Changeset 735b1c for src/boundary.cpp

Timestamp:

Mar 1, 2011, 10:16:39 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:

5309ba

Parents:

a479fa

git-author:

Frederik Heber <heber@…> (02/22/11 00:15:33)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:39)

Message:

ParticleInfo::ParticleInfo_nr is protected and accessed via getter/setter.

• many changes (~400) in molecule- and tesselation-related functions.

File:

• src/boundary.cpp (modified) (2 diffs)

src/boundary.cpp

@@ -909 +909 @@
             DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is outer point." << endl);
             // copy atom ...
-            CopyAtoms[(*iter)->ParticleInfo_nr] = (*iter)->clone();
-            (*CopyAtoms[(*iter)->ParticleInfo_nr]).setPosition(Inserter);
-            Filling->AddAtom(CopyAtoms[(*iter)->ParticleInfo_nr]);
-            DoLog(1) && (Log() << Verbose(1) << "Filling atom " << **iter << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->ParticleInfo_nr]->getPosition()) << "." << endl);
+            CopyAtoms[(*iter)->getNr()] = (*iter)->clone();
+            (*CopyAtoms[(*iter)->getNr()]).setPosition(Inserter);
+            Filling->AddAtom(CopyAtoms[(*iter)->getNr()]);
+            DoLog(1) && (Log() << Verbose(1) << "Filling atom " << **iter << ", translated to " << AtomTranslations << ", at final position is " << (CopyAtoms[(*iter)->getNr()]->getPosition()) << "." << endl);
           } else {
             DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is inner point, within boundary or outside of MaxDistance." << endl);
-            CopyAtoms[(*iter)->ParticleInfo_nr] = NULL;
+            CopyAtoms[(*iter)->getNr()] = NULL;
             continue;
           }
@@ -927 +927 @@
             if ((*BondRunner)->leftatom == *AtomRunner) {
               Binder = (*BondRunner);
-              if ((CopyAtoms[Binder->leftatom->ParticleInfo_nr] != NULL) && (CopyAtoms[Binder->rightatom->ParticleInfo_nr] != NULL)) {
-                Log()  << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->ParticleInfo_nr] << " and " << *CopyAtoms[Binder->rightatom->ParticleInfo_nr]<< "." << endl;
-                Filling->AddBond(CopyAtoms[Binder->leftatom->ParticleInfo_nr], CopyAtoms[Binder->rightatom->ParticleInfo_nr], Binder->BondDegree);
+              if ((CopyAtoms[Binder->leftatom->getNr()] != NULL) && (CopyAtoms[Binder->rightatom->getNr()] != NULL)) {
+                Log()  << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->getNr()] << " and " << *CopyAtoms[Binder->rightatom->getNr()]<< "." << endl;
+                Filling->AddBond(CopyAtoms[Binder->leftatom->getNr()], CopyAtoms[Binder->rightatom->getNr()], Binder->BondDegree);
               }
             }