Changeset 95634f for src

Timestamp:

Oct 15, 2008, 6:20:51 PM (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:

e198c7

Parents:

19f3d6

Message:

Analyzer now prints usable ShieldingsPAS data and plot files (so that comparison per order is possible).

File:

• src/analyzer.cpp (modified) (5 diffs)

src/analyzer.cpp

@@ -105 +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;
   }
 
@@ -116 +120 @@
   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 +215 @@
   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();
+
+  
   // +++++++++++++++++++++++++++++++++++++++ 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;
@@ -232 +252 @@
   // ++++++++++++++++++++++++++++++++++++++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;
@@ -359 +387 @@
   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;
+    CreatePlotHeader(output, "ShieldingsPAS-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;
+    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;
+    }
+    output << "'ShieldingsPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
+    output.close();  
+  }
+
   // create Makefile
   if(!OpenOutputFile(output, argv[3], "Makefile")) return 1;