Changeset f14a52

Timestamp:

Jun 23, 2008, 11:23:50 AM (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:

1f066fe

Parents:

256520

Message:

StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond for non-hydrogen atoms by accident

This happened because the adding was hidden in the "*out << ... << endl;" directive. I put it onto an extra line and surrounded it with "*out <<" and so on so that it may still be used.

File:

• src/molecules.cpp (modified) (6 diffs)

src/molecules.cpp

@@ -3123 +3123 @@
 //          *out << ", whose son is " << *SonList[OtherFather->nr] << "." << endl; 
           if (OtherFather->nr > FatherOfRunner->nr) { // add bond (nr check is for adding only one of both variants: ab, ba)
-//            *out << Verbose(3) << "Adding Bond: " << Leaf->AddBond(Runner, SonList[OtherFather->nr], ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree) << "." << endl;
+//            *out << Verbose(3) << "Adding Bond: ";
+//            *out << 
+            Leaf->AddBond(Runner, SonList[OtherFather->nr], ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree);
+//            *out << "." << endl;
             //NumBonds[Runner->nr]++;
           } else { 
@@ -3743 +3746 @@
   bool flag = true;
 
-//  *out << Verbose(1) << "Begin of ScanForPeriodicCorrection." << endl;
+  *out << Verbose(1) << "Begin of ScanForPeriodicCorrection." << endl;
 
   ColorList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
@@ -3757 +3760 @@
       for (int i=NDIM;i--;) {
         tmp = fabs(Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i]);
-        //*out << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
+        *out << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
         if (tmp > BondDistance) {
           OtherBinder = Binder->next; // note down binding partner for later re-insertion
           unlink(Binder);   // unlink bond
-//          *out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
+          *out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
           flag = true;
           break;
@@ -3775 +3778 @@
       }
       TranslationVector.MatrixMultiplication(matrix);
-      //*out << "Translation vector is ";
-      //TranslationVector.Output(out);
-      //*out << endl;
+      *out << "Translation vector is ";
+      TranslationVector.Output(out);
+      *out << endl;
       // apply to all atoms of first component via BFS
       for (int i=AtomCount;i--;)
@@ -3799 +3802 @@
       link(Binder, OtherBinder);
     } else {
-//      *out << Verbose(2) << "No corrections for this fragment." << endl;
+      *out << Verbose(2) << "No corrections for this fragment." << endl;
     }
     //delete(CompStack);
@@ -3808 +3811 @@
   Free((void **)&ColorList, "molecule::ScanForPeriodicCorrection: *ColorList");
   Free((void **)&matrix, "molecule::ScanForPeriodicCorrection: *matrix");
-//  *out << Verbose(1) << "End of ScanForPeriodicCorrection." << endl;
+  *out << Verbose(1) << "End of ScanForPeriodicCorrection." << endl;
 };