MC-SPEC:  Specify how to do the Markov chain simulation.

MC-spec writes records to a log file that specify the operations
making up a single Markov chain iteration, and that also specify how
dynamic trajectories are to be computed.  When invoked with just a log
file as argument, it displays the specifications stored at the given
index, or the last specifications stored if no index is given.

MC-spec is often invoked several times during a single simulation run.
The last specification in the log file is used for further iterations.


    mc-spec log-file { operation-spec } [ / trajectory-spec ]

    mc-spec log-file [ index ]

The log file must already exist.  For the first form, specifications
are appended to the log file with index equal that of the last record
in the file, or 0 if the log file has no non-negative records.

For the second form, with no index specified, the last specifications
stored in the log file are displayed.  If an index is specified in the
second form, the specifications in the record with the given index are

An operation-spec may be one of the following:

    repeat times

        Repeat the following operations the specified number of times.
        The repeated group of operations is terminated by 'end', or
        the end of the list.


        Terminates a group of operations.

    heatbath [ decay ]

        Do a heatbath update of the momentum variables.


        Negate the momentum variables.

    metropolis [ stepsize-adjust[:stepsize-alpha] ]  

        Do a simple Metropolis update, to all components at once.

    met-1 [ stepsize-adjust[:stepsize-alpha] [ first[:last] ] ]

        Do single-component Metropolis updates, for the range of components 
        given.  The default if no components are given is all components. 
        The default for last if first alone is given is last=first.

    dynamic steps [ stepsize-adjust[:stepsize-alpha] ] 

        Follow a dynamical trajectory for the given number of steps, 
        always accepting the result (hence does not leave distribution 
        exactly invariant).

    permuted-dynamic steps [ stepsize-adjust[:stepsize-alpha] ] 

        Like 'dynamic', but the order of approximations is randomly

    hybrid steps[:window[:jump]] 
         [ stepsize-adjust[:stepsize-alpha] ] 

        Use the results of following a dynamical trajectory as a 
        candidate state for a Metropolis update.  Only steps at multiples 
        of 'jump' are looked at; 'steps' must be a multiple of 'jump'.  
        The momentum is negated if the proposal is accepted to make the 
        step reversible.

    tempered-hybrid temper-factor steps[:window[:jump]] 
                  [ stepsize-adjust[:stepsize-alpha] ] 

        Like hybrid, but the trajectory is "tempered" by multiplying
        the momenta by temper-factor in the first half of the portion
        of the trajectory outside any windows, and by 1/temper-factor
        in the second half.

    slice-1 [ stepsize-adjust[:stepsize-alpha] [ max-steps [ first[:last] ] ] ]

        Do single-component slice sampling, for the range of components 
        given.  The max-steps argument gives the maximum number of 
        intervals to create when stepping out, with zero indicating no
        limit (this is the default).  The default for the range of components
        (first:last) is all components.  The default for last if first alone 
        is given is last=first.  Components are numbered starting with zero.

    slice-over [ refinements [ refresh-prob [ stepsize-adjust[:stepsize-alpha] 
                 [ max-steps [ first[:last] ] ] ] ] ]

        Do overrelaxed slice sampling, for the range of components given.
        The endpoints are computed using the given number of refinements
        (default zero).  The refresh probability is the probability of doing 
        an ordinary slice sampling update rather than an overrelaxed one; 
        it defaults to zero.  The default maximum number of steps is zero
        (indicating no limit).  The default range of components if no range is 
        given is all components. The default for last if first alone is given 
        is last=first.


        Do a metropolis update of the simulated tempering inverse
        temperature, with a proposal of changing the temperature 
        index in accord with the current tempering direction.  The 
        direction is negated if the proposal is accepted to make the 
        step reversible.


        Randomize the tempering direction.


        Negate the tempering direction.


        Prints the current values of those quantities specified in the
        "xxx-mc" command on standard output, preceded by an index that
        is reset to zero every iteration.


        Perform a tempered transition, with components given by the
        following operations (terminated by 'end').  The components
        are done in forward order for the first half of the tempered
        transition, in reverse order for the second.  For this to  
        work, the components must be reversible in themselves.  

    (any other that starts with a letter)

        Invoke the application-specific update procedure, passing the
        name of the operation.

Certain of these operations are normally used in standard combinations, 
in particular the following:

 heatbath hybrid <steps>                 Standard hybrid Monte Carlo
 heatbath <decay> hybrid <steps> negate  Persistent Hybrid Monte Carlo 
 rand-dir sim-temp                       Standard simulated tempering
 sim-temp neg-dir                        Persistent Simulated tempering 

All individual operations are reversible, except for 'dynamic',
'permuted-dynamic', and perhaps the application-specific operations.
However, note that in general sequential combinations of reversible
operations are not reversible.

Defaults are decay of zero, stepsize-adjust of one, stepsize-alpha of
infinity, window of one, and jump of one.  A minus sign before a
stepsize-adjust value results in the adjustment being applied to
uniform stepsizes of one; otherwise, the adjustment is applied to the
application-specific stepsizes (which may be non-uniform).  A minus
sign in front of stepsize alpha means that instead of the usual Gamma
distribution for stepsizes, a distribution over 'alpha' orders of
magnitude, uniform in the log domain, centred at the value found using
stepsize-adjust, is used.

Currently, the trajectory specification can have only the following

    leapfrog [ halfp | halfq ] [ N-approx ]

        Use the leapfrog method, repeated N-approx times using a randomly
        selected ordering of that number of energy approximations (whose
        average must be the true value).  The default for N-approx is one.
        The "halfp" or "halfq" option specifies whether the half-steps
        at the beginning and end of the trajectory are for p (momentum)
        or q (position).  The default is "halfp".

The default if no specification is given is "leapfrog halfp 1".

The list of operations is stored in a record of type 'o'; the
trajectory specification in a record of type 't'.

            Copyright (c) 1995 by Radford M. Neal