Changeset 3bdb6d

Timestamp:

Oct 17, 2011, 4:18:54 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

592be9

Parents:

2fadb6f

git-author:

Frederik Heber <heber@…> (09/16/11 10:07:33)

git-committer:

Frederik Heber <heber@…> (10/17/11 16:18:54)

Message:

Moved all stuff related to elements into own subfolder and has its own convenience library.

• this induced massive changes in includes in other files.
• we adapted PeriodentafelUnitTest to not get instance from world, but we create it ourselves.
• also moved all .db files related to elements into subfolder Element/.

Location:

src

Files:

• Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (1 diff)
• Actions/AnalysisAction/PairCorrelationAction.cpp (modified) (1 diff)
• Actions/AnalysisAction/PointCorrelationAction.cpp (modified) (1 diff)
• Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) (1 diff)
• Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) (1 diff)
• Actions/AtomAction/AddAction.cpp (modified) (1 diff)
• Actions/AtomAction/ChangeElementAction.cpp (modified) (1 diff)
• Actions/CommandAction/ElementDbAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) (1 diff)
• Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) (1 diff)
• Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) (1 diff)
• Actions/ValueStorage.cpp (modified) (1 diff)
• Analysis/analysis_bonds.cpp (modified) (1 diff)
• Analysis/analysis_correlation.cpp (modified) (1 diff)
• Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) (1 diff)
• Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) (1 diff)
• Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) (1 diff)
• Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) (1 diff)
• Analysis/unittests/CountBondsUnitTest.cpp (modified) (1 diff)
• AtomicInfo.cpp (modified) (1 diff)
• Bond/bond.cpp (modified) (1 diff)
• Descriptors/AtomTypeDescriptor.cpp (modified) (1 diff)
• Dynamics/MinimiseConstrainedPotential.cpp (modified) (1 diff)
• Element/Hbondangle.db (moved) (moved from src/Hbondangle.db )
• Element/Hbonddistance.db (moved) (moved from src/Hbonddistance.db )
• Element/Makefile.am (added)
• Element/element.cpp (moved) (moved from src/element.cpp )
• Element/element.hpp (moved) (moved from src/element.hpp )
• Element/elements.db (moved) (moved from src/elements.db )
• Element/elements_db.cpp (moved) (moved from src/elements_db.cpp )
• Element/elements_db.hpp (moved) (moved from src/elements_db.hpp )
• Element/orbitals.db (moved) (moved from src/orbitals.db )
• Element/periodentafel.cpp (moved) (moved from src/periodentafel.cpp )
• Element/periodentafel.hpp (moved) (moved from src/periodentafel.hpp )
• Element/valence.db (moved) (moved from src/valence.db )
• Formula.cpp (modified) (1 diff)
• Fragmentation/analyzer.cpp (modified) (1 diff)
• Fragmentation/joiner.cpp (modified) (1 diff)
• Graph/BondGraph.cpp (modified) (2 diffs)
• Graph/BondGraph.hpp (modified) (1 diff)
• Graph/CyclicStructureAnalysis.cpp (modified) (1 diff)
• Graph/unittests/BondGraphUnitTest.cpp (modified) (1 diff)
• Makefile.am (modified) (8 diffs)
• Parser/MpqcParser.cpp (modified) (2 diffs)
• Parser/PcpParser.cpp (modified) (2 diffs)
• Parser/PdbParser.cpp (modified) (1 diff)
• Parser/TremoloParser.cpp (modified) (1 diff)
• Parser/XyzParser.cpp (modified) (1 diff)
• Parser/unittests/ParserMpqcUnitTest.cpp (modified) (1 diff)
• Parser/unittests/ParserPcpUnitTest.cpp (modified) (1 diff)
• Parser/unittests/ParserPdbUnitTest.cpp (modified) (1 diff)
• Parser/unittests/ParserTremoloUnitTest.cpp (modified) (2 diffs)
• Parser/unittests/ParserXyzUnitTest.cpp (modified) (1 diff)
• Tesselation/boundary.cpp (modified) (1 diff)
• Thermostats/Berendsen.cpp (modified) (1 diff)
• Thermostats/GaussianThermostat.cpp (modified) (1 diff)
• Thermostats/Langevin.cpp (modified) (1 diff)
• Thermostats/NoseHoover.cpp (modified) (1 diff)
• Thermostats/Woodcock.cpp (modified) (1 diff)
• UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) (1 diff)
• UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) (1 diff)
• UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) (1 diff)
• UIElements/Makefile.am (modified) (1 diff)
• UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) (1 diff)
• UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) (1 diff)
• UIElements/Qt4/Query/ElementQtQuery.cpp (modified) (1 diff)
• UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) (1 diff)
• UIElements/TextUI/Query/ElementTextQuery.cpp (modified) (1 diff)
• UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) (1 diff)
• UIElements/TextUI/TextWindow.cpp (modified) (1 diff)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) (1 diff)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) (1 diff)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) (1 diff)
• UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) (1 diff)
• World.cpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom_atominfo.cpp (modified) (1 diff)
• atom_bondedparticle.cpp (modified) (1 diff)
• builder_init.cpp (modified) (1 diff)
• config.cpp (modified) (2 diffs)
• molecule.cpp (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (2 diffs)
• molecule_geometry.cpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)
• moleculelist.cpp (modified) (2 diffs)
• unittests/ElementUnitTest.cpp (modified) (1 diff)
• unittests/LinkedCellUnitTest.cpp (modified) (1 diff)
• unittests/ListOfBondsUnitTest.cpp (modified) (1 diff)
• unittests/Makefile.am (modified) (2 diffs)
• unittests/PeriodentafelUnitTest.cpp (modified) (5 diffs)

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -25 +25 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -25 +25 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/Actions/AnalysisAction/PointCorrelationAction.cpp

@@ -25 +25 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

@@ -24 +24 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -26 +26 @@
 #include "CodePatterns/Log.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "PointCloudAdaptor.hpp"
 #include "Tesselation/tesselation.hpp"

src/Actions/AtomAction/AddAction.cpp

@@ -22 +22 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "atom.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Log.hpp"
 #include "molecule.hpp"

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -22 +22 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "atom.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Log.hpp"
 #include "LinearAlgebra/Vector.hpp"

src/Actions/CommandAction/ElementDbAction.cpp

@@ -25 +25 @@
 
 #include "config.hpp"
-#include "element.hpp"    // we need element because of serialization!
-#include "periodentafel.hpp"
+#include "Element/element.hpp"    // we need element because of serialization!
+#include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

@@ -25 +25 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 

src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp

@@ -23 +23 @@
 #include "Descriptors/AtomSelectionDescriptor.hpp"
 #include "atom.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp

@@ -23 +23 @@
 #include "Descriptors/AtomTypeDescriptor.hpp"
 #include "atom.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Actions/ValueStorage.cpp

@@ -37 +37 @@
 #include "atom.hpp"
 #include "Box.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/Analysis/analysis_bonds.cpp

@@ -23 +23 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Analysis/analysis_correlation.cpp

@@ -27 +27 @@
 #include "Tesselation/BoundaryTriangleSet.hpp"
 #include "Box.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"

src/Analysis/unittests/AnalysisBondsUnitTest.cpp

@@ -31 +31 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp

@@ -31 +31 @@
 
 #include "atom.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 #include "linkedcell.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

@@ -31 +31 @@
 #include "CodePatterns/Assert.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 #include "linkedcell.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "PointCloudAdaptor.hpp"
 #include "Tesselation/tesselation.hpp"

src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp

@@ -32 +32 @@
 #include "atom.hpp"
 #include "Tesselation/boundary.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 #include "linkedcell.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Tesselation/tesselation.hpp"
 #include "World.hpp"

src/Analysis/unittests/CountBondsUnitTest.cpp

@@ -33 +33 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/AtomicInfo.cpp

@@ -22 +22 @@
 #include "atom.hpp"
 #include "AtomicInfo.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "LinearAlgebra/Vector.hpp"
 

src/Bond/bond.cpp

@@ -23 +23 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 
 

src/Descriptors/AtomTypeDescriptor.cpp

@@ -25 +25 @@
 #include "atom.hpp"
 #include "World.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 
 AtomTypeDescriptor_impl::AtomTypeDescriptor_impl(const element* _type) :

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -26 +26 @@
 #include "atom.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Info.hpp"

src/Formula.cpp

@@ -25 +25 @@
 
 #include "World.hpp"
-#include "periodentafel.hpp"
-#include "element.hpp"
+#include "Element/periodentafel.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Range.hpp"

src/Fragmentation/analyzer.cpp

@@ -29 +29 @@
 #include "datacreator.hpp"
 #include "parser.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Fragmentation/joiner.cpp

@@ -27 +27 @@
 #include "datacreator.hpp"
 #include "parser.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Graph/BondGraph.cpp

@@ -26 +26 @@
 #include "Graph/BondGraph.hpp"
 #include "Box.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
@@ -33 +33 @@
 #include "molecule.hpp"
 #include "Fragmentation/parser.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/Graph/BondGraph.hpp

@@ -26 +26 @@
 #include "CodePatterns/Range.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "linkedcell.hpp"
 #include "IPointCloud.hpp"

src/Graph/CyclicStructureAnalysis.cpp

@@ -28 +28 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 

src/Graph/unittests/BondGraphUnitTest.cpp

@@ -33 +33 @@
 #include "Bond/bond.hpp"
 #include "CodePatterns/Log.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"

src/Makefile.am

@@ -9 +9 @@
 include Actions/Makefile.am
 include Analysis/Makefile.am
+include Element/Makefile.am
 include Graph/Makefile.am
 include Helpers/Makefile.am
@@ -175 +176 @@
   config.cpp \
   ConfigFileBuffer.cpp \
-  element.cpp \
-  elements_db.cpp \
   Formula.cpp \
   graph.cpp \
@@ -185 +184 @@
   molecule_geometry.cpp \
   molecule_graph.cpp \
-  periodentafel.cpp \
   ThermoStatContainer.cpp \
   UIElements/UIFactory.cpp \
@@ -204 +202 @@
   config.hpp \
   ConfigFileBuffer.hpp \
-  element.hpp \
-  elements_db.hpp \
   Formula.hpp \
   graph.hpp \
   linkedcell.hpp \
   molecule.hpp \
-  periodentafel.hpp \
   ThermoStatContainer.hpp \
   types.hpp \
@@ -271 +266 @@
 libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER} 
 
-molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
+molecuilder_DATA = Element/elements.db Element/valence.db Element/orbitals.db Element/Hbonddistance.db Element/Hbondangle.db
 
 molecuilder_CXXFLAGS = $(AM_CPPFLAGS) 
@@ -303 +298 @@
         $(GUI_LIBS)
 
-joiner_SOURCES = Fragmentation/joiner.cpp Fragmentation/datacreator.cpp datacreator.hpp Fragmentation/periodentafel.hpp
+joiner_SOURCES = Fragmentation/joiner.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
 joiner_LDADD = \
         libMolecuilder.la \
@@ -309 +304 @@
         libMolecuilderShapes.la \
         libMolecuilderHelpers.la \
+        libMolecuilderElement.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \
         $(BOOST_THREAD_LIBS)
 
-analyzer_SOURCES = Fragmentation/analyzer.cpp Fragmentation/datacreator.cpp periodentafel.hpp Fragmentation/datacreator.hpp 
+analyzer_SOURCES = Fragmentation/analyzer.cpp Fragmentation/datacreator.cpp Fragmentation/datacreator.hpp
 analyzer_LDADD = \
         libMolecuilder.la \
@@ -319 +315 @@
         libMolecuilderShapes.la \
         libMolecuilderHelpers.la \
+        libMolecuilderElement.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         ${CodePatterns_LIBS} \

src/Parser/MpqcParser.cpp

@@ -29 +29 @@
 #include "atom.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 #include "CodePatterns/Log.hpp"
@@ -35 +35 @@
 #include "CodePatterns/Verbose.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/Parser/PcpParser.cpp

@@ -27 +27 @@
 #include "config.hpp"
 #include "ConfigFileBuffer.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
@@ -34 +34 @@
 #include "molecule.hpp"
 #include "PcpParser.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"

src/Parser/PdbParser.cpp

@@ -28 +28 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Parser/PdbParser.hpp"

src/Parser/TremoloParser.cpp

@@ -29 +29 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include <map>

src/Parser/XyzParser.cpp

@@ -28 +28 @@
 #include "atom.hpp"
 #include "molecule.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 
 using namespace std;

src/Parser/unittests/ParserMpqcUnitTest.cpp

@@ -28 +28 @@
 #include "World.hpp"
 #include "atom.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"
 #include "CodePatterns/Assert.hpp"

src/Parser/unittests/ParserPcpUnitTest.cpp

@@ -27 +27 @@
 #include "World.hpp"
 #include "atom.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"

src/Parser/unittests/ParserPdbUnitTest.cpp

@@ -27 +27 @@
 #include "World.hpp"
 #include "atom.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"

src/Parser/unittests/ParserTremoloUnitTest.cpp

@@ -26 +26 @@
 #include "atom.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Parser/MpqcParser.hpp"
 #include "Parser/PdbParser.hpp"
@@ -32 +32 @@
 #include "Parser/TremoloParser.hpp"
 #include "Parser/XyzParser.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"

src/Parser/unittests/ParserXyzUnitTest.cpp

@@ -27 +27 @@
 #include "World.hpp"
 #include "atom.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "CodePatterns/Log.hpp"
 #include "Descriptors/AtomTypeDescriptor.hpp"

src/Tesselation/boundary.cpp

@@ -30 +30 @@
 #include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "LinearAlgebra/Plane.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"

src/Thermostats/Berendsen.cpp

@@ -14 +14 @@
 
 #include "Berendsen.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "config.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Thermostats/GaussianThermostat.cpp

@@ -19 +19 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "AtomSet.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "config.hpp"
 #include "World.hpp"

src/Thermostats/Langevin.cpp

@@ -14 +14 @@
 
 #include "Langevin.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "config.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Thermostats/NoseHoover.cpp

@@ -15 +15 @@
 #include "NoseHoover.hpp"
 
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "config.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Thermostats/Woodcock.cpp

@@ -15 +15 @@
 #include "Woodcock.hpp"
 
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "config.hpp"
 #include "CodePatterns/Verbose.hpp"

src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp

@@ -24 +24 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp

@@ -24 +24 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/CommandLineUI/TypeEnumContainer.cpp

@@ -34 +34 @@
 #include "LinearAlgebra/BoxVector.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
 #include "RandomNumbers/RandomNumberDistribution_Parameters.hpp"

src/UIElements/Makefile.am

@@ -270 +270 @@
         libMolecuilderShapes.la \
         libMolecuilderHelpers.la \
+        libMolecuilderElement.la \
         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
         libMolecuilderRandomNumbers.la \

src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp

@@ -24 +24 @@
 
 #include "CodePatterns/MemDebug.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp

@@ -26 +26 @@
 
 #include "CodePatterns/MemDebug.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/Qt4/Query/ElementQtQuery.cpp

@@ -27 +27 @@
 #include "UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp"
 
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/Qt4/Query/ElementsQtQuery.cpp

@@ -27 +27 @@
 #include "UIElements/Qt4/Pipe/ElementsQtQueryPipe.hpp"
 
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/TextUI/Query/ElementTextQuery.cpp

@@ -26 +26 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/TextUI/Query/ElementsTextQuery.cpp

@@ -27 +27 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/TextUI/TextWindow.cpp

@@ -45 +45 @@
 // all needed due to config::SaveAll()
 #include "config.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 
 // config::SaveAll() and enumerate()

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp

@@ -33 +33 @@
 
 #include "Helpers/defs.hpp"
-#include "element.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp

@@ -30 +30 @@
 
 #include "Descriptors/AtomIdDescriptor.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp

@@ -32 +32 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Helpers/defs.hpp"
 #include "LinearAlgebra/Line.hpp"

src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp

@@ -145 +145 @@
 //#include "atom.hpp"
 //#include "Bond/bond.hpp"
-//#include "element.hpp"
+//#include "Element/element.hpp"
 //#include "molecule.hpp"
-//#include "periodentafel.hpp"
+//#include "Element/periodentafel.hpp"
 //#include "World.hpp"
 //

src/World.cpp

@@ -40 +40 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "ThermoStatContainer.hpp"
 #include "WorldTime.hpp"

src/atom.cpp

@@ -23 +23 @@
 #include "CodePatterns/Log.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Fragmentation/parser.hpp"
 #include "LinearAlgebra/Vector.hpp"

src/atom_atominfo.cpp

@@ -23 +23 @@
 #include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Fragmentation/parser.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"

src/atom_bondedparticle.cpp

@@ -26 +26 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "WorldTime.hpp"
 

src/builder_init.cpp

@@ -26 +26 @@
 #include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Tesselation/tesselationhelpers.hpp"
 #include "UIElements/UIFactory.hpp"

src/config.cpp

@@ -34 +34 @@
 #include "config.hpp"
 #include "ConfigFileBuffer.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Helpers/helpers.hpp"
@@ -40 +40 @@
 #include "molecule.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"

src/molecule.cpp

@@ -32 +32 @@
 #include "CodePatterns/Log.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "graph.hpp"
 #include "Graph/BondGraph.hpp"
@@ -42 +42 @@
 #include "linkedcell.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Tesselation/tesselation.hpp"
 #include "World.hpp"

src/molecule_fragmentation.cpp

@@ -28 +28 @@
 #include "CodePatterns/Log.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Graph/CheckAgainstAdjacencyFile.hpp"
@@ -36 +36 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/molecule_geometry.cpp

@@ -26 +26 @@
 #include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "LinearAlgebra/leastsquaremin.hpp"

src/molecule_graph.cpp

@@ -31 +31 @@
 #include "config.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Helpers/defs.hpp"

src/moleculelist.cpp

@@ -32 +32 @@
 #include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Helpers/helpers.hpp"
@@ -40 +40 @@
 #include "Parser/MpqcParser.hpp"
 #include "Parser/FormatParserStorage.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "Tesselation/tesselation.hpp"
 #include "World.hpp"

src/unittests/ElementUnitTest.cpp

@@ -26 +26 @@
 #include <sstream>
 
-#include "element.hpp"
+#include "Element/element.hpp"
 
 // include headers that implement a archive in simple text format

src/unittests/LinkedCellUnitTest.cpp

@@ -30 +30 @@
 #include "atom.hpp"
 #include "Descriptors/MoleculeDescriptor.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "linkedcell.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "PointCloudAdaptor.hpp"
 #include "World.hpp"

src/unittests/ListOfBondsUnitTest.cpp

@@ -30 +30 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "element.hpp"
+#include "Element/element.hpp"
 #include "molecule.hpp"
-#include "periodentafel.hpp"
+#include "Element/periodentafel.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"

src/unittests/Makefile.am

@@ -101 +101 @@
 ElementUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ElementUnitTest.cpp \
-        ../element.cpp \
-        ElementUnitTest.hpp \
-        ../element.hpp
+        ElementUnitTest.hpp
 ElementUnitTest_LDADD = \
+        ../libMolecuilderElement.la \
         $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
 
@@ -125 +124 @@
         PeriodentafelUnitTest.cpp \
         PeriodentafelUnitTest.hpp
-PeriodentafelUnitTest_LDADD = ${ALLLIBS}
+PeriodentafelUnitTest_LDADD = \
+                ../libMolecuilderElement.la \
+                ../libMolecuilderHelpers.la \
+        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
 
 WorldTimeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \

src/unittests/PeriodentafelUnitTest.cpp

@@ -29 +29 @@
 #include "CodePatterns/Assert.hpp"
 
-#include "World.hpp"
-#include "element.hpp"
-#include "elements_db.hpp"
-#include "periodentafel.hpp"
+#include "Element/element.hpp"
+#include "Element/elements_db.hpp"
+#include "Element/periodentafel.hpp"
 
 #include "PeriodentafelUnitTest.hpp"
@@ -53 +52 @@
 {
   // make sure world is present
-  tafel = World::getInstance().getPeriode();
+  tafel = new periodentafel();
   CPPUNIT_ASSERT(tafel != NULL && "could not obtain periodentafel");
 };
@@ -60 +59 @@
 void periodentafelTest::tearDown()
 {
-  World::purgeInstance();
+  delete tafel;
 };
 
@@ -124 +123 @@
 }
 
-std::string gatherUndoInformation()
+std::string gatherUndoInformation(const periodentafel *tafel)
 {
   // create undo state
   std::stringstream undostream;
   boost::archive::text_oarchive oa(undostream);
-  oa << World::getInstance().getPeriode();
+  oa << tafel;
   return undostream.str();
 }
@@ -139 +138 @@
 {
   // write element to stream
-  std::stringstream stream(gatherUndoInformation());
+  std::stringstream stream(gatherUndoInformation(tafel));
 //  boost::archive::text_oarchive oa(stream);
 //  oa << World::getInstance().getPeriode();