Changeset b4b7c3 for src

Timestamp:

Aug 6, 2008, 8:50:52 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:

d7e30c

Parents:

fb9364

Message:

pcp.speed is parsed and analyzed again (Time matrices).

This was commented out before.

File:

• src/analyzer.cpp (modified) (4 diffs)

src/analyzer.cpp

@@ -85 +85 @@
   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 (!Time.ParseMatrix(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;
@@ -159 +159 @@
   }
   
-//  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++)
-//      output << scientific << Time.Matrix[ Time.MatrixCounter ][j][k] << "\t";
-//    output << endl;
-//  }
-//  output << endl;
+  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++)
+      output << scientific << Time.Matrix[ Time.MatrixCounter ][j][k] << "\t";
+    output << endl;
+  }
+  output << endl;
   output.close();
 
@@ -181 +181 @@
   // ======================================= Creating the data files ==============================================================
 
-//  // +++++++++++++++++++++++++++++++++++++++ Plotting Simtime vs Bond Order
-//  if (!OpenOutputFile(output, argv[3], "SimTime-Order.dat" )) return false;
-//  Time.SetLastMatrix(0., 0);
-//  output << "#Order\tFrag.No.\t" << Time.Header << endl;
-//  for (int BondOrder=0;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];
-//        }
-//    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;
-//  }
-//  output.close();
+  // +++++++++++++++++++++++++++++++++++++++ Plotting Simtime vs Bond Order
+  if (!OpenOutputFile(output, argv[3], "SimTime-Order.dat" )) return false;
+  Time.SetLastMatrix(0., 0);
+  output << "#Order\tFrag.No.\t" << Time.Header << endl;
+  for (int BondOrder=0;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];
+        }
+    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;
+  }
+  output.close();
 
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in energy to full QM
@@ -264 +264 @@
   
   // +++++++++++++++++++++++++++++++++++++++ Plotting Simtime vs Bond Order
-  //if (!CreatePlotOrder(Time, KeySet, argv[3], "SimTime-Order", 1, "below", "y", "",  1, 1, "bond order k", "Evaluation time [s]", Orderxrange.str().c_str(), "", "1" , "with linespoints", EnergyPlotLine)) return 1;
+  if (!CreatePlotOrder(Time, KeySet, argv[3], "SimTime-Order", 1, "below", "y", "",  1, 1, "bond order k", "Evaluation time [s]", Orderxrange.str().c_str(), "", "1" , "with linespoints", EnergyPlotLine)) return 1;
   
   // +++++++++++++++++++++++++++++++++++++++ Plotting deviation in energy to full QM