| 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 |
|
|
| 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 |
| 608 |
|
\label{oopseFig:dynamicPropsProcess} |
| 609 |
|
\end{figure} |
| 610 |
|
|
| 645 |
– |
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} |
| 650 |
+ |
\label{appendix:dynamicPropsOptions} |
| 651 |
|
\\ \hline |
| 652 |
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 653 |
|
\endhead |
