Changeset 75363b for src/Fragmentation/Fragmentation.cpp

Timestamp:

Oct 25, 2011, 12:08:03 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, Candidate_v1.7.0, 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:

730d7a

Parents:

42127c

git-author:

Frederik Heber <heber@…> (10/20/11 10:17:10)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

Extracted functions from fragmentation_helpers and placed them in KeySet or Graph class.

• KeySet: ScanBufferIntoKeySet()
• Graph: ParseKeySetFile(), StoreKeySetFile(), ParseTEFactorsFile(), StoreTEFactorsFile(), GraphToIndexedKeySet()

File:

• src/Fragmentation/Fragmentation.cpp (modified) (7 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -83 +83 @@
   bool CheckOrder = false;
   Graph **FragmentList = NULL;
-  Graph *ParsedFragmentList = NULL;
   Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
@@ -126 +125 @@
 
   // ===== 3. if structure still valid, parse key set file and others =====
-  FragmentationToDo = FragmentationToDo && ParseKeySetFile(prefix, ParsedFragmentList);
+  Graph ParsedFragmentList;
+  FragmentationToDo = FragmentationToDo && ParsedFragmentList.ParseKeySetFile(prefix);
 
   // ===== 4. check globally whether there's something to do actually (first adaptivity check)
@@ -138 +138 @@
     ListOfLocalAtoms[i] = NULL;
   FragmentCounter = 0;
-  Subgraphs->next->AssignKeySetsToFragment(mol, ParsedFragmentList, ListOfLocalAtoms, FragmentList, FragmentCounter, true);
+  Subgraphs->next->AssignKeySetsToFragment(mol, &ParsedFragmentList, ListOfLocalAtoms, FragmentList, FragmentCounter, true);
   delete[](ListOfLocalAtoms);
 
@@ -146 +146 @@
   AtomMask[mol->getAtomCount()] = false;
   FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
-  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, prefix))) {
+  while ((CheckOrder = CheckOrderAtSite(AtomMask, &ParsedFragmentList, Order, prefix))) {
     FragmentationToDo = FragmentationToDo || CheckOrder;
     AtomMask[mol->getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
@@ -171 +171 @@
   delete[](RootStack);
   delete[](AtomMask);
-  delete(ParsedFragmentList);
 
   // ==================================== End of FRAGMENTATION ============================================
@@ -224 +223 @@
 
     // store keysets file
-    StoreKeySetFile(TotalGraph, prefix);
+    TotalGraph.StoreKeySetFile(prefix);
 
     {
@@ -465 +464 @@
       return false;
     }
-    map<int,KeySet> *IndexKeySetList = GraphToIndexedKeySet(GlobalKeySetList);
+    map<int,KeySet> *IndexKeySetList = GlobalKeySetList->GraphToIndexedKeySet();
 
     // parse the EnergyPerFragment file