--- trunk/tengDissertation/Appendix.tex	2006/06/07 02:49:09	2813
+++ trunk/tengDissertation/Appendix.tex	2006/06/07 18:34:05	2815
@@ -1,5 +1,5 @@
 \appendix
-\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)}
+\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine}
 
 Designing object-oriented software is hard, and designing reusable
 object-oriented scientific software is even harder. Absence of
@@ -14,14 +14,68 @@ documents which is crucial to the maintenance and exte
 coordination to enforce design and programming guidelines. Moreover,
 most MD programs also suffer from missing design and implement
 documents which is crucial to the maintenance and extensibility.
+Along the way of studying structural and dynamic processes in
+condensed phase systems like biological membranes and nanoparticles,
+we developed and maintained an Object-Oriented Parallel Simulation
+Engine ({\sc OOPSE}). This new molecular dynamics package has some
+unique features
+\begin{enumerate}
+  \item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard
+atom types (transition metals, point dipoles, sticky potentials,
+Gay-Berne ellipsoids, or other "lumpy"atoms with orientational
+degrees of freedom), as well as rigid bodies.
+  \item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap
+Beowulf clusters to obtain very efficient parallelism.
+  \item {\sc OOPSE} integrates the equations of motion using advanced methods for
+orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T
+ensembles.
+  \item {\sc OOPSE} can carry out simulations on metallic systems using the
+Embedded Atom Method (EAM) as well as the Sutton-Chen potential.
+  \item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals.
+  \item  {\sc OOPSE} can simulate systems containing the extremely efficient
+extended-Soft Sticky Dipole (SSD/E) model for water.
+\end{enumerate}
 
 \section{\label{appendixSection:architecture }Architecture}
 
+Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE}
+uses C++ Standard Template Library (STL) and fortran modules as the
+foundation. As an extensive set of the STL and Fortran90 modules,
+{\sc Base Classes} provide generic implementations of mathematical
+objects (e.g., matrices, vectors, polynomials, random number
+generators) and advanced data structures and algorithms(e.g., tuple,
+bitset, generic data, string manipulation). The molecular data
+structures for the representation of atoms, bonds, bends, torsions,
+rigid bodies and molecules \textit{etc} are contained in the {\sc
+Kernel} which is implemented with {\sc Base Classes} and are
+carefully designed to provide maximum extensibility and flexibility.
+The functionality required for applications is provide by the third
+layer which contains Input/Output, Molecular Mechanics and Structure
+modules. Input/Output module not only implements general methods for
+file handling, but also defines a generic force field interface.
+Another important component of Input/Output module is the meta-data
+file parser, which is rewritten using ANother Tool for Language
+Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular
+Mechanics module consists of energy minimization and a wide
+varieties of integration methods(see Chap.~\ref{chapt:methodology}).
+The structure module contains a flexible and powerful selection
+library which syntax is elaborated in
+Sec.~\ref{appendixSection:syntax}. The top layer is made of the main
+program of the package, \texttt{oopse} and it corresponding parallel
+version \texttt{oopse\_MPI}, as well as other useful utilities, such
+as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}),
+\texttt{DynamicProps} (see
+Sec.~\ref{appendixSection:appendixSection:DynamicProps}),
+\texttt{Dump2XYZ} (see
+Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro}
+(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics})
+\textit{etc}.
+
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{architecture.eps}
-\caption[The architecture of {\sc oopse}-3.0] {The architecture of
-{\sc oopse}-3.0.} \label{appendixFig:architecture}
+\caption[The architecture of {\sc OOPSE}] {Overview of the structure
+of {\sc OOPSE}} \label{appendixFig:architecture}
 \end{figure}
 
 \section{\label{appendixSection:desginPattern}Design Pattern}
@@ -58,8 +112,10 @@ the modern scientific software applications, such as J
 
 As one of the latest advanced techniques emerged from
 object-oriented community, design patterns were applied in some of
-the modern scientific software applications, such as JMol, OOPSE
-\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}.
+the modern scientific software applications, such as JMol, {\sc
+OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}.
+The following sections enumerates some of the patterns used in {\sc
+OOPSE}.
 
 \subsection{\label{appendixSection:singleton}Singleton}
 The Singleton pattern ensures that only one instance of a class is
@@ -74,7 +130,6 @@ that will be created.
 subclasses can then override to specify the derived type of product
 that will be created.
 
-
 \subsection{\label{appendixSection:visitorPattern}Visitor}
 The purpose of the Visitor Pattern is to encapsulate an operation
 that you want to perform on the elements of a data structure. In
@@ -82,9 +137,6 @@ that you are operating on.
 structure without the need of changing the classes of the elements
 that you are operating on.
 
-
-\subsection{\label{appendixSection:templateMethod}Template Method}
-
 \section{\label{appendixSection:concepts}Concepts}
 
 OOPSE manipulates both traditional atoms as well as some objects
@@ -110,7 +162,7 @@ Every Molecule, Atom and DirectionalAtom in {\sc oopse
 DirectionalAtom}s which behaves as a single unit.
 \end{itemize}
 
-Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their
+Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
 own names which are specified in the {\tt .md} file. In contrast,
 RigidBodies are denoted by their membership and index inside a
 particular molecule: [MoleculeName]\_RB\_[index] (the contents
@@ -121,15 +173,14 @@ expression}}
 \section{\label{appendixSection:syntax}Syntax of the Select Command}
 
 The most general form of the select command is: {\tt select {\it
-expression}}
+expression}}. This expression represents an arbitrary set of
+StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are
+composed of either name expressions, index expressions, predefined
+sets, user-defined expressions, comparison operators, within
+expressions, or logical combinations of the above expression types.
+Expressions can be combined using parentheses and the Boolean
+operators.
 
-This expression represents an arbitrary set of StuntDoubles (Atoms
-or RigidBodies) in {\sc oopse}. Expressions are composed of either
-name expressions, index expressions, predefined sets, user-defined
-expressions, comparison operators, within expressions, or logical
-combinations of the above expression types. Expressions can be
-combined using parentheses and the Boolean operators.
-
 \subsection{\label{appendixSection:logical}Logical expressions}
 
 The logical operators allow complex queries to be constructed out of
@@ -211,10 +262,9 @@ expression}}
 Users can define arbitrary terms to represent groups of
 StuntDoubles, and then use the define terms in select commands. The
 general form for the define command is: {\bf define {\it term
-expression}}
+expression}}. Once defined, the user can specify such terms in
+boolean expressions
 
-Once defined, the user can specify such terms in boolean expressions
-
 {\tt define SSDWATER SSD or SSD1 or SSDRF}
 
 {\tt select SSDWATER}
@@ -259,10 +309,10 @@ and other atoms of type $B$, $g_{AB}(r)$.  StaticProps
 some or all of the configurations that are contained within a dump
 file. The most common example of a static property that can be
 computed is the pair distribution function between atoms of type $A$
-and other atoms of type $B$, $g_{AB}(r)$.  StaticProps can also be
-used to compute the density distributions of other molecules in a
-reference frame {\it fixed to the body-fixed reference frame} of a
-selected atom or rigid body.
+and other atoms of type $B$, $g_{AB}(r)$.  {\tt StaticProps} can
+also be used to compute the density distributions of other molecules
+in a reference frame {\it fixed to the body-fixed reference frame}
+of a selected atom or rigid body.
 
 There are five seperate radial distribution functions availiable in
 OOPSE. Since every radial distrbution function invlove the
@@ -316,6 +366,25 @@ their body-fixed frames.} \label{oopseFig:gofr}
 Any two directional objects (DirectionalAtoms and RigidBodies) have
 a set of two angles ($\theta$, and $\omega$) between the z-axes of
 their body-fixed frames.} \label{oopseFig:gofr}
+\end{figure}
+
+Due to the fact that the selected StuntDoubles from two selections
+may be overlapped, {\tt StaticProps} performs the calculation in
+three stages which are illustrated in
+Fig.~\ref{oopseFig:staticPropsProcess}.
+
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{staticPropsProcess.eps}
+\caption[A representation of the three-stage correlations in
+\texttt{StaticProps}]{Three-stage processing in
+\texttt{StaticProps}. $S_1$ and $S_2$ are the numbers of selected
+stuntdobules from {\tt -{}-sele1} and {\tt -{}-sele2} respectively,
+while $C$ is the number of stuntdobules appearing at both sets. The
+first stage($S_1-C$ and $S_2$) and second stages ($S_1$ and $S_2-C$)
+are completely non-overlapping. On the contrary, the third stage($C$
+and $C$) are completely overlapping}
+\label{oopseFig:staticPropsProcess}
 \end{figure}
 
 The options available for {\tt StaticProps} are as follows:
@@ -379,6 +448,21 @@ The options available for DynamicProps are as follows:
 different vectors).  The ability to use two selection scripts to
 select different types of atoms is already present in the code.
 
+For large simulations, the trajectory files can sometimes reach
+sizes in excess of several gigabytes. In order to effectively
+analyze that amount of data. In order to prevent a situation where
+the program runs out of memory due to large trajectories,
+\texttt{dynamicProps} will estimate the size of free memory at
+first, and determine the number of frames in each block, which
+allows the operating system to load two blocks of data
+simultaneously without swapping. Upon reading two blocks of the
+trajectory, \texttt{dynamicProps} will calculate the time
+correlation within the first block and the cross correlations
+between the two blocks. This second block is then freed and then
+incremented and the process repeated until the end of the
+trajectory. Once the end is reached, the first block is freed then
+incremented, until all frame pairs have been correlated in time.
+
 The options available for DynamicProps are as follows:
 \begin{longtable}[c]{|EFG|}
 \caption{DynamicProps Command-line Options}
@@ -406,8 +490,9 @@ be opened by other molecular dynamics viewers such as 
 \subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ}
 
 Dump2XYZ can transform an OOPSE dump file into a xyz file which can
-be opened by other molecular dynamics viewers such as Jmol and VMD.
-The options available for Dump2XYZ are as follows:
+be opened by other molecular dynamics viewers such as Jmol and
+VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as
+follows:
 
 
 \begin{longtable}[c]{|EFG|}
@@ -437,8 +522,8 @@ converted. \\
      & {\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}.
 \end{longtable}
 
-\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
-
+\subsection{\label{appendixSection:hydrodynamics}Hydro}
+The options available for Hydro are as follows:
 \begin{longtable}[c]{|EFG|}
 \caption{Hydrodynamics Command-line Options}
 \\ \hline
@@ -451,5 +536,5 @@ converted. \\
   -i & {\tt -{}-input}  &             input dump file \\
   -o & {\tt -{}-output} &             output file prefix  (default=`hydro') \\
   -b & {\tt -{}-beads}  &                   generate the beads only, hydrodynamics calculation will not be performed (default=off)\\
-     & {\tt -{}-model}  &                 hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
+     & {\tt -{}-model}  &                 hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\
 \end{longtable}
