Changeset dfe653 for doc/userguide

Timestamp:

Aug 30, 2025, 2:41:31 PM (2 months ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

9928ece

Parents:

d25515

git-author:

Frederik Heber <frederik.heber@…> (08/13/25 22:05:47)

git-committer:

Frederik Heber <frederik.heber@…> (08/30/25 14:41:31)

Message:

TESTFIX: Finalizes evaluate stability regression test.

• recomputed the homology file for H2 and C3H8 for 20 MD steps in order to provide a proper stability evaluation.
• DOC: extended userguide on how to obtain homologies in the first place.
• TESTFIX: evaluate-stability lacked argument.

File:

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

doc/userguide/userguide.xml

@@ -2282 +2282 @@
         <para>Homologies -- in the sense used here -- are then nothing else but containers for a specific
         type of fragment of all the different, calculated configurations (i.e.
-        varying nuclear coordinates of the same fragment, i.e. same atoms with identical bonding).</para>
-        <para>Now, we explain the actions that parse and store
+        varying nuclear coordinates of the same fragment, i.e. same atoms with identical bonding).</para>
+        <para>Homologies are created inside MoleCuilder from fragment calculations
+        by using the action 
+        <programlisting>... --analyse-fragment-results</programlisting>.
+        This computes the energy of the molecule from the fragments and also the
+        fragment energies. These are put into the internal homology container.</para>
+        <para>Now, we explain the actions that parse and store those
         homologies.</para>
         <programlisting>... --parse-homologies homologies.dat</programlisting>