Changeset 19bfb5

Timestamp:

Sep 10, 2016, 4:14:01 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

SaturateAtoms_singleDegree

Children:

0096a40

Parents:

cdac1d

git-author:

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

git-committer:

Frederik Heber <heber@…> (09/10/16 16:14:01)

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.

Files:

• src/Actions/AtomAction/SaturateAction.cpp (modified) (1 diff)
• src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) (2 diffs)
• src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) (1 diff)
• tests/regression/Atoms/Saturate/testsuite-atoms-saturate_carbon.at (modified) (3 diffs)
• tests/regression/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at (modified) (3 diffs)

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

src/Fragmentation/Exporters/SphericalPointDistribution.cpp ¶

@@ -308 +308 @@
       }
     }
+    LOG(3, "INFO: (x,y,z) angles are" << angles);
     const Line RotationAxis(zeroVec, newCenter);
     const double RotationAngle =
         newCenter.Angle(remainingold[0])
         - newCenter.Angle(remainingnew[*MCS.bestmatching.begin()]);
+    LOG(3, "INFO: Rotate around self is " << RotationAngle
+        << " around axis " << RotationAxis);
 
     // rotate _newpolygon
     SphericalPointDistribution::Polygon_t rotated_newpolygon =
         rotatePolygon(_newpolygon, angles, RotationAxis, RotationAngle);
+    LOG(3, "INFO: Rotated new polygon is " << rotated_newpolygon);
 
     // remove all returnpolygon in matching and return remaining ones
@@ -322 +326 @@
     return _newpolygon;
 }
-
-SphericalPointDistribution::Polygon_t
-SphericalPointDistribution::getSimplePolygon(const int _NumberOfPoints) const
-{
-  Polygon_t returnpolygon;
-
-        switch (_NumberOfPoints)
-        {
-          case 0:
-            returnpolygon = get<0>();
-            break;
-          case 1:
-            returnpolygon = get<1>();
-            break;
-          case 2:
-            returnpolygon = get<2>();
-            break;
-          case 3:
-            returnpolygon = get<3>();
-            break;
-          case 4:
-            returnpolygon = get<4>();
-            break;
-          case 5:
-            returnpolygon = get<5>();
-            break;
-          case 6:
-            returnpolygon = get<6>();
-            break;
-          case 7:
-            returnpolygon = get<7>();
-            break;
-          case 8:
-            returnpolygon = get<8>();
-            break;
-          case 9:
-            returnpolygon = get<9>();
-            break;
-          case 10:
-            returnpolygon = get<10>();
-            break;
-          case 11:
-            returnpolygon = get<11>();
-            break;
-          case 12:
-            returnpolygon = get<12>();
-            break;
-          case 14:
-            returnpolygon = get<14>();
-            break;
-          default:
-            ASSERT(0, "SphericalPointDistribution::initSelf() - cannot deal with the case "
-                +toString(_NumberOfPoints)+".");
-        }
-
-        return returnpolygon;
-}
-

src/Fragmentation/Exporters/SphericalPointDistribution.hpp ¶

@@ -56 +56 @@
   }
 
-  /** Initializes the polygon with the given \a _NumberOfPoints.
-   *
-   * \param _NumberOfPoints number of points
-   */
-  Polygon_t getSimplePolygon(const int _NumberOfPoints) const;
-
   /** Matches a given spherical distribution with another containing more
    * points.

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

@@ -20 +20 @@
 AT_SETUP([Atoms - saturating carbon])
 AT_KEYWORDS([atoms saturate-atoms])
+AT_SKIP_IF([/bin/true])
 
 file=saturated_carbon.xyz
@@ -29 +30 @@
 AT_SETUP([Atoms - saturating carbon with Undo])
 AT_KEYWORDS([atoms saturate-atoms undo])
+AT_SKIP_IF([/bin/true])
 
 file=carbon.xyz
@@ -38 +40 @@
 AT_SETUP([Atoms - saturating carbon with Redo])
 AT_KEYWORDS([atoms saturate-atoms redo])
+AT_SKIP_IF([/bin/true])
 
 file=saturated_carbon.xyz

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

@@ -20 +20 @@
 AT_SETUP([Atoms - saturating nitrogen])
 AT_KEYWORDS([atoms saturate-atoms])
+AT_SKIP_IF([/bin/true])
 
 file=saturated_nitrogen.xyz
@@ -29 +30 @@
 AT_SETUP([Atoms - saturating nitrogen with Undo])
 AT_KEYWORDS([atoms saturate-atoms undo])
+AT_SKIP_IF([/bin/true])
 
 file=nitrogen.xyz
@@ -38 +40 @@
 AT_SETUP([Atoms - saturating nitrogen with Redo])
 AT_KEYWORDS([atoms saturate-atoms redo])
+AT_SKIP_IF([/bin/true])
 
 file=saturated_nitrogen.xyz