Changeset ce0ca4 for src/Fragmentation/Exporters/SphericalPointDistribution.hpp

Timestamp:

Aug 20, 2014, 1:06:16 PM (11 years ago)

Author:

Frederik Heber <heber@…>

Children:

f5fa48

Parents:

c8d2e7

git-author:

Frederik Heber <heber@…> (07/18/14 16:24:53)

git-committer:

Frederik Heber <heber@…> (08/20/14 13:06:16)

Message:

Added getAssociatedPoints().

• the general problem with getRemainingPoints() for saturating fragments with dangling bonds is that we violate the "Saturation Consistency Principle": Common saturation hydrogens for a specific fragments must remain at the exact same position for all containing fragments.
• only there do we ascertain that the eigenvalue is (due to the invariance of hydrogen to changes in its chemical neighborhood, valid to a good degree) actually removed by higher order fragments.
• this function is the first step to calculate a "global" set of saturation positions per atom.
• added also getIdentityAssociation() in case the association is trivial (i.e. in case of only bonds of degree 1).

File:

• src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) (1 diff)

src/Fragmentation/Exporters/SphericalPointDistribution.hpp

@@ -126 +126 @@
     IndexList_t indices;
   };
+
+  struct PolygonWithIndexTuples
+  {
+    //!> array with points
+    VectorArray_t polygon;
+    //!> list with tuples of indices for the above points, defining subset
+    IndexTupleList_t indices;
+  };
+
+  /** Returns associated \a _N points equally distributed on a sphere's surface
+   * with respect to the given set of points \a _polygon.
+   *
+   * This function is similar to getRemainingPoints() in that both calculate
+   * a matching between the given points \a _polygon and the \a _N equally
+   * distributed points. The difference is that getRemainingPoints() returns
+   * the unmatched points. This function however is supposed to match (almost)
+   * all and return for each of the points a respective set of points where to
+   * place saturation hydrogens.
+   *
+   * This set of points is then used as a "global" reference set over all
+   * fragments (\sa FragmentationFragmentationAction::performCall()) such that
+   * the common saturation hydrogens for the same atom over all containing
+   * fragments remain at exactly the same position, the saturation consistency
+   * principle. Only by that do we maintain same eigenvalues and hence minimal
+   * disturbance (due to approximate invariance of hydrogen to its chemical
+   * neighborhood) when using the fragmention method with closed-shell
+   * calculations requiring this saturation of dangling bonds.
+   *
+   * \param _polygon already filled places to match
+   * \param _N desired total number fo points
+   * \return a set of positions and a list of tuples of indices such that each
+   *        point in \a _polygon is related to one of the tuples and designates
+   *        those positions where a number of hydrogens should be placed when
+   *        the bond associated with this point is removed, i.e. the bond
+   *        becomes a dangling one.
+   */
+  PolygonWithIndexTuples getAssociatedPoints(
+      const WeightedPolygon_t &_polygon,
+      const int _N);
+
+  static PolygonWithIndexTuples getIdentityAssociation(
+      const WeightedPolygon_t &_polygon);
 
   static Vector calculateCenterOfMinimumDistance(