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\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{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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The absence of modern software development practices has been a |
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bottleneck limiting progress in the Scientific Computing |
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community\cite{Wilson2006}. In the last 20 years , a large number of |
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few MD packages\cite{Brooks1983, Vincent1995, Kale1999} 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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contributed by scientists without official computer science |
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training. The development of most MD applications are lack of strong |
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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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. Most of these are commercial programs that are either poorly |
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written or extremely complicated to use correctly. This situation |
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prevents researchers from reusing or extending those packages to do |
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cutting-edge research effectively. In the process of studying |
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structural and dynamic processes in condensed phase systems like |
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biological membranes and nanoparticles, we developed an open source |
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Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
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molecular dynamics package has some 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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|
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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, |
42 |
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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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Mainly written by C++ and Fortran90, {\sc OOPSE} uses C++ Standard |
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Template Library (STL) and fortran modules as a foundation. As an |
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extensive set of the STL and Fortran90 modules, {\sc Base Classes} |
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> |
provide generic implementations of mathematical objects (e.g., |
40 |
> |
matrices, vectors, polynomials, random number generators) and |
41 |
> |
advanced data structures and algorithms(e.g., tuple, bitset, generic |
42 |
> |
data and string manipulation). The molecular data structures for the |
43 |
> |
representation of atoms, bonds, bends, torsions, rigid bodies and |
44 |
> |
molecules \textit{etc} are contained in the {\sc Kernel} which is |
45 |
> |
implemented with {\sc Base Classes} and are carefully designed to |
46 |
> |
provide maximum extensibility and flexibility. The functionality |
47 |
> |
required for applications is provided by the third layer which |
48 |
> |
contains Input/Output, Molecular Mechanics and Structure modules. |
49 |
> |
The Input/Output module not only implements general methods for file |
50 |
> |
handling, but also defines a generic force field interface. Another |
51 |
> |
important component of Input/Output module is the parser for |
52 |
> |
meta-data files, which has been implemented using the ANother Tool |
53 |
> |
for Language Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. |
54 |
> |
The Molecular Mechanics module consists of energy minimization and a |
55 |
> |
wide varieties of integration methods(see |
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> |
Chap.~\ref{chapt:methodology}). The structure module contains a |
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> |
flexible and powerful selection library which syntax is elaborated |
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> |
in Sec.~\ref{appendixSection:syntax}. The top layer is made of the |
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main program of the package, \texttt{oopse} and it corresponding |
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parallel version \texttt{oopse\_MPI}, as well as other useful |
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utilities, such as \texttt{StatProps} (see |
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Sec.~\ref{appendixSection:StaticProps}), \texttt{DynamicProps} (see |
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Sec.~\ref{appendixSection:DynamicProps}), \texttt{Dump2XYZ} (see |
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Sec.~\ref{appendixSection:Dump2XYZ}), \texttt{Hydro} (see |
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Sec.~\ref{appendixSection:hydrodynamics}) \textit{etc}. |
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|
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\begin{figure} |
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\centering |
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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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\section{\label{appendixSection:desginPattern}Design Patterns} |
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|
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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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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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different problems as necessary. As one of the latest advanced |
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techniques to emerge from object-oriented community, design patterns |
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were applied in some of the modern scientific software applications, |
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such as JMol, {\sc OOPSE}\cite{Meineke2005} and |
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PROTOMOL\cite{Matthey2004} \textit{etc}. The following sections |
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enumerates some of the patterns used in {\sc OOPSE}. |
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|
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Patterns are usually described using a format that includes the |
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following information: |
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\begin{enumerate} |
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\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
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discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
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in the literature. In this case it is common practice to document these nicknames or synonyms under |
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the heading of \emph{Aliases} or \emph{Also Known As}. |
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\item The \emph{motivation} or \emph{context} that this pattern applies |
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to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
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\item The \emph{solution} to the problem that the pattern |
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addresses. It describes how to construct the necessary work products. The description may include |
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pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
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collaborations, to show how the problem is solved. |
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\item The \emph{consequences} of using the given solution to solve a |
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problem, both positive and negative. |
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\end{enumerate} |
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\subsection{\label{appendixSection:singleton}Singletons} |
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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, {\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 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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point of access to the object. Although the singleton pattern can be |
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implemented in various ways to account for different aspects of the |
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software designs, such as lifespan control \textit{etc}, we only use |
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the static data approach in {\sc OOPSE}. The declaration and |
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implementation of IntegratorFactory class are given by declared in |
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List.~\ref{appendixScheme:singletonDeclaration} and |
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Scheme.~\ref{appendixScheme:singletonImplementation} respectively. |
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Since the 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 Methods} |
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|
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The Factory Method pattern is a creational pattern and 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 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 Scheme.~\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 |
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Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the |
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modern C++ template technique to avoid excess subclassing. |
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|
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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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 |
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element classes into other visitor classes, which is equivalent to |
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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 |
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> |
structure of a Visitor pattern which is used extensively in {\tt |
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> |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
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> |
distinct operations are performed on different StuntDoubles (See the |
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class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
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> |
in Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
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remain stable, it is easy to define a visit operation (see |
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Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
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Note that using Composite pattern\cite{Gamma1994}, CompositeVisitor |
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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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|
\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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> |
class IntegratorFactory { public: |
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> |
static IntegratorFactory* getInstance(); 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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> |
|
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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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|
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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 |
162 |
– |
requirement, a single instance. Another consequence of this approach |
163 |
– |
is the automatic destruction since static data are destroyed upon |
164 |
– |
program termination. |
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|
|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
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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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< |
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. |
172 |
< |
{\tt Integrator} class Parameterized Factory pattern where factory |
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< |
method ({\tt createIntegrator} member function) creates products |
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< |
based on the identifier (see |
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< |
List.~\ref{appendixScheme:factoryDeclaration}). If the identifier |
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< |
has been already registered, the factory method will invoke the |
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< |
corresponding creator (see List.~\ref{integratorCreator}) which |
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< |
utilizes the modern C++ template technique to avoid subclassing. |
179 |
< |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of {\tt IntegratorFactory} class.},label={appendixScheme:factoryDeclaration}] |
180 |
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|
181 |
< |
class IntegratorFactory { |
182 |
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public: |
169 |
> |
class IntegratorFactory { public: |
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|
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
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|
172 |
|
bool registerIntegrator(IntegratorCreator* creator) { |
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|
CreatorMapType creatorMap_; |
187 |
|
}; |
188 |
|
\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}] |
191 |
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|
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|
class IntegratorCreator { |
193 |
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public: |
193 |
> |
public: |
194 |
|
IntegratorCreator(const string& ident) : ident_(ident) {} |
195 |
|
|
196 |
|
const string& getIdent() const { return ident_; } |
201 |
|
string ident_; |
202 |
|
}; |
203 |
|
|
204 |
< |
template<class ConcreteIntegrator> |
205 |
< |
class IntegratorBuilder : public IntegratorCreator { |
206 |
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public: |
207 |
< |
IntegratorBuilder(const string& ident) |
208 |
< |
: IntegratorCreator(ident) {} |
209 |
< |
virtual Integrator* create(SimInfo* info) const { |
210 |
< |
return new ConcreteIntegrator(info); |
211 |
< |
} |
204 |
> |
template<class ConcreteIntegrator> class IntegratorBuilder : public |
205 |
> |
IntegratorCreator { |
206 |
> |
public: |
207 |
> |
IntegratorBuilder(const string& ident) |
208 |
> |
: IntegratorCreator(ident) {} |
209 |
> |
virtual Integrator* create(SimInfo* info) const { |
210 |
> |
return new ConcreteIntegrator(info); |
211 |
> |
} |
212 |
|
}; |
213 |
|
\end{lstlisting} |
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|
215 |
< |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
228 |
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|
229 |
< |
The purpose of the Visitor Pattern is to encapsulate an operation |
230 |
< |
that you want to perform on the elements. The operation being |
231 |
< |
performed on a structure can be switched without changing the |
232 |
< |
interfaces of the elements. In other words, one can add virtual |
233 |
< |
functions into a set of classes without modifying their interfaces. |
234 |
< |
Fig.~\ref{appendixFig:visitorUML} demonstrates the structure of |
235 |
< |
Visitor pattern which is used extensively in {\tt Dump2XYZ}. In |
236 |
< |
order to convert an OOPSE dump file, a series of distinct and |
237 |
< |
unrelated operations are performed on different StuntDoubles. |
238 |
< |
Visitor allows one to keep related operations together by packing |
239 |
< |
them into one class. {\tt BaseAtomVisitor} is a typical example of |
240 |
< |
visitor in {\tt Dump2XYZ} program{see |
241 |
< |
List.~\ref{appendixScheme:visitor}}. In contrast to the operations, |
242 |
< |
the object structure or element classes rarely change(See |
243 |
< |
Fig.~\ref{oopseFig:heirarchy} and |
244 |
< |
List.~\ref{appendixScheme:element}). |
215 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
216 |
|
|
217 |
+ |
class StuntDouble { |
218 |
+ |
public: |
219 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
220 |
+ |
}; |
221 |
|
|
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\begin{figure} |
223 |
< |
\centering |
224 |
< |
\includegraphics[width=\linewidth]{visitor.eps} |
225 |
< |
\caption[The UML class diagram of Visitor patten] {The UML class |
226 |
< |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
227 |
< |
\end{figure} |
222 |
> |
class Atom: public StuntDouble { |
223 |
> |
public: |
224 |
> |
virtual void accept{BaseVisitor* v*} { |
225 |
> |
v->visit(this); |
226 |
> |
} |
227 |
> |
}; |
228 |
|
|
229 |
< |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
230 |
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|
231 |
< |
class BaseVisitor{ |
232 |
< |
public: |
233 |
< |
virtual void visit(Atom* atom); |
259 |
< |
virtual void visit(DirectionalAtom* datom); |
260 |
< |
virtual void visit(RigidBody* rb); |
229 |
> |
class DirectionalAtom: public Atom { |
230 |
> |
public: |
231 |
> |
virtual void accept{BaseVisitor* v*} { |
232 |
> |
v->visit(this); |
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> |
} |
234 |
|
}; |
235 |
|
|
236 |
< |
class BaseAtomVisitor:public BaseVisitor{ public: |
237 |
< |
virtual void visit(Atom* atom); |
238 |
< |
virtual void visit(DirectionalAtom* datom); |
239 |
< |
virtual void visit(RigidBody* rb); |
236 |
> |
class RigidBody: public StuntDouble { |
237 |
> |
public: |
238 |
> |
virtual void accept{BaseVisitor* v*} { |
239 |
> |
v->visit(this); |
240 |
> |
} |
241 |
|
}; |
242 |
|
|
243 |
|
\end{lstlisting} |
244 |
|
|
245 |
< |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
245 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
246 |
|
|
247 |
< |
class StuntDouble { |
248 |
< |
public: |
249 |
< |
virtual void accept(BaseVisitor* v) = 0; |
247 |
> |
class BaseVisitor{ |
248 |
> |
public: |
249 |
> |
virtual void visit(Atom* atom); |
250 |
> |
virtual void visit(DirectionalAtom* datom); |
251 |
> |
virtual void visit(RigidBody* rb); |
252 |
|
}; |
253 |
|
|
254 |
< |
class Atom: public StuntDouble { |
255 |
< |
public: |
256 |
< |
virtual void accept{BaseVisitor* v*} { |
257 |
< |
v->visit(this); |
258 |
< |
} |
254 |
> |
class BaseAtomVisitor:public BaseVisitor{ |
255 |
> |
public: |
256 |
> |
virtual void visit(Atom* atom); |
257 |
> |
virtual void visit(DirectionalAtom* datom); |
258 |
> |
virtual void visit(RigidBody* rb); |
259 |
|
}; |
260 |
|
|
261 |
< |
class DirectionalAtom: public Atom { |
262 |
< |
public: |
263 |
< |
virtual void accept{BaseVisitor* v*} { |
264 |
< |
v->visit(this); |
261 |
> |
class CompositeVisitor: public BaseVisitor { |
262 |
> |
public: |
263 |
> |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
264 |
> |
typedef VistorListType::iterator VisitorListIterator; |
265 |
> |
virtual void visit(Atom* atom) { |
266 |
> |
VisitorListIterator i; |
267 |
> |
BaseVisitor* curVisitor; |
268 |
> |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
269 |
> |
atom->accept(*i); |
270 |
> |
} |
271 |
|
} |
290 |
– |
}; |
272 |
|
|
273 |
< |
class RigidBody: public StuntDouble { |
274 |
< |
public: |
275 |
< |
virtual void accept{BaseVisitor* v*} { |
276 |
< |
v->visit(this); |
273 |
> |
virtual void visit(DirectionalAtom* datom) { |
274 |
> |
VisitorListIterator i; |
275 |
> |
BaseVisitor* curVisitor; |
276 |
> |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
277 |
> |
atom->accept(*i); |
278 |
> |
} |
279 |
|
} |
297 |
– |
}; |
280 |
|
|
281 |
+ |
virtual void visit(RigidBody* rb) { |
282 |
+ |
VisitorListIterator i; |
283 |
+ |
std::vector<Atom*> myAtoms; |
284 |
+ |
std::vector<Atom*>::iterator ai; |
285 |
+ |
myAtoms = rb->getAtoms(); |
286 |
+ |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
287 |
+ |
rb->accept(*i); |
288 |
+ |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
289 |
+ |
(*ai)->accept(*i); |
290 |
+ |
} |
291 |
+ |
} |
292 |
+ |
|
293 |
+ |
void addVisitor(BaseVisitor* v, int priority); |
294 |
+ |
protected: |
295 |
+ |
VistorListType visitorList; |
296 |
+ |
}; |
297 |
|
\end{lstlisting} |
298 |
|
|
299 |
+ |
\begin{figure} |
300 |
+ |
\centering |
301 |
+ |
\includegraphics[width=\linewidth]{visitor.eps} |
302 |
+ |
\caption[The UML class diagram of Visitor patten] {The UML class |
303 |
+ |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
304 |
+ |
\end{figure} |
305 |
+ |
|
306 |
+ |
\begin{figure} |
307 |
+ |
\centering |
308 |
+ |
\includegraphics[width=\linewidth]{hierarchy.eps} |
309 |
+ |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
310 |
+ |
the class hierarchy. Objects below others on the diagram inherit |
311 |
+ |
data structures and functions from their parent classes above them.} |
312 |
+ |
\label{oopseFig:hierarchy} |
313 |
+ |
\end{figure} |
314 |
+ |
|
315 |
|
\section{\label{appendixSection:concepts}Concepts} |
316 |
|
|
317 |
|
OOPSE manipulates both traditional atoms as well as some objects |
318 |
|
that {\it behave like atoms}. These objects can be rigid |
319 |
|
collections of atoms or atoms which have orientational degrees of |
320 |
< |
freedom. A diagram of the class heirarchy is illustrated in |
321 |
< |
Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
320 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
321 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
322 |
|
DirectionalAtom in {\sc OOPSE} have their own names which are |
323 |
< |
specified in the {\tt .md} file. In contrast, RigidBodies are |
323 |
> |
specified in the meta data file. In contrast, RigidBodies are |
324 |
|
denoted by their membership and index inside a particular molecule: |
325 |
|
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
326 |
|
on the specifics of the simulation). The names of rigid bodies are |
327 |
|
generated automatically. For example, the name of the first rigid |
328 |
|
body in a DMPC molecule is DMPC\_RB\_0. |
329 |
< |
%\begin{figure} |
330 |
< |
%\centering |
331 |
< |
%\includegraphics[width=\linewidth]{heirarchy.eps} |
332 |
< |
%\caption[Class heirarchy for ojects in {\sc OOPSE}]{ A diagram of |
333 |
< |
%the class heirarchy. |
334 |
< |
%\begin{itemize} |
335 |
< |
%\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
336 |
< |
%integrators and minimizers. |
323 |
< |
%\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
324 |
< |
%\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
325 |
< |
%\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
326 |
< |
%DirectionalAtom}s which behaves as a single unit. |
327 |
< |
%\end{itemize} |
328 |
< |
%} \label{oopseFig:heirarchy} |
329 |
< |
%\end{figure} |
329 |
> |
\begin{itemize} |
330 |
> |
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
331 |
> |
integrators and minimizers. |
332 |
> |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
333 |
> |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
334 |
> |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
335 |
> |
DirectionalAtom}s which behaves as a single unit. |
336 |
> |
\end{itemize} |
337 |
|
|
338 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
339 |
|
|
340 |
< |
The most general form of the select command is: {\tt select {\it |
341 |
< |
expression}}. This expression represents an arbitrary set of |
335 |
< |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
336 |
< |
composed of either name expressions, index expressions, predefined |
337 |
< |
sets, user-defined expressions, comparison operators, within |
338 |
< |
expressions, or logical combinations of the above expression types. |
339 |
< |
Expressions can be combined using parentheses and the Boolean |
340 |
< |
operators. |
340 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
341 |
> |
StuntDoubles. The most general form of the select command is: |
342 |
|
|
343 |
+ |
{\tt select {\it expression}}. |
344 |
+ |
|
345 |
+ |
This expression represents an arbitrary set of StuntDoubles (Atoms |
346 |
+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
347 |
+ |
name expressions, index expressions, predefined sets, user-defined |
348 |
+ |
expressions, comparison operators, within expressions, or logical |
349 |
+ |
combinations of the above expression types. Expressions can be |
350 |
+ |
combined using parentheses and the Boolean operators. |
351 |
+ |
|
352 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
353 |
|
|
354 |
|
The logical operators allow complex queries to be constructed out of |
480 |
|
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
481 |
|
also be used to compute the density distributions of other molecules |
482 |
|
in a reference frame {\it fixed to the body-fixed reference frame} |
483 |
< |
of a selected atom or rigid body. |
483 |
> |
of a selected atom or rigid body. Due to the fact that the selected |
484 |
> |
StuntDoubles from two selections may be overlapped, {\tt |
485 |
> |
StaticProps} performs the calculation in three stages which are |
486 |
> |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
487 |
> |
|
488 |
> |
\begin{figure} |
489 |
> |
\centering |
490 |
> |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
491 |
> |
\caption[A representation of the three-stage correlations in |
492 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
493 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
494 |
> |
numbers of selected StuntDobules from {\tt -{}-sele1} and {\tt |
495 |
> |
-{}-sele2} respectively, while $C$ is the number of StuntDobules |
496 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
497 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
498 |
> |
the contrary, the third stage($C$ and $C$) are completely |
499 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
500 |
> |
\end{figure} |
501 |
|
|
502 |
+ |
\begin{figure} |
503 |
+ |
\centering |
504 |
+ |
\includegraphics[width=3in]{definition.eps} |
505 |
+ |
\caption[Definitions of the angles between directional objects]{Any |
506 |
+ |
two directional objects (DirectionalAtoms and RigidBodies) have a |
507 |
+ |
set of two angles ($\theta$, and $\omega$) between the z-axes of |
508 |
+ |
their body-fixed frames.} \label{oopseFig:gofr} |
509 |
+ |
\end{figure} |
510 |
+ |
|
511 |
|
There are five seperate radial distribution functions availiable in |
512 |
|
OOPSE. Since every radial distrbution function invlove the |
513 |
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
551 |
|
\end{description} |
552 |
|
|
553 |
|
The vectors (and angles) associated with these angular pair |
554 |
< |
distribution functions are most easily seen in the figure below: |
554 |
> |
distribution functions are most easily seen in |
555 |
> |
Fig.~\ref{oopseFig:gofr}. |
556 |
|
|
520 |
– |
\begin{figure} |
521 |
– |
\centering |
522 |
– |
\includegraphics[width=3in]{definition.eps} |
523 |
– |
\caption[Definitions of the angles between directional objects]{ \\ |
524 |
– |
Any two directional objects (DirectionalAtoms and RigidBodies) have |
525 |
– |
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
526 |
– |
their body-fixed frames.} \label{oopseFig:gofr} |
527 |
– |
\end{figure} |
528 |
– |
|
529 |
– |
Due to the fact that the selected StuntDoubles from two selections |
530 |
– |
may be overlapped, {\tt StaticProps} performs the calculation in |
531 |
– |
three stages which are illustrated in |
532 |
– |
Fig.~\ref{oopseFig:staticPropsProcess}. |
533 |
– |
|
534 |
– |
\begin{figure} |
535 |
– |
\centering |
536 |
– |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
537 |
– |
\caption[A representation of the three-stage correlations in |
538 |
– |
\texttt{StaticProps}]{This diagram illustrates three-stage |
539 |
– |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
540 |
– |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
541 |
– |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
542 |
– |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
543 |
– |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
544 |
– |
the contrary, the third stage($C$ and $C$) are completely |
545 |
– |
overlapping} \label{oopseFig:staticPropsProcess} |
546 |
– |
\end{figure} |
547 |
– |
|
557 |
|
The options available for {\tt StaticProps} are as follows: |
558 |
|
\begin{longtable}[c]{|EFG|} |
559 |
|
\caption{StaticProps Command-line Options} |
616 |
|
select different types of atoms is already present in the code. |
617 |
|
|
618 |
|
For large simulations, the trajectory files can sometimes reach |
619 |
< |
sizes in excess of several gigabytes. In order to effectively |
620 |
< |
analyze that amount of data. In order to prevent a situation where |
621 |
< |
the program runs out of memory due to large trajectories, |
622 |
< |
\texttt{dynamicProps} will estimate the size of free memory at |
623 |
< |
first, and determine the number of frames in each block, which |
615 |
< |
allows the operating system to load two blocks of data |
619 |
> |
sizes in excess of several gigabytes. In order to prevent a |
620 |
> |
situation where the program runs out of memory due to large |
621 |
> |
trajectories, \texttt{dynamicProps} will first estimate the size of |
622 |
> |
free memory, and determine the number of frames in each block, which |
623 |
> |
will allow the operating system to load two blocks of data |
624 |
|
simultaneously without swapping. Upon reading two blocks of the |
625 |
|
trajectory, \texttt{dynamicProps} will calculate the time |
626 |
|
correlation within the first block and the cross correlations |