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  • doc/userguide/userguide.xml

    r0ea063 r9bce96  
    21092109            a fragment of order 1, e.g. a single hydrogen atom.</para>
    21102110          </note>
    2111         </section>
    2112 
    2113         <section xml:id='potentials.fit-compound-potential'>
    2114           <title xml:id='potentials.fit-compound-potential.title'>Fitting
    2115           many empirical potentials simultaneously</title>
    2116 
    21172111
    21182112          <para>Another way is using a file containing a specific set of
    … …  
    21202114
    21212115          <programlisting>
    2122                 ... --fit-compound-potential \
     2116                ... --fit-potential \
    21232117                    --fragment-charges 8 1 1 \
    21242118                    --potential-file water.potentials \
    … …  
    21422136          type of analysis.</para>
    21432137
    2144           <para>Note that you can combine the two ways, i.e. start with a
    2145           fit-potential call but give an empty potential file. The resulting
    2146           parameters are stored in it. Fit other potentials and give different
    2147           file names for each in turn. Eventually, you have to combine the file
    2148           in a text editor at the moment. And perform a fit-compound-potential
    2149           with this file.</para>
    2150         </section>
    2151 
    2152        
    2153         <section xml:id='potentials.parse-potential'>
    2154           <title xml:id='potentials.parse-potential.title'>Parsing an
    2155           empirical potentials file</title>
    2156 
    2157           <para>Responsible for the compound potential is every potential
    2158           function whose signature matches with the designated fragment-charges
    2159           and who is currently known to an internal instance called the
    2160           PotentialRegistry.</para>
    2161 
    2162           <para>More potentials can be registered (fit-potential will also
    2163           register the potential it fits) by parsing them from a file.</para>
    2164 
    2165           <programlisting>
    2166                 ... --parse-potentials water.potentials
    2167           </programlisting>
    2168 
    2169           <note>Currently, only <productname>TREMOLO</productname> potential
    2170           files are understood and can be parsed.</note>
    2171         </section>
    2172 
    2173         <section xml:id='potentials.save-potential'>
    2174           <title xml:id='potentials.save-potential.title'>Saving an
    2175           empirical potentials file</title>
    2176 
    2177           <para>The opposite to parse-potentials is save-potentials that writes
    2178           every potential currently known to the PotentialRegistry to the given
    2179           file along with the currently fitted parameters</para>
    2180 
    2181           <programlisting>
    2182                 ... --save-potentials water.potentials
    2183           </programlisting>
    2184 
    2185           <note>Again, only the <productname>TREMOLO</productname> potential
    2186           format is understood currently and is written.</note>
     2138          <para>Note that you can combine the two ways, i.e. start with the
     2139          first but give an empty potential file. The resulting parameters are
     2140          stored in this way. Fit other potentials and give different file
     2141          names for each. Eventually, you have to combine the file in a text
     2142          editor at the moment.</para>
    21872143        </section>
    21882144
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