# # ChangeLog for src/Actions/Makefile.am # # Generated by Trac 1.4.4 # Dec 27, 2024, 2:54:11 PM Thu, 11 Jun 2015 23:21:40 GMT Frederik Heber [f3db60] * doc/userguide/userguide.xml (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/DryRunAction.cpp (added) * src/Actions/CommandAction/DryRunAction.def (added) * src/Actions/CommandAction/DryRunAction.hpp (added) * src/Actions/CommandAction/NoDryRunAction.cpp (added) * src/Actions/CommandAction/NoDryRunAction.def (added) * src/Actions/CommandAction/NoDryRunAction.hpp (added) * src/Actions/DryRunAdvocate.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/DryRun/post/session.py (added) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (added) * tests/regression/Options/DryRun/testsuite-options-dryrun.at (added) * tests/regression/Options/DryRun/testsuite-options-no-dryrun.at (added) * tests/regression/Options/testsuite-options.at (modified) Added DryRun and NoDryRun actions. - actions (un)set a flag inside ... Fri, 13 Feb 2015 09:17:52 GMT Frederik Heber [2fcef3] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/SaturateAction.cpp (added) * src/Actions/AtomAction/SaturateAction.def (added) * src/Actions/AtomAction/SaturateAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/Saturate/post/carbon.xyz (added) * tests/regression/Atoms/Saturate/post/nitrogen.xyz (added) * tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (added) * tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (added) * tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added SaturateAction that uses SphericalPointDistribution. - added ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [066442] * doc/userguide/userguide.xml (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (added) * src/Actions/MoleculeAction/TranslateAction.def (added) * src/Actions/MoleculeAction/TranslateAction.hpp (added) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (modified) Added TranslateMolecule action. - added translate-molecule to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [a84e8d] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.hpp (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/box.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/empty.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/id2_4_missing.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/water_id2_4.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/pre/box.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/box.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/empty.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/id2_4_missing.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/water_id2_4.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/pre/box.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at (added) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) Added Push/PopMolecules selection action. - added push-molecule to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [3213f2] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/PopAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/PopAtomsAction.hpp (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/PopAtomSelection/post/empty.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/pre/test.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/testsuite-selection-pop-atom-selection.at (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/empty.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/pre/test.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/testsuite-selection-push-atom-selection.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added Push/PopAtom selection actions. - added push-atom to ... Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [867473] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RemoveAction.cpp (added) * src/Actions/MoleculeAction/RemoveAction.def (added) * src/Actions/MoleculeAction/RemoveAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/Remove/post/id0_2_missing.pdb (added) * tests/regression/Molecules/Remove/post/water_box.pdb (added) * tests/regression/Molecules/Remove/pre/water_box.pdb (added) * tests/regression/Molecules/Remove/testsuite-molecules-remove.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added new RemoveAction for molecules. - also add regression test. ... Sun, 19 Oct 2014 17:12:11 GMT Frederik Heber [5c8807] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 ... Sun, 19 Oct 2014 17:09:30 GMT Frederik Heber [9e1bfb] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:08:51 GMT Frederik Heber [0ea063] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (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/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Extracted SavePotentialsAction. - PotentialTrainer::StorePotentials ... Sun, 19 Oct 2014 17:08:50 GMT Frederik Heber [f1eabd] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * tests/Python/AllActions/options.dat (modified) Extracted ParsePotentialsAction from FitCompoundPotentialAction. Sun, 19 Oct 2014 17:08:36 GMT Frederik Heber [98d166] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) Split FitPotentialAction into two actions. - FitPotentialAction ... Thu, 18 Sep 2014 23:32:23 GMT Frederik Heber [bbf6dc] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/MirrorAction.cpp (added) * src/Actions/AtomAction/MirrorAction.def (added) * src/Actions/AtomAction/MirrorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/Mirror/post/test-mirrored.xyz (added) * tests/regression/Atoms/Mirror/post/test.xyz (added) * tests/regression/Atoms/Mirror/pre/test.xyz (added) * tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added AtomMirrorAction. - also added regression tests. Thu, 18 Sep 2014 17:23:14 GMT Frederik Heber [c7fe90] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added TranslateToOriginAction. - also added regression test. Thu, 18 Sep 2014 17:19:38 GMT Frederik Heber [f4b626a] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added AverageMoleculeForceAction for measuring average force acting ... Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [aa55d0] * src/Actions/FillAction/SuspendInMoleculeAction.cpp (added) * src/Actions/FillAction/SuspendInMoleculeAction.def (added) * src/Actions/FillAction/SuspendInMoleculeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (deleted) * src/Actions/MoleculeAction/SuspendInWaterAction.def (deleted) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (deleted) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) Moved and renamed SuspendInWaterAction from Molecule.. to ... Wed, 10 Sep 2014 19:10:26 GMT Frederik Heber [16c7dd] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (deleted) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (deleted) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified) * tests/regression/Filling/FillVoidWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/post/test.xyz (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillVoidWithMolecule/pre/water.data (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (deleted) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (deleted) * tests/regression/Filling/FillWithMolecule/post/propane.xyz (deleted) * tests/regression/Filling/FillWithMolecule/post/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/pre/test.conf (deleted) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Removed FillVoidWithMolecule and FillWithMolecule actions. - these ... Wed, 10 Sep 2014 18:59:16 GMT Frederik Heber [6801f4] * src/Actions/FillAction/FillVolumeAction.cpp (added) * src/Actions/FillAction/FillVolumeAction.def (added) * src/Actions/FillAction/FillVolumeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Filling/Mesh/MeshAdaptor.hpp (modified) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeVolumeFillerPreparator.hpp (added) * tests/regression/Filling/FillVolume/post/water_cylinder.xyz (added) * tests/regression/Filling/FillVolume/post/water_undo.xyz (added) * tests/regression/Filling/FillVolume/pre/water.xyz (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at (added) * tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at (added) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Added FillVolumeAction for filling a Shape's volume. - added ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [e5f61ba] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (added) * src/Actions/FragmentationAction/StructuralOptimizationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added MakroAction StructureOptimizationAction. - performs similarly ... Wed, 20 Aug 2014 12:58:30 GMT Frederik Heber [1a48d2] * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (added) * src/Actions/MoleculeAction/ForceAnnealingAction.def (added) * src/Actions/MoleculeAction/ForceAnnealingAction.hpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (added) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (added) * tests/regression/Molecules/ForceAnnealing/post/test.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test.forces (added) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added ForceAnnealingAction. - also added regression test. - ... Sat, 16 Aug 2014 15:52:31 GMT Frederik Heber [343c5a] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (added) * src/Actions/GraphAction/CorrectBondDegreeAction.def (added) * src/Actions/GraphAction/CorrectBondDegreeAction.hpp (added) * src/Actions/Makefile.am (modified) * tests/Calculations/testsuite-calculations-anthracene.at (modified) * tests/Calculations/testsuite-calculations-coronene.at (modified) * tests/Calculations/testsuite-calculations-naphthalene.at (modified) * tests/Calculations/testsuite-calculations-phenanthrene.at (modified) Added CorrectBondDegreeAction and fixed Calculation tests. - pdb ... Mon, 14 Jul 2014 11:16:23 GMT Frederik Heber [d8821e] * Makefile.am (modified) * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Element/Makefile.am (modified) * src/Element/element.hpp (modified) * src/Element/ion.cpp (added) * src/Element/ion.hpp (added) * src/Element/periodentafel.cpp (modified) * src/Element/periodentafel.hpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/IonUnitTest.cpp (added) * src/Element/unittests/IonUnitTest.hpp (added) * src/Element/unittests/Makefile.am (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (added) * src/Fragmentation/Automation/MPQCCommandFragmentController.hpp (added) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/ResultContainer.hpp (added) * src/Fragmentation/Automation/ResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController.hpp (modified) * src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp (added) * src/Fragmentation/Automation/SpecificFragmentController_ResultContainer_impl.hpp (deleted) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/analyzer.cpp (deleted) * src/Fragmentation/datacreator.cpp (deleted) * src/Fragmentation/datacreator.hpp (deleted) * src/Fragmentation/joiner.cpp (deleted) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/Jobs/JobMarket/FragmentJob.cpp (added) * src/Jobs/JobMarket/FragmentJob.hpp (added) * src/Jobs/JobMarket/FragmentResult.cpp (added) * src/Jobs/JobMarket/FragmentResult.hpp (added) * src/Jobs/JobMarket/JobId.cpp (added) * src/Jobs/JobMarket/JobId.hpp (added) * src/Jobs/JobMarket/SystemCommandJob.cpp (added) * src/Jobs/JobMarket/SystemCommandJob.hpp (added) * src/Jobs/JobMarket/types.hpp (added) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) * src/Potentials/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/cleanUp.cpp (modified) * src/documentation/constructs/potentials.dox (modified) * tests/Calculations/Makefile.am (added) * tests/Calculations/atlocal.in (added) * tests/Calculations/molecuilder.in 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tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment14/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment15/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment16/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment17/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment18/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment19/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment20/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragment21/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragmentForces-Factors.dat (deleted) * tests/Fragmentations/Joining/heptan/pre/BondFragmentKeySets.dat (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.energy.all (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.forces.all (deleted) * tests/Fragmentations/Joining/heptan/pre/pcp.speed (deleted) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (deleted) * tests/Fragmentations/Makefile.am (modified) * tests/Fragmentations/joiner.in (deleted) * tests/Fragmentations/testsuite.at (modified) * tests/Makefile.am (modified) * tests/regression/Fragmentation/FragmentationAutomation/pre/test.conf (added) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [786d28] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Lib..FragmentationAutomation and lib..Jobs now also compiled without ... Fri, 27 Jun 2014 21:32:02 GMT Frederik Heber [26b4eb4] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionStatusList.cpp (added) * src/Actions/ActionStatusList.hpp (added) * src/Actions/Makefile.am (modified) Added observable ActionStatusList to ActionQueue. - this allows to ... Tue, 20 May 2014 09:11:52 GMT Frederik Heber [975b83] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Python/PythonScripting_impl.hpp (modified) * tests/Python/AllActions/moltest.py (modified) Added ActionQueue::insertAction(). - this is preparatory for ... Tue, 20 May 2014 08:47:10 GMT Frederik Heber [cc6e5c] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (deleted) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.hpp (deleted) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (deleted) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (deleted) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (deleted) * src/Actions/AnalysisAction/CalculateMolarMassAction.hpp (deleted) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/Reaction.hpp (deleted) * src/Actions/Reaction_impl.hpp (deleted) * src/Actions/Reaction_impl_header.hpp (deleted) * src/Actions/Reaction_impl_pre.hpp (deleted) * src/Actions/pyMoleCuilder.cpp (deleted) * src/Makefile.am (modified) * src/Python/Makefile.am (modified) * src/Python/PythonScripting_impl.hpp (modified) * src/Python/exit.cpp (added) * src/Python/getBoundingBox.cpp (moved) * src/Python/getDomainVolume.cpp (moved) * src/Python/getSelectedMolarMass.cpp (moved) * src/Python/modules.hpp (added) * src/Python/reinit.cpp (added) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (modified) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (deleted) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (deleted) * tests/regression/Analysis/CalculateMolarMass/pre/argon.xyz (deleted) * tests/regression/Analysis/CalculateMolarMass/pre/water.xyz (deleted) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (deleted) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * utils/Python/boxmaker.py.in (modified) Replaced Reactions by simple function exported to pyMoleCuilder. - ... Tue, 20 May 2014 08:47:03 GMT Frederik Heber [0d4168] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/unittests/ContinuousValueTest.cpp (modified) * src/Parameters/unittests/DiscreteValueTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/builder_init.cpp (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Allow setting of invalid values in Value class, Action::performCall() ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [16893f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.cpp (added) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (added) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added ClearFragmentationResultsAction. - As we retain summed ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [12d946] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/LoadSessionAction.cpp (added) * src/Actions/CommandAction/LoadSessionAction.def (added) * src/Actions/CommandAction/LoadSessionAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (added) * tests/regression/Options/testsuite-options.at (modified) Implemented LoadSessionAction. - this it also used in ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [992839] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/toPythonString.cpp (added) * src/Actions/toPythonString.hpp (added) * tests/regression/Options/Session/post/complextest.py (added) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Added more complex python example to regression test of store ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [9b56f34] * src/Actions/ActionSequence.cpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/toCLIString.cpp (added) * src/Actions/toCLIString.hpp (added) ActionParameters need special format when given to CLI. - ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [bad589] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (added) * src/Actions/CommandAction/StoreSessionAction.def (added) * src/Actions/CommandAction/StoreSessionAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/Session/post/test.sh (added) * tests/regression/Options/Session/testsuite-options-store-session.at (added) * tests/regression/Options/testsuite-options.at (modified) Added StoreSessionAction to store the current session to file. Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [b5b01e] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionParameters.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/ActionState.hpp (added) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/Reaction.hpp (modified) * src/Actions/Reaction_impl.hpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) ActionState extracted into own header file, rename Action::state_ptr ... Thu, 19 Sep 2013 20:23:52 GMT Frederik Heber [f92ef3] * src/Actions/Action.hpp (modified) * src/Actions/ActionParameters.hpp (added) * src/Actions/Makefile.am (modified) Extracted ActionParameters into own header file. Thu, 19 Sep 2013 20:23:51 GMT Frederik Heber [628577] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (added) * src/Actions/ActionQueue.hpp (added) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/PythonScripting.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/cleanUp.cpp (modified) Introduced ActionQueue which contains internal ActionRegistry. - ... Mon, 12 Aug 2013 11:30:33 GMT Frederik Heber [f5724f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitParticleChargesAction.cpp (moved) * src/Actions/PotentialAction/FitParticleChargesAction.def (moved) * src/Actions/PotentialAction/FitParticleChargesAction.hpp (moved) * src/Actions/PotentialAction/FitPotentialAction.cpp (moved) * src/Actions/PotentialAction/FitPotentialAction.def (moved) * src/Actions/PotentialAction/FitPotentialAction.hpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (moved) * src/Actions/PotentialAction/ParseHomologiesAction.def (moved) * src/Actions/PotentialAction/ParseHomologiesAction.hpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (moved) * src/Actions/PotentialAction/SaveHomologiesAction.def (moved) * src/Actions/PotentialAction/SaveHomologiesAction.hpp (moved) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitParticleCharges/pre/homology_grid.dat (moved) * tests/regression/Potential/FitParticleCharges/pre/water.pdb (moved) * tests/regression/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at (moved) * tests/regression/Potential/FitPotential/pre/angle_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/harmonic_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/improper_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/length_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/lj_homology.dat (moved) * tests/regression/Potential/FitPotential/pre/torsion_homology.dat (moved) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (moved) * tests/regression/Potential/testsuite-potential.at (added) * tests/regression/testsuite.at (modified) Moved all FragmentationActions related to potentials into own menu ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [c4a323] * src/Actions/FragmentationAction/FitParticleChargesAction.cpp (added) * src/Actions/FragmentationAction/FitParticleChargesAction.def (added) * src/Actions/FragmentationAction/FitParticleChargesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Fragmentation/FitParticleCharges/pre/homology_grid.dat (added) * tests/regression/Fragmentation/FitParticleCharges/pre/water.pdb (added) * tests/regression/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added FitParticleChargesAction for fitting partial nuclei charges to ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [d449a9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Actions/FragmentationAction/ParseHomologiesAction.cpp (added) * src/Actions/FragmentationAction/ParseHomologiesAction.def (added) * src/Actions/FragmentationAction/ParseHomologiesAction.hpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.cpp (added) * src/Actions/FragmentationAction/SaveHomologiesAction.def (added) * src/Actions/FragmentationAction/SaveHomologiesAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Split off parsing and saving of homologies into new Actions. Fri, 09 Aug 2013 14:20:18 GMT Frederik Heber [39986b] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (added) * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) Added new MakroAction MolecularDynamicsAction. - this resides ... Thu, 11 Jul 2013 21:44:01 GMT Frederik Heber [9c1324] * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_header.hpp (added) * src/Actions/MakroAction_impl_pre.hpp (added) Equipped MakroAction with some boost::preprocessor magic, ... Fri, 03 May 2013 11:58:26 GMT Frederik Heber [48d20d] * configure.ac (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (added) * src/Actions/FragmentationAction/FitPotentialAction.def (added) * src/Actions/FragmentationAction/FitPotentialAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/LevMartester.cpp (deleted) * src/Makefile.am (modified) * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/potentials.dox (modified) * src/documentation/install.dox (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/pre/angle_homology.dat (added) * tests/regression/Fragmentation/FitPotential/pre/length_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added new action FitPotentialAction to fit empirical potentials. - ... Tue, 16 Apr 2013 06:30:39 GMT Frederik Heber [214240] * src/Actions/Makefile.am (modified) * src/Analysis/Makefile.am (modified) * src/Atom/Makefile.am (modified) * src/Element/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Helpers/Makefile.am (modified) * src/LinkedCell/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Potentials/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) FIX: Most of the includedirs were wrongly set. - each just needs to ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [a3427f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (added) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (added) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (added) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (added) * src/Fragmentation/Summation/Containers/Makefile.am (modified) Split FragmentationAutomationAction into calculation and analysis. ... Mon, 15 Apr 2013 10:28:25 GMT Frederik Heber [bae7bc] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (added) * src/Actions/FragmentationAction/ParseFragmentJobsAction.def (added) * src/Actions/FragmentationAction/ParseFragmentJobsAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified) * src/Fragmentation/Automation/FragmentationResults.cpp (modified) * src/Fragmentation/Automation/FragmentationResults.hpp (modified) Outsourced parsing of fragment files into ParseFragmentJobsAction ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [22b786] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (added) * src/Actions/GraphAction/UpdateMoleculesAction.def (added) * src/Actions/GraphAction/UpdateMoleculesAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) Made SubgraphDissection a MakroAction and added ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [560cbf] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (added) * src/Actions/GraphAction/DestroyAdjacencyAction.def (added) * src/Actions/GraphAction/DestroyAdjacencyAction.hpp (added) * src/Actions/Makefile.am (modified) * tests/regression/Graph/DestroyAdjacency/pre/ethane.pdb (added) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added a DestroyAdjacencyAction with undo/redo. - also added ... Fri, 22 Mar 2013 00:03:38 GMT Frederik Heber [5589e7e] * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (added) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/post/BondFragment0.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/pre/C6-0.Sheet.Aligned.xyz (added) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added StoreSaturatedFragmentAction to save a set of atoms satured ... Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [29ea65] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (added) * src/Actions/ShapeAction/StretchShapeAction.def (added) * src/Actions/ShapeAction/StretchShapeAction.hpp (added) * src/UIElements/Views/Qt4/QtShapeController.cpp (modified) * tests/Python/AllActions/options.dat (modified) StretchShapeAction added Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [a2bbb1] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (added) * src/Actions/ShapeAction/RotateShapeAction.def (added) * src/Actions/ShapeAction/RotateShapeAction.hpp (added) RotateShapeAction added Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber [0b5057] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (added) * src/Actions/ShapeAction/TranslateShapeAction.def (added) * src/Actions/ShapeAction/TranslateShapeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) TranslateShapeAction added Fri, 14 Dec 2012 17:38:49 GMT Frederik Heber [8b886f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (added) * src/Actions/MoleculeAction/ChangeBondAngleAction.def (added) * src/Actions/MoleculeAction/ChangeBondAngleAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/ChangeBondAngle/post/water.pdb (added) * tests/regression/Molecules/ChangeBondAngle/pre/water.pdb (added) * tests/regression/Molecules/ChangeBondAngle/testsuite-molecules-change-bond-angle.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added ChangeBondAngleAction that changes the bond angle while keeping ... Fri, 14 Dec 2012 14:30:23 GMT Frederik Heber [f63e41] * src/Actions/BondAction/BondAddAction.cpp (added) * src/Actions/BondAction/BondAddAction.def (added) * src/Actions/BondAction/BondAddAction.hpp (added) * src/Actions/BondAction/BondRemoveAction.cpp (added) * src/Actions/BondAction/BondRemoveAction.def (added) * src/Actions/BondAction/BondRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Bond/Add/post/test.pdb (added) * tests/regression/Bond/Add/pre/test.pdb (added) * tests/regression/Bond/Add/testsuite-bond-add.at (added) * tests/regression/Bond/Remove/post/test.pdb (added) * tests/regression/Bond/Remove/pre/test.pdb (added) * tests/regression/Bond/Remove/testsuite-bond-remove.at (added) * tests/regression/Bond/testsuite-bond.at (added) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added Actions to add and remove a bond in between two atoms. - ... Fri, 16 Nov 2012 11:10:27 GMT Frederik Heber [f20da5] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (added) * src/Actions/ShapeAction/RemoveShapeAction.def (added) * src/Actions/ShapeAction/RemoveShapeAction.hpp (added) RemoveShapeAction added Fri, 16 Nov 2012 11:10:27 GMT Frederik Heber [842aac] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.def (modified) * src/Actions/ShapeAction/SetShapeAction.cpp (deleted) * src/Actions/ShapeAction/SetShapeAction.def (deleted) * src/Actions/ShapeAction/SetShapeAction.hpp (deleted) * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeFactory.hpp (modified) * src/Shapes/unittests/ShapeFactoryUnitTest.cpp (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) Refactoring: FillSurfaceAction uses ShapeRegistry Thu, 15 Nov 2012 17:31:11 GMT Frederik Heber [d475a6] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (added) * src/Actions/ShapeAction/CombineShapesAction.def (added) * src/Actions/ShapeAction/CombineShapesAction.hpp (added) * tests/Python/AllActions/options.dat (modified) CombineShapesAction added Thu, 15 Nov 2012 17:31:10 GMT Frederik Heber [2c004d] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.def (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (added) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.def (added) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) SelectionNotShapeByNameAction added Thu, 15 Nov 2012 17:31:10 GMT Frederik Heber [a27dcb] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (added) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.def (added) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.hpp (added) SelectionNotAllShapesAction added Thu, 15 Nov 2012 17:31:09 GMT Frederik Heber [663606] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (added) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.def (added) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) SelectionShapeByNameAction added Thu, 15 Nov 2012 17:31:09 GMT Frederik Heber [70bce9] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (added) * src/Actions/SelectionAction/Shapes/AllShapesAction.def (added) * src/Actions/SelectionAction/Shapes/AllShapesAction.hpp (added) AllShapesAction added Thu, 15 Nov 2012 17:31:08 GMT Frederik Heber [6131d8] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (added) * src/Actions/ShapeAction/CreateShapeAction.def (added) * src/Actions/ShapeAction/CreateShapeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) CreateShapeAction added Thu, 15 Nov 2012 17:31:07 GMT Frederik Heber [eff536] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.def (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.def (added) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.def (added) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.hpp (added) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) AllAtomsInsideCuboid/SphereAction > AllAtomsInsideVolumeAction (using ... Thu, 15 Nov 2012 17:31:07 GMT Frederik Heber [09eaac] * src/Actions/FillAction/FillSurfaceAction.cpp (moved) * src/Actions/FillAction/FillSurfaceAction.def (moved) * src/Actions/FillAction/FillSurfaceAction.hpp (moved) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) FillSphericalSurfaceAction > FillSurfaceAction (using shape factory) Thu, 15 Nov 2012 17:31:06 GMT Frederik Heber [4dc309] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/SetShapeAction.cpp (added) * src/Actions/ShapeAction/SetShapeAction.def (added) * src/Actions/ShapeAction/SetShapeAction.hpp (added) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/Python/AllActions/options.dat (modified) SetShapeAction added Fri, 26 Oct 2012 13:11:18 GMT Frederik Heber [3a51bd] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (added) * src/Actions/MoleculeAction/StretchBondAction.def (added) * src/Actions/MoleculeAction/StretchBondAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/StretchBond/post/ethane.xyz (added) * tests/regression/Molecules/StretchBond/pre/ethane.xyz (added) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added new StretchBondAction to stretch the bond within a molecule. ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [94d5ac6] * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * LinearAlgebra/src/unittests/LineUnitTest.cpp (modified) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (modified) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (modified) * LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (modified) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (modified) * LinearAlgebra/src/unittests/UnitTestMain.cpp (modified) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (modified) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (added) * src/Actions/CommandAction/HelpRedistributeAction.def (added) * src/Actions/CommandAction/HelpRedistributeAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified) * src/AtomIdSet.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Filling/Cluster.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Generators/NodeGenerator.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/RandomInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SurfaceInserter.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/Mesh.cpp (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (modified) * src/Filling/Predicates/FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (modified) * src/Filling/unittests/ClusterUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp (modified) * src/Filling/unittests/Ops_FillPredicateUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.cpp (modified) * src/Jobs/unittests/MPQCCommandJobUnitTest.cpp (modified) * src/Jobs/unittests/MPQCDataUnitTest.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parameters/Validators/Specific/BoundaryConditionValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxLengthValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.cpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.cpp (modified) * src/Parameters/Validators/Specific/FormulaValidator.cpp (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorNotZeroValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.cpp (modified) * src/Parameters/unittests/ContinuousParameterTest.cpp (modified) * src/Parameters/unittests/ContinuousValueTest.cpp (modified) * src/Parameters/unittests/DiscreteParameterTest.cpp (modified) * src/Parameters/unittests/DiscreteValueTest.cpp (modified) * src/Parameters/unittests/Ops_ValidatorTest.cpp (modified) * src/Parameters/unittests/stubs/ActionNameValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxLengthValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxVectorValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser_ElementKeys.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/BaseShapesUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified) * src/Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (modified) * src/Tesselation/ApproximateShapeArea.cpp (modified) * src/Tesselation/ApproximateShapeVolume.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/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/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.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/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.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/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (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/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/Query.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/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.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/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/controller.cpp (modified) * src/controller_AddOn_MPQCCommandJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/AtomIdSetUnitTest.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/Box_BoundaryConditionsUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/MoleculeUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/JobMarket/mpqc.cpp (modified) FIX: As we use GSL internally, we are as of now required to use GPL ... Mon, 27 Aug 2012 11:36:58 GMT Michael Ankele [a55e6f] * src/Actions/Makefile.am (modified) * src/Actions/ValueStorage.cpp (deleted) * src/Actions/ValueStorage.hpp (deleted) * src/cleanUp.cpp (modified) really remove ValueStorage Fri, 10 Aug 2012 15:56:44 GMT Frederik Heber [5e7ebe] * src/Actions/Makefile.am (modified) DISTCHECKFIX: AllActionHeaders.hpp must not appear as nobase_ and ... Thu, 09 Aug 2012 12:51:34 GMT Michael Ankele [5bcbc7] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.def (added) * src/Actions/WorldAction/OutputAction.hpp (added) OutputAction added Thu, 09 Aug 2012 12:51:10 GMT Michael Ankele [072f0e] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/WorldAction/OutputAsAction.cpp (moved) * src/Actions/WorldAction/OutputAsAction.def (moved) * src/Actions/WorldAction/OutputAsAction.hpp (moved) * tests/Python/AllActions/missing.dat (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-save.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-save.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * utils/Python/boxmaker.py.in (modified) Refactoring: renamed OutputAction -> OutputAsAction Tue, 10 Jul 2012 15:41:00 GMT Frederik Heber [004d5c] * JobMarket/AUTHORS (deleted) * JobMarket/COPYING (deleted) * JobMarket/ChangeLog (deleted) * JobMarket/INSTALL (deleted) * JobMarket/JobMarket-debug.pc.in (deleted) * JobMarket/JobMarket.pc.in (deleted) * JobMarket/Makefile.am (deleted) * JobMarket/NEWS (deleted) * JobMarket/README (deleted) * JobMarket/bootstrap (deleted) * JobMarket/build-aux/README (deleted) * JobMarket/configure.ac (deleted) * JobMarket/configure.scan (deleted) * JobMarket/doc/Doxyfile (deleted) * JobMarket/doc/Makefile.am (deleted) * JobMarket/doc/am_doxygen_include.am (deleted) * JobMarket/libJobMarket_config.h.in (deleted) * JobMarket/m4 (deleted) * JobMarket/src/JobMarket/Connection.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerCommand.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.cpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions.cpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.hpp (deleted) * JobMarket/src/JobMarket/Controller/FragmentController.cpp (deleted) * JobMarket/src/JobMarket/Controller/FragmentController.hpp (deleted) * JobMarket/src/JobMarket/Controller/controller.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_AddOn.hpp (deleted) * JobMarket/src/JobMarket/Controller/controller_AddOn_SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.hpp (deleted) * JobMarket/src/JobMarket/Controller/controller_main.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_main.hpp (deleted) * JobMarket/src/JobMarket/ControllerChoices.hpp (deleted) * JobMarket/src/JobMarket/DefaultOptions.cpp (deleted) * JobMarket/src/JobMarket/DefaultOptions.hpp (deleted) * JobMarket/src/JobMarket/ExitflagContainer.hpp (deleted) * JobMarket/src/JobMarket/FragmentQueue.cpp (deleted) * JobMarket/src/JobMarket/FragmentQueue.hpp (deleted) * JobMarket/src/JobMarket/FragmentScheduler.cpp (deleted) * JobMarket/src/JobMarket/FragmentScheduler.hpp (deleted) * JobMarket/src/JobMarket/GlobalJobId.cpp (deleted) * JobMarket/src/JobMarket/GlobalJobId.hpp (deleted) * JobMarket/src/JobMarket/JobId.cpp (deleted) * JobMarket/src/JobMarket/JobId.hpp (deleted) * JobMarket/src/JobMarket/Jobs/FragmentJob.cpp (deleted) * JobMarket/src/JobMarket/Jobs/FragmentJob.hpp (deleted) * JobMarket/src/JobMarket/Jobs/SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Jobs/SystemCommandJob.hpp (deleted) * JobMarket/src/JobMarket/Listener.cpp (deleted) * JobMarket/src/JobMarket/Listener.hpp (deleted) * JobMarket/src/JobMarket/Makefile.am (deleted) * JobMarket/src/JobMarket/Operations/AsyncOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/AsyncOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Operation.hpp (deleted) * JobMarket/src/JobMarket/Operations/OperationQueue.cpp (deleted) * JobMarket/src/JobMarket/Operations/OperationQueue.hpp (deleted) * JobMarket/src/JobMarket/Operations/OperationRegistry.cpp (deleted) * JobMarket/src/JobMarket/Operations/OperationRegistry.hpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/SyncOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/SyncOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.hpp (deleted) * JobMarket/src/JobMarket/Pool/PoolWorker.cpp (deleted) * JobMarket/src/JobMarket/Pool/PoolWorker.hpp (deleted) * JobMarket/src/JobMarket/Pool/WorkerPool.cpp (deleted) * JobMarket/src/JobMarket/Pool/WorkerPool.hpp (deleted) * JobMarket/src/JobMarket/Results/FragmentResult.cpp (deleted) * JobMarket/src/JobMarket/Results/FragmentResult.hpp (deleted) * JobMarket/src/JobMarket/ServerOptions.cpp (deleted) * JobMarket/src/JobMarket/ServerOptions.hpp (deleted) * JobMarket/src/JobMarket/SignalHandler.cpp (deleted) * JobMarket/src/JobMarket/SignalHandler.hpp (deleted) * JobMarket/src/JobMarket/SignalOptions.cpp (deleted) * JobMarket/src/JobMarket/SignalOptions.hpp (deleted) * JobMarket/src/JobMarket/WorkerAddress.cpp (deleted) * JobMarket/src/JobMarket/WorkerAddress.hpp (deleted) * JobMarket/src/JobMarket/WorkerChoices.hpp (deleted) * JobMarket/src/JobMarket/WorkerOptions.cpp (deleted) * JobMarket/src/JobMarket/WorkerOptions.hpp (deleted) * JobMarket/src/JobMarket/atexit.cpp (deleted) * JobMarket/src/JobMarket/atexit.hpp (deleted) * JobMarket/src/JobMarket/poolworker.cpp (deleted) * JobMarket/src/JobMarket/poolworker_main.cpp (deleted) * JobMarket/src/JobMarket/poolworker_main.hpp (deleted) * JobMarket/src/JobMarket/server.cpp (deleted) * JobMarket/src/JobMarket/server_main.cpp (deleted) * JobMarket/src/JobMarket/server_main.hpp (deleted) * JobMarket/src/JobMarket/types.hpp (deleted) * JobMarket/src/documentation/Makefile.am (deleted) * JobMarket/src/documentation/jobmarket.dox (deleted) * JobMarket/src/documentation/mainpage.dox (deleted) * JobMarket/src/unittests/FragmentJobUnitTest.cpp (deleted) * JobMarket/src/unittests/FragmentJobUnitTest.hpp (deleted) * JobMarket/src/unittests/FragmentQueueUnitTest.cpp (deleted) * JobMarket/src/unittests/FragmentQueueUnitTest.hpp (deleted) * JobMarket/src/unittests/FragmentResultUnitTest.cpp (deleted) * JobMarket/src/unittests/FragmentResultUnitTest.hpp (deleted) * JobMarket/src/unittests/Makefile.am (deleted) * JobMarket/src/unittests/OperationQueueUnitTest.cpp (deleted) * JobMarket/src/unittests/OperationQueueUnitTest.hpp (deleted) * JobMarket/src/unittests/SystemCommandJobUnitTest.cpp (deleted) * JobMarket/src/unittests/SystemCommandJobUnitTest.hpp (deleted) * JobMarket/src/unittests/UnitTestMain.cpp (deleted) * JobMarket/src/unittests/WorkerAddressUnitTest.cpp (deleted) * JobMarket/src/unittests/WorkerAddressUnitTest.hpp (deleted) * JobMarket/src/unittests/WorkerPoolUnitTest.cpp (deleted) * JobMarket/src/unittests/WorkerPoolUnitTest.hpp (deleted) * JobMarket/src/unittests/stubs/AsyncOperationStub.hpp (deleted) * JobMarket/src/unittests/stubs/FragmentJobStub.cpp (deleted) * JobMarket/src/unittests/stubs/FragmentJobStub.hpp (deleted) * JobMarket/src/unittests/stubs/FragmentResultStub.cpp (deleted) * JobMarket/src/unittests/stubs/ObserverStub.cpp (deleted) * JobMarket/src/unittests/stubs/ObserverStub.hpp (deleted) * JobMarket/tests/CodeChecks/Makefile.am (deleted) * JobMarket/tests/CodeChecks/atlocal.in (deleted) * JobMarket/tests/CodeChecks/testsuite-config_h.at (deleted) * JobMarket/tests/CodeChecks/testsuite-date_in_dox.at (deleted) * JobMarket/tests/CodeChecks/testsuite-header-dist.at (deleted) * JobMarket/tests/CodeChecks/testsuite-memdebug.at (deleted) * JobMarket/tests/CodeChecks/testsuite-project-disclaimer.at (deleted) * JobMarket/tests/Makefile.am (deleted) * JobMarket/tests/regression/atlocal.in (deleted) * JobMarket/tests/regression/testsuite-addingjobs.at (deleted) * JobMarket/tests/regression/testsuite-checkstate.at (deleted) * JobMarket/tests/regression/testsuite-completerun.at (deleted) * JobMarket/tests/regression/testsuite-enrollinpool.at (deleted) * JobMarket/tests/regression/testsuite-getresults.at (deleted) * JobMarket/tests/regression/testsuite-resubmitjobs.at (deleted) * JobMarket/tests/regression/testsuite-server-shutdown.at (deleted) * JobMarket/tests/regression/testsuite-server-worker.at (deleted) * JobMarket/tests/regression/testsuite.at (deleted) * Makefile.am (modified) * configure.ac (modified) * m4/ax_jobmarket.m4 (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Server.cpp (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/Makefile.am (modified) * tests/CodeChecks/testsuite-globallistofactions_hpp.at (modified) * tests/JobMarket/Makefile.am (moved) * tests/JobMarket/atlocal.in (added) * tests/JobMarket/molecuilder.in (added) * tests/JobMarket/mpqc.cpp (moved) * tests/JobMarket/pre/BondFragment00.in (moved) * tests/JobMarket/pre/BondFragment00.out (moved) * tests/JobMarket/pre/BondFragment01.out (moved) * tests/JobMarket/pre/BondFragment02.out (moved) * tests/JobMarket/pre/BondFragment03.out (moved) * tests/JobMarket/pre/BondFragment04.out (moved) * tests/JobMarket/pre/BondFragment05.out (moved) * tests/JobMarket/pre/BondFragment06.out (moved) * tests/JobMarket/pre/BondFragmentAdjacency.dat (moved) * tests/JobMarket/pre/BondFragmentForces-Factors.dat (moved) * tests/JobMarket/pre/BondFragmentKeySets.dat (moved) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (moved) * tests/JobMarket/testsuite-jobmarket-mpqc-jobs.at (moved) * tests/JobMarket/testsuite-jobmarket-stand-in-mpqc.at (moved) * tests/JobMarket/testsuite-jobmarket.at (added) * tests/JobMarket/testsuite.at (moved) * tests/Makefile.am (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Removed JobMarket as it is now in its own repository. - added ... Fri, 06 Jul 2012 10:18:48 GMT Frederik Heber [edecba] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-molecuilderrun.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added Action to use the JobMarket for FragmentationAutomation. - ... Fri, 06 Apr 2012 11:45:30 GMT Frederik Heber [531f27] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (added) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.def (added) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-Exttypes/post/test-right.exttypes (added) * tests/regression/Parser/Tremolo-Exttypes/post/test-wrong.exttypes (added) * tests/regression/Parser/Tremolo-Exttypes/pre/test.xyz (added) * tests/regression/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Added SaveSelectedAtomsAsExtTypesAction that creates a tremolo- ... Fri, 06 Apr 2012 11:44:09 GMT Frederik Heber [57dd40] * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/UndoRedoHelpers.cpp (added) * src/Actions/UndoRedoHelpers.hpp (added) * src/documentation/constructs/actions.dox (modified) Extracted removal and adding of atoms from AtomicInfo to ... Fri, 06 Apr 2012 11:44:09 GMT Frederik Heber [4187a7] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (deleted) * src/Actions/MoleculeAction/CreateMicelleAction.def (deleted) * src/Actions/MoleculeAction/CreateMicelleAction.hpp (deleted) * tests/regression/Filling/SphericalSurface/post/tensid.data (added) * tests/regression/Filling/SphericalSurface/pre/tensid.data (added) * tests/regression/Filling/SphericalSurface/pre/tensid.potentials (moved) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (added) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (deleted) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (deleted) * tests/regression/Molecules/CreateMicelle/testsuite-molecules-create-micelle.at (deleted) * tests/regression/Molecules/testsuite-molecules.at (modified) Removed MoleculeAction/CreateMicelleAction, is replaced by ... Fri, 06 Apr 2012 11:44:09 GMT Frederik Heber [2db053] * src/Actions/FillAction/FillSphericalSurfaceAction.cpp (added) * src/Actions/FillAction/FillSphericalSurfaceAction.def (added) * src/Actions/FillAction/FillSphericalSurfaceAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) Added action to fill selected atoms on sphere surface. Tue, 03 Apr 2012 07:55:55 GMT Frederik Heber [ebc499] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.hpp (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/InvertAtoms/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/pre/box.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_missing.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_present.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/pre/box.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (added) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) Added InvertMoleculesAction and InvertAtomsAction. - World has two ... Tue, 03 Apr 2012 07:55:43 GMT Frederik Heber [61c364] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.hpp (added) * src/Descriptors/AtomOrderDescriptor.cpp (added) * src/Descriptors/AtomOrderDescriptor.hpp (added) * src/Descriptors/AtomOrderDescriptor_impl.hpp (added) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (modified) * src/Makefile.am (modified) * src/World.hpp (modified) * tests/Python/AllActions/moltest.py (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByOrder/post/empty.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/pre/test.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at (added) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-unselect-atom-by-order.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added AtomOrderDescription along with SelectionAtomByOrder. - added ... Fri, 30 Mar 2012 09:18:17 GMT Frederik Heber [a88452] * src/Actions/FillAction/FillRegularGridAction.cpp (added) * src/Actions/FillAction/FillRegularGridAction.def (added) * src/Actions/FillAction/FillRegularGridAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/Python/AllActions/options.dat (modified) Added new Action subfolder, menu, and CommandLine options map, and ... Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber [c52e08] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (added) * src/Actions/WorldAction/SetBoundaryConditionsAction.def (added) * src/Actions/WorldAction/SetBoundaryConditionsAction.hpp (added) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/Box_BoundaryConditions.hpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (added) * tests/regression/Domain/testsuite-domain.at (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water-bounced.xyz (added) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water-wrapped.xyz (added) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water.xyz (added) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added new action SetBoundaryConditionsAction. - Added new ... Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [c015b3] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * tests/Makefile.am (modified) * tests/Python/AllActions/getPossibleOptions.sh (moved) * tests/Python/AllActions/listcmds.py (moved) * tests/Python/AllActions/missing.dat (moved) * tests/Python/AllActions/moltest.py (moved) * tests/Python/AllActions/moltest_check.py (moved) * tests/Python/AllActions/options.dat (moved) * tests/Python/AllActions/testsuite-python-allactions.at (added) * tests/Python/AllActions/testsuite-python-options_dat.at (added) * tests/Python/BoxMaker/post/out.data (moved) * tests/Python/BoxMaker/post/out.xyz (moved) * tests/Python/BoxMaker/pre/argon.data (moved) * tests/Python/BoxMaker/pre/argon.potentials (moved) * tests/Python/BoxMaker/pre/argon.tremolo (moved) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (added) * tests/Python/CommandHelp/testsuite-python-commandhelp.at (moved) * tests/Python/Makefile.am (added) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (moved) * tests/Python/atlocal.in (added) * tests/Python/run.in (moved) * tests/Python/testsuite.at (added) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (deleted) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (deleted) * tests/regression/Python/BoxMaker/testsuite-python-boxmaker.at (deleted) * tests/regression/Python/testsuite-python.at (deleted) * tests/regression/testsuite.at (modified) * utils/Makefile.am (modified) Added enable-switches for Qt-based GUI and python module and scripts. ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [48d3c0] * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) DISTCHECKFIX: Added some missing header files in src/Actions. - ... Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [24da48] * src/Actions/Makefile.am (modified) DISTCHECKFIX: Added missing ActionTraits.hpp to src/Actions/Makefile.am. Mon, 07 Nov 2011 18:34:45 GMT Frederik Heber [c1ab1f] * src/Actions/Makefile.am (modified) DISTCHECKFIX: Added all Reaction...hpp to src/Actions/Makefile.am. Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [f89b45] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/listcmds.py (added) * tests/regression/Python/AllActions/moltest.py (modified) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) Added Reaction CalculateBoundingBoxAction. - calculate bounding box ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [55f299] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateMolarMass/pre/argon.xyz (added) * tests/regression/Analysis/CalculateMolarMass/pre/water.xyz (added) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/options.dat (modified) Added Reaction CalculateMolarMassAction. - calculate molar mass ... Mon, 07 Nov 2011 12:24:07 GMT Frederik Heber [54088a] * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (added) * tests/regression/Python/testsuite-python.at (modified) Added first Reaction named CalculateCellVolumeAction. - this sets ... Mon, 07 Nov 2011 12:24:02 GMT Frederik Heber [3139b2] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionTrait.cpp (moved) * src/Actions/ActionTrait.hpp (added) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) Renamed ActionTrait and ActionTraits. - the specialized Trait ... Mon, 07 Nov 2011 12:24:00 GMT Frederik Heber [c20b35] * src/Actions/Makefile.am (modified) Added commented-out stuff for a extra libMolecuilderActionPython.la. ... Mon, 07 Nov 2011 12:23:52 GMT Frederik Heber [949953] * src/Actions/Action_impl_python.hpp (added) * src/Actions/Action_impl_undef.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Makefile.am (modified) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (added) * src/cleanUp.hpp (added) pyMoleCuilder now has full functionality. - For each header file ... Mon, 07 Nov 2011 10:46:25 GMT Frederik Heber [83e90c] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/GlobalListOfActions.hpp (added) * src/Actions/Makefile.am (modified) New function ActionRegistry::fillRegistry() fills instead of static ... Thu, 03 Nov 2011 09:52:29 GMT Frederik Heber [7ba268] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/World.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0023.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0024.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0025.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0026.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0027.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0028.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0029.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0030.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0031.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_histogram_Y.0032.dat (added) * 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tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (added) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox-mirrored_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/pre/water.xyz (moved) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/emptybox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/post/hydrogenbox_histogram.dat (moved) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (moved) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'DipoleAngularCorrelation' into mergeMaster Conflicts: ... Mon, 31 Oct 2011 11:16:17 GMT Frederik Heber [41d023] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetMpqcParametersAction.cpp (deleted) * src/Actions/ParserAction/SetParserParametersAction.cpp (added) * src/Actions/ParserAction/SetParserParametersAction.def (moved) * src/Actions/ParserAction/SetParserParametersAction.hpp (moved) * src/Parser/FormatParser_Parameters.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (moved) * tests/regression/Parser/SetParameters/Mpqc/pre/test.xyz (moved) * tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-theory.at (moved) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (moved) * tests/regression/Parser/SetParameters/Psi3/pre/test.xyz (added) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-wavefunction.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Renamed SetMpqcParametersAction to SetParserParametersAction and ... Tue, 25 Oct 2011 15:28:06 GMT Frederik Heber [208237b] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (added) * src/Actions/AnalysisAction/DipoleCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) Renamed DipoleAngularCorrelation(Action) -> DipoleCorrelation(Action) ... Thu, 06 Oct 2011 09:15:04 GMT Frederik Heber [81c980b] * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (added) * src/Actions/ParserAction/SetTremoloAtomdataAction.def (added) * src/Actions/ParserAction/SetTremoloAtomdataAction.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/pre/argon.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Added new action to set the ATOMDATA in tremolo's .data output file. ... Wed, 05 Oct 2011 09:18:20 GMT Frederik Heber [807c0e] * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (moved) * src/Actions/MoleculeAction/CreateMicelleAction.def (added) * src/Actions/MoleculeAction/CreateMicelleAction.hpp (added) * src/Makefile.am (modified) Daniel has recently changed his mizelledata to work as an action ... Wed, 21 Sep 2011 20:04:30 GMT Frederik Heber [e69c87] * src/Actions/Action.cpp (modified) * src/Actions/ActionExceptions.hpp (added) * src/Actions/ActionHistory.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/boundary.cpp (modified) * src/builder_init.cpp (modified) * tests/regression/Analysis/AngularDipoleCorrelation-Empty/testsuite-analysis-angular-dipole-correlation-empty.at (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) * tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified) * tests/regression/Atoms/RemoveCuboid/post/test-cuboid.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/post/test-withoutcuboid.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/post/test.xyz-sorted (moved) * tests/regression/Atoms/RemoveCuboid/pre/test.xyz (moved) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (moved) * tests/regression/Atoms/RemoveSphere/post/test-sphere.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/post/test-withoutsphere.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/post/test.xyz-sorted (moved) * tests/regression/Atoms/RemoveSphere/pre/test.xyz (moved) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (moved) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (added) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (deleted) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (added) * tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (added) * tests/regression/Molecules/Copy/post/tensid-undo.data (added) * tests/regression/Molecules/Copy/post/test-undo.xyz (added) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) * tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/Translation-Periodic/post/test-undo.conf (added) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/post/test-undo.conf (added) * tests/regression/Molecules/Translation/post/test2-undo.conf (added) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified) * tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-basis.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-maxiterations.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters-theory.at (added) * tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc.at (modified) * tests/regression/Parser/Pcp/post/empty.conf (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp.at (modified) * tests/regression/Parser/Pdb/post/empty.pdb (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb.at (modified) * tests/regression/Parser/Tremolo/post/empty.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo.at (modified) * tests/regression/Parser/Xyz/post/empty.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz.at (modified) * tests/regression/Parser/testsuite-parser.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) Splitted off Undo and Redo parts into own tests (3-step rule). - ... Thu, 21 Apr 2011 16:26:04 GMT Frederik Heber [dd8990] * src/Actions/Makefile.am (modified) FIX: .def files of Actions have not been present in Makefile.am, ... Thu, 21 Apr 2011 16:25:23 GMT Frederik Heber [3001c9] * src/Actions/Makefile.am (modified) FIX: LoadAction.cpp and RemoveAction.cpp were doubly included instead ... Thu, 21 Apr 2011 16:23:50 GMT Frederik Heber [7159ed] * src/Actions/Makefile.am (modified) DISTFIX: Missing header files in Actions/Makefile.am - missing: ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [455573] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Large Commit: SUBDIRS in src/Makefile.am replaced by include. - ... Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber [bf4b9f] * LinearAlgebra/.gitignore (added) * LinearAlgebra/AUTHORS (added) * LinearAlgebra/COPYING (added) * LinearAlgebra/ChangeLog (added) * LinearAlgebra/INSTALL (added) * LinearAlgebra/LinearAlgebra-debug.pc.in (added) * LinearAlgebra/LinearAlgebra.pc.in (moved) * LinearAlgebra/Makefile.am (added) * LinearAlgebra/NEWS (added) * LinearAlgebra/README (added) * LinearAlgebra/bootstrap (added) * LinearAlgebra/build-aux/README (added) * LinearAlgebra/configure.ac (added) * LinearAlgebra/doc/Doxyfile (added) * LinearAlgebra/doc/Makefile.am (added) * LinearAlgebra/libLinearAlgebra_config.h.in (added) * LinearAlgebra/m4 (added) * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * 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LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * LinearAlgebra/src/unittests/Makefile.am (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (added) * LinearAlgebra/src/unittests/UnitTestMain.cpp (added) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * LinearAlgebra/tests/CodeChecks/Makefile.am (added) * LinearAlgebra/tests/CodeChecks/atlocal.in (added) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added) * LinearAlgebra/tests/CodeChecks/testsuite.at (added) * Makefile.am (modified) * bootstrap (modified) * build-aux/README (added) * config/depcomp (deleted) * config/install-sh (deleted) * config/ltmain.sh (deleted) * config/missing (deleted) * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra from folder src/ into distinct sub-package. - ...