Changeset dcbb5d

Timestamp:

Dec 3, 2012, 9:50:00 AM (12 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:

b4f72c

Parents:

ca8bea

git-author:

Frederik Heber <heber@…> (09/20/12 13:12:32)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:00)

Message:

REFACTOR: Replaced SortIndex by a distinct class to allow replacement.

Location:

src

Files:

• Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) (4 diffs)
• Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) (1 diff)
• Fragmentation/Graph.cpp (modified) (1 diff)
• Fragmentation/Makefile.am (modified) (2 diffs)
• Fragmentation/SortIndex.cpp (added)
• Fragmentation/SortIndex.hpp (added)
• MoleculeListClass.hpp (modified) (2 diffs)
• moleculelist.cpp (modified) (3 diffs)

src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

@@ -44 +44 @@
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/SortIndex.hpp"
 #include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
@@ -88 +89 @@
 
   // ===== 9. Save fragments' configuration and keyset files et al to disk ===
-  // create the SortIndex from BFS labels to order in the config file
-  std::map<atomId_t, int> SortIndex;
-  CreateMappingLabelsToConfigSequence(SortIndex);
-
   LOG(1, "Writing " << BondFragments.ListOfMolecules.size() << " possible bond fragmentation configs");
   bool write_status = true;
@@ -109 +106 @@
 
   // store force index reference file
-  BondFragments.StoreForcesFile(prefix, SortIndex);
+  {
+    SortIndex_t SortIndex(mol);
+    BondFragments.StoreForcesFile(prefix, SortIndex);
+  }
 
   // store keysets file
@@ -254 +254 @@
 }
 
-/** Create a SortIndex to map from atomic labels to the sequence in which the atoms are given in the config file.
- * \param &SortIndex Mapping array of size molecule::AtomCount
- * \return true - success, false - failure of SortIndex alloc
- */
-bool ExportGraph_ToFiles::CreateMappingLabelsToConfigSequence(std::map<atomId_t, int> &SortIndex)
-{
-  if (!SortIndex.empty()) {
-    LOG(1, "SortIndex has " << SortIndex.size() << " entries and is not empty as expected.");
-    return false;
-  }
-
-  int AtomNo = 0;
-  for(molecule::const_iterator iter=mol->begin();iter!=mol->end();++iter){
-    const int id = (*iter)->getNr();
-#ifndef NDEBUG
-      std::pair<std::map<atomId_t, int>::const_iterator, bool> inserter =
-#endif
-    SortIndex.insert( std::make_pair(id, AtomNo++) );
-    ASSERT( inserter.second ,
-        "ExportGraph_ToFiles::CreateMappingLabelsToConfigSequence() - same SortIndex set twice.");
-  }
-
-  return true;
-}
-

src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

@@ -48 +48 @@
   int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
   void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
-  bool CreateMappingLabelsToConfigSequence(std::map<atomId_t, int> &SortIndex);
-
 
 private:

src/Fragmentation/Graph.cpp

@@ -156 +156 @@
   }
   output.close();
-  output.clear();
 
   return status;

src/Fragmentation/Makefile.am

@@ -18 +18 @@
         Fragmentation/MatrixContainer.cpp \
         Fragmentation/PowerSetGenerator.cpp \
+        Fragmentation/SortIndex.cpp \
         Fragmentation/UniqueFragments.cpp
 
@@ -42 +43 @@
         Fragmentation/MoleculeMask.hpp \
         Fragmentation/PowerSetGenerator.hpp \
+        Fragmentation/SortIndex.hpp \
         Fragmentation/UniqueFragments.hpp
 

src/MoleculeListClass.hpp

@@ -27 +27 @@
 class molecule;
 class periodentafel;
+class SortIndex_t;
 class World;
 
@@ -45 +46 @@
 
   bool AddHydrogenCorrection(std::string &path);
-  bool StoreForcesFile(std::string &path, const std::map<atomId_t, int> &SortIndex);
+  bool StoreForcesFile(std::string &path, const SortIndex_t &SortIndex);
   void insert(molecule *mol);
   void erase(molecule *mol);

src/moleculelist.cpp

@@ -51 +51 @@
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/SortIndex.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Helpers/helpers.hpp"
@@ -492 +493 @@
  * \return true - file written successfully, false - writing failed
  */
-bool MoleculeListClass::StoreForcesFile(std::string &path, const std::map<atomId_t, int> &SortIndex)
+bool MoleculeListClass::StoreForcesFile(std::string &path, const SortIndex_t &SortIndex)
 {
   bool status = true;
@@ -512 +513 @@
               if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
                 const atomId_t fatherid = (*atomIter)->GetTrueFather()->getNr();
-                const std::map<atomId_t, int>::const_iterator iter = SortIndex.find(fatherid);
-                if( iter != SortIndex.end())
-                  ForcesFile << iter->second << "\t";
-                else
-                  ForcesFile << "-1\t";
+                ForcesFile << SortIndex.find(fatherid) << "\t";
               } else
                 // otherwise a -1 to indicate an added saturation hydrogen