Changeset b4f72c for src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

Timestamp:

Dec 3, 2012, 9:50:01 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:

2ab6b6

Parents:

dcbb5d

git-author:

Frederik Heber <heber@…> (09/20/12 13:44:17)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

ExportGraph_ToFiles now does not require molecule reference anymore.

• SortIndex is now just a dummy (identity) map.
• FragmentationAction combines all graphs from each Fragmentationm call and exports these in one go.

File:

• src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) (9 diffs)

src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

@@ -54 +54 @@
  *
  * @param _graph instance of Graph containing keyset of each fragment
- * @param _mol molecule as reference
- */
-ExportGraph_ToFiles::ExportGraph_ToFiles(const Graph &_graph, molecule *&_mol, const enum HydrogenSaturation _saturation) :
+ * @param saturation whether to saturate dangling bonds with hydrogen or not
+ */
+ExportGraph_ToFiles::ExportGraph_ToFiles(const Graph &_graph, const enum HydrogenSaturation _saturation) :
                 ExportGraph(_graph),
-                mol(_mol),
                 BondFragments(World::getPointer()),
                 saturation(_saturation)
@@ -107 +106 @@
   // store force index reference file
   {
-    SortIndex_t SortIndex(mol);
+    SortIndex_t SortIndex;
     BondFragments.StoreForcesFile(prefix, SortIndex);
   }
@@ -113 +112 @@
   // store keysets file
   TotalGraph.StoreKeySetFile(prefix);
-
-  {
-    // store Adjacency file
-    std::string filename = prefix + ADJACENCYFILE;
-    mol->StoreAdjacencyToFile(filename);
-  }
 
   // store Hydrogen saturation correction file
@@ -137 +130 @@
     LOG(2, "DEBUG: Fragment No." << (*runner).second.first << " with TEFactor "
                 << (*runner).second.second << ".");
-    BondFragments.insert(StoreFragmentFromKeySet(mol, test, World::getInstance().getConfig()));
+    BondFragments.insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
     ++count;
   }
@@ -147 +140 @@
  * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
  * molecule and adds missing hydrogen where bonds were cut.
- * \param *mol reference molecule
  * \param &Leaflet pointer to KeySet structure
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
  * \return pointer to constructed molecule
  */
-molecule * ExportGraph_ToFiles::StoreFragmentFromKeySet(molecule *mol, KeySet &Leaflet, bool IsAngstroem)
+molecule * ExportGraph_ToFiles::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
 {
   Info info(__func__);
@@ -158 +150 @@
   molecule *Leaf = World::getInstance().createMolecule();
 
-  StoreFragmentFromKeySet_Init(mol, Leaf, Leaflet, SonList);
+  StoreFragmentFromKeySet_Init(Leaf, Leaflet, SonList);
   // create the bonds between all: Make it an induced subgraph and add hydrogen
 //  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
-  CreateInducedSubgraphOfFragment(mol, Leaf, SonList, IsAngstroem);
+  CreateInducedSubgraphOfFragment(Leaf, SonList, IsAngstroem);
 
   //Leaflet->Leaf->ScanForPeriodicCorrection(out);
@@ -168 +160 @@
 
 /** Initializes some value for putting fragment of \a *mol into \a *Leaf.
- * \param *mol total molecule
  * \param *Leaf fragment molecule
  * \param &Leaflet pointer to KeySet structure
@@ -174 +165 @@
  * \return number of atoms in fragment
  */
-int ExportGraph_ToFiles::StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
+int ExportGraph_ToFiles::StoreFragmentFromKeySet_Init(molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
 {
   atom *FatherOfRunner = NULL;
 
   // first create the minimal set of atoms from the KeySet
+  World &world = World::getInstance();
   int size = 0;
   for(KeySet::const_iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
-    FatherOfRunner = mol->FindAtom((*runner));  // find the id
+    FatherOfRunner = world.getAtom(AtomById(*runner));  // find the id
     SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
     size++;
@@ -189 +181 @@
 
 /** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
- * \param *out output stream for debugging messages
- * \param *mol total molecule
  * \param *Leaf fragment molecule
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
- * \param SonList list which atom of \a *Leaf is a son of which atom in \a *mol
- */
-void ExportGraph_ToFiles::CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
+ * \param SonList list which atom of \a *Leaf is another atom's son
+ */
+void ExportGraph_ToFiles::CreateInducedSubgraphOfFragment(molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
 {
   bool LonelyFlag = false;