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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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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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\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}-3.0] {The architecture of |
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{\sc oopse}-3.0.} \label{appendixFig:architecture} |
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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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subclasses can then override to specify the derived type of product |
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that will be created. |
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\subsection{\label{appendixSection:visitorPattern}Visitor} |
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The purpose of the Visitor Pattern is to encapsulate an operation |
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that you want to perform on the elements of a data structure. In |
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structure without the need of changing the classes of the elements |
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that you are operating on. |
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\subsection{\label{appendixSection:templateMethod}Template Method} |
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\section{\label{appendixSection:concepts}Concepts} |
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OOPSE manipulates both traditional atoms as well as some objects |
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DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
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Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
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own names which are specified in the {\tt .md} file. In contrast, |
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RigidBodies are denoted by their membership and index inside a |
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particular molecule: [MoleculeName]\_RB\_[index] (the contents |
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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The most general form of the select command is: {\tt select {\it |
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expression}} |
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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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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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\subsection{\label{appendixSection:logical}Logical expressions} |
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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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Once defined, the user can specify such terms in boolean expressions |
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{\tt define SSDWATER SSD or SSD1 or SSDRF} |
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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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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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Any two directional objects (DirectionalAtoms and RigidBodies) have |
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a set of two angles ($\theta$, and $\omega$) between the z-axes of |
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their body-fixed frames.} \label{oopseFig:gofr} |
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\end{figure} |
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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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\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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The options available for {\tt StaticProps} are as follows: |
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different vectors). The ability to use two selection scripts to |
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select different types of atoms is already present in the code. |
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For large simulations, the trajectory files can sometimes reach |
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sizes in excess of several gigabytes. In order to effectively |
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analyze that amount of data. In order to prevent a situation where |
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the program runs out of memory due to large trajectories, |
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\texttt{dynamicProps} will estimate the size of free memory at |
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first, and determine the number of frames in each block, which |
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allows the operating system to load two blocks of data |
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simultaneously without swapping. Upon reading two blocks of the |
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trajectory, \texttt{dynamicProps} will calculate the time |
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correlation within the first block and the cross correlations |
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between the two blocks. This second block is then freed and then |
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incremented and the process repeated until the end of the |
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trajectory. Once the end is reached, the first block is freed then |
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incremented, until all frame pairs have been correlated in time. |
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This process is illustrated in |
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Fig.~\ref{oopseFig:dynamicPropsProcess}. |
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
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\caption[A representation of the block correlations in |
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\texttt{dynamicProps}]{This diagram illustrates block correlations |
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processing in \texttt{dynamicProps}. The shaded region represents |
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the self correlation of the block, and the open blocks are read one |
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at a time and the cross correlations between blocks are calculated.} |
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\label{oopseFig:dynamicPropsProcess} |
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\end{figure} |
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The options available for DynamicProps are as follows: |
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\begin{longtable}[c]{|EFG|} |
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\caption{DynamicProps Command-line Options} |
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\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
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Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
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be opened by other molecular dynamics viewers such as Jmol and VMD. |
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The options available for Dump2XYZ are as follows: |
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be opened by other molecular dynamics viewers such as Jmol and |
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VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
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follows: |
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\begin{longtable}[c]{|EFG|} |
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& {\tt -{}-refsele} & In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}. |
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\end{longtable} |
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\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
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\subsection{\label{appendixSection:hydrodynamics}Hydro} |
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The options available for Hydro are as follows: |
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\begin{longtable}[c]{|EFG|} |
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\caption{Hydrodynamics Command-line Options} |
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\\ \hline |
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-i & {\tt -{}-input} & input dump file \\ |
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-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
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-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
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& {\tt -{}-model} & hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
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& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
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\end{longtable} |
