Changeset 674220

Timestamp:

Oct 30, 2008, 4:13:32 PM (17 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:

a98603

Parents:

450d63

git-author:

Frederik Heber <heber@…> (10/30/08 00:55:19)

git-committer:

Frederik Heber <heber@…> (10/30/08 16:13:32)

Message:

Implemented analysis of magnetic susceptibilites.

This is very similar to Sigma(PAS), however not with ForceMatrix class but with EnergyMatrix. This is still not finished and yet not working. However, it does not impact on other functions of joiner or analyzer.

Location:

src

Files:

• analyzer.cpp (modified) (8 diffs)
• joiner.cpp (modified) (9 diffs)
• parser.hpp (modified) (1 diff)

src/analyzer.cpp

@@ -29 +29 @@
   ForceMatrix Shielding;
   ForceMatrix ShieldingPAS;
+  ForceMatrix Chi;
+  ForceMatrix ChiPAS;
   EnergyMatrix Time;
   EnergyMatrix EnergyFragments;
@@ -35 +37 @@
   ForceMatrix ShieldingFragments;
   ForceMatrix ShieldingPASFragments;
+  ForceMatrix ChiFragments;
+  ForceMatrix ChiPASFragments;
   KeySetsContainer KeySet;
   ofstream output;
@@ -90 +94 @@
     if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
     if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
+    if (!Chi.ParseFragmentMatrix(argv[1], dir, ChiSuffix, 1, 0)) return 1;
+    if (!ChiPAS.ParseFragmentMatrix(argv[1], dir, ChiPASSuffix, 1, 0)) return 1;
   }
 
@@ -109 +115 @@
     if(!ShieldingFragments.ParseIndices(argv[1])) return 1;
     if(!ShieldingPASFragments.ParseIndices(argv[1])) return 1;
+    if(!Chi.ParseIndices(argv[1])) return 1;
+    if(!ChiPAS.ParseIndices(argv[1])) return 1;
+    if (!ChiFragments.AllocateMatrix(Chi.Header, Chi.MatrixCounter, Chi.RowCounter, Chi.ColumnCounter)) return 1;
+    if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
+    if(!ChiFragments.ParseIndices(argv[1])) return 1;
+    if(!ChiPASFragments.ParseIndices(argv[1])) return 1;
   }
 
@@ -122 +134 @@
     if (!ShieldingFragments.ParseFragmentMatrix(argv[1], dir, ShieldingFragmentSuffix, 1, 0)) return 1;
     if (!ShieldingPASFragments.ParseFragmentMatrix(argv[1], dir, ShieldingPASFragmentSuffix, 1, 0)) return 1;
+    if (!ChiFragments.ParseFragmentMatrix(argv[1], dir, ChiFragmentSuffix, 1, 0)) return 1;
+    if (!ChiPASFragments.ParseFragmentMatrix(argv[1], dir, ChiPASFragmentSuffix, 1, 0)) return 1;
   }
 
@@ -159 +173 @@
       for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
         output << scientific << ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k] << "\t";
+      output << endl;
+    }
+    output << endl;
+
+    output << endl << "Total Chis" << endl << "===============" << endl << Chi.Header[Hessian.MatrixCounter] << endl;
+    for(int j=0;j<Chi.RowCounter[Chi.MatrixCounter];j++) {
+      for(int k=0;k<Chi.ColumnCounter[Chi.MatrixCounter];k++)
+        output << scientific << Chi.Matrix[ Chi.MatrixCounter ][j][k] << "\t";
+      output << endl;
+    }
+    output << endl;
+  
+    output << endl << "Total Chis PAS" << endl << "===============" << endl << ChiPAS.Header[ChiPAS.MatrixCounter] << endl;
+    for(int j=0;j<ChiPAS.RowCounter[ChiPAS.MatrixCounter];j++) {
+      for(int k=0;k<ChiPAS.ColumnCounter[ChiPAS.MatrixCounter];k++)
+        output << scientific << ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t";
       output << endl;
     }
@@ -228 +258 @@
       output << endl;
     }
-  }
-  output.close();
+    output.close();
+    if (!CreateDataDeltaForcesOrderPerAtom(ChiPAS, ChiPASFragments, KeySet, argv[3], "DeltaChisPAS-Order", "Plot of error between approximated Chis and full Chis versus the Bond Order", datum)) return 1;
+    if (!CreateDataForcesOrderPerAtom(ChiPASFragments, KeySet, argv[3], "ChisPAS-Order", "Plot of approximated Chis versus the Bond Order", datum)) return 1;
+    if (!AppendOutputFile(output, argv[3], "ChisPAS-Order.dat" )) return false;
+    output << endl << "# Full" << endl;
+    for(int j=0;j<ChiPAS.RowCounter[ChiPAS.MatrixCounter];j++) {
+      output << j << "\t";
+      for(int k=0;k<ChiPAS.ColumnCounter[ChiPAS.MatrixCounter];k++)
+        output << scientific <<  ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t"; //*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
+      output << endl;
+    }
+    output.close();
+  }
 
   
@@ -404 +445 @@
     }
     output << "'ShieldingsPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
+    output.close();  
+    output2.close();  
+
+    if(!OpenOutputFile(output, argv[3], "ChisPAS-Order.pyx")) return 1;
+    if(!OpenOutputFile(output2, argv[3], "DeltaChisPAS-Order.pyx")) return 1;
+    CreatePlotHeader(output, "ChisPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical Chi value [ppm]");
+    CreatePlotHeader(output2, "DeltaChisPAS-Order", 1, "top right", NULL, NULL,  1, 5, "nuclei index", "iso chemical Chi value [ppm]");
+    output << "set boxwidth " << step << endl;
+    output << "plot [0:" << ChiPAS.RowCounter[ChiPAS.MatrixCounter]+10 << "]\\" << endl;
+    output2 << "plot [0:" << ChiPAS.RowCounter[ChiPAS.MatrixCounter]+10 << "]\\" << endl;
+    for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+      output << "'ChisPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1+" << step*(double)BondOrder << "):7 with boxes, \\" << endl;
+      output2 << "'DeltaChisPAS-Order.dat' index " << BondOrder << " title 'Order " << BondOrder+1 << "' using ($1):7 with linespoints";
+      if (BondOrder-1 != KeySet.Order)
+        output2 << ", \\" << endl;
+    }
+    output << "'ChisPAS-Order.dat' index " << KeySet.Order << " title 'Full' using ($1+" << step*(double)KeySet.Order << "):7 with boxes" << endl;
     output.close();  
     output2.close();  

src/joiner.cpp

@@ -28 +28 @@
   ForceMatrix ShieldingFragments;
   ForceMatrix ShieldingPASFragments;
+  EnergyMatrix Chi;
+  EnergyMatrix ChiPAS;
+  EnergyMatrix ChiFragments;
+  EnergyMatrix ChiPASFragments;
   KeySetsContainer KeySet;  
   stringstream prefix;
@@ -66 +70 @@
     if (!Shielding.ParseFragmentMatrix(argv[1], dir, ShieldingSuffix, 1, 0)) return 1;
     if (!ShieldingPAS.ParseFragmentMatrix(argv[1], dir, ShieldingPASSuffix, 1, 0)) return 1;
+    if (!Chi.ParseFragmentMatrix(argv[1], dir, ChiSuffix, 1, 0)) return 1;
+    if (!ChiPAS.ParseFragmentMatrix(argv[1], dir, ChiPASSuffix, 1, 0)) return 1;
   }
 
@@ -79 +85 @@
     if(!Shielding.ParseIndices(argv[1])) return 1;
     if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
+    if(!Chi.ParseIndices(argv[1])) return 1;
+    if(!ChiPAS.ParseIndices(argv[1])) return 1;
   }
 
   // ---------- Parse the KeySets into an array ---------------
   if (!KeySet.ParseKeySets(argv[1], Force.RowCounter, Force.MatrixCounter)) return 1;
-
   if (!KeySet.ParseManyBodyTerms()) return 1;
+
   if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
   if (Hcorrected)  HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
@@ -91 +99 @@
     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 (!ChiFragments.AllocateMatrix(Chi.Header, Chi.MatrixCounter, Chi.RowCounter, Chi.ColumnCounter)) return 1;
+    if (!ChiPASFragments.AllocateMatrix(ChiPAS.Header, ChiPAS.MatrixCounter, ChiPAS.RowCounter, ChiPAS.ColumnCounter)) return 1;
   }
   
@@ -99 +109 @@
     if(!Shielding.SetLastMatrix(0., 2)) return 1;
     if(!ShieldingPAS.SetLastMatrix(0., 2)) return 1;
+    if(!Chi.SetLastMatrix(0., 2)) return 1;
+    if(!ChiPAS.SetLastMatrix(0., 2)) return 1;
   }
 
@@ -119 +131 @@
     if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return 1;
     if (periode != NULL) { // also look for PAS values
-      cout << "Summing shieldings of order " << BondOrder+1 << " ..." << endl;
+      cout << "Summing shieldings and susceptibilities of order " << BondOrder+1 << " ..." << endl;
       if (!ShieldingFragments.SumSubManyBodyTerms(Shielding, KeySet, BondOrder)) return 1;
       if (!Shielding.SumSubForces(ShieldingFragments, KeySet, BondOrder, 1.)) return 1;
       if (!ShieldingPASFragments.SumSubManyBodyTerms(ShieldingPAS, KeySet, BondOrder)) return 1;
       if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
+      if (!ChiFragments.SumSubManyBodyTerms(Chi, KeySet, BondOrder)) return 1;
+      if (!Chi.SumSubForces(ChiFragments, KeySet, BondOrder, 1.)) return 1;
+      if (!ChiPASFragments.SumSubManyBodyTerms(ChiPAS, KeySet, BondOrder)) return 1;
+      if (!ChiPAS.SumSubForces(ChiPASFragments, KeySet, BondOrder, 1.)) return 1;
     }
 
@@ -138 +154 @@
       if (!Shielding.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingSuffix)) return 1;
       if (!ShieldingPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ShieldingPASSuffix)) return 1;
+      if (!Chi.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ChiSuffix)) return 1;
+      if (!ChiPAS.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ChiPASSuffix)) return 1;
     }
   }
@@ -160 +178 @@
     prefix << dir << ShieldingPASFragmentSuffix;
     if (!ShieldingPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
+    prefix.str(" ");
+    prefix << dir << ChiFragmentSuffix;
+    if (!ChiFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
+    prefix.str(" ");
+    prefix << dir << ChiPASFragmentSuffix;
+    if (!ChiPASFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
   }
 
@@ -169 +193 @@
     if (!Shielding.WriteLastMatrix(argv[1], dir, ShieldingFragmentSuffix)) return 1;
     if (!ShieldingPAS.WriteLastMatrix(argv[1], dir, ShieldingPASFragmentSuffix)) return 1;
+    if (!Chi.WriteLastMatrix(argv[1], dir, ChiFragmentSuffix)) return 1;
+    if (!ChiPAS.WriteLastMatrix(argv[1], dir, ChiPASFragmentSuffix)) return 1;
   }
 

src/parser.hpp

@@ -25 +25 @@
 #define ShieldingFragmentSuffix ".sigma_all_fragment.all"
 #define ShieldingPASFragmentSuffix ".sigma_all_PAS_fragment.all"
+#define ChiSuffix ".chi_all.csv"
+#define ChiPASSuffix ".chi_all_PAS.csv"
+#define ChiFragmentSuffix ".chi_all_fragment.all"
+#define ChiPASFragmentSuffix ".chi_all_PAS_fragment.all"
 #define TimeSuffix ".speed"
 #define EnergyFragmentSuffix ".energyfragment.all"