Changeset 3af1f0 for src/moleculelist.cpp

Timestamp:

Apr 8, 2009, 11:25:03 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:

d67150

Parents:

ca2587

Message:

MoleculeListClass::Enumerate() lists center and size of molecule, fix of MoleculeListClass::ReturnIndex()

• MoleculeListClass::Enumerate(): Vector Center and size (greatest distance from center) is also given
• MoleculeListClass::ReturnIndex(): BUGFIX - counter instead of molecule::IndexNr was still used

File:

• src/moleculelist.cpp (modified) (2 diffs)

src/moleculelist.cpp

@@ -128 +128 @@
   atom *Walker = NULL;
   int Counts[MAX_ELEMENTS];
+  double size=0;
+  Vector Origin;
 
   // header
-  *out << "Index\tName\tNo.Atoms\tformula" << endl;
+  *out << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
   cout << Verbose(0) << "-----------------------------------------------" << endl;
   if (ListOfMolecules.size() == 0)
     *out << "\tNone" << endl;
   else {
+    Origin.Zero();
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
       // reset element counts
       for (int j = 0; j<MAX_ELEMENTS;j++)
         Counts[j] = 0;
-      // count atoms per element
+      // count atoms per element and determine size of bounding sphere
+      size=0.;
       Walker = (*ListRunner)->start;
       while (Walker->next != (*ListRunner)->end) {
         Walker = Walker->next;
         Counts[Walker->type->Z]++;
+        if (Walker->x.DistanceSquared(&Origin) > size)
+          size = Walker->x.DistanceSquared(&Origin);
       }
       // output Index, Name, number of atoms, chemical formula
       *out << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
       Elemental = (*ListRunner)->elemente->end;
-      while(Elemental != (*ListRunner)->elemente->start) {
+      while(Elemental->previous != (*ListRunner)->elemente->start) {
         Elemental = Elemental->previous;
         if (Counts[Elemental->Z] != 0)
           *out << Elemental->symbol << Counts[Elemental->Z];
       }
-      *out << endl;
+      // Center and size
+      *out << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
     }
   }
@@ -164 +171 @@
 molecule * MoleculeListClass::ReturnIndex(int index)
 {
-  int count = 1;
-  MoleculeList::iterator ListRunner = ListOfMolecules.begin();
-  for(; ((ListRunner != ListOfMolecules.end()) && (count < index)); ListRunner++);
-  if (count == index)
-    return (*ListRunner);
-  else
-    return NULL;
+  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
+    if ((*ListRunner)->IndexNr == index)
+      return (*ListRunner);
+  return NULL;
 };