# # ChangeLog for src # # Generated by Trac 1.6 # Jul 4, 2025, 3:32:17 PM Sun, 28 Feb 2016 18:00:02 GMT Frederik Heber [df0c80] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Filling/Makefile.am (modified) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.cpp (added) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.hpp (added) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.hpp (modified) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-minimum-distance-to-surface.at (modified) FIX: Filling actions did not use minimum distance for tesselated ... Sun, 28 Feb 2016 17:59:42 GMT Frederik Heber [50d49d] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (moved) * src/Actions/PotentialAction/FitPartialChargesAction.def (moved) * src/Actions/PotentialAction/FitPartialChargesAction.hpp (moved) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Potential/FitParticleCharges/testsuite-potential-fit-partial-charges.at (moved) * tests/GuiChecks/Potential/testsuite-potential.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitPartialCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitPartialCharges/pre/water.pdb (moved) * tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at (moved) * tests/regression/Potential/testsuite-potential.at (modified) FIX: Renamed FitParticleCharges -> FitPartialCharges. - fitting ... Fri, 26 Feb 2016 09:54:40 GMT Frederik Heber [0824dd] * src/documentation/constructs/qt-gui.dox (modified) Enhanced documentation for Qt constructs. Fri, 26 Feb 2016 09:54:40 GMT Frederik Heber [4a187d] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene also takes note of empty molecule. - this is for the ... Fri, 26 Feb 2016 09:54:40 GMT Frederik Heber [1187c5] * src/Atom/atom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) FIX: QtObservedAtom's AtomMoleculeIndex was not informed of molecule ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [640cbd] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: emit changed signal before moleculeEmptied. Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [e29427] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene RemovedMolecules now uses QtObservedMolecule* as key. ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [805fdc] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene's moleculesAtomRemoved was checking ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [5c9604] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) SignedOn_t in QtObservedInstanceBoard is again just a set. - we do ... Fri, 26 Feb 2016 09:46:19 GMT Frederik Heber [8b59dd] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) Removed last...removed in QtObservedInstanceBoard. - this does not ... Fri, 26 Feb 2016 09:46:18 GMT Frederik Heber [92af1b] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) tempcommit: Removed atomDelayed stuff in QtObservedInstanceBoard's ... Fri, 26 Feb 2016 09:46:18 GMT Frederik Heber [96e145] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) AtomInserted/Removed of QtObservedMolecule sends ptr as unique key. ... Fri, 26 Feb 2016 09:46:18 GMT Frederik Heber [bcf9cd] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) GLWorldScene places GLMoleculeObject_molecule into extra list before ... Sun, 14 Feb 2016 12:34:30 GMT Frederik Heber [23221f] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) Removed RefCounted... again. Sun, 14 Feb 2016 12:34:29 GMT Frederik Heber [59f1bc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/documentation/constructs/qt-gui.dox (modified) All ..Inserted/..Removed signals now go through GLWorldScene. - ... Sun, 14 Feb 2016 12:34:29 GMT Frederik Heber [03e69e] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: GLMoleculeObject_.. does not care whether selection state did ... Sun, 14 Feb 2016 12:34:29 GMT Frederik Heber [8281cc] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) FIX: Making sure that atomInserted is received from same source in ... Sun, 14 Feb 2016 12:34:29 GMT Frederik Heber [1c0961] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: indexChanged from QtObserved... transmit both old and new id. Sun, 14 Feb 2016 12:34:29 GMT Frederik Heber [62a0ee] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) QtObserved... now count the subjectKilled() from the containes ... Sun, 14 Feb 2016 12:34:28 GMT Frederik Heber [1b07b1] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) QtObservedInstanceBoard now sends QtObserved..::ptr around in ... Sun, 14 Feb 2016 12:34:28 GMT Frederik Heber [e7ed12] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) Combined checks into checkRemoval() in ObservedValuesContainer. Sun, 14 Feb 2016 12:34:28 GMT Frederik Heber [387a84] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) FIX: Added mutex to ObservedValuesContainer to ensure atomic access. Sun, 14 Feb 2016 12:34:27 GMT Frederik Heber [5aec20] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) QtElementList must not use atom but only QtObservedAtom. Sun, 14 Feb 2016 12:34:27 GMT Frederik Heber [4cac6c] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) CHECK: Don't admonish empty missed states in GLWorldScene? - ... Sun, 14 Feb 2016 12:34:27 GMT Frederik Heber [7ded1c] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) GLMoleculeObject_atom and .._molecule don't get QtObserved... right ... Sun, 14 Feb 2016 12:34:27 GMT Frederik Heber [3fe318] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) CHECK: tempcommit: Removed Cacheable of TesselationHull for ... Sun, 14 Feb 2016 12:34:27 GMT Frederik Heber [aa41a3] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) QtMoleculeList must not use QtObservedMolecules in lists but only ... Sun, 14 Feb 2016 12:34:26 GMT Frederik Heber [6bce88] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) ObservedValuesContainer now asserts that observedinstance has been ... Sun, 14 Feb 2016 12:34:26 GMT Frederik Heber [393342] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) FIX: ObservesValuesContainer uses internal struct for two iterators ... Sun, 14 Feb 2016 12:34:26 GMT Frederik Heber [0af22d] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) FIX: ObservedValuesContainer uses deque for internal observed values. ... Sun, 14 Feb 2016 12:33:43 GMT Frederik Heber [b43585] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp (deleted) * src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp (deleted) Removed QtSelectionChangedAgent. - it is no longer used. We either ... Sun, 14 Feb 2016 12:33:43 GMT Frederik Heber [0f368b] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp (modified) Removed QtSelectionAgent usage in QtMoleculeListView. - instead we ... Sun, 14 Feb 2016 12:33:43 GMT Frederik Heber [5cd3a33] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) Removed QtSelectionUsage in GLWorldView and related. - instead ... Sun, 14 Feb 2016 12:33:42 GMT Frederik Heber [9e9100] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Added ObservedValue for selection status of atoms and molecules to ... Sun, 14 Feb 2016 12:33:42 GMT Frederik Heber [6d4925] * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) FIX: QtObservedInstanceBoard needs to allow delayed atomInserted from ... Sun, 14 Feb 2016 12:33:42 GMT Frederik Heber [42d7dc] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) QtInfoBox disconnects signals. Sun, 14 Feb 2016 12:33:42 GMT Frederik Heber [4e6ffe] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) FIX: ObservedValue need to be removed with a bit of delay. - ... Sun, 14 Feb 2016 12:33:42 GMT Frederik Heber [04c3a3] * src/UIElements/Qt4/InstanceBoard/ObservedValue_wCallback.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) QtObservedAtom, ..Molecule, and ObservedValue_wCallback have flag to ... Sun, 14 Feb 2016 12:33:41 GMT Frederik Heber [b2c2e4] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) FIX: Qt's parent properly set from QtMainWindow's point of view. Sun, 14 Feb 2016 12:33:41 GMT Frederik Heber [cf9287] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) Equipped QtInfoBox with mutex and split clearTabs(). - this avoids ... Sun, 14 Feb 2016 12:33:41 GMT Frederik Heber [3b9aa1] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) FIX: All ObservedValue getters now return const references. - this ... Fri, 12 Feb 2016 23:15:40 GMT Frederik Heber [367489] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) QtInfoBox now obtains information completely from ... Fri, 12 Feb 2016 23:15:40 GMT Frederik Heber [5a9e34] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Extended QtObservedMolecule by Center, NonHydrogenCount, and BondCount. Fri, 12 Feb 2016 23:15:40 GMT Frederik Heber [fe493f] * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) Extended QtObservedAtom by Name and Molecule. Fri, 12 Feb 2016 23:15:40 GMT Frederik Heber [deb5ee] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed molecule's AboutToBeRemoved channel. Fri, 12 Feb 2016 23:15:39 GMT Frederik Heber [ca1535] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) All QtMoleculeItem now heed QtObservedMolecule and QtMoleculeList ... Fri, 12 Feb 2016 23:15:39 GMT Frederik Heber [1b6415a] * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Added AtomCount and FormulaChanged to QtObservedMolecule. Fri, 12 Feb 2016 23:15:24 GMT Frederik Heber [ab628c] * src/UIElements/Qt4/InstanceBoard/ObservedValue_wCallback.hpp (modified) FIX: ObservedValue_wCallback needs to call callback() only on last ... Fri, 12 Feb 2016 23:15:24 GMT Frederik Heber [68418e] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) ObservedValuesContainer now stores QtObserved.. instances directly. ... Fri, 12 Feb 2016 23:15:24 GMT Frederik Heber [90821d] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) Moved countSubjectKilled related code from QtObservedInstanceBoard ... Fri, 12 Feb 2016 23:15:24 GMT Frederik Heber [494478] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValue_UpdateAtoms.hpp (moved) * src/UIElements/Qt4/InstanceBoard/ObservedValue_wCallback.hpp (moved) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Extracted all ObservedValue functionality out of ... Fri, 12 Feb 2016 23:15:23 GMT Frederik Heber [65c323] * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) Extracted all ObservedValue functionality out of ... Fri, 12 Feb 2016 23:15:23 GMT Frederik Heber [41e287] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer.hpp (added) * src/UIElements/Qt4/InstanceBoard/ObservedValuesContainer_impl.hpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Extracted functions handling refcounting of ObservedValues into ... Fri, 12 Feb 2016 23:15:23 GMT Frederik Heber [98c35c] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/ObservedValue_types.hpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (modified) Added rudimentary getter and returner for ObservedAtom/..Molecule() ... Fri, 12 Feb 2016 23:15:22 GMT Frederik Heber [0070aa] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.cpp (added) * src/UIElements/Qt4/InstanceBoard/QtObservedMolecule.hpp (added) Added QtObservedAtom and ..Molecule() instances. Fri, 12 Feb 2016 23:15:07 GMT Frederik Heber [2f7988] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.cpp (moved) * src/UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp (moved) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) Moved and renamed QtInstanceInformationBoard -> ... Fri, 12 Feb 2016 23:15:07 GMT Frederik Heber [0f7ffe] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) Changed connections between GLWorldScene, GLWorldView and ... Fri, 12 Feb 2016 23:15:06 GMT Frederik Heber [8d5fbf1] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtInstanceInformationBoard.cpp (modified) * src/UIElements/Views/Qt4/QtInstanceInformationBoard.hpp (modified) GLMoleculeObject_atom, _bond, _molecule all use ... Fri, 12 Feb 2016 23:15:06 GMT Frederik Heber [47f0e4] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) FIX: QtMoleculeItem not signing off after subjectKilled(). Fri, 12 Feb 2016 23:15:06 GMT Frederik Heber [15c8a9] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/UIElements/Views/Qt4/QtInstanceInformationBoard.cpp (added) * src/UIElements/Views/Qt4/QtInstanceInformationBoard.hpp (added) Added QtInstanceInformationBoard that handles ObservedValues through ... Fri, 12 Feb 2016 23:15:06 GMT Frederik Heber [026bef] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/ObservedValue_UpdateAtoms.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/ObservedValue_wCallback.hpp (modified) Changed GLMoleculeObject_...:countSubjectKilled() to taking id ... Fri, 12 Feb 2016 23:15:05 GMT Frederik Heber [099f67] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) GLMoleculeObject_bond's ObservedValues is now all static. - again, ... Fri, 12 Feb 2016 23:15:05 GMT Frederik Heber [16bd37] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) GLMoleculeObject_atom's ObservedValues is now all static. - this is ... Fri, 12 Feb 2016 23:15:05 GMT Frederik Heber [8688ef] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/ObservedValue_UpdateAtoms.hpp (added) GLMoleculeObject_molecule's ObservedValues is now all static. - ... Fri, 12 Feb 2016 23:15:05 GMT Frederik Heber [7a205a] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: GLMoleculeObject_molecule::updateAtoms() used DisplayAtoms ... Fri, 12 Feb 2016 23:15:05 GMT Frederik Heber [2831b3] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) FIX: QtInfoBox only updatePage() when ref still present (no ... Fri, 12 Feb 2016 23:15:04 GMT Frederik Heber [7c7c4a] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/ObservedValue_wCallback.hpp (added) FIX: All ObservedValue's of GLMoleculeObject_atom/bond/molecule ... Fri, 12 Feb 2016 23:15:04 GMT Frederik Heber [e25448] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: GLMoleculeObject_molecule::subjectKilled() should not call ... Fri, 12 Feb 2016 23:15:04 GMT Frederik Heber [7cf0eb] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: GLWorldScene has additional moleculePrepared... slots and ... Fri, 12 Feb 2016 23:15:04 GMT Frederik Heber [4ab5dc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: GLMoleculeObject_molecule still contained hack to get upper ... Fri, 12 Feb 2016 23:15:03 GMT Frederik Heber [b375e7] * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (modified) QtFavoriteActions uses ObservedValue for checking last queued ... Thu, 11 Feb 2016 08:07:50 GMT Frederik Heber [db842b] * src/molecule.hpp (modified) FIX: molecule's BoundingBoxSweepingAxis used unordered set of ... Thu, 11 Feb 2016 08:07:50 GMT Frederik Heber [951aa6] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed molecule's resetFormula() and doCountBonds() and ... Thu, 11 Feb 2016 08:07:50 GMT Frederik Heber [29f7c1] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Molecule now has maps with old values for bond counts and element ... Thu, 11 Feb 2016 08:07:50 GMT Frederik Heber [c0f2fc] * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) atom now uses associate... and disassociatedAtomWithMolecule(). - ... Thu, 11 Feb 2016 08:07:12 GMT Frederik Heber [eb6552] * src/Makefile.am (modified) * src/MoleculeListClass.hpp (deleted) * src/moleculelist.cpp (deleted) Deleted MoleculeListClass. - finally ... some veeeery old legacy ... Thu, 11 Feb 2016 08:07:11 GMT Frederik Heber [2affd1] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.hpp (modified) Removed molecules_deprecated from World and unnecessary includes of ... Thu, 11 Feb 2016 08:07:11 GMT Frederik Heber [df5b8c] * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) Replaced MoleculeListClass in ExportGraph by vector of molecules. - ... Thu, 11 Feb 2016 08:07:11 GMT Frederik Heber [2bfc5b] * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_bonds.hpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.hpp (modified) Replaced MoleculeListClass in analysis_bonds by vector of molecules. ... Thu, 11 Feb 2016 08:07:11 GMT Frederik Heber [ada8df] * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) Removed FindEmbeddingHole which lacked implementation so far. Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [d4ba3f] * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomObserver.hpp (modified) * src/Atom/atom.cpp (modified) * src/EntityObserver.hpp (added) * src/EntityObserver_impl.hpp (added) * src/LinkedCell/unittests/Makefile.am (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (deleted) * src/Makefile.am (modified) * src/MoleculeObserver.cpp (modified) * src/MoleculeObserver.hpp (modified) * src/molecule.cpp (modified) Extracted common code out of Molecule/AtomObserver into ... Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [5d8f4f] * src/Atom/AtomObserver.hpp (modified) * src/Makefile.am (modified) * src/MoleculeObserver.cpp (added) * src/MoleculeObserver.hpp (added) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) Added MoleculeObserver as pendant to AtomObserver for molecules. Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [4a328f] * src/Atom/AtomObserver.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.hpp (modified) FIX: AtomObserver was not up-to-date with respect to atom's channels. Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [7f1865d] * src/World.cpp (modified) * src/World.hpp (modified) Added template functions to (un)set vector of instances in a row. Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [b71881] * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_observable.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Added select() and unselect() functions to atom and molecule, also ... Thu, 11 Feb 2016 08:06:49 GMT Frederik Heber [687ef1] * src/builder_init.cpp (modified) FIX: molecuilder.py is now loaded after GUI is done initializing. - ... Thu, 11 Feb 2016 08:06:48 GMT Frederik Heber [cbd409] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Added Cacheable MoleculeCenter to molecule which is cleverly updated. Thu, 11 Feb 2016 08:03:36 GMT Frederik Heber [d93d2c] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_IndexedEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeForces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_VMGEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_VMGForces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_IndexedEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeForces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_VMGEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_VMGForces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_OBC.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_PBC.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentShortRangeResults.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) FIX: Long-range forces were not added onto atom's forces. - this ... Tue, 09 Feb 2016 07:11:37 GMT Frederik Heber [45b45d] * src/Parser/PdbParser.cpp (modified) FIX: PdbParser would calculate trajectors over all atoms, not just ... Tue, 09 Feb 2016 07:11:37 GMT Frederik Heber [7daf73] * src/Analysis/analysis_correlation.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/types.hpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * tests/regression/Molecules/Remove/post/id0_2_missing.pdb (modified) * tests/regression/Molecules/Remove/post/water_box.pdb (modified) LinkedCell's LinkedList is now a vector and no longer a set. - this ... Tue, 09 Feb 2016 07:11:35 GMT Frederik Heber [b40690] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) Fit..PotentialAction now allow setting maximum number of optimization ... Tue, 09 Feb 2016 07:10:23 GMT Frederik Heber [b8f2ea] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) FIX: PotentialTrainer did not use user-specified threshold so far. ... Mon, 08 Feb 2016 10:28:17 GMT Frederik Heber [08111a] * src/Actions/MoleculeAction/RemoveAction.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) FIX: Added copy cstor for AtomicInfo. - otherwise AtomicInfo is ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [918a6c] * src/Atom/atom.cpp (modified) * src/Atom/atom_observable.hpp (modified) Added extra signal MoleculeChanged to AtomObservable. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [8ad68b] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) AddAction and UndoRedoHelpers' AddAtomsFromAtomicInfo use recreate..(). Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [5cf341] * src/World.cpp (modified) * src/World.hpp (modified) Added recreateAtom() and recreateMolecule() to World. - in order to ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [840d02] * src/molecule.cpp (modified) FIX: not using const ref in binding updateBoundingBox() for molecule. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [7eec64] * src/World.cpp (modified) FIX: World needs to first destroy the molecule, then release its ids. ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [4965d9f] * src/World.cpp (modified) FIX: World::destroy..() did not emit SelectionChanged signal. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [50c45f] * src/UIElements/Qt4/QtMainWindow.cpp (modified) FIX: Fitting domain to window on QtMainWindow's init.