Changeset c67ff9 for src/molecule.cpp

Timestamp:

Mar 30, 2012, 9:16:31 AM (14 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, Candidate_v1.7.0, 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.

File:

• src/molecule.cpp (modified) (4 diffs)

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)
+