Changeset 812155

Timestamp:

Feb 17, 2012, 3:24:18 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:

9f8b01

Parents:

8bf9c6

git-author:

Frederik Heber <heber@…> (02/06/12 18:35:40)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:18)

Message:

TremoloParser::save() redistributes ids in a continuous manner.

• i.e. we reset the local to global id associations, set them beforehand and then save the set of atoms.

File:

• src/Parser/TremoloParser.cpp (modified) (3 diffs)

src/Parser/TremoloParser.cpp

@@ -162 +162 @@
   //LOG(3, "INFO: additionalAtomData contains: " << additionalAtomData);
 
+  // distribute continuous indices
+  resetIdAssociations();
+  atomId_t lastid = 0;
+  for (atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
+    associateLocaltoGlobalId(++lastid, (*atomIt)->getId());
+  }
+
+  // store
   *file << "# ATOMDATA";
   for (it=usedFields.begin(); it < usedFields.end(); it++) {
@@ -267 +275 @@
       case TremoloKey::Id :
         LOG(3, "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getId()+1);
-        *file << currentAtom->getId()+1 << "\t";
+        *file << getLocalId(currentAtom->getId()) << "\t";
         break;
       case TremoloKey::neighbors :
@@ -321 +329 @@
   for (BondList::const_iterator iter = ListOfBonds.begin();
       iter != ListOfBonds.end(); ++iter)
-    sortedBonds.insert((*iter)->GetOtherAtom(currentAtom)->getId());
+    sortedBonds.insert(getLocalId((*iter)->GetOtherAtom(currentAtom)->getId()));
   // print indices
   sortedIndices::const_iterator currentBond = sortedBonds.begin();
   for (int i = 0; i < numberOfNeighbors; i++) {
-    *file << (currentBond != sortedBonds.end() ? (*currentBond)+1 : 0) << "\t";
+    *file << (currentBond != sortedBonds.end() ? (*currentBond) : 0) << "\t";
     if (currentBond != sortedBonds.end())
       ++currentBond;