Changeset 55c494 for doc/userguide

Timestamp:

May 19, 2021, 7:06:29 PM (4 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

b3bd7d

Parents:

15fc6a

git-author:

Frederik Heber <frederik.heber@…> (05/14/21 09:52:02)

git-committer:

Frederik Heber <frederik.heber@…> (05/19/21 19:06:29)

Message:

Added GeneratePotentialsAction.

• this generates all potential combinations for a given fragment.
• exposed PotentialFactory::getDefaultInstance() for constant instance to be able to gather more information about the potential such as the binding model.
• DOCU: Added documentation.
• TEST: Added regression test case.

File:

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

doc/userguide/userguide.xml

@@ -2464 +2464 @@
           <note>Currently, only <productname>TREMOLO</productname>potential files are understood and can be parsed.</note>
         </section>
+        <section xml:id="potentials.generate-potentials">
+          <title xml:id="potentials.generate-potentials.title">Generate empirical potentials</title>
+          <para>The actions to fit potentials take either a single potential name or a 
+          potentials file. In order to create all potentials that would match with its
+          particle types the following action can be called:
+          <programlisting>
+                  ... --generate-potentials
+                  --fragment-charges 8 1 1
+          </programlisting>
+          Here, it would create all potentials for a fragment specifying a water 
+          molecule: harmonic_bond for O and H, morse for O and H, harmonic_angle
+          for H, O, and H (and not for O, H, H, or other combinations as these
+          subgraphs do not exists for the molecule H-O-H), and tersoff for the
+          types O and H.
+        </para>
+        </section>
         <section xml:id="potentials.save-potential">
           <title xml:id="potentials.save-potential.title">Saving an empirical potentials file</title>