| 261 |
|
\endfoot |
| 262 |
|
-h & {\tt -{}-help} & Print help and exit \\ |
| 263 |
|
-V & {\tt -{}-version} & Print version and exit \\ |
| 264 |
< |
-i & {\tt -{}-input=filename} & input dump file \\ |
| 265 |
< |
-o & {\tt -{}-output=filename} & output file name \\ |
| 266 |
< |
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
| 264 |
> |
-i & {\tt -{}-input} & input dump file \\ |
| 265 |
> |
-o & {\tt -{}-output} & output file name \\ |
| 266 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
| 267 |
|
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
| 268 |
|
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
| 269 |
|
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
| 270 |
|
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
| 271 |
|
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
| 272 |
|
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
| 273 |
< |
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
| 274 |
< |
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
| 275 |
< |
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
| 276 |
< |
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 273 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
| 274 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
| 275 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
| 276 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 277 |
|
converted. \\ |
| 278 |
|
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
| 279 |
|
& {\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}. |
| 355 |
|
\endfoot |
| 356 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 357 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 358 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 359 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 360 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
| 361 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
| 362 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
| 363 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 364 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
| 365 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
| 366 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
| 367 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 368 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
| 369 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
| 370 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
| 358 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 359 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 360 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
| 361 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
| 362 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
| 363 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 364 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
| 365 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
| 366 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
| 367 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 368 |
> |
& {\tt -{}-molname} & molecule name \\ |
| 369 |
> |
& {\tt -{}-begin} & begin internal index \\ |
| 370 |
> |
& {\tt -{}-end} & end internal index \\ |
| 371 |
|
\hline |
| 372 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 373 |
|
\hline |
| 416 |
|
\endfoot |
| 417 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 418 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 419 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 420 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 421 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
| 422 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 419 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 420 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 421 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
| 422 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 423 |
|
\hline |
| 424 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 425 |
|
\hline |
