Changeset ea7176 for src/molecule_fragmentation.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, Candidate_v1.7.0, 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_fragmentation.cpp (modified) (15 diffs)

src/molecule_fragmentation.cpp

@@ -435 +435 @@
 
   // initialize mask list
-  for(int i=AtomCount;i--;)
+  for(int i=getAtomCount();i--;)
     AtomMask[i] = false;
 
   if (Order < 0) { // adaptive increase of BondOrder per site
-    if (AtomMask[AtomCount] == true)  // break after one step
+    if (AtomMask[getAtomCount()] == true)  // break after one step
       return false;
 
@@ -483 +483 @@
       }
     }
-    if ((Order == 0) && (AtomMask[AtomCount] == false))  // single stepping, just check
+    if ((!Order) && (!AtomMask[getAtomCount()]))  // single stepping, just check
       status = true;
 
@@ -494 +494 @@
   }
 
-  PrintAtomMask(AtomMask, AtomCount); // for debugging
+  PrintAtomMask(AtomMask, getAtomCount()); // for debugging
 
   return status;
@@ -510 +510 @@
     return false;
   }
-  SortIndex = Malloc<int>(AtomCount, "molecule::CreateMappingLabelsToConfigSequence: *SortIndex");
-  for(int i=AtomCount;i--;)
+  SortIndex = Malloc<int>(getAtomCount(), "molecule::CreateMappingLabelsToConfigSequence: *SortIndex");
+  for(int i=getAtomCount();i--;)
     SortIndex[i] = -1;
 
@@ -595 +595 @@
   MoleculeListClass *BondFragments = NULL;
   int *SortIndex = NULL;
-  int *MinimumRingSize = new int[AtomCount];
+  int *MinimumRingSize = new int[getAtomCount()];
   int FragmentCounter;
   MoleculeLeafClass *MolecularWalker = NULL;
@@ -623 +623 @@
 
   // create lookup table for Atom::nr
-  FragmentationToDo = FragmentationToDo && CreateFatherLookupTable(ListOfAtoms, AtomCount);
+  FragmentationToDo = FragmentationToDo && CreateFatherLookupTable(ListOfAtoms, getAtomCount());
 
   // === compare it with adjacency file ===
@@ -633 +633 @@
 
   // analysis of the cycles (print rings, get minimum cycle length) for each subgraph
-  for(int i=AtomCount;i--;)
-    MinimumRingSize[i] = AtomCount;
+  for(int i=getAtomCount();i--;)
+    MinimumRingSize[i] = getAtomCount();
   MolecularWalker = Subgraphs;
   FragmentCounter = 0;
@@ -671 +671 @@
   // ===== 6b. prepare and go into the adaptive (Order<0), single-step (Order==0) or incremental (Order>0) cycle
   KeyStack *RootStack = new KeyStack[Subgraphs->next->Count()];
-  AtomMask = new bool[AtomCount+1];
-  AtomMask[AtomCount] = false;
+  AtomMask = new bool[getAtomCount()+1];
+  AtomMask[getAtomCount()] = false;
   FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
   while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, MinimumRingSize, configuration->configpath))) {
     FragmentationToDo = FragmentationToDo || CheckOrder;
-    AtomMask[AtomCount] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
+    AtomMask[getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
     // ===== 6b. fill RootStack for each subgraph (second adaptivity check) =====
     Subgraphs->next->FillRootStackForSubgraphs(RootStack, AtomMask, (FragmentCounter = 0));
@@ -811 +811 @@
 bool molecule::ParseOrderAtSiteFromFile(char *path)
 {
-  unsigned char *OrderArray = Calloc<unsigned char>(AtomCount, "molecule::ParseOrderAtSiteFromFile - *OrderArray");
-  bool *MaxArray = Calloc<bool>(AtomCount, "molecule::ParseOrderAtSiteFromFile - *MaxArray");
+  unsigned char *OrderArray = Calloc<unsigned char>(getAtomCount(), "molecule::ParseOrderAtSiteFromFile - *OrderArray");
+  bool *MaxArray = Calloc<bool>(getAtomCount(), "molecule::ParseOrderAtSiteFromFile - *MaxArray");
   bool status;
   int AtomNr, value;
@@ -917 +917 @@
   atom *OtherFather = NULL;
   atom *FatherOfRunner = NULL;
-  Leaf->CountAtoms();
 
 #ifdef ADDHYDROGEN
@@ -955 +954 @@
       eLog() << Verbose(1) << "Son " << (*iter)->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl;
     }
-    if ((LonelyFlag) && (Leaf->AtomCount > 1)) {
+    if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {
       Log() << Verbose(0) << *(*iter) << "has got bonds only to hydrogens!" << endl;
     }
@@ -975 +974 @@
 molecule * molecule::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
 {
-  atom **SonList = Calloc<atom*>(AtomCount, "molecule::StoreFragmentFromStack: **SonList");
+  atom **SonList = Calloc<atom*>(getAtomCount(), "molecule::StoreFragmentFromStack: **SonList");
   molecule *Leaf = World::get()->createMolecule();
 
@@ -1602 +1601 @@
   FragmentSearch.FragmentSet = new KeySet;
   FragmentSearch.Root = FindAtom(RootKeyNr);
-  FragmentSearch.ShortestPathList = Malloc<int>(AtomCount, "molecule::PowerSetGenerator: *ShortestPathList");
-  for (int i=AtomCount;i--;) {
+  FragmentSearch.ShortestPathList = Malloc<int>(getAtomCount(), "molecule::PowerSetGenerator: *ShortestPathList");
+  for (int i=getAtomCount();i--;) {
     FragmentSearch.ShortestPathList[i] = -1;
   }
@@ -1707 +1706 @@
   Vector Translationvector;
   //class StackClass<atom *> *CompStack = NULL;
-  class StackClass<atom *> *AtomStack = new StackClass<atom *>(AtomCount);
+  class StackClass<atom *> *AtomStack = new StackClass<atom *>(getAtomCount());
   bool flag = true;
 
   Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl;
 
-  ColorList = Calloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
+  ColorList = Calloc<enum Shading>(getAtomCount(), "molecule::ScanForPeriodicCorrection: *ColorList");
   while (flag) {
     // remove bonds that are beyond bonddistance
@@ -1746 +1745 @@
       Log() << Verbose(0) << endl;
       // apply to all atoms of first component via BFS
-      for (int i=AtomCount;i--;)
+      for (int i=getAtomCount();i--;)
         ColorList[i] = white;
       AtomStack->Push(Binder->leftatom);