Changeset cbd409 for src/molecule.cpp

Timestamp:

Feb 11, 2016, 8:06:48 AM (9 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:

687ef1

Parents:

d93d2c

git-author:

Frederik Heber <heber@…> (01/20/16 20:02:03)

git-committer:

Frederik Heber <heber@…> (02/11/16 08:06:48)

Message:

Added Cacheable MoleculeCenter to molecule which is cleverly updated.

File:

• src/molecule.cpp (modified) (8 diffs)

src/molecule.cpp

@@ -72 +72 @@
 
 // static entities
-static Observable::channels_t getBoundingBoxChannels()
+static Observable::channels_t getAtomPositionsChannels()
 {
   Observable::channels_t channels;
@@ -96 +96 @@
   BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
-  last_atom(0)
+  last_atom(0),
+  molcenter(zeroVec)
 {
   // add specific channels
@@ -107 +108 @@
   BoundingBox.reset(
       new Cacheable<BoundingBoxInfo>(
-          this, boost::bind(&molecule::updateBoundingBox, this), "molecule_BoundingBox", getBoundingBoxChannels()));
+          this, boost::bind(&molecule::updateBoundingBox, this), "molecule_BoundingBox", getAtomPositionsChannels()));
+  MoleculeCenter.reset(
+      new Cacheable<Vector>(
+          this, boost::bind(&molecule::updateMoleculeCenter, this), "molecule_center", getAtomPositionsChannels()));
 
   strcpy(name,World::getInstance().getDefaultName().c_str());
@@ -272 +276 @@
   }
   {
+    molcenter -= _atom->getPosition();
+  }
+  {
     NOTIFY(AtomNrChanged);
     atomIdPool.releaseId(_atom->getNr());
@@ -306 +313 @@
       if (oldinfo != newinfo)
         NOTIFY(BoundingBoxChanged);
+    }
+    {
+      molcenter += key->getPosition();
     }
     NOTIFY(AtomNrChanged);
@@ -1092 +1102 @@
 }
 
+Vector molecule::updateMoleculeCenter() const
+{
+  return (1./(double)getAtomCount())*molcenter;
+}
+
 molecule::BoundingBoxInfo molecule::getBoundingBox() const
 {
   return **BoundingBox;
+}
+
+Vector molecule::getMoleculeCenter() const
+{
+  return **MoleculeCenter;
 }
 
@@ -1116 +1136 @@
         // emit others about one of our atoms moved
         _lastchangedatomid = _atom->getId();
-        // update entry in map
+        // update entry in map and also molecule center
         BoundingBoxInfo oldinfo = updateBoundingBox();
         for (int i=0;i<NDIM;++i) {
@@ -1123 +1143 @@
               "molecule::recieveNotification() - could not find atom "+toString(_atom->getId())
               +" in BoundingBoxSweepingAxis.");
+          molcenter[i] -= iter->second;
           BoundingBoxSweepingAxis[i].left.erase(iter);
+          const Vector &position = _atom->getPosition();
           BoundingBoxSweepingAxis[i].left.insert(
-              std::make_pair(_atom->getId(), _atom->getPosition()[i]) );
+              std::make_pair(_atom->getId(), position[i]) );
+          molcenter[i] += position[i];
         }
         BoundingBoxInfo newinfo = updateBoundingBox();
         OBSERVE;
         NOTIFY(AtomMoved);
+        NOTIFY(MoleculeCenterChanged);
         if (oldinfo != newinfo)
           NOTIFY(BoundingBoxChanged);