# # ChangeLog for tests/regression # # Generated by Trac 1.6 # May 23, 2025, 4:44:25 PM Tue, 28 Jul 2015 13:42:43 GMT Frederik Heber [7d146a] * Makefile.am (modified) * configure.ac (modified) * src/Tesselation/TriangleMatcher/Makefile.am (added) * src/Tesselation/TriangleMatcher/Triangle.hpp (added) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (added) * src/Tesselation/TriangleMatcher/types.hpp (added) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/testsuite-tesselation.at (modified) * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (modified) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/Convex/proline/testsuite-proline.at (modified) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/NonConvex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/NonConvex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/NonConvex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/NonConvex/proline/testsuite-proline.at (modified) * tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/trianglematcher.in (added) * tests/regression/Makefile.am (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/regression/Tesselation/TriangleMatcher/pre/convex.dat (added) * tests/regression/Tesselation/TriangleMatcher/pre/convex_none.dat (added) * tests/regression/Tesselation/TriangleMatcher/pre/convex_other.dat (added) * tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (added) * tests/regression/Tesselation/testsuite-tesselation.at (modified) * tests/regression/trianglematcher.in (added) Added TriangleMatcher to safely compare tesselation .dat files. - ... Tue, 23 Jun 2015 06:29:02 GMT Frederik Heber [7774f7] * tests/GuiChecks/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified) * tests/GuiChecks/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified) FIX: parser-parameters in regression tests basis and maxiter ... Tue, 23 Jun 2015 06:29:02 GMT Frederik Heber [23110a] * tests/GuiChecks/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified) * tests/GuiChecks/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified) * tests/GuiChecks/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (modified) FIX: Regression test set-parameters-mpqc undo compared against wrong ... 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 ... Sun, 17 May 2015 07:41:44 GMT Frederik Heber [22ac22a] * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) FIX: Fastparsing regression test contained one broken line. - this ... Fri, 13 Feb 2015 09:18:04 GMT Frederik Heber [88afc9] * doc/userguide/userguide.xml (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondAddAction.def (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.def (modified) * tests/regression/Bond/Add/post/test_multiple.pdb (added) * tests/regression/Bond/Add/pre/test_multiple.pdb (added) * tests/regression/Bond/Add/testsuite-bond-add.at (modified) * tests/regression/Bond/Add/testsuite-bond-add_multiple.at (added) * tests/regression/Bond/Remove/post/test_multiple.pdb (added) * tests/regression/Bond/Remove/post/test_multiple_undo.pdb (added) * tests/regression/Bond/Remove/pre/test_multiple.pdb (added) * tests/regression/Bond/Remove/pre/test_multiple_undo.pdb (added) * tests/regression/Bond/Remove/testsuite-bond-remove.at (modified) * tests/regression/Bond/Remove/testsuite-bond-remove_multiple.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Enhanced add-bonds and remove-bonds to multiply selected pairs of ... 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 ... Tue, 10 Feb 2015 14:09:08 GMT Frederik Heber [c26617] * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Bond/BondInfo.cpp (modified) * tests/regression/Molecules/Remove/post/water_box.pdb (modified) Undoing atom/molecule removal will also recreate bonds. - TESTFIX: ... Tue, 03 Feb 2015 08:01:55 GMT Frederik Heber [c0db90] * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) * tests/regression/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at (modified) FIX: We must use --help directly instead of --actionname in checking ... Mon, 02 Feb 2015 19:20:43 GMT Frederik Heber [55feff5] * src/Actions/CommandAction/HelpAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Removed extra option actionname from HelpAction. - this shortens ... 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 ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [2440ce] * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.def (modified) * tests/regression/Filling/SuspendInWater/pre/single_molecule.conf (added) * tests/regression/Filling/SuspendInWater/pre/test.conf (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) FIX: Changed SuspendInMoleculeAction to catch segfault when rho=1 was ... 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, 11 Jan 2015 16:42:43 GMT Frederik Heber [d7cad1] * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) Extended selection action for Molecule ids to multiple ids. Sun, 19 Oct 2014 17:13:12 GMT Frederik Heber [565695] * tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.dat (added) * tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.r3d (added) * tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.dat (deleted) * tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.r3d (deleted) * tests/regression/Tesselation/BigConvex/post/test.conf (deleted) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) TESTFIX: Regression test Tesselation/BigConvex is now working. Sun, 19 Oct 2014 17:13:12 GMT Frederik Heber [bcb831] * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) Added SphereRadius parameter to ConvexEnvelopeAction. Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [d45a5b] * src/Tesselation/tesselation.cpp (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume ... 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 ... 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. Mon, 15 Sep 2014 21:46:01 GMT Frederik Heber [7e1a88] * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) MEMFIX: Thrown ParserException causes mem leak in LoadAction - also ... Mon, 15 Sep 2014 15:05:28 GMT Frederik Heber [7f1b51] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/LoadSessionAction.def (modified) * src/Actions/CommandAction/StoreSessionAction.def (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.def (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.def (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Specifics/Value_atom.cpp (added) * src/Parameters/Specifics/Value_atom.hpp (added) * src/Parameters/Specifics/Value_element.cpp (added) * src/Parameters/Specifics/Value_element.hpp (added) * src/Parameters/Specifics/Value_molecule.cpp (added) * src/Parameters/Specifics/Value_molecule.hpp (added) * src/Parameters/Specifics/Value_string.cpp (moved) * src/Parameters/Specifics/Value_string.hpp (moved) * src/Parameters/Validators/Ops_Validator_impl.hpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.hpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.hpp (modified) * src/Parameters/Validators/Validator.hpp (modified) * src/Parameters/Validators/getFlatListFromHierarchyOfValidators.hpp (added) * src/Parameters/Value.hpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/Qt4/QMenu_tooltip.hpp (added) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/QtUIFactory.hpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextUIFactory.hpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (added) * src/World.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) Merge branch 'GUI_Fixes' into stable Mon, 15 Sep 2014 14:28:50 GMT Frederik Heber [b73545] * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (modified) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialRegistry.hpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/cleanUp.cpp (modified) * src/documentation/tests/tests.dox (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) Merge branch 'MemFixes' into stable Conflicts: ... 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 19:00:56 GMT Frederik Heber [df9f20] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.def (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (added) * src/Filling/Inserter/SurfaceRandomInserter.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (added) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.hpp (added) * tests/regression/Filling/FillSurface/post/tensid-undo.data (moved) * tests/regression/Filling/FillSurface/post/tensid.data (moved) * tests/regression/Filling/FillSurface/post/water_cube.xyz (added) * tests/regression/Filling/FillSurface/post/water_cylinder.xyz (added) * tests/regression/Filling/FillSurface/post/water_sphere.xyz (added) * tests/regression/Filling/FillSurface/post/water_undo.xyz (added) * tests/regression/Filling/FillSurface/pre/tensid.data (moved) * tests/regression/Filling/FillSurface/pre/tensid.potentials (moved) * tests/regression/Filling/FillSurface/pre/water.xyz (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at (added) * tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at (added) * tests/regression/Filling/SphericalSurface/testsuite-fill-spherical-surface.at (deleted) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Refactored FillSurfaceAction to also use FillerPreparators. - added ... 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, 10 Sep 2014 07:55:15 GMT Frederik Heber [36f45c] * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid-with-surface.at (moved) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid.at (moved) * tests/regression/Filling/SphericalSurface/testsuite-fill-spherical-surface.at (moved) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in ... Wed, 10 Sep 2014 07:45:55 GMT Frederik Heber [a090e3] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) FIX: FillRegularGridAction requires filler molecule at origin. - ... Tue, 09 Sep 2014 22:19:15 GMT Frederik Heber [0fe135] * src/UIElements/Dialog.cpp (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) In QTUI empty dialogs no longer have to be confirmed. - this was ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [62c378a] * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) FIX: Made checks in random number engine and distribution regression ... Thu, 28 Aug 2014 08:53:32 GMT Frederik Heber [520029] * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) FIX: regression test add atoms outside boundary had given boundary ... 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. - ... Wed, 20 Aug 2014 12:58:29 GMT Frederik Heber [d5f7b8] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-testsuite-in-makefile.at (added) * tests/CodeChecks/testsuite.at (modified) * tests/regression/Makefile.am (modified) Added CodeCheck for ensuring testsuite..at's appear in ... Wed, 20 Aug 2014 12:58:29 GMT Frederik Heber [1e45f1f] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * tests/regression/Molecules/VerletIntegration/post/test-undo.conf (added) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) Extended VerletIntegrationAction wirth Undo/Redo. - using new ... Mon, 14 Jul 2014 11:15:18 GMT Frederik Heber [a61dbb] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (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) In CommandLineUI actions are skipped after failing action. - ... Fri, 27 Jun 2014 11:45:16 GMT Frederik Heber [1b1fa5] * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_missing.xyz (modified) * tests/regression/Selection/Molecules/InvertMolecules/pre/box.xyz (modified) TESTFIX: Reduced size of loaded file for regression test ... Fri, 27 Jun 2014 11:45:16 GMT Frederik Heber [89604a] * tests/regression/Selection/Molecules/AllMolecules/post/box.xyz (modified) * tests/regression/Selection/Molecules/AllMolecules/pre/box.xyz (modified) TESTFIX: Changed size of loaded file for unselection AllMolecules ... Fri, 27 Jun 2014 11:45:15 GMT Frederik Heber [f678fc4] * tests/regression/Filling/RegularGrid/post/double_sles-undo.data (modified) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified) TESTFIX: Reduced box size in FillRegularGrid to speed up regression test. Fri, 27 Jun 2014 11:45:15 GMT Frederik Heber [e4157b] * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox-mirrored_histogram.dat (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/post/waterbox_histogram.dat (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) TESTFIX: Reduced box size in DipoleCorrelation-DiscreteAngle ... Fri, 27 Jun 2014 11:45:15 GMT Frederik Heber [6d3cb8] * tests/regression/Molecules/BondFile/pre/silica.dbond.0000 (modified) TESTFIX: reduced dbond file size in regression test Molecules/BondFile. Fri, 27 Jun 2014 11:45:15 GMT Frederik Heber [2cc1cb] * tests/regression/Filling/SphericalSurface/post/tensid.data (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) TESTFIX: FillSphericalSurface regression now with just 20 instead of ... Fri, 27 Jun 2014 11:45:13 GMT Frederik Heber [1dbbeb] * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) TESTFIX: reduced required threshold for fit-potential regression ... Fri, 27 Jun 2014 11:43:27 GMT Frederik Heber [0932c2] * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) * src/documentation/constructs/potentials.dox (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed ... Tue, 20 May 2014 09:14:56 GMT Frederik Heber [415ddd] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Python/Makefile.am (modified) * src/Python/PythonScripting_impl.hpp (modified) * src/Python/wait.cpp (added) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) * src/builder_init.hpp (modified) * src/cleanUp.cpp (modified) * src/cleanUp.hpp (modified) * src/documentation/Makefile.am (modified) * src/documentation/userinterfaces/python.dox (modified) * tests/regression/Options/Session/pre/complexwait.py (added) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * utils/Python/boxmaker.py.in (modified) ActionQueue now contains a run thread. - otherwise the progress bar ... 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() ... Tue, 29 Apr 2014 12:42:44 GMT Frederik Heber [607245] * tests/regression/Options/Session/pre/complextest.py (added) * tests/regression/Options/Session/pre/test.py (added) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) TESTFIX: regression test load-session uses python scripts in pre. - ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [f47e00b] * src/Actions/FragmentationAction/MolecularDynamicsAction.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/complextest.sh (modified) FIX: SubgraphDissectionAction is now a MakroAction, fixed store- ... Tue, 29 Apr 2014 12:42:22 GMT Frederik Heber [57388c9] * src/Python/PythonScripting.cpp (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) FIX: Test on skipping load/store session from python script was wrong ... Mon, 21 Oct 2013 10:33:11 GMT Frederik Heber [5e1443] * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) DISTFIX: regression tests Options Sessions do not check correctly for ... Thu, 17 Oct 2013 07:24:50 GMT Frederik Heber [92f978] * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) FIX: store-.. and load-session regression tests were skipped on wrong ... Thu, 17 Oct 2013 07:24:42 GMT Frederik Heber [d29b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_OBC.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_PBC.dat (modified) Longrange energy is now also calculated for level 1. - level 1 sum ... Thu, 17 Oct 2013 07:24:41 GMT Frederik Heber [6531a7] * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Energy.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Forces.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_LongRangeEnergy.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Times.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_VMGEnergy.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Eigenhistogram.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Eigenvalues.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_LongRangeEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/BondFragment_VMGEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_LongRangeEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/BondFragment_VMGEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults.dat (deleted) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_OBC.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults_PBC.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Split regression test on analysing long range results into OBC and ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [c8d13f5] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * src/Fragmentation/Summation/IndexSet.hpp (modified) * src/Fragmentation/Summation/writeIndexedTable.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (modified) Summed up results are now handed-over to FragmentationResultContainer ... Thu, 17 Oct 2013 07:24:25 GMT Frederik Heber [47cee7] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/HeaderPrinter.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/ValuePrinter.hpp (modified) * src/Fragmentation/Summation/writeIndexedTable.hpp (added) * src/Fragmentation/Summation/writeTable.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_IndexedEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Writing out energy file with value and contribution per index set - ... Thu, 17 Oct 2013 07:24:06 GMT Frederik Heber [0588e9] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FragmentMolecule/pre/benzene.pdb (added) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) AnalyseFragmentationResultsAction now also calculates and prints ... Sat, 21 Sep 2013 08:58:26 GMT Frederik Heber [1f86ae] * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) ENABLEFIX: load-session and store-session regression check for ... 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 20:23:53 GMT Frederik Heber [893426] * configure.ac (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/Session/post/complextest.sh (added) * tests/regression/Options/Session/testsuite-options-store-session-cli.at (added) * tests/regression/Options/Session/testsuite-options-store-session-python.at (moved) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/runpython.in (added) Split regression test testsuite-options-store-session in two files. ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [9e4655] * src/Actions/ActionQueue.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/SessionTypeValidator.cpp (added) * src/Parameters/Validators/Specific/SessionTypeValidator.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Options/Session/post/test.py (added) Added sessiontype option to StoreSessionAction. - added ... Thu, 19 Sep 2013 20:23:53 GMT Frederik Heber [f6ff216] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/Reaction_impl_pre.hpp (modified) * tests/regression/Options/Session/post/test.sh (modified) FIX: Removed " " around every printed parameter. 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. 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 ... Mon, 12 Aug 2013 11:30:31 GMT Frederik Heber [321470] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) FIX: Fragmentation's OrderAtSite was written per molecule and with ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [6550cf] * tests/regression/Fragmentation/FitPotential/pre/harmonic_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added regression test for harmonic_bond potential. Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [791a12] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/improper_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added improper potential based on torsion potential with flipped ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [e2037e] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (added) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (added) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Fragmentation/FitPotential/pre/torsion_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added FourBodyPotential_Torsion. - also added regression test to ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [1413f4] * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (added) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (added) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp (added) * tests/regression/Fragmentation/FitPotential/pre/lj_homology.dat (added) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added LennardJones pair potential. - this is for later fitting ... Fri, 09 Aug 2013 14:20:37 GMT Frederik Heber [4792ab] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Added set-threshold option to FitPotentialAction. - TESTFIX: ... 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 14:20:37 GMT Frederik Heber [e355b31] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added both_sampled_potential to VMGData, analogous 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. Thu, 11 Jul 2013 21:43:31 GMT Frederik Heber [bcb593] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/VerletIntegration/post/test.conf (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) FIX: VerletIntegrationAction now assumes forces have just been ... Tue, 09 Jul 2013 06:21:28 GMT Frederik Heber [f73351] * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * tests/regression/Atoms/Add/post/empty.conf (modified) * tests/regression/Domain/ChangeBox/post/test-undo.conf (modified) * tests/regression/Domain/ChangeBox/post/test.conf (modified) FIX: Some Thermostats would cause NaN on zero temperature. - ... Tue, 09 Jul 2013 06:21:05 GMT Frederik Heber [e5ebaf] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Forces obtained from fragmentation summation are now set. - i.e. ... Mon, 08 Jul 2013 14:22:04 GMT Frederik Heber [a315e8] * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/EmptyStringValidator.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Potential type is given via extra option not "fit-potential". - ... Mon, 08 Jul 2013 14:22:03 GMT Frederik Heber [baccf6] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) FitPotentialAction now uses new CompoundPotential to fit. - ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [1e242a] * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Angle. - regression test ... Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [919c8a] * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) Removed energy_offset from PairPotential_Morse. - regression test ... Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [85dee9] * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) FIX: regression test FitPotentialAction was always skipped. - we ... Wed, 12 Jun 2013 10:11:59 GMT Frederik Heber [5aaa43] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/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/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.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/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/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.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/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/testsuite.at (modified) FIX: Fixed new copyright line since start of 2013 in CodeChecks test. ... 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. - ... Fri, 03 May 2013 09:46:45 GMT Frederik Heber [e2925fd] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenhistogram.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Eigenvalues.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Energy.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Forces.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_LongRangeEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/BondFragment_VMGEnergy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/BondFragment_Times.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentLongRangeResults.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentShortRangeResults.dat (moved) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Split long-range calculations into two parts to overcome ... Wed, 01 May 2013 07:52:55 GMT Frederik Heber [6ff62c] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenhistogram.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Energy.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Forces.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Times.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added DoValenceOnly has new option to FragmentationAutomationAction. ... Wed, 17 Apr 2013 18:55:54 GMT Frederik Heber [30f2815] * src/Parser/MpqcParser.cpp (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n.in (added) * tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (added) * tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (added) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) MpqcParser now also understands "_n_ atoms geometry" lines. - ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [eb32b6] * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) Eigenvalue summation uses two sets: added and subtracted values. - ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [5c867e] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (added) * src/Fragmentation/Summation/SetValues/Eigenvalues.hpp (added) * src/Fragmentation/Summation/SetValues/Histogram.hpp (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenhistogram.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Added new SetValue Eigenvalues to just add up the set of eigenvalues. ... Mon, 15 Apr 2013 18:13:36 GMT Frederik Heber [e95c8b] * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Eigenvalues.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) Re-added printing of eigenvalues as histogram. - TEST: added check ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [55e1bc] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Energy.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Forces.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/BondFragment_Times.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/pre/BondFragmentResults.dat (added) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) FragmentationResultContainer is serializable. - ... 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 ... Mon, 08 Apr 2013 11:56:08 GMT Frederik Heber [055ad7] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.def (modified) * tests/regression/Graph/CreateAdjacency/post/ethane-half.pdb (added) * tests/regression/Graph/CreateAdjacency/post/ethane.pdb (added) * tests/regression/Graph/CreateAdjacency/pre/ethane.xyz (added) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added Undo/Redo functionality to CreateAdjacencyAction. - also ... 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 ... Mon, 18 Mar 2013 14:46:12 GMT Frederik Heber [d5b90b] * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * tests/regression/Parser/Xyz/post/HugeCoordinates.xyz (added) * tests/regression/Parser/Xyz/pre/HugeCoordinates.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) FIX: XyzParser had lacking precision beyond coordinates of 100000. ... Sun, 17 Mar 2013 18:27:37 GMT Frederik Heber [e9bdef] * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_values_Y.0035.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (modified) * tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (modified) TESTFIX: Analysis' DipoleAngularCorrelation() and BinData() suffered ...