Changeset f3dc4c

Timestamp:

Aug 18, 2008, 8:27:34 AM (16 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

8f019c

Parents:

9e5a04d

Message:

Time analysis is back in

File:

• src/analyzer.cpp (modified) (7 diffs)

src/analyzer.cpp

@@ -29 +29 @@
   ForceMatrix Shielding;
   ForceMatrix ShieldingPAS;
-  MatrixContainer Time;
+  EnergyMatrix Time;
   EnergyMatrix EnergyFragments;
   EnergyMatrix HcorrectionFragments;
@@ -51 +51 @@
   bool Hcorrected = true;
   double norm;
+  int counter;
   
   cout << "ANOVA Analyzer" << endl;
@@ -82 +83 @@
   
   // ------------- Parse through all Fragment subdirs --------
-  if (!Energy.ParseMatrix(argv[1], dir, EnergySuffix,0,0)) return 1;
-  Hcorrected = Hcorrection.ParseMatrix(argv[1], "", HCORRECTIONSUFFIX,0,0);
-  if (!Force.ParseMatrix(argv[1], dir, ForcesSuffix,0,0)) return 1;
-  if (!Time.ParseMatrix(argv[1], dir, TimeSuffix, 10,1)) return 1;
+  if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix,0,0)) return 1;
+  Hcorrected = Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX,0,0);
+  if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix,0,0)) return 1;
+  if (!Time.ParseFragmentMatrix(argv[1], dir, TimeSuffix, 10,1)) return 1;
   if (periode != NULL) { // also look for PAS values
-    if (!Shielding.ParseMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
-    if (!ShieldingPAS.ParseMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
+    if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
+    if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
   }
 
@@ -111 +112 @@
   
   // ---------- Parse fragment files created by 'joiner' into an array -------------
-  if (!EnergyFragments.ParseMatrix(argv[1], dir, EnergyFragmentSuffix,0,0)) return 1;
-  if (Hcorrected) HcorrectionFragments.ParseMatrix(argv[1], dir, HcorrectionFragmentSuffix,0,0);
-  if (!ForceFragments.ParseMatrix(argv[1], dir, ForceFragmentSuffix,0,0)) return 1;
+  if (!EnergyFragments.ParseFragmentMatrix(argv[1], dir, EnergyFragmentSuffix,0,0)) return 1;
+  if (Hcorrected) HcorrectionFragments.ParseFragmentMatrix(argv[1], dir, HcorrectionFragmentSuffix,0,0);
+  if (!ForceFragments.ParseFragmentMatrix(argv[1], dir, ForceFragmentSuffix,0,0)) return 1;
   if (periode != NULL) { // also look for PAS values
-    if (!ShieldingFragments.ParseMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
-    if (!ShieldingPASFragments.ParseMatrix(argv[1], dir, ShieldingPASSuffix, 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;
   }
 
@@ -160 +161 @@
   
   output << endl << "Total Times" << endl << "===============" << endl << Time.Header << endl;
-  Time.SetLastMatrix(0., 0);
-  for (int BondOrder=KeySet.Order;BondOrder--;)
-    for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;)
-      for(int j=Time.RowCounter[Time.MatrixCounter];j--;)
-        for(int k=Time.ColumnCounter;k--;) {
-          Time.Matrix[ Time.MatrixCounter ][j][k] += Time.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
-        }
   for(int j=0;j<Time.RowCounter[Time.MatrixCounter];j++) {
-    for(int k=0;k<Time.ColumnCounter;k++)
+    for(int k=0;k<Time.ColumnCounter;k++) {
       output << scientific << Time.Matrix[ Time.MatrixCounter ][j][k] << "\t";
+    }
     output << endl;
   }
   output << endl;
   output.close();
+  for(int k=0;k<Time.ColumnCounter;k++)
+    Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter] ][k] = Time.Matrix[ Time.MatrixCounter ][Time.RowCounter[Time.MatrixCounter]-1][k];
 
   // +++++++++++++++ ANALYZING ++++++++++++++++++++++++++++++
@@ -182 +179 @@
 
   // +++++++++++++++++++++++++++++++++++++++ Plotting Simtime vs Bond Order
+  // +++++++++++++++++++++++++++++++++++++++ Plotting Delta Simtime vs Bond Order
   if (!OpenOutputFile(output, argv[3], "SimTime-Order.dat" )) return false;
-  Time.SetLastMatrix(0., 0);
+  if (!OpenOutputFile(output2, argv[3], "DeltaSimTime-Order.dat" )) return false;
+  for(int j=Time.RowCounter[Time.MatrixCounter];j--;)
+    for(int k=Time.ColumnCounter;k--;) {
+      Time.Matrix[ Time.MatrixCounter ][j][k] = 0.;
+    }
+  counter = 0;
   output << "#Order\tFrag.No.\t" << Time.Header << endl;
+  output2 << "#Order\tFrag.No.\t" << Time.Header << endl;
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;)
@@ -191 +195 @@
           Time.Matrix[ Time.MatrixCounter ][j][k] += Time.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
         }
-    output << BondOrder+1 << "\t" << KeySet.FragmentsPerOrder[BondOrder];
-    for(int k=0;k<Time.ColumnCounter;k++)
-      output << "\t" << scientific << Time.Matrix[ Time.MatrixCounter ][1][k];
-    output << endl;
+    counter += KeySet.FragmentsPerOrder[BondOrder];
+    output << BondOrder+1 << "\t" << counter;
+    output2 << BondOrder+1 << "\t" << counter;
+    for(int k=0;k<Time.ColumnCounter;k++) {
+      output << "\t" << scientific << Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter]-1 ][k];
+      if (fabs(Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter] ][k]) > MYEPSILON)
+        output2 << "\t" << scientific << Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter]-1 ][k] / Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter] ][k];
+      else
+        output2 << "\t" << scientific << Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter]-1 ][k];
+    }
+    output << endl;
+    output2 << endl;
   }
   output.close();
+  output2.close();
+
 
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in energy to full QM