Changes in src/analyzer.cpp [5bc4d0:f05407]

File:

• src/analyzer.cpp (modified) (9 diffs, 1 prop)

src/analyzer.cpp

@@ -29 +29 @@
   ForceMatrix Shielding;
   ForceMatrix ShieldingPAS;
-  ForceMatrix Chi;
-  ForceMatrix ChiPAS;
   EnergyMatrix Time;
   EnergyMatrix EnergyFragments;
@@ -37 +35 @@
   ForceMatrix ShieldingFragments;
   ForceMatrix ShieldingPASFragments;
-  ForceMatrix ChiFragments;
-  ForceMatrix ChiPASFragments;
   KeySetsContainer KeySet;
   ofstream output;
@@ -94 +90 @@
     if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
     if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
-    if (!Chi.ParseFragmentMatrix(argv[1], dir, ChiSuffix, 1, 0)) return 1;
-    if (!ChiPAS.ParseFragmentMatrix(argv[1], dir, ChiPASSuffix, 1, 0)) return 1;
   }
 
@@ -111 +105 @@
     if(!Shielding.ParseIndices(argv[1])) return 1;
     if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
-    if (!ShieldingFragments.AllocateMatrix(Shielding.Header, Shielding.MatrixCounter, Shielding.RowCounter, Shielding.ColumnCounter)) return 1;
-    if (!ShieldingPASFragments.AllocateMatrix(ShieldingPAS.Header, ShieldingPAS.MatrixCounter, ShieldingPAS.RowCounter, ShieldingPAS.ColumnCounter)) return 1;
-    if(!ShieldingFragments.ParseIndices(argv[1])) return 1;
-    if(!ShieldingPASFragments.ParseIndices(argv[1])) return 1;
-    if(!Chi.ParseIndices(argv[1])) return 1;
-    if(!ChiPAS.ParseIndices(argv[1])) return 1;
-    if (!ChiFragments.AllocateMatrix(Chi.Header, Chi.MatrixCounter, Chi.RowCounter, Chi.ColumnCounter)) return 1;
-    if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
-    if(!ChiFragments.ParseIndices(argv[1])) return 1;
-    if(!ChiPASFragments.ParseIndices(argv[1])) return 1;
   }
 
@@ -132 +116 @@
   if (!ForceFragments.ParseFragmentMatrix(argv[1], dir, ForceFragmentSuffix,0,0)) return 1;
   if (periode != NULL) { // also look for PAS values
-    if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingFragmentSuffix, 1, 0)) return 1;
-    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASFragmentSuffix, 1, 0)) return 1;
-    if (!ChiFragments.ParseFragmentMatrix(argv[1], dir, ChiFragmentSuffix, 1, 0)) return 1;
-    if (!ChiPASFragments.ParseFragmentMatrix(argv[1], dir, ChiPASFragmentSuffix, 1, 0)) return 1;
+    if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
+    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
   }
 
@@ -173 +155 @@
       for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
         output << scientific << ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k] << "\t";
-      output << endl;
-    }
-    output << endl;
-
-    output << endl << "Total Chis" << endl << "===============" << endl << Chi.Header[Chi.MatrixCounter] << endl;
-    for(int j=0;j<Chi.RowCounter[Chi.MatrixCounter];j++) {
-      for(int k=0;k<Chi.ColumnCounter;k++)
-        output << scientific << Chi.Matrix[ Chi.MatrixCounter ][j][k] << "\t";
-      output << endl;
-    }
-    output << endl;
-  
-    output << endl << "Total Chis PAS" << endl << "===============" << endl << ChiPAS.Header[ChiPAS.MatrixCounter] << endl;
-    for(int j=0;j<ChiPAS.RowCounter[ChiPAS.MatrixCounter];j++) {
-      for(int k=0;k<ChiPAS.ColumnCounter;k++)
-        output << scientific << ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t";
       output << endl;
     }
@@ -245 +211 @@
   output2.close();
 
-  // +++++++++++++++++++++++++++++++++++++++ Plotting shieldings
-
-  if (periode != NULL) { // also look for PAS values
-    if (!CreateDataDeltaForcesOrderPerAtom(ShieldingPAS, ShieldingPASFragments, KeySet, argv[3], "DeltaShieldingsPAS-Order", "Plot of error between approximated shieldings and full shieldings versus the Bond Order", datum)) return 1;
-    if (!CreateDataForcesOrderPerAtom(ShieldingPASFragments, KeySet, argv[3], "ShieldingsPAS-Order", "Plot of approximated shieldings versus the Bond Order", datum)) return 1;
-    if (!AppendOutputFile(output, argv[3], "ShieldingsPAS-Order.dat" )) return false;
-    output << endl << "# Full" << endl;
-    for(int j=0;j<ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter];j++) {
-      output << j << "\t";
-      for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
-        output << scientific <<  ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k] << "\t"; //*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
-      output << endl;
-    }
-    output.close();
-    if (!CreateDataDeltaForcesOrderPerAtom(ChiPAS, ChiPASFragments, KeySet, argv[3], "DeltaChisPAS-Order", "Plot of error between approximated Chis and full Chis versus the Bond Order", datum)) return 1;
-    if (!CreateDataForcesOrderPerAtom(ChiPASFragments, KeySet, argv[3], "ChisPAS-Order", "Plot of approximated Chis versus the Bond Order", datum)) return 1;
-    if (!AppendOutputFile(output, argv[3], "ChisPAS-Order.dat" )) return false;
-    output << endl << "# Full" << endl;
-    for(int j=0;j<ChiPAS.RowCounter[ChiPAS.MatrixCounter];j++) {
-      output << j << "\t";
-      for(int k=0;k<ChiPAS.ColumnCounter;k++)
-        output << scientific <<  ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t"; //*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
-      output << endl;
-    }
-    output.close();
-  }
-
-  
+
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in energy to full QM
   if (!CreateDataDeltaEnergyOrder(Energy, EnergyFragments, KeySet, argv[3], "DeltaEnergies-Order", "Plot of error between approximated and full energies energies versus the Bond Order", datum)) return 1;
@@ -293 +232 @@
   // ++++++++++++++++++++++++++++++++++++++Plotting Forces vs. Order
   if (!CreateDataForcesOrderPerAtom(ForceFragments, KeySet, argv[3], "Forces-Order", "Plot of approximated forces versus the Bond Order", datum)) return 1;
-  if (!AppendOutputFile(output, argv[3], "Forces-Order.dat" )) return false;
-  output << endl << "# Full" << endl;
-  for(int j=0;j<Force.RowCounter[Force.MatrixCounter];j++) {
-    output << j << "\t";
-    for(int k=0;k<Force.ColumnCounter;k++)
-      output << scientific <<  Force.Matrix[ Force.MatrixCounter ][j][k] << "\t";
-    output << endl;
-  }
-  output.close();
+
   // min force
   if (!CreateDataForcesOrder(ForceFragments, KeySet, argv[3], "MinForces-Order", "Plot of min approximated forces versus the Bond Order", datum, CreateMinimumForce)) return 1;
@@ -428 +359 @@
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MaxForces-FragmentOrder", 5, "below", "y", "set boxwidth 0.2", 1, 1, "bond order", "maximum of approximated forces [Ht/a.u.]", Orderxrange.str().c_str(), yrange.str().c_str(), "1" , "with boxes fillcolor", BoxesForcePlotLine)) return 1;
  
-  // +++++++++++++++++++++++++++++++=Ploting approximated and true shielding for each atom
-  if (periode != NULL) { // also look for PAS values
-    if(!OpenOutputFile(output, argv[3], "ShieldingsPAS-Order.pyx")) return 1;
-    if(!OpenOutputFile(output2, argv[3], "DeltaShieldingsPAS-Order.pyx")) return 1;
-    CreatePlotHeader(output, "ShieldingsPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical shielding value [ppm]");
-    CreatePlotHeader(output2, "DeltaShieldingsPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical shielding value [ppm]");
-    double step=0.8/KeySet.Order;
-    output << "set boxwidth " << step << endl;
-    output << "plot [0:" << ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter]+10 << "]\\" << endl;
-    output2 << "plot [0:" << ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter]+10 << "]\\" << endl;
-    for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
-      output << "'ShieldingsPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1+" << step*(double)BondOrder << "):7 with boxes, \\" << endl;
-      output2 << "'DeltaShieldingsPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1):7 with linespoints";
-      if (BondOrder-1 != KeySet.Order)
-        output2 << ", \\" << endl;
-    }
-    output << "'ShieldingsPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
-    output.close();  
-    output2.close();  
-
-    if(!OpenOutputFile(output, argv[3], "ChisPAS-Order.pyx")) return 1;
-    if(!OpenOutputFile(output2, argv[3], "DeltaChisPAS-Order.pyx")) return 1;
-    CreatePlotHeader(output, "ChisPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical Chi value [ppm]");
-    CreatePlotHeader(output2, "DeltaChisPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical Chi value [ppm]");
-    output << "set boxwidth " << step << endl;
-    output << "plot [0:" << ChiPAS.RowCounter[ChiPAS.MatrixCounter]+10 << "]\\" << endl;
-    output2 << "plot [0:" << ChiPAS.RowCounter[ChiPAS.MatrixCounter]+10 << "]\\" << endl;
-    for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
-      output << "'ChisPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1+" << step*(double)BondOrder << "):7 with boxes, \\" << endl;
-      output2 << "'DeltaChisPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1):7 with linespoints";
-      if (BondOrder-1 != KeySet.Order)
-        output2 << ", \\" << endl;
-    }
-    output << "'ChisPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
-    output.close();  
-    output2.close();  
-  }
-
   // create Makefile
   if(!OpenOutputFile(output, argv[3], "Makefile")) return 1;