Changeset 9d83b6 for src/atom_bondedparticle.cpp

Timestamp:

Feb 24, 2011, 6:51:32 PM (15 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, Candidate_v1.7.1, 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:

a2bdbe

Parents:

c0d9eb

git-author:

Frederik Heber <heber@…> (02/24/11 14:41:13)

git-committer:

Frederik Heber <heber@…> (02/24/11 18:51:32)

Message:

BondedParticleInfo now has vector<BondList>

• vector<BondList> ListOfBonds is private, getter for (non-)const access.
• Access everywhere to ListOfBonds replaced by respective getter.
• Access is as of now always to time step zero.
• greatest impact is on molecule... files, and ListOfBondsUnitTest.

File:

• src/atom_bondedparticle.cpp (modified) (14 diffs)

src/atom_bondedparticle.cpp

@@ -27 +27 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "WorldTime.hpp"
 
 /** Constructor of class BondedParticle.
@@ -32 +33 @@
 BondedParticle::BondedParticle()
 {
+  ListOfBonds.push_back(BondList());
 };
 
@@ -38 +40 @@
 BondedParticle::~BondedParticle()
 {
-  BondList::const_iterator Runner;
-  while (!ListOfBonds.empty()) {
-    Runner = ListOfBonds.begin();
-    removewithoutcheck(*Runner);
+  BondList::iterator Runner;
+  for (std::vector<BondList>::iterator iter = ListOfBonds.begin();
+      !ListOfBonds.empty();
+      iter = ListOfBonds.begin()) {
+    while (!(*iter).empty()) {
+      Runner = (*iter).begin();
+      removewithoutcheck(*Runner);
+    }
+    ListOfBonds.erase(iter);
   }
 };
@@ -58 +65 @@
 void BondedParticle::OutputBondOfAtom() const
 {
+  const BondList& ListOfBonds = getListOfBonds();
   DoLog(4) && (Log() << Verbose(4) << "Atom " << getName() << "/" << nr << " with " << ListOfBonds.size() << " bonds: " << endl);
   int TotalDegree = 0;
@@ -72 +80 @@
 void BondedParticle::OutputAdjacency(ofstream * const AdjacencyFile) const
 {
+  const BondList& ListOfBonds = getListOfBonds();
   *AdjacencyFile << nr << "\t";
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
@@ -84 +93 @@
 void BondedParticle::OutputBonds(ofstream * const BondFile) const
 {
+  const BondList& ListOfBonds = getListOfBonds();
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
     if (nr < (*Runner)->GetOtherAtom(this)->nr)
@@ -113 +123 @@
   if (Binder != NULL) {
     if (Binder->Contains(this)) {
+      BondList& ListOfBonds = getListOfBonds();
       ListOfBonds.push_back(Binder);
       status = true;
@@ -125 +136 @@
 
 /** Removes a given bond from atom::ListOfBonds.
+ * @param _step time step to access
  * \param *Binder bond to remove
  */
@@ -132 +144 @@
   if (Binder != NULL) {
     if (Binder->Contains(this)) {
+      BondList& ListOfBonds = getListOfBonds();
       ListOfBonds.remove(Binder);
       status = true;
@@ -148 +161 @@
 void BondedParticle::UnregisterAllBond()
 {
+  BondList& ListOfBonds = getListOfBonds();
   ListOfBonds.clear();
 };
@@ -165 +179 @@
   //Log() << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
   if ((int)(getType()->getNoValenceOrbitals()) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
+    const BondList& ListOfBonds = getListOfBonds();
     for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner)) {
       OtherWalker = (*Runner)->GetOtherAtom(this);
@@ -170 +185 @@
       //Log() << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << OtherNoBonds << "?" << endl;
       if ((int)(OtherWalker->getType()->getNoValenceOrbitals()) > OtherNoBonds) { // check if possible candidate
-        if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherWalker->ListOfBonds.size())) { // pick the one with fewer number of bonds first
+        const BondList& OtherListOfBonds = OtherWalker->getListOfBonds();
+        if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherListOfBonds.size())) { // pick the one with fewer number of bonds first
           CandidateBond = (*Runner);
           //Log() << Verbose(3) << "New candidate is " << *CandidateBond << "." << endl;
@@ -194 +210 @@
 {
   int NoBonds = 0;
+  const BondList& ListOfBonds = getListOfBonds();
   for (BondList::const_iterator Runner = ListOfBonds.begin();
       Runner != ListOfBonds.end();
@@ -209 +226 @@
   bool status = false;
 
-  for (BondList::iterator runner = ListOfBonds.begin(); runner != ListOfBonds.end(); runner++) {
+  const BondList& ListOfBonds = getListOfBonds();
+  for (BondList::const_iterator runner = ListOfBonds.begin(); runner != ListOfBonds.end(); runner++) {
     status = status || ((*runner)->Contains(BondPartner));
   }