Changeset d4c9ae

Timestamp:

May 20, 2010, 3:51:14 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

93dfc7b

Parents:

5702280

Message:

Removed the DistanceToPlane method in the Vector class in favor of a method that computes the distance to arbitrary spaces

Location:

src

Files:

• Plane.cpp (modified) (1 diff)
• Plane.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (3 diffs)
• tesselation.cpp (modified) (2 diffs)
• tesselation.hpp (modified) (2 diffs)
• tesselationhelpers.cpp (modified) (2 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/Plane.cpp

@@ -91 +91 @@
   offset = normalVector->ScalarProduct(_offsetVector);
 }
+
+/**
+ * copy constructor
+ */
+Plane::Plane(const Plane& plane) :
+  normalVector(new Vector(*plane.normalVector)),
+  offset(plane.offset)
+{}
+
 
 Plane::~Plane()

src/Plane.hpp

@@ -26 +26 @@
   Plane(const Vector &_normalVector, double _offset)  throw(ZeroVectorException);
   Plane(const Vector &_normalVector, const Vector &_offsetVector) throw(ZeroVectorException);
+  Plane(const Plane& plane);
   virtual ~Plane();
 

src/molecule_fragmentation.cpp

@@ -593 +593 @@
     MolecularWalker = MolecularWalker->next;
     // fill the bond structure of the individually stored subgraphs
-  MolecularWalker->FillBondStructureFromReference(this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
+    MolecularWalker->FillBondStructureFromReference(this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
@@ -1672 +1672 @@
   while (flag) {
     // remove bonds that are beyond bonddistance
-    for(int i=NDIM;i--;)
-      Translationvector[i] = 0.;
+    Translationvector.Zero();
     // scan all bonds
     Binder = first;
@@ -1726 +1725 @@
     //delete(CompStack);
   }
-
   // free allocated space from ReturnFullMatrixforSymmetric()
   delete(AtomStack);

src/tesselation.cpp

@@ -21 +21 @@
 #include "Plane.hpp"
 #include "Exceptions/LinearDependenceException.hpp"
+#include "Helpers/Assert.hpp"
 
 class molecule;
@@ -680 +681 @@
   center->Scale(1. / 3.);
   DoLog(1) && (Log() << Verbose(1) << "INFO: Center is at " << *center << "." << endl);
+}
+
+/**
+ * gets the Plane defined by the three triangle Basepoints
+ */
+Plane BoundaryTriangleSet::getPlane() const{
+  ASSERT(endpoints[0] && endpoints[1] && endpoints[2], "Triangle not fully defined");
+
+  return Plane(*endpoints[0]->node->node,
+               *endpoints[1]->node->node,
+               *endpoints[2]->node->node);
 }
 

src/tesselation.hpp

@@ -38 +38 @@
 class PointCloud;
 class Tesselation;
+class Plane;
 
 /********************************************** definitions *********************************/
@@ -165 +166 @@
     bool IsPresentTupel(const BoundaryPointSet * const Points[3]) const;
     bool IsPresentTupel(const BoundaryTriangleSet * const T) const;
+
+    Plane getPlane() const;
 
     class BoundaryPointSet *endpoints[3];

src/tesselationhelpers.cpp

@@ -16 +16 @@
 #include "vector_ops.hpp"
 #include "verbose.hpp"
+#include "Plane.hpp"
 
 double DetGet(gsl_matrix * const A, const int inPlace)
@@ -687 +688 @@
     return -1;
   }
-  distance = x->DistanceToPlane(triangle->NormalVector, *triangle->endpoints[0]->node->node);
+  distance = x->DistanceToSpace(triangle->getPlane());
   return distance;
 };

src/vector.cpp

@@ -266 +266 @@
  * \return distance to plane
  */
-double Vector::DistanceToPlane(const Vector &PlaneNormal, const Vector &PlaneOffset) const
-{
-  return GetDistanceVectorToPlane(PlaneNormal,PlaneOffset).Norm();
+double Vector::DistanceToSpace(const Space &space) const
+{
+  return space.distance(*this);
 };
 

src/vector.hpp

@@ -40 +40 @@
   double DistanceSquared(const Vector &y) const;
   Vector GetDistanceVectorToPlane(const Vector &PlaneNormal, const Vector &PlaneOffset) const;
-  double DistanceToPlane(const Vector &PlaneNormal, const Vector &PlaneOffset) const;
+  double DistanceToSpace(const Space& space) const;
   double PeriodicDistance(const Vector &y, const double * const cell_size) const;
   double PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const;