[Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.7
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- Log -----------------------------------------------------------------
-----------------------------------------------------------------------
Summary of changes:
LinearAlgebra/src/LinearAlgebra/Makefile.am | 7 +-
LinearAlgebra/src/LinearAlgebra/Plane.cpp | 7 +-
LinearAlgebra/src/LinearAlgebra/Vector.cpp | 35 ++-
LinearAlgebra/src/LinearAlgebra/Vector.hpp | 9 +-
LinearAlgebra/src/LinearAlgebra/VectorContent.cpp | 3 +-
LinearAlgebra/src/unittests/Makefile.am | 7 +-
Makefile.am | 8 +-
configure.ac | 12 +-
m4/boost.m4 | 438 +++++++++++++-----
m4/qwt.m4 | 2 +-
src/Actions/ActionQueue.cpp | 2 +-
src/Actions/ActionRegistry.cpp | 24 +-
src/Actions/Action_impl_python.hpp | 24 +-
src/Actions/AtomAction/RemoveAction.def | 3 -
.../FragmentationAction/FragmentationAction.cpp | 112 +++++-
.../FragmentationAutomationAction.cpp | 14 +-
.../StoreSaturatedFragmentAction.cpp | 6 +-
.../StructuralOptimizationAction.cpp | 117 +++++
.../StructuralOptimizationAction.def | 36 ++
.../StructuralOptimizationAction.hpp | 22 +
src/Actions/GlobalListOfActions.hpp | 183 ++++----
.../GraphAction/CorrectBondDegreeAction.cpp | 164 +++++++
.../GraphAction/CorrectBondDegreeAction.def | 37 ++
.../GraphAction/CorrectBondDegreeAction.hpp | 22 +
src/Actions/Makefile.am | 15 +-
.../MoleculeAction/ForceAnnealingAction.cpp | 166 +++++++
.../MoleculeAction/ForceAnnealingAction.def | 40 ++
.../MoleculeAction/ForceAnnealingAction.hpp | 22 +
.../MoleculeAction/VerletIntegrationAction.cpp | 97 ++++-
.../MoleculeAction/VerletIntegrationAction.def | 8 +-
src/Actions/UndoRedoHelpers.cpp | 72 +++-
src/Actions/UndoRedoHelpers.hpp | 60 +++-
src/Actions/unittests/Makefile.am | 13 +-
src/Analysis/unittests/Makefile.am | 11 +-
src/Atom/AtomicInfo.cpp | 3 +
src/Atom/AtomicInfo.hpp | 1 +
src/Atom/TesselPoint.cpp | 6 +
src/Atom/TesselPoint.hpp | 8 +
src/Atom/atom.cpp | 9 +
src/Atom/atom.hpp | 8 +
src/Atom/atom_atominfo.cpp | 12 +
src/Atom/atom_atominfo.hpp | 17 +
src/Atom/atom_bondedparticleinfo.cpp | 6 +
src/Atom/atom_bondedparticleinfo.hpp | 8 +-
src/Atom/unittests/Makefile.am | 6 +-
src/Descriptors/unittests/Makefile.am | 6 +-
src/Dynamics/AtomicForceManipulator.hpp | 144 ++++++
src/Dynamics/ForceAnnealing.hpp | 159 +++++++
src/Dynamics/MinimiseConstrainedPotential.cpp | 2 +-
src/Dynamics/MinimiseConstrainedPotential.hpp | 2 +-
src/Dynamics/VerletForceIntegration.hpp | 151 +-----
src/Element/elements_db.cpp | 24 +-
src/Element/unittests/Makefile.am | 9 +-
src/Filling/unittests/Makefile.am | 20 +-
.../Automation/MPQCCommandFragmentController.cpp | 9 +-
.../Automation/MPQCCommandFragmentController.hpp | 11 +
.../Automation/MPQCFragmentController.cpp | 5 +-
src/Fragmentation/Automation/Makefile.am | 2 +-
...gmentController_ReceiveResultContainer_impl.hpp | 8 +-
src/Fragmentation/Exporters/ExportGraph.cpp | 261 ++++++-----
src/Fragmentation/Exporters/ExportGraph.hpp | 14 +-
.../Exporters/ExportGraph_ToFiles.cpp | 7 +-
.../Exporters/ExportGraph_ToFiles.hpp | 3 +-
src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp | 5 +-
src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp | 5 +-
src/Fragmentation/Exporters/SaturatedBond.cpp | 132 ++++++
src/Fragmentation/Exporters/SaturatedBond.hpp | 89 ++++
src/Fragmentation/Exporters/SaturatedFragment.cpp | 258 +++++++++--
src/Fragmentation/Exporters/SaturatedFragment.hpp | 46 ++-
.../Exporters/SaturationDistanceMaximizer.cpp | 302 ++++++++++++
.../Exporters/SaturationDistanceMaximizer.hpp | 147 ++++++
src/Fragmentation/Exporters/unittests/Makefile.am | 24 +-
.../unittests/SaturatedFragmentUnitTest.cpp | 9 +-
.../SaturationDistanceMaximizerUnitTest.cpp | 137 ++++++
.../SaturationDistanceMaximizerUnitTest.hpp | 43 ++
.../unittests/stubs/SaturatedBondStub.cpp | 73 +++
src/Fragmentation/Fragmentation.cpp | 2 +-
src/Fragmentation/Homology/unittests/Makefile.am | 10 +-
src/Fragmentation/Interfragmenter.cpp | 12 +-
src/Fragmentation/Makefile.am | 4 +
src/Fragmentation/Summation/Containers/Makefile.am | 2 +-
.../Summation/Containers/unittests/Makefile.am | 6 +-
.../Summation/Converter/DataConverter.hpp | 8 +
src/Fragmentation/Summation/Converter/Makefile.am | 2 +-
src/Fragmentation/Summation/Makefile.am | 2 +-
src/Fragmentation/Summation/SetValues/Makefile.am | 2 +-
.../Summation/SetValues/unittests/Makefile.am | 14 +-
src/Fragmentation/Summation/unittests/Makefile.am | 16 +-
src/Fragmentation/unittests/Makefile.am | 6 +-
src/FunctionApproximation/unittests/Makefile.am | 6 +-
src/Graph/BreadthFirstSearchAdd.cpp | 190 --------
src/Graph/BreadthFirstSearchAdd.hpp | 82 ----
src/Graph/CyclicStructureAnalysis.cpp | 253 ++++++-----
src/Graph/CyclicStructureAnalysis.hpp | 6 +-
src/Graph/Makefile.am | 2 -
src/Graph/unittests/Makefile.am | 6 +-
src/Jobs/Makefile.am | 2 +-
src/Jobs/unittests/Makefile.am | 6 +-
src/LinkedCell/unittests/Makefile.am | 24 +-
src/Makefile.am | 120 ++---
src/Parameters/Makefile.am | 1 +
src/Parameters/unittests/Makefile.am | 12 +-
src/Parser/Parameters/unittests/Makefile.am | 34 +-
src/Parser/PdbParser.cpp | 9 +-
src/Parser/unittests/Makefile.am | 18 +-
src/Parser/unittests/ParserPdbUnitTest.cpp | 14 +
src/Potentials/Specifics/unittests/Makefile.am | 18 +-
src/Potentials/unittests/Makefile.am | 9 +-
src/RandomNumbers/Makefile.am | 8 +-
src/RandomNumbers/unittests/Makefile.am | 12 +-
src/Shapes/Makefile.am | 3 +
src/Shapes/unittests/Makefile.am | 49 +--
src/Tesselation/Makefile.am | 74 +++
src/Tesselation/unittests/Makefile.am | 8 +-
src/UIElements/CommandLineUI/unittests/Makefile.am | 4 +-
src/UIElements/Makefile.am | 4 +-
src/UIElements/Menu/unittests/Makefile.am | 10 +-
src/UIElements/Views/Qt4/Plotting/Makefile.am | 2 +-
src/UIElements/Views/Qt4/QDebugStream.hpp | 7 +-
src/UIElements/Views/Qt4/QtTimeLine.cpp | 16 +-
src/builder_init.cpp | 27 +-
src/documentation/install.dox | 11 +-
src/molecule.cpp | 494 ++++++++++----------
src/molecule.hpp | 2 +-
src/unittests/Makefile.am | 91 +++-
.../testsuite-calculations-1_2-dimethoxyethane.at | 2 +-
.../testsuite-calculations-1_2-dimethylbenzene.at | 2 +-
...testsuite-calculations-2-methylcyclohexanone.at | 2 +-
...testsuite-calculations-N_N-dimethylacetamide.at | 2 +-
.../testsuite-calculations-anthracene.at | 3 +-
.../Calculations/testsuite-calculations-benzene.at | 2 +-
.../testsuite-calculations-cholesterol.at | 2 +-
.../testsuite-calculations-coronene.at | 3 +-
.../testsuite-calculations-cycloheptane.at | 2 +-
...estsuite-calculations-dimethyl_bromomalonate.at | 2 +-
.../Calculations/testsuite-calculations-glucose.at | 2 +-
.../Calculations/testsuite-calculations-heptan.at | 2 +-
.../testsuite-calculations-isoleucine.at | 2 +-
.../testsuite-calculations-naphthalene.at | 3 +-
.../testsuite-calculations-neohexane.at | 2 +-
.../testsuite-calculations-phenanthrene.at | 3 +-
.../Calculations/testsuite-calculations-proline.at | 2 +-
.../testsuite-calculations-putrescine.at | 2 +-
.../testsuite-calculations-tartaric_acid.at | 2 +-
tests/CodeChecks/Makefile.am | 3 +-
.../CodeChecks/testsuite-testsuite-in-makefile.at | 53 +++
tests/CodeChecks/testsuite.at | 2 +
.../testsuite-fragmenting-anthracene-order1.at | 2 +-
.../testsuite-fragmenting-anthracene-order2.at | 2 +-
.../testsuite-fragmenting-anthracene-order3.at | 2 +-
.../testsuite-fragmenting-anthracene-order4.at | 2 +-
.../testsuite-fragmenting-anthracene-order5.at | 2 +-
.../testsuite-fragmenting-anthracene-order6.at | 2 +-
.../testsuite-fragmenting-coronene-order1.at | 2 +-
.../testsuite-fragmenting-coronene-order2.at | 2 +-
.../testsuite-fragmenting-coronene-order3.at | 2 +-
.../testsuite-fragmenting-coronene-order4.at | 2 +-
.../testsuite-fragmenting-coronene-order5.at | 2 +-
.../testsuite-fragmenting-coronene-order6.at | 2 +-
.../testsuite-fragmenting-naphthalene-order1.at | 2 +-
.../testsuite-fragmenting-naphthalene-order2.at | 2 +-
.../testsuite-fragmenting-naphthalene-order3.at | 2 +-
.../testsuite-fragmenting-naphthalene-order4.at | 2 +-
.../testsuite-fragmenting-naphthalene-order5.at | 2 +-
.../testsuite-fragmenting-naphthalene-order6.at | 2 +-
.../testsuite-fragmenting-phenanthrene-order1.at | 2 +-
.../testsuite-fragmenting-phenanthrene-order2.at | 2 +-
.../testsuite-fragmenting-phenanthrene-order3.at | 2 +-
.../testsuite-fragmenting-phenanthrene-order4.at | 2 +-
.../testsuite-fragmenting-phenanthrene-order5.at | 2 +-
.../testsuite-fragmenting-phenanthrene-order6.at | 2 +-
tests/Fragmentations/testsuite.at | 2 +-
tests/JobMarket/Makefile.am | 4 +-
tests/Makefile.am | 4 +-
tests/regression/Makefile.am | 36 +-
.../Molecules/ForceAnnealing/post/test-undo.conf | 83 ++++
.../Molecules/ForceAnnealing/post/test.conf | 83 ++++
.../pre/test.conf | 0
.../pre/test.forces | 0
.../testsuite-molecules-force-annealing.at | 56 +++
.../VerletIntegration/post/test-undo.conf | 83 ++++
.../testsuite-molecules-verlet-integration.at | 8 +-
tests/regression/Molecules/testsuite-molecules.at | 3 +
183 files changed, 4592 insertions(+), 1627 deletions(-)
create mode 100644 src/Actions/FragmentationAction/StructuralOptimizationAction.cpp
create mode 100644 src/Actions/FragmentationAction/StructuralOptimizationAction.def
create mode 100644 src/Actions/FragmentationAction/StructuralOptimizationAction.hpp
create mode 100644 src/Actions/GraphAction/CorrectBondDegreeAction.cpp
create mode 100644 src/Actions/GraphAction/CorrectBondDegreeAction.def
create mode 100644 src/Actions/GraphAction/CorrectBondDegreeAction.hpp
create mode 100644 src/Actions/MoleculeAction/ForceAnnealingAction.cpp
create mode 100644 src/Actions/MoleculeAction/ForceAnnealingAction.def
create mode 100644 src/Actions/MoleculeAction/ForceAnnealingAction.hpp
create mode 100644 src/Dynamics/AtomicForceManipulator.hpp
create mode 100644 src/Dynamics/ForceAnnealing.hpp
create mode 100644 src/Fragmentation/Exporters/SaturatedBond.cpp
create mode 100644 src/Fragmentation/Exporters/SaturatedBond.hpp
create mode 100644 src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp
create mode 100644 src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp
create mode 100644 src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp
create mode 100644 src/Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.hpp
create mode 100644 src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp
delete mode 100644 src/Graph/BreadthFirstSearchAdd.cpp
delete mode 100644 src/Graph/BreadthFirstSearchAdd.hpp
create mode 100644 src/Tesselation/Makefile.am
create mode 100644 tests/CodeChecks/testsuite-testsuite-in-makefile.at
create mode 100644 tests/regression/Molecules/ForceAnnealing/post/test-undo.conf
create mode 100644 tests/regression/Molecules/ForceAnnealing/post/test.conf
copy tests/regression/Molecules/{VerletIntegration => ForceAnnealing}/pre/test.conf (100%)
copy tests/regression/Molecules/{VerletIntegration => ForceAnnealing}/pre/test.forces (100%)
create mode 100644 tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at
create mode 100644 tests/regression/Molecules/VerletIntegration/post/test-undo.conf
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