Changeset 104524 for src

Timestamp:

Jun 9, 2010, 2:04:54 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:

94d131

Parents:

c78d44

git-author:

Frederik Heber <heber@…> (06/09/10 11:21:58)

git-committer:

Frederik Heber <heber@…> (06/09/10 14:04:54)

Message:

Changed PairCorrelationAction to incorporate all three cases and handled different parameters needed for each, changed queryElement to list of elements.

PairCorrelationAction:

• PairCorrelationAction has now three cases for Pair, Point and Surface.
• removed PairCorrelationToPointAction, PairCorrelationToSurfaceAction files and from Makefile.am

queryElement:

• queryElement, ElementCommandLineQuery, ElementTextQuery, ElementQuery all changed to use vector<element *>* instead of element
• ChangeElementAction changed accordingly
• oldmenu::AddAtoms() changed accordingly

Others:

• CommandLineWindow::populateAnalysisActions() - missing MolecularVolumeAction and PrinicipalAxisSystemAction.

Location:

src

Files:

• Actions/AnalysisAction/PairCorrelationAction.cpp (modified) (4 diffs)
• Actions/AnalysisAction/PairCorrelationToPointAction.cpp (deleted)
• Actions/AnalysisAction/PairCorrelationToPointAction.hpp (deleted)
• Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (deleted)
• Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp (deleted)
• Actions/AtomAction/ChangeElementAction.cpp (modified) (1 diff)
• Actions/Makefile.am (modified) (1 diff)
• Legacy/oldmenu.cpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineDialog.cpp (modified) (4 diffs)
• UIElements/CommandLineUI/CommandLineDialog.hpp (modified) (2 diffs)
• UIElements/CommandLineUI/CommandLineWindow.cpp (modified) (2 diffs)
• UIElements/Dialog.cpp (modified) (2 diffs)
• UIElements/Dialog.hpp (modified) (3 diffs)
• UIElements/TextUI/TextDialog.cpp (modified) (5 diffs)
• UIElements/TextUI/TextDialog.hpp (modified) (2 diffs)

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -9 +9 @@
 #include "CommandLineParser.hpp"
 #include "analysis_correlation.hpp"
+#include "boundary.hpp"
+#include "linkedcell.hpp"
 #include "log.hpp"
 #include "element.hpp"
+#include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "vector.hpp"
 #include "World.hpp"
 
@@ -35 +39 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
   int ranges[3] = {1, 1, 1};
+  double BinEnd = 0.;
   double BinStart = 0.;
-  double BinEnd = 0.;
+  double BinWidth = 0.;
+  molecule *Boundary = NULL;
   string outputname;
   string binoutputname;
@@ -42 +48 @@
   ofstream output;
   ofstream binoutput;
-  const element *elemental1;
-  const element *elemental2;
+  std::vector< element *> elements;
+  string type;
+  Vector Point;
+  BinPairMap *binmap = NULL;
+  MoleculeListClass *molecules = World::getInstance().getMolecules();
 
-  dialog->queryElement("elements", &elemental1, MapOfActions::getInstance().getDescription("elements"));
-  dialog->queryElement("elements", &elemental2, MapOfActions::getInstance().getDescription("elements"));
+  // 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;
+  }
+
+  // second dialog: Obtain parameters specific to this type
+  dialog = UIFactory::getInstance().makeDialog();
+  if (type == "P")
+    dialog->queryVector("position", &Point, World::getInstance().getDomain(), 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"));
@@ -57 +81 @@
     binoutput.open(binoutputname.c_str());
     PairCorrelationMap *correlationmap = NULL;
-    if (periodic)
-      correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elemental1, elemental2, ranges);
-    else
-      correlationmap = PairCorrelation(World::getInstance().getMolecules(), elemental1, elemental2);
-    //OutputCorrelationToSurface(&output, correlationmap);
-    BinPairMap *binmap = BinData( correlationmap, 0.5, BinStart, BinEnd );
+    if (type == "E") {
+      PairCorrelationMap *correlationmap = NULL;
+      if (periodic)
+        correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elements, ranges);
+      else
+        correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
+      //OutputCorrelationToSurface(&output, correlationmap);
+      binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+    } 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);
+      //OutputCorrelationToSurface(&output, correlationmap);
+      binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+    } 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);
+      OutputCorrelationToSurface(&output, surfacemap);
+      // 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 );
+    } else
+      return Action::failure;
     OutputCorrelation ( &binoutput, binmap );
     output.close();

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -34 +34 @@
 Action::state_ptr AtomChangeElementAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  int Z = -1;
   atom *first = NULL;
-  element *elemental = NULL;
+  std::vector<element *> elements;
 
-  dialog->queryElement(NAME, (const element **) &elemental, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryElement(NAME, &elements, MapOfActions::getInstance().getDescription(NAME));
   dialog->queryAtom("atom-by-id", &first, MapOfActions::getInstance().getDescription("atom-by-id"));
 
   if(dialog->display()) {
     delete dialog;
-    DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << elemental << "." << endl);
-    if (elemental != NULL) {
-      first->type = elemental;
+    ASSERT(elements.size() == 1, "Unequal to one element specified when changing an atom's element");
+    DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << elements.at(0) << "." << endl);
+    if (elements.at(0) != NULL) {
+      first->type = elements.at(0);
       return Action::success;
     } else

src/Actions/Makefile.am

@@ -36 +36 @@
   AnalysisAction/MolecularVolumeAction.cpp \
   AnalysisAction/PairCorrelationAction.cpp \
-  AnalysisAction/PairCorrelationToPointAction.cpp \
-  AnalysisAction/PairCorrelationToSurfaceAction.cpp \
   AnalysisAction/PrincipalAxisSystemAction.cpp
 ANALYSISACTIONHEADER = \
   AnalysisAction/MolecularVolumeAction.hpp \
   AnalysisAction/PairCorrelationAction.hpp \
-  AnalysisAction/PairCorrelationToPointAction.hpp \
-  AnalysisAction/PairCorrelationToSurfaceAction.hpp \
   AnalysisAction/PrincipalAxisSystemAction.hpp
 

src/Legacy/oldmenu.cpp

@@ -84 +84 @@
         Dialog *dialog = UIFactory::getInstance().makeDialog();
         first = World::getInstance().createAtom();
+        std::vector<element *> elements;
         dialog->queryVector("Please enter coordinates: ",&first->x,World::getInstance().getDomain(), false);
-        dialog->queryElement("Please choose element: ",&first->type);
+        dialog->queryElement("Please choose element: ",&elements);
         if(dialog->display()){
-          mol->AddAtom(first);  // add to molecule
+          if (elements.size() == 1) {
+            first->type = elements.at(0);
+            mol->AddAtom(first);  // add to molecule
+          } else {
+            DoeLog(1) && (eLog() << Verbose(1) << "Unequal to one element given for element of new atom." << endl);
+          }
         }
         else{

src/UIElements/CommandLineUI/CommandLineDialog.cpp

@@ -7 +7 @@
 
 
-#include <cassert>
 #include <iostream>
+#include <vector>
 
 #include <Descriptors/AtomDescriptor.hpp>
@@ -80 +80 @@
 }
 
-void CommandLineDialog::queryElement(const char* title, const element **target, string _description){
+void CommandLineDialog::queryElement(const char* title, std::vector<element *> *target, string _description){
   registerQuery(new ElementCommandLineQuery(title,target, _description));
 }
@@ -231 +231 @@
 }
 
-CommandLineDialog::ElementCommandLineQuery::ElementCommandLineQuery(string title, const element **target, string _description) :
+CommandLineDialog::ElementCommandLineQuery::ElementCommandLineQuery(string title, std::vector<element *> *target, string _description) :
     Dialog::ElementQuery(title,target, _description)
 {}
@@ -240 +240 @@
 bool CommandLineDialog::ElementCommandLineQuery::handle() {
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
-  int Z;
+  periodentafel *periode = World::getInstance().getPeriode();
+  element *elemental = NULL;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
     vector<int> AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
-    vector<int>::iterator ElementRunner = AllElements.begin();
-    Z = *ElementRunner;
-    // TODO: So far, this does not really erase the element in the parsed list.
-    AllElements.erase(ElementRunner);
-    tmp = World::getInstance().getPeriode()->FindElement(Z);
-    return true;
-  } else
-    return false;
-}
+    for (vector<int>::iterator ZRunner = AllElements.begin(); ZRunner != AllElements.end(); ++ZRunner) {
+      elemental = periode->FindElement(*ZRunner);
+      ASSERT(elemental != NULL, "Invalid element specified in ElementCommandLineQuery");
+      elements.push_back(elemental);
+    }
+    return true;
+  } else
+    return false;
+}

src/UIElements/CommandLineUI/CommandLineDialog.hpp

@@ -36 +36 @@
   virtual void queryVector(const char*,Vector *,const double * const,bool, std::string = "");
   virtual void queryBox(const char*,double ** const, std::string = "");
-  virtual void queryElement(const char*,const element **, std::string = "");
+  virtual void queryElement(const char*, std::vector<element *> *, std::string = "");
 
 protected:
@@ -105 +105 @@
   class ElementCommandLineQuery : public Dialog::ElementQuery {
   public:
-    ElementCommandLineQuery(std::string title, const element **_target, std::string _description = "");
+    ElementCommandLineQuery(std::string title, std::vector<element *> *_target, std::string _description = "");
     virtual ~ElementCommandLineQuery();
     virtual bool handle();

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -12 +12 @@
 
 #include "Actions/ActionRegistry.hpp"
+#include "Actions/AnalysisAction/MolecularVolumeAction.hpp"
 #include "Actions/AnalysisAction/PairCorrelationAction.hpp"
-#include "Actions/AnalysisAction/PairCorrelationToPointAction.hpp"
-#include "Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp"
+#include "Actions/AnalysisAction/PrincipalAxisSystemAction.hpp"
 #include "Actions/AtomAction/AddAction.hpp"
 #include "Actions/AtomAction/ChangeElementAction.hpp"
@@ -95 +95 @@
 void CommandLineWindow::populateAnalysisActions()
 {
+  new AnalysisMolecularVolumeAction();
   new AnalysisPairCorrelationAction();
-  new AnalysisPairCorrelationToPointAction();
-  new AnalysisPairCorrelationToSurfaceAction();
+  new AnalysisPrincipalAxisSystemAction();
 }
 

src/UIElements/Dialog.cpp

@@ -199 +199 @@
 
 // Element Queries
-Dialog::ElementQuery::ElementQuery(std::string title, const element **_target, std::string _description) :
+Dialog::ElementQuery::ElementQuery(std::string title, std::vector<element *> *_target, std::string _description) :
   Query(title, _description),
-  tmp(0),
   target(_target)
   {}
@@ -208 +207 @@
 
 void Dialog::ElementQuery::setResult(){
-  *target=tmp;
-}
+  *target=elements;
+}

src/UIElements/Dialog.hpp

@@ -11 +11 @@
 #include<string>
 #include<list>
+#include<vector>
 
 class atom;
@@ -32 +33 @@
   virtual void queryVector(const char*,Vector *,const double *const,bool, std::string = "")=0;
   virtual void queryBox(const char*,double ** const, std::string = "")=0;
-  virtual void queryElement(const char*,const element **, std::string = "")=0;
+  virtual void queryElement(const char*, std::vector<element *> *, std::string = "")=0;
 
   virtual bool display();
@@ -172 +173 @@
   class ElementQuery : public Query {
   public:
-    ElementQuery(std::string title, const element**_target, std::string _description = "");
+    ElementQuery(std::string title, std::vector<element *> *_target, std::string _description = "");
     virtual ~ElementQuery();
     virtual bool handle()=0;
     virtual void setResult();
   protected:
-    const element *tmp;
+    std::vector<element *> elements;
   private:
-    const element **target;
+    std::vector<element *> * const target;
   };
 

src/UIElements/TextUI/TextDialog.cpp

@@ -72 +72 @@
 }
 
-void TextDialog::queryElement(const char* title, const element **target, string description){
+void TextDialog::queryElement(const char* title, std::vector<element *> *target, string description){
   registerQuery(new ElementTextQuery(title,target,description));
 }
@@ -281 +281 @@
 }
 
-TextDialog::ElementTextQuery::ElementTextQuery(std::string title, const element **target, std::string _description) :
-    Dialog::ElementQuery(title,target,_description)
+TextDialog::ElementTextQuery::ElementTextQuery(std::string title, std::vector<element *> *_target, std::string _description) :
+    Dialog::ElementQuery(title,_target,_description)
 {}
 
@@ -291 +291 @@
   bool badInput=false;
   bool aborted = false;
+  element * tmp = NULL;
   do{
     badInput = false;
@@ -307 +308 @@
           Log() << Verbose(0) << "No element with this atomic number!" << endl;
           badInput = true;
+        } else {
+          elements.push_back(tmp);
         }
       }
@@ -329 +332 @@
           Log() << Verbose(0) << "No element with this shorthand!" << endl;
           badInput = true;
+        } else {
+          elements.push_back(tmp);
         }
       }

src/UIElements/TextUI/TextDialog.hpp

@@ -33 +33 @@
   virtual void queryVector(const char*,Vector *,const double * const,bool, std::string = "");
   virtual void queryBox(const char*,double ** const, std::string = "");
-  virtual void queryElement(const char*,const element **, std::string = "");
+  virtual void queryElement(const char*, std::vector<element *> *, std::string = "");
 
 protected:
@@ -102 +102 @@
   class ElementTextQuery : public Dialog::ElementQuery {
   public:
-    ElementTextQuery(std::string title, const element **_target, std::string _description = NULL);
+    ElementTextQuery(std::string title, std::vector<element *> *_target, std::string _description = NULL);
     virtual ~ElementTextQuery();
     virtual bool handle();