Changeset f39735 for molecuilder/src/analyzer.cpp

Timestamp:

Jul 23, 2009, 1:45:24 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

47548d

Parents:

560995 (diff), 1b2aa1 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• molecuilder/src/analyzer.cpp (modified) (18 diffs)

molecuilder/src/analyzer.cpp

@@ -3 +3 @@
  * Takes evaluated fragments (energy and forces) and does evaluation of how sensible the BOSSANOVA
  * approach was, e.g. in the decay of the many-body-contributions.
- *    
+ *
  */
 
@@ -9 +9 @@
 
 #include "datacreator.hpp"
-#include "helpers.hpp" 
+#include "helpers.hpp"
 #include "parser.hpp"
-#include "periodentafel.hpp" 
+#include "periodentafel.hpp"
 
 // include config.h
@@ -55 +55 @@
   stringstream yrange;
   char *dir = NULL;
-  bool NoHCorrection = false;
   bool NoHessian = false;
   bool NoTime = false;
+  bool NoHCorrection = true;
   int counter;
-  
+
   cout << "ANOVA Analyzer" << endl;
   cout << "==============" << endl;
-  
+
   // Get the command line options
   if (argc < 4) {
@@ -76 +76 @@
     strcat(dir, argv[2]);
   }
-  
+
   if (argc > 4) {
     cout << "Loading periodentafel." << endl;
@@ -82 +82 @@
     periode->LoadPeriodentafel(argv[4]);
   }
-  
+
   // Test the given directory
   if (!TestParams(argc, argv))
@@ -88 +88 @@
 
   // +++++++++++++++++ PARSING +++++++++++++++++++++++++++++++
-  
+
   // ------------- Parse through all Fragment subdirs --------
   if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix,0,0)) return 1;
@@ -113 +113 @@
 
   // ---------- Parse the TE Factors into an array -----------------
-  if (!Energy.InitialiseIndices()) return 1;
-  if (!NoHCorrection) 
-    Hcorrection.InitialiseIndices();
-  
+  if (!Energy.ParseIndices()) return 1;
+  if (!NoHCorrection) Hcorrection.ParseIndices();
+
   // ---------- Parse the Force indices into an array ---------------
   if (!Force.ParseIndices(argv[1])) return 1;
@@ -148 +147 @@
   if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
   if (!KeySet.ParseManyBodyTerms()) return 1;
-  
+
   // ---------- Parse fragment files created by 'joiner' into an array -------------
   if (!EnergyFragments.ParseFragmentMatrix(argv[1], dir, EnergyFragmentSuffix,0,0)) return 1;
@@ -164 +163 @@
 
   // +++++++++++++++ TESTING ++++++++++++++++++++++++++++++
-  
+
   // print energy and forces to file
   filename.str("");
@@ -245 +244 @@
 
   // +++++++++++++++ ANALYZING ++++++++++++++++++++++++++++++
-  
+
   cout << "Analyzing ..." << endl;
 
@@ -330 +329 @@
   }
 
-  
+
   // +++++++++++++++++++++++++++++++++++++++ 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;
-  
+
   // +++++++++++++++++++++++++++++++++++Plotting Energies vs. Order
   if (!CreateDataEnergyOrder(EnergyFragments, KeySet, argv[3], "Energies-Order", "Plot of approximated energies versus the Bond Order", datum)) return 1;
-  
+
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in forces to full QM
   if (!CreateDataDeltaForcesOrderPerAtom(Force, ForceFragments, KeySet, argv[3], "DeltaForces-Order", "Plot of error between approximated forces and full forces versus the Bond Order", datum)) return 1;
@@ -399 +398 @@
 
   // ======================================= Creating the plot files ==============================================================
- 
+
   Orderxrange << "[1:" << KeySet.Order << "]";
   Fragmentxrange << "[0:" << KeySet.FragmentCounter+1 << "]";
@@ -411 +410 @@
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in energy to full QM
   if (!CreatePlotOrder(Energy, KeySet, argv[3], "DeltaEnergies-Order", 1, "outside", "y", "",  1, 1, "bond order k", "absolute error in energy [Ht]", Orderxrange.str().c_str(), yrange.str().c_str(), "1" , "with linespoints", AbsEnergyPlotLine)) return 1;
-  
+
   // +++++++++++++++++++++++++++++++++++Plotting Energies vs. Order
   if (!CreatePlotOrder(Energy, KeySet, argv[3], "Energies-Order", 1, "outside", "", "",  1, 1, "bond order k", "approximate energy [Ht]", Orderxrange.str().c_str(), "", "1" , "with linespoints", EnergyPlotLine)) return 1;
@@ -429 +428 @@
   if(!OpenOutputFile(output, argv[3], "DeltaMinMeanMaxTotalForce-Order.pyx")) return 1;
   CreatePlotHeader(output, "DeltaMinMeanMaxTotalForce-Order", 1, "bottom left", "y", NULL,  1, 1, "bond order k", "absolute error in total forces [Ht/a.u.]");
-  output << "plot " << Orderxrange.str().c_str() << " [1e-8:1e+0] \\" << endl;  
+  output << "plot " << Orderxrange.str().c_str() << " [1e-8:1e+0] \\" << endl;
   output << "'DeltaMinForces-Order.dat' title 'minimum' using 1:(sqrt($" << 8 << "*$" << 8 << "+$" << 8+1 << "*$" << 8+1 << "+$" << 8+2 << "*$" << 8+2 << ")) with linespoints, \\" << endl;
   output << "'DeltaMeanForces-Order.dat' title 'mean' using 1:(abs($" << 8 << ")) with linespoints, \\" << endl;
   output << "'DeltaMaxForces-Order.dat' title 'maximum' using 1:(sqrt($" << 8 << "*$" << 8 << "+$" << 8+1 << "*$" << 8+1 << "+$" << 8+2 << "*$" << 8+2 << ")) with linespoints" << endl;
-  output.close();  
+  output.close();
 
   // ++++++++++++++++++++++++++++++++++++++Plotting Forces vs. Order
@@ -448 +447 @@
   if(!OpenOutputFile(output, argv[3],"MinMeanMaxTotalForce-Order.pyx")) return 1;
   CreatePlotHeader(output, "MinMeanMaxTotalForce-Order", 1, "bottom left", "y", NULL, 1, 1, "bond order k", "absolute total force [Ht/a.u.]");
-  output << "plot "<< Orderxrange.str().c_str() << " [1e-8:1e+0] \\" << endl;  
+  output << "plot "<< Orderxrange.str().c_str() << " [1e-8:1e+0] \\" << endl;
   output << "'MinForces-Order.dat' title 'minimum' using 1:(sqrt($" << 8 << "*$" << 8 << "+$" << 8+1 << "*$" << 8+1 << "+$" << 8+2 << "*$" << 8+2 << ")) with linespoints, \\" << endl;
   output << "'MeanForces-Order.dat' title 'mean' using 1:(abs($" << 8 << ")) with linespoints, \\" << endl;
   output << "'MaxForces-Order.dat' title 'maximum' using 1:(sqrt($" << 8 << "*$" << 8 << "+$" << 8+1 << "*$" << 8+1 << "+$" << 8+2 << "*$" << 8+2 << ")) with linespoints" << endl;
-  output.close();  
+  output.close();
 
   // ++++++++++++++++++++++++++++++++++++++Plotting vector sum vs. Order
@@ -471 +470 @@
   // min
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MinForces-Fragment", 5, "below", "y", "set boxwidth 0.2", 1, 5, "fragment number", "minimum of approximated forces [Ht/a.u.]", Fragmentxrange.str().c_str(), yrange.str().c_str(), "2" , "with boxes fillcolor", BoxesForcePlotLine)) return 1;
-    
+
   // mean
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MeanForces-Fragment", 5, "below", "y", "set boxwidth 0.2", 1, 5, "fragment number", "mean of approximated forces [Ht/a.u.]", Fragmentxrange.str().c_str(), yrange.str().c_str(), "2" , "with boxes fillcolor", BoxesFirstForceValuePlotLine)) return 1;
-    
+
   // max
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MaxForces-Fragment", 5, "below", "y", "set boxwidth 0.2", 1, 5, "fragment number", "maximum of approximated forces [Ht/a.u.]", Fragmentxrange.str().c_str(), yrange.str().c_str(), "2" , "with boxes fillcolor", BoxesForcePlotLine)) return 1;
@@ -481 +480 @@
   // min
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MinForces-FragmentOrder", 5, "below", "y", "set boxwidth 0.2", 1, 1, "bond order", "minimum of approximated forces [Ht/a.u.]", Orderxrange.str().c_str(), yrange.str().c_str(), "1" , "with boxes fillcolor", BoxesForcePlotLine)) return 1;
-    
+
   // mean
   if (!CreatePlotOrder(ForceFragments, KeySet, argv[3], "MeanForces-FragmentOrder", 5, "below", "y", "set boxwidth 0.2", 1, 1, "bond order", "mean of approximated forces [Ht/a.u.]", Orderxrange.str().c_str(), yrange.str().c_str(), "1" , "with boxes fillcolor", BoxesFirstForceValuePlotLine)) return 1;
-    
+
   // max
   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
@@ -553 +552 @@
   output << "\trm -rf $(EPS)" << endl;
   output.close();
- 
+
   // ++++++++++++++++ exit ++++++++++++++++++++++++++++++++++
   delete(periode);