Changeset 3dadd5


Ignore:
Timestamp:
Sep 14, 2016, 1:36:04 PM (9 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().
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/AtomAction/SaturateAction.cpp

    r1af2ae r3dadd5  
    8484    // check for any bonds and get vacant positions
    8585    SphericalPointDistribution::Polygon_t vacant_positions;
    86 //    const BondList& ListOfBonds = _atom->getListOfBonds();
    87 //    SphericalPointDistribution PointSphere(typical_distance);
    88 //    if (ListOfBonds.size() == 0) {
    89 //      vacant_positions = PointSphere.getSimplePolygon(_atom->getType()->getNoValenceOrbitals());
    90 //      LOG(3, "DEBUG: Using ideal positions as " << vacant_positions);
    91 //    } else {
    92 //      // get ideal polygon and currently occupied positions
    93 //      const SphericalPointDistribution::Polygon_t ideal_positions =
    94 //          PointSphere.getSimplePolygon(_atom->getType()->getNoValenceOrbitals());
    95 //      LOG(3, "DEBUG: ideal positions are " << ideal_positions);
    96 //      SphericalPointDistribution::Polygon_t current_positions;
    97 //      for (BondList::const_iterator bonditer = ListOfBonds.begin();
    98 //          bonditer != ListOfBonds.end(); ++bonditer) {
    99 //        const Vector position =
    100 //            (*bonditer)->GetOtherAtom(_atom)->getPosition().getVectorToPoint(_atom->getPosition());
    101 //        current_positions.push_back((1./position.Norm())*position);
    102 //      }
    103 //      LOG(3, "DEBUG: current occupied positions are " << current_positions);
    104 //
    105 //      // find the best matching rotated polygon
    106 //      vacant_positions = SphericalPointDistribution::matchSphericalPointDistributions(
    107 //          current_positions,
    108 //          ideal_positions);
    109 //      LOG(3, "DEBUG: Resulting vacant positions are " << vacant_positions);
    110 //
    111 //      // scale vacant positions to typical_distance
    112 //      std::for_each(
    113 //          vacant_positions.begin(), vacant_positions.end(),
    114 //          boost::bind(&Vector::Scale, _1, boost::cref(typical_distance)));
    115 //    }
     86    const BondList& ListOfBonds = _atom->getListOfBonds();
     87    SphericalPointDistribution PointSphere(typical_distance);
     88    if (ListOfBonds.size() == 0) {
     89      vacant_positions = PointSphere.getSimplePolygon(_atom->getType()->getNoValenceOrbitals());
     90      LOG(3, "DEBUG: Using ideal positions as " << vacant_positions);
     91    } else {
     92      // get ideal polygon and currently occupied positions
     93      const SphericalPointDistribution::Polygon_t ideal_positions =
     94          PointSphere.getSimplePolygon(_atom->getType()->getNoValenceOrbitals());
     95      LOG(3, "DEBUG: ideal positions are " << ideal_positions);
     96      SphericalPointDistribution::WeightedPolygon_t current_positions;
     97      for (BondList::const_iterator bonditer = ListOfBonds.begin();
     98          bonditer != ListOfBonds.end(); ++bonditer) {
     99        const Vector position =
     100            (*bonditer)->GetOtherAtom(_atom)->getPosition().getVectorToPoint(_atom->getPosition());
     101        current_positions.push_back(
     102            std::make_pair( (1./position.Norm())*position, (*bonditer)->getDegree() ));
     103      }
     104      LOG(3, "DEBUG: current occupied positions are " << current_positions);
     105
     106      // find the best matching rotated polygon
     107      vacant_positions = PointSphere.getRemainingPoints(
     108          current_positions,
     109          _atom->getType()->getNoValenceOrbitals());
     110      LOG(3, "DEBUG: Resulting vacant positions are " << vacant_positions);
     111
     112      // scale vacant positions to typical_distance
     113      std::for_each(
     114          vacant_positions.begin(), vacant_positions.end(),
     115          boost::bind(&Vector::Scale, _1, boost::cref(typical_distance)));
     116      LOG(3, "DEBUG: Rescaled vacant positions are " << vacant_positions);
     117    }
    116118
    117119    // add the hydrogens

  • src/Fragmentation/Exporters/SphericalPointDistribution.cpp

    r1af2ae r3dadd5  
    10291029    return points;
    10301030}
     1031
     1032SphericalPointDistribution::Polygon_t
     1033SphericalPointDistribution::getSimplePolygon(const int _NumberOfPoints) const
     1034{
     1035  Polygon_t returnpolygon;
     1036
     1037        switch (_NumberOfPoints)
     1038        {
     1039          case 0:
     1040            returnpolygon = get<0>();
     1041            break;
     1042          case 1:
     1043            returnpolygon = get<1>();
     1044            break;
     1045          case 2:
     1046            returnpolygon = get<2>();
     1047            break;
     1048          case 3:
     1049            returnpolygon = get<3>();
     1050            break;
     1051          case 4:
     1052            returnpolygon = get<4>();
     1053            break;
     1054          case 5:
     1055            returnpolygon = get<5>();
     1056            break;
     1057          case 6:
     1058            returnpolygon = get<6>();
     1059            break;
     1060          case 7:
     1061            returnpolygon = get<7>();
     1062            break;
     1063          case 8:
     1064            returnpolygon = get<8>();
     1065            break;
     1066          case 9:
     1067            returnpolygon = get<9>();
     1068            break;
     1069          case 10:
     1070            returnpolygon = get<10>();
     1071            break;
     1072          case 11:
     1073            returnpolygon = get<11>();
     1074            break;
     1075          case 12:
     1076            returnpolygon = get<12>();
     1077            break;
     1078          case 14:
     1079            returnpolygon = get<14>();
     1080            break;
     1081          default:
     1082            ASSERT(0, "SphericalPointDistribution::initSelf() - cannot deal with the case "
     1083                +toString(_NumberOfPoints)+".");
     1084        }
     1085
     1086        return returnpolygon;
     1087}
     1088

  • src/Fragmentation/Exporters/SphericalPointDistribution.hpp

    r1af2ae r3dadd5  
    7373    return Polygon_t();
    7474  }
     75
     76  /** Initializes the polygon with the given \a _NumberOfPoints.
     77   *
     78   * \param _NumberOfPoints number of points
     79   */
     80  Polygon_t getSimplePolygon(const int _NumberOfPoints) const;
    7581
    7682  /** Returns vacant spots to fill to get a complete spherical point distribution from

  • tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at

    r1af2ae r3dadd5  
    2020AT_SETUP([Atoms - saturating carbon])
    2121AT_KEYWORDS([atoms saturate-atoms])
    22 AT_SKIP_IF([/bin/true])
    2322
    2423file=saturated_carbon.xyz
    … …  
    3029AT_SETUP([Atoms - saturating carbon with Undo])
    3130AT_KEYWORDS([atoms saturate-atoms undo])
    32 AT_SKIP_IF([/bin/true])
    3331
    3432file=carbon.xyz
    … …  
    4038AT_SETUP([Atoms - saturating carbon with Redo])
    4139AT_KEYWORDS([atoms saturate-atoms redo])
    42 AT_SKIP_IF([/bin/true])
    4340
    4441file=saturated_carbon.xyz

  • tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at

    r1af2ae r3dadd5  
    2020AT_SETUP([Atoms - saturating nitrogen])
    2121AT_KEYWORDS([atoms saturate-atoms])
    22 AT_SKIP_IF([/bin/true])
    2322
    2423file=saturated_nitrogen.xyz
    … …  
    3029AT_SETUP([Atoms - saturating nitrogen with Undo])
    3130AT_KEYWORDS([atoms saturate-atoms undo])
    32 AT_SKIP_IF([/bin/true])
    3331
    3432file=nitrogen.xyz
    … …  
    4038AT_SETUP([Atoms - saturating nitrogen with Redo])
    4139AT_KEYWORDS([atoms saturate-atoms redo])
    42 AT_SKIP_IF([/bin/true])
    4340
    4441file=saturated_nitrogen.xyz
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