Changeset 23fb72

Timestamp:

Oct 25, 2011, 12:08:03 PM (13 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:

f67817f

Parents:

f6d1d0

git-author:

Frederik Heber <heber@…> (10/18/11 12:02:04)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

Encapsulated UniqueFragments::Root with getter/setter.

Location:

src

Files:

• Fragmentation/UniqueFragments.cpp (modified) (1 diff)
• Fragmentation/UniqueFragments.hpp (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (7 diffs)

src/Fragmentation/UniqueFragments.cpp

@@ -259 +259 @@
   delete(FragmentSet);
 }
+
+/** Getter for UniqueFragments:Root.
+ *
+ * @return const ref to root atom.
+ */
+const atom *UniqueFragments::getRoot() const
+{
+  return Root;
+}
+
+/** Setter for UniqueFragments:Root.
+ *
+ * @param _root root atom to set
+ */
+void UniqueFragments::setRoot(atom *_root)
+{
+  Root=_root;
+}

src/Fragmentation/UniqueFragments.hpp

@@ -45 +45 @@
   void Cleanup();
 
-  atom *Root;
+  const atom *getRoot() const;
+  void setRoot(atom *_root);
+
   KeySet *FragmentSet;
   int FragmentCounter;
@@ -53 +55 @@
   AllSPBonds BondsPerSPList;
 
+
 private:
-  config *configuration;
+  atom *Root;
+
+private:
   int ANOVAOrder;
   int CurrentIndex;

src/molecule_fragmentation.cpp

@@ -688 +688 @@
 
   Log() << Verbose(1+verbosity) << "Begin of SPFragmentGenerator." << endl;
-  Log() << Verbose(1+verbosity) << "We are " << RootDistance << " away from Root, which is " << *FragmentSearch->Root << ", SubOrder is " << SubOrder << ", SetDimension is " << SetDimension << " and this means " <<  NumCombinations-1 << " combination(s)." << endl;
+  Log() << Verbose(1+verbosity) << "We are " << RootDistance << " away from Root, which is " << *FragmentSearch->getRoot() << ", SubOrder is " << SubOrder << ", SetDimension is " << SetDimension << " and this means " <<  NumCombinations-1 << " combination(s)." << endl;
 
   // initialised touched list (stores added atoms on this level)
@@ -722 +722 @@
 
           // then iterate
-          Log() << Verbose(2+verbosity) << "Calling subset generator " << SP << " away from root " << *FragmentSearch->Root << " with sub set dimension " << SubSetDimension << "." << endl;
+          Log() << Verbose(2+verbosity) << "Calling subset generator " << SP << " away from root " << *FragmentSearch->getRoot() << " with sub set dimension " << SubSetDimension << "." << endl;
           SPFragmentGenerator(FragmentSearch, SP, BondsList, SubSetDimension, SubOrder-bits);
         }
@@ -744 +744 @@
   }
   delete[](TouchedList);
-  Log() << Verbose(1+verbosity) << "End of SPFragmentGenerator, " << RootDistance << " away from Root " << *FragmentSearch->Root << " and SubOrder is " << SubOrder << "." << endl;
+  Log() << Verbose(1+verbosity) << "End of SPFragmentGenerator, " << RootDistance << " away from Root " << *FragmentSearch->getRoot() << " and SubOrder is " << SubOrder << "." << endl;
 };
 
@@ -768 +768 @@
 
   DoLog(0) && (Log() << Verbose(0) << endl);
-  DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl);
+  DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.getRoot() << "." << endl);
 
   FragmentSearch.SetSPList(Order);
@@ -783 +783 @@
   if (SP >= (Order-1)) {
     // start with root (push on fragment stack)
-    DoLog(0) && (Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->getNr() << "." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.getRoot() << ", local nr is " << FragmentSearch.getRoot()->getNr() << "." << endl);
     FragmentSearch.FragmentSet->clear();
     DoLog(0) && (Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl);
@@ -802 +802 @@
   // remove root from stack
   DoLog(0) && (Log() << Verbose(0) << "Removing root again from stack." << endl);
-  FragmentSearch.FragmentSet->erase(FragmentSearch.Root->getNr());
+  FragmentSearch.FragmentSet->erase(FragmentSearch.getRoot()->getNr());
 
   // free'ing the bonds lists
@@ -900 +900 @@
       FragmentSearch.TEFactor = 1.;
       FragmentSearch.Leaflet = FragmentLowerOrdersList[RootNr][0];      // set to insertion graph
-      FragmentSearch.Root = Walker;
+      FragmentSearch.setRoot(Walker);
       NumMoleculesOfOrder[RootNr] = PowerSetGenerator(Walker->AdaptiveOrder, FragmentSearch, CompleteMolecule);