Changeset c4d4df

Timestamp:

Oct 13, 2009, 4:42:58 PM (15 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:

06c7a3, f74d08

Parents:

93d120

git-author:

Frederik Heber <heber@…> (10/13/09 16:14:49)

git-committer:

Frederik Heber <heber@…> (10/13/09 16:42:58)

Message:

Pair correlation analysis added.

• new file analysis_correlation.cpp with the following functions: PairCorrelation(), CorrelationToPoint(), CorrelationToSurface(), GetBin(), OutputCorrelation(), and templates GetMinMax(), BinData()
• three new unit tests: AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest (each in own file)
• new function DistanceToTrianglePlane() in tesselationhelpers.cpp
• new function Vector::DistanceToPlane() calculates distance to a plane

Unit tests are working fine.

Location:

src

Files:

• Makefile.am (modified) (1 diff)
• analysis_correlation.cpp (added)
• analysis_correlation.hpp (added)
• tesselationhelpers.cpp (modified) (1 diff)
• tesselationhelpers.hpp (modified) (1 diff)
• unittests/AnalysisCorrelationToPointUnitTest.cpp (added)
• unittests/AnalysisCorrelationToPointUnitTest.hpp (added)
• unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (added)
• unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (added)
• unittests/AnalysisPairCorrelationUnitTest.cpp (added)
• unittests/AnalysisPairCorrelationUnitTest.hpp (added)
• unittests/Makefile.am (modified) (1 diff)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/Makefile.am

@@ -1 @@
-SOURCE = atom.cpp bond.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
-HEADER = atom.hpp bond.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
+SOURCE = analysis_correlation.cpp atom.cpp bond.cpp boundary.cpp config.cpp element.cpp ellipsoid.cpp graph.cpp helpers.cpp leastsquaremin.cpp linkedcell.cpp memoryusageobserver.cpp moleculelist.cpp molecule.cpp molecule_dynamics.cpp molecule_fragmentation.cpp molecule_geometry.cpp molecule_graph.cpp molecule_pointcloud.cpp parser.cpp periodentafel.cpp tesselation.cpp tesselationhelpers.cpp vector.cpp verbose.cpp
+HEADER = analysis_correlation.hpp atom.hpp bond.hpp boundary.hpp config.hpp defs.hpp element.hpp ellipsoid.hpp graph.hpp helpers.hpp leastsquaremin.hpp linkedcell.hpp lists.hpp memoryallocator.hpp memoryusageobserver.hpp molecule.hpp molecule_template.hpp parser.hpp periodentafel.hpp stackclass.hpp tesselation.hpp tesselationhelpers.hpp vector.hpp verbose.hpp
 
 BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)

src/tesselationhelpers.cpp

@@ -679 +679 @@
 };
 
+/** Returns the distance to the plane defined by \a *triangle
+ * \param *out output stream for debugging
+ * \param *x Vector to calculate distance to
+ * \param *triangle triangle defining plane
+ * \return distance between \a *x and plane defined by \a *triangle, -1 - if something went wrong
+ */
+double DistanceToTrianglePlane(ofstream *out, Vector *x, BoundaryTriangleSet *triangle)
+{
+  double distance = 0.;
+  if (x == NULL) {
+    return -1;
+  }
+  distance = x->DistanceToPlane(out, &triangle->NormalVector, triangle->endpoints[0]->node->node);
+  return distance;
+};
 
 /** Creates the objects in a VRML file.

src/tesselationhelpers.hpp

@@ -68 +68 @@
 void WriteVrmlFile(ofstream *out, ofstream *vrmlfile, class Tesselation *Tess, PointCloud *cloud);
 void CalculateConcavityPerBoundaryPoint(ofstream *out, class Tesselation *TesselStruct);
+double DistanceToTrianglePlane(ofstream *out, Vector *x, BoundaryTriangleSet *triangle);
 
 bool CheckListOfBaselines(ofstream *out, Tesselation *TesselStruct);

src/unittests/Makefile.am

@@ -1 +1 @@
 INCLUDES = -I$(top_srcdir)/src
 
-noinst_PROGRAMS =  ActOnAllTest MemoryAllocatorUnitTest MemoryUsageObserverUnitTest VectorUnitTest
+noinst_PROGRAMS =  ActOnAllUnitTest AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest MemoryAllocatorUnitTest MemoryUsageObserverUnitTest VectorUnitTest
 
-TESTS = ActOnAllTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest VectorUnitTest
+TESTS = ActOnAllUnitTest AnalysisCorrelationToPointUnitTest AnalysisCorrelationToSurfaceUnitTest AnalysisPairCorrelationUnitTest MemoryUsageObserverUnitTest MemoryAllocatorUnitTest VectorUnitTest
 check_PROGRAMS = $(TESTS)
 
-ActOnAllTest_SOURCES = ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp memoryallocator.hpp
-ActOnAllTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
-ActOnAllTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
-ActOnAllTest_LDADD = ../libmolecuilder.a
+ActOnAllUnitTest_SOURCES = ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp memoryallocator.hpp
+ActOnAllUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
+ActOnAllUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
+ActOnAllUnitTest_LDADD = ../libmolecuilder.a
 
+AnalysisCorrelationToPointUnitTest_SOURCES = analysis_correlation.hpp AnalysisCorrelationToPointUnitTest.cpp AnalysisCorrelationToPointUnitTest.hpp
+AnalysisCorrelationToPointUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
+AnalysisCorrelationToPointUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
+AnalysisCorrelationToPointUnitTest_LDADD = ../libmolecuilder.a
+
+AnalysisCorrelationToSurfaceUnitTest_SOURCES = analysis_correlation.hpp AnalysisCorrelationToSurfaceUnitTest.cpp AnalysisCorrelationToSurfaceUnitTest.hpp
+AnalysisCorrelationToSurfaceUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
+AnalysisCorrelationToSurfaceUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
+AnalysisCorrelationToSurfaceUnitTest_LDADD = ../libmolecuilder.a
+
+AnalysisPairCorrelationUnitTest_SOURCES = analysis_correlation.hpp AnalysisPairCorrelationUnitTest.cpp AnalysisPairCorrelationUnitTest.hpp
+AnalysisPairCorrelationUnitTest_CXXFLAGS = $(CPPUNIT_CFLAGS)
+AnalysisPairCorrelationUnitTest_LDFLAGS = $(CPPUNIT_LIBS) -ldl
+AnalysisPairCorrelationUnitTest_LDADD = ../libmolecuilder.a
 
 VectorUnitTest_SOURCES = defs.hpp helpers.hpp leastsquaremin.hpp memoryallocator.hpp memoryusageobserver.hpp vectorunittest.cpp vectorunittest.hpp vector.hpp verbose.hpp 

src/vector.cpp

@@ -256 +256 @@
     return false;
   }
+};
+
+/** Calculates the minimum distance of this vector to the plane.
+ * \param *out output stream for debugging
+ * \param *PlaneNormal normal of plane
+ * \param *PlaneOffset offset of plane
+ * \return distance to plane
+ */
+double Vector::DistanceToPlane(ofstream *out, Vector *PlaneNormal, Vector *PlaneOffset)
+{
+  Vector temp;
+
+  // first create part that is orthonormal to PlaneNormal with withdraw
+  temp.CopyVector(this);
+  temp.SubtractVector(PlaneOffset);
+  temp.MakeNormalVector(PlaneNormal);
+  temp.Scale(-1.);
+  // then add connecting vector from plane to point
+  temp.AddVector(this);
+  temp.SubtractVector(PlaneOffset);
+
+  return temp.Norm();
 };
 

src/vector.hpp

@@ -31 +31 @@
   double Distance(const Vector *y) const;
   double DistanceSquared(const Vector *y) const;
+  double DistanceToPlane(ofstream *out, Vector *PlaneNormal, Vector *PlaneOffset);
   double PeriodicDistance(const Vector *y, const double *cell_size) const;
   double PeriodicDistanceSquared(const Vector *y, const double *cell_size) const;