Changeset 0c42f2 for src/Actions

Timestamp:

Sep 12, 2016, 2:03:11 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, 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:

6cb1cd

Parents:

64cafb2

git-author:

Frederik Heber <heber@…> (05/10/16 20:04:47)

git-committer:

Frederik Heber <heber@…> (09/12/16 14:03:11)

Message:

Extended SaturateAction to be able to deal with bonded atoms.

• TESTFIX: Removed XFAIL from SaturateAction regression tests again.

File:

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

src/Actions/AtomAction/SaturateAction.cpp

@@ -75 +75 @@
     }
     ASSERT( mol != NULL,
-        "ChangeElementAction::performCall() - mol is still NULL." );
+        "AtomSaturateAction::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)));
-//    }
+    // radius of polygon on sphere
+    double typical_distance = _atom->getType()->getHBondDistance(0);
+    if (typical_distance == -1.)
+      typical_distance = 1.;
+
+    // check for any bonds and get vacant positions
+    SphericalPointDistribution::Polygon_t vacant_positions;
+    const BondList& ListOfBonds = _atom->getListOfBonds();
+    SphericalPointDistribution PointSphere(typical_distance);
+    if (ListOfBonds.size() == 0) {
+      vacant_positions = PointSphere.getSimplePolygon(_atom->getType()->getNoValenceOrbitals());
+      LOG(3, "DEBUG: Using ideal positions as " << vacant_positions);
+    } else {
+      // get ideal polygon and currently occupied positions
+      const SphericalPointDistribution::Polygon_t ideal_positions =
+          PointSphere.getSimplePolygon(_atom->getType()->getNoValenceOrbitals());
+      LOG(3, "DEBUG: ideal positions are " << ideal_positions);
+      SphericalPointDistribution::Polygon_t current_positions;
+      for (BondList::const_iterator bonditer = ListOfBonds.begin();
+          bonditer != ListOfBonds.end(); ++bonditer) {
+        const Vector position =
+            (*bonditer)->GetOtherAtom(_atom)->getPosition().getVectorToPoint(_atom->getPosition());
+        current_positions.push_back((1./position.Norm())*position);
+      }
+      LOG(3, "DEBUG: current occupied positions are " << current_positions);
+
+      // find the best matching rotated polygon
+      vacant_positions = SphericalPointDistribution::matchSphericalPointDistributions(
+          current_positions,
+          ideal_positions);
+      LOG(3, "DEBUG: Resulting vacant positions are " << vacant_positions);
+
+      // scale vacant positions to typical_distance
+      std::for_each(
+          vacant_positions.begin(), vacant_positions.end(),
+          boost::bind(&Vector::Scale, _1, boost::cref(typical_distance)));
+    }
+
+    // add the hydrogens
+    const Vector AtomsPosition = _atom->getPosition();
+    for (SphericalPointDistribution::Polygon_t::const_iterator iter = vacant_positions.begin();
+        iter != vacant_positions.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)));
+    }
   }