Changeset 6cb1cd for src/Actions/AtomAction

Timestamp:

Sep 12, 2016, 2:03:15 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, 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:

7e81ca

Parents:

0c42f2

git-author:

Frederik Heber <heber@…> (05/10/16 20:35:20)

git-committer:

Frederik Heber <heber@…> (09/12/16 14:03:15)

Message:

Removing SphericalPointDistribution::getSimplePolygon() to allow for easy rebasing of very old branch on top.

• SaturateAtoms does not use SphericalPointDistribution at the moment.
• TESTFIX: associated regression tests are skipped.

File:

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

src/Actions/AtomAction/SaturateAction.cpp

@@ -84 +84 @@
     // 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)));
-    }
+//    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