document flags that were missing in the man page and the help message

doc/lammps.1

@@ -122,6 +122,38 @@ to perform client/server messaging with another application.
 .B LAMMPS
 can act as either a client or server (or both).
 .TP
+\fB\-mdi '<mdi_flags>'\fR
+This flag is only recognized and used when
+.B LAMMPS
+has support for the MolSSI
+Driver Interface (MDI) included as part of the MDI package.  This flag is
+specific to the MDI library and controls how
+.B LAMMPS
+interacts with MDI.  There are usually multiple flags that have to follow it
+and those have to be placed in quotation marks.  For more information about
+how to launch LAMMPS in MDI client/server mode please refer to the
+MDI How-to at  https://docs.lammps.org/Howto_mdi.html
+.TP
+\fB\-c\fR or \fB\-cite <style or filename>\fR
+Select how and where to output a reminder about citing contributions
+to the
+.B LAMMPS
+code that were used during the run. Available keywords
+for styles are "both", "none", "screen", or "log".  Any other keyword
+will be considered a file name to write the detailed citation info to
+instead of logfile or screen.  Default is the "log" style where there
+is a short summary in the screen output and detailed citations
+in BibTeX format in the logfile.  The option "both" selects the detailed
+output for both, "none", the short output for both, and "screen" will
+write the detailed info to the screen and the short version to the log
+file.  If a dedicated citation info file is requested, the screen and
+log file output will be in the short format (same as with "none").
+
+See https://docs.lammps.org/Intro_citing.html for more details on
+how to correctly reference and cite
+.B LAMMPS
+.
+.TP
 \fB\-nc\fR or \fB\-nocite\fR
 Disable writing the "log.cite" file which is normally written to
 list references for specific cite-able features used during a
@@ -218,8 +250,19 @@ and then "omp") and thus requires two arguments. Along with the
 "-package" command-line switch, this is a convenient mechanism for
 invoking styles from accelerator packages and setting their options
 without having to edit an input script.
+.TP
+\fB\-sr\fR or \fB\-skiprun\fR
+Insert the command "timer timeout 0 every 1" at the
+beginning of an input file or after a "clear" command.
+This has the effect that the entire
+.B LAMMPS
+input script is processed without executing actual
+"run" or "minimize" or similar commands (their main loops are skipped).
+This can be helpful and convenient to test input scripts of long running
+calculations for correctness to avoid having them crash after a
+long time due to a typo or syntax error in the middle or at the end.
 
-See https://lammps.sandia.gov/doc/Run_options.html for additional
+See https://docs.lammps.org/Run_options.html for additional
 details and discussions on command-line options.
 
 .SH LAMMPS BASICS

src/lammps.cpp

@@ -1178,6 +1178,7 @@ void _noopt LAMMPS::help()
           "                            : convert restart to dump file (-r2dump)\n"
           "-reorder topology-specs     : processor reordering (-r)\n"
           "-screen none/filename       : where to send screen output (-sc)\n"
+          "-skiprun                    : skip loops in run and minimize (-sr)\n"
           "-suffix gpu/intel/opt/omp   : style suffix to apply (-sf)\n"
           "-var varname value          : set index style variable (-v)\n\n",
           exename);