Changeset 0a7fad

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:

325687

Parents:

1cc661

git-author:

Frederik Heber <heber@…> (05/11/11 07:46:24)

git-committer:

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

Message:

Refactored part of code in DipoleAngularCorrelation into new method CalculateZeroAngularDipole().

Location:

src/Analysis

Files:

• analysis_correlation.cpp (modified) (2 diffs)
• analysis_correlation.hpp (modified) (1 diff)

src/Analysis/analysis_correlation.cpp

@@ -117 +117 @@
 }
 
-
-/** 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.
- * \param &atoms list of atoms of the molecules taking part (Note: molecules may
- * change over time as bond structure is recalculated, hence we need the atoms)
- * \return Map of doubles with values the pair of the two atoms.
- */
-DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms)
-{
-  Info FunctionInfo(__func__);
-  DipoleAngularCorrelationMap *outmap = new DipoleAngularCorrelationMap;
+/** Calculates the angular dipole zero orientation from current time step.
+ * \param atoms vector of atoms to calculate it for
+ * \return map with orientation vector for each atomic id given in \a atoms.
+ */
+std::map<atomId_t, Vector> CalculateZeroAngularDipole(std::vector<atom *> &atoms)
+{
+  // calculate molecules for this time step
   std::set<molecule *> molecules;
-
-  // store original time step
-  const unsigned int oldtime = WorldTime::getTime();
-  World::getInstance().setTime(0);
-  // calculate molecules for this time step
   BOOST_FOREACH(atom *_atom, atoms)
     molecules.insert(_atom->getMolecule());
-
-  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
-    LOG(2, "INFO: Atom " << _atom->getId() << " "
-        << *dynamic_cast<AtomInfo *>(_atom) <<".");
-
 
   // get zero orientation for each molecule.
@@ -153 +137 @@
     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.");
+  LOG(1,"INFO: We calculated zero orientation for a total of " << molecules.size() << " molecule(s).");
+
+  return ZeroVector;
+}
+
+/** 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.
+ * \param &atoms list of atoms of the molecules taking part (Note: molecules may
+ * change over time as bond structure is recalculated, hence we need the atoms)
+ * \return Map of doubles with values the pair of the two atoms.
+ */
+DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms)
+{
+  Info FunctionInfo(__func__);
+  DipoleAngularCorrelationMap *outmap = new DipoleAngularCorrelationMap;
+
+  // store original time step
+  const unsigned int oldtime = WorldTime::getTime();
+  World::getInstance().setTime(0);
+
+  // calculate molecules for this time step
+  std::set<molecule *> molecules;
+  BOOST_FOREACH(atom *_atom, atoms)
+    molecules.insert(_atom->getMolecule());
+
+  BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
+    LOG(2, "INFO: Atom " << _atom->getId() << " "
+        << *dynamic_cast<AtomInfo *>(_atom) <<".");
+
+
+  // get zero orientation for each molecule.
+  std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(atoms);
 
   // go through every time step

src/Analysis/analysis_correlation.hpp

@@ -56 +56 @@
 
 range<size_t> getMaximumTrajectoryBounds(std::vector<atom *> &atoms);
+std::map<atomId_t, Vector> CalculateZeroAngularDipole(std::vector<atom *> &atoms);
 
 DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms);