Add help text, add manual entry.

doc/cpptraj.lyx

@@ -419,7 +419,7 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \end_layout
 
 \begin_layout LyX-Code
-        [--rng {marsaglia|stdlib|mt|pcg32|xo128}]
+        [--rng {marsaglia|stdlib|mt|pcg32|xo128}] [--charge <mask>]
 \end_layout
 
 \begin_deeper
@@ -580,7 +580,11 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \end_layout
 
 \begin_layout Description
--mr <mask> : Print selected residue numbers to STDOUT.
+-mr
+\begin_inset space ~
+\end_inset
+
+<mask> : Print selected residue numbers to STDOUT.
  Selected residues are written out as 'Selected= 1 2 3 ...'
 \end_layout
 
@@ -593,11 +597,27 @@ cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>]
 \end_layout
 
 \begin_layout Description
-–resmask <mask> : Print detailed residue selection to STDOUT.
+–resmask
+\begin_inset space ~
+\end_inset
+
+<mask> Print detailed residue selection to STDOUT.
 \end_layout
 
 \begin_layout Description
---rng <type> : Change default random number generator.
+--rng
+\begin_inset space ~
+\end_inset
+
+<type> Change default random number generator.
+\end_layout
+
+\begin_layout Description
+--charge
+\begin_inset space ~
+\end_inset
+
+<mask> Print total charge (in e-) of atoms selected by <mask> to STDOUT.
 \end_layout
 
 \end_deeper

src/Cpptraj.cpp

@@ -73,7 +73,7 @@ void Cpptraj::Usage() {
             "               [-h | --help] [-V | --version] [--defines] [-debug <#>]\n"
             "               [--interactive] [--log <logfile>] [-tl]\n"
             "               [-ms <mask>] [-mr <mask>] [--mask <mask>] [--resmask <mask>]\n"
-            "               [--rng %s]\n"
+            "               [--rng %s] [--charge <mask>]\n"
             "\t-p <Top0>        : * Load <Top0> as a topology file.\n"
             "\t-i <Input0>      : * Read input from file <Input0>.\n"
             "\t-y <trajin>      : * Read from trajectory file <trajin>; same as input 'trajin <trajin>'.\n"
@@ -96,8 +96,8 @@ void Cpptraj::Usage() {
             "\t-mr <mask>       : Print selected residue numbers to STDOUT.\n"
             "\t--mask <mask>    : Print detailed atom selection to STDOUT.\n"
             "\t--resmask <mask> : Print detailed residue selection to STDOUT.\n"
-            "\t--charge <mask>  : Print total charge in e- of atoms selected by <mask>.\n"
             "\t--rng <type>     : Change default random number generator.\n"
+            "\t--charge <mask>  : Print total charge in e- of atoms selected by <mask>.\n"
             "      * Denotes flag may be specified multiple times.\n"
             "\n", CpptrajState::RngKeywords());
 }