Changeset 68cfd1 for molecuilder/src/analyzer.cpp

Timestamp:

Sep 28, 2008, 5:55:04 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

a7b3b8

Parents:

556157

Message:

corrected molecule::VerletForceIntegration() and analyzer creates data and plot file for shielding values

File:

• molecuilder/src/analyzer.cpp (modified) (3 diffs)

molecuilder/src/analyzer.cpp

@@ -116 +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, ShieldingSuffix, 1, 0)) return 1;
-    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
+    if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingFragmentSuffix, 1, 0)) return 1;
+    if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASFragmentSuffix, 1, 0)) return 1;
   }
 
@@ -211 +211 @@
   output2.close();
 
-
+  // +++++++++++++++++++++++++++++++++++++++ Plotting shieldings
+  if (periode != NULL) { // also look for PAS values
+    if (!OpenOutputFile(output, argv[3], "ShieldingPAS-Atom.dat" )) return false;
+    output << "#" << ShieldingPAS.Header << endl;
+    for(int j=0;j<ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter];j++) {
+      for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
+        output << scientific << ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k]*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
+      output << endl;
+    }
+    output << endl << endl; // another two newlines to partition the data
+    for(int j=0;j<ShieldingPASFragments.RowCounter[ShieldingPASFragments.MatrixCounter];j++) {
+      for(int k=0;k<ShieldingPASFragments.ColumnCounter;k++)
+        output << scientific << ShieldingPASFragments.Matrix[ ShieldingPASFragments.MatrixCounter ][j][k]*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
+      output << endl;
+    }
+    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;
@@ -359 +378 @@
   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], "ShieldingPAS-Atom.pyx")) return 1;
+    CreatePlotHeader(output, "ShieldingPAS-Atom", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "chemical shielding value [ppm]");
+    output << "plot \\" << endl;  
+    output << "'ShieldingPAS-Atom.dat' index 0 title 'DFT' using 2:6 with linespoints, \\" << endl;
+    output << "'ShieldingPAS-Atom.dat' index 1 title 'BOSSANOVA' using 2:6 with linespoints" << endl;
+    output.close();  
+  }
+
   // create Makefile
   if(!OpenOutputFile(output, argv[3], "Makefile")) return 1;