First step in reorganizing the installation of the musrfit documentation (further commits will follow)

src/external/BMWtools/TTrimSPDataHandler.cpp

@@ -42,7 +42,7 @@ using namespace std;
 // Constructor of the TrimSPData class -- reading all available trim.SP-rge-files with a given name into std::vectors
 //--------------------
 
-TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool debug) {
+TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool debug, unsigned int highRes) {
 
   // 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!
@@ -101,6 +101,12 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool
         vnzz.clear();
         goodFile = false;
 
+        fIsNormalized.push_back(false);
+
+        if (highRes) {
+          UseHighResolution(iter->first);
+        }
+
       } else {
         cerr << "TTrimSPData::TTrimSPData: " << energyStr << " does not seem to be a valid unmodified TRIM.SP output file!" << endl;
         continue;
@@ -113,9 +119,6 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool
 
   fOrigDataNZ = fDataNZ;
 
-  for(unsigned int i(0); i<fEnergy.size();++i)
-    fIsNormalized.push_back(false);
-
   fEnergyIter = fEnergy.end();
 }
 
@@ -146,7 +149,7 @@ void TTrimSPData::UseHighResolution(double e) {
     }
     fDataZ[i] = vecZ;
     fDataNZ[i] = vecNZ;
-    fOrigDataNZ[i] = vecNZ;
+    //fOrigDataNZ[i] = vecNZ;
     fDZ[i] = 1.;
     fIsNormalized[i] = false;
     return;
@@ -494,7 +497,7 @@ void TTrimSPData::ConvolveGss(double w, double e) const {
   if(fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     z = fDataZ[i];
-    nz = fOrigDataNZ[i];
+    nz = fDataNZ[i];
 
     for(unsigned int k(0); k<z.size(); k++) {
       gss.push_back(exp(-z[k]*z[k]/200.0/w/w));

src/external/BMWtools/TTrimSPDataHandler.h

@@ -43,7 +43,7 @@ class TTrimSPData {
 
 public:
 
-  TTrimSPData(const string&, map<double, string>&, bool debug = false);
+  TTrimSPData(const string&, map<double, string>&, bool debug = false, unsigned int highRes = 0);
 
   ~TTrimSPData() {
     fDataZ.clear();
@@ -60,6 +60,7 @@ public:
   vector<double> OrigDataNZ(double) const;
   double DataDZ(double) const;
   void UseHighResolution(double);
+  void SetOriginal() {fOrigDataNZ = fDataNZ;}
   void WeightLayers(double, const vector<double>&, const vector<double>&) const;
   double LayerFraction(double, unsigned int, const vector<double>&) const;
   double GetNofZ(double, double) const;

src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEM.cpp

@@ -33,6 +33,7 @@
 #include <functional>
 #include <string>
 #include <iostream>
+#include <fstream>
 using namespace std;
 
 #include <TSAXParser.h>
@@ -257,7 +258,7 @@ TMeanFieldsForScBilayer::TMeanFieldsForScBilayer() {
   string rge_path(startupHandler->GetDataPath());
   map<double, string> energy_vec(startupHandler->GetEnergies());
 
-  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug(), 1);
 
   // clean up
   if (saxParser) {
@@ -272,10 +273,16 @@ TMeanFieldsForScBilayer::TMeanFieldsForScBilayer() {
 }
 
 // Operator-method that returns the mean field for a given implantation energy
-// Parameters: field, deadlayer, layer1, layer2, lambda1, lambda2, weight1 (deadlayer), weight2, weight3, weight4 (substrate)
+// Parameters: field, deadlayer, layer1, layer2, lambda1, lambda2, weight1 (deadlayer), weight2, weight3, weight4 (substrate),
+//             [Gss width for profile convolution]
 
 double TMeanFieldsForScBilayer::operator()(double E, const vector<double> &par_vec) const{
-  
+
+  double width(0.0);
+  if (par_vec.size() == 11) {
+    width = par_vec[10];
+  }
+
   vector<double> interfaces;
   interfaces.push_back(par_vec[1]);
   interfaces.push_back(par_vec[1]+par_vec[2]);
@@ -299,12 +306,12 @@ double TMeanFieldsForScBilayer::operator()(double E, const vector<double> &par_v
   energyIter = find(energies.begin(), energies.end(), E);
 
   if (energyIter != energies.end()) { // implantation profile found - no interpolation needed
-    return CalcMeanB(E, interfaces, weights, BofZ);
+    return CalcMeanB(E, interfaces, weights, BofZ, width);
   } else {
     if (E < energies.front())
-      return CalcMeanB(energies.front(), interfaces, weights, BofZ);
+      return CalcMeanB(energies.front(), interfaces, weights, BofZ, width);
     if (E > energies.back())
-      return CalcMeanB(energies.back(), interfaces, weights, BofZ);
+      return CalcMeanB(energies.back(), interfaces, weights, BofZ, width);
 
     energyIter = find_if(energies.begin(), energies.end(), bind2nd( greater<double>(), E));
 //    cout << *(energyIter - 1) << " " << *(energyIter) << endl;
@@ -312,22 +319,32 @@ double TMeanFieldsForScBilayer::operator()(double E, const vector<double> &par_v
     double E1(*(energyIter - 1));
     double E2(*(energyIter));
 
-    double B1(CalcMeanB(E1, interfaces, weights, BofZ));
-    double B2(CalcMeanB(E2, interfaces, weights, BofZ));
+    double B1(CalcMeanB(E1, interfaces, weights, BofZ, width));
+    double B2(CalcMeanB(E2, interfaces, weights, BofZ, width));
 
     return B1 + (B2-B1)/(E2-E1)*(E-E1);
   }
 }
 
-double TMeanFieldsForScBilayer::CalcMeanB (double E, const vector<double>& interfaces, const vector<double>& weights, const TLondon1D_2L& BofZ) const {
-  //calcData->UseHighResolution(E);
+double TMeanFieldsForScBilayer::CalcMeanB (double E, const vector<double>& interfaces, const vector<double>& weights, const TLondon1D_2L& BofZ, double width=0.0) const {
+    //fImpProfile->UseHighResolution(E);
+    //fImpProfile->ConvolveGss(width, E);
+    //fImpProfile->SetOriginal();
     fImpProfile->WeightLayers(E, interfaces, weights);
+    fImpProfile->ConvolveGss(width, E);
     fImpProfile->Normalize(E);
 
     vector<double> z(fImpProfile->DataZ(E));
     vector<double> nz(fImpProfile->DataNZ(E));
     double dz(fImpProfile->DataDZ(E));
 
+  if (E==20.0){
+  ofstream of("Implantation-profile-normal.dat");
+  for (unsigned int i(0); i<z.size(); i++) {
+    of << z[i] << " " << nz[i] << endl;
+  }
+  of.close();
+ }
     // calculate mean field
 
     double meanB(0.);

src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEM.h

@@ -85,7 +85,7 @@ public:
   virtual Bool_t GlobalPartIsValid() const { return true; }
 
   double operator()(double, const vector<double>&) const;
-  double CalcMeanB (double, const vector<double>&, const vector<double>&, const TLondon1D_2L&) const;
+  double CalcMeanB (double, const vector<double>&, const vector<double>&, const TLondon1D_2L&, double) const;
 
 private:
   TTrimSPData *fImpProfile;