--- trunk/tengDissertation/Appendix.tex	2006/06/07 01:49:15	2807
+++ trunk/tengDissertation/Appendix.tex	2006/06/07 02:02:44	2809
@@ -261,19 +261,19 @@ The options available for Dump2XYZ are as follows:
 \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') \\
+  -i & {\tt -{}-input}  &             input dump file \\
+  -o & {\tt -{}-output} &             output file name \\
+  -n & {\tt -{}-frame}   &                 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
+     & {\tt -{}-repeatX}  &                 The number of images to repeat in the x direction  (default=`0') \\
+     & {\tt -{}-repeatY} &                 The number of images to repeat in the y direction  (default=`0') \\
+     &  {\tt -{}-repeatZ}  &                The number of images to repeat in the z direction  (default=`0') \\
+  -s & {\tt -{}-selection} & 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}.
@@ -355,19 +355,19 @@ The options available for {\tt StaticProps} are as fol
 \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 \\
+  -i& {\tt -{}-input}          &  input dump file \\
+  -o& {\tt -{}-output}         &  output file name \\
+  -n& {\tt -{}-step}                &  process every n frame  (default=`1') \\
+  -r& {\tt -{}-nrbins}              &  number of bins for distance  (default=`100') \\
+  -a& {\tt -{}-nanglebins}          &  number of bins for cos(angle)  (default= `50') \\
+  -l& {\tt -{}-length}           &  maximum length (Defaults to 1/2 smallest length of first frame) \\
+    & {\tt -{}-sele1}   & select the first StuntDouble set \\
+    & {\tt -{}-sele2}   & select the second StuntDouble set \\
+    & {\tt -{}-sele3}   & select the third StuntDouble set \\
+    & {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\
+    & {\tt -{}-molname}           & molecule name \\
+    & {\tt -{}-begin}                & begin internal index \\
+    & {\tt -{}-end}                  & end internal index \\
 \hline
 \multicolumn{3}{|l|}{One option from the following group of options is required:} \\
 \hline
@@ -416,10 +416,10 @@ The options available for DynamicProps are as follows:
 \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) \\
+  -i& {\tt -{}-input}         & input dump file \\
+  -o& {\tt -{}-output}        & output file name \\
+    & {\tt -{}-sele1} & select first StuntDouble set \\
+    & {\tt -{}-sele2} & 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