Changeset 2390e6 for doc/userguide

Timestamp:

Apr 28, 2021, 10:02:49 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

e0e77e

Parents:

87c1cc

git-author:

Frederik Heber <frederik.heber@…> (04/17/21 09:41:33)

git-committer:

Frederik Heber <frederik.heber@…> (04/28/21 22:02:49)

Message:

SaturateAction may use outer shell information.

• when considering the outer shell, then we look at both occupied and unoccupied orbitals. The ideal polygon will be created for the number of all orbitals, but only the unoccupied will be allowed to be taken by either present bonds or saturation hydrogens.
• SphericalPointDistribution allows to occupy less than present points.
• I have tested this manually by adding oxygen, saturation, adding carbon, saturating again, then turning oxygen into nitrogen and saturating. Results were always exactly as hoped for.
• DOCU: Added note to action in userguide.

File:

• doc/userguide/userguide.xml (modified) (1 diff)

doc/userguide/userguide.xml

@@ -1070 +1070 @@
           and approximately with same distance to their nearest neighbor 
           hydrogens. Already present bonds (i.e. the position of neighboring 
-          atoms) are taken into account and left intact.</para>
+          atoms) are taken into account and left intact.</para>
+          <programlisting>^M
+  ... --saturate-atoms --use-outer-shell 1^M
+   </programlisting>
+          <para>This will not simply consider the number of unoccupied orbitals
+          of the respective element. Instead it will take the outermost shell
+          into consideration and use the number of orbitals in total as the
+          ideal polyhedra but only taking the number of unoccupied orbitals as
+          free nodes, i.e. where to saturate with hydrogens. For example, 
+          nitrogen will then fill an tetrahedron (4 orbitals in outer shell)
+          where one orbital is already fully occupied and 3 nodes in the 
+          tetrahedron remain to fill up with hydrogens.
+          Without the outer shell, saturate atoms would simply consider a 
+          triangle as the ideal polyhedron and fill its 3 corners.</para>
         </section>
         <section xml:id="atoms.bondify-atom">