Changeset d02e07 for src

Timestamp:

Jul 22, 2010, 7:11:35 PM (15 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:

75dc28

Parents:

0c9cc3

Message:

Split PairCorrelation into Pair, Point and SurfaceCorrelation.

• also converted to new createDialog().

Location:

src/Actions

Files:

• AnalysisAction/PairCorrelationAction.cpp (modified) (2 diffs)
• AnalysisAction/PairCorrelationAction.hpp (modified) (1 diff)
• AnalysisAction/PointCorrelationAction.cpp (added)
• AnalysisAction/PointCorrelationAction.hpp (added)
• AnalysisAction/SurfaceCorrelationAction.cpp (added)
• AnalysisAction/SurfaceCorrelationAction.hpp (added)
• Makefile.am (modified) (1 diff)
• MapOfActions.cpp (modified) (5 diffs)
• MapOfActions.hpp (modified) (4 diffs)

src/Actions/AnalysisAction/PairCorrelationAction.cpp ¶

@@ -38 +38 @@
 {}
 
+Dialog* AnalysisPairCorrelationAction::createDialog() {
+  Dialog *dialog = UIFactory::getInstance().makeDialog();
+  int ranges[3] = {1, 1, 1};
+  double BinEnd = 0.;
+  double BinStart = 0.;
+  double BinWidth = 0.;
+  molecule *Boundary = NULL;
+  string outputname;
+  string binoutputname;
+  bool periodic;
+  ofstream output;
+  ofstream binoutput;
+  std::vector< element *> elements;
+  string type;
+  Vector Point;
+  BinPairMap *binmap = NULL;
+
+  dialog->queryElement("elements", &elements, MapOfActions::getInstance().getDescription("elements"));
+  dialog->queryDouble("bin-start", &BinStart, MapOfActions::getInstance().getDescription("bin-start"));
+  dialog->queryDouble("bin-width", &BinWidth, MapOfActions::getInstance().getDescription("bin-width"));
+  dialog->queryDouble("bin-end", &BinEnd, MapOfActions::getInstance().getDescription("bin-end"));
+  dialog->queryString("output-file", &outputname, MapOfActions::getInstance().getDescription("output-file"));
+  dialog->queryString("bin-output-file", &binoutputname, MapOfActions::getInstance().getDescription("bin-output-file"));
+  dialog->queryBoolean("periodic", &periodic, MapOfActions::getInstance().getDescription("periodic"));
+
+  return dialog;
+}
+
 Action::state_ptr AnalysisPairCorrelationAction::performCall() {
-  Dialog *dialog = UIFactory::getInstance().makeDialog();
   int ranges[3] = {1, 1, 1};
   double BinEnd = 0.;
@@ -56 +83 @@
   MoleculeListClass *molecules = World::getInstance().getMolecules();
 
-  // first dialog: Obtain which type of correlation
-  dialog->queryString(NAME, &type, MapOfActions::getInstance().getDescription(NAME));
-  if(dialog->display()) {
-    delete dialog;
-  } else {
-    delete dialog;
-    return Action::failure;
-  }
+  // obtain information
+  MapOfActions::getInstance().queryCurrentValue("elements", elements);
+  MapOfActions::getInstance().queryCurrentValue("bin-start", BinStart);
+  MapOfActions::getInstance().queryCurrentValue("bin-width", BinWidth);
+  MapOfActions::getInstance().queryCurrentValue("bin-end", BinEnd);
+  MapOfActions::getInstance().queryCurrentValue("output-file", outputname);
+  MapOfActions::getInstance().queryCurrentValue("bin-output-file", binoutputname);
+  MapOfActions::getInstance().queryCurrentValue("periodic", periodic);
 
-  // second dialog: Obtain parameters specific to this type
-  dialog = UIFactory::getInstance().makeDialog();
-  if (type == "P")
-    dialog->queryVector("position", &Point, false, MapOfActions::getInstance().getDescription("position"));
-  if (type == "S")
-    dialog->queryMolecule("molecule-by-id", &Boundary, MapOfActions::getInstance().getDescription("molecule-by-id"));
-  dialog->queryElement("elements", &elements, MapOfActions::getInstance().getDescription("elements"));
-  dialog->queryDouble("bin-start", &BinStart, MapOfActions::getInstance().getDescription("bin-start"));
-  dialog->queryDouble("bin-width", &BinWidth, MapOfActions::getInstance().getDescription("bin-width"));
-  dialog->queryDouble("bin-end", &BinEnd, MapOfActions::getInstance().getDescription("bin-end"));
-  dialog->queryString("output-file", &outputname, MapOfActions::getInstance().getDescription("output-file"));
-  dialog->queryString("bin-output-file", &binoutputname, MapOfActions::getInstance().getDescription("bin-output-file"));
-  dialog->queryBoolean("periodic", &periodic, MapOfActions::getInstance().getDescription("periodic"));
-
-  if(dialog->display()) {
-    output.open(outputname.c_str());
-    binoutput.open(binoutputname.c_str());
-    if (type == "E") {
-      PairCorrelationMap *correlationmap = NULL;
-      if (periodic)
-        correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elements, ranges);
-      else
-        correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
-      OutputPairCorrelation(&output, correlationmap);
-      binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
-      OutputCorrelation ( &binoutput, binmap );
-      delete(binmap);
-      delete(correlationmap);
-    } else if (type == "P")  {
-      cout << "Point to correlate to is  " << Point << endl;
-      CorrelationToPointMap *correlationmap = NULL;
-      if (periodic)
-        correlationmap  = PeriodicCorrelationToPoint(molecules, elements, &Point, ranges);
-      else
-        correlationmap = CorrelationToPoint(molecules, elements, &Point);
-      OutputCorrelationToPoint(&output, correlationmap);
-      binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
-      OutputCorrelation ( &binoutput, binmap );
-      delete(binmap);
-      delete(correlationmap);
-    } else if (type == "S") {
-      ASSERT(Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
-      const double radius = 4.;
-      double LCWidth = 20.;
-      if (BinEnd > 0) {
-        if (BinEnd > 2.*radius)
-          LCWidth = BinEnd;
-        else
-          LCWidth = 2.*radius;
-      }
-
-      // get the boundary
-      class Tesselation *TesselStruct = NULL;
-      const LinkedCell *LCList = NULL;
-      // find biggest molecule
-      int counter  = molecules->ListOfMolecules.size();
-      bool *Actives = new bool[counter];
-      counter = 0;
-      for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-        Actives[counter++] = (*BigFinder)->ActiveFlag;
-        (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
-      }
-      LCList = new LinkedCell(Boundary, LCWidth);
-      FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
-      CorrelationToSurfaceMap *surfacemap = NULL;
-      if (periodic)
-        surfacemap = PeriodicCorrelationToSurface( molecules, elements, TesselStruct, LCList, ranges);
-      else
-        surfacemap = CorrelationToSurface( molecules, elements, TesselStruct, LCList);
-      delete LCList;
-      OutputCorrelationToSurface(&output, surfacemap);
-      // re-set ActiveFlag
-      counter = 0;
-      for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-        (*BigFinder)->ActiveFlag = Actives[counter++];
-      }
-      delete[] Actives;
-      // check whether radius was appropriate
-      {
-        double start; double end;
-        GetMinMax( surfacemap, start, end);
-        if (LCWidth < end)
-          DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
-      }
-      binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
-      OutputCorrelation ( &binoutput, binmap );
-      delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!
-      delete(binmap);
-      delete(surfacemap);
-    } else {
-      return Action::failure;
-    }
-    output.close();
-    binoutput.close();
-    delete dialog;
-    return Action::success;
-  } else {
-    delete dialog;
-    return Action::failure;
-  }
+  // execute action
+  output.open(outputname.c_str());
+  binoutput.open(binoutputname.c_str());
+  PairCorrelationMap *correlationmap = NULL;
+  if (periodic)
+    correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elements, ranges);
+  else
+    correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
+  OutputPairCorrelation(&output, correlationmap);
+  binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+  OutputCorrelation ( &binoutput, binmap );
+  delete(binmap);
+  delete(correlationmap);
+  output.close();
+  binoutput.close();
+  return Action::success;
 }
 
 Action::state_ptr AnalysisPairCorrelationAction::performUndo(Action::state_ptr _state) {
-//  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
-
-  return Action::failure;
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
-//
-//  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
+  return Action::success;
 }
 
 Action::state_ptr AnalysisPairCorrelationAction::performRedo(Action::state_ptr _state){
-  return Action::failure;
+  return Action::success;
 }
 
 bool AnalysisPairCorrelationAction::canUndo() {
-  return false;
+  return true;
 }
 
 bool AnalysisPairCorrelationAction::shouldUndo() {
-  return false;
+  return true;
 }
 

src/Actions/AnalysisAction/PairCorrelationAction.hpp ¶

@@ -21 +21 @@
   virtual const std::string getName();
 private:
+  virtual Dialog * createDialog();
   virtual Action::state_ptr performCall();
   virtual Action::state_ptr performUndo(Action::state_ptr);

src/Actions/Makefile.am ¶

@@ -36 +36 @@
   AnalysisAction/MolecularVolumeAction.cpp \
   AnalysisAction/PairCorrelationAction.cpp \
-  AnalysisAction/PrincipalAxisSystemAction.cpp
+  AnalysisAction/PointCorrelationAction.cpp \
+  AnalysisAction/PrincipalAxisSystemAction.cpp \
+  AnalysisAction/SurfaceCorrelationAction.cpp
 ANALYSISACTIONHEADER = \
   AnalysisAction/MolecularVolumeAction.hpp \
   AnalysisAction/PairCorrelationAction.hpp \
-  AnalysisAction/PrincipalAxisSystemAction.hpp
+  AnalysisAction/PointCorrelationAction.hpp \
+  AnalysisAction/PrincipalAxisSystemAction.hpp \
+  AnalysisAction/SurfaceCorrelationAction.hpp
 
 ATOMACTIONSOURCE = \

src/Actions/MapOfActions.cpp ¶

@@ -10 +10 @@
 using namespace std;
 
+#include "Actions/MapOfActions.hpp"
+#include "Descriptors/AtomIdDescriptor.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Patterns/Singleton_impl.hpp"
-#include "Actions/MapOfActions.hpp"
 #include "Helpers/Assert.hpp"
 
@@ -21 +23 @@
 
 #include "atom.hpp"
+#include "Box.hpp"
 #include "CommandLineParser.hpp"
 #include "element.hpp"
 #include "log.hpp"
+#include "Matrix.hpp"
 #include "molecule.hpp"
+#include "periodentafel.hpp"
+#include "vector.hpp"
 #include "verbose.hpp"
 
@@ -30 +36 @@
 #include "Actions/AnalysisAction/MolecularVolumeAction.hpp"
 #include "Actions/AnalysisAction/PairCorrelationAction.hpp"
+#include "Actions/AnalysisAction/PointCorrelationAction.hpp"
 #include "Actions/AnalysisAction/PrincipalAxisSystemAction.hpp"
+#include "Actions/AnalysisAction/SurfaceCorrelationAction.hpp"
 #include "Actions/AtomAction/AddAction.hpp"
 #include "Actions/AtomAction/ChangeElementAction.hpp"
@@ -497 +505 @@
 }
 
+void MapOfActions::queryCurrentValue(const char * name, class atom * &_T)
+{
+  int atomID = -1;
+  if (typeid( atom ) == *TypeMap[name])
+    atomID = lexical_cast<int>(CurrentValue[name].c_str());
+  else
+    throw IllegalTypeException(__FILE__,__LINE__);
+  _T = World::getInstance().getAtom(AtomById(atomID));
+}
+
+void MapOfActions::queryCurrentValue(const char * name, class element * &_T)  {
+  int Z = -1;
+  if (typeid( element ) == *TypeMap[name])
+    Z = lexical_cast<int>(CurrentValue[name].c_str());
+  else
+    throw IllegalTypeException(__FILE__,__LINE__);
+  _T = World::getInstance().getPeriode()->FindElement(Z);
+}
+
+void MapOfActions::queryCurrentValue(const char * name, class molecule * &_T) {
+  int molID = -1;
+  if (typeid( molecule ) == *TypeMap[name])
+    molID = lexical_cast<int>(CurrentValue[name].c_str());
+  else
+    throw IllegalTypeException(__FILE__,__LINE__);
+  _T = World::getInstance().getMolecule(MoleculeById(molID));
+}
+
+void MapOfActions::queryCurrentValue(const char * name, class Box &_T) {
+  Matrix M;
+  double tmp;
+  if (typeid( BoxValue ) == *TypeMap[name]) {
+    std::istringstream stream(CurrentValue[name]);
+    stream >> tmp;
+    M.set(0,0,tmp);
+    stream >> tmp;
+    M.set(0,1,tmp);
+    M.set(1,0,tmp);
+    stream >> tmp;
+    M.set(0,2,tmp);
+    M.set(2,0,tmp);
+    stream >> tmp;
+    M.set(1,1,tmp);
+    stream >> tmp;
+    M.set(1,2,tmp);
+    M.set(2,1,tmp);
+    stream >> tmp;
+    M.set(2,2,tmp);
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::queryCurrentValue(const char * name, class Vector &_T) {
+  if (typeid( VectorValue ) == *TypeMap[name]) {
+    std::istringstream stream(CurrentValue[name]);
+    stream >> _T[0];
+    stream >> _T[1];
+    stream >> _T[2];
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::queryCurrentValue(const char * name, std::vector<element *>&_T)
+{
+  int Z = -1;
+  element *elemental = NULL;
+  if (typeid( std::vector<element *> ) == *TypeMap[name]) {
+    std::istringstream stream(CurrentValue[name]);
+    while (!stream.fail()) {
+      stream >> Z;
+      elemental = World::getInstance().getPeriode()->FindElement(Z);
+      if (elemental != NULL)
+        _T.push_back(elemental);
+    }
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+
+void MapOfActions::setCurrentValue(const char * name, class atom * &_T)
+{
+  if (typeid( atom ) == *TypeMap[name]) {
+    std::ostringstream stream;
+    stream << _T->getId();
+    CurrentValue[name] = stream.str();
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::setCurrentValue(const char * name, class element * &_T)
+{
+  if (typeid( element ) == *TypeMap[name]) {
+    std::ostringstream stream;
+    stream << _T->Z;
+    CurrentValue[name] = stream.str();
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::setCurrentValue(const char * name, class molecule * &_T)
+{
+  if (typeid( molecule ) == *TypeMap[name]) {
+    std::ostringstream stream;
+    stream << _T->getId();
+    CurrentValue[name] = stream.str();
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::setCurrentValue(const char * name, class Box &_T)
+{
+  const Matrix &M = _T.getM();
+  if (typeid( Box ) == *TypeMap[name]) {
+    std::ostringstream stream;
+    stream << M.at(0,0) << " ";
+    stream << M.at(0,1) << " ";
+    stream << M.at(0,2) << " ";
+    stream << M.at(1,1) << " ";
+    stream << M.at(1,2) << " ";
+    stream << M.at(2,2) << " ";
+    CurrentValue[name] = stream.str();
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::setCurrentValue(const char * name, class Vector &_T)
+{
+  if (typeid( Vector ) == *TypeMap[name]){
+    std::ostringstream stream;
+    stream << _T[0] << " ";
+    stream << _T[1] << " ";
+    stream << _T[2] << " ";
+    CurrentValue[name] = stream.str();
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+void MapOfActions::setCurrentValue(const char * name, std::vector<element *>&_T)
+{
+  if (typeid( std::vector<element *> ) == *TypeMap[name]) {
+    std::ostringstream stream;
+    for (std::vector<element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
+      stream << (*iter)->Z;
+    }
+    CurrentValue[name] = stream.str();
+  } else
+    throw IllegalTypeException(__FILE__,__LINE__);
+}
+
+
 
 void MapOfActions::populateActions()
@@ -502 +660 @@
   new AnalysisMolecularVolumeAction();
   new AnalysisPairCorrelationAction();
+  new AnalysisPointCorrelationAction();
   new AnalysisPrincipalAxisSystemAction();
+  new AnalysisSurfaceCorrelationAction();
 
   new AtomAddAction();

src/Actions/MapOfActions.hpp ¶

@@ -14 +14 @@
 #include <map>
 #include <set>
+#include <vector>
 #include <typeinfo>
 
@@ -20 +21 @@
 #include "Exceptions/IllegalTypeException.hpp"
 #include "Patterns/Singleton.hpp"
+
+class Box;
+class atom;
+class element;
+class molecule;
+class Vector;
 
 namespace po = boost::program_options;
@@ -154 +161 @@
   void populateActions();
 
+  void queryCurrentValue(const char * name, class atom * &_T);
+  void queryCurrentValue(const char * name, class element * &_T);
+  void queryCurrentValue(const char * name, class molecule * &_T);
+  void queryCurrentValue(const char * name, class Box &_T);
+  void queryCurrentValue(const char * name, class Vector &_T);
+  void queryCurrentValue(const char * name, std::vector<element *>&_T);
   template<typename T> void queryCurrentValue(const char * name, T &_T)
   {
@@ -162 +175 @@
   }
 
+  void setCurrentValue(const char * name, class atom * &_T);
+  void setCurrentValue(const char * name, class element * &_T);
+  void setCurrentValue(const char * name, class molecule * &_T);
+  void setCurrentValue(const char * name, class Box &_T);
+  void setCurrentValue(const char * name, class Vector &_T);
+  void setCurrentValue(const char * name, std::vector<element *>&_T);
   template<class T> void setCurrentValue(const char * name, T &_T)
   {