Changeset cda81d for src/Actions

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.

File:

• src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (1 diff)

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -50 +50 @@
   // obtain information
   getParametersfromValueStorage();
-
-  // open files
-  ofstream output;
-  ofstream binoutput;
-  output.open(params.outputname.string().c_str());
-  binoutput.open(params.binoutputname.string().c_str());
+  ASSERT(!params.periodic, "AnalysisDipoleAngularCorrelationAction() - periodic case not implemented.");
 
   // get selected atoms
   std::vector<atom*> atoms = World::getInstance().getSelectedAtoms();
-  LOG(0, "STATUS: There are " << atoms.size() << " selected atoms.");
-  ASSERT(!params.periodic, "AnalysisDipoleAngularCorrelationAction() - periodic case not implemented.");
+  ASSERT(!atoms.size(), "AnalysisDipoleAngularCorrelationAction() - not atoms selected.");
 
-  // obtain zero dipole orientation from first time step
+  // get current time step
   const unsigned int oldtime = WorldTime::getTime();
+
+  // obtain zero dipole orientation
   World::getInstance().setTime(0);
   std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(atoms);
+
+  // go through each step of common trajectory of all atoms in set
+  range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
+  for (size_t step = 0; step < timesteps.first; ++step) {
+    // calculate dipoles relative to zero orientation
+    DipoleAngularCorrelationMap *correlationmap = NULL;
+    correlationmap = DipoleAngularCorrelation(atoms, step, ZeroVector);
+
+    // output correlation map
+    ofstream output;
+    std::string filename = params.outputname.string()+"."+toString(step)+".dat";
+    output.open(filename.c_str());
+    OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
+    output.close();
+
+    // bin map
+    BinPairMap *binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
+
+    // free correlation map
+    delete(correlationmap);
+
+    // output binned map
+    ofstream binoutput;
+    std::string binfilename = params.binoutputname.string()+"."+toString(step)+".dat";
+    binoutput.open(binfilename.c_str());
+    OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
+    binoutput.close();
+
+    // free binned map
+    delete(binmap);
+  }
+
+  // reset to old time step
   World::getInstance().setTime(oldtime);
-
-  // calculate dipoles relative to zero orientation and put into maps
-  DipoleAngularCorrelationMap *correlationmap = NULL;
-  correlationmap = DipoleAngularCorrelation(atoms, ZeroVector);
-  OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
-
-  // bin maps
-  BinPairMap *binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
-  OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
-
-  // free maps
-  delete(binmap);
-  delete(correlationmap);
-
-  // close files
-  output.close();
-  binoutput.close();
 
   // exit