--- trunk/tengDissertation/Appendix.tex	2006/06/07 02:02:44	2809
+++ trunk/tengDissertation/Appendix.tex	2006/06/07 02:24:27	2811
@@ -76,8 +76,6 @@ that you are operating on.
 
 \subsection{\label{appendixSection:templateMethod}Template Method}
 
-\section{\label{appendixSection:analysisFramework}Analysis Framework}
-
 \section{\label{appendixSection:concepts}Concepts}
 
 OOPSE manipulates both traditional atoms as well as some objects
@@ -243,43 +241,9 @@ atoms.
 select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
 atoms.
 
-\section{\label{appendixSection:tools}Tools which use the selection command}
 
-\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
-
-Dump2XYZ can transform an OOPSE dump file into a xyz file which can
-be opened by other molecular dynamics viewers such as Jmol and VMD.
-The options available for Dump2XYZ are as follows:
-
-
-\begin{longtable}[c]{|EFG|}
-\caption{Dump2XYZ Command-line Options}
-\\ \hline
-{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
-\endhead
-\hline
-\endfoot
-  -h & {\tt -{}-help} &                        Print help and exit \\
-  -V & {\tt -{}-version} &                     Print version and exit \\
-  -i & {\tt -{}-input}  &             input dump file \\
-  -o & {\tt -{}-output} &             output file name \\
-  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
-  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
-  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
-  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
-  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
-  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
-  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
-     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
-     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
-     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
-  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
-converted. \\
-     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
-     & {\tt -{}-refsele} &  In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}.
-\end{longtable}
+\section{\label{appendixSection:analysisFramework}Analysis Framework}
 
-
 \subsection{\label{appendixSection:StaticProps}StaticProps}
 
 {\tt StaticProps} can compute properties which are averaged over
@@ -428,4 +392,55 @@ The options available for DynamicProps are as follows:
   -d& {\tt -{}-dcorr}                  & compute dipole correlation function
 \end{longtable}
 
+\section{\label{appendixSection:tools}Other Useful Utilities}
+
+\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
+
+Dump2XYZ can transform an OOPSE dump file into a xyz file which can
+be opened by other molecular dynamics viewers such as Jmol and VMD.
+The options available for Dump2XYZ are as follows:
+
+
+\begin{longtable}[c]{|EFG|}
+\caption{Dump2XYZ Command-line Options}
+\\ \hline
+{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
+\endhead
+\hline
+\endfoot
+  -h & {\tt -{}-help} &                        Print help and exit \\
+  -V & {\tt -{}-version} &                     Print version and exit \\
+  -i & {\tt -{}-input}  &             input dump file \\
+  -o & {\tt -{}-output} &             output file name \\
+  -n & {\tt -{}-frame}   &                 print every n frame  (default=`1') \\
+  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
+  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
+  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
+  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
+  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
+  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
+     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
+     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
+     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
+  -s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
+converted. \\
+     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
+     & {\tt -{}-refsele} &  In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}.
+\end{longtable}
+
 \subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
+
+\begin{longtable}[c]{|EFG|}
+\caption{Hydrodynamics Command-line Options}
+\\ \hline
+{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
+\endhead
+\hline
+\endfoot
+  -h & {\tt -{}-help} &                        Print help and exit \\
+  -V & {\tt -{}-version} &                     Print version and exit \\
+  -i & {\tt -{}-input}  &             input dump file \\
+  -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
+  -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
+     & {\tt -{}-model}  &                 hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
+\end{longtable}
