XXX-MC:  Run Markov chain simulation.

There is a version of this program for each 'mc' application (eg,
net-mc).  The version of this program for a given application runs a
Markov chain simulation, using the application-specific routines for
that application, as specified in a previous call of 'mc-spec'.

Usage:

    xxx-mc [ -c coupled-log-file ] log-file ["@"]iteration [ save-mod ] 
           [ quantities | "tt[12]" ] [ / decay [ temperature ] ]
 
Here 'xxx' is a prefix identifying the particular incarnation of this
program.

This program performs a Markov chain Monte Carlo simulation starting
with the last iteration saved in log-file and continuing up to the
indicated iteration (or if the iteration is immediately preceded by
"@", until a total of iteration minutes of cpu-time have been used,
for all iterations).  The log file must contain specifications for how
to run the simulation, as created by mc-spec; the last such in the log
file is used.  Results of the simulation are appended to the log file
for iterations that are divisible by save-mod, which defaults to one
(every iteration saved).

The 'quantities' parameter specifies what is to be printed on standard
output when 'plot' specifications are encountered.  The default is
nothing.  If "tt1" or "tt2" are specified, the progress of tempered
trajectories and tempered transitions is plotted, the details
depending on the digit (you'll have to look at the program code to
learn more).

If a decay parameter is specified, it overrides the decay parameter in
the specification of any "heatbath" operations.  The temperature
parameter controls the level of noise added in heatbath operations and
the acceptance test for metropolis and hybrid updates, and may also
affect application specific updates.  It defaults to one.  (Note that
this temperature is not the same as any temperature involved in
tempering operations.)

The -c option is used when the simulation is "coupled" to a previously
performed simulation, whose results are stored in coupled-log-file.
It causes the simulation to be terminated if and when the iteration
written to log-file exactly matches the corresponding iteration in
coupled-log-file, ignoring the records of type "i" that record the
iteration statistics.  When this situation is detected, the remaining
iterations to be performed are simply copied from coupled-log-file to
log-file.  The "k" quantity (normally cumulative compute time) will be
set to -1e-4 for such copied iterations.  Coupling is not allowed if
the number of iterations to do is specified by a time limit rather
than a maximum iteration number.

            Copyright (c) 1995-2004 by Radford M. Neal