Code health, performance, security, and test-coverage pass on NFsim - from Jules

CMakeLists.txt

@@ -42,6 +42,7 @@ set(SUB_DIRS
     src/NFtest/complex
     src/NFtest/templateMolecule
     src/NFtest/mappingSet
+    src/NFtest/reactantTree
     src/NFscheduler
     src/NFreactions/transformations
     src/NFreactions/reactions

CMakeLists.x86.txt

@@ -33,6 +33,10 @@ set(SUB_DIRS
     src/NFtest/reactionClass
     src/NFtest/observable
     src/NFtest/molecule
+    src/NFtest/mappingSet
+    src/NFtest/templateMolecule
+    src/NFtest/complex
+    src/NFtest/reactantTree
     src/NFscheduler 
     src/NFreactions/transformations 
     src/NFreactions/reactions 

src/NFcore/moleculeType.cpp

@@ -238,10 +238,10 @@ void MoleculeType::addEquivalentComponents(vector <vector <string> > &identicalC
 
 
 bool MoleculeType::isIntegerComponent(const string& cName) const {
-	for(int c=0; c<numOfComponents; c++)
-			if(compName[c].compare(cName)==0) {
-				return this->isIntegerCompState[c];
-			}
+	auto it = compNameMap.find(cName);
+	if (it != compNameMap.end()) {
+		return this->isIntegerCompState[it->second];
+	}
 	cerr<<"!!! error !!! cannot find site name "<< cName << " in MoleculeType: "<<name;
 	cerr<<"in function isIntegerComponent(string cName).  "<<endl;
 	this->printDetails();

src/NFcore/reactionClass.cpp

@@ -406,19 +406,6 @@ string ReactionClass::fire(double random_A_number, bool track) {
 	}
 
 
-	// // output something if the reaction was tagged
-	// if(tagged) {
-	// 	for(unsigned int k=0; k<n_reactants; k++) {
-	// 		cout<<" [";
-	// 		for(unsigned int p=0; p<mappingSet[k]->getNumOfMappings();p++) {
-	// 			Molecule *mForTag = mappingSet[k]->get(p)->getMolecule();
-	// 			cout<<" "<<mForTag->getMoleculeTypeName()<<mForTag->getUniqueID();
-	// 		}
-	// 		cout<<" ]";
-	// 	}
-	// 	cout<<endl;
-	// }
-
 	// Generate the set of possible products that we need to update
 	// (excluding new molecules, we'll get those later --Justin)
 	this->transformationSet->getListOfProducts(mappingSet,products,traversalLimit);

src/NFcore/system.cpp

@@ -660,12 +660,6 @@ void System::prepareForSimulation()
 	//Note!!  : the order of preparing the system matters!  You have to prepare
 	//some things before others, because certain things require other
 
-	//First, set the observables up correctly, so when functions evaluate, they get the
-	//correct values
-	//for(molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ ) {
-	//	(*molTypeIter)->addAllToObservables();
-	//}
-
   	//First, we have to prep all the functions...
   	for( functionIter = globalFunctions.begin(); functionIter != globalFunctions.end(); functionIter++ )
   		(*functionIter)->prepareForSimulation(this);
@@ -754,14 +748,6 @@ void System::prepareForSimulation()
 
   	//cout<<"here 7..."<<endl;
 
-  	//add all the molecules to the appropriate observables
-  	//NOT NECESSARY - molecules are added to observables when they are prepared
-  	//for(obsIter=obsToOutput.begin(); obsIter != obsToOutput.end(); obsIter++)
-  	//	(*obsIter)->clear();
-  	//for(molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ ) {
-  	//	(*molTypeIter)->addAllToObservables();
-  	//}
-
   	//Add the complexes to Species observables
   	int match = 0;
   	for(obsIter = speciesObservables.begin(); obsIter != speciesObservables.end(); obsIter++)
@@ -906,9 +892,6 @@ void System::update_A_tot(ReactionClass *r, double old_a, double new_a)
 {
 	a_tot = selector->update(r,old_a,new_a);
 
-	//BUILT IN DIRECT SEARCH
-	//a_tot-=old_a;
-	//a_tot+=new_a;
 }
 
 
@@ -917,16 +900,6 @@ double System::recompute_A_tot()
 	a_tot = selector->refactorPropensities();
 	return a_tot;
 
-
-//  BUILT IN DIRECT SEARCH
-//	//Loop through the reactions and add up the rates
-//	a_tot = 0;
-//	for(rxnIter = allReactions.begin(); rxnIter != allReactions.end(); rxnIter++ )
-//	{
-//		a_tot += (*rxnIter)->update_a();
-//		if(DEBUG) (*rxnIter)->printDetails();
-//	}
-//	return a_tot;
 }
 
 

src/NFfunction/muParser/muParserFixes.h

@@ -58,117 +58,5 @@
 #endif
 
 
-//---------------------------------------------------------------------------
-//
-// MSVC6
-//
-//---------------------------------------------------------------------------
-
-
-#if defined(_MSC_VER) && _MSC_VER==1200
-
-/** \brief Macro to replace the MSVC6 auto_ptr with the _my_auto_ptr class.
-
-    Hijack auto_ptr and replace it with a version that actually does
-    what an auto_ptr normally does. If you use std::auto_ptr in your other code
-    might either explode or work much better. The original crap created
-    by Microsoft, called auto_ptr and bundled with MSVC6 is not standard compliant.
-*/
-#define auto_ptr _my_auto_ptr
-
-// This is another stupidity that needs to be undone in order to de-pollute
-// the global namespace!
-#undef min
-#undef max
-
-
-namespace std
-{
-  typedef ::size_t size_t;
-
-  //---------------------------------------------------------------------------
-  /** \brief MSVC6 fix: Put rand into namespace std. */
-  using ::rand;
-
-  //---------------------------------------------------------------------------
-  /** \brief MSVC6 fix: Put strlen into namespace std. */
-  using ::strlen;
-
-  //---------------------------------------------------------------------------
-  /** \brief MSVC6 fix: Put strncmp into namespace std. */
-  using ::strncmp;
-
-  //---------------------------------------------------------------------------
-  template<typename T>
-  T max(T a, T b)
-  {
-    return (a>b) ? a : b;
-  }
-
-  //---------------------------------------------------------------------------
-  template<typename T>
-  T min(T a, T b)
-  {
-    return (a<b) ? a : b;
-  }
-
-  //---------------------------------------------------------------------------
-  /** Standard compliant auto_ptr redefinition for MSVC6.
-
-    The code is taken from VS.NET 2003, slightly modified to reduce
-    it's dependencies from other classes.
-  */
-  template<class _Ty>
-  class _my_auto_ptr
-  {
-  public:
-    typedef _Ty element_type;
-
-	  explicit _my_auto_ptr(_Ty *_Ptr = 0)
-	    :_Myptr(_Ptr)
-	  {}
-
-	  _my_auto_ptr(_my_auto_ptr<_Ty>& _Right)
-	    :_Myptr(_Right.release())
-	  {}
-
-	  template<class _Other>
-    operator _my_auto_ptr<_Other>()
-	  {
-      return (_my_auto_ptr<_Other>(*this));
-	  }
-
-	  template<class _Other>
-	  _my_auto_ptr<_Ty>& operator=(_my_auto_ptr<_Other>& _Right)
-	  {
-      reset(_Right.release());
-	    return (*this);
-	  }
-
-	 ~auto_ptr()              { delete _Myptr;    }
-	  _Ty& operator*() const  { return (*_Myptr); }
-	  _Ty *operator->() const	{ return (&**this);	}
-	  _Ty *get() const        { return (_Myptr);	}
-
-    _Ty *release()
-    {
-		  _Ty *_Tmp = _Myptr;
-		  _Myptr = 0;
-		  return (_Tmp);
-		}
-
-	  void reset(_Ty* _Ptr = 0)
-		{
-		  if (_Ptr != _Myptr)
-			  delete _Myptr;
-		  _Myptr = _Ptr;
-    }
-
-  private:
-	    _Ty *_Myptr;
-	}; // class _my_auto_ptr
-} // namespace std
-
-#endif // Microsoft Visual Studio Version 6.0
 
 #endif // include guard

src/NFinput/NFinput.cpp

@@ -667,12 +667,6 @@ bool NFinput::initMoleculeTypes(
 			firstSymSiteToAppend.clear();
 		}
 
-		// prints out allowed state map
-		//for ( std::map< string, int, std::less< int > >::const_iterator iter = allowedStates.begin();
-		//      iter != allowedStates.end(); ++iter )
-		//      cout << iter->first << '\t' << iter->second << '\n';
-
-
 		//Getting here means we read everything we could successfully
 		return true;
 	} catch (...) {
@@ -996,12 +990,6 @@ static bool processSingleSpecies(
 				usedComponentNames.clear();
 
 
-				//We dont' have to do this anymore, because we handled it earlier!
-				//int eqClassCount = mt->getNumOfEquivalencyClasses();
-				//int *currentCount = new int[eqClassCount];
-				//for(int i=0; i<eqClassCount; i++) { currentCount[i]=1; }
-				//string *eqCompNames = mt->getEquivalencyClassCompNames();
-
 				//loop to create the actual molecules of this type
 				vector <Molecule *> currentM;
 				molecules.push_back(currentM);
@@ -1016,21 +1004,11 @@ static bool processSingleSpecies(
 						mids.push_back(mol->getMoleculeType()->getTypeID());
 						mgids.push_back(mol->getUniqueID());
 
-						//for(int i=0; i<eqClassCount; i++) { currentCount[i]=1; }
-
 						//Loop through the states and set the ones we need to set
 						int k=0;
 						for(snIter = stateName.begin(); snIter != stateName.end(); k++, snIter++ )
 						{
-							//if(mt->isEquivalentComponent((*snIter))) {
-							//	int eqNum = mt->getEquivalencyClassNumber((*snIter));
-							//	std::stringstream numStream; numStream << currentCount[eqNum];
-							//	string postFix = numStream.str();
-							//	m->setComponentState((*snIter)+postFix, (int)stateValue.at(k));
-							//	currentCount[eqNum]++;
-							//} else {
-								mol->setComponentState((*snIter), (int)stateValue.at(k));
-							//}
+							mol->setComponentState((*snIter), (int)stateValue.at(k));
 
 							// AS2023 - this is here to reduce the number of operations written
 							// note that the default molecule starts the component state at the 
@@ -1064,8 +1042,6 @@ static bool processSingleSpecies(
 
 				}
 
-				//delete [] currentCount;
-
 				//Reset the states for the next wave...
 				stateName.clear();
 				stateValue.clear();

src/NFinput/parseSymRxns.cpp

@@ -372,7 +372,7 @@ void createFullSymMaps(
 //saves all possible names for all possible components
 void assembleFullSymmetryList(
 		vector <vector <vector <component> > > &symmetries, //for output
-		vector <string> &moleculeIds,    //also for output
+		map <string, int> &moleculeIds,    //also for output
 		map<string,component> &symComps, //the input of symmetric components
 		bool isRxnCenter  //set to true if you are looking at reaction centers
 		)
@@ -392,13 +392,13 @@ void assembleFullSymmetryList(
 			string thisMoleculeId = id.substr(0,length);
 			int moleculeIndex = -1;
 
-			for(unsigned int i=0; i<moleculeIds.size(); i++) {
-				if(moleculeIds.at(i).compare(thisMoleculeId)==0)
-					moleculeIndex = i; break;
+			map<string, int>::iterator mIt = moleculeIds.find(thisMoleculeId);
+			if (mIt != moleculeIds.end()) {
+				moleculeIndex = mIt->second;
 			}
 			if(moleculeIndex==-1) {
 				moleculeIndex = moleculeIds.size();
-				moleculeIds.push_back(thisMoleculeId);
+				moleculeIds[thisMoleculeId] = moleculeIndex;
 
 				//Create the vector to store all of our potential permutations
 				vector <vector <component> > v;
@@ -430,7 +430,7 @@ void assembleFullSymmetryList(
 //saves all possible names for all possible components
 void assembleFullSymmetryListOnRxnCenter(
 		vector <vector <vector <component> > > &symmetries, //for output
-		vector <string> &moleculeIds,    //also for output
+		map <string, int> &moleculeIds,    //also for output
 		map<string,component> &symComps //the input of symmetric components
 		)
 {
@@ -449,14 +449,13 @@ void assembleFullSymmetryListOnRxnCenter(
 			string thisMoleculeId = id.substr(0,length);
 			int moleculeIndex = -1;
 
-			for(unsigned int i=0; i<moleculeIds.size(); i++) {
-				if(moleculeIds.at(i).compare(thisMoleculeId)==0) {
-					moleculeIndex = i; break;
-				}
+			map<string, int>::iterator mIt = moleculeIds.find(thisMoleculeId);
+			if (mIt != moleculeIds.end()) {
+				moleculeIndex = mIt->second;
 			}
 			if(moleculeIndex==-1) {
 				moleculeIndex = moleculeIds.size();
-				moleculeIds.push_back(thisMoleculeId);
+				moleculeIds[thisMoleculeId] = moleculeIndex;
 
 				//Create the vector to store all of our potential permutations
 				vector <vector <component> > v;
@@ -528,7 +527,7 @@ bool isMoleculePermuationValid(
 //
 void assembleOffRxnCenterSymClasses(
 		vector <vector <vector <string> > > &offRxnCenterSymClasses, //the output
-		vector <string> &moleculeIds, //input list of molecule names
+		map <string, int> &moleculeIds, //input list of molecule names
 		map<string,component> &symComps)  //input list of symmetric components off the rxn center
 {
 	offRxnCenterSymClasses.clear();
@@ -550,12 +549,9 @@ void assembleOffRxnCenterSymClasses(
 		string thisMoleculeId = id.substr(0,length);
 
 		int mIndex = -1;
-		for(unsigned int i=0; i<moleculeIds.size(); i++) {
-			if(thisMoleculeId.compare(moleculeIds.at(i))==0) {
-				//cout<<" found at index: "<<i<<endl;
-				mIndex=i;
-				break;
-			}
+		map<string, int>::iterator mIt = moleculeIds.find(thisMoleculeId);
+		if (mIt != moleculeIds.end()) {
+			mIndex = mIt->second;
 		}
 		if(mIndex==-1) { cout<<"ERROR in parseSymRxns.cpp - in assebmly of off rxn center sym classes"<<endl; exit(1); }
 
@@ -662,7 +658,7 @@ bool NFinput::generateRxnPermutations(vector<map<string,component> > &permutatio
 	if(verbose) cout<<"\t\t\tGenerating symmetric permutations..."<<endl;
 
 	vector <vector <vector <component> > > symmetries;
-	vector <string> moleculeIds;
+	map <string, int> moleculeIds;
 
 	//Assemble the list of possible components for each symmetric class on a reaction center
 	assembleFullSymmetryListOnRxnCenter(symmetries,moleculeIds,symRxnCenter);