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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} |
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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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coordination to enforce design and programming guidelines. Moreover, |
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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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Along the way of studying structural and dynamic processes in |
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condensed phase systems like biological membranes and nanoparticles, |
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we developed and maintained an Object-Oriented Parallel Simulation |
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Engine ({\sc OOPSE}). This new molecular dynamics package has some |
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unique features |
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\begin{enumerate} |
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\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
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atom types (transition metals, point dipoles, sticky potentials, |
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Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
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degrees of freedom), as well as rigid bodies. |
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\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
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Beowulf clusters to obtain very efficient parallelism. |
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\item {\sc OOPSE} integrates the equations of motion using advanced methods for |
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orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T |
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ensembles. |
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\item {\sc OOPSE} can carry out simulations on metallic systems using the |
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Embedded Atom Method (EAM) as well as the Sutton-Chen potential. |
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\item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals. |
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\item {\sc OOPSE} can simulate systems containing the extremely efficient |
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extended-Soft Sticky Dipole (SSD/E) model for water. |
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\end{enumerate} |
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\section{\label{appendixSection:architecture }Architecture} |
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Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE} |
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uses C++ Standard Template Library (STL) and fortran modules as the |
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foundation. As an extensive set of the STL and Fortran90 modules, |
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{\sc Base Classes} provide generic implementations of mathematical |
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objects (e.g., matrices, vectors, polynomials, random number |
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generators) and advanced data structures and algorithms(e.g., tuple, |
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bitset, generic data, string manipulation). The molecular data |
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structures for the representation of atoms, bonds, bends, torsions, |
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rigid bodies and molecules \textit{etc} are contained in the {\sc |
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Kernel} which is implemented with {\sc Base Classes} and are |
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carefully designed to provide maximum extensibility and flexibility. |
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The functionality required for applications is provide by the third |
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layer which contains Input/Output, Molecular Mechanics and Structure |
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modules. Input/Output module not only implements general methods for |
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file handling, but also defines a generic force field interface. |
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Another important component of Input/Output module is the meta-data |
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file parser, which is rewritten using ANother Tool for Language |
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Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular |
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Mechanics module consists of energy minimization and a wide |
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varieties of integration methods(see Chap.~\ref{chapt:methodology}). |
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The structure module contains a flexible and powerful selection |
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library which syntax is elaborated in |
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Sec.~\ref{appendixSection:syntax}. The top layer is made of the main |
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program of the package, \texttt{oopse} and it corresponding parallel |
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version \texttt{oopse\_MPI}, as well as other useful utilities, such |
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as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
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\texttt{DynamicProps} (see |
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Sec.~\ref{appendixSection:appendixSection:DynamicProps}), |
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\texttt{Dump2XYZ} (see |
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Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} |
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(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) |
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\textit{etc}. |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{architecture.eps} |
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\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
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of {\sc OOPSE}} \label{appendixFig:architecture} |
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\end{figure} |
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|
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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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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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As one of the latest advanced techniques emerged from |
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object-oriented community, design patterns were applied in some of |
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the modern scientific software applications, such as JMol, OOPSE |
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\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
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the modern scientific software applications, such as JMol, {\sc |
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OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
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The following sections enumerates some of the patterns used in {\sc |
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OOPSE}. |
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\subsection{\label{appendixSection:singleton}Singleton} |
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The Singleton pattern ensures that only one instance of a class is |
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subclasses can then override to specify the derived type of product |
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that will be created. |
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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The purpose of the Visitor Pattern is to encapsulate an operation |
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that you want to perform on the elements of a data structure. In |
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structure without the need of changing the classes of the elements |
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that you are operating on. |
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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|
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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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|
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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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|
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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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DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
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Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
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own names which are specified in the {\tt .md} file. In contrast, |
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RigidBodies are denoted by their membership and index inside a |
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particular molecule: [MoleculeName]\_RB\_[index] (the contents |
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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The most general form of the select command is: {\tt select {\it |
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expression}} |
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expression}}. This expression represents an arbitrary set of |
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StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
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composed of either name expressions, index expressions, predefined |
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sets, user-defined expressions, comparison operators, within |
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expressions, or logical combinations of the above expression types. |
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Expressions can be combined using parentheses and the Boolean |
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operators. |
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|
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This expression represents an arbitrary set of StuntDoubles (Atoms |
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or RigidBodies) in {\sc oopse}. Expressions are composed of either |
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name expressions, index expressions, predefined sets, user-defined |
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expressions, comparison operators, within expressions, or logical |
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combinations of the above expression types. Expressions can be |
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combined using parentheses and the Boolean operators. |
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|
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\subsection{\label{appendixSection:logical}Logical expressions} |
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The logical operators allow complex queries to be constructed out of |
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Users can define arbitrary terms to represent groups of |
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StuntDoubles, and then use the define terms in select commands. The |
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general form for the define command is: {\bf define {\it term |
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expression}} |
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expression}}. Once defined, the user can specify such terms in |
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boolean expressions |
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|
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Once defined, the user can specify such terms in boolean expressions |
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|
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{\tt define SSDWATER SSD or SSD1 or SSDRF} |
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|
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{\tt select SSDWATER} |
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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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|
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\section{\label{appendixSection:tools}Tools which use the selection command} |
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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=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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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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|
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\subsection{\label{appendixSection:StaticProps}StaticProps} |
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|
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{\tt StaticProps} can compute properties which are averaged over |
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some or all of the configurations that are contained within a dump |
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file. The most common example of a static property that can be |
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computed is the pair distribution function between atoms of type $A$ |
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and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
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used to compute the density distributions of other molecules in a |
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reference frame {\it fixed to the body-fixed reference frame} of a |
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selected atom or rigid body. |
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and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
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also be used to compute the density distributions of other molecules |
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in a reference frame {\it fixed to the body-fixed reference frame} |
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of a selected atom or rigid body. |
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|
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There are five seperate radial distribution functions availiable in |
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OOPSE. Since every radial distrbution function invlove the |
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their body-fixed frames.} \label{oopseFig:gofr} |
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\end{figure} |
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|
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Due to the fact that the selected StuntDoubles from two selections |
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may be overlapped, {\tt StaticProps} performs the calculation in |
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three stages which are illustrated in |
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Fig.~\ref{oopseFig:staticPropsProcess}. |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
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\caption[A representation of the three-stage correlations in |
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\texttt{StaticProps}]{This diagram illustrates three-stage |
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processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
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numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
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-{}-sele2} respectively, while $C$ is the number of stuntdobules |
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appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
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second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
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the contrary, the third stage($C$ and $C$) are completely |
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overlapping} \label{oopseFig:staticPropsProcess} |
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\end{figure} |
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|
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The options available for {\tt StaticProps} are as follows: |
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\begin{longtable}[c]{|EFG|} |
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\caption{StaticProps Command-line Options} |
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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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different vectors). The ability to use two selection scripts to |
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select different types of atoms is already present in the code. |
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|
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For large simulations, the trajectory files can sometimes reach |
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sizes in excess of several gigabytes. In order to effectively |
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analyze that amount of data. In order to prevent a situation where |
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the program runs out of memory due to large trajectories, |
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\texttt{dynamicProps} will estimate the size of free memory at |
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first, and determine the number of frames in each block, which |
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allows the operating system to load two blocks of data |
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simultaneously without swapping. Upon reading two blocks of the |
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trajectory, \texttt{dynamicProps} will calculate the time |
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correlation within the first block and the cross correlations |
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between the two blocks. This second block is then freed and then |
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incremented and the process repeated until the end of the |
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trajectory. Once the end is reached, the first block is freed then |
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incremented, until all frame pairs have been correlated in time. |
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This process is illustrated in |
| 466 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
| 467 |
+ |
|
| 468 |
+ |
\begin{figure} |
| 469 |
+ |
\centering |
| 470 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
| 471 |
+ |
\caption[A representation of the block correlations in |
| 472 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
| 473 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
| 474 |
+ |
the self correlation of the block, and the open blocks are read one |
| 475 |
+ |
at a time and the cross correlations between blocks are calculated.} |
| 476 |
+ |
\label{oopseFig:dynamicPropsProcess} |
| 477 |
+ |
\end{figure} |
| 478 |
+ |
|
| 479 |
|
The options available for DynamicProps are as follows: |
| 480 |
|
\begin{longtable}[c]{|EFG|} |
| 481 |
|
\caption{DynamicProps Command-line Options} |
| 486 |
|
\endfoot |
| 487 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 488 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 489 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 490 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 491 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
| 492 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 489 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 490 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 491 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
| 492 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 493 |
|
\hline |
| 494 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 495 |
|
\hline |
| 498 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
| 499 |
|
\end{longtable} |
| 500 |
|
|
| 501 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
| 501 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
| 502 |
> |
|
| 503 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
| 504 |
> |
|
| 505 |
> |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
| 506 |
> |
be opened by other molecular dynamics viewers such as Jmol and |
| 507 |
> |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
| 508 |
> |
follows: |
| 509 |
> |
|
| 510 |
> |
|
| 511 |
> |
\begin{longtable}[c]{|EFG|} |
| 512 |
> |
\caption{Dump2XYZ Command-line Options} |
| 513 |
> |
\\ \hline |
| 514 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 515 |
> |
\endhead |
| 516 |
> |
\hline |
| 517 |
> |
\endfoot |
| 518 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
| 519 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
| 520 |
> |
-i & {\tt -{}-input} & input dump file \\ |
| 521 |
> |
-o & {\tt -{}-output} & output file name \\ |
| 522 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
| 523 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
| 524 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
| 525 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
| 526 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
| 527 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
| 528 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
| 529 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
| 530 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
| 531 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
| 532 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 533 |
> |
converted. \\ |
| 534 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
| 535 |
> |
& {\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}. |
| 536 |
> |
\end{longtable} |
| 537 |
> |
|
| 538 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
| 539 |
> |
The options available for Hydro are as follows: |
| 540 |
> |
\begin{longtable}[c]{|EFG|} |
| 541 |
> |
\caption{Hydrodynamics Command-line Options} |
| 542 |
> |
\\ \hline |
| 543 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 544 |
> |
\endhead |
| 545 |
> |
\hline |
| 546 |
> |
\endfoot |
| 547 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
| 548 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
| 549 |
> |
-i & {\tt -{}-input} & input dump file \\ |
| 550 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
| 551 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
| 552 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
| 553 |
> |
\end{longtable} |
