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\appendix |
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\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)} |
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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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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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|
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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=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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\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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\section{\label{appendixSection:desginPattern}Design Pattern} |
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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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created. All objects that use an instance of that class use the same |
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instance. |
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The Singleton pattern not only provides a mechanism to restrict |
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instantiation of a class to one object, but also provides a global |
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point of access to the object. Currently implemented as a global |
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variable, the logging utility which reports error and warning |
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messages to the console in {\sc OOPSE} is a good candidate for |
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applying the Singleton pattern to avoid the global namespace |
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pollution.Although the singleton pattern can be implemented in |
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various ways to account for different aspects of the software |
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designs, such as lifespan control \textit{etc}, we only use the |
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static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class |
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is declared as |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}] |
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|
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class IntegratorFactory { |
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public: |
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static IntegratorFactory* getInstance(); |
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protected: |
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IntegratorFactory(); |
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private: |
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static IntegratorFactory* instance_; |
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}; |
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|
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\end{lstlisting} |
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The corresponding implementation is |
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\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}] |
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|
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IntegratorFactory::instance_ = NULL; |
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|
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IntegratorFactory* getInstance() { |
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if (instance_ == NULL){ |
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instance_ = new IntegratorFactory; |
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} |
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return instance_; |
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} |
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|
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\end{lstlisting} |
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Since constructor is declared as {\tt protected}, a client can not |
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instantiate {\tt IntegratorFactory} directly. Moreover, since the |
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member function {\tt getInstance} serves as the only entry of access |
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to {\tt IntegratorFactory}, this approach fulfills the basic |
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requirement, a single instance. Another consequence of this approach |
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is the automatic destruction since static data are destroyed upon |
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program termination. |
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|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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The Factory Method pattern is a creational pattern which deals with |
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the problem of creating objects without specifying the exact class |
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of object that will be created. Factory Method solves this problem |
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by defining a separate method for creating the objects, which |
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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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|
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Categoried as a creational pattern, the Factory Method pattern deals |
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with the problem of creating objects without specifying the exact |
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class of object that will be created. Factory Method is typically |
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implemented by delegating the creation operation to the subclasses. |
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|
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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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this way, you can change the operation being performed on a |
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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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Registers a creator with a type identifier. Looks up the type |
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identifier in the internal map. If it is found, it invokes the |
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corresponding creator for the type identifier and returns its |
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result. |
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}] |
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|
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class IntegratorFactory { |
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public: |
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typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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|
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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bool registerIntegrator(IntegratorCreator* creator); |
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|
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Integrator* createIntegrator(const string& id, SimInfo* info); |
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|
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private: |
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CreatorMapType creatorMap_; |
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}; |
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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}] |
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|
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bool IntegratorFactory::unregisterIntegrator(const string& id) { |
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return creatorMap_.erase(id) == 1; |
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} |
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|
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Integrator* IntegratorFactory::createIntegrator(const string& id, |
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SimInfo* info) { |
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CreatorMapType::iterator i = creatorMap_.find(id); |
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if (i != creatorMap_.end()) { |
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return (i->second)->create(info); |
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} else { |
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return NULL; |
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} |
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} |
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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}] |
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|
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class IntegratorCreator { |
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public: |
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IntegratorCreator(const string& ident) : ident_(ident) {} |
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|
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const string& getIdent() const { return ident_; } |
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|
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virtual Integrator* create(SimInfo* info) const = 0; |
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|
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private: |
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string ident_; |
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}; |
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|
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template<class ConcreteIntegrator> |
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class IntegratorBuilder : public IntegratorCreator { |
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public: |
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IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {} |
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virtual Integrator* create(SimInfo* info) const { |
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return new ConcreteIntegrator(info); |
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} |
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}; |
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\end{lstlisting} |
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|
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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|
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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. The operation being |
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performed on a structure can be switched without changing the |
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interfaces of the elements. In other words, one can add virtual |
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functions into a set of classes without modifying their interfaces. |
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The UML class diagram of Visitor patten is shown in |
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Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
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Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
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extensively. |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{visitor.eps} |
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\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
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of {\sc OOPSE}} \label{appendixFig:visitorUML} |
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\end{figure} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
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|
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class BaseVisitor{ |
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public: |
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virtual void visit(Atom* atom); |
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virtual void visit(DirectionalAtom* datom); |
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virtual void visit(RigidBody* rb); |
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}; |
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|
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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|
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class StuntDouble { |
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public: |
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virtual void accept(BaseVisitor* v) = 0; |
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}; |
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|
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class Atom: public StuntDouble { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class DirectionalAtom: public Atom { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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class RigidBody: public StuntDouble { |
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public: |
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virtual void accept{BaseVisitor* v*} { |
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v->visit(this); |
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} |
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}; |
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|
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\end{lstlisting} |
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|
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\section{\label{appendixSection:concepts}Concepts} |
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|
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OOPSE manipulates both traditional atoms as well as some objects |
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that {\it behave like atoms}. These objects can be rigid |
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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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|
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freedom. A diagram of the class heirarchy is illustrated in |
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Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
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DirectionalAtom in {\sc OOPSE} have their own names which are |
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specified in the {\tt .md} file. In contrast, RigidBodies are |
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denoted by their membership and index inside a particular molecule: |
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[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
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on the specifics of the simulation). The names of rigid bodies are |
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generated automatically. For example, the name of the first rigid |
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body in a DMPC molecule is DMPC\_RB\_0. |
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{heirarchy.eps} |
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\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class |
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heirarchy of StuntDoubles in {\sc OOPSE}. |
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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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integrators and minimizers. |
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\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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|
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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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inside the brackets depend on the specifics of the simulation). The |
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names of rigid bodies are generated automatically. For example, the |
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name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
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} \label{oopseFig:heirarchy} |
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\end{figure} |
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|
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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|
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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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|
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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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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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+ |
|
541 |
|
The options available for {\tt StaticProps} are as follows: |
542 |
|
\begin{longtable}[c]{|EFG|} |
543 |
|
\caption{StaticProps Command-line Options} |
599 |
|
different vectors). The ability to use two selection scripts to |
600 |
|
select different types of atoms is already present in the code. |
601 |
|
|
602 |
+ |
For large simulations, the trajectory files can sometimes reach |
603 |
+ |
sizes in excess of several gigabytes. In order to effectively |
604 |
+ |
analyze that amount of data. In order to prevent a situation where |
605 |
+ |
the program runs out of memory due to large trajectories, |
606 |
+ |
\texttt{dynamicProps} will estimate the size of free memory at |
607 |
+ |
first, and determine the number of frames in each block, which |
608 |
+ |
allows the operating system to load two blocks of data |
609 |
+ |
simultaneously without swapping. Upon reading two blocks of the |
610 |
+ |
trajectory, \texttt{dynamicProps} will calculate the time |
611 |
+ |
correlation within the first block and the cross correlations |
612 |
+ |
between the two blocks. This second block is then freed and then |
613 |
+ |
incremented and the process repeated until the end of the |
614 |
+ |
trajectory. Once the end is reached, the first block is freed then |
615 |
+ |
incremented, until all frame pairs have been correlated in time. |
616 |
+ |
This process is illustrated in |
617 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
618 |
+ |
|
619 |
+ |
\begin{figure} |
620 |
+ |
\centering |
621 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
622 |
+ |
\caption[A representation of the block correlations in |
623 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
624 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
625 |
+ |
the self correlation of the block, and the open blocks are read one |
626 |
+ |
at a time and the cross correlations between blocks are calculated.} |
627 |
+ |
\label{oopseFig:dynamicPropsProcess} |
628 |
+ |
\end{figure} |
629 |
+ |
|
630 |
|
The options available for DynamicProps are as follows: |
631 |
|
\begin{longtable}[c]{|EFG|} |
632 |
|
\caption{DynamicProps Command-line Options} |
653 |
|
|
654 |
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
655 |
|
|
656 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
657 |
< |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
658 |
< |
The options available for Dump2XYZ are as follows: |
656 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
657 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
658 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
659 |
> |
as follows: |
660 |
|
|
661 |
|
|
662 |
|
\begin{longtable}[c]{|EFG|} |
686 |
|
& {\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}. |
687 |
|
\end{longtable} |
688 |
|
|
689 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
689 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
690 |
|
|
691 |
+ |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
692 |
+ |
center of resistance. Both tensors at the center of diffusion can |
693 |
+ |
also be reported from the program, as well as the coordinates for |
694 |
+ |
the beads which are used to approximate the arbitrary shapes. The |
695 |
+ |
options available for Hydro are as follows: |
696 |
|
\begin{longtable}[c]{|EFG|} |
697 |
|
\caption{Hydrodynamics Command-line Options} |
698 |
|
\\ \hline |
705 |
|
-i & {\tt -{}-input} & input dump file \\ |
706 |
|
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
707 |
|
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
708 |
< |
& {\tt -{}-model} & hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
708 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
709 |
|
\end{longtable} |