ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/tengDissertation/Appendix.tex
(Generate patch)

Comparing trunk/tengDissertation/Appendix.tex (file contents):
Revision 2883 by tim, Sun Jun 25 17:39:42 2006 UTC vs.
Revision 2906 by tim, Wed Jun 28 19:25:13 2006 UTC

# Line 552 | Line 552 | distribution functions are most easily seen in
552  
553   The vectors (and angles) associated with these angular pair
554   distribution functions are most easily seen in
555 < Fig.~\ref{oopseFig:gofr}.
556 <
557 < The options available for {\tt StaticProps} are as follows:
558 < \begin{longtable}[c]{|EFG|}
559 < \caption{StaticProps Command-line Options}
560 < \\ \hline
561 < {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
562 < \endhead
563 < \hline
564 < \endfoot
565 <  -h& {\tt -{}-help}                    &  Print help and exit \\
566 <  -V& {\tt -{}-version}                 &  Print version and exit \\
567 <  -i& {\tt -{}-input}          &  input dump file \\
568 <  -o& {\tt -{}-output}         &  output file name \\
569 <  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
570 <  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
571 <  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
572 <  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
573 <    & {\tt -{}-sele1}   & select the first StuntDouble set \\
574 <    & {\tt -{}-sele2}   & select the second StuntDouble set \\
575 <    & {\tt -{}-sele3}   & select the third StuntDouble set \\
576 <    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
577 <    & {\tt -{}-molname}           & molecule name \\
578 <    & {\tt -{}-begin}                & begin internal index \\
579 <    & {\tt -{}-end}                  & end internal index \\
580 < \hline
581 < \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
582 < \hline
583 <    &  {\tt -{}-gofr}                    &  $g(r)$ \\
584 <    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
585 <    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
586 <    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
587 <    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
588 <    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
589 <    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
590 <    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
591 <    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
592 < \end{longtable}
555 > Fig.~\ref{oopseFig:gofr}. The options available for {\tt
556 > StaticProps} are showed in Table.~\ref{appendix:staticPropsOptions}.
557  
558   \subsection{\label{appendixSection:DynamicProps}DynamicProps}
559  
# Line 629 | Line 593 | This process is illustrated in
593   trajectory. Once the end is reached, the first block is freed then
594   incremented, until all frame pairs have been correlated in time.
595   This process is illustrated in
596 < Fig.~\ref{oopseFig:dynamicPropsProcess}.
596 > Fig.~\ref{oopseFig:dynamicPropsProcess} and the options available
597 > for DynamicProps are showed in
598 > Table.~\ref{appendix:dynamicPropsOptions}
599  
600   \begin{figure}
601   \centering
# Line 642 | Line 608 | at a time and the cross correlations between blocks ar
608   \label{oopseFig:dynamicPropsProcess}
609   \end{figure}
610  
611 < The options available for DynamicProps are as follows:
611 > \begin{longtable}[c]{|EFG|}
612 > \caption{STATICPROPS COMMAND-LINE OPTIONS}
613 > \label{appendix:staticPropsOptions}
614 > \\ \hline
615 > {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
616 > \endhead
617 > \hline
618 > \endfoot
619 >  -h& {\tt -{}-help}                    &  Print help and exit \\
620 >  -V& {\tt -{}-version}                 &  Print version and exit \\
621 >  -i& {\tt -{}-input}          &  input dump file \\
622 >  -o& {\tt -{}-output}         &  output file name \\
623 >  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
624 >  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
625 >  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
626 >  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
627 >    & {\tt -{}-sele1}   & select the first StuntDouble set \\
628 >    & {\tt -{}-sele2}   & select the second StuntDouble set \\
629 >    & {\tt -{}-sele3}   & select the third StuntDouble set \\
630 >    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
631 >    & {\tt -{}-molname}           & molecule name \\
632 >    & {\tt -{}-begin}                & begin internal index \\
633 >    & {\tt -{}-end}                  & end internal index \\
634 > \hline
635 > \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
636 > \hline
637 >    &  {\tt -{}-gofr}                    &  $g(r)$ \\
638 >    &  {\tt -{}-r\_theta}                 &  $g(r, \cos(\theta))$ \\
639 >    &  {\tt -{}-r\_omega}                 &  $g(r, \cos(\omega))$ \\
640 >    &  {\tt -{}-theta\_omega}             &  $g(\cos(\theta), \cos(\omega))$ \\
641 >    &  {\tt -{}-gxyz}                    &  $g(x, y, z)$ \\
642 >    &  {\tt -{}-p2}                      &  $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\
643 >    &  {\tt -{}-scd}                     &  $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\
644 >    &  {\tt -{}-density}                 &  density plot ({\tt -{}-sele1} must be specified) \\
645 >    &  {\tt -{}-slab\_density}           &  slab density ({\tt -{}-sele1} must be specified)
646 > \end{longtable}
647 >
648   \begin{longtable}[c]{|EFG|}
649 < \caption{DynamicProps Command-line Options}
649 > \caption{DYNAMICPROPS COMMAND-LINE OPTIONS}
650 > \label{appendix:dynamicPropsOptions}
651   \\ \hline
652   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
653   \endhead
# Line 673 | Line 676 | as follows:
676   and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are
677   as follows:
678  
676 –
679   \begin{longtable}[c]{|EFG|}
680 < \caption{Dump2XYZ Command-line Options}
680 > \caption{DUMP2XYZ COMMAND-LINE OPTIONS}
681   \\ \hline
682   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
683   \endhead
# Line 709 | Line 711 | options available for Hydro are as follows:
711   the beads which are used to approximate the arbitrary shapes. The
712   options available for Hydro are as follows:
713   \begin{longtable}[c]{|EFG|}
714 < \caption{Hydrodynamics Command-line Options}
714 > \caption{HYDRODYNAMICS COMMAND-LINE OPTIONS}
715   \\ \hline
716   {\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline
717   \endhead

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines