Changeset be0c61

Timestamp:

Oct 25, 2011, 3:33:14 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:

1cc661

Parents:

4b8630

git-author:

Frederik Heber <heber@…> (05/11/11 07:42:43)

git-committer:

Frederik Heber <heber@…> (10/25/11 15:33:14)

Message:

FIX: DipoleAngularCorrelation() - ZeroVector is now map over atoms, not vector over molecules.

• Molecules are not consistent over trajectories, atoms however are.
• hence, we store the ZeroVector for each atom of a molecule, not per molecule.

File:

• src/Analysis/analysis_correlation.cpp (modified) (2 diffs)

src/Analysis/analysis_correlation.cpp

@@ -139 +139 @@
   // get zero orientation for each molecule.
   LOG(0,"STATUS: Calculating dipoles for first time step ...");
-  std::vector<Vector> ZeroVector;
-  ZeroVector.resize(molecules.size(), zeroVec);
-  size_t i=0;
+  std::map<atomId_t, Vector> ZeroVector;
   BOOST_FOREACH(molecule *_mol, molecules) {
     const Vector Dipole = getDipole(_mol->begin(), _mol->end());
-    ZeroVector[i] = Dipole;
-    LOG(2,"INFO: Zero alignment for molecule " << _mol->getId() << " is " << ZeroVector[i]);
-    ++i;
-  }
-  LOG(1,"INFO: There is a total of " << i << " molecules.");
+    for(molecule::const_iterator iter = _mol->begin(); iter != _mol->end(); ++iter)
+      ZeroVector[(*iter)->getId()] = Dipole;
+    LOG(2,"INFO: Zero alignment for molecule " << _mol->getId() << " is " << Dipole);
+  }
+  LOG(1,"INFO: We calculated zero orientation for a total of " << molecules.size() << " molecules.");
 
   // go through every time step
@@ -162 +160 @@
       const Vector Dipole = getDipole(_mol->begin(), _mol->end());
       LOG(2,"INFO: Dipole vector at time step " << step << " for for molecule " << _mol->getId() << " is " << Dipole);
-      const double angle = Dipole.Angle(ZeroVector[i]) * (180./M_PI);
-      LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getId() << " is " << angle << ".");
-      outmap->insert ( make_pair (angle, *_mol->begin() ) );
+      molecule::const_iterator iter = _mol->begin();
+      ASSERT(ZeroVector.count((*iter)->getId()),
+          "DipoleAngularCorrelation() - ZeroVector for atom "+toString(**iter)+" not present.");
+      const double angle = Dipole.Angle(ZeroVector[(*iter)->getId()]) * (180./M_PI);
+      LOG(1,"INFO: Resulting relative angle for molecule " << **iter << " is " << angle << ".");
+      outmap->insert ( make_pair (angle, *iter ) );
       ++i;
     }