Changeset ea7176 for src/molecule_graph.cpp

Timestamp:

Mar 19, 2010, 1:29:01 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

e0b6fd

Parents:

80c63d

Message:

FIX: Made AtomCount a Cacheable so that the number of atoms in a molecule will always be correct

All unittests working.
All Complete testcases fail.

File:

• src/molecule_graph.cpp (modified) (9 diffs)

src/molecule_graph.cpp

@@ -125 +125 @@
 
   // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
-  CountAtoms();
-  Log() << Verbose(1) << "AtomCount " << AtomCount << " and bonddistance is " << bonddistance << "." << endl;
-
-  if ((AtomCount > 1) && (bonddistance > 1.)) {
+  Log() << Verbose(1) << "AtomCount " << getAtomCount() << " and bonddistance is " << bonddistance << "." << endl;
+
+  if ((getAtomCount() > 1) && (bonddistance > 1.)) {
     Log() << Verbose(2) << "Creating Linked Cell structure ... " << endl;
     LC = new LinkedCell(this, bonddistance);
@@ -191 +190 @@
     ActOnAllAtoms( &atom::OutputBondOfAtom );
   } else
-    Log() << Verbose(1) << "AtomCount is " << AtomCount << ", thus no bonds, no connections!." << endl;
+    Log() << Verbose(1) << "AtomCount is " << getAtomCount() << ", thus no bonds, no connections!." << endl;
   Log() << Verbose(0) << "End of CreateAdjacencyList." << endl;
   if (free_BG)
@@ -233 +232 @@
     Log() << Verbose(0) << " done." << endl;
   } else {
-    Log() << Verbose(1) << "BondCount is " << BondCount << ", no bonds between any of the " << AtomCount << " atoms." << endl;
+    Log() << Verbose(1) << "BondCount is " << BondCount << ", no bonds between any of the " << getAtomCount() << " atoms." << endl;
   }
   Log() << Verbose(0) << No << " bonds could not be corrected." << endl;
@@ -453 +452 @@
 void DepthFirstSearchAnalysis_Init(struct DFSAccounting &DFS, const molecule * const mol)
 {
-  DFS.AtomStack = new StackClass<atom *> (mol->AtomCount);
+  DFS.AtomStack = new StackClass<atom *> (mol->getAtomCount());
   DFS.CurrentGraphNr = 0;
   DFS.ComponentNumber = 0;
@@ -847 +846 @@
       Root = *iter;
 
-      if (MinimumRingSize[Root->GetTrueFather()->nr] == mol->AtomCount) { // check whether MinimumRingSize is set, if not BFS to next where it is
+      if (MinimumRingSize[Root->GetTrueFather()->nr] == mol->getAtomCount()) { // check whether MinimumRingSize is set, if not BFS to next where it is
         Walker = Root;
 
         //Log() << Verbose(1) << "---------------------------------------------------------------------------------------------------------" << endl;
-        CyclicStructureAnalysis_BFSToNextCycle(Root, Walker, MinimumRingSize, mol->AtomCount);
+        CyclicStructureAnalysis_BFSToNextCycle(Root, Walker, MinimumRingSize, mol->getAtomCount());
 
       }
@@ -881 +880 @@
   int MinRingSize = -1;
 
-  InitializeBFSAccounting(BFS, AtomCount);
+  InitializeBFSAccounting(BFS, getAtomCount());
 
   //Log() << Verbose(1) << "Back edge list - ";
@@ -1117 +1116 @@
     CurrentBondsOfAtom = -1; // we count one too far due to line end
     // parse into structure
-    if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
+    if ((AtomNr >= 0) && (AtomNr < getAtomCount())) {
       Walker = ListOfAtoms[AtomNr];
       while (!line.eof())
@@ -1296 +1295 @@
     AddedAtomList[Root->nr] = Mol->AddCopyAtom(Root);
 
-  BreadthFirstSearchAdd_Init(BFS, Root, BondOrder, AtomCount, AddedAtomList);
+  BreadthFirstSearchAdd_Init(BFS, Root, BondOrder, getAtomCount(), AddedAtomList);
 
   // and go on ... Queue always contains all lightgray vertices
@@ -1407 +1406 @@
 
   Log() << Verbose(2) << "Begin of BuildInducedSubgraph." << endl;
-  BuildInducedSubgraph_Init(ParentList, Father->AtomCount);
+  BuildInducedSubgraph_Init(ParentList, Father->getAtomCount());
   BuildInducedSubgraph_FillParentList(this, Father, ParentList);
   status = BuildInducedSubgraph_CreateBondsFromParent(this, Father, ParentList);