Changeset 0bbfa1 for src/Parser

Timestamp:

Dec 16, 2010, 5:32:22 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:

92d756

Parents:

93fd43e

git-author:

Frederik Heber <heber@…> (12/08/10 01:10:03)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:22)

Message:

BUGFIX: Parsing a second .data file failed.

• atomIdMap was not cleared in TremoloParser::load().
• neighbors of first parsing get processed again after second parsing, hence bonds are added twice.

Location:

src/Parser

Files:

• TremoloAtomInfoContainer.cpp (modified) (1 diff)
• TremoloAtomInfoContainer.hpp (modified) (1 diff)
• TremoloParser.cpp (modified) (5 diffs)

src/Parser/TremoloAtomInfoContainer.cpp

@@ -35 +35 @@
   GrpTypeNo("0"),
   torsion("-"),
-  neighbors(std::vector<int>(0, 5))
+  neighbors(std::vector<int>(0, 5)),
+  neighbors_processed(false)
 {}
 

src/Parser/TremoloAtomInfoContainer.hpp

@@ -39 +39 @@
   std::string torsion;
   std::vector<int> neighbors;
+  bool neighbors_processed;
 };
 

src/Parser/TremoloParser.cpp

@@ -90 +90 @@
   string::size_type location;
 
+  // reset atomIdMap, for we now get new serials
+  atomIdMap.clear();
   usedFields.clear();
+
   molecule *newmol = World::getInstance().createMolecule();
   newmol->ActiveFlag = true;
@@ -220 +223 @@
         ? (*currentBond)->GetOtherAtom(currentAtom)->getId()+1 : 0) << "\t";
     if (currentBond != currentAtom->ListOfBonds.end())
-      currentBond++;
+      ++currentBond;
   }
 }
@@ -310 +313 @@
  * Reads neighbor information for one atom from the input.
  *
- * \param stream where to read the information from
- * \param number of neighbors to read
- * \param world id of the atom the information belongs to
+ * \param line stream where to read the information from
+ * \param numberOfNeighbors number of neighbors to read
+ * \param atomid world id of the atom the information belongs to
  */
 void TremoloParser::readNeighbors(stringstream* line, int numberOfNeighbors, int atomId) {
@@ -320 +323 @@
     // 0 is used to fill empty neighbor positions in the tremolo file.
     if (neighborId > 0) {
+//      std::cout << "Atom with global id " << atomId << " has neighbour with serial " << neighborId << std::endl;
       additionalAtomData[atomId].neighbors.push_back(neighborId);
     }
@@ -356 +360 @@
     currentInfo != additionalAtomData.end(); currentInfo++
   ) {
-    for(vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
-      neighbor != currentInfo->second.neighbors.end(); neighbor++
-    ) {
-      World::getInstance().getAtom(AtomById(currentInfo->first))
-          ->addBond(World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
+    if (!currentInfo->second.neighbors_processed) {
+      for(vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
+        neighbor != currentInfo->second.neighbors.end(); neighbor++
+      ) {
+//        std::cout << "Creating bond between ("
+//            << currentInfo->first
+//            << ") and ("
+//            << atomIdMap[*neighbor] << "|" << *neighbor << ")" << std::endl;
+        World::getInstance().getAtom(AtomById(currentInfo->first))
+            ->addBond(World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
+      }
+      currentInfo->second.neighbors_processed = true;
     }
   }