Changeset c550dd for src

Timestamp:

Jul 1, 2010, 2:37:53 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:

4b94bb

Parents:

205d9b

Message:

Removed the VectorIsInParallelepiped in favor of more general methods in the Shape class

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• atom.hpp (modified) (2 diffs)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (2 diffs)
• unittests/vectorunittest.cpp (modified) (1 diff)
• unittests/vectorunittest.hpp (modified) (2 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/atom.cpp

@@ -17 +17 @@
 #include "World.hpp"
 #include "molecule.hpp"
+#include "Shapes/Shape.hpp"
 
 /************************************* Functions for class atom *************************************/
@@ -112 +113 @@
  * \return true - is inside, false - is not
  */
-bool atom::IsInParallelepiped(const Vector offset, const Matrix& parallelepiped) const
-{
-  return (node->IsInParallelepiped(offset, parallelepiped));
+bool atom::IsInShape(const Shape& shape) const
+{
+  return shape.isInside(*node);
 };
 

src/atom.hpp

@@ -35 +35 @@
 class World;
 class molecule;
+class Shape;
 
 /********************************************** declarations *******************************/
@@ -66 +67 @@
   double DistanceToVector(const Vector &origin) const;
   double DistanceSquaredToVector(const Vector &origin) const;
-  bool IsInParallelepiped(const Vector offset, const Matrix &parallelepiped) const;
+  bool IsInShape(const Shape&) const;
 
   // getter and setter

src/molecule.cpp

@@ -659 +659 @@
  * @param three vectors forming the matrix that defines the shape of the parallelpiped
  */
-molecule* molecule::CopyMoleculeFromSubRegion(const Vector offset, const Matrix &parallelepiped) const {
+molecule* molecule::CopyMoleculeFromSubRegion(const Shape &region) const {
   molecule *copy = World::getInstance().createMolecule();
 
   BOOST_FOREACH(atom *iter,atoms){
-    if(iter->IsInParallelepiped(offset,parallelepiped)){
+    if(iter->IsInShape(region)){
       copy->AddCopyAtom(iter);
     }

src/molecule.hpp

@@ -53 +53 @@
 class periodentafel;
 class Vector;
+class Shape;
 
 /******************************** Some definitions for easier reading **********************************/
@@ -316 +317 @@
 
   molecule *CopyMolecule();
-  molecule* CopyMoleculeFromSubRegion(const Vector offset, const Matrix &parallelepiped) const;
+  molecule* CopyMoleculeFromSubRegion(const Shape&) const;
 
   /// Fragment molecule by two different approaches:

src/unittests/vectorunittest.cpp

@@ -215 +215 @@
   CPPUNIT_ASSERT(testVector.ScalarProduct(three) < MYEPSILON);
 }
-
-
-/**
- * UnitTest for Vector::IsInParallelepiped().
- */
-void VectorTest::IsInParallelepipedTest()
-{
-  Matrix parallelepiped;
-  parallelepiped.at(0,0) = 1;
-  parallelepiped.at(1,0) = 0;
-  parallelepiped.at(2,0) = 0;
-  parallelepiped.at(0,1) = 0;
-  parallelepiped.at(1,1) = 1;
-  parallelepiped.at(2,1) = 0;
-  parallelepiped.at(0,2) = 0;
-  parallelepiped.at(1,2) = 0;
-  parallelepiped.at(2,2) = 1;
-
-  fixture = zero;
-  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-  fixture = Vector(2.5,2.5,2.5);
-  CPPUNIT_ASSERT_EQUAL( true, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-  fixture = Vector(1.,1.,1.);
-  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-  fixture = Vector(3.5,3.5,3.5);
-  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-  fixture = Vector(2.,2.,2.);
-  CPPUNIT_ASSERT_EQUAL( true, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-  fixture = Vector(2.,3.,2.);
-  CPPUNIT_ASSERT_EQUAL( true, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-  fixture = Vector(-2.,2.,-1.);
-  CPPUNIT_ASSERT_EQUAL( false, fixture.IsInParallelepiped(Vector(2.,2.,2.), parallelepiped) );
-}
-

src/unittests/vectorunittest.hpp

@@ -27 +27 @@
     CPPUNIT_TEST ( ProjectionTest );
     CPPUNIT_TEST ( NormalsTest );
-    CPPUNIT_TEST ( IsInParallelepipedTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -45 +44 @@
     void LineIntersectionTest();
     void VectorRotationTest();
-    void IsInParallelepipedTest();
 
 private:

src/vector.cpp

@@ -543 +543 @@
 }
 
-/**
- * Checks whether this vector is within the parallelepiped defined by the given three vectors and
- * their offset.
- *
- * @param offest for the origin of the parallelepiped
- * @param three vectors forming the matrix that defines the shape of the parallelpiped
- */
-bool Vector::IsInParallelepiped(const Vector &offset, const Matrix& _parallelepiped) const
-{
-  Matrix parallelepiped = _parallelepiped.invert();
-  Vector a = parallelepiped * ((*this)-offset);
-  bool isInside = true;
-
-  for (int i=NDIM;i--;)
-    isInside = isInside && ((a[i] <= 1) && (a[i] >= 0));
-
-  return isInside;
-}
-
 
 // some comonly used vectors

src/vector.hpp

@@ -60 +60 @@
   bool GetOneNormalVector(const Vector &x1);
   bool MakeNormalTo(const Vector &y1);
-  bool IsInParallelepiped(const Vector &offset, const Matrix& _parallelepiped) const;
   std::pair<Vector,Vector> partition(const Vector&) const;
   std::pair<pointset,Vector> partition(const pointset&) const;