Changeset bf46da for src

Timestamp:

May 8, 2008, 3:52:11 PM (17 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:

a529de

Parents:

87f6c9

Message:

new function molecule::CreateMappingLabelsToConfigSequence() creates SortIndex in molecule::FragmentMolecule()

further and now final abstraction of FragmentMolecule()

Location:

src

Files:

• moleculelist.cpp (modified) (1 diff)
• molecules.cpp (modified) (4 diffs)
• molecules.hpp (modified) (1 diff)

src/moleculelist.cpp

@@ -503 +503 @@
   if (FragmentList == NULL) {
     KeySetCounter = Count();
-    FragmentList = (Graph **) Malloc(sizeof(Graph *)*KeySetCounter, "molecule::FragmentMolecule - **BondFragments");
+    FragmentList = (Graph **) Malloc(sizeof(Graph *)*KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
     for(int i=0;i<KeySetCounter;i++)
       FragmentList[i] = NULL;

src/molecules.cpp

@@ -2161 +2161 @@
 };
 
+/** Create a SortIndex to map from BFS labels to the sequence in which the atoms are given in the config file.
+ * \param *out output stream for debugging
+ * \param *&SortIndex Mapping array of size molecule::AtomCount
+ * \return true - success, false - failure of SortIndex alloc
+ */
+bool molecule::CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex)
+{
+  element *runner = elemente->start;
+  int AtomNo = 0;
+  atom *Walker = NULL;
+  
+  if (SortIndex != NULL) {
+    *out << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl;
+    return false;
+  }
+  SortIndex = (int *) Malloc(sizeof(int)*AtomCount, "molecule::FragmentMolecule: *SortIndex");
+  for(int i=0;i<AtomCount;i++)
+    SortIndex[i] = -1;
+  while (runner->next != elemente->end) { // go through every element
+    runner = runner->next;
+    if (ElementsInMolecule[runner->Z]) { // if this element got atoms
+      Walker = start;
+      while (Walker->next != end) { // go through every atom of this element
+        Walker = Walker->next;
+        if (Walker->type->Z == runner->Z) // if this atom fits to element
+          SortIndex[Walker->nr] = AtomNo++;
+      }
+    }
+  }
+  return true;
+};
+
 /** Performs a many-body bond order analysis for a given bond order.
  * -# parses adjacency, keysets and orderatsite files
@@ -2181 +2213 @@
 {
         MoleculeListClass *BondFragments = NULL;
-  atom *Walker = NULL;
   int *SortIndex = NULL;
-  element *runner = NULL;
-  int AtomNo;
   int MinimumRingSize;
   int FragmentCounter;
@@ -2302 +2331 @@
   // ===== 9. Save fragments' configuration and keyset files et al to disk ===
   if (BondFragments->NumberOfMolecules != 0) {
-    // create a SortIndex to map from BFS labels to the sequence in which the atoms are given in the config file
-    SortIndex = (int *) Malloc(sizeof(int)*AtomCount, "molecule::FragmentMolecule: *SortIndex");
-    for(int i=0;i<AtomCount;i++)
-      SortIndex[i] = -1;
-    runner = elemente->start;
-    AtomNo = 0;
-    while (runner->next != elemente->end) { // go through every element
-      runner = runner->next;
-      if (ElementsInMolecule[runner->Z]) { // if this element got atoms
-        Walker = start;
-        while (Walker->next != end) { // go through every atom of this element
-          Walker = Walker->next;
-          if (Walker->type->Z == runner->Z) // if this atom fits to element
-            SortIndex[Walker->nr] = AtomNo++;
-        }
-      }
-    }
+    // create the SortIndex from BFS labels to order in the config file
+    CreateMappingLabelsToConfigSequence(out, SortIndex);
+    
     *out << Verbose(1) << "Writing " << BondFragments->NumberOfMolecules << " possible bond fragmentation configs" << endl;
     if (BondFragments->OutputConfigForListOfFragments(out, configuration, SortIndex))
@@ -2343 +2358 @@
     *out << Verbose(1) << "Freeing bond memory" << endl;
     delete(FragmentList); // remove bond molecule from memory
-    FragmentList = NULL;
     Free((void **)&SortIndex, "molecule::FragmentMolecule: *SortIndex"); 
   } else

src/molecules.hpp

@@ -348 +348 @@
   bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
   bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
+  bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
   bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
   void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);