Changeset 3aa8a5 for src/Fragmentation

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:

4694df

Parents:

5197e5

git-author:

Frederik Heber <heber@…> (09/21/12 16:22:50)

git-committer:

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

Message:

REFACTOR: AdjacencyList now just contains a single internal map.

• map may either be created from world for a given vector of atomids or parsed from file.
• Moved molecule::StoreAdjacencyFromFile() over to StoreToFile().
• removed atom_bondedparticle::OutputAdjacency().
• changed comparison functions into operator<,>,==,!=().
• adapted FragmentationAction and SaveAdjacencyAction due to new calls, the former also needs to check the adjacency file for existence.
• SaveAdjacencyAction does not split given filename into path and name anymore.
• TESTFIX: Fragmentation-MaxOrder is working again, removed XFAIL_IF.
• TESTFIX: Rewrite of AdjacencyListUnitTest due to heavily changed interface of AdjacencyList. Also wrongadjacencyfile3 was buggy.
• TESTFIX: regression test SaveAdjacency replaced tab by space and removed tab after last entry in test.adj.

Location:

src/Fragmentation

Files:

• Fragmentation.cpp (modified) (4 diffs)
• fragmentation_helpers.cpp (modified) (1 diff)

src/Fragmentation/Fragmentation.cpp

@@ -100 +100 @@
 {
   std::fstream File;
-  bool FragmentationToDo = true;
   bool CheckOrder = false;
   int TotalNumberOfKeySets = 0;
@@ -118 +117 @@
 
   // ++++++++++++++++++++++++++++ INITIAL STUFF: Bond structure analysis, file parsing, ... ++++++++++++++++++++++++++++++++++++++++++
+  bool FragmentationToDo = true;
 
   // ===== 1. Check whether bond structure is same as stored in files ====
@@ -124 +124 @@
   {
     const std::vector<atomId_t> globalids = getGlobalIdsFromLocalIds(*mol, atomids);
-    FragmentationToDo = FragmentationToDo && FileChecker.CheckAgainstSubset(globalids);
+    AdjacencyList WorldAdjacency(globalids);
+    FragmentationToDo = FragmentationToDo && (FileChecker > WorldAdjacency);
   }
 
@@ -170 +171 @@
   LOG(1, "STATUS: We have created " << TotalGraph.size() << " fragments.");
 
-  {
-    // store Adjacency file
-    std::string filename = prefix + ADJACENCYFILE;
-    mol->StoreAdjacencyToFile(filename);
-  }
 
   // store adaptive orders into file

src/Fragmentation/fragmentation_helpers.cpp

@@ -140 +140 @@
 };
 
-
 const std::vector<atomId_t> getGlobalIdsFromLocalIds(const molecule &mol, const std::vector<atomId_t> &atomids)
 {
   std::vector<atomId_t> globalids;
-  globalids.reserve(atomids.size());
-  BOOST_FOREACH( atomId_t id, atomids ) {
-    molecule::const_iterator iter = mol.begin();
-    for (; iter != mol.end(); ++iter) {
-      if ( (*iter)->getNr() == (int)id)
-        break;
-    }
-    ASSERT( iter != mol.end(),
-        "getGlobalIdsFromLocalIds() - could not find id "+toString(id)
-        +" in molecule "+toString(mol.getName()));
-    globalids.push_back( (*iter)->getId() );
-  }
+  std::transform(atomids.begin(), atomids.end(), std::back_inserter(globalids),
+      boost::bind( &atom::getId,
+          boost::bind( &molecule::FindAtom, boost::cref(mol), _1 ))
+  );
   return globalids;
 }