Changeset 9d83b6 for src/Actions

Timestamp:

Feb 24, 2011, 6:51:32 PM (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:

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.

Location:

src/Actions

Files:

• FragmentationAction/ConstructBondGraphAction.cpp (modified) (5 diffs)
• FragmentationAction/SubgraphDissectionAction.cpp (modified) (1 diff)
• MoleculeAction/CopyAction.cpp (modified) (1 diff)

src/Actions/FragmentationAction/ConstructBondGraphAction.cpp

@@ -32 +32 @@
 #include "molecule.hpp"
 #include "World.hpp"
+#include "WorldTime.hpp"
 
 #include <iostream>
@@ -67 +68 @@
   // remove every bond from the selected atoms' list
   int AtomCount = 0;
-  for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection(); AtomRunner != World::getInstance().endAtomSelection(); ++AtomRunner) {
+  for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection();
+      AtomRunner != World::getInstance().endAtomSelection();
+      ++AtomRunner) {
     AtomCount++;
-    for(BondList::iterator BondRunner = (AtomRunner->second)->ListOfBonds.begin(); !(AtomRunner->second)->ListOfBonds.empty(); BondRunner = (AtomRunner->second)->ListOfBonds.begin())
+    BondList& ListOfBonds = (AtomRunner->second)->getListOfBonds();
+    for(BondList::iterator BondRunner = ListOfBonds.begin();
+        !ListOfBonds.empty();
+        BondRunner = ListOfBonds.begin())
       if ((*BondRunner)->leftatom == AtomRunner->second)
         delete((*BondRunner));
@@ -81 +87 @@
     DoLog(2) && (Log() << Verbose(2) << "Creating Linked Cell structure ... " << endl);
     LinkedCell::LinkedNodes list;
-    for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection(); AtomRunner != World::getInstance().endAtomSelection(); ++AtomRunner) {
+    for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection();
+        AtomRunner != World::getInstance().endAtomSelection();
+        ++AtomRunner) {
       list.push_back(AtomRunner->second);
     }
@@ -92 +100 @@
     std::map<TesselPoint *, int> AtomIds;
     int i=0;
-    for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection(); AtomRunner != World::getInstance().endAtomSelection(); ++AtomRunner) {
+    for (World::AtomSelectionIterator AtomRunner = World::getInstance().beginAtomSelection();
+        AtomRunner != World::getInstance().endAtomSelection();
+        ++AtomRunner) {
       AtomIds.insert(pair<TesselPoint *, int> (AtomRunner->second, i++) );
     }
@@ -104 +114 @@
 //          Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
           if (List != NULL) {
-            for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
+            for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin();
+                Runner != List->end();
+                Runner++) {
               Walker = dynamic_cast<atom*>(*Runner);
               ASSERT(Walker,"Tesselpoint that was not an atom retrieved from LinkedNode");

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -78 +78 @@
     vector <atom *> allatoms = World::getInstance().getAllAtoms();
     for(vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
-      BondCount += (*AtomRunner)->ListOfBonds.size();
-//      for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+      const BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+      BondCount += ListOfBonds.size();
+//      for(BondList::iterator BondRunner = ListOfBonds.begin();
+//          !ListOfBonds.empty();
+//          BondRunner = ListOfBonds.begin()) {
 //        delete(*BondRunner);
+//      }
       mol->AddAtom(*AtomRunner);
     }

src/Actions/MoleculeAction/CopyAction.cpp

@@ -59 +59 @@
   MoleculeCopyState *state = assert_cast<MoleculeCopyState*>(_state.get());
 
-  for (molecule::iterator AtomRunner = state->copy->begin(); !state->copy->empty(); AtomRunner = state->copy->begin()) {
-    for(BondList::iterator BondRunner = (*AtomRunner)->ListOfBonds.begin(); !(*AtomRunner)->ListOfBonds.empty(); BondRunner = (*AtomRunner)->ListOfBonds.begin())
+  for (molecule::iterator AtomRunner = state->copy->begin();
+      !state->copy->empty();
+      AtomRunner = state->copy->begin()) {
+    BondList& ListOfBonds = (*AtomRunner)->getListOfBonds();
+    for(BondList::iterator BondRunner = ListOfBonds.begin();
+        !ListOfBonds.empty();
+        BondRunner = ListOfBonds.begin()) {
       delete(*BondRunner);
+    }
     atom *Walker = *AtomRunner;
     state->copy->erase(AtomRunner);