Changes in src/datacreator.cpp [f66195:042f82]

File:

• src/datacreator.cpp (modified) (45 diffs)

src/datacreator.cpp

@@ -8 +8 @@
 
 #include "datacreator.hpp"
-#include "helpers.hpp"
-#include "parser.hpp"
 
 //=========================== FUNCTIONS============================
@@ -51 +49 @@
 /** Plots an energy vs. order.
  * \param &Fragments EnergyMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
  * \param *prefix prefix in filename (without ending)
  * \param *msg message to be place in first line as a comment
  * \return true if file was written successfully
  */
-bool CreateDataEnergyOrder(class EnergyMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
+bool CreateDataEnergyOrder(class EnergyMatrix &Fragments, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum)
 {
   stringstream filename;
@@ -65 +63 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "#Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    for(int i=KeySets.FragmentsPerOrder[BondOrder];i--;) {
-      for(int j=Fragments.RowCounter[ KeySets.OrderSet[BondOrder][i] ];j--;)
-        for(int k=Fragments.ColumnCounter[ KeySets.OrderSet[BondOrder][i] ];k--;)
-          Fragments.Matrix[Fragments.MatrixCounter][j][k] += Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][k];
-    }
-    output << BondOrder+1 << "\t" << KeySets.FragmentsPerOrder[BondOrder];
-    for (int l=0;l<Fragments.ColumnCounter[Fragments.MatrixCounter];l++)
+  output << "#Order\tFrag.No.\t" << Fragments.Header << endl;
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;) {
+      for(int j=Fragments.RowCounter[ KeySet.OrderSet[BondOrder][i] ];j--;)
+        for(int k=Fragments.ColumnCounter;k--;)
+          Fragments.Matrix[Fragments.MatrixCounter][j][k] += Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
+    }
+    output << BondOrder+1 << "\t" << KeySet.FragmentsPerOrder[BondOrder];
+    for (int l=0;l<Fragments.ColumnCounter;l++)
       output << scientific << "\t" << Fragments.Matrix[Fragments.MatrixCounter][ Fragments.RowCounter[Fragments.MatrixCounter]-1 ][l];
     output << endl;
@@ -84 +82 @@
  * \param &Energy EnergyMatrix class containing reference values (in MatrixCounter matrix)
  * \param &Fragments EnergyMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
  * \param *prefix prefix in filename (without ending)
  * \param *msg message to be place in first line as a comment
  * \return true if file was written successfully
  */
-bool CreateDataDeltaEnergyOrder(class EnergyMatrix &Energy, class EnergyMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
+bool CreateDataDeltaEnergyOrder(class EnergyMatrix &Energy, class EnergyMatrix &Fragments, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum)
 {
   stringstream filename;
@@ -98 +96 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "#Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
+  output << "#Order\tFrag.No.\t" << Fragments.Header << endl;
   Fragments.SetLastMatrix(Energy.Matrix[Energy.MatrixCounter],0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    for(int i=KeySets.FragmentsPerOrder[BondOrder];i--;) {
-      for(int j=Fragments.RowCounter[ KeySets.OrderSet[BondOrder][i] ];j--;)
-        for(int k=Fragments.ColumnCounter[ KeySets.OrderSet[BondOrder][i] ];k--;)
-          Fragments.Matrix[Fragments.MatrixCounter][j][k] -= Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][k];
-    }
-    output << BondOrder+1 << "\t" << KeySets.FragmentsPerOrder[BondOrder];
-    for (int l=0;l<Fragments.ColumnCounter[Energy.MatrixCounter];l++)
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;) {
+      for(int j=Fragments.RowCounter[ KeySet.OrderSet[BondOrder][i] ];j--;)
+        for(int k=Fragments.ColumnCounter;k--;)
+          Fragments.Matrix[Fragments.MatrixCounter][j][k] -= Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
+    }
+    output << BondOrder+1 << "\t" << KeySet.FragmentsPerOrder[BondOrder];
+    for (int l=0;l<Fragments.ColumnCounter;l++)
       if (fabs(Energy.Matrix[Energy.MatrixCounter][ Energy.RowCounter[Energy.MatrixCounter]-1 ][l]) < MYEPSILON)
         output << scientific << "\t" << Fragments.Matrix[Fragments.MatrixCounter][ Fragments.RowCounter[Fragments.MatrixCounter]-1 ][l];
@@ -120 +118 @@
 /** Plot forces vs. order.
  * \param &Fragments ForceMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
  * \param *prefix prefix in filename (without ending)
  * \param *msg message to be place in first line as a comment
@@ -126 +124 @@
  * \return true if file was written successfully
  */
-bool CreateDataForcesOrder(class ForceMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix,const  char *msg, const char *datum, void (*CreateForce)(class MatrixContainer &, int))
+bool CreateDataForcesOrder(class ForceMatrix &Fragments, class KeySetsContainer &KeySet, const char *dir, const char *prefix,const  char *msg, const char *datum, void (*CreateForce)(class MatrixContainer &, int))
 {
   stringstream filename;
@@ -135 +133 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
+  output << "# Order\tFrag.No.\t" << Fragments.Header << endl;
   Fragments.SetLastMatrix(0.,0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    Fragments.SumSubForces(Fragments, KeySets, BondOrder, 1.);
-    output << BondOrder+1 << "\t" << KeySets.FragmentsPerOrder[BondOrder];
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    Fragments.SumSubForces(Fragments, KeySet, BondOrder, 1.);
+    output << BondOrder+1 << "\t" << KeySet.FragmentsPerOrder[BondOrder];
     CreateForce(Fragments, Fragments.MatrixCounter);
-    for (int l=0;l<Fragments.ColumnCounter[Fragments.MatrixCounter];l++)
+    for (int l=0;l<Fragments.ColumnCounter;l++)
        output << scientific << "\t" << Fragments.Matrix[Fragments.MatrixCounter][ Fragments.RowCounter[Fragments.MatrixCounter] ][l];
     output << endl;
@@ -152 +150 @@
  * \param &Force ForceMatrix containing reference values (in MatrixCounter matrix)
  * \param &Fragments ForceMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
  * \param *prefix prefix in filename (without ending)
  * \param *msg message to be place in first line as a comment
@@ -158 +156 @@
  * \return true if file was written successfully
  */
-bool CreateDataDeltaForcesOrder(class ForceMatrix &Force, class ForceMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum, void (*CreateForce)(class MatrixContainer &, int))
+bool CreateDataDeltaForcesOrder(class ForceMatrix &Force, class ForceMatrix &Fragments, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum, void (*CreateForce)(class MatrixContainer &, int))
 {
   stringstream filename;
@@ -167 +165 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
+  output << "# Order\tFrag.No.\t" << Fragments.Header << endl;
   Fragments.SetLastMatrix(Force.Matrix[Force.MatrixCounter],0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    Fragments.SumSubForces(Fragments, KeySets, BondOrder, -1.);
-    output << BondOrder+1 << "\t" << KeySets.FragmentsPerOrder[BondOrder];
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    Fragments.SumSubForces(Fragments, KeySet, BondOrder, -1.);
+    output << BondOrder+1 << "\t" << KeySet.FragmentsPerOrder[BondOrder];
     CreateForce(Fragments, Fragments.MatrixCounter);
-    for (int l=0;l<Fragments.ColumnCounter[Fragments.MatrixCounter];l++)
+    for (int l=0;l<Fragments.ColumnCounter;l++)
        output << scientific << "\t" << Fragments.Matrix[Fragments.MatrixCounter][ Fragments.RowCounter[Fragments.MatrixCounter] ][l];
     output << endl;
@@ -184 +182 @@
  * \param &Force ForceMatrix containing reference values (in MatrixCounter matrix)
  * \param &Fragments ForceMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
  * \param *prefix prefix in filename (without ending)
  * \param *msg message to be place in first line as a comment
@@ -190 +188 @@
  * \return true if file was written successfully
  */
-bool CreateDataDeltaForcesOrderPerAtom(class ForceMatrix &Force, class ForceMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
+bool CreateDataDeltaForcesOrderPerAtom(class ForceMatrix &Force, class ForceMatrix &Fragments, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum)
 {
   stringstream filename;
@@ -200 +198 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
+  output << "# AtomNo\t" << Fragments.Header << endl;
   Fragments.SetLastMatrix(Force.Matrix[Force.MatrixCounter], 0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     //cout << "Current order is " << BondOrder << "." << endl;
-    Fragments.SumSubForces(Fragments, KeySets, BondOrder, -1.);
+    Fragments.SumSubForces(Fragments, KeySet, BondOrder, -1.);
     // errors per atom
     output << endl << "#Order\t" << BondOrder+1 << endl;
     for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) {
       output << Fragments.Indices[Fragments.MatrixCounter][j] << "\t";
-      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++) {
+      for (int l=0;l<Fragments.ColumnCounter;l++) {
         if (((l+1) % 3) == 0) {
           norm = 0.;
@@ -215 +213 @@
             norm += Force.Matrix[Force.MatrixCounter][ j ][l+m]*Force.Matrix[Force.MatrixCounter][ j ][l+m];
           norm = sqrt(norm);
-        }                                                                                                    
+        }
 //        if (norm < MYEPSILON)
           output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
@@ -231 +229 @@
 /** Plot forces error vs. vs atom vs. order.
  * \param &Fragments ForceMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
  * \param *prefix prefix in filename (without ending)
  * \param *msg message to be place in first line as a comment
@@ -237 +235 @@
  * \return true if file was written successfully
  */
-bool CreateDataForcesOrderPerAtom(class ForceMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
+bool CreateDataForcesOrderPerAtom(class ForceMatrix &Fragments, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum)
 {
   stringstream filename;
@@ -246 +244 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
+  output << "# AtomNo\t" << Fragments.Header << endl;
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     //cout << "Current order is " << BondOrder << "." << endl;
-    Fragments.SumSubForces(Fragments, KeySets, BondOrder, 1.);
+    Fragments.SumSubForces(Fragments, KeySet, BondOrder, 1.);
     // errors per atom
     output << endl << "#Order\t" << BondOrder+1 << endl;
     for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) {
       output << Fragments.Indices[Fragments.MatrixCounter][j] << "\t";
-      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++)
+      for (int l=0;l<Fragments.ColumnCounter;l++)
         output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
       output << endl;
@@ -264 +262 @@
 };
 
-
-/** Plot hessian error vs. vs atom vs. order.
- * \param &Hessian HessianMatrix containing reference values (in MatrixCounter matrix)
- * \param &Fragments HessianMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
- * \param *prefix prefix in filename (without ending)
- * \param *msg message to be place in first line as a comment
- * \param *datum current date and time
- * \return true if file was written successfully
- */
-bool CreateDataDeltaHessianOrderPerAtom(class HessianMatrix &Hessian, class HessianMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
-{
-  stringstream filename;
-  ofstream output;
-
-  filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
-  cout << msg << endl;
-  output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
-  Fragments.SetLastMatrix(Hessian.Matrix[Hessian.MatrixCounter], 0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    //cout << "Current order is " << BondOrder << "." << endl;
-    Fragments.SumSubHessians(Fragments, KeySets, BondOrder, -1.);
-    // errors per atom
-    output << endl << "#Order\t" << BondOrder+1 << endl;
-    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
-      output << Fragments.Indices[Fragments.MatrixCounter][j] << "\t";
-      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++) {
-        output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
-      }
-      output << endl;
-    }
-    output << endl;
-  }
-  output.close();
-  return true;
-};
-
-/** Plot hessian error vs. vs atom vs. order in the frobenius norm.
- * \param &Hessian HessianMatrix containing reference values (in MatrixCounter matrix)
- * \param &Fragments HessianMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
- * \param *prefix prefix in filename (without ending)
- * \param *msg message to be place in first line as a comment
- * \param *datum current date and time
- * \return true if file was written successfully
- */
-bool CreateDataDeltaFrobeniusOrderPerAtom(class HessianMatrix &Hessian, class HessianMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
-{
-  stringstream filename;
-  ofstream output;
-  double norm = 0;
-  double tmp;
-
-  filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
-  cout << msg << endl;
-  output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t";
-  Fragments.SetLastMatrix(Hessian.Matrix[Hessian.MatrixCounter], 0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    output << "Order" << BondOrder+1 << "\t";
-  }
-  output << endl;
-  output << Fragments.RowCounter[ Fragments.MatrixCounter ] << "\t";
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    //cout << "Current order is " << BondOrder << "." << endl;
-    Fragments.SumSubHessians(Fragments, KeySets, BondOrder, -1.);
-    // frobenius norm of errors per atom
-    norm = 0.;
-    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
-      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++) {
-        tmp = Fragments.Matrix[Fragments.MatrixCounter][ j ][l];
-        norm += tmp*tmp;
-      }
-    }
-    output << scientific << sqrt(norm)/(Fragments.RowCounter[ Fragments.MatrixCounter ]*Fragments.ColumnCounter[ Fragments.MatrixCounter] ) << "\t";
-  }
-  output << endl;
-  output.close();
-  return true;
-};
-
-/** Plot hessian error vs. vs atom vs. order.
- * \param &Fragments HessianMatrix class containing matrix values
- * \param KeySets KeySetContainer class holding bond KeySetContainer::Order
- * \param *prefix prefix in filename (without ending)
- * \param *msg message to be place in first line as a comment
- * \param *datum current date and time
- * \return true if file was written successfully
- */
-bool CreateDataHessianOrderPerAtom(class HessianMatrix &Fragments, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum)
-{
-  stringstream filename;
-  ofstream output;
-
-  filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
-  cout << msg << endl;
-  output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t" << Fragments.Header[ Fragments.MatrixCounter ] << endl;
-  Fragments.SetLastMatrix(0., 0);
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    //cout << "Current order is " << BondOrder << "." << endl;
-    Fragments.SumSubHessians(Fragments, KeySets, BondOrder, 1.);
-    // errors per atom
-    output << endl << "#Order\t" << BondOrder+1 << endl;
-    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
-      output << Fragments.Indices[Fragments.MatrixCounter][j] << "\t";
-      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++)
-        output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
-      output << endl;
-    }
-    output << endl;
-  }
-  output.close();
-  return true;
-};
-
 /** Plot matrix vs. fragment.
  */
-bool CreateDataFragment(class MatrixContainer &Fragment, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum, void (*CreateFragment)(class MatrixContainer &, int))
+bool CreateDataFragment(class MatrixContainer &Fragment, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum, void (*CreateFragment)(class MatrixContainer &, int))
 {
   stringstream filename;
@@ -395 +273 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum << endl;
-  output << "#Order\tFrag.No.\t" << Fragment.Header[ Fragment.MatrixCounter ] << endl;
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
-    for(int i=0;i<KeySets.FragmentsPerOrder[BondOrder];i++) {
-      output << BondOrder+1 << "\t" << KeySets.OrderSet[BondOrder][i]+1;
-      CreateFragment(Fragment, KeySets.OrderSet[BondOrder][i]);
-      for (int l=0;l<Fragment.ColumnCounter[ KeySets.OrderSet[BondOrder][i] ];l++)
-        output << scientific << "\t" << Fragment.Matrix[ KeySets.OrderSet[BondOrder][i] ][ Fragment.RowCounter[ KeySets.OrderSet[BondOrder][i] ] ][l];
+  output << "#Order\tFrag.No.\t" << Fragment.Header << endl;
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    for(int i=0;i<KeySet.FragmentsPerOrder[BondOrder];i++) {
+      output << BondOrder+1 << "\t" << KeySet.OrderSet[BondOrder][i]+1;
+      CreateFragment(Fragment, KeySet.OrderSet[BondOrder][i]);
+      for (int l=0;l<Fragment.ColumnCounter;l++)
+        output << scientific << "\t" << Fragment.Matrix[ KeySet.OrderSet[BondOrder][i] ][ Fragment.RowCounter[ KeySet.OrderSet[BondOrder][i] ] ][l];
       output << endl;
     }
@@ -411 +289 @@
 /** Copies fragment energy values into last matrix of \a Matrix with greatest total energy.
  * \param &Matrix MatrixContainer with all fragment energy values
- * \param &KeySets KeySetsContainer with associations of each fragment to a bond order
+ * \param &KeySet KeySetsContainer with associations of each fragment to a bond order
  * \param BondOrder current bond order
  */
-void CreateMaxFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySets, int BondOrder)
+void CreateMaxFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySet, int BondOrder)
 {
   for(int j=Fragments.RowCounter[ Fragments.MatrixCounter ];j--;) {
-    for(int i=KeySets.FragmentsPerOrder[BondOrder];i--;) {
-      if (fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) < fabs(Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][1])) {
-        for (int k=Fragments.ColumnCounter[ Fragments.MatrixCounter ];k--;)
-          Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][k];
+    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;) {
+      if (fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) < fabs(Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][1])) {
+        for (int k=Fragments.ColumnCounter;k--;)
+          Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       }
     }
@@ -428 +306 @@
 /** Copies fragment energy values into last matrix of \a Matrix with smallest total energy.
  * \param &Matrix MatrixContainer with all fragment energy values
- * \param &KeySets KeySetsContainer with associations of each fragment to a bond order
+ * \param &KeySet KeySetsContainer with associations of each fragment to a bond order
  * \param BondOrder current bond order
  */
-void CreateMinFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySets, int BondOrder)
+void CreateMinFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySet, int BondOrder)
 {
   for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) {
     int i=0;
     do {  // first get a minimum value unequal to 0
-      for (int k=Fragments.ColumnCounter[ Fragments.MatrixCounter ];k--;)
-        Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][k];
+      for (int k=Fragments.ColumnCounter;k--;)
+        Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       i++;
-    } while ((fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) < MYEPSILON) && (i<KeySets.FragmentsPerOrder[BondOrder]));
-    for(;i<KeySets.FragmentsPerOrder[BondOrder];i++) { // then find lowest
-      if (fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) > fabs(Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][1])) {
-        for (int k=Fragments.ColumnCounter[ Fragments.MatrixCounter ];k--;)
-          Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySets.OrderSet[BondOrder][i] ][j][k];
+    } while ((fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) < MYEPSILON) && (i<KeySet.FragmentsPerOrder[BondOrder]));
+    for(;i<KeySet.FragmentsPerOrder[BondOrder];i++) { // then find lowest
+      if (fabs(Fragments.Matrix[ Fragments.MatrixCounter ][j][1]) > fabs(Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][1])) {
+        for (int k=Fragments.ColumnCounter;k--;)
+          Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       }
     }
@@ -451 +329 @@
 /** Plot matrix vs. fragment.
  */
-bool CreateDataFragmentOrder(class MatrixContainer &Fragment, class KeySetsContainer &KeySets, const char *dir, const char *prefix, const char *msg, const char *datum, void (*CreateFragmentOrder)(class MatrixContainer &, class KeySetsContainer &, int))
+bool CreateDataFragmentOrder(class MatrixContainer &Fragment, class KeySetsContainer &KeySet, const char *dir, const char *prefix, const char *msg, const char *datum, void (*CreateFragmentOrder)(class MatrixContainer &, class KeySetsContainer &, int))
 {
   stringstream filename;
@@ -460 +338 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "#Order\tFrag.No.\t" << Fragment.Header[ Fragment.MatrixCounter ] << endl;
+  output << "#Order\tFrag.No.\t" << Fragment.Header << endl;
   // max
-  for (int BondOrder=0;BondOrder<KeySets.Order;BondOrder++) {
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     Fragment.SetLastMatrix(0.,0);
-    CreateFragmentOrder(Fragment, KeySets, BondOrder);
-    output << BondOrder+1 << "\t" << KeySets.FragmentsPerOrder[BondOrder];
-    for (int l=0;l<Fragment.ColumnCounter[ Fragment.MatrixCounter ];l++)
+    CreateFragmentOrder(Fragment, KeySet, BondOrder);
+    output << BondOrder+1 << "\t" << KeySet.FragmentsPerOrder[BondOrder];
+    for (int l=0;l<Fragment.ColumnCounter;l++)
       output << scientific << "\t" << Fragment.Matrix[ Fragment.MatrixCounter ][ Fragment.RowCounter[ Fragment.MatrixCounter ]-1 ][l];
     output << endl;
@@ -480 +358 @@
 void CreateEnergy(class MatrixContainer &Energy, int MatrixNumber)
 {
-  for(int k=0;k<Energy.ColumnCounter[MatrixNumber];k++)
+  for(int k=0;k<Energy.ColumnCounter;k++)
     Energy.Matrix[MatrixNumber][ Energy.RowCounter[MatrixNumber] ] [k] =  Energy.Matrix[MatrixNumber][ Energy.RowCounter[MatrixNumber]-1 ] [k];
 };
@@ -491 +369 @@
 void CreateMinimumForce(class MatrixContainer &Force, int MatrixNumber)
 {
-  for (int l=Force.ColumnCounter[MatrixNumber];l--;)
+  for (int l=Force.ColumnCounter;l--;)
     Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] = 0.;
-  for (int l=5;l<Force.ColumnCounter[MatrixNumber];l+=3) {
+  for (int l=5;l<Force.ColumnCounter;l+=3) {
     double stored = 0;
     int k=0;
@@ -526 +404 @@
 {
   int divisor = 0;
-  for (int l=Force.ColumnCounter[MatrixNumber];l--;)
+  for (int l=Force.ColumnCounter;l--;)
     Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] = 0.;
-  for (int l=5;l<Force.ColumnCounter[MatrixNumber];l+=3) {
+  for (int l=5;l<Force.ColumnCounter;l+=3) {
     double tmp = 0;
     for (int k=Force.RowCounter[MatrixNumber];k--;) {
@@ -550 +428 @@
 void CreateMaximumForce(class MatrixContainer &Force, int MatrixNumber)
 {
-  for (int l=5;l<Force.ColumnCounter[MatrixNumber];l+=3) {
+  for (int l=5;l<Force.ColumnCounter;l+=3) {
     double stored = 0;
     for (int k=Force.RowCounter[MatrixNumber];k--;) {
@@ -582 +460 @@
 void CreateVectorSumForce(class MatrixContainer &Force, int MatrixNumber)
 {
-  for (int l=Force.ColumnCounter[MatrixNumber];l--;)
+  for (int l=Force.ColumnCounter;l--;)
     Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] = 0.;
-  for (int l=0;l<Force.ColumnCounter[MatrixNumber];l++) {
+  for (int l=0;l<Force.ColumnCounter;l++) {
     for (int k=Force.RowCounter[MatrixNumber];k--;)
       Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l] += Force.Matrix[MatrixNumber][k][l];
@@ -620 +498 @@
 /** Creates the pyxplotfile for energy data.
  * \param Matrix MatrixContainer with matrix values
- * \param KeySets contains bond order
+ * \param KeySet contains bond order
  * \param *dir directory
  * \param *prefix prefix for all filenames (without ending)
@@ -637 +515 @@
  * \return true if file was written successfully
  */
-bool CreatePlotOrder(class MatrixContainer &Matrix, const class KeySetsContainer &KeySets, const char *dir, const char *prefix, const int keycolumns, const char *key, const char *logscale, const char *extraline, const int mxtics, const int xtics, const char *xlabel, const char *ylabel, const char *xrange, const char *yrange, const char *xargument, const char *uses, void (*CreatePlotLines)(ofstream &, class MatrixContainer &, const char *, const char *, const char *))
+bool CreatePlotOrder(class MatrixContainer &Matrix, const class KeySetsContainer &KeySet, const char *dir, const char *prefix, const int keycolumns, const char *key, const char *logscale, const char *extraline, const int mxtics, const int xtics, const char *xlabel, const char *ylabel, const char *xrange, const char *yrange, const char *xargument, const char *uses, void (*CreatePlotLines)(ofstream &, class MatrixContainer &, const char *, const char *, const char *))
 {
   stringstream filename;
@@ -660 +538 @@
 void AbsEnergyPlotLine(ofstream &output, class MatrixContainer &Energy, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Energy.Header[ Energy.MatrixCounter ]);
+  stringstream line(Energy.Header);
   string token;
 
   getline(line, token, '\t');
-  for (int i=2; i<= Energy.ColumnCounter[Energy.MatrixCounter];i++) {
+  for (int i=2; i<= Energy.ColumnCounter;i++) {
     getline(line, token, '\t');
     while (token[0] == ' ') // remove leading white spaces
       token.erase(0,1);
     output << "'" << prefix << ".dat' title '" << token << "' using " << xargument << ":(abs($" << i+2 << ")) " << uses;
-    if (i != (Energy.ColumnCounter[Energy.MatrixCounter]))
+    if (i != (Energy.ColumnCounter))
       output << ", \\";
     output << endl;
@@ -684 +562 @@
 void EnergyPlotLine(ofstream &output, class MatrixContainer &Energy, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Energy.Header[Energy.MatrixCounter]);
+  stringstream line(Energy.Header);
   string token;
 
   getline(line, token, '\t');
-  for (int i=1; i<= Energy.ColumnCounter[Energy.MatrixCounter];i++) {
+  for (int i=1; i<= Energy.ColumnCounter;i++) {
     getline(line, token, '\t');
     while (token[0] == ' ') // remove leading white spaces
       token.erase(0,1);
     output << "'" << prefix << ".dat' title '" << token << "' using " << xargument << ":" << i+2 << " " << uses;
-    if (i != (Energy.ColumnCounter[Energy.MatrixCounter]))
+    if (i != (Energy.ColumnCounter))
       output << ", \\";
     output << endl;
@@ -708 +586 @@
 void ForceMagnitudePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header[Force.MatrixCounter]);
+  stringstream line(Force.Header);
   string token;
 
@@ -716 +594 @@
   getline(line, token, '\t');
   getline(line, token, '\t');
-  for (int i=7; i< Force.ColumnCounter[Force.MatrixCounter];i+=NDIM) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     getline(line, token, '\t');
     while (token[0] == ' ') // remove leading white spaces
@@ -722 +600 @@
     token.erase(token.length(), 1);  // kill residual index char (the '0')
     output << "'" << prefix << ".dat' title '" << token << "' using " << xargument << ":(sqrt($" << i+1 << "*$" << i+1 << "+$" << i+2 << "*$" << i+2 << "+$" << i+3 << "*$" << i+3 << ")) " << uses;
-    if (i != (Force.ColumnCounter[Force.MatrixCounter]-1))
+    if (i != (Force.ColumnCounter-1))
       output << ", \\";
     output << endl;
@@ -739 +617 @@
 void AbsFirstForceValuePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header[Force.MatrixCounter]);
+  stringstream line(Force.Header);
   string token;
 
@@ -747 +625 @@
   getline(line, token, '\t');
   getline(line, token, '\t');
-  for (int i=7; i< Force.ColumnCounter[Force.MatrixCounter];i+=NDIM) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     getline(line, token, '\t');
     while (token[0] == ' ') // remove leading white spaces
@@ -753 +631 @@
     token.erase(token.length(), 1);  // kill residual index char (the '0')
     output << "'" << prefix << ".dat' title '" << token << "' using " << xargument << ":(abs($" << i+1 << ")) " << uses;
-    if (i != (Force.ColumnCounter[Force.MatrixCounter]-1))
+    if (i != (Force.ColumnCounter-1))
       output << ", \\";
     output << endl;
@@ -770 +648 @@
 void BoxesForcePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header[Force.MatrixCounter]);
-  char *fillcolor[5] = {"black", "red", "blue", "green", "cyan"};
+  stringstream line(Force.Header);
+  const char *fillcolor[5] = {"black", "red", "blue", "green", "cyan"};
   string token;
 
@@ -779 +657 @@
   getline(line, token, '\t');
   getline(line, token, '\t');
-  for (int i=7; i< Force.ColumnCounter[Force.MatrixCounter];i+=NDIM) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     getline(line, token, '\t');
     while (token[0] == ' ') // remove leading white spaces
@@ -785 +663 @@
     token.erase(token.length(), 1);  // kill residual index char (the '0')
     output << "'" << prefix << ".dat' title '" << token << "' using ($" << xargument << "+" << fixed << setprecision(1) << (double)((i-7)/3)*0.2 << "):(sqrt($" << i+1 << "*$" << i+1 << "+$" << i+2 << "*$" << i+2 << "+$" << i+3 << "*$" << i+3 << ")) " << uses << " " << fillcolor[(i-7)/3];
-    if (i != (Force.ColumnCounter[Force.MatrixCounter]-1))
+    if (i != (Force.ColumnCounter-1))
       output << ", \\";
     output << endl;
@@ -802 +680 @@
 void BoxesFirstForceValuePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header[Force.MatrixCounter]);
-  char *fillcolor[5] = {"black", "red", "blue", "green", "cyan"};
+  stringstream line(Force.Header);
+  const char *fillcolor[5] = {"black", "red", "blue", "green", "cyan"};
   string token;
 
@@ -811 +689 @@
   getline(line, token, '\t');
   getline(line, token, '\t');
-  for (int i=7; i< Force.ColumnCounter[Force.MatrixCounter];i+=NDIM) {
+  for (int i=7; i< Force.ColumnCounter;i+=NDIM) {
     getline(line, token, '\t');
     while (token[0] == ' ') // remove leading white spaces
@@ -817 +695 @@
     token.erase(token.length(), 1);  // kill residual index char (the '0')
     output << "'" << prefix << ".dat' title '" << token << "' using ($" << xargument << "+" << fixed << setprecision(1) << (double)((i-7)/3)*0.2 << "):" << i+1 << " " << uses << " " << fillcolor[(i-7)/3];
-    if (i != (Force.ColumnCounter[Force.MatrixCounter]-1))
+    if (i != (Force.ColumnCounter-1))
       output << ", \\";
     output << endl;