Changeset 1f91f4

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.

Location:

src

Files:

• Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) (1 diff)
• boundary.cpp (modified) (2 diffs)
• molecule.hpp (modified) (2 diffs)
• molecule_geometry.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();
 

src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

@@ -50 +50 @@
     mol = iter->second;
     DoLog(0) && (Log() << Verbose(0) << "Converting to prinicipal axis system." << endl);
-    RealSpaceMatrix InertiaTensor;
-    Vector *CenterOfGravity = mol->DetermineCenterOfGravity();
 
-    // reset inertia tensor
-    InertiaTensor.setZero();
+    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 for debugging
-    DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << InertiaTensor << endl);
-
-    // diagonalize to determine principal axis system
-    Vector Eigenvalues = InertiaTensor.transformToEigenbasis();
-
-    for(int i=0;i<NDIM;i++)
-      DoLog(0) && (Log() << Verbose(0) << "eigenvalue = " << Eigenvalues[i] << ", eigenvector = " << InertiaTensor.column(i) << endl);
-
-    // check whether we rotate or not
-    DoLog(0) && (Log() << Verbose(0) << "Transforming molecule into PAS ... ");
-
-    // obtain first column, eigenvector to biggest eigenvalue
-    Vector BiggestEigenvector(InertiaTensor.column(Eigenvalues.SmallestComponent()));
-    Vector DesiredAxis(params.Axis);
-
-    // Creation Line that is the rotation axis
-    DesiredAxis.VectorProduct(BiggestEigenvector);
-    Line RotationAxis(Vector(0.,0.,0.), DesiredAxis);
-
-    // determine angle
-    const double alpha = BiggestEigenvector.Angle(params.Axis);
-
-    DoLog(0) && (Log() << Verbose(0) << alpha << endl);
-
-    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      *(*iter) -= *CenterOfGravity;
-      (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
-      *(*iter) += *CenterOfGravity;
-    }
-    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
+    mol->RotateToPrincipalAxisSystem(params.Axis);
 
     // summing anew for debugging (resulting matrix has to be diagonal!)
-    // reset inertia tensor
-    InertiaTensor.setZero();
-
-    // 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 for debugging
-      DoLog(0) && (Log() << Verbose(0) << "The inertia tensor is:" << InertiaTensor << endl);
-    }
-
-    // free everything
-    delete(CenterOfGravity);
+    InertiaTensor = mol->getInertiaTensor();
   }
   return Action::success;

src/boundary.cpp

@@ -18 +18 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
 #include "BoundaryPointSet.hpp"
 #include "BoundaryLineSet.hpp"
@@ -693 +692 @@
   // transform to PAS by Action
   Vector MainAxis(0.,0.,1.);
-  MoleculeRotateToPrincipalAxisSystem(MainAxis);
+  mol->RotateToPrincipalAxisSystem(MainAxis);
 
   IsAngstroem = configuration->GetIsAngstroem();

src/molecule.hpp

@@ -47 +47 @@
 class MoleculeListClass;
 class periodentafel;
+class RealSpaceMatrix;
 class Vector;
 class Shape;
@@ -208 +209 @@
   bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
   double VolumeOfConvexEnvelope(bool IsAngstroem);
+  RealSpaceMatrix getInertiaTensor() const;
+  void RotateToPrincipalAxisSystem(Vector &Axis);
 
   double ConstrainedPotential(struct EvaluatePotential &Params);

src/molecule_geometry.cpp

@@ -225 +225 @@
 };
 
+/** Calculate the inertia tensor of a the molecule.
+ *
+ * @return inertia tensor
+ */
+RealSpaceMatrix molecule::getInertiaTensor() const
+{
+  RealSpaceMatrix InertiaTensor;
+  Vector *CenterOfGravity = DetermineCenterOfGravity();
+
+  // reset inertia tensor
+  InertiaTensor.setZero();
+
+  // sum up inertia tensor
+  for (molecule::const_iterator iter = begin(); iter != 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 "
+      << getName() <<  " is:"
+      << InertiaTensor << endl);
+
+  delete CenterOfGravity;
+  return InertiaTensor;
+}
+
+/** Rotates the molecule in such a way that biggest principal axis corresponds
+ * to given \a Axis.
+ *
+ * @param Axis Axis to align with biggest principal axis
+ */
+void molecule::RotateToPrincipalAxisSystem(Vector &Axis)
+{
+  Vector *CenterOfGravity = DetermineCenterOfGravity();
+  RealSpaceMatrix InertiaTensor = getInertiaTensor();
+
+  // diagonalize to determine principal axis system
+  Vector Eigenvalues = InertiaTensor.transformToEigenbasis();
+
+  for(int i=0;i<NDIM;i++)
+    DoLog(0) && (Log() << Verbose(0) << "eigenvalue = " << Eigenvalues[i] << ", eigenvector = " << InertiaTensor.column(i) << endl);
+
+  DoLog(0) && (Log() << Verbose(0) << "Transforming to PAS ... ");
+
+  // obtain first column, eigenvector to biggest eigenvalue
+  Vector BiggestEigenvector(InertiaTensor.column(Eigenvalues.SmallestComponent()));
+  Vector DesiredAxis(Axis);
+
+  // Creation Line that is the rotation axis
+  DesiredAxis.VectorProduct(BiggestEigenvector);
+  Line RotationAxis(Vector(0.,0.,0.), DesiredAxis);
+
+  // determine angle
+  const double alpha = BiggestEigenvector.Angle(Axis);
+
+  DoLog(0) && (Log() << Verbose(0) << "Rotation angle is " << alpha << endl);
+
+  // and rotate
+  for (molecule::iterator iter = begin(); iter != end(); ++iter) {
+    *(*iter) -= *CenterOfGravity;
+    (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
+    *(*iter) += *CenterOfGravity;
+  }
+  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
+
+  delete CenterOfGravity;
+}
 
 /** Scales all atoms by \a *factor.