Small changes in libTFitPofB to get rid of annoying messages (if the debug flag is not set)

src/external/TFitPofB-lib/classes/TFitPofBStartupHandler.cpp

@@ -49,7 +49,8 @@ ClassImpQ(TFitPofBStartupHandler)
 /**
  * <p>
  */
-TFitPofBStartupHandler::TFitPofBStartupHandler() : fDeltat(0.), fDeltaB(0.), fNSteps(0), fGridSteps(0)
+TFitPofBStartupHandler::TFitPofBStartupHandler() :
+ fDebug(false), fLEM(false), fVortex(false), fDataPath(""), fDeltat(0.), fDeltaB(0.), fWisdomFile(""), fNSteps(0), fGridSteps(0)
 {
 }
 
@@ -318,7 +319,7 @@ void TFitPofBStartupHandler::CheckLists()
     if(fDebug)
       cout << endl << "TFitPofBStartupHandler::CheckLists: check data path ..." << endl;
     if (!fDataPath.size()) {
-      cout << "TFitPofBStartupHandler::CheckLists: This is not going to work, you have to set a valid data path where to find the rge-files in the xml-file!" << endl;
+      cerr << "TFitPofBStartupHandler::CheckLists: This is not going to work, you have to set a valid data path where to find the rge-files in the xml-file!" << endl;
       assert(fDataPath.size());
     } else {
       if(fDebug)
@@ -329,19 +330,19 @@ void TFitPofBStartupHandler::CheckLists()
     if(fDebug)
       cout << endl << "TFitPofBStartupHandler::CheckLists: check energy list ..." << endl;
     if (fEnergyList.size() != fEnergyLabelList.size()) {
-      cout << "TFitPofBStartupHandler::CheckLists: The number of energies and energy labels are different! Please fix it!" << endl \
+      cerr << "TFitPofBStartupHandler::CheckLists: The number of energies and energy labels are different! Please fix it!" << endl \
            << "TFitPofBStartupHandler::CheckLists: The program will be terminated now!" << endl;
       assert(fEnergyList.size() == fEnergyLabelList.size());
     }
     if (fEnergyList.empty()) {
-      cout << "TFitPofBStartupHandler::CheckLists: Energy list empty!" << endl \
+      cerr << "TFitPofBStartupHandler::CheckLists: Energy list empty!" << endl \
            << "TFitPofBStartupHandler::CheckLists: Trying to use the standard energies: 0.0 to 35.0 keV in 0.1 keV steps" << endl;
       for (double x(0.0); x<= 35.0; x+=0.1) {
         fEnergyList.push_back(x);
       }
     }
     if (fEnergyLabelList.empty()) {
-      cout << "TFitPofBStartupHandler::CheckLists: Energy label list empty!" << endl \
+      cerr << "TFitPofBStartupHandler::CheckLists: Energy label list empty!" << endl \
            << "TFitPofBStartupHandler::CheckLists: Trying to use the specified energies as labels in the format %02.1f..." << endl \
            << "TFitPofBStartupHandler::CheckLists: Most probably this will go wrong and should therefore be fixed in the xml-file!" << endl;
       char eChar[5];
@@ -376,7 +377,6 @@ void TFitPofBStartupHandler::CheckLists()
   }
 
   if (fVortex) {
-
     // check if any number of steps for the theory function is specified
     if(fDebug)
       cout << endl << "TFitPofBStartupHandler::CheckLists: check number of steps for Vortex grid ..." << endl;

src/external/TFitPofB-lib/classes/TLondon1D.cpp

@@ -179,7 +179,7 @@ TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec);
+    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 
     fPofB = new TPofBCalc(fParForPofB);
 
@@ -327,7 +327,7 @@ TLondon1D1L::TLondon1D1L() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec);
+    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 
     fPofB = new TPofBCalc(fParForPofB);
 
@@ -510,7 +510,7 @@ TLondon1D2L::TLondon1D2L() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec);
+    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 
     fPofB = new TPofBCalc(fParForPofB);
 
@@ -680,7 +680,7 @@ TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.01); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec);
+    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 
     fPofB = new TPofBCalc(fParForPofB);
 
@@ -827,7 +827,7 @@ TLondon1D3L::TLondon1D3L() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec);
+    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 
     fPofB = new TPofBCalc(fParForPofB);
 
@@ -996,7 +996,7 @@ TLondon1D3LS::TLondon1D3LS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec);
+    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 
     fPofB = new TPofBCalc(fParForPofB);
 
@@ -1159,7 +1159,7 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
 //     fParForPofB.push_back(startupHandler->GetDeltaB());
 //     fParForPofB.push_back(0.0);
 // 
-//     fImpProfile = new TTrimSPData(rge_path, energy_vec);
+//     fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
 // 
 //     fPofT = new TPofTCalc(fWisdom, fParForPofT);
 // 

src/external/TFitPofB-lib/classes/TTrimSPDataHandler.cpp

@@ -41,24 +41,9 @@ using namespace std;
 
 //--------------------
 // Constructor of the TrimSPData class -- reading all available trim.SP-rge-files with a given name into std::vectors
-// The rge-file names have to contain the Implantation energy just before the rge-extension in the format %02u_%1u
-// Example: string path("/home/user/TrimSP/SomeSample-");
-//          string energyArr[] = {"02_1", "02_5", "03_5", "05_0", "07_5", "10_0", "12_5"};
-//          vector<string> energyVec(energyArr, energyArr+(sizeof(energyArr)/sizeof(energyArr[0])));
-//
-// This will read the files "/home/user/TrimSP/SomeSample-02_1.rge", "/home/user/TrimSP/SomeSample-02_5.rge" and so on.
-//
-// Alternative supported energy formats in the energyVec are, e.g. for E=2.1keV:
-// <some_path>02-1.rge
-// <some_path>02.1.rge
-// <some_path>021.rge
-//
-// <some_path>21.rge is explicitly not possible since it is not clear, if this denotes 2.1keV or 21.0keV!
-//
-// Also always use the same format within one energyVec - otherwise sorting of the vector will not work properly!
 //--------------------
 
-TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies) {
+TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool debug) {
 
   // sort the energies in ascending order - this might be useful for later applications (energy-interpolations etc.)
   // after the change from the vector to the map this is not necessary any more - since maps are always ordered!
@@ -75,7 +60,7 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies) {
 
     ifstream *rgeFile = new ifstream(energyStr.c_str());
     if(! *rgeFile) {
-      cout << "TTrimSPData::TTrimSPData: file " << energyStr << " not found! Try next energy..." << endl;
+      cerr << "TTrimSPData::TTrimSPData: file " << energyStr << " not found! Try next energy..." << endl;
       delete rgeFile;
       rgeFile = 0;
     } else {
@@ -97,10 +82,10 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies) {
           vnzz.push_back(nzz);
         }
 
-        fDZ.push_back(vzz[1]-vzz[0]);
+        fDZ.push_back(0.5*(vzz[2]-vzz[0])); // it happens that TRIM.SP uses different step sizes in one output file, therefore take the average
 
         while(zz < 2100.0){
-          zz += *(fDZ.end()-1);
+          zz += fDZ.back();
           vzz.push_back(zz);
           vnzz.push_back(0.0);
         }
@@ -124,11 +109,12 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies) {
     }
   }
 
-  cout << "TTrimSPData::TTrimSPData: Read in " << fDataNZ.size() << " implantation profiles in total." << endl;
+  if (debug)
+    cout << "TTrimSPData::TTrimSPData: Read in " << fDataNZ.size() << " implantation profiles in total." << endl;
 
   fOrigDataNZ = fDataNZ;
 
-  for(unsigned int i(0); i<fEnergy.size();i++)
+  for(unsigned int i(0); i<fEnergy.size();++i)
     fIsNormalized.push_back(false);
 
   fEnergyIter = fEnergy.end();

src/external/TFitPofB-lib/include/TFitPofBStartupHandler.h

@@ -67,6 +67,7 @@ class TFitPofBStartupHandler : public TQObject {
     virtual const string GetWisdomFile() const { return fWisdomFile; }
     virtual const unsigned int GetNSteps() const { return fNSteps; }
     virtual const unsigned int GetGridSteps() const { return fGridSteps; }
+    virtual const bool GetDebug() const { return fDebug; }
 
   private:
     enum EKeyWords {eEmpty, eComment, eDebug, eLEM, eVortex, eDataPath, eEnergyLabel, \

src/external/TFitPofB-lib/include/TTrimSPDataHandler.h

@@ -44,7 +44,7 @@ class TTrimSPData {
 
 public:
 
-  TTrimSPData(const string&, map<double, string>&);
+  TTrimSPData(const string&, map<double, string>&, bool debug = false);
 
   ~TTrimSPData() {
     fDataZ.clear();