Changeset 9f8b01

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:

3867a7

Parents:

812155

git-author:

Frederik Heber <heber@…> (02/07/12 12:25:24)

git-committer:

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

Message:

FIX: TremoloParser::processNeighbors() always ran through all neighbors.

• processNeighbors() now receives a vector of atoms whose neighbors to process.

Location:

src/Parser

Files:

• TremoloParser.cpp (modified) (3 diffs)
• TremoloParser.hpp (modified) (1 diff)

src/Parser/TremoloParser.cpp ¶

@@ -38 +38 @@
 
 
+#include <algorithm>
 #include <boost/tokenizer.hpp>
 #include <iostream>
@@ -136 +137 @@
     }
   }
+  LOG(3, "usedFields after load contains: " << usedFields);
+
   // refresh atom::nr and atom::name
-  newmol->getAtomCount();
-
-  LOG(3, "usedFields after load contains: " << usedFields);
-
-  processNeighborInformation();
+  std::vector<atomId_t> atoms(newmol->getAtomCount());
+  std::transform(newmol->begin(), newmol->end(), atoms.begin(),
+      boost::bind(&atom::getId, _1));
+  processNeighborInformation(atoms);
   adaptImprData();
   adaptTorsion();
@@ -515 +517 @@
  * are found by their current ID and mapped to the corresponding atoms with the
  * Id found in the parsed file.
- */
-void FormatParser< tremolo >::processNeighborInformation() {
+ *
+ * @param atoms vector with all newly added (global) atomic ids
+ */
+void FormatParser< tremolo >::processNeighborInformation(const std::vector<atomId_t> &atoms) {
   if (!isUsedField("neighbors")) {
     return;
   }
 
-  for(std::map<const atomId_t, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
-    currentInfo != additionalAtomData.end(); currentInfo++
-  ) {
-    if (!currentInfo->second.neighbors_processed) {
-      for(std::vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
-        neighbor != currentInfo->second.neighbors.end(); neighbor++
-      ) {
-        LOG(3, "INFO: Creating bond between ("
-            << currentInfo->first
-            << ") and ("
-            << getGlobalId(*neighbor) << "|" << *neighbor << ")");
-        ASSERT(getGlobalId(*neighbor) != -1,
-            "FormatParser< tremolo >::processNeighborInformation() - global id to local id "
-            +toString(*neighbor)+" is unknown.");
-        World::getInstance().getAtom(AtomById(currentInfo->first))
-            ->addBond(WorldTime::getTime(), World::getInstance().getAtom(AtomById(getGlobalId(*neighbor))));
-      }
-      currentInfo->second.neighbors_processed = true;
-    }
+  for (std::vector<atomId_t>::const_iterator iter = atoms.begin(); iter != atoms.end(); ++iter) {
+    ASSERT(additionalAtomData.count(*iter) != 0,
+        "FormatParser< tremolo >::processNeighborInformation() - global id "
+        +toString(*iter)+" unknown in additionalAtomData.");
+    TremoloAtomInfoContainer &currentInfo = additionalAtomData[*iter];
+    ASSERT (!currentInfo.neighbors_processed,
+        "FormatParser< tremolo >::processNeighborInformation() - neighbors of new atom "
+        +toString(*iter)+" are already processed.");
+    for(std::vector<int>::const_iterator neighbor = currentInfo.neighbors.begin();
+      neighbor != currentInfo.neighbors.end(); neighbor++
+    ) {
+      LOG(3, "INFO: Creating bond between ("
+          << *iter
+          << ") and ("
+          << getGlobalId(*neighbor) << "|" << *neighbor << ")");
+      ASSERT(getGlobalId(*neighbor) != -1,
+          "FormatParser< tremolo >::processNeighborInformation() - global id to local id "
+          +toString(*neighbor)+" is unknown.");
+      World::getInstance().getAtom(AtomById(*iter))
+          ->addBond(WorldTime::getTime(), World::getInstance().getAtom(AtomById(getGlobalId(*neighbor))));
+    }
+    currentInfo.neighbors_processed = true;
   }
 }

src/Parser/TremoloParser.hpp ¶

@@ -65 +65 @@
   void parseAtomDataKeysLine(std::string line, int offset);
   void readNeighbors(std::stringstream* line, int numberOfNeighbors, int atomId);
-  void processNeighborInformation();
+  void processNeighborInformation(const std::vector<atomId_t> &atoms);
   void adaptImprData();
   void adaptTorsion();