--- 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}