# # ChangeLog for / # # Generated by Trac 1.4.4 # Mar 24, 2025, 10:50:27 AM Tue, 10 Apr 2018 06:43:31 GMT Frederik Heber [441d40] * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) TESTFIX: bondgraph annealing is working better than expected. Tue, 10 Apr 2018 06:43:31 GMT Frederik Heber [90050b] * src/Dynamics/ForceAnnealing.hpp (modified) Center of weight translation removed from GatheredUpdates. Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [07d4b1] * src/Dynamics/BondVectors.cpp (modified) * src/Dynamics/BondVectors.hpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) BondVectors::getRemnant...() now requires atom's gradient. - No ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [f433ec] * src/Dynamics/BondVectors.cpp (modified) * src/Dynamics/BondVectors.hpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * src/Dynamics/unittests/BondVectorsUnitTest.cpp (modified) * src/Dynamics/unittests/Makefile.am (modified) * src/Makefile.am (modified) We now obtain weights via levmar minimization. - this should yield ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [7b4e67] * src/Dynamics/unittests/BondVectorsUnitTest.cpp (modified) * src/Dynamics/unittests/BondVectorsUnitTest.hpp (modified) * src/Dynamics/unittests/Makefile.am (modified) Added failing weights test case to BondVectors. - TESTFIX: Marked ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [c1c6cb] * src/Dynamics/unittests/BondVectorsUnitTest.cpp (added) * src/Dynamics/unittests/BondVectorsUnitTest.hpp (added) * src/Dynamics/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Added unit tests for BondVectors. - Added tests on up-to-date ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [825d33] * src/Dynamics/BondVectors.cpp (modified) * src/Dynamics/BondVectors.hpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) Extracted calculation of weights per atom into BondVectors. Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [9861d0] * src/Dynamics/BondVectors.cpp (modified) * src/Dynamics/BondVectors.hpp (modified) * src/Dynamics/BondVectors_impl.hpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) BondVectors now return subset of BondVectors for a given atom. - ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [2f3905] * src/Dynamics/ForceAnnealing.hpp (modified) Fixing annealWithBondgraph(). Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [038ccd] * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) TESTFIX: Needed to change ForceAnnealing Python and regression test ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [be729b] * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing::anneal() now only once reduces deltat. - TESTFIX: ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [6458e7] * src/Dynamics/ForceAnnealing.hpp (modified) ForceAnnealing can now be used either atom- or bond-centered. - ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [77d0cd] * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) ForceAnnealing now uses BondVectors to optimize the structure from ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [d51e62] * src/Dynamics/BondVectors.cpp (added) * src/Dynamics/BondVectors.hpp (added) * src/Dynamics/BondVectors_impl.hpp (added) * src/Makefile.am (modified) Added helper class BondVectors. Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [355915] * src/Dynamics/ForceAnnealing.hpp (modified) ForceAnnealing now calculates force on either side of bond in ... Tue, 10 Apr 2018 06:43:29 GMT Frederik Heber [e77580] * src/Dynamics/ForceAnnealing.hpp (modified) ForceAnnealing converts atomic forces to bond forces and optimize ... Tue, 10 Apr 2018 06:43:29 GMT Frederik Heber [d3e1d5] * src/FunctionApproximation/FunctionApproximation.cpp (modified) FIX: unnecessary output iterator present in ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [e21d55] * src/Dynamics/ForceAnnealing.hpp (modified) FIX: annealWithBondgraph() did not check for zero GradientDifference. ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [075357] * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (added) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (added) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (added) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (added) * tests/Python/ForceAnnealing/pre/ising_model_chain.py (added) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (added) * tests/Python/Makefile.am (modified) * tests/Python/numpy_check.py (added) * tests/Python/testsuite.at (modified) TEST: Adding Python test on ForceAnnealing using an Ising model with ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [41de6e] * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/pre/test.forces (modified) TESTFIX: ForceAnnealing regression test used zero force. - all ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [9bb8c8] * src/Dynamics/ForceAnnealing.hpp (modified) FIX: maxComponents was not chosen by absolute magnitude. Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [c87d6e] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo2.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test2.conf (added) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealingAction's Undo removes trajectory item if it was added. ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [6145577] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) FIX: ForceAnnealingAction's Undo is again working. - ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [8c6b68] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) atom::removeStep() extended to removing interval of steps. - ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [efd020] * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) Readded step-world-time to StructuralOptimization. - adapted ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [12f16c] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) ForceAnnealing first parses forces, then copies step and finally ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [2bb3be] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) Removed DoOutput param from ForceAnnealing. - TESTFIX: Modifying ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [866dec] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) ForceAnnealing no longer resets forces, AnalyseFragmentResults now ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [216840] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) ForceAnnealing accepts option deltat. Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [b2acca] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing can now be used either atom- or bond-centered. - new ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [ecfcf6] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) FIX: ForceAnnealing would not reset force components prior to loading ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [8ddd07] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/AtomicForceManipulator.hpp (modified) Sorting given selected atoms by ids in ForceAnnealing. Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [0477b0] * src/Atom/AtomSet.hpp (modified) Added sortByIds() to AtomSetMixin. Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [56b4c6] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added damping-factor as another option to ForceAnnealing for proper ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [985d1f] * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) FIX: Removed step-world-tme from StructuralOptimizationAction. - ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [cdfb6f] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) ForceAnnealing now shifts atoms in the bond graph to anneal forces, ... Tue, 10 Apr 2018 06:42:56 GMT Frederik Heber [a5c293] * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/SyncOperation.cpp (modified) FIX: SyncOperation now checks error codes from connect and close. - ... Tue, 10 Apr 2018 06:42:56 GMT Frederik Heber [1e58bb] * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-mpqc-jobs.at (modified) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-vmg-jobs.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting-water.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) * tests/integration/molecuilder_poolworker.in (modified) FIX: Integration tests now abort safely when one of the programs ... Thu, 05 Apr 2018 21:03:48 GMT Frederik Heber [456f19] * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (modified) SpecificFragmentController checks whether there are still workers ... Thu, 05 Apr 2018 13:19:33 GMT Frederik Heber [0542e2] * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/ControllerChoices.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.hpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_ControllerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Makefile.am (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/GetNumberWorkersOperation.cpp (added) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/GetNumberWorkersOperation.hpp (added) * ThirdParty/JobMarket/tests/regression/Makefile.am (modified) * ThirdParty/JobMarket/tests/regression/testsuite-numberworkers.at (added) * ThirdParty/JobMarket/tests/regression/testsuite.at (modified) Added GetNumberWorkersOperation, Controller returns number of ... Thu, 05 Apr 2018 13:19:33 GMT Frederik Heber [1181a3] * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.hpp (modified) ControllerListener now also gets const ref to WorkerPool. - this is ... Thu, 05 Apr 2018 13:19:33 GMT Frederik Heber [354a5f] * ThirdParty/JobMarket/src/JobMarket/Pool/PoolGuard.cpp (modified) FIX: PoolGuard did not decrease WaitingOp counter when checkalive op ... Thu, 05 Apr 2018 13:19:33 GMT Frederik Heber [bca6b6] * ThirdParty/JobMarket/src/JobMarket/Operations/OperationQueue.cpp (modified) OperationQueue states when queue is empty (instead of all are running). Wed, 04 Apr 2018 16:59:48 GMT Frederik Heber [322d58] * doc/userguide/userguide.xml (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/GuiChecks/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) * tests/integration/testsuite-integration.at (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing now uses step width according to Barzilai-Borwein ... Wed, 04 Apr 2018 16:59:48 GMT Frederik Heber [1e49e6] * src/Dynamics/ForceAnnealing.hpp (modified) Added reset() function to ForceAnnealing. Wed, 04 Apr 2018 16:59:37 GMT Frederik Heber [9b32071] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-testsuite-integration-unique-ports.at (added) * tests/CodeChecks/testsuite.at (modified) TESTS: Added CodeCheck on uniqueness of ports in integration tests. Wed, 04 Apr 2018 16:59:36 GMT Frederik Heber [53a85a] * tests/integration/Makefile.am (modified) * tests/integration/PotentialFitting/pre/water.pdb (added) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting-water.at (added) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting.at (added) * tests/integration/testsuite-integration.at (modified) Added integration test on Potential Fitting for water. - we fit ... Wed, 04 Apr 2018 16:59:36 GMT Frederik Heber [167523] * tests/integration/Makefile.am (modified) * tests/integration/StructureOptimization/pre/ethane.pdb (added) * tests/integration/StructureOptimization/pre/methane.pdb (added) * tests/integration/StructureOptimization/pre/water.pdb (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization.at (added) * tests/integration/testsuite-integration.at (modified) Added integration tests on Structure Optimization. - we use the ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [37fe17] * data/molecules/methane.pdb (added) * tests/integration/Makefile.am (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (added) * tests/integration/MolecularDynamics/post/ethane_initial_steps.data (added) * tests/integration/MolecularDynamics/post/methane.ekin (added) * tests/integration/MolecularDynamics/post/methane_initial_steps.data (added) * tests/integration/MolecularDynamics/post/water-system.ekin (added) * tests/integration/MolecularDynamics/post/water-system_initial_steps.data (added) * tests/integration/MolecularDynamics/pre/ethane.pdb (added) * tests/integration/MolecularDynamics/pre/methane.pdb (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics.at (modified) TESTS: Added MD tests on methane, ethane, and water-filled system. Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [7e4d0a6] * src/Fragmentation/Fragmentation.cpp (modified) FIX: Fragmentation does no longer use getTrueFather(). - in a very ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [0aae02] * tests/integration/Makefile.am (modified) * tests/integration/MolecularDynamics/post/water.ekin (added) * tests/integration/MolecularDynamics/post/water_initial_steps.data (added) * tests/integration/MolecularDynamics/pre/water.pdb (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics.at (added) * tests/integration/testsuite-integration.at (modified) Added integration test molecular dynamics of a water molecule. - we ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [f4b6bc9] * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (modified) * src/Actions/ParserAction/SetParserParametersAction.def (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Dialog_impl_pre.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) Query::handle() no longer returns bool but has internal result flag. ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [775f3f] * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (modified) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/Convex/proline/testsuite-proline.at (modified) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (modified) TESTFIX: Convex Tesselation did not specify nonconvex-file which they ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [6491d3] * tests/integration/FragmentJobs/pre/ethane.pdb (moved) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-mpqc-jobs.at (moved) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-vmg-jobs.at (moved) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs.at (added) * tests/integration/Makefile.am (modified) * tests/integration/testsuite-integration.at (modified) Moved fragment jobs integration test into subfolder. Wed, 04 Apr 2018 16:58:46 GMT Frederik Heber [6c2ae0] * ThirdParty/CodePatterns/src/Helpers/Verbose.cpp (modified) FIX: Verbose assumed Info::Verbosity is non-negative. - while ... Wed, 12 Jul 2017 19:12:47 GMT Frederik Heber [d86d97] * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.hpp (modified) * tests/regression/DiffFragmentResultContainer.cpp (modified) FIX: FragmentResultsContainer is no longer purged during run. - so ... Wed, 12 Jul 2017 19:12:47 GMT Frederik Heber [9a1e099] * tests/regression/Fragmentation/DiffFragmentResultContainer/pre/alkane_results.dat (added) * tests/regression/Fragmentation/DiffFragmentResultContainer/pre/water_results.dat (added) * tests/regression/Fragmentation/DiffFragmentResultContainer/testsuite-fragmentation-difffragmenresultcontainer.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test on DiffFragmentResultContainer. Wed, 12 Jul 2017 19:12:47 GMT Frederik Heber [3c9ac3] * src/UIElements/Views/Qt4/QtGeometryList.cpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.hpp (modified) Qt..Lists now take note of subjectKilled propery. Wed, 12 Jul 2017 19:12:43 GMT Frederik Heber [4c6f0d] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/GuiChecks/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) FIX: server-port was invalid. - now, we use empty string as param ... Wed, 12 Jul 2017 19:11:51 GMT Frederik Heber [7516f6] * src/UIElements/Views/Qt4/QtGeometryList.cpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.hpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.hpp (modified) FIX: several Qt...Lists required mutex to control refill triggered by ... Wed, 12 Jul 2017 19:11:51 GMT Frederik Heber [b10593] * configure.ac (modified) * tests/GuiChecks/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added) * tests/GuiChecks/Atoms/testsuite-atoms.at (modified) * tests/GuiChecks/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) * tests/GuiChecks/Geometry/testsuite-geometry-common.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/GuiChecks/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/GuiChecks/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (added) * tests/GuiChecks/Molecules/testsuite-molecules.at (modified) * tests/GuiChecks/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (added) * tests/GuiChecks/Parser/testsuite-parser.at (modified) * tests/GuiChecks/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/GuiChecks/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/GuiChecks/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/GuiChecks/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) * tests/GuiChecks/atlocal.in (modified) * tests/GuiChecks/difffragmentresultcontainer.in (added) Recreated all GuiChecks. - GuiChecks lacked ... Wed, 12 Jul 2017 19:11:50 GMT Frederik Heber [ecacf0] * tests/regression/Makefile.am (modified) FIX: regression test Makefile.am lacked difffragmentresultcontainer ... Wed, 12 Jul 2017 19:11:50 GMT Frederik Heber [a9db89] * tests/regression/Geometry/testsuite-geometry-common.at (modified) FIX: regression test Geometry common still used position instead of ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [92d0e6] * tests/Examples/ManyWaysTranslateAtom/testsuite-examples-many-ways-translate-atom.at (modified) ManyWaysToTranslateAtom: Added stretch-bond test. Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [d1134d] * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (modified) * tests/regression/Molecules/RotateAroundBond/post/benzene_90degree.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/benzene.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (modified) FIX: rotate-around-bond now rotates only one side of mol's bond ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [4a6ef3] * src/Graph/BreadthFirstSearchGatherer.hpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.cpp (modified) Moved AlwaysTruePredicate from BoostGraphCreatorUnitTest into ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [e0b960] * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.cpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.hpp (modified) Edges may be added and removed in BoostGraphCreator. - TESTS: added ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [966ce7] * src/Graph/BreadthFirstSearchGatherer.cpp (modified) * src/Graph/BreadthFirstSearchGatherer.hpp (modified) BreadthFirstSearchGatherer::getDistances() added. Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [e3ec8a8] * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BreadthFirstSearchGatherer.cpp (modified) * src/Graph/BreadthFirstSearchGatherer.hpp (modified) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.cpp (modified) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.hpp (modified) Extended BreadthFirstSearchGatherer to allow BFS with limited ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [0dc8bf2] * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/unittests/BoostGraphCreatorUnitTest.cpp (added) * src/Graph/unittests/BoostGraphCreatorUnitTest.hpp (added) * src/Graph/unittests/Makefile.am (modified) Added unit test for BoostGraphCreator. Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [1356af] * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BoostGraphCreator_impl.hpp (added) * src/Graph/Makefile.am (modified) Moved BoostGraphCreator::createFromRange into extra impl module. Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [6e5b8d] * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.cpp (added) * src/Graph/unittests/BreadthFirstSearchGathererUnitTest.hpp (added) * src/Graph/unittests/Makefile.am (modified) Added BreadthFirstSearchGathererUnitTest. Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [bccbe9] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BoostGraphHelpers.hpp (added) * src/Graph/BreadthFirstSearchGatherer.cpp (added) * src/Graph/BreadthFirstSearchGatherer.hpp (added) * src/Graph/Makefile.am (modified) Extracted extraction (subset of) nodes from BoostGraph into ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [d24ef58] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Graph/BoostGraphCreator.cpp (added) * src/Graph/BoostGraphCreator.hpp (added) * src/Graph/Makefile.am (modified) Extracted conversion to boost::graph into distinct struct. - ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [3b74fa] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/StretchBond/post/benzene.pdb (added) * tests/regression/Molecules/StretchBond/pre/benzene.pdb (added) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Rewrite of StretchBondAction to take bondgraph into account. - i.e. ... Wed, 12 Jul 2017 19:10:22 GMT Frederik Heber [0716eac] * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def (modified) SelectMoleculeByOrder and SelectionAtomByOrder now allows multiple ... Wed, 12 Jul 2017 19:10:21 GMT Frederik Heber [f56e14] * tests/Examples/Makefile.am (modified) * tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz (added) * tests/Examples/ManyWaysTranslateAtom/pre/water.xyz (added) * tests/Examples/ManyWaysTranslateAtom/testsuite-examples-many-ways-translate-atom.at (added) * tests/Examples/testsuite-examples.at (modified) Added Examples testcase for the many ways to translate an atom blog ... Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [70f2a1] * doc/userguide/userguide.xml (modified) DOCU: Added restrictions of file formats to userguide. Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [33af20] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (modified) TremoloParser::save() now supports multiple time steps. - TESTS: ... Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [0e894a] * src/Parser/FormatParser_common.cpp (modified) * src/Parser/FormatParser_common.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) Extracted getMinMaxTrajectories() into FormatParser_common. Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [220d2c] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/post/water_multipletimesteps.data (added) * tests/regression/Parser/Tremolo/post/water_multipletimesteps_fail.data (added) * tests/regression/Parser/Tremolo/pre/water_multipletimesteps.data (added) * tests/regression/Parser/Tremolo/pre/water_multipletimesteps_fail.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (added) * tests/regression/Parser/testsuite-parser.at (modified) TremoloParser::load() can deal with multiple time steps. - TESTS: ... Mon, 03 Jul 2017 15:07:28 GMT Frederik Heber [95b64f] * src/Atom/atom_atominfo.cpp (modified) Implemented missing AtomInfo::setAtStep(). Mon, 03 Jul 2017 15:06:53 GMT Frederik Heber [3cfb31] * src/documentation/constructs/potentials.dox (modified) DOCU: Updated potentials.dox. Mon, 03 Jul 2017 15:06:53 GMT Frederik Heber [b52710e] * doc/userguide/userguide.xml (modified) DOCU: Enhanced documentation of fit-potential to explain new ... Mon, 03 Jul 2017 15:06:34 GMT Frederik Heber [8f2f4e] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene::removeShape() invalidated iter before delete. Mon, 03 Jul 2017 15:06:31 GMT Frederik Heber [3f6aac] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByName/post/ethane-H5_missing.pdb (added) * tests/regression/Selection/Atoms/AtomByName/pre/ethane.pdb (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added (Un)selectAtomByName. - Descriptor for AtomByName was already ... Mon, 03 Jul 2017 15:01:38 GMT Frederik Heber [9a4772] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) AnalyseFragmentResults now always prints energy table, verbosity 1. Mon, 03 Jul 2017 15:01:38 GMT Frederik Heber [f1cacb] * doc/userguide/userguide.xml (modified) Fixed several small issues with the userguide. - additional ... Mon, 03 Jul 2017 15:00:00 GMT Frederik Heber [4dfe724] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) FIX: QtGui again reacts to WorldTime changes. - QtObservedAtom now ... Mon, 03 Jul 2017 15:00:00 GMT Frederik Heber [70fee0] * ThirdParty/CodePatterns/src/CodePatterns/ObservedValue.hpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/ObservedValueUnitTest.cpp (modified) ObservedValue has forceUpdate() public function to externally force ... Mon, 03 Jul 2017 14:59:32 GMT Frederik Heber [8e9217] * configure.ac (modified) Changed email address to bug@molecuilder.com. Thu, 22 Jun 2017 22:28:16 GMT Frederik Heber [310445] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/RandomPerturbationAction.cpp (added) * src/Actions/AtomAction/RandomPerturbationAction.def (added) * src/Actions/AtomAction/RandomPerturbationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/RandomPerturbation/post/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/pre/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added RandomPerturbationAction. - this should be when doing ... Wed, 21 Jun 2017 22:02:50 GMT Frederik Heber [78ea3c] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/World.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) Merge branch 'Docu_Python_wait' into Candidate_v1.6.1 Conflicts: ... Wed, 21 Jun 2017 22:02:14 GMT Frederik Heber [be848d] * doc/userguide/userguide.xml (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.def (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.def (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.cpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.def (added) * src/Actions/GeometryAction/GeometryRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/Values.hpp (modified) * src/Geometry/GeometryObject.cpp (added) * src/Geometry/GeometryObject.hpp (added) * src/Geometry/GeometryRegistry.cpp (added) * src/Geometry/GeometryRegistry.hpp (added) * src/Geometry/Makefile.am (added) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Specifics/Parameter_vector.cpp (added) * src/Parameters/Specifics/Parameter_vector.hpp (added) * src/Parameters/Specifics/Value_vector.cpp (added) * src/Parameters/Specifics/Value_vector.hpp (added) * src/Parameters/Validators/Specific/GeometryNameValidator.cpp (added) * src/Parameters/Validators/Specific/GeometryNameValidator.hpp (added) * src/Parameters/Validators/Specific/PresentGeometryNameValidator.cpp (added) * src/Parameters/Validators/Specific/PresentGeometryNameValidator.hpp (added) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/GlobalListOfParameterQueries.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/Views/Qt4/QtGeometryList.cpp (added) * src/UIElements/Views/Qt4/QtGeometryList.hpp (added) * src/cleanUp.cpp (modified) * tests/GuiChecks/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (added) * tests/GuiChecks/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (added) * tests/GuiChecks/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (added) * tests/GuiChecks/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (added) * tests/GuiChecks/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/GuiChecks/Geometry/testsuite-geometry-common.at (added) * tests/GuiChecks/Geometry/testsuite-geometry.at (added) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/testsuite.at (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Geometry/DistanceToVector/post/test.xyz (added) * tests/regression/Geometry/DistanceToVector/pre/test.xyz (added) * tests/regression/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (added) * tests/regression/Geometry/InputToVector/post/test.xyz (added) * tests/regression/Geometry/InputToVector/pre/test.xyz (added) * tests/regression/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (added) * tests/regression/Geometry/PlaneToVector/post/test.xyz (added) * tests/regression/Geometry/PlaneToVector/pre/test.xyz (added) * tests/regression/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (added) * tests/regression/Geometry/PositionToVector/post/test.xyz (added) * tests/regression/Geometry/PositionToVector/pre/test.xyz (added) * tests/regression/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (added) * tests/regression/Geometry/Remove/post/test.xyz (added) * tests/regression/Geometry/Remove/pre/test.xyz (added) * tests/regression/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/regression/Geometry/testsuite-geometry-common.at (added) * tests/regression/Geometry/testsuite-geometry.at (added) * tests/regression/Makefile.am (modified) * tests/regression/Options/DryRun/post/session.py (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/pre/complextest.py (modified) * tests/regression/testsuite.at (modified) Merge branch 'GeometryObjects' into Candidate_v1.6.1 Wed, 21 Jun 2017 21:52:01 GMT Frederik Heber [101d2d] * doc/userguide/userguide.xml (modified) DOCU: Added note on necessity of wait() to Python section. Wed, 21 Jun 2017 21:51:24 GMT Frederik Heber [7294dc] * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: Fixing the use of the trajectories that were changed to maps. ... Wed, 21 Jun 2017 21:15:15 GMT Frederik Heber [9f2071] * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: World::setTime() now correctly copies the current state to the ... Tue, 20 Jun 2017 20:02:18 GMT Frederik Heber [137845] * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) StepWorldTime now has a single argument. - this was not possible ... Tue, 20 Jun 2017 20:02:18 GMT Frederik Heber [15d21e] * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) CommandLineParser is now able to parse negative numbers. - before ... Tue, 20 Jun 2017 20:01:46 GMT Frederik Heber [da7ef9] * src/Actions/Action.hpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) FIX: STATUS msg only pushed to GUI, now also always in log.