Changeset 71e7c7

Timestamp:

Jul 23, 2009, 11:31:00 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:

986c80

Parents:

631dcb (diff), cc36a5 (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.

Message:

Merge branch 'test'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/datacreator.cpp
molecuilder/src/joiner.cpp

all Chi.. matrices were EnergyMatrix instead of ForceMatrix, despite in all branches (test, master, Thermostat) always some ParseIndices was called for them, which is only implemented in the ForceMatrix. I change hence to ForceMatrix and removed the comments from ParseIndices(). But this is untested.

Location:

src

Files:

• analyzer.cpp (modified) (2 diffs)
• joiner.cpp (modified) (3 diffs)

src/analyzer.cpp

@@ -222 +222 @@
     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[Chi.MatrixCounter];k++)
+      for(int k=0;k<ChiPAS.ColumnCounter[ChiPAS.MatrixCounter];k++)
         output << scientific << ChiPAS.Matrix[ ChiPAS.MatrixCounter ][j][k] << "\t";
       output << endl;
@@ -523 +523 @@
     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

@@ -34 +34 @@
   ForceMatrix ShieldingFragments;
   ForceMatrix ShieldingPASFragments;
-  EnergyMatrix Chi;
-  EnergyMatrix ChiPAS;
-  EnergyMatrix ChiFragments;
-  EnergyMatrix ChiPASFragments;
+  ForceMatrix Chi;
+  ForceMatrix ChiPAS;
+  ForceMatrix ChiFragments;
+  ForceMatrix ChiPASFragments;
   KeySetsContainer KeySet;  
   stringstream prefix;
@@ -104 +104 @@
     if(!Shielding.ParseIndices(argv[1])) return 1;
     if(!ShieldingPAS.ParseIndices(argv[1])) return 1;
-    //if(!Chi.ParseIndices()) return 1;
-    //if(!ChiPAS.ParseIndices()) return 1;
+    if(!Chi.ParseIndices(argv[1])) return 1;
+    if(!ChiPAS.ParseIndices(argv[1])) return 1;
   }
 
@@ -167 +167 @@
       if (!ShieldingPAS.SumSubForces(ShieldingPASFragments, KeySet, BondOrder, 1.)) return 1;
       if (!ChiFragments.SumSubManyBodyTerms(Chi, KeySet, BondOrder)) return 1;
-      if (!Chi.SumSubEnergy(ChiFragments, NULL, KeySet, BondOrder, 1.)) return 1;
+      if (!Chi.SumSubForces(ChiFragments, KeySet, BondOrder, 1.)) return 1;
       if (!ChiPASFragments.SumSubManyBodyTerms(ChiPAS, KeySet, BondOrder)) return 1;
-      if (!ChiPAS.SumSubEnergy(ChiPASFragments, NULL,KeySet, BondOrder, 1.)) return 1;
+      if (!ChiPAS.SumSubForces(ChiPASFragments, KeySet, BondOrder, 1.)) return 1;
     }