Changeset a479fa for src/moleculelist.cpp

Timestamp:

Mar 1, 2011, 10:16:38 AM (14 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:

735b1c

Parents:

5702cdb

git-author:

Frederik Heber <heber@…> (02/21/11 23:50:41)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Renamed ParticleInfo::nr to ParticleInfo::ParticleInfo_nr for easier privatization.

File:

• src/moleculelist.cpp (modified) (10 diffs)

src/moleculelist.cpp

@@ -140 +140 @@
           aList[Counter] = Count + (aCounter++);
         else
-          aList[Counter] = (*aiter)->GetTrueFather()->nr;
+          aList[Counter] = (*aiter)->GetTrueFather()->ParticleInfo_nr;
         if ((*biter)->GetTrueFather() == NULL)
           bList[Counter] = Count + (bCounter++);
         else
-          bList[Counter] = (*biter)->GetTrueFather()->nr;
+          bList[Counter] = (*biter)->GetTrueFather()->ParticleInfo_nr;
         Counter++;
       }
@@ -367 +367 @@
           // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
           Binder = *((*runner)->getListOfBonds().begin());
-          if (((*runner)->getType()->getAtomicNumber() == 1) && ((*runner)->nr > (*iter)->nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
+          if (((*runner)->getType()->getAtomicNumber() == 1) && ((*runner)->ParticleInfo_nr > (*iter)->ParticleInfo_nr) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
             // 4. evaluate the morse potential for each matrix component and add up
             distance = (*runner)->distance(*(*iter));
@@ -462 +462 @@
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
                 //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
-                ForcesFile << SortIndex[(*atomIter)->GetTrueFather()->nr] << "\t";
+                ForcesFile << SortIndex[(*atomIter)->GetTrueFather()->ParticleInfo_nr] << "\t";
               } else
                 // otherwise a -1 to indicate an added saturation hydrogen
@@ -808 +808 @@
     for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
       Father = (*iter)->GetTrueFather();
-      AtomNo = Father->nr; // global id of the current walker
+      AtomNo = Father->ParticleInfo_nr; // global id of the current walker
       const BondList& ListOfBonds = Father->getListOfBonds();
       for (BondList::const_iterator Runner = ListOfBonds.begin();
           Runner != ListOfBonds.end();
           ++Runner) {
-        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->nr]; // local copy of current bond partner of walker
+        OtherWalker = ListOfLocalAtoms[(*Runner)->GetOtherAtom((*iter)->GetTrueFather())->ParticleInfo_nr]; // local copy of current bond partner of walker
         if (OtherWalker != NULL) {
-          if (OtherWalker->nr > (*iter)->nr)
+          if (OtherWalker->ParticleInfo_nr > (*iter)->ParticleInfo_nr)
             Leaf->AddBond((*iter), OtherWalker, (*Runner)->BondDegree);
         } else {
-          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->nr << "] is NULL!" << endl);
+          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << (*Runner)->GetOtherAtom((*iter)->GetTrueFather())->ParticleInfo_nr << "] is NULL!" << endl);
           status = false;
         }
@@ -837 +837 @@
  * \param *out output stream for debugging
  * \param *&RootStack stack to be filled
- * \param *AtomMask defines true/false per global Atom::nr to mask in/out each nuclear site
+ * \param *AtomMask defines true/false per global Atom::ParticleInfo_nr to mask in/out each nuclear site
  * \param &FragmentCounter counts through the fragments in this MoleculeLeafClass
  * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
@@ -851 +851 @@
       for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
         Father = (*iter)->GetTrueFather();
-        if (AtomMask[Father->nr]) // apply mask
+        if (AtomMask[Father->ParticleInfo_nr]) // apply mask
 #ifdef ADDHYDROGEN
           if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
 #endif
-          RootStack[FragmentCounter].push_front((*iter)->nr);
+          RootStack[FragmentCounter].push_front((*iter)->ParticleInfo_nr);
       }
       if (next != NULL)
@@ -871 +871 @@
 };
 
-/** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
+/** Fills a lookup list of father's Atom::ParticleInfo_nr -> atom for each subgraph.
  * \param *out output stream from debugging
  * \param **&ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
@@ -891 +891 @@
 };
 
-/** The indices per keyset are compared to the respective father's Atom::nr in each subgraph and thus put into \a **&FragmentList.
+/** The indices per keyset are compared to the respective father's Atom::ParticleInfo_nr in each subgraph and thus put into \a **&FragmentList.
  * \param *out output stream fro debugging
  * \param *reference reference molecule with the bond structure to be copied
@@ -928 +928 @@
     KeySet *TempSet = new KeySet;
     for (Graph::iterator runner = KeySetList->begin(); runner != KeySetList->end(); runner++) { // key sets contain global numbers!
-      if (ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->nr] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
+      if (ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->ParticleInfo_nr] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
         // translate keyset to local numbers
         for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-          TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->nr]->nr);
+          TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->ParticleInfo_nr]->ParticleInfo_nr);
         // insert into FragmentList
         FragmentList[FragmentCounter]->insert(GraphPair(*TempSet, pair<int, double> (KeySetCounter++, (*runner).second.second)));
@@ -972 +972 @@
     for (Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
       for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-        TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->nr);
+        TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->ParticleInfo_nr);
       TotalGraph.insert(GraphPair(*TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
       TempSet->clear();