Changeset 9ec12c

Timestamp:

Sep 10, 2016, 4:14:02 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

SaturateAtoms_singleDegree

Children:

aa91e63

Parents:

899cc9

git-author:

Frederik Heber <heber@…> (05/10/16 21:50:32)

git-committer:

Frederik Heber <heber@…> (09/10/16 16:14:02)

Message:

SaturateAction reduces polygon edge count by surplus bond degrees.

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
+      SphericalPointDistribution::Polygon_t current_positions;
+      int number_vacant_positions = _atom->getType()->getNoValenceOrbitals();
+      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);
+        number_vacant_positions -= (*bonditer)->getDegree() - 1;
+      }
+      LOG(3, "DEBUG: current occupied positions are " << current_positions);
+      ASSERT( number_vacant_positions >= 0,
+          "AtomSaturateAction::performCall() - negative number of vacant positions?");
+      LOG(3, "DEBUG: There remain " << number_vacant_positions << " vacant positions.");
+
+      const SphericalPointDistribution::Polygon_t ideal_positions =
+          PointSphere.getSimplePolygon(number_vacant_positions);
+      LOG(3, "DEBUG: ideal positions are " << ideal_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