Changeset aeb694 for src

Timestamp:

Sep 19, 2013, 8:24:28 PM (11 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:

d5521e

Parents:

f06cbb

git-author:

Frederik Heber <heber@…> (08/30/13 23:18:46)

git-committer:

Frederik Heber <heber@…> (09/19/13 20:24:28)

Message:

Added molecule::getBoundingShape() (renamed old to ...Sphere()).

• renamed molecule::getBoundingShape() to molecule::getBoundingSphere().
• new molecule::getBoundingShape() creates vdW spheres around every atom.
• for this to be any fast we require the Cacheable change for And and OrShapes.

Location:

src

Files:

• Actions/FillAction/FillRegularGridAction.cpp (modified) (1 diff)
• Actions/FillAction/FillSurfaceAction.cpp (modified) (1 diff)
• UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)
• unittests/MoleculeUnitTest.cpp (modified) (1 diff)
• unittests/MoleculeUnitTest.hpp (modified) (2 diffs)

src/Actions/FillAction/FillRegularGridAction.cpp

@@ -140 +140 @@
     {
       Filler *fillerFunction = new Filler(*mesh, Andpredicate, *inserter);
-      // TODO: When molecule::getBoundingShape() does not use a sphere anymore,
+      // TODO: When molecule::getBoundingSphere() does not use a sphere anymore,
       // we need to check whether we rotate the molecule randomly. For this to
       // work we need a sphere!
-      const Shape s = filler->getBoundingShape(params.RandAtomDisplacement.get());
+      const Shape s = filler->getBoundingSphere(params.RandAtomDisplacement.get());
       ClusterInterface::Cluster_impl cluster( new Cluster(filler->getAtomIds(), s) );
       CopyAtoms_withBonds copyMethod;

src/Actions/FillAction/FillSurfaceAction.cpp

@@ -125 +125 @@
     {
       Filler *fillerFunction = new Filler(*mesh, *voidnode_predicate, *inserter);
-      ClusterInterface::Cluster_impl cluster( new Cluster( filler->getAtomIds(), filler->getBoundingShape() ) );
+      ClusterInterface::Cluster_impl cluster( new Cluster( filler->getAtomIds(), filler->getBoundingSphere() ) );
       CopyAtoms_withBonds copyMethod;
       Filler::ClusterVector_t ClonedClusters;

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

@@ -82 +82 @@
 void GLMoleculeObject_molecule::updateBoundingBox()
 {
-  Shape shape = _molecule->getBoundingShape();
+  Shape shape = _molecule->getBoundingSphere();
   Vector v = shape.getCenter();
   setPosition(QVector3D(v[0], v[1], v[2]));

src/molecule.cpp

@@ -958 +958 @@
 }
 
-Shape molecule::getBoundingShape(const double boundary) const
+Shape molecule::getBoundingShape(const double scale) const
+{
+  // create Sphere around every atom
+  if (empty())
+    return Nowhere();
+  const_iterator iter = begin();
+  const Vector center = (*iter)->getPosition();
+  const double vdWRadius = (*iter)->getElement().getVanDerWaalsRadius();
+  Shape BoundingShape = Sphere(center, vdWRadius*scale);
+  for(++iter; iter != end(); ++iter) {
+    const Vector center = (*iter)->getPosition();
+    const double vdWRadius = (*iter)->getElement().getVanDerWaalsRadius();
+    if (vdWRadius*scale != 0.)
+      BoundingShape = Sphere(center, vdWRadius*scale) || BoundingShape;
+  }
+  return BoundingShape;
+}
+
+Shape molecule::getBoundingSphere(const double boundary) const
 {
   // get center and radius

src/molecule.hpp

@@ -244 +244 @@
    *        and the shape's surface)
    */
-  Shape getBoundingShape(const double boundary = 0.) const;
+  Shape getBoundingSphere(const double boundary = 0.) const;
+
+  /** Creates the bounding box by adding van der Waals-Spheres around every atom.
+   *
+   * \param scale extra scale parameter to enlarge the spheres artifically
+   */
+  Shape getBoundingShape(const double scale = 1.) const;
 
   /// remove atoms from molecule.

src/unittests/MoleculeUnitTest.cpp

@@ -80 +80 @@
 }
 
+/** Unit test for molecule::getBoundingSphere() with a linear chain
+ *
+ */
+void MoleculeUnittest::getBoundingSphereTest_linearchain()
+{
+  // prepare a chain of atoms
+  double offset = 0.;
+  BOOST_FOREACH(atom *_atom, atomVector) {
+    _atom->setPosition( Vector(offset, 0., 0.) );
+    offset += 1.;
+  }
+
+  {
+    // get bounding shape
+    Shape s = mol->getBoundingSphere();
+
+    // check that each atom is truely inside the shape
+    BOOST_FOREACH(atom *_atom, atomVector) {
+      CPPUNIT_ASSERT( s.isInside(_atom->getPosition()) );
+    }
+  }
+}
+
+/** Unit test for molecule::getBoundingSphere() with a v-shaped molecule.
+ *
+ */
+void MoleculeUnittest::getBoundingSphereTest_vshaped()
+{
+  double xoffset = -2.5;
+  double yoffset = -2.5;
+  double yadder = -1;
+  BOOST_FOREACH(atom *_atom, atomVector) {
+    _atom->setPosition( Vector(xoffset, yoffset, 0.) );
+    xoffset += 1.;
+    yoffset -= yadder;
+    if (yoffset <= 0) {
+      yadder = 1.;
+    }
+  }
+
+  {
+    // get bounding shape
+    Shape s = mol->getBoundingSphere();
+
+    // check that each atom is truely inside the shape
+    BOOST_FOREACH(atom *_atom, atomVector) {
+      CPPUNIT_ASSERT( s.isInside(_atom->getPosition()) );
+    }
+  }
+}
+
 /** Unit test for molecule::getBoundingShape() with a linear chain
  *

src/unittests/MoleculeUnitTest.hpp

@@ -25 +25 @@
 {
   CPPUNIT_TEST_SUITE( MoleculeUnittest );
+  CPPUNIT_TEST ( getBoundingSphereTest_linearchain );
+  CPPUNIT_TEST ( getBoundingSphereTest_vshaped );
   CPPUNIT_TEST ( getBoundingShapeTest_linearchain );
   CPPUNIT_TEST ( getBoundingShapeTest_vshaped );
@@ -33 +35 @@
   void tearDown();
 
+  void getBoundingSphereTest_linearchain();
+  void getBoundingSphereTest_vshaped();
   void getBoundingShapeTest_linearchain();
   void getBoundingShapeTest_vshaped();