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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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|
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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 |
26 |
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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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|
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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=\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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|
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Design patterns are optimal solutions to commonly-occurring problems |
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|
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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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|
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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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|
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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}. IntegratorFactory class is |
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declared as |
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|
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
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|
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class IntegratorFactory { |
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public: |
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static IntegratorFactory* |
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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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|
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The corresponding implementation is |
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|
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\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},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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|
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Since constructor is declared as protected, a client can not |
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instantiate IntegratorFactory directly. Moreover, since the member |
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function getInstance serves as the only entry of access to |
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IntegratorFactory, this approach fulfills the basic requirement, a |
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single instance. Another consequence of this approach is the |
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automatic destruction since static data are destroyed upon program |
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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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Parameterized Factory pattern where factory method ( |
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createIntegrator member function) creates products based on the |
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identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
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the identifier has been already registered, the factory method will |
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invoke the corresponding creator (see List.~\ref{integratorCreator}) |
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which utilizes the modern C++ template technique to avoid excess |
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subclassing. |
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|
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},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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bool registerIntegrator(IntegratorCreator* creator) { |
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return creatorMap_.insert(creator->getIdent(), creator).second; |
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} |
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|
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Integrator* createIntegrator(const string& id, SimInfo* info) { |
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Integrator* result = NULL; |
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CreatorMapType::iterator i = creatorMap_.find(id); |
198 |
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if (i != creatorMap_.end()) { |
199 |
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result = (i->second)->create(info); |
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} |
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return result; |
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} |
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|
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private: |
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CreatorMapType creatorMap_; |
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}; |
207 |
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\end{lstlisting} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
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|
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class IntegratorCreator { |
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public: |
213 |
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IntegratorCreator(const string& ident) : ident_(ident) {} |
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|
215 |
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const string& getIdent() const { return ident_; } |
216 |
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|
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virtual Integrator* create(SimInfo* info) const = 0; |
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|
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private: |
220 |
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string ident_; |
221 |
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}; |
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|
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template<class ConcreteIntegrator> |
224 |
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class IntegratorBuilder : public IntegratorCreator { |
225 |
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public: |
226 |
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IntegratorBuilder(const string& ident) |
227 |
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: IntegratorCreator(ident) {} |
228 |
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virtual Integrator* create(SimInfo* info) const { |
229 |
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return new ConcreteIntegrator(info); |
230 |
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} |
231 |
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}; |
232 |
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\end{lstlisting} |
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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 |
71 |
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that you want to perform on the elements of a data structure. In |
72 |
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this way, you can change the operation being performed on a |
73 |
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structure without the need of changing the classes of the elements |
74 |
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that you are operating on. |
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|
|
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The visitor pattern is designed to decouple the data structure and |
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algorithms used upon them by collecting related operation from |
238 |
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element classes into other visitor classes, which is equivalent to |
239 |
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adding virtual functions into a set of classes without modifying |
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their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
241 |
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structure of Visitor pattern which is used extensively in {\tt |
242 |
+ |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
243 |
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distinct operations are performed on different StuntDoubles (See the |
244 |
+ |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
245 |
+ |
in List.~\ref{appendixScheme:element}). Since the hierarchies |
246 |
+ |
remains stable, it is easy to define a visit operation (see |
247 |
+ |
List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
248 |
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Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
249 |
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manages a priority visitor list and handles the execution of every |
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visitor in the priority list on different StuntDoubles. |
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|
|
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< |
\subsection{\label{appendixSection:templateMethod}Template Method} |
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\begin{figure} |
253 |
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\centering |
254 |
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\includegraphics[width=\linewidth]{visitor.eps} |
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\caption[The UML class diagram of Visitor patten] {The UML class |
256 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
257 |
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\end{figure} |
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|
|
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\section{\label{appendixSection:analysisFramework}Analysis Framework} |
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\begin{figure} |
260 |
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\centering |
261 |
> |
\includegraphics[width=\linewidth]{hierarchy.eps} |
262 |
> |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
263 |
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the class hierarchy. } \label{oopseFig:hierarchy} |
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\end{figure} |
265 |
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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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|
268 |
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class StuntDouble { public: |
269 |
> |
virtual void accept(BaseVisitor* v) = 0; |
270 |
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}; |
271 |
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|
272 |
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class Atom: public StuntDouble { public: |
273 |
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virtual void accept{BaseVisitor* v*} { |
274 |
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v->visit(this); |
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} |
276 |
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}; |
277 |
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|
278 |
> |
class DirectionalAtom: public Atom { public: |
279 |
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virtual void accept{BaseVisitor* v*} { |
280 |
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v->visit(this); |
281 |
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} |
282 |
> |
}; |
283 |
> |
|
284 |
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class RigidBody: public StuntDouble { public: |
285 |
> |
virtual void accept{BaseVisitor* v*} { |
286 |
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v->visit(this); |
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> |
} |
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> |
}; |
289 |
> |
|
290 |
> |
\end{lstlisting} |
291 |
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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}] |
293 |
|
|
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class BaseVisitor{ |
295 |
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public: |
296 |
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virtual void visit(Atom* atom); |
297 |
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virtual void visit(DirectionalAtom* datom); |
298 |
+ |
virtual void visit(RigidBody* rb); |
299 |
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}; |
300 |
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|
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class BaseAtomVisitor:public BaseVisitor{ public: |
302 |
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virtual void visit(Atom* atom); |
303 |
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virtual void visit(DirectionalAtom* datom); |
304 |
+ |
virtual void visit(RigidBody* rb); |
305 |
+ |
}; |
306 |
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|
307 |
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class SSDAtomVisitor:public BaseAtomVisitor{ public: |
308 |
+ |
virtual void visit(Atom* atom); |
309 |
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virtual void visit(DirectionalAtom* datom); |
310 |
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virtual void visit(RigidBody* rb); |
311 |
+ |
}; |
312 |
+ |
|
313 |
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class CompositeVisitor: public BaseVisitor { |
314 |
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public: |
315 |
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|
316 |
+ |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
317 |
+ |
typedef VistorListType::iterator VisitorListIterator; |
318 |
+ |
virtual void visit(Atom* atom) { |
319 |
+ |
VisitorListIterator i; |
320 |
+ |
BaseVisitor* curVisitor; |
321 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
322 |
+ |
atom->accept(*i); |
323 |
+ |
} |
324 |
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} |
325 |
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|
326 |
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virtual void visit(DirectionalAtom* datom) { |
327 |
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VisitorListIterator i; |
328 |
+ |
BaseVisitor* curVisitor; |
329 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) { |
330 |
+ |
atom->accept(*i); |
331 |
+ |
} |
332 |
+ |
} |
333 |
+ |
|
334 |
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virtual void visit(RigidBody* rb) { |
335 |
+ |
VisitorListIterator i; |
336 |
+ |
std::vector<Atom*> myAtoms; |
337 |
+ |
std::vector<Atom*>::iterator ai; |
338 |
+ |
myAtoms = rb->getAtoms(); |
339 |
+ |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
340 |
+ |
rb->accept(*i); |
341 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
342 |
+ |
(*ai)->accept(*i); |
343 |
+ |
} |
344 |
+ |
} |
345 |
+ |
|
346 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
347 |
+ |
|
348 |
+ |
protected: |
349 |
+ |
VistorListType visitorList; |
350 |
+ |
}; |
351 |
+ |
|
352 |
+ |
\end{lstlisting} |
353 |
+ |
|
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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 |
357 |
|
that {\it behave like atoms}. These objects can be rigid |
358 |
|
collections of atoms or atoms which have orientational degrees of |
359 |
< |
freedom. Here is a diagram of the class heirarchy: |
360 |
< |
|
361 |
< |
%\begin{figure} |
362 |
< |
%\centering |
363 |
< |
%\includegraphics[width=3in]{heirarchy.eps} |
364 |
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%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
365 |
< |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
366 |
< |
%selection syntax allows the user to select any of the objects that |
367 |
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%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
95 |
< |
%\end{figure} |
96 |
< |
|
359 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
360 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
361 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
362 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
363 |
> |
denoted by their membership and index inside a particular molecule: |
364 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
365 |
> |
on the specifics of the simulation). The names of rigid bodies are |
366 |
> |
generated automatically. For example, the name of the first rigid |
367 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
368 |
|
\begin{itemize} |
369 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
370 |
|
integrators and minimizers. |
374 |
|
DirectionalAtom}s which behaves as a single unit. |
375 |
|
\end{itemize} |
376 |
|
|
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Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
107 |
– |
own names which are specified in the {\tt .md} file. In contrast, |
108 |
– |
RigidBodies are denoted by their membership and index inside a |
109 |
– |
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
110 |
– |
inside the brackets depend on the specifics of the simulation). The |
111 |
– |
names of rigid bodies are generated automatically. For example, the |
112 |
– |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
113 |
– |
|
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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 |
380 |
< |
expression}} |
379 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
380 |
> |
StuntDoubles. The most general form of the select command is: |
381 |
|
|
382 |
+ |
{\tt select {\it expression}}. |
383 |
+ |
|
384 |
|
This expression represents an arbitrary set of StuntDoubles (Atoms |
385 |
< |
or RigidBodies) in {\sc oopse}. Expressions are composed of either |
385 |
> |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
386 |
|
name expressions, index expressions, predefined sets, user-defined |
387 |
|
expressions, comparison operators, within expressions, or logical |
388 |
|
combinations of the above expression types. Expressions can be |
469 |
|
Users can define arbitrary terms to represent groups of |
470 |
|
StuntDoubles, and then use the define terms in select commands. The |
471 |
|
general form for the define command is: {\bf define {\it term |
472 |
< |
expression}} |
472 |
> |
expression}}. Once defined, the user can specify such terms in |
473 |
> |
boolean expressions |
474 |
|
|
209 |
– |
Once defined, the user can specify such terms in boolean expressions |
210 |
– |
|
475 |
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
476 |
|
|
477 |
|
{\tt select SSDWATER} |
507 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
508 |
|
atoms. |
509 |
|
|
246 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
510 |
|
|
511 |
< |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
249 |
< |
|
250 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
251 |
< |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
252 |
< |
The options available for Dump2XYZ are as follows: |
253 |
< |
|
254 |
< |
|
255 |
< |
\begin{longtable}[c]{|EFG|} |
256 |
< |
\caption{Dump2XYZ Command-line Options} |
257 |
< |
\\ \hline |
258 |
< |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
259 |
< |
\endhead |
260 |
< |
\hline |
261 |
< |
\endfoot |
262 |
< |
-h & {\tt -{}-help} & Print help and exit \\ |
263 |
< |
-V & {\tt -{}-version} & Print version and exit \\ |
264 |
< |
-i & {\tt -{}-input} & input dump file \\ |
265 |
< |
-o & {\tt -{}-output} & output file name \\ |
266 |
< |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
267 |
< |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
268 |
< |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
269 |
< |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
270 |
< |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
271 |
< |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
272 |
< |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
273 |
< |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
274 |
< |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
275 |
< |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
276 |
< |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
277 |
< |
converted. \\ |
278 |
< |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
279 |
< |
& {\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}. |
280 |
< |
\end{longtable} |
511 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
512 |
|
|
282 |
– |
|
513 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
514 |
|
|
515 |
|
{\tt StaticProps} can compute properties which are averaged over |
516 |
|
some or all of the configurations that are contained within a dump |
517 |
|
file. The most common example of a static property that can be |
518 |
|
computed is the pair distribution function between atoms of type $A$ |
519 |
< |
and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
520 |
< |
used to compute the density distributions of other molecules in a |
521 |
< |
reference frame {\it fixed to the body-fixed reference frame} of a |
522 |
< |
selected atom or rigid body. |
519 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
520 |
> |
also be used to compute the density distributions of other molecules |
521 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
522 |
> |
of a selected atom or rigid body. |
523 |
|
|
524 |
|
There are five seperate radial distribution functions availiable in |
525 |
|
OOPSE. Since every radial distrbution function invlove the |
575 |
|
their body-fixed frames.} \label{oopseFig:gofr} |
576 |
|
\end{figure} |
577 |
|
|
578 |
+ |
Due to the fact that the selected StuntDoubles from two selections |
579 |
+ |
may be overlapped, {\tt StaticProps} performs the calculation in |
580 |
+ |
three stages which are illustrated in |
581 |
+ |
Fig.~\ref{oopseFig:staticPropsProcess}. |
582 |
+ |
|
583 |
+ |
\begin{figure} |
584 |
+ |
\centering |
585 |
+ |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
586 |
+ |
\caption[A representation of the three-stage correlations in |
587 |
+ |
\texttt{StaticProps}]{This diagram illustrates three-stage |
588 |
+ |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
589 |
+ |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
590 |
+ |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
591 |
+ |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
592 |
+ |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
593 |
+ |
the contrary, the third stage($C$ and $C$) are completely |
594 |
+ |
overlapping} \label{oopseFig:staticPropsProcess} |
595 |
+ |
\end{figure} |
596 |
+ |
|
597 |
|
The options available for {\tt StaticProps} are as follows: |
598 |
|
\begin{longtable}[c]{|EFG|} |
599 |
|
\caption{StaticProps Command-line Options} |
655 |
|
different vectors). The ability to use two selection scripts to |
656 |
|
select different types of atoms is already present in the code. |
657 |
|
|
658 |
+ |
For large simulations, the trajectory files can sometimes reach |
659 |
+ |
sizes in excess of several gigabytes. In order to effectively |
660 |
+ |
analyze that amount of data. In order to prevent a situation where |
661 |
+ |
the program runs out of memory due to large trajectories, |
662 |
+ |
\texttt{dynamicProps} will estimate the size of free memory at |
663 |
+ |
first, and determine the number of frames in each block, which |
664 |
+ |
allows the operating system to load two blocks of data |
665 |
+ |
simultaneously without swapping. Upon reading two blocks of the |
666 |
+ |
trajectory, \texttt{dynamicProps} will calculate the time |
667 |
+ |
correlation within the first block and the cross correlations |
668 |
+ |
between the two blocks. This second block is then freed and then |
669 |
+ |
incremented and the process repeated until the end of the |
670 |
+ |
trajectory. Once the end is reached, the first block is freed then |
671 |
+ |
incremented, until all frame pairs have been correlated in time. |
672 |
+ |
This process is illustrated in |
673 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
674 |
+ |
|
675 |
+ |
\begin{figure} |
676 |
+ |
\centering |
677 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
678 |
+ |
\caption[A representation of the block correlations in |
679 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
680 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
681 |
+ |
the self correlation of the block, and the open blocks are read one |
682 |
+ |
at a time and the cross correlations between blocks are calculated.} |
683 |
+ |
\label{oopseFig:dynamicPropsProcess} |
684 |
+ |
\end{figure} |
685 |
+ |
|
686 |
|
The options available for DynamicProps are as follows: |
687 |
|
\begin{longtable}[c]{|EFG|} |
688 |
|
\caption{DynamicProps Command-line Options} |
705 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
706 |
|
\end{longtable} |
707 |
|
|
708 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
708 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
709 |
> |
|
710 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
711 |
> |
|
712 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
713 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
714 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
715 |
> |
as follows: |
716 |
> |
|
717 |
> |
|
718 |
> |
\begin{longtable}[c]{|EFG|} |
719 |
> |
\caption{Dump2XYZ Command-line Options} |
720 |
> |
\\ \hline |
721 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
722 |
> |
\endhead |
723 |
> |
\hline |
724 |
> |
\endfoot |
725 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
726 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
727 |
> |
-i & {\tt -{}-input} & input dump file \\ |
728 |
> |
-o & {\tt -{}-output} & output file name \\ |
729 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
730 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
731 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
732 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
733 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
734 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
735 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
736 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
737 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
738 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
739 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
740 |
> |
converted. \\ |
741 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
742 |
> |
& {\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}. |
743 |
> |
\end{longtable} |
744 |
> |
|
745 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
746 |
> |
|
747 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
748 |
> |
center of resistance. Both tensors at the center of diffusion can |
749 |
> |
also be reported from the program, as well as the coordinates for |
750 |
> |
the beads which are used to approximate the arbitrary shapes. The |
751 |
> |
options available for Hydro are as follows: |
752 |
> |
\begin{longtable}[c]{|EFG|} |
753 |
> |
\caption{Hydrodynamics Command-line Options} |
754 |
> |
\\ \hline |
755 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
756 |
> |
\endhead |
757 |
> |
\hline |
758 |
> |
\endfoot |
759 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
760 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
761 |
> |
-i & {\tt -{}-input} & input dump file \\ |
762 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
763 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
764 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
765 |
> |
\end{longtable} |