Changeset a251a3

Timestamp:

May 26, 2008, 10:52:00 AM (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:

9a1b84

Parents:

040f93

Message:

molecule::CreateAdjacencyList() now needs IsAngstroem as parameter

This is necessary, as the database values (covalent radii et al) are in Angstroem, hence don't match if we use Bohrradii as length unit instead. CreateAdjacencyList() converts units and now finds correct bond structure and fragments properly.

Location:

src

Files:

• builder.cpp (modified) (3 diffs)
• molecules.cpp (modified) (5 diffs)
• molecules.hpp (modified) (1 diff)

src/builder.cpp

@@ -931 +931 @@
                 cout << Verbose(0) << "Creating connection matrix..." << endl;
                 start = clock();
-                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]));
+                mol->CreateAdjacencyList((ofstream *)&cout, atof(argv[argptr++]), configuration.GetIsAngstroem());
                 cout << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl;
                 if (mol->first->next != mol->last) {
@@ -1116 +1116 @@
           }
           if (mol->first->next != mol->last) // if connect matrix is present already, redo it
-            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance);
+            mol->CreateAdjacencyList((ofstream *)&cout, mol->BondDistance, configuration.GetIsAngstroem());
           // free memory
           delete[](Elements);
@@ -1159 +1159 @@
         cin >> tmp1;
         start = clock();
-        mol->CreateAdjacencyList((ofstream *)&cout, tmp1);
+        mol->CreateAdjacencyList((ofstream *)&cout, tmp1, configuration.GetIsAngstroem());
         //mol->CreateListOfBondsPerAtom((ofstream *)&cout);
         Subgraphs = mol->DepthFirstSearchAnalysis((ofstream *)&cout, false, MinimumRingSize);

src/molecules.cpp

@@ -1318 +1318 @@
  * \param *out out stream for printing the matrix, NULL if no output
  * \param bonddistance length of linked cells (i.e. maximum minimal length checked)
- */
-void molecule::CreateAdjacencyList(ofstream *out, double bonddistance)
+ * \param IsAngstroem whether coordinate system is gauged to Angstroem or Bohr radii
+ */
+void molecule::CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem)
 {
   atom *Walker = NULL, *OtherWalker = NULL;
@@ -1329 +1330 @@
   vector x;
  
-  BondDistance = bonddistance;
+  BondDistance = bonddistance; // * ((IsAngstroem) ? 1. : 1./AtomicLengthToAngstroem);
   *out << Verbose(0) << "Begin of CreateAdjacencyList." << endl;
   // remove every bond from the list
@@ -1407 +1408 @@
                         /// \todo periodic check is missing here!
                         //*out << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistance(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
-                        MinDistance = OtherWalker->type->CovalentRadius + Walker->type->CovalentRadius;  
+                        MinDistance = OtherWalker->type->CovalentRadius + Walker->type->CovalentRadius;
+                        MinDistance *= (IsAngstroem) ? 1. : 1./AtomicLengthToAngstroem;
                         MaxDistance = MinDistance + BONDTHRESHOLD;
                         MinDistance -= BONDTHRESHOLD;
@@ -1414 +1416 @@
                           *out << Verbose(0) << "Adding Bond between " << *Walker << " and " << *OtherWalker << "." << endl;
                           AddBond(Walker->father, OtherWalker->father, 1);  // also increases molecule::BondCount
+                          BondCount++;
                         } else {
                           //*out << Verbose(1) << "Not Adding: Wrong label order or distance too great." << endl;
@@ -1428 +1431 @@
         delete(CellList[i]);
       }
-    Free((void **)&CellList, "molecule::CreateAdjacencyList - ** CellList"); 
-  
+    Free((void **)&CellList, "molecule::CreateAdjacencyList - ** CellList");
+    
     // create the adjacency list per atom
     CreateListOfBondsPerAtom(out);

src/molecules.hpp

@@ -279 +279 @@
 
   /// Initialising routines in fragmentation  
-  void CreateAdjacencyList(ofstream *out, double bonddistance);
+  void CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem);
   void CreateListOfBondsPerAtom(ofstream *out);