Changeset 9879f6 for src/molecule_fragmentation.cpp

Timestamp:

Mar 5, 2010, 10:16:47 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, 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:

d3347e

Parents:

e87acf

git-author:

Frederik Heber <heber@…> (03/05/10 10:08:44)

git-committer:

Frederik Heber <heber@…> (03/05/10 10:16:47)

Message:

Huge Refactoring due to class molecule now being an STL container.

• molecule::start and molecule::end were dropped. Hence, the usual construct Walker = start while (Walker->next != end) {

Walker = walker->next
...

}
was changed to
for (molecule::iterator iter = begin(); iter != end(); ++iter) {

...

}
and (*iter) used instead of Walker.

• Two build errors remain (beside some more in folder Actions, Patterns and unittest) in molecule_pointcloud.cpp and molecule.cpp
• lists.cpp was deleted as specialization of atom* was not needed anymore
• link, unlink, add, remove, removewithoutcheck all are not needed for atoms anymore, just for bonds (where first, last entries remain in molecule)
• CreateFatherLookupTable() was put back into class molecule.
• molecule::InternalPointer is now an iterator
• class PointCloud: GoToPrevious() and GetTerminalPoint() were dropped as not needed.
• some new STL functions in class molecule: size(), empty(), erase(), find() and insert()

File:

• src/molecule_fragmentation.cpp (modified) (13 diffs)

src/molecule_fragmentation.cpp

@@ -38 +38 @@
   int FragmentCount;
   // get maximum bond degree
-  atom *Walker = start;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-    c = (Walker->ListOfBonds.size() > c) ? Walker->ListOfBonds.size() : c;
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    c = ((*iter)->ListOfBonds.size() > c) ? (*iter)->ListOfBonds.size() : c;
   }
   FragmentCount = NoNonHydrogen*(1 << (c*order));
@@ -358 +356 @@
 map<double, pair<int,int> >  * ReMapAdaptiveCriteriaListToValue(map<int, pair<double,int> > *AdaptiveCriteriaList, molecule *mol)
 {
-  atom *Walker = mol->start;
+  atom *Walker = NULL;
   map<double, pair<int,int> > *FinalRootCandidates = new map<double, pair<int,int> > ;
   Log() << Verbose(1) << "Root candidate list is: " << endl;
@@ -390 +388 @@
 bool MarkUpdateCandidates(bool *AtomMask, map<double, pair<int,int> > &FinalRootCandidates, int Order, molecule *mol)
 {
-  atom *Walker = mol->start;
+  atom *Walker = NULL;
   int No = -1;
   bool status = false;
@@ -434 +432 @@
 bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path)
 {
-  atom *Walker = start;
   bool status = false;
 
@@ -456 +453 @@
     if (AdaptiveCriteriaList->empty()) {
       eLog() << Verbose(2) << "Unable to parse file, incrementing all." << endl;
-      while (Walker->next != end) {
-        Walker = Walker->next;
+      for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
     #ifdef ADDHYDROGEN
-        if (Walker->type->Z != 1) // skip hydrogen
+        if ((*iter)->type->Z != 1) // skip hydrogen
     #endif
         {
-          AtomMask[Walker->nr] = true;  // include all (non-hydrogen) atoms
+          AtomMask[(*iter)->nr] = true;  // include all (non-hydrogen) atoms
           status = true;
         }
@@ -477 +473 @@
     Free(&FinalRootCandidates);
   } else { // global increase of Bond Order
-    while (Walker->next != end) {
-      Walker = Walker->next;
+    for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
   #ifdef ADDHYDROGEN
-      if (Walker->type->Z != 1) // skip hydrogen
+      if ((*iter)->type->Z != 1) // skip hydrogen
   #endif
       {
-        AtomMask[Walker->nr] = true;  // include all (non-hydrogen) atoms
-        if ((Order != 0) && (Walker->AdaptiveOrder < Order)) // && (Walker->AdaptiveOrder < MinimumRingSize[Walker->nr]))
+        AtomMask[(*iter)->nr] = true;  // include all (non-hydrogen) atoms
+        if ((Order != 0) && ((*iter)->AdaptiveOrder < Order)) // && ((*iter)->AdaptiveOrder < MinimumRingSize[(*iter)->nr]))
           status = true;
       }
@@ -523 +518 @@
 
   return true;
+};
+
+
+
+/** Creates a lookup table for true father's Atom::Nr -> atom ptr.
+ * \param *start begin of list (STL iterator, i.e. first item)
+ * \paran *end end of list (STL iterator, i.e. one past last item)
+ * \param **Lookuptable pointer to return allocated lookup table (should be NULL on start)
+ * \param count optional predetermined size for table (otherwise we set the count to highest true father id)
+ * \return true - success, false - failure
+ */
+bool molecule::CreateFatherLookupTable(atom **&LookupTable, int count)
+{
+  bool status = true;
+  int AtomNo;
+
+  if (LookupTable != NULL) {
+    Log() << Verbose(0) << "Pointer for Lookup table is not NULL! Aborting ..." <<endl;
+    return false;
+  }
+
+  // count them
+  if (count == 0) {
+    for (molecule::iterator iter = begin(); iter != end(); ++iter) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron
+      count = (count < (*iter)->GetTrueFather()->nr) ? (*iter)->GetTrueFather()->nr : count;
+    }
+  }
+  if (count <= 0) {
+    Log() << Verbose(0) << "Count of lookup list is 0 or less." << endl;
+    return false;
+  }
+
+  // allocate and fill
+  LookupTable = Calloc<atom *>(count, "CreateFatherLookupTable - **LookupTable");
+  if (LookupTable == NULL) {
+    eLog() << Verbose(0) << "LookupTable memory allocation failed!" << endl;
+    performCriticalExit();
+    status = false;
+  } else {
+    for (molecule::iterator iter = begin(); iter != end(); ++iter) {
+      AtomNo = (*iter)->GetTrueFather()->nr;
+      if ((AtomNo >= 0) && (AtomNo < count)) {
+        //*out << "Setting LookupTable[" << AtomNo << "] to " << *(*iter) << endl;
+        LookupTable[AtomNo] = (*iter);
+      } else {
+        Log() << Verbose(0) << "Walker " << *(*iter) << " exceeded range of nuclear ids [0, " << count << ")." << endl;
+        status = false;
+        break;
+      }
+    }
+  }
+
+  return status;
 };
 
@@ -575 +623 @@
 
   // create lookup table for Atom::nr
-  FragmentationToDo = FragmentationToDo && CreateFatherLookupTable(start, end, ListOfAtoms, AtomCount);
+  FragmentationToDo = FragmentationToDo && CreateFatherLookupTable(ListOfAtoms, AtomCount);
 
   // === compare it with adjacency file ===
@@ -871 +919 @@
   Leaf->CountAtoms();
 
-  atom *Runner = Leaf->start;
-  while (Runner->next != Leaf->end) {
-    Runner = Runner->next;
+#ifdef ADDHYDROGEN
+  molecule::const_iterator runner;
+#endif
+  for (molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ) {
     LonelyFlag = true;
-    FatherOfRunner = Runner->father;
+    FatherOfRunner = (*iter)->father;
     if (SonList[FatherOfRunner->nr] != NULL)  {  // check if this, our father, is present in list
       // create all bonds
@@ -886 +935 @@
 //            Log() << Verbose(3) << "Adding Bond: ";
 //            Log() << Verbose(0) <<
-            Leaf->AddBond(Runner, SonList[OtherFather->nr], (*BondRunner)->BondDegree);
+            Leaf->AddBond((*iter), SonList[OtherFather->nr], (*BondRunner)->BondDegree);
 //            Log() << Verbose(0) << "." << endl;
-            //NumBonds[Runner->nr]++;
+            //NumBonds[(*iter)->nr]++;
           } else {
 //            Log() << Verbose(3) << "Not adding bond, labels in wrong order." << endl;
@@ -896 +945 @@
 //          Log() << Verbose(0) << ", who has no son in this fragment molecule." << endl;
 #ifdef ADDHYDROGEN
-          //Log() << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
-          if(!Leaf->AddHydrogenReplacementAtom((*BondRunner), Runner, FatherOfRunner, OtherFather, IsAngstroem))
+          //Log() << Verbose(3) << "Adding Hydrogen to " << (*iter)->Name << " and a bond in between." << endl;
+          if(!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
             exit(1);
 #endif
-          //NumBonds[Runner->nr] += Binder->BondDegree;
+          //NumBonds[(*iter)->nr] += Binder->BondDegree;
         }
       }
     } else {
-      eLog() << Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl;
+      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)) {
-      Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl;
+      Log() << Verbose(0) << *(*iter) << "has got bonds only to hydrogens!" << endl;
     }
 #ifdef ADDHYDROGEN
-    while ((Runner->next != Leaf->end) && (Runner->next->type->Z == 1)) // skip added hydrogen
-      Runner = Runner->next;
+    while ((iter != Leaf->end()) && ((*iter)->type->Z == 1)) // skip added hydrogen
+      iter++;
 #endif
   }
@@ -1559 +1608 @@
 
   // Construct the complete KeySet which we need for topmost level only (but for all Roots)
-  atom *Walker = start;
   KeySet CompleteMolecule;
-  while (Walker->next != end) {
-    Walker = Walker->next;
-    CompleteMolecule.insert(Walker->GetTrueFather()->nr);
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    CompleteMolecule.insert((*iter)->GetTrueFather()->nr);
   }
 
@@ -1574 +1621 @@
     RootKeyNr = RootStack.front();
     RootStack.pop_front();
-    Walker = FindAtom(RootKeyNr);
+    atom *Walker = FindAtom(RootKeyNr);
     // check cyclic lengths
     //if ((MinimumRingSize[Walker->GetTrueFather()->nr] != -1) && (Walker->GetTrueFather()->AdaptiveOrder+1 > MinimumRingSize[Walker->GetTrueFather()->nr])) {