Changeset 6e5084 for src/Actions/AnalysisAction

Timestamp:

Aug 6, 2010, 1:32:00 PM (15 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:

eaf4ae

Parents:

a439e5

git-author:

Frederik Heber <heber@…> (08/05/10 14:34:18)

git-committer:

Frederik Heber <heber@…> (08/06/10 13:32:00)

Message:

Fixed PrincipalAxisSystemAction.

• PrincipalAxisSystemAction:performCall() now has initial parts of former molecule::PrincipalAxisSystem()
• RotateToPrincipalAxisSystemAction::performCall () now has former molecule::PrincipalAxisSystem()
• call in PrepareClustersinWater() replaced by call to this Action
• changes in PrincipalAxisSystemAction/RotateToPrincipalAxisSystemAction:
  • use Matrix class for InertiaTensor
  • use Vector class for axis
  • use Line class for rotation axis

File:

• src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) (3 diffs)

src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

@@ -10 +10 @@
 #include "Actions/AnalysisAction/PrincipalAxisSystemAction.hpp"
 #include "Actions/ActionRegistry.hpp"
-#include "molecule.hpp"
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
+#include "LinearAlgebra/Matrix.hpp"
+#include "LinearAlgebra/Vector.hpp"
+#include "element.hpp"
+#include "molecule.hpp"
 
 #include <iostream>
@@ -46 +49 @@
 Action::state_ptr AnalysisPrincipalAxisSystemAction::performCall() {
   molecule *mol = NULL;
+  Matrix InertiaTensor;
 
   ValueStorage::getInstance().queryCurrentValue(NAME, mol);
@@ -51 +55 @@
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     molecule *mol = iter->second;
-    mol->PrincipalAxisSystem(false);
+    Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
+
+    // reset inertia tensor
+    InertiaTensor.zero();
+
+    // sum up inertia tensor
+    for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+      Vector x = (*iter)->x;
+      x -= *CenterOfGravity;
+      InertiaTensor.at(0,0) += (*iter)->type->mass*(x[1]*x[1] + x[2]*x[2]);
+      InertiaTensor.at(0,1) += (*iter)->type->mass*(-x[0]*x[1]);
+      InertiaTensor.at(0,2) += (*iter)->type->mass*(-x[0]*x[2]);
+      InertiaTensor.at(1,0) += (*iter)->type->mass*(-x[1]*x[0]);
+      InertiaTensor.at(1,1) += (*iter)->type->mass*(x[0]*x[0] + x[2]*x[2]);
+      InertiaTensor.at(1,2) += (*iter)->type->mass*(-x[1]*x[2]);
+      InertiaTensor.at(2,0) += (*iter)->type->mass*(-x[2]*x[0]);
+      InertiaTensor.at(2,1) += (*iter)->type->mass*(-x[2]*x[1]);
+      InertiaTensor.at(2,2) += (*iter)->type->mass*(x[0]*x[0] + x[1]*x[1]);
+    }
+    // print InertiaTensor for debugging
+    DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << InertiaTensor << endl);
   }
   return Action::success;