Changeset 3dadd5 for src/Actions

Timestamp:

Sep 14, 2016, 1:36:04 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:

c4abf2

Parents:

1af2ae

git-author:

Frederik Heber <heber@…> (05/10/16 21:23:50)

git-committer:

Frederik Heber <heber@…> (09/14/16 13:36:04)

Message:

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

This reverts commit c8fd68b29755db45c6c61c8b73eba4c88480c5bf.

Conflicts:

src/Fragmentation/Exporters/SphericalPointDistribution.cpp
src/Fragmentation/Exporters/SphericalPointDistribution.hpp

• needed to reattach SphericalPointDistribution::getSimplifiedPolygon() that was removed in order to ease rebasing a very old branch on top.
• SaturateAction changed to use WeightedPolygon_t and getRemainingPoints().

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::WeightedPolygon_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(
+            std::make_pair( (1./position.Norm())*position, (*bonditer)->getDegree() ));
+      }
+      LOG(3, "DEBUG: current occupied positions are " << current_positions);
+
+      // find the best matching rotated polygon
+      vacant_positions = PointSphere.getRemainingPoints(
+          current_positions,
+          _atom->getType()->getNoValenceOrbitals());
+      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)));
+      LOG(3, "DEBUG: Rescaled vacant positions are " << vacant_positions);
+    }
 
     // add the hydrogens