Changeset 44a59b for src

Timestamp:

Oct 17, 2009, 5:06:42 PM (15 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:

07051c

Parents:

09048c

Message:

Renamed and rewritten CreateAdjacencyList2().

• rename CreateAdjacencyList2() -> CreateAdjacencyListFromDbondFile()
• initially written by Christian Neuen who was at that time not familiar with all the functions already present. The code is now shortened and tighter.

Signed-off-by: Frederik Heber <heber@…>

Location:

src

Files:

• builder.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)

src/builder.cpp

@@ -1666 +1666 @@
                 cout << "Parsing bonds from " << argv[argptr] << "." << endl;
                 ifstream *input = new ifstream(argv[argptr]);
-                mol->CreateAdjacencyList2((ofstream *)&cout, input);
+                mol->CreateAdjacencyListFromDbondFile((ofstream *)&cout, input);
                 input->close();
                 argptr+=1;

src/molecule.hpp

@@ -245 +245 @@
 
   /// Initialising routines in fragmentation
-  void CreateAdjacencyList2(ofstream *out, ifstream *output);
+  void CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *output);
   void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
   void CreateListOfBondsPerAtom(ofstream *out);

src/molecule_graph.cpp

@@ -21 +21 @@
  * We obtain an outside file with the indices of atoms which are bondmembers.
  */
-void molecule::CreateAdjacencyList2(ofstream *out, ifstream *input)
+void molecule::CreateAdjacencyListFromDbondFile(ofstream *out, ifstream *input)
 {
 
   // 1 We will parse bonds out of the dbond file created by tremolo.
-      int atom1, atom2, temp;
-      atom *Walker, *OtherWalker;
-
-          if (!input)
-          {
-            cout << Verbose(1) << "Opening silica failed \n";
-          };
-
-      *input >> ws >> atom1;
-      *input >> ws >> atom2;
-          cout << Verbose(1) << "Scanning file\n";
-          while (!input->eof()) // Check whether we read everything already
-          {
-        *input >> ws >> atom1;
-        *input >> ws >> atom2;
-            if(atom2<atom1) //Sort indices of atoms in order
-            {
-              temp=atom1;
-              atom1=atom2;
-              atom2=temp;
-            };
-
-            Walker=start;
-            while(Walker-> nr != atom1) // Find atom corresponding to first index
-            {
-              Walker = Walker->next;
-            };
-            OtherWalker = Walker->next;
-            while(OtherWalker->nr != atom2) // Find atom corresponding to second index
-            {
-              OtherWalker= OtherWalker->next;
-            };
-            AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
-
-          }
-
-          CreateListOfBondsPerAtom(out);
-
+  int atom1, atom2;
+  atom *Walker, *OtherWalker;
+
+  if (!input)
+  {
+    cout << Verbose(1) << "Opening silica failed \n";
+  };
+
+  *input >> ws >> atom1;
+  *input >> ws >> atom2;
+  cout << Verbose(1) << "Scanning file\n";
+  while (!input->eof()) // Check whether we read everything already
+  {
+    *input >> ws >> atom1;
+    *input >> ws >> atom2;
+
+    if(atom2<atom1) //Sort indices of atoms in order
+      flip(atom1, atom2);
+    Walker=FindAtom(atom1);
+    OtherWalker=FindAtom(atom2);
+    AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
+  }
+
+  CreateListOfBondsPerAtom(out);
 };