Changeset ec9bd2


Ignore:
Timestamp:
May 25, 2016, 7:13:59 AM (9 years ago)
Author:
Frederik Heber <heber@…>
Parents:
9cf90e
git-author:
Frederik Heber <heber@…> (05/10/16 21:23:50)
git-committer:
Frederik Heber <heber@…> (05/25/16 07:13:59)
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

    r9cf90e rec9bd2  
    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

    r9cf90e rec9bd2  
    10271027    return points;
    10281028}
     1029
     1030SphericalPointDistribution::Polygon_t
     1031SphericalPointDistribution::getSimplePolygon(const int _NumberOfPoints) const
     1032{
     1033  Polygon_t returnpolygon;
     1034
     1035        switch (_NumberOfPoints)
     1036        {
     1037          case 0:
     1038            returnpolygon = get<0>();
     1039            break;
     1040          case 1:
     1041            returnpolygon = get<1>();
     1042            break;
     1043          case 2:
     1044            returnpolygon = get<2>();
     1045            break;
     1046          case 3:
     1047            returnpolygon = get<3>();
     1048            break;
     1049          case 4:
     1050            returnpolygon = get<4>();
     1051            break;
     1052          case 5:
     1053            returnpolygon = get<5>();
     1054            break;
     1055          case 6:
     1056            returnpolygon = get<6>();
     1057            break;
     1058          case 7:
     1059            returnpolygon = get<7>();
     1060            break;
     1061          case 8:
     1062            returnpolygon = get<8>();
     1063            break;
     1064          case 9:
     1065            returnpolygon = get<9>();
     1066            break;
     1067          case 10:
     1068            returnpolygon = get<10>();
     1069            break;
     1070          case 11:
     1071            returnpolygon = get<11>();
     1072            break;
     1073          case 12:
     1074            returnpolygon = get<12>();
     1075            break;
     1076          case 14:
     1077            returnpolygon = get<14>();
     1078            break;
     1079          default:
     1080            ASSERT(0, "SphericalPointDistribution::initSelf() - cannot deal with the case "
     1081                +toString(_NumberOfPoints)+".");
     1082        }
     1083
     1084        return returnpolygon;
     1085}
     1086

  • src/Fragmentation/Exporters/SphericalPointDistribution.hpp

    r9cf90e rec9bd2  
    7171    ASSERT(0, "SphericalPointDistribution::getConnections() - not specialized for "+toString(N)+".");
    7272  }
     73
     74  /** Initializes the polygon with the given \a _NumberOfPoints.
     75   *
     76   * \param _NumberOfPoints number of points
     77   */
     78  Polygon_t getSimplePolygon(const int _NumberOfPoints) const;
    7379
    7480  /** Returns vacant spots to fill to get a complete spherical point distribution from

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

    r9cf90e rec9bd2  
    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

    r9cf90e rec9bd2  
    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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