Changeset 0eb8f4

Timestamp:

Sep 26, 2012, 5:24:33 PM (13 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:

6f0507e

Parents:

52575c

git-author:

Gregor Bollerhey <bollerhe@…> (06/18/12 14:43:14)

git-committer:

Frederik Heber <heber@…> (09/26/12 17:24:33)

Message:

Cylinder implementation.

Taken from somehow broken branch, so rebase was not possible,
unfortunately.

The cylinder shape is centered on (0 0 0) and its height (z-Axis)
ranges from -1 to 1. Different scalings can be applied with the special
constructor.

Location:

src/Shapes

Files:

• BaseShapes.cpp (modified) (2 diffs)
• BaseShapes.hpp (modified) (1 diff)
• BaseShapes_impl.hpp (modified) (1 diff)
• ShapeType.hpp (modified) (1 diff)
• unittests/BaseShapesUnitTest.cpp (modified) (1 diff)
• unittests/BaseShapesUnitTest.hpp (modified) (2 diffs)

src/Shapes/BaseShapes.cpp ¶

@@ -29 +29 @@
 #include "CodePatterns/Assert.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Line.hpp"
 #include "LinearAlgebra/Plane.hpp"
@@ -36 +37 @@
 #include <cmath>
 #include <algorithm>
+
+// CYLINDER CODE
+// ----------------------------------------------------------------------------
+bool Cylinder_impl::isInside(const Vector &point) const {
+  return (Vector(point[0], point[1], 0.0).NormSquared() < 1.0+MYEPSILON) &&
+      (point[2] > -1.0-MYEPSILON) && (point[2] < 1.0+MYEPSILON);
+}
+
+bool Cylinder_impl::isOnSurface(const Vector &point) const {
+  return fabs(Vector(point[0], point[1], 0.0).NormSquared()-1.0)<MYEPSILON &&
+      (point[2] > -1.0-MYEPSILON) && (point[2] < 1.0+MYEPSILON);
+
+}
+
+Vector Cylinder_impl::getNormal(const Vector &point) const throw(NotOnSurfaceException) {
+  if(!isOnSurface(point)){
+    throw NotOnSurfaceException() << ShapeVector(&point);
+  }
+
+  if ((fabs(point[2]-1)<MYEPSILON) || (fabs(point[2])<MYEPSILON))
+      return Vector(0.0, 0.0, point[2]);
+  else
+    return Vector(point[0], point[1], 0.0);
+}
+
+Vector Cylinder_impl::getCenter() const
+{
+  return Vector(0.0, 0.0, 0.0);
+}
+
+double Cylinder_impl::getRadius() const
+{
+    return 1.0;
+}
+
+double Cylinder_impl::getVolume() const
+{
+        return M_PI*2.0; // pi r^2 h
+}
+
+double Cylinder_impl::getSurfaceArea() const
+{
+        return 2.0*M_PI*2.0; // 2 pi r h
+}
+
+LineSegmentSet Cylinder_impl::getLineIntersections(const Line &line) const {
+    // TODO
+        ASSERT(0, "Cylinder_impl::getLineIntersections - not implemented.");
+}
+
+std::string Cylinder_impl::toString() const
+{
+  return "Cylinder()";
+}
+
+enum ShapeType Cylinder_impl::getType() const
+{
+        return CylinderType;
+}
+
+std::vector<Vector> Cylinder_impl::getHomogeneousPointsOnSurface(const size_t N) const {
+    // TODO
+    ASSERT(0, "Cylinder_impl::getHomogeneousPointsOnSurface - not implemented.");
+}
+
+std::vector<Vector> Cylinder_impl::getHomogeneousPointsInVolume(const size_t N) const {
+    // TODO
+    ASSERT(0, "Cylinder_impl::getHomogeneousPointsInVolume - not implemented.");
+}
+
+Shape Cylinder() {
+  Shape::impl_ptr impl = Shape::impl_ptr(new Cylinder_impl());
+  return Shape(impl);
+}
+
+Shape Cylinder(const Vector &center, const double xrot, const double yrot,
+        const double height, const double radius)
+{
+    RealSpaceMatrix rot;
+    rot.setRotation(xrot, yrot, 0.0);
+
+    return translate(
+                transform(
+                    stretch(
+                        Cylinder(),
+                    Vector(radius, radius, height*0.5)),
+                rot),
+            center);
+}
+// ----------------------------------------------------------------------------
 
 bool Sphere_impl::isInside(const Vector &point) const{

src/Shapes/BaseShapes.hpp ¶

@@ -17 +17 @@
 #include "Shapes/Shape.hpp"
 
+Shape Cylinder();
+Shape Cylinder(const Vector &center, const double xrot, const double yrot,
+        const double height, const double radius);
 Shape Sphere();
 Shape Sphere(const Vector &center,double radius);

src/Shapes/BaseShapes_impl.hpp ¶

@@ -21 +21 @@
 #include "Shapes/ShapeExceptions.hpp"
 #include "Shapes/ShapeType.hpp"
+
+class Cylinder_impl : public Shape_impl {
+  virtual bool isInside(const Vector &point) const;
+  virtual bool isOnSurface(const Vector &point) const;
+  virtual Vector getNormal(const Vector &point) const throw(NotOnSurfaceException);
+  virtual Vector getCenter() const;
+  virtual double getRadius() const;
+  virtual double getVolume() const;
+  virtual double getSurfaceArea() const;
+  virtual LineSegmentSet getLineIntersections(const Line&) const;
+  virtual std::string toString() const;
+  virtual enum ShapeType getType() const;
+  virtual std::vector<Vector> getHomogeneousPointsOnSurface(const size_t N) const;
+  virtual std::vector<Vector> getHomogeneousPointsInVolume(const size_t N) const;
+};
 
 class Sphere_impl : public Shape_impl {

src/Shapes/ShapeType.hpp ¶

@@ -22 +22 @@
         PolygonType,
         CombinedType,
-        MAX_ShapeType
+        MAX_ShapeType,
+    CylinderType
 };
 

src/Shapes/unittests/BaseShapesUnitTest.cpp ¶

@@ -78 +78 @@
 {}
 
+void BaseShapesTest::cylinderTest()
+{
+    Shape s = Cylinder();
+    // z = 0
+    // Quadrant 1 1
+    CPPUNIT_ASSERT( s.isInside(v000));
+    CPPUNIT_ASSERT( s.isInside(v100));
+    CPPUNIT_ASSERT(!s.isInside(v110));
+    CPPUNIT_ASSERT( s.isInside(v010));
+    // Quadrant 0 1
+    CPPUNIT_ASSERT(!s.isInside(v210));
+    CPPUNIT_ASSERT( s.isInside(v200));
+    // Quadrant 0 0
+    CPPUNIT_ASSERT(!s.isInside(v220));
+    CPPUNIT_ASSERT( s.isInside(v020));
+    // Quadrant 1 0
+    CPPUNIT_ASSERT(!s.isInside(v120));
+    
+    // z = 1
+    // Quadrant 1 1
+    CPPUNIT_ASSERT( s.isInside(v001));
+    CPPUNIT_ASSERT( s.isInside(v101));
+    CPPUNIT_ASSERT(!s.isInside(v111));
+    CPPUNIT_ASSERT( s.isInside(v011));
+    // Quadrant 0 1
+    CPPUNIT_ASSERT(!s.isInside(v211));
+    CPPUNIT_ASSERT( s.isInside(v201));
+    // Quadrant 0 0
+    CPPUNIT_ASSERT(!s.isInside(v221));
+    CPPUNIT_ASSERT( s.isInside(v021));
+    // Quadrant 1 0
+    CPPUNIT_ASSERT(!s.isInside(v121));
+    
+    // z = 2
+    // Quadrant 1 1
+    CPPUNIT_ASSERT( s.isInside(v002));
+    CPPUNIT_ASSERT( s.isInside(v102));
+    CPPUNIT_ASSERT(!s.isInside(v112));
+    CPPUNIT_ASSERT( s.isInside(v012));
+    // Quadrant 0 1
+    CPPUNIT_ASSERT(!s.isInside(v212));
+    CPPUNIT_ASSERT( s.isInside(v202));
+    // Quadrant 0 0
+    CPPUNIT_ASSERT(!s.isInside(v222));
+    CPPUNIT_ASSERT( s.isInside(v022));
+    // Quadrant 1 0
+    CPPUNIT_ASSERT(!s.isInside(v122));
+
+
+    // More special cylinder
+    s = Cylinder(Vector(0.5, 0.5, 0.0), 0.0, 30.0/180.0*M_PI, 4.0, 1.5);
+
+    CPPUNIT_ASSERT(!s.isInside(v222));
+    CPPUNIT_ASSERT(!s.isInside(v022));
+    CPPUNIT_ASSERT(!s.isInside(v122));
+    CPPUNIT_ASSERT( s.isInside(v202));
+    CPPUNIT_ASSERT( s.isInside(v002));
+    CPPUNIT_ASSERT( s.isInside(v102));
+    CPPUNIT_ASSERT( s.isInside(v212));
+    CPPUNIT_ASSERT( s.isInside(v012));
+    CPPUNIT_ASSERT( s.isInside(v112));
+    
+    CPPUNIT_ASSERT(!s.isInside(v220));
+    CPPUNIT_ASSERT(!s.isInside(v020));
+    CPPUNIT_ASSERT(!s.isInside(v120));
+    CPPUNIT_ASSERT( s.isInside(v200));
+    CPPUNIT_ASSERT( s.isInside(v000));
+    CPPUNIT_ASSERT( s.isInside(v100));
+    CPPUNIT_ASSERT( s.isInside(v210));
+    CPPUNIT_ASSERT( s.isInside(v010));
+    CPPUNIT_ASSERT( s.isInside(v110));
+    
+    CPPUNIT_ASSERT(!s.isInside(v221));
+    CPPUNIT_ASSERT(!s.isInside(v021));
+    CPPUNIT_ASSERT(!s.isInside(v121));
+    CPPUNIT_ASSERT(!s.isInside(v201));
+    CPPUNIT_ASSERT( s.isInside(v001));
+    CPPUNIT_ASSERT( s.isInside(v101));
+    CPPUNIT_ASSERT(!s.isInside(v211));
+    CPPUNIT_ASSERT( s.isInside(v011));
+    CPPUNIT_ASSERT( s.isInside(v111));
+}
 
 void BaseShapesTest::baseShapesTest(){

src/Shapes/unittests/BaseShapesUnitTest.hpp ¶

@@ -30 +30 @@
   CPPUNIT_TEST ( operatorTest );
   CPPUNIT_TEST ( PointsOnSurfaceTest );
+  CPPUNIT_TEST ( cylinderTest );
   CPPUNIT_TEST_SUITE_END();
 
@@ -41 +42 @@
   void operatorTest();
   void PointsOnSurfaceTest();
+  void cylinderTest();
 
   // a lot of vectors.