Changeset 64cafb2 for src/Actions/AtomAction

Timestamp:

Sep 10, 2016, 4:01:20 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

0c42f2, cdac1d

Parents:

d32f60

git-author:

Frederik Heber <heber@…> (05/10/16 18:33:50)

git-committer:

Frederik Heber <heber@…> (09/10/16 16:01:20)

Message:

Revert "Trimmed down SphericalPointDistribution to what is needed at the moment."

This reverts commit 0241c59e7f10c73f87336715af0aadac2b2d4db1.

• TESTFIX: SaturateAtoms regression tests are marked as XFAIL.
• commented-out addHydrogen section in SaturateAction.

File:

• src/Actions/AtomAction/SaturateAction.cpp (modified) (1 diff)

src/Actions/AtomAction/SaturateAction.cpp

@@ -77 +77 @@
         "ChangeElementAction::performCall() - mol is still NULL." );
 
-    // add the hydrogens
-    const Vector AtomsPosition = _atom->getPosition();
-    double typical_distance = _atom->getType()->getHBondDistance(0);
-    if (typical_distance == -1.)
-      typical_distance = 1.;
-    SphericalPointDistribution PointSphere(typical_distance);
-    PointSphere.initSelf(_atom->getType()->getNoValenceOrbitals());
-    for (SphericalPointDistribution::Polygon_t::const_iterator iter = PointSphere.points.begin();
-        iter != PointSphere.points.end(); ++iter) {
-      // for every Vector add a point relative to atom's position
-      atom * hydrogenAtom = World::getInstance().createAtom();
-      hydrogenAtom->setType(hydrogen);
-      hydrogenAtom->setPosition(AtomsPosition + *iter);
-      mol->AddAtom(hydrogenAtom);
-      // add bond
-      _atom->addBond(WorldTime::getTime(), hydrogenAtom);
-      // mark down for undo state
-      addedHydrogens.push_back(AtomicInfo(*(hydrogenAtom)));
-    }
+//    // add the hydrogens
+//    const Vector AtomsPosition = _atom->getPosition();
+//    double typical_distance = _atom->getType()->getHBondDistance(0);
+//    if (typical_distance == -1.)
+//      typical_distance = 1.;
+//    SphericalPointDistribution PointSphere(typical_distance);
+//    PointSphere.initSelf(_atom->getType()->getNoValenceOrbitals());
+//    for (SphericalPointDistribution::Polygon_t::const_iterator iter = PointSphere.points.begin();
+//        iter != PointSphere.points.end(); ++iter) {
+//      // for every Vector add a point relative to atom's position
+//      atom * hydrogenAtom = World::getInstance().createAtom();
+//      hydrogenAtom->setType(hydrogen);
+//      hydrogenAtom->setPosition(AtomsPosition + *iter);
+//      mol->AddAtom(hydrogenAtom);
+//      // add bond
+//      _atom->addBond(WorldTime::getTime(), hydrogenAtom);
+//      // mark down for undo state
+//      addedHydrogens.push_back(AtomicInfo(*(hydrogenAtom)));
+//    }
   }