/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment01/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment02/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment03/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment04/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment05/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment06/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment07/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment08/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment09/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment10/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment11/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment12/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment13/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.speed (added) * tests/Fragmentations/Joining/heptan/pre/BondFragmentForces-Factors.dat (added) * tests/Fragmentations/Joining/heptan/pre/BondFragmentKeySets.dat (added) * tests/Fragmentations/Joining/heptan/pre/pcp.energy.all (added) * tests/Fragmentations/Joining/heptan/pre/pcp.forces.all (added) * tests/Fragmentations/Joining/heptan/pre/pcp.speed (added) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (added) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/analyzer.in (added) * tests/Fragmentations/joiner.in (added) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (modified) Added (simple) regression tests for joiner and analyzer for heptan. ... Thu, 13 Oct 2011 18:28:54 GMT Frederik Heber <heber@…> [88f629] * tests/Joiner/BondFragment00/pcp.energy.all (added) * tests/Joiner/BondFragment00/pcp.forces.all (added) * tests/Joiner/BondFragment00/pcp.speed (added) * tests/Joiner/BondFragment01/pcp.energy.all (added) * tests/Joiner/BondFragment01/pcp.forces.all (added) * tests/Joiner/BondFragment01/pcp.speed (added) * tests/Joiner/BondFragment02/pcp.energy.all (added) * tests/Joiner/BondFragment02/pcp.forces.all (added) * tests/Joiner/BondFragment02/pcp.speed (added) * tests/Joiner/BondFragment03/pcp.energy.all (added) * tests/Joiner/BondFragment03/pcp.forces.all (added) * tests/Joiner/BondFragment03/pcp.speed (added) * tests/Joiner/BondFragment04/pcp.energy.all (added) * tests/Joiner/BondFragment04/pcp.forces.all (added) * tests/Joiner/BondFragment04/pcp.speed (added) * tests/Joiner/BondFragment05/pcp.energy.all (added) * tests/Joiner/BondFragment05/pcp.forces.all (added) * tests/Joiner/BondFragment05/pcp.speed (added) * tests/Joiner/BondFragment06/pcp.energy.all (added) * tests/Joiner/BondFragment06/pcp.forces.all (added) * tests/Joiner/BondFragment06/pcp.speed (added) * tests/Joiner/BondFragment07/pcp.energy.all (added) * tests/Joiner/BondFragment07/pcp.forces.all (added) * tests/Joiner/BondFragment07/pcp.speed (added) * tests/Joiner/BondFragment08/pcp.energy.all (added) * tests/Joiner/BondFragment08/pcp.forces.all (added) * tests/Joiner/BondFragment08/pcp.speed (added) * tests/Joiner/BondFragment09/pcp.energy.all (added) * tests/Joiner/BondFragment09/pcp.forces.all (added) * tests/Joiner/BondFragment09/pcp.speed (added) * tests/Joiner/BondFragment10/pcp.energy.all (added) * tests/Joiner/BondFragment10/pcp.forces.all (added) * tests/Joiner/BondFragment10/pcp.speed (added) * tests/Joiner/BondFragment11/pcp.energy.all (added) * tests/Joiner/BondFragment11/pcp.forces.all (added) * tests/Joiner/BondFragment11/pcp.speed (added) * tests/Joiner/BondFragment12/pcp.energy.all (added) * tests/Joiner/BondFragment12/pcp.forces.all (added) * tests/Joiner/BondFragment12/pcp.speed (added) * tests/Joiner/BondFragment13/pcp.energy.all (added) * tests/Joiner/BondFragment13/pcp.forces.all (added) * tests/Joiner/BondFragment13/pcp.speed (added) * tests/Joiner/BondFragment14/pcp.energy.all (added) * tests/Joiner/BondFragment14/pcp.forces.all (added) * tests/Joiner/BondFragment14/pcp.speed (added) * tests/Joiner/BondFragment15/pcp.energy.all (added) * tests/Joiner/BondFragment15/pcp.forces.all (added) * tests/Joiner/BondFragment15/pcp.speed (added) * tests/Joiner/BondFragment16/pcp.energy.all (added) * tests/Joiner/BondFragment16/pcp.forces.all (added) * tests/Joiner/BondFragment16/pcp.speed (added) * tests/Joiner/BondFragment17/pcp.energy.all (added) * tests/Joiner/BondFragment17/pcp.forces.all (added) * tests/Joiner/BondFragment17/pcp.speed (added) * tests/Joiner/BondFragment18/pcp.energy.all (added) * tests/Joiner/BondFragment18/pcp.forces.all (added) * tests/Joiner/BondFragment18/pcp.speed (added) * tests/Joiner/BondFragment19/pcp.energy.all (added) * tests/Joiner/BondFragment19/pcp.forces.all (added) * tests/Joiner/BondFragment19/pcp.speed (added) * tests/Joiner/BondFragment20/pcp.energy.all (added) * tests/Joiner/BondFragment20/pcp.forces.all (added) * tests/Joiner/BondFragment20/pcp.speed (added) * tests/Joiner/BondFragment21/pcp.energy.all (added) * tests/Joiner/BondFragment21/pcp.forces.all (added) * tests/Joiner/BondFragment21/pcp.speed (added) * tests/Joiner/BondFragmentForces-Factors.dat (added) * tests/Joiner/BondFragmentKeySets.dat (added) * tests/Joiner/pcp.energy.all (added) * tests/Joiner/pcp.forces.all (added) * tests/Joiner/pcp.speed (added) Added initial testset of files for regression test on joiner. Thu, 13 Oct 2011 14:02:41 GMT Frederik Heber <heber@…> [a8b10a] * src/Makefile.am (modified) FIX: Shifted ANALYSIS... in src/Makefile.am to alphabetical ordering. Thu, 13 Oct 2011 14:02:41 GMT Frederik Heber <heber@…> [f17b5f] * src/Parser/FormatParser.hpp (modified) FIX: FormatParser does not depend on parser.hpp. Thu, 13 Oct 2011 14:02:40 GMT Frederik Heber <heber@…> [5930bc] * src/Descriptors/AtomIdDescriptor.hpp (modified) FIX: AtomIdDescriptor just needs types.hpp include. Thu, 13 Oct 2011 14:02:40 GMT Frederik Heber <heber@…> [2329be] * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) FIX: Inclusion of Box.hpp is not required in AtomCommandLineQuery. Thu, 13 Oct 2011 14:02:40 GMT Frederik Heber <heber@…> [61ff05] * src/Actions/CommandAction/ElementDbAction.cpp (modified) FIX: ElementDbAction uses CleanupPeriodentafel() instead of deleting ... Thu, 13 Oct 2011 13:03:40 GMT Frederik Heber <heber@…> [ce7fdc] * 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/ActionSequence.cpp (modified) * src/Actions/ActionSequence.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/DipoleAngularCorrelationAction.cpp (modified) * 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/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (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/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (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/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionRegistry.hpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/OptionTrait.hpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * 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/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.hpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.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/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/WorldTime.hpp (modified) * src/World_calculations.hpp (modified) * src/builder_init.cpp (modified) HUGE: All Action-related codes resides now in namespace MoleCuilder. ... Thu, 13 Oct 2011 13:03:40 GMT Frederik Heber <heber@…> [e0f8c8] * configure.ac (modified) Set version to 1.1.4. - FIX: Removed AC_SUBST for LinearAlgebra ... Thu, 13 Oct 2011 13:00:58 GMT Frederik Heber <heber@…> [7ff53f] * src/UIElements/Makefile.am (modified) DISTCHECKFIX: moc_*.cpp and ui_*.h files added to MOSTLYCLEANFILES.