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\appendix |
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\chapter{\label{chapt:appendix}APPENDIX} |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)} |
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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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last 20 years , there are quite a few MD packages that were |
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Scientific Computing community\cite{Wilson2006}. For instance, in |
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the 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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poorly organized or extremely complex. Usually, these packages were |
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most MD programs also suffer from missing design and implement |
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documents which is crucial to the maintenance and extensibility. |
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\section{\label{appendixSection:architecture }Architecture} |
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{architecture.eps} |
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\caption[The architecture of {\sc oopse}-3.0] {The architecture |
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of{\sc oopse}-3.0.} \label{appendixFig:architecture} |
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\end{figure} |
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\section{\label{appendixSection:desginPattern}Design Pattern} |
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Design patterns are optimal solutions to commonly-occurring problems |
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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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For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
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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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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} & 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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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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\subsection{\label{appendixSection:StaticProps}StaticProps} |
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-d& {\tt -{}-dcorr} & compute dipole correlation function |
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\end{longtable} |
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\section{\label{appendixSection:tools}Other Useful Utilities} |
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\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
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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} & 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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\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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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} |
