Changeset 208237b for src/Analysis

Timestamp:

Oct 25, 2011, 3:28:06 PM (13 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:

df8759

Parents:

5fd0f4

git-author:

Frederik Heber <heber@…> (02/11/11 22:28:51)

git-committer:

Frederik Heber <heber@…> (10/25/11 15:28:06)

Message:

Renamed DipoleAngularCorrelation(Action) -> DipoleCorrelation(Action) and new DipoleAngularCorrelation(Action).

• DipoleCorrelation performs dipole orientation calculation.
• DipoleAngularCorrelation calculates the change in dipole orienation over time.
• new action DipoleAngularCorrelationAction

Location:

src/Analysis

Files:

• analysis_correlation.cpp (modified) (6 diffs)
• analysis_correlation.hpp (modified) (3 diffs)

src/Analysis/analysis_correlation.cpp

@@ -30 +30 @@
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "Formula.hpp"
+#include "LinearAlgebra/Vector.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "Tesselation/tesselation.hpp"
@@ -36 +39 @@
 #include "Tesselation/triangleintersectionlist.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "World.hpp"
-#include "Box.hpp"
+#include "WorldTime.hpp"
 
 #include "analysis_correlation.hpp"
@@ -90 +89 @@
 
 /** Calculates the dipole angular correlation for given molecule type.
+ * Calculate the change of the dipole orientation angle over time.
  * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
  * Angles are given in degrees.
@@ -107 +107 @@
   }
 
-  outmap = new DipoleAngularCorrelationMap;
+  // store original time step
+  const unsigned int oldtime = WorldTime::getTime();
+  World::getInstance().setTime(0);
+
+  // get highest trajectory size
+  size_t max_timesteps = 0;
+  BOOST_FOREACH(molecule *_mol, molecules) {
+    for(molecule::const_iterator iter = _mol->begin();
+        iter != _mol->end();
+        ++iter) {
+      if ((*iter)->getTrajectorySize() > max_timesteps)
+        max_timesteps  = (*iter)->getTrajectorySize();
+    }
+  }
+  // get zero orientation for each molecule.
+  std::vector<Vector> ZeroVector;
+  ZeroVector.resize(molecules.size(), zeroVec);
+  size_t i=0;
+  BOOST_FOREACH(molecule *_mol, molecules) {
+    const Vector Dipole = getDipole(_mol->begin(), _mol->end());
+    ZeroVector[i] = Dipole;
+    ++i;
+  }
+  // go through every time step
+  for (size_t step = 1; step < max_timesteps; ++step) {
+    World::getInstance().setTime(step);
+    size_t i=0;
+    BOOST_FOREACH(molecule *_mol, molecules) {
+      const Vector Dipole = getDipole(_mol->begin(), _mol->end());
+      const double angle = Dipole.Angle(ZeroVector[i]) * (180./M_PI);
+      DoLog(1) && (Log() << Verbose(1) << "Angle for molecule "
+          << _mol->getId() << " at time step " << step << " is " << angle << "." << endl);
+      outmap->insert ( make_pair (angle, _mol ) );
+      ++i;
+    }
+  }
+
+
+  // set original time step again
+  World::getInstance().setTime(oldtime);
+
+  // and return results
+  return outmap;
+};
+
+/** Calculates the dipole correlation for given molecule type.
+ * I.e. we calculate how the angle between any two given dipoles in the
+ * systems behaves. Sort of pair correlation but distance is replaced by
+ * the orientation distance, i.e. an angle.
+ * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
+ * Angles are given in degrees.
+ * \param *molecules vector of molecules
+ * \return Map of doubles with values the pair of the two atoms.
+ */
+DipoleCorrelationMap *DipoleCorrelation(std::vector<molecule *> &molecules)
+{
+  Info FunctionInfo(__func__);
+  DipoleCorrelationMap *outmap = new DipoleCorrelationMap;
+//  double distance = 0.;
+//  Box &domain = World::getInstance().getDomain();
+//
+  if (molecules.empty()) {
+    DoeLog(1) && (eLog()<< Verbose(1) <<"No molecule given." << endl);
+    return outmap;
+  }
+
   for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin();
       MolWalker != molecules.end(); ++MolWalker) {
@@ -503 +568 @@
 void OutputDipoleAngularCorrelation_Header( ofstream * const file )
 {
-  *file << "\tAtom1\tAtom2";
-};
-
-/** Prints values stored in DipoleAngularCorrelationMap iterator.
+  *file << "\tMolecule1\tMolecule2";
+};
+
+/** Prints values stored in DipoleCorrelationMap iterator.
  *
  * @param file stream to print to
@@ -512 +577 @@
  */
 void OutputDipoleAngularCorrelation_Value( ofstream * const file, DipoleAngularCorrelationMap::const_iterator &runner )
+{
+  *file << runner->second->getId();
+};
+
+
+/** Adds header part that is unique to DipoleAngularCorrelationMap.
+ *
+ * @param file stream to print to
+ */
+void OutputDipoleCorrelation_Header( ofstream * const file )
+{
+  *file << "\tMolecule";
+};
+
+/** Prints values stored in DipoleCorrelationMap iterator.
+ *
+ * @param file stream to print to
+ * @param runner iterator pointing at values to print
+ */
+void OutputDipoleCorrelation_Value( ofstream * const file, DipoleCorrelationMap::const_iterator &runner )
 {
   *file << runner->second.first->getId() << "\t" << runner->second.second->getId();

src/Analysis/analysis_correlation.hpp

@@ -46 +46 @@
 
 typedef multimap<double, pair<atom *, atom *> > PairCorrelationMap;
-typedef multimap<double, pair<molecule *, molecule *> > DipoleAngularCorrelationMap;
+typedef multimap<double, molecule * > DipoleAngularCorrelationMap;
+typedef multimap<double, pair<molecule *, molecule *> > DipoleCorrelationMap;
 typedef multimap<double, pair<atom *, const Vector *> > CorrelationToPointMap;
 typedef multimap<double, pair<atom *, BoundaryTriangleSet *> > CorrelationToSurfaceMap;
@@ -54 +55 @@
 
 DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<molecule *> &molecules);
+DipoleCorrelationMap *DipoleCorrelation(std::vector<molecule *> &molecules);
 PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements);
 CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point );
@@ -65 +67 @@
 void OutputDipoleAngularCorrelation_Header( ofstream * const file );
 void OutputDipoleAngularCorrelation_Value( ofstream * const file, DipoleAngularCorrelationMap::const_iterator &runner );
+void OutputDipoleCorrelation_Header( ofstream * const file );
+void OutputDipoleCorrelation_Value( ofstream * const file, DipoleCorrelationMap::const_iterator &runner );
 void OutputPairCorrelation_Header( ofstream * const file );
 void OutputPairCorrelation_Value( ofstream * const file, PairCorrelationMap::const_iterator &runner );