Changeset 52ed5b for src/Atom

Timestamp:

Feb 17, 2012, 3:24:20 PM (13 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:

ea7a50

Parents:

cdaae6

git-author:

Frederik Heber <heber@…> (02/08/12 17:36:46)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:20)

Message:

Ids handed out by molecule now start with 1.

• this required some changes because of the shifted molecular indices, especially in:
  • BondedParticle::OutputAdjacency(): removed +1
  • BondedParticle::OutputBonds(): same
  • Fragmentation::StoreFragmentFromKeySet(): increased array size
  • Fragmentation::CreateMappingLabelsToConfigSequence() : same
  • CheckAgainstAdjacencyFile::ParseInExternalMap(): decreased index by one. This is actually broken and only working if World's and molecular indices coincide.
  • molecule::CreateFatherLookupTable(): increased array size
• TESTFIX: CheckAgainstAdjacencyFileUnitTest had its internal file strings' indices decreased by one.

File:

• src/Atom/atom_bondedparticle.cpp (modified) (2 diffs)

src/Atom/atom_bondedparticle.cpp

@@ -72 +72 @@
 {
   const BondList& ListOfBonds = getListOfBonds();
-  *AdjacencyFile << getNr()+1 << "\t";
+  *AdjacencyFile << getNr() << "\t";
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
-    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr()+1 << "\t";
+    *AdjacencyFile << (*Runner)->GetOtherAtom(this)->getNr() << "\t";
   *AdjacencyFile << endl;
 };
@@ -87 +87 @@
   for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
     if (getNr() < (*Runner)->GetOtherAtom(this)->getNr())
-      *BondFile << getNr()+1 << "\t" << (*Runner)->GetOtherAtom(this)->getNr()+1 << "\n";
+      *BondFile << getNr() << "\t" << (*Runner)->GetOtherAtom(this)->getNr() << "\n";
 };