Changeset 3c349b for src/bondgraph.cpp

Timestamp:

Nov 3, 2009, 4:34:31 PM (16 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:

f4e1f5

Parents:

ae38fb

Message:

"not working parsed molecule into subgraph splitting"-BUG fixed, BugFinder branch can be closed.

• config::Load() - atoms were not in the right order for MaxOrder-test (12). Hence, the BondFragmentAdjacency could not be parsed. Now, we just take the subgraphs as the association of each atom to a molecule, i.e. we make a list and then re-link each atom to its new connected subgraph molecule, which is returned as the MoleculeListClass.

other fixes:

• BondGraph::SetMaxDistanceToMaxOfCovalentRadii() - parses the molecule and set to max of covalent radii of elements found therein
• BondGraph::ConstructBondGraph() - SetMaxDistanceToMaxOfCovalentRadii() called before CreateAdjacencyList() to have current max_distance
• BUGFIX: molecule::CreateAdjacencyList() - BondCount was not set to zero after cleaning of list
• FIX: CreateFatherLookupTable() - as we use Calloc(), initialization to NULL was unnecessary

File:

• src/bondgraph.cpp (modified) (2 diffs)

src/bondgraph.cpp

@@ -84 +84 @@
     return false;
 
-  if (BondLengthMatrix == NULL) // no bond length matrix parsed?
+  if (BondLengthMatrix == NULL) { // no bond length matrix parsed?
+    SetMaxDistanceToMaxOfCovalentRadii(out, mol);
     mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
-  else
+  } else
     mol->CreateAdjacencyList(out, max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
 
@@ -105 +106 @@
 };
 
-/** Determines the maximum of all element::CovalentRadius.
+/** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
  * \param *out output stream for debugging
- * \param *periode periodentafel with all elements.
+ * \param *mol molecule with all atoms and their respective elements.
  */
-double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const periodentafel * const periode)
+double BondGraph::SetMaxDistanceToMaxOfCovalentRadii(ofstream * const out, const molecule * const mol)
 {
   max_distance = 0.;
 
-  element * Runner = periode->start;
-  while (Runner->next != periode->end) {
+  atom *Runner = mol->start;
+  while (Runner->next != mol->end) {
     Runner = Runner->next;
-    if (Runner->CovalentRadius > max_distance)
-      max_distance = Runner->CovalentRadius;
+    if (Runner->type->CovalentRadius > max_distance)
+      max_distance = Runner->type->CovalentRadius;
   }
   max_distance *= 2.;