Changeset f10b0c for src/Actions/AnalysisAction

Timestamp:

Jun 11, 2012, 9:53:19 AM (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, Candidate_v1.7.0, 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:

95f965

Parents:

b9c69d

git-author:

Michael Ankele <ankele@…> (04/24/12 13:55:16)

git-committer:

Frederik Heber <heber@…> (06/11/12 09:53:19)

Message:

disastrously big and ugly commit

• using new Parameter<T> classes:
  • Actions
  • Queries (all UIs)

• TODO:
  • actions crash cause Value is unset
  • no query<BoxVector>

Location:

src/Actions/AnalysisAction

Files:

• DipoleAngularCorrelationAction.cpp (modified) (5 diffs)
• DipoleCorrelationAction.cpp (modified) (1 diff)
• PairCorrelationAction.cpp (modified) (2 diffs)
• PointCorrelationAction.cpp (modified) (1 diff)
• SurfaceCorrelationAction.cpp (modified) (3 diffs)

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -56 +56 @@
 
   // select atoms and obtain zero dipole orientation
-  Formula DipoleFormula(params.DipoleFormula);
-  World::getInstance().setTime(params.timestepzero);
+  Formula DipoleFormula(params.DipoleFormula.get());
+  World::getInstance().setTime(params.timestepzero.get());
   World::getInstance().clearMoleculeSelection(); // TODO: This should be done in setTime or where molecules are re-done
   World::getInstance().selectAllMolecules(MoleculeByFormula(DipoleFormula));
@@ -71 +71 @@
       +toString(DipoleFormula)+" selects no atoms.");
   range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
-  ASSERT(params.timestepzero < timesteps.first,
+  ASSERT(params.timestepzero.get() < timesteps.first,
     "AnalysisDipoleAngularCorrelationAction::performCall() - time step zero "
-    +toString(params.timestepzero)+" is beyond trajectory range ("
+    +toString(params.timestepzero.get())+" is beyond trajectory range ("
     +toString(timesteps.first)+") of some atoms.");
-  for (size_t step = params.timestepzero; step < timesteps.first; ++step) {
+  for (size_t step = params.timestepzero.get(); step < timesteps.first; ++step) {
     // calculate dipoles relative to zero orientation
     DipoleAngularCorrelationMap *correlationmap = NULL;
@@ -87 +87 @@
     // output correlation map
     ofstream output;
-    std::string filename = params.outputname.string()+"."+stepname+".dat";
+    std::string filename = params.outputname.get().string()+"."+stepname+".dat";
     output.open(filename.c_str());
     OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
@@ -93 +93 @@
 
     // bin map
-    BinPairMap *binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
+    BinPairMap *binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
 
     // free correlation map
@@ -100 +100 @@
     // output binned map
     ofstream binoutput;
-    std::string binfilename = params.binoutputname.string()+"."+stepname+".dat";
+    std::string binfilename = params.binoutputname.get().string()+"."+stepname+".dat";
     binoutput.open(binfilename.c_str());
     OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );

src/Actions/AnalysisAction/DipoleCorrelationAction.cpp

@@ -48 +48 @@
 
   // execute action
-  output.open(params.outputname.string().c_str());
-  binoutput.open(params.binoutputname.string().c_str());
+  output.open(params.outputname.get().string().c_str());
+  binoutput.open(params.binoutputname.get().string().c_str());
   DipoleCorrelationMap *correlationmap = NULL;
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   LOG(0, "STATUS: There are " << molecules.size() << " selected molecules.");
-  ASSERT(!params.periodic, "AnalysisDipoleCorrelationAction() - periodic case not implemented.");
+  ASSERT(!params.periodic.get(), "AnalysisDipoleCorrelationAction() - periodic case not implemented.");
   correlationmap = DipoleCorrelation(molecules);
   OutputCorrelationMap<DipoleCorrelationMap>(&output, correlationmap, OutputDipoleCorrelation_Header, OutputDipoleCorrelation_Value);
-  binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
+  binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
   delete(binmap);

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -51 +51 @@
 
   // execute action
-  output.open(params.outputname.string().c_str());
-  binoutput.open(params.binoutputname.string().c_str());
+  output.open(params.outputname.get().string().c_str());
+  binoutput.open(params.binoutputname.get().string().c_str());
   PairCorrelationMap *correlationmap = NULL;
-  ASSERT(params.elements.size() == 2,
+  ASSERT(params.elements.get().size() == 2,
       "AnalysisPairCorrelationAction::performCall() - Exactly two elements are required for pair correlation.");
-  std::vector<const element *>::const_iterator elemiter = params.elements.begin();
+  std::vector<const element *>::const_iterator elemiter = params.elements.get().begin();
   const World::AtomComposite atoms_first = World::getInstance().getAllAtoms(AtomByType(*(elemiter++)));
   const World::AtomComposite atoms_second = World::getInstance().getAllAtoms(AtomByType(*(elemiter++)));
-  ASSERT(elemiter == params.elements.end(),
+  ASSERT(elemiter == params.elements.get().end(),
       "AnalysisPairCorrelationAction::performCall() - Exactly two elements are required for pair correlation.");
-  double max_distance = params.BinEnd;
-  if (params.BinEnd <= 0.) {
+  double max_distance = params.BinEnd.get();
+  if (params.BinEnd.get() <= 0.) {
     // find max distance within box from diagonal
     const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
@@ -69 +69 @@
   correlationmap = PairCorrelation(atoms_first, atoms_second, max_distance);
   OutputCorrelationMap<PairCorrelationMap>(&output, correlationmap, OutputPairCorrelation_Header, OutputPairCorrelation_Value);
-  binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
+  binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
   delete(binmap);

src/Actions/AnalysisAction/PointCorrelationAction.cpp

@@ -50 +50 @@
 
   // execute action
-  output.open(params.outputname.string().c_str());
-  binoutput.open(params.binoutputname.string().c_str());
-  cout << "Point to correlate to is  " << params.Point << endl;
+  output.open(params.outputname.get().string().c_str());
+  binoutput.open(params.binoutputname.get().string().c_str());
+  cout << "Point to correlate to is  " << params.Point.get() << endl;
   CorrelationToPointMap *correlationmap = NULL;
-  for(std::vector<const element *>::iterator iter = params.elements.begin(); iter != params.elements.end(); ++iter)
+  for(std::vector<const element *>::const_iterator iter = params.elements.get().begin(); iter != params.elements.get().end(); ++iter)
     cout << "element is " << (*iter)->getSymbol() << endl;
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
-  if (params.periodic)
-    correlationmap  = PeriodicCorrelationToPoint(molecules, params.elements, &params.Point, ranges);
+  if (params.periodic.get())
+    correlationmap  = PeriodicCorrelationToPoint(molecules, params.elements.get(), &params.Point.get(), ranges);
   else
-    correlationmap = CorrelationToPoint(molecules, params.elements, &params.Point);
+    correlationmap = CorrelationToPoint(molecules, params.elements.get(), &params.Point.get());
   OutputCorrelationMap<CorrelationToPointMap>(&output, correlationmap, OutputCorrelationToPoint_Header, OutputCorrelationToPoint_Value);
-  binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );
+  binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
   delete(binmap);

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -53 +53 @@
 
   // execute action
-  output.open(params.outputname.string().c_str());
-  binoutput.open(params.binoutputname.string().c_str());
-  molecule *surfacemol = const_cast<molecule *>(params.Boundary);
+  output.open(params.outputname.get().string().c_str());
+  binoutput.open(params.binoutputname.get().string().c_str());
+  molecule *surfacemol = const_cast<molecule *>(params.Boundary.get());
   ASSERT(surfacemol != NULL, "No molecule specified for SurfaceCorrelation.");
   const double radius = 4.;
   double LCWidth = 20.;
-  if (params.BinEnd > 0) {
-    if (params.BinEnd > 2.*radius)
-      LCWidth = params.BinEnd;
+  if (params.BinEnd.get() > 0) {
+    if (params.BinEnd.get() > 2.*radius)
+      LCWidth = params.BinEnd.get();
     else
       LCWidth = 2.*radius;
@@ -76 +76 @@
   FindNonConvexBorder(surfacemol, TesselStruct, LCList, radius, NULL);
   CorrelationToSurfaceMap *surfacemap = NULL;
-  if (params.periodic)
-    surfacemap = PeriodicCorrelationToSurface( molecules, params.elements, TesselStruct, LCList, ranges);
+  if (params.periodic.get())
+    surfacemap = PeriodicCorrelationToSurface( molecules, params.elements.get(), TesselStruct, LCList, ranges);
   else
-    surfacemap = CorrelationToSurface( molecules, params.elements, TesselStruct, LCList);
+    surfacemap = CorrelationToSurface( molecules, params.elements.get(), TesselStruct, LCList);
   delete LCList;
   OutputCorrelationMap<CorrelationToSurfaceMap>(&output, surfacemap, OutputCorrelationToSurface_Header, OutputCorrelationToSurface_Value);
@@ -89 +89 @@
       ELOG(1, "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << ".");
   }
-  binmap = BinData( surfacemap, params.BinWidth, params.BinStart, params.BinEnd );
+  binmap = BinData( surfacemap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
   OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
   delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!