Changeset 276ac6 for src

Timestamp:

Feb 27, 2013, 12:42:37 PM (12 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:

5a4955

Parents:

a82127

git-author:

Frederik Heber <heber@…> (12/14/12 15:56:00)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:42:37)

Message:

FIX: ExportGraph_ToFiles needs to know about hydrogen treatment to not copy present hydrogens.

• we only copy if hydrogen is excluded.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) (3 diffs)
• Fragmentation/Exporters/ExportGraph_ToFiles.hpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -166 +166 @@
   {
     const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
-    ExportGraph_ToFiles exporter(TotalGraph, saturation);
+    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+    ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation);
     exporter.setPrefix(params.prefix.get());
     exporter.setOutputTypes(params.types.get());

src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp

@@ -54 +54 @@
  *
  * @param _graph instance of Graph containing keyset of each fragment
- * @param saturation whether to saturate dangling bonds with hydrogen or not
- */
-ExportGraph_ToFiles::ExportGraph_ToFiles(const Graph &_graph, const enum HydrogenSaturation _saturation) :
+ * @param _treatment whether to always add already present hydrogens or not
+ * @param _saturation whether to saturate dangling bonds with hydrogen or not
+ */
+ExportGraph_ToFiles::ExportGraph_ToFiles(
+    const Graph &_graph,
+    const enum HydrogenTreatment _treatment,
+    const enum HydrogenSaturation _saturation) :
                 ExportGraph(_graph),
                 BondFragments(World::getPointer()),
+                treatment(_treatment),
                 saturation(_saturation)
 {}
@@ -225 +230 @@
             if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
               exit(1);
+          } else if ((treatment == ExcludeHydrogen) && (OtherFather->getElementNo() == (atomicNumber_t)1)) {
+            // just copy the atom if it's a hydrogen
+            atom * const OtherWalker = Leaf->AddCopyAtom(OtherFather);
+            Leaf->AddBond((*iter), OtherWalker, (*BondRunner)->BondDegree);
           }
           //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
@@ -230 +239 @@
       }
     } else {
-    ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
+      ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
     }
     if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {

src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp

@@ -30 +30 @@
 {
 public:
-        ExportGraph_ToFiles(const Graph &_graph, const enum HydrogenSaturation _saturation);
+        ExportGraph_ToFiles(
+            const Graph &_graph,
+            const enum HydrogenTreatment _treatment,
+            const enum HydrogenSaturation _saturation);
         virtual ~ExportGraph_ToFiles();
 
@@ -57 +60 @@
   //!> list of parser types for which a configuration file per fragment is stored
   std::vector<std::string> typelist;
+  //!> whether to always add already present hydrogens or not
+  const enum HydrogenTreatment treatment;
   //!> whether to saturate dangling bonds or not
   const enum HydrogenSaturation saturation;