Changeset cda81d for src/Analysis

Timestamp:

Oct 27, 2011, 4:45:47 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:

a2b0ce

Parents:

9e1709

git-author:

Frederik Heber <heber@…> (05/11/11 08:10:27)

git-committer:

Frederik Heber <heber@…> (10/27/11 16:45:47)

Message:

DipoleAngularCorrelation is now calculated per time step not over all time steps combined.

• DipoleAngularCorrelation() gets time step to calculate orientation for.
• AnalysisDipoleAngularCorrelationAction::performCall() loops over all present time steps and calls DipoleAngularCorrelation() for each.

• TESTFIX: Regression tests Analysis/DipoleAngularCorrelation are marked as XFAIL until new tests are installed.

Location:

src/Analysis

Files:

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

src/Analysis/analysis_correlation.cpp

@@ -148 +148 @@
  * \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)
+ * \param timestep time step to calculate angular correlation for (relative to
+ *  \a ZeroVector)
  * \param ZeroVector map with Zero orientation vector for each atom in \a atoms.
- *   Is filled if size of map does not match size of \a atoms.
+ *   Is filled from initial time step if size of map does not match size of \a atoms.
  * \return Map of doubles with values the pair of the two atoms.
  */
 DipoleAngularCorrelationMap *DipoleAngularCorrelation(
     std::vector<atom *> &atoms,
+    const size_t timestep,
     std::map<atomId_t, Vector> &ZeroVector
     )
@@ -160 +163 @@
   DipoleAngularCorrelationMap *outmap = new DipoleAngularCorrelationMap;
 
+  // get zero orientation for each molecule if not given
+  if (ZeroVector.size() != atoms.size()) {
+    ZeroVector.clear();
+    ZeroVector = CalculateZeroAngularDipole(atoms);
+  }
+
   // store original time step
   const unsigned int oldtime = WorldTime::getTime();
-  World::getInstance().setTime(0);
-
-  // calculate molecules for this time step
+
+  // set time step
+  World::getInstance().setTime(timestep);
+
+  // get all molecules for this time step
+  LOG(0,"STATUS: Gathering molecules for time step " << timestep << " ...");
   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 atom if not given
-  if (ZeroVector.size() != atoms.size()) {
-    ZeroVector.clear();
-    ZeroVector = CalculateZeroAngularDipole(atoms);
-  }
-
-  // go through every time step
-  LOG(0,"STATUS: Calculating dipoles of following time steps ...");
-  range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
-  for (size_t step = 1; step < timesteps.first; ++step) {
-    World::getInstance().setTime(step);
-    // recalculate molecules for this time step
-    molecules.clear();
-    BOOST_FOREACH(atom *_atom, atoms)
-      molecules.insert(_atom->getMolecule());
-    size_t i=0;
-    BOOST_FOREACH(molecule *_mol, molecules) {
-      const Vector Dipole = getDipole(_mol->begin(), _mol->end());
-      LOG(2,"INFO: Dipole vector at time step " << step << " for for molecule "
-          << _mol->getId() << " is " << Dipole);
-      molecule::const_iterator iter = _mol->begin();
-      ASSERT(ZeroVector.count((*iter)->getId()),
-          "DipoleAngularCorrelation() - ZeroVector for atom "+toString(**iter)+" not present.");
-      double angle = 0.;
-      LOG(2, "INFO: ZeroVector of first atom " << **iter << " is "
-          << ZeroVector[(*iter)->getId()] << ".");
-      LOG(4, "INFO: Squared norm of difference vector is "
-          << (ZeroVector[(*iter)->getId()] - Dipole).NormSquared() << ".");
-      if ((ZeroVector[(*iter)->getId()] - Dipole).NormSquared() > MYEPSILON)
-        angle = Dipole.Angle(ZeroVector[(*iter)->getId()]) * (180./M_PI);
-      else
-        LOG(2, "INFO: Both vectors (almost) coincide, numerically unstable, angle set to zero.");
-      LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getName()
-          << " is " << angle << ".");
-      outmap->insert ( make_pair (angle, *iter ) );
-      ++i;
-    }
-  }
-
-
-  // set original time step again
+  // calculate dipoles for each
+  LOG(0,"STATUS: Calculating dipoles for time step " << timestep << " ...");
+  size_t i=0;
+  BOOST_FOREACH(molecule *_mol, molecules) {
+    const Vector Dipole = getDipole(_mol->begin(), _mol->end());
+    LOG(2,"INFO: Dipole vector at time step " << timestep << " for for molecule "
+        << _mol->getId() << " is " << Dipole);
+    molecule::const_iterator iter = _mol->begin();
+    ASSERT(ZeroVector.count((*iter)->getId()),
+        "DipoleAngularCorrelation() - ZeroVector for atom "+toString(**iter)+" not present.");
+    double angle = 0.;
+    LOG(2, "INFO: ZeroVector of first atom " << **iter << " is "
+        << ZeroVector[(*iter)->getId()] << ".");
+    LOG(4, "INFO: Squared norm of difference vector is "
+        << (ZeroVector[(*iter)->getId()] - Dipole).NormSquared() << ".");
+    if ((ZeroVector[(*iter)->getId()] - Dipole).NormSquared() > MYEPSILON)
+      angle = Dipole.Angle(ZeroVector[(*iter)->getId()]) * (180./M_PI);
+    else
+      LOG(2, "INFO: Both vectors (almost) coincide, numerically unstable, angle set to zero.");
+    LOG(1,"INFO: Resulting relative angle for molecule " << _mol->getName()
+        << " is " << angle << ".");
+    outmap->insert ( make_pair (angle, *iter ) );
+    ++i;
+  }
+
+  // re-set to original time step again
   World::getInstance().setTime(oldtime);
   LOG(0,"STATUS: Done.");

src/Analysis/analysis_correlation.hpp

@@ -58 +58 @@
 std::map<atomId_t, Vector> CalculateZeroAngularDipole(std::vector<atom *> &atoms);
 
-DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms, std::map<atomId_t, Vector> &ZeroVector);
+DipoleAngularCorrelationMap *DipoleAngularCorrelation(std::vector<atom *> &atoms, const size_t timestep, std::map<atomId_t, Vector> &ZeroVector);
 DipoleCorrelationMap *DipoleCorrelation(std::vector<molecule *> &molecules);
 PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements);