Changeset c67ff9

Timestamp:

Mar 30, 2012, 9:16:31 AM (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:

9e1d01

Parents:

8e1f901

git-author:

Frederik Heber <heber@…> (03/21/12 11:56:06)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:16:31)

Message:

Added molecule::getBoundingShape() and unit test MoleculeUnitTest on it.

• We now simply have a function to get a sphere as a suitable bounding shape which allows easy construction of a new cluster.

Location:

src

Files:

• molecule.cpp (modified) (4 diffs)
• molecule.hpp (modified) (6 diffs)
• unittests/Makefile.am (modified) (4 diffs)
• unittests/MoleculeUnitTest.cpp (added)
• unittests/MoleculeUnitTest.hpp (added)

src/molecule.cpp ¶

@@ -44 +44 @@
 #include "LinkedCell/linkedcell.hpp"
 #include "IdPool_impl.hpp"
+#include "Shapes/BaseShapes.hpp"
 #include "Tesselation/tesselation.hpp"
 #include "World.hpp"
@@ -548 +549 @@
 
 /** Creates a copy of this molecule.
+ * \param offset translation Vector for the new molecule relative to old one
  * \return copy of molecule
  */
-molecule *molecule::CopyMolecule() const
+molecule *molecule::CopyMolecule(const Vector &offset) const
 {
   molecule *copy = World::getInstance().createMolecule();
@@ -558 +560 @@
   for (iterator iter = begin(); iter != end(); ++iter) {
     atom * const copy_atom = copy->AddCopyAtom(*iter);
+    copy_atom->setPosition(copy_atom->getPosition() + offset);
     FatherFinder.insert( std::make_pair( *iter, copy_atom ) );
   }
@@ -1022 +1025 @@
 }
 
+Shape molecule::getBoundingShape() const
+{
+  // get center and radius
+  Vector center;
+  double radius = 0.;
+  {
+    center.Zero();
+    for(const_iterator iter = begin(); iter != end(); ++iter)
+      center += (*iter)->getPosition();
+    center *= 1./(double)size();
+    for(const_iterator iter = begin(); iter != end(); ++iter) {
+      const Vector &position = (*iter)->getPosition();
+      const double temp_distance = position.DistanceSquared(center);
+      if (temp_distance > radius)
+        radius = temp_distance;
+    }
+  }
+  // convert radius to true value and add some small boundary
+  radius = sqrt(radius) + 1e+6*std::numeric_limits<double>::epsilon();
+  LOG(1, "INFO: The " << size() << " atoms of the molecule are contained in a sphere at "
+      << center << " with radius " << radius << ".");
+
+  Shape BoundingShape(Sphere(center, radius));
+  LOG(1, "INFO: Created sphere at " << BoundingShape.getCenter() << " and radius "
+      << BoundingShape.getRadius() << ".");
+  return BoundingShape;
+}
+
 // construct idpool
 CONSTRUCT_IDPOOL(atomId_t, continuousId)
+

src/molecule.hpp ¶

@@ -33 +33 @@
 #include "IdPool_policy.hpp"
 #include "IdPool.hpp"
+#include "Shapes/Shape.hpp"
 #include "types.hpp"
 
@@ -49 +50 @@
 class MoleculeLeafClass;
 class MoleculeListClass;
-class periodentafel;
+class MoleculeUnittest;
 class RealSpaceMatrix;
 class Vector;
-class Shape;
 
 /************************************* Class definitions ****************************************/
@@ -61 +61 @@
 class molecule : public Observable
 {
+  //!> grant unit test access
+  friend class MoleculeUnittest;
+  //!> function may access cstor
   friend molecule *NewMolecule();
+  //!> function may access dstor
   friend void DeleteMolecule(molecule *);
 
@@ -138 +142 @@
     return atomIds.find(key);
   }
+
+  /** Returns the set of atomic ids contained in this molecule.
+   *
+   * @return set of atomic ids
+   */
   const atomIdSet & getAtomIds() const {
     return atomIds.getAtomIds();
@@ -189 +198 @@
 
 public:
+
+  /** Function to create a bounding spherical shape for the currently associated atoms.
+   *
+   */
+  Shape getBoundingShape() const;
 
   /// remove atoms from molecule.
@@ -241 +255 @@
   bond * CopyBond(atom *left, atom *right, bond *CopyBond);
 
-  molecule *CopyMolecule() const;
+  molecule *CopyMolecule(const Vector &offset = zeroVec) const;
   molecule* CopyMoleculeFromSubRegion(const Shape&) const;
 

src/unittests/Makefile.am ¶

@@ -33 +33 @@
   FormulaUnittest \
   ListOfBondsUnitTest \
+  MoleculeUnitTest \
   WorldTimeUnitTest
 
@@ -87 +88 @@
   FormulaUnitTest.cpp \
   ListOfBondsUnitTest.cpp \
+  MoleculeUnitTest.cpp \
   WorldTimeUnitTest.cpp
 
@@ -110 +112 @@
   FormulaUnitTest.hpp \
   ListOfBondsUnitTest.hpp \
+  MoleculeUnitTest.hpp \
   WorldTimeUnitTest.hpp
   
@@ -148 +151 @@
 ListOfBondsUnitTest_LDADD = $(ALLLIBS)
 
+MoleculeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
+        MoleculeUnitTest.cpp \
+        MoleculeUnitTest.hpp
+MoleculeUnitTest_LDADD = \
+        ../libMolecuilderUI.la \
+        ../libMolecuilder.la \
+        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la
+
 WorldTimeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         WorldTimeUnitTest.cpp \