Changes in doc/userguide/userguide.xml [c7fe90:0ea063]

File:

• doc/userguide/userguide.xml (modified) (6 diffs)

doc/userguide/userguide.xml

@@ -954 +954 @@
           mind the boundary conditions, i.e. might shift atoms outside of the
           domain.</para>
-        </section>
-
-        <section xml:id='atoms.translate-to-origin'>
-          <title xml:id='atoms.translate-to-origin.title'>Translating atoms</title>
-
-          <para>The following Action is convenient to place a subset of atoms
-          at a known position, the origin, and then translate to some other
-          absolute coordinate. It calculates the average position of the set
-          of selected atoms and then translates all atoms by the negative of
-          this center, i.e. the center is afterwards at the origin.</para>
-
-          <programlisting>... --translate-to-origin</programlisting>
         </section>
 
@@ -1756 +1744 @@
         </section>
 
-        <section xml:id='analysis.molecular-volume'>
-          <title xml:id='analysis.molecular-volume.title'>Molecular Volume
+        <section xml:id='analysis.molecullar-volume'>
+          <title xml:id='analysis.molecullar-volume.title'>Molecular Volume
           </title>
           
@@ -1765 +1753 @@
           that each node of the tesselation consists of an atom of the
           molecule.</para>
-
-          <programlisting>... --molecular-volume</programlisting>
-        </section>
-
-        <section xml:id='analysis.average-molecule-force'>
-          <title xml:id='analysis.average-molecule-forcetitle'>Average force
-          acting on a molecule</title>
-          
-          <para>This sums up all the forces of each atom of a currently 
-          selected molecule and returns the average force vector. This should
-          give you the general direction of acceleration of the molecule.
-          </para>
 
           <programlisting>... --molecular-volume</programlisting>
@@ -2133 +2109 @@
             a fragment of order 1, e.g. a single hydrogen atom.</para>
           </note>
+        </section>
+
+        <section xml:id='potentials.fit-compound-potential'>
+          <title xml:id='potentials.fit-compound-potential.title'>Fitting
+          many empirical potentials simultaneously</title>
+
 
           <para>Another way is using a file containing a specific set of
@@ -2138 +2120 @@
 
           <programlisting>
-                ... --fit-potential \
+                ... --fit-compound-potential \
                     --fragment-charges 8 1 1 \
                     --potential-file water.potentials \
@@ -2160 +2142 @@
           type of analysis.</para>
 
-          <para>Note that you can combine the two ways, i.e. start with the
-          first but give an empty potential file. The resulting parameters are
-          stored in this way. Fit other potentials and give different file
-          names for each. Eventually, you have to combine the file in a text
-          editor at the moment.</para>
+          <para>Note that you can combine the two ways, i.e. start with a
+          fit-potential call but give an empty potential file. The resulting
+          parameters are stored in it. Fit other potentials and give different
+          file names for each in turn. Eventually, you have to combine the file
+          in a text editor at the moment. And perform a fit-compound-potential
+          with this file.</para>
+        </section>
+
+        
+        <section xml:id='potentials.parse-potential'>
+          <title xml:id='potentials.parse-potential.title'>Parsing an
+          empirical potentials file</title>
+
+          <para>Responsible for the compound potential is every potential
+          function whose signature matches with the designated fragment-charges
+          and who is currently known to an internal instance called the
+          PotentialRegistry.</para>
+
+          <para>More potentials can be registered (fit-potential will also
+          register the potential it fits) by parsing them from a file.</para>
+
+          <programlisting>
+                ... --parse-potentials water.potentials
+          </programlisting>
+
+          <note>Currently, only <productname>TREMOLO</productname> potential
+          files are understood and can be parsed.</note>
+        </section>
+
+        <section xml:id='potentials.save-potential'>
+          <title xml:id='potentials.save-potential.title'>Saving an
+          empirical potentials file</title>
+
+          <para>The opposite to parse-potentials is save-potentials that writes
+          every potential currently known to the PotentialRegistry to the given
+          file along with the currently fitted parameters</para>
+
+          <programlisting>
+                ... --save-potentials water.potentials
+          </programlisting>
+
+          <note>Again, only the <productname>TREMOLO</productname> potential
+          format is understood currently and is written.</note>
         </section>