Changeset 2cc75c3 for src

Timestamp:

Oct 18, 2009, 4:09:26 PM (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:

df8b19

Parents:

ef9aae

Message:

Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr.

Note that this is still only possible due to ListOfBondsPerAtom() -> atom::ListOfBonds() switch.

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• atom.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (2 diffs)

src/atom.cpp

@@ -292 +292 @@
 };
 
+/** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
+ * \param *file output stream
+ */
+void atom::OutputOrder(ofstream *file)
+{
+  *file << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
+  //cout << Verbose(2) << "Storing: " << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << "." << endl;
+};
+
+/** Initialises the component number array.
+ * Size is set to atom::ListOfBonds.size()+1 (last is th encode end by -1)
+ */
+void atom::InitComponentNr()
+{
+  if (ComponentNr != NULL)
+    Free(&ComponentNr);
+  ComponentNr = Malloc<int>(ListOfBonds.size()+1, "atom::InitComponentNumbers: *ComponentNr");
+  for (int i=ListOfBonds.size()+1;i--;)
+    ComponentNr[i] = -1;
+};
+
 /** Puts a given bond into atom::ListOfBonds.
  * \param *Binder bond to insert
@@ -471 +492 @@
 };
 
-/** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
- * \param *file output stream
- */
-void atom::OutputOrder(ofstream *file)
-{
-  *file << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
-  //cout << Verbose(2) << "Storing: " << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << "." << endl;
-}
-
 /** Returns squared distance to a given vector.
  * \param origin vector to calculate distance to

src/atom.hpp

@@ -104 +104 @@
   void OutputGraphInfo(ofstream *out) const;
   void OutputComponentNumber(ofstream *out) const;
+  void InitComponentNr();
   int CountBonds() const;
   int CorrectBondDegree(ofstream *out);

src/molecule_graph.cpp

@@ -388 +388 @@
   ResetAllBondsToUnused();
   ResetAllAtomNumbers();
-  InitComponentNumbers();
+  ActOnAllAtoms( &atom::InitComponentNr );
   BackEdgeStack->ClearStack();
   while (Root != end) { // if there any atoms at all
@@ -781 +781 @@
   } else
       cerr << "Error: Given vertex is NULL!" << endl;
-};
-
-/** Allocates memory for all atom::*ComponentNr in this molecule and sets each entry to -1.
- */
-void molecule::InitComponentNumbers()
-{
-  atom *Walker = start;
-  while(Walker->next != end) {
-    Walker = Walker->next;
-    if (Walker->ComponentNr != NULL)
-      Free(&Walker->ComponentNr);
-    Walker->ComponentNr = Malloc<int>(Walker->ListOfBonds.size()+1, "molecule::InitComponentNumbers: *Walker->ComponentNr");
-    for (int i=Walker->ListOfBonds.size()+1;i--;)
-      Walker->ComponentNr[i] = -1;
-  }
 };