Changes in doc/userguide/userguide.xml [0ea063:8544b32]

File:

• doc/userguide/userguide.xml (modified) (7 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.mirror-atoms'>
+          <title xml:id='atoms.mirror-atoms.title'>Mirroring atoms</title>
+
+          <para>Present (and selected) atoms can be mirrored with respect to
+          a certain plane. You have to specify the normal vector of the plane
+          and the offset with respect to the origin as follows</para>
+
+          <programlisting>
+                ... --mirror-atoms "1,0,0" \
+                    --plane-offset 10.1 \
+                    --periodic 0
+          </programlisting>
+        </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>
 
@@ -1744 +1770 @@
         </section>
 
-        <section xml:id='analysis.molecullar-volume'>
-          <title xml:id='analysis.molecullar-volume.title'>Molecular Volume
+        <section xml:id='analysis.molecular-volume'>
+          <title xml:id='analysis.molecular-volume.title'>Molecular Volume
           </title>
           
@@ -1753 +1779 @@
           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>
@@ -2367 +2405 @@
           Non-convex envelope</title>
           
-          <para>This will create a non-convex envelope for a molecule.</para>
+          <para>This will create a non-convex envelope for a molecule and store
+          it to a file for viewing with external programs.</para>
 
           <programlisting>
@@ -2376 +2415 @@
           <para>This tesselation file can be conveniently viewed with 
           <productname>TecPlot</productname> or with one of the Tcl script 
-          in the util folder with <productname>VMD</productname>.</para>
+          in the util folder with <productname>VMD</productname>. Also,
+          still pictures can be produced with <productname>Raster3D
+          </productname>.
+          <note>The required file header.r3d can be found in a subfolder of
+          the util folder.</note>
+          </para>
         </section>
 
@@ -2383 +2427 @@
           envelope</title>
           
-          <para>This will create a convex envelope for a molecule.</para>
+          <para>This will create a convex envelope for a molecule and give the
+          volumes of both the non-convex and the convex envelope. This is good
+          for measuring the space a molecule takes up, e.g. when filling a 
+          domain and taking care of correct densities.</para>
 
           <programlisting>
@@ -2390 +2437 @@
           </programlisting>
 
-          <para>This tesselation file can be conveniently viewed with 
+          <para>This tesselation file can be likewise viewed with 
           <productname>TecPlot</productname> or with one of the Tcl script 
           in the util folder with <productname>VMD</productname>.</para>