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\appendix |
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\chapter{\label{chapt:appendix}APPENDIX} |
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Designing object-oriented software is hard, and designing reusable |
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object-oriented scientific software is even harder. Absence of |
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applying modern software development practices is the bottleneck of |
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Scientific Computing community\cite{wilson}. For instance, in the |
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Scientific Computing community\cite{Wilson}. For instance, in the |
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last 20 years , there are quite a few MD packages that were |
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developed to solve common MD problems and perform robust simulations |
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. However, many of the codes are legacy programs that are either |
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Design patterns are optimal solutions to commonly-occurring problems |
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in software design. Although originated as an architectural concept |
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for buildings and towns by Christopher Alexander \cite{alexander}, |
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software patterns first became popular with the wide acceptance of |
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the book, Design Patterns: Elements of Reusable Object-Oriented |
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Software \cite{gamma94}. Patterns reflect the experience, knowledge |
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and insights of developers who have successfully used these patterns |
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in their own work. Patterns are reusable. They provide a ready-made |
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solution that can be adapted to different problems as necessary. |
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Pattern are expressive. they provide a common vocabulary of |
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solutions that can express large solutions succinctly. |
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for buildings and towns by Christopher Alexander |
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\cite{Alexander1987}, software patterns first became popular with |
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the wide acceptance of the book, Design Patterns: Elements of |
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Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
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the experience, knowledge and insights of developers who have |
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successfully used these patterns in their own work. Patterns are |
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reusable. They provide a ready-made solution that can be adapted to |
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different problems as necessary. Pattern are expressive. they |
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provide a common vocabulary of solutions that can express large |
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solutions succinctly. |
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Patterns are usually described using a format that includes the |
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following information: |
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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\section{\label{appendixSection:concepts}Concepts} |
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OOPSE manipulates both traditional atoms as well as some objects |
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collections of atoms or atoms which have orientational degrees of |
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freedom. Here is a diagram of the class heirarchy: |
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{heirarchy.eps} |
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\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
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The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
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selection syntax allows the user to select any of the objects that |
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are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
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\end{figure} |
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%\begin{figure} |
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%\centering |
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%\includegraphics[width=3in]{heirarchy.eps} |
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%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
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%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
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%selection syntax allows the user to select any of the objects that |
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%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
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%\end{figure} |
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\begin{itemize} |
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\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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\subsection{\label{appendixSection:name}Name expressions} |
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\begin{center} |
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\begin{tabular}{|llp{3in}|} |
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\begin{tabular}{|llp{2in}|} |
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\hline {\bf type of expression} & {\bf examples} & {\bf translation |
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of |
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examples} \\ |
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\end{center} |
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For example, the phrase {\tt select mass > 16.0 and charge < -2} |
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wouldselect StuntDoubles which have mass greater than 16.0 and |
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would select StuntDoubles which have mass greater than 16.0 and |
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charges less than -2. |
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\subsection{\label{appendixSection:within}Within expressions} |
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select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
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atoms. |
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\section{\label{appendixSection:tools}Tools which use the selection command} |
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\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
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be opened by other molecular dynamics viewers such as Jmol and VMD. |
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The options available for Dump2XYZ are as follows: |
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\begin{longtable}[c]{|EFG|} |
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\caption{Dump2XYZ Command-line Options} |
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\\ \hline |
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{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
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\endhead |
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\hline |
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\endfoot |
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-h & {\tt -{}-help} & Print help and exit \\ |
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-V & {\tt -{}-version} & Print version and exit \\ |
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-i & {\tt -{}-input=filename} & input dump file \\ |
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-o & {\tt -{}-output=filename} & output file name \\ |
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-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
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-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
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-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
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-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
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-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
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-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
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-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
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& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
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& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
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& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
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-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
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converted. \\ |
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& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
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& {\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}. |
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\end{longtable} |
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\subsection{\label{appendixSection:StaticProps}StaticProps} |
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{\tt StaticProps} can compute properties which are averaged over |
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{definition.pdf} |
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\includegraphics[width=3in]{definition.eps} |
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\caption[Definitions of the angles between directional objects]{ \\ |
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Any two directional objects (DirectionalAtoms and RigidBodies) have |
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a set of two angles ($\theta$, and $\omega$) between the z-axes of |
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\endfoot |
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-h& {\tt -{}-help} & Print help and exit \\ |
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-V& {\tt -{}-version} & Print version and exit \\ |
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-i& {\tt -{}-input=filename} & input dump file \\ |
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-o& {\tt -{}-output=filename} & output file name \\ |
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-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
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-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
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-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
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-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
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& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
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& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
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& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
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& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
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& {\tt -{}-molname=STRING} & molecule name \\ |
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& {\tt -{}-begin=INT} & begin internal index \\ |
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& {\tt -{}-end=INT} & end internal index \\ |
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-i& {\tt -{}-input} & input dump file \\ |
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-o& {\tt -{}-output} & output file name \\ |
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-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
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-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
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-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
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-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
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& {\tt -{}-sele1} & select the first StuntDouble set \\ |
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& {\tt -{}-sele2} & select the second StuntDouble set \\ |
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& {\tt -{}-sele3} & select the third StuntDouble set \\ |
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& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
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& {\tt -{}-molname} & molecule name \\ |
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& {\tt -{}-begin} & begin internal index \\ |
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& {\tt -{}-end} & end internal index \\ |
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\hline |
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\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
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\hline |
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\endfoot |
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-h& {\tt -{}-help} & Print help and exit \\ |
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-V& {\tt -{}-version} & Print version and exit \\ |
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-i& {\tt -{}-input=filename} & input dump file \\ |
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-o& {\tt -{}-output=filename} & output file name \\ |
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& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
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& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
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-i& {\tt -{}-input} & input dump file \\ |
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-o& {\tt -{}-output} & output file name \\ |
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& {\tt -{}-sele1} & select first StuntDouble set \\ |
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& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
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\hline |
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\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
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\hline |
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-d& {\tt -{}-dcorr} & compute dipole correlation function |
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\end{longtable} |
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|
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\section{\label{appendixSection:tools}Other Useful Utilities} |
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|
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\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
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|
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Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
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be opened by other molecular dynamics viewers such as Jmol and VMD. |
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The options available for Dump2XYZ are as follows: |
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|
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|
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\begin{longtable}[c]{|EFG|} |
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\caption{Dump2XYZ Command-line Options} |
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\\ \hline |
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{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
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\endhead |
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\hline |
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\endfoot |
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-h & {\tt -{}-help} & Print help and exit \\ |
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-V & {\tt -{}-version} & Print version and exit \\ |
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-i & {\tt -{}-input} & input dump file \\ |
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-o & {\tt -{}-output} & output file name \\ |
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-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
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-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
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-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
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-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
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-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
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-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
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-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
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& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
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& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
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& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
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-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
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converted. \\ |
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& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
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& {\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}. |
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\end{longtable} |
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|
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\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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|
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\begin{longtable}[c]{|EFG|} |
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\caption{Hydrodynamics Command-line Options} |
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\\ \hline |
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{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
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\endhead |
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\hline |
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\endfoot |
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-h & {\tt -{}-help} & Print help and exit \\ |
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-V & {\tt -{}-version} & Print version and exit \\ |
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-i & {\tt -{}-input} & input dump file \\ |
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-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
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-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
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& {\tt -{}-model} & hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
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\end{longtable} |
