Changeset 999eaf for doc/userguide/userguide.xml

Timestamp:

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

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

6b7765

Parents:

5aa337

git-author:

Frederik Heber <frederik.heber@…> (04/18/21 08:23:36)

git-committer:

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

Message:

Added EvaluateStabilityAction to estimate a molecule's stability.

• removes every bond and checks the energies of the products against the educt equipped with enough hydrogen molecules to compensate for the cut bond times its degree.
• outputs a CSV file with entries per bond.
• extended HomologyGraph to allow direct use of AtomIdSet, i.e. atomic ids coming from a selection in the World or from the molecule.
• DOCU: Added subsection on this action to section homology.
• TEST: Added regression test case.

File:

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

doc/userguide/userguide.xml

@@ -2291 +2291 @@
         <filename>homologies.dat</filename>.</para>
       </section>
+      <section xml:id="homology.evaluate-stability">
+         <title xml:id="homology.evaluate-stability.title">Evaluate Stability</title>
+         <para>The homologies can be used to quickly get an approximation on
+         the ground state energy of a molecule.
+         <warning>This does not accurately take the current geometry into account.</warning>
+         In other words, it will produce the equilibrium energy for the given
+         molecule.
+         Using this, there is an action that evaluates the stability of a molecule
+         by removing each bond, saturating the ends and comparing the ground
+         state energy of the two products to the educt plus the ground state
+         energy of as many hydrogen molecules to match the cut bond's degree.
+         <programlisting>... --evaluate-stability output.csv</programlisting>
+         This writes a table of educt and product names along with their summed
+         energies. The comparison between educt and product energy in each row
+         yields whether this molecule is overall stable.
+         <note>Be aware that this calculation is based on saturation, i.e. hydrogens
+         are added to saturate dangling bonds. These additional atoms need to
+         be compensated and for this reason there is an additional educt, a
+         number of hydrogen molecules.</note>
+         </para>
+      </section>
       <section xml:id="atomfragments">
         <title xml:id="atomfragments.title">AtomFragments</title>