Changeset ea430a for src

Timestamp:

Feb 3, 2011, 9:51:18 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:

67c92b

Parents:

9df680

git-author:

Frederik Heber <heber@…> (12/15/10 17:23:34)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

Initial versions of DipoleAngularCorrelation().

• no implementation yet, just function signatures.

Location:

src

Files:

• analysis_correlation.cpp (modified) (2 diffs)
• analysis_correlation.hpp (modified) (3 diffs)

src/analysis_correlation.cpp

@@ -28 +28 @@
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Formula.hpp"
 #include "molecule.hpp"
 #include "tesselation.hpp"
@@ -37 +38 @@
 #include "World.hpp"
 #include "Box.hpp"
+
+/** Calculates the dipole angular correlation for given molecule type.
+ * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
+ * \param *molecules vector of molecules
+ * \param &elements vector of elements to correlate
+ * \return Map of doubles with values the pair of the two atoms.
+ */
+DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<molecule *> &molecules, const Formula &formula)
+{
+  Info FunctionInfo(__func__);
+  DipoleAngularCorrelationMap *outmap = NULL;
+//  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++)
+//    (*MolWalker)->doCountAtoms();
+//
+//  // create all possible pairs of elements
+//  set <pair<const element *,const element *> > PairsOfElements;
+//  if (elements.size() >= 2) {
+//    for (vector<const element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
+//      for (vector<const element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
+//        if (type1 != type2) {
+//          PairsOfElements.insert( make_pair(*type1,*type2) );
+//          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << *(*type1) << " and " << *(*type2) << "." << endl);
+//        }
+//  } else if (elements.size() == 1) { // one to all are valid
+//    const element *elemental = *elements.begin();
+//    PairsOfElements.insert( pair<const element *,const element*>(elemental,0) );
+//    PairsOfElements.insert( pair<const element *,const element*>(0,elemental) );
+//  } else { // all elements valid
+//    PairsOfElements.insert( pair<element *, element*>((element *)NULL, (element *)NULL) );
+//  }
+//
+//  outmap = new PairCorrelationMap;
+//  for (std::vector<molecule *>::const_iterator MolWalker = molecules.begin(); MolWalker != molecules.end(); MolWalker++){
+//    DoLog(2) && (Log()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
+//    for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
+//      DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
+//      for (std::vector<molecule *>::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules.end(); MolOtherWalker++){
+//        DoLog(2) && (Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl);
+//        for (molecule::const_iterator runner = (*MolOtherWalker)->begin(); runner != (*MolOtherWalker)->end(); ++runner) {
+//          DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << **runner << "." << endl);
+//          if ((*iter)->getId() < (*runner)->getId()){
+//            for (set <pair<const element *, const element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
+//              if ((PairRunner->first == (**iter).getType()) && (PairRunner->second == (**runner).getType())) {
+//                distance = domain.periodicDistance((*iter)->getPosition(),(*runner)->getPosition());
+//                //Log() << Verbose(1) <<"Inserting " << *(*iter) << " and " << *(*runner) << endl;
+//                outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
+//              }
+//          }
+//        }
+//      }
+//    }
+//  }
+  return outmap;
+};
 
 

src/analysis_correlation.hpp

@@ -33 +33 @@
 
 class BoundaryTriangleSet;
+class Formula;
 class element;
 class LinkedCell;
@@ -41 +42 @@
 
 typedef multimap<double, pair<atom *, atom *> > PairCorrelationMap;
+typedef multimap<double, pair<molecule *, molecule *> > DipoleAngularCorrelationMap;
 typedef multimap<double, pair<atom *, const Vector *> > CorrelationToPointMap;
 typedef multimap<double, pair<atom *, BoundaryTriangleSet *> > CorrelationToSurfaceMap;
@@ -47 +49 @@
 /********************************************** declarations *******************************/
 
+DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<molecule *> &molecules, const Formula &formula);
 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 );