Changeset 9291d04 for src/molecule_geometry.cpp

Timestamp:

Feb 27, 2013, 12:42:36 PM (13 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:

39a07a

Parents:

c7c615

git-author:

Frederik Heber <heber@…> (12/11/12 10:39:30)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:42:36)

Message:

Split saturation with hydrogen of treatment of hydrogen.

• now saturation means dangling bonds are saturated, and treatment means that in a bond graph hydrogen is skipped.
• FragmentationAction and DepthFirstSearchAction adapted in options.

File:

• src/molecule_geometry.cpp (modified) (3 diffs)

src/molecule_geometry.cpp

@@ -371 +371 @@
 /** Determines center of molecule (yet not considering atom masses).
  * \param center reference to return vector
- * \param saturation whether to treat hydrogen special or not
- */
-void molecule::DeterminePeriodicCenter(Vector &center, const enum HydrogenSaturation saturation)
+ * \param treatment whether to treat hydrogen special or not
+ */
+void molecule::DeterminePeriodicCenter(Vector &center, const enum HydrogenTreatment treatment)
 {
   const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
@@ -387 +387 @@
     flag = true;
     for (const_iterator iter = begin(); iter != end(); ++iter) {
-      if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) {
+      if ((treatment == IncludeHydrogen) || ((*iter)->getType()->getAtomicNumber() != 1)) {
         Testvector = inversematrix * (*iter)->getPosition();
         Translationvector.Zero();
@@ -413 +413 @@
         Center += Testvector;
         LOG(1, "vector is: " << Testvector);
-        if (saturation == DoSaturate) {
+        if (treatment == ExcludeHydrogen) {
           // now also change all hydrogens
           for (BondList::const_iterator Runner = ListOfBonds.begin();