trunk/tengDissertation/Appendix.tex

\appendix
\chapter{\label{chapt:appendix}APPENDIX}

Designing object-oriented software is hard, and designing reusable
object-oriented scientific software is even harder. Absence of
applying modern software development practices is the bottleneck of
Scientific Computing community\cite{Wilson}. For instance, in the
last 20 years , there are quite a few MD packages that were
developed to solve common MD problems and perform robust simulations
. However, many of the codes are legacy programs that are either
poorly organized or extremely complex. Usually, these packages were
contributed by scientists without official computer science
training. The development of most MD applications are lack of strong
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.

\section{\label{appendixSection:desginPattern}Design Pattern}

Design patterns are optimal solutions to commonly-occurring problems
in software design. Although originated as an architectural concept
for buildings and towns by Christopher Alexander
\cite{Alexander1987}, software patterns first became popular with
the wide acceptance of the book, Design Patterns: Elements of
Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect
the experience, knowledge and insights of developers who have
successfully used these patterns in their own work. Patterns are
reusable. They provide a ready-made solution that can be adapted to
different problems as necessary. Pattern are expressive. they
provide a common vocabulary of solutions that can express large
solutions succinctly.

Patterns are usually described using a format that includes the
following information:
\begin{enumerate}
  \item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for
  discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name
  in the literature. In this case it is common practice to document these nicknames or synonyms under
  the heading of \emph{Aliases} or \emph{Also Known As}.
  \item The \emph{motivation} or \emph{context} that this pattern applies
  to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern
  \item The \emph{solution} to the problem that the pattern
  addresses. It describes how to construct the necessary work products. The description may include
  pictures, diagrams and prose which identify the pattern's structure, its participants, and their
  collaborations, to show how the problem is solved.
  \item The \emph{consequences} of using the given solution to solve a
  problem, both positive and negative.
\end{enumerate}

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}.

\subsection{\label{appendixSection:singleton}Singleton}
The Singleton pattern ensures that only one instance of a class is
created. All objects that use an instance of that class use the same
instance.

\subsection{\label{appendixSection:factoryMethod}Factory Method}
The Factory Method pattern is a creational pattern which deals with
the problem of creating objects without specifying the exact class
of object that will be created. Factory Method solves this problem
by defining a separate method for creating the objects, which
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
this way, you can change the operation being performed on a
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:analysisFramework}Analysis Framework}

\section{\label{appendixSection:concepts}Concepts}

OOPSE manipulates both traditional atoms as well as some objects
that {\it behave like atoms}.  These objects can be rigid
collections of atoms or atoms which have orientational degrees of
freedom.  Here is a diagram of the class heirarchy:

%\begin{figure}
%\centering
%\includegraphics[width=3in]{heirarchy.eps}
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The
%selection syntax allows the user to select any of the objects that
%are descended from a StuntDouble.} \label{oopseFig:heirarchy}
%\end{figure}

\begin{itemize}
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
integrators and minimizers.
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation.
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom.
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
DirectionalAtom}s which behaves as a single unit.
\end{itemize}

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
inside the brackets depend on the specifics of the simulation). The
names of rigid bodies are generated automatically. For example, the
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.

\section{\label{appendixSection:syntax}Syntax of the Select Command}

The most general form of the select command is: {\tt select {\it
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.

\subsection{\label{appendixSection:logical}Logical expressions}

The logical operators allow complex queries to be constructed out of
simpler ones using the standard boolean connectives {\bf and}, {\bf
or}, {\bf not}. Parentheses can be used to alter the precedence of
the operators.

\begin{center}
\begin{tabular}{|ll|}
\hline
{\bf logical operator} & {\bf equivalent operator}  \\
\hline
and & ``\&'', ``\&\&'' \\
or & ``$|$'', ``$||$'', ``,'' \\
not & ``!''  \\
\hline
\end{tabular}
\end{center}

\subsection{\label{appendixSection:name}Name expressions}

\begin{center}
\begin{tabular}{|llp{2in}|}
\hline {\bf type of expression} & {\bf examples} & {\bf translation
of
examples} \\
\hline expression without ``.'' & select DMPC & select all
StuntDoubles
belonging to all DMPC molecules \\
 & select C* & select all atoms which have atom types beginning with C
\\
 & select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but
only select the rigid bodies, and not the atoms belonging to them). \\
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the
O\_TIP3P
atoms belonging to TIP3P molecules \\
 & select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to
the first
RigidBody in each DMPC molecule \\
 & select DMPC.20 & select the twentieth StuntDouble in each DMPC
molecule \\
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* &
select all atoms
belonging to all rigid bodies within all DMPC molecules \\
\hline
\end{tabular}
\end{center}

\subsection{\label{appendixSection:index}Index expressions}

\begin{center}
\begin{tabular}{|lp{4in}|}
\hline
{\bf examples} & {\bf translation of examples} \\
\hline
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\
select 20 to 30 & select all of the StuntDoubles belonging to
molecules which have global indices between 20 (inclusive) and 30
(exclusive) \\
\hline
\end{tabular}
\end{center}

\subsection{\label{appendixSection:predefined}Predefined sets}

\begin{center}
\begin{tabular}{|ll|}
\hline
{\bf keyword} & {\bf description} \\
\hline
all & select all StuntDoubles \\
none & select none of the StuntDoubles \\
\hline
\end{tabular}
\end{center}

\subsection{\label{appendixSection:userdefined}User-defined expressions}

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}}

Once defined, the user can specify such terms in boolean expressions

{\tt define SSDWATER SSD or SSD1 or SSDRF}

{\tt select SSDWATER}

\subsection{\label{appendixSection:comparison}Comparison expressions}

StuntDoubles can be selected by using comparision operators on their
properties. The general form for the comparison command is: a
property name, followed by a comparision operator and then a number.

\begin{center}
\begin{tabular}{|l|l|}
\hline
{\bf property} & mass, charge \\
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'',
``$<=$'', ``$!=$'' \\
\hline
\end{tabular}
\end{center}

For example, the phrase {\tt select mass > 16.0 and charge < -2}
would select StuntDoubles which have mass greater than 16.0 and
charges less than -2.

\subsection{\label{appendixSection:within}Within expressions}

The ``within'' keyword allows the user to select all StuntDoubles
within the specified distance (in Angstroms) from a selection,
including the selected atom itself. The general form for within
selection is: {\tt select within(distance, expression)}

For example, the phrase {\tt select within(2.5, PO4 or NC4)} would
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4
atoms.

\section{\label{appendixSection:tools}Tools which use the selection command}

\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:


\begin{longtable}[c]{|EFG|}
\caption{Dump2XYZ Command-line Options}
\\ \hline
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
\endhead
\hline
\endfoot
  -h & {\tt -{}-help} &                        Print help and exit \\
  -V & {\tt -{}-version} &                     Print version and exit \\
  -i & {\tt -{}-input=filename}  &             input dump file \\
  -o & {\tt -{}-output=filename} &             output file name \\
  -n & {\tt -{}-frame=INT}   &                 print every n frame  (default=`1') \\
  -w & {\tt -{}-water}       &                 skip the the waters  (default=off) \\
  -m & {\tt -{}-periodicBox} &                 map to the periodic box  (default=off)\\
  -z & {\tt -{}-zconstraint}  &                replace the atom types of zconstraint molecules  (default=off) \\
  -r & {\tt -{}-rigidbody}  &                  add a pseudo COM atom to rigidbody  (default=off) \\
  -t & {\tt -{}-watertype} &                   replace the atom type of water model (default=on) \\
  -b & {\tt -{}-basetype}  &                   using base atom type  (default=off) \\
     & {\tt -{}-repeatX=INT}  &                 The number of images to repeat in the x direction  (default=`0') \\
     & {\tt -{}-repeatY=INT} &                 The number of images to repeat in the y direction  (default=`0') \\
     &  {\tt -{}-repeatZ=INT}  &                The number of images to repeat in the z direction  (default=`0') \\
  -s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be
converted. \\
     & {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\
     & {\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:StaticProps}StaticProps}

{\tt StaticProps} can compute properties which are averaged over
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.

There are five seperate radial distribution functions availiable in
OOPSE. Since every radial distrbution function invlove the
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt
-{}-sele2} must be specified to tell StaticProps which bodies to
include in the calculation.

\begin{description}
\item[{\tt -{}-gofr}] Computes the pair distribution function,
\begin{equation*}
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A}
\sum_{j \in B} \delta(r - r_{ij}) \rangle
\end{equation*}
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution
function. The angle is defined by the intermolecular vector
$\vec{r}$ and $z$-axis of DirectionalAtom A,
\begin{equation*}
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos
\theta_{ij} - \cos \theta)\rangle
\end{equation*}
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution
function. The angle is defined by the $z$-axes of the two
DirectionalAtoms A and B.
\begin{equation*}
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos
\omega_{ij} - \cos \omega)\rangle
\end{equation*}
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular
space $\theta, \omega$ defined by the two angles mentioned above.
\begin{equation*}
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A}
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos
\omega)\rangle
\end{equation*}
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type
B in the body frame of particle A. Therefore, {\tt -{}-originsele}
and {\tt -{}-refsele} must be given to define A's internal
coordinate set as the reference frame for the calculation.
\end{description}

The vectors (and angles) associated with these angular pair
distribution functions are most easily seen in the figure below:

\begin{figure}
\centering
\includegraphics[width=3in]{definition.eps}
\caption[Definitions of the angles between directional objects]{ \\
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}

The options available for {\tt StaticProps} are as follows:
\begin{longtable}[c]{|EFG|}
\caption{StaticProps Command-line Options}
\\ \hline
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
\endhead
\hline
\endfoot
  -h& {\tt -{}-help}                    &  Print help and exit \\
  -V& {\tt -{}-version}                 &  Print version and exit \\
  -i& {\tt -{}-input=filename}          &  input dump file \\
  -o& {\tt -{}-output=filename}         &  output file name \\
  -n& {\tt -{}-step=INT}                &  process every n frame  (default=`1') \\
  -r& {\tt -{}-nrbins=INT}              &  number of bins for distance  (default=`100') \\
  -a& {\tt -{}-nanglebins=INT}          &  number of bins for cos(angle)  (default= `50') \\
  -l& {\tt -{}-length=DOUBLE}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
    & {\tt -{}-sele1=selection script}   & select the first StuntDouble set \\
    & {\tt -{}-sele2=selection script}   & select the second StuntDouble set \\
    & {\tt -{}-sele3=selection script}   & select the third StuntDouble set \\
    & {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\
    & {\tt -{}-molname=STRING}           & molecule name \\
    & {\tt -{}-begin=INT}                & begin internal index \\
    & {\tt -{}-end=INT}                  & end internal index \\
\hline
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\
\hline
    &  {\tt -{}-gofr}                    &  $g(r)$ \\
    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
\end{longtable}

\subsection{\label{appendixSection:DynamicProps}DynamicProps}

{\tt DynamicProps} computes time correlation functions from the
configurations stored in a dump file.  Typical examples of time
correlation functions are the mean square displacement and the
velocity autocorrelation functions.   Once again, the selection
syntax can be used to specify the StuntDoubles that will be used for
the calculation.  A general time correlation function can be thought
of as:
\begin{equation}
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle
\end{equation}
where $\vec{u}_A(t)$ is a vector property associated with an atom of
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different
vector property associated with an atom of type $B$ at a different
time $t^{\prime}$.  In most autocorrelation functions, the vector
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and
$B$) are identical, and the three calculations built in to {\tt
DynamicProps} make these assumptions.  It is possible, however, to
make simple modifications to the {\tt DynamicProps} code to allow
the use of {\it cross} time correlation functions (i.e. with
different vectors).  The ability to use two selection scripts to
select different types of atoms is already present in the code.

The options available for DynamicProps are as follows:
\begin{longtable}[c]{|EFG|}
\caption{DynamicProps Command-line Options}
\\ \hline
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
\endhead
\hline
\endfoot
  -h& {\tt -{}-help}                   & Print help and exit \\
  -V& {\tt -{}-version}                & Print version and exit \\
  -i& {\tt -{}-input=filename}         & input dump file \\
  -o& {\tt -{}-output=filename}        & output file name \\
    & {\tt -{}-sele1=selection script} & select first StuntDouble set \\
    & {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\
\hline
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\
\hline
  -r& {\tt -{}-rcorr}                  & compute mean square displacement \\
  -v& {\tt -{}-vcorr}                  & compute velocity correlation function \\
  -d& {\tt -{}-dcorr}                  & compute dipole correlation function
\end{longtable}

\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics}
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