Changeset 1f91f4 for src/Actions/AnalysisAction

Timestamp:

Feb 3, 2011, 9:51:19 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, 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:

3f9eba

Parents:

4782599

git-author:

Frederik Heber <heber@…> (01/10/11 22:31:40)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:19)

Message:

factored functionality in PrincipalAxisSystemAction() and RotateToPrincipalAxisSystemAction() into class molecule:

• new functions in molecule
  • getInertiaTensor()
  • RotateToPrincipalAxisSystem()
• PrepareClustersinWater() then does not need to call an Action anymore.

File:

• src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) (1 diff)

src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

@@ -40 +40 @@
 /** =========== define the function ====================== */
 Action::state_ptr AnalysisPrincipalAxisSystemAction::performCall() {
-  RealSpaceMatrix InertiaTensor;
-
   DoLog(0) && (Log() << Verbose(0) << "Evaluating prinicipal axis." << endl);
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     molecule *mol = iter->second;
-    Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
 
-    // reset inertia tensor
-    InertiaTensor.setZero();
+    // get inertia tensor
+    RealSpaceMatrix InertiaTensor = mol->getInertiaTensor();
 
-    // sum up inertia tensor
-    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      Vector x = (*iter)->getPosition();
-      x -= *CenterOfGravity;
-      const double mass = (*iter)->getType()->getMass();
-      InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
-      InertiaTensor.at(0,1) += mass*(-x[0]*x[1]);
-      InertiaTensor.at(0,2) += mass*(-x[0]*x[2]);
-      InertiaTensor.at(1,0) += mass*(-x[1]*x[0]);
-      InertiaTensor.at(1,1) += mass*(x[0]*x[0] + x[2]*x[2]);
-      InertiaTensor.at(1,2) += mass*(-x[1]*x[2]);
-      InertiaTensor.at(2,0) += mass*(-x[2]*x[0]);
-      InertiaTensor.at(2,1) += mass*(-x[2]*x[1]);
-      InertiaTensor.at(2,2) += mass*(x[0]*x[0] + x[1]*x[1]);
-    }
-    // print InertiaTensor
-    DoLog(0) && (Log() << Verbose(0) << "The inertia tensor of molecule "
-        << mol->getName() <<  " is:"
-        << InertiaTensor << endl);
-
-    // diagonalize matrix
+                // diagonalize matrix
     Vector EigenValues = InertiaTensor.transformToEigenbasis();