new hyper examples

potential.  In practice a {Dcut} value of ~10 Angstroms seems to work

well for many solid-state systems.

NOTE: You must also insure that ghost atom communication is performed

for a distance of at least {Dcut} + {cutevent} where {cutevent} = the

distance one or more atoms move (between quenched states) to be

considered an "event".  It is an argument to the "compute

event/displace" command used to detect events.  By default the ghost

communication distance is set by the pair_style cutoff, which will

typically be < {Dcut}.  The "comm_modify cutoff"_comm_modify.html

command can be used to set the ghost cutoff explicitly, e.g.

comm_modify cutoff 12.0 :pre

This fix does not know the {cutevent} parameter, but uses half the

bond length as an estimate to warn if the ghost cutoff is not long

enough.

As described above the {alpha} argument is a pre-factor in the

boostostat update equation for each bond's Cij prefactor.  {Alpha} is

specified in time units, similar to other thermostat or barostat

fix-ID = ID of a fix that applies a global or local bias potential, can be NULL :l

compute-ID = ID of a compute that identifies when an event has occurred :l

zero or more keyword/value pairs may be appended :l

keyword = {min} or {time} or {dump} or {rebond} :l

keyword = {min} or {dump} or {rebond} :l

  {min} values = etol ftol maxiter maxeval

    etol = stopping tolerance for energy, used in quenching

    ftol = stopping tolerance for force, used in quenching

    maxiter = max iterations of minimize, used in quenching

    maxeval = max number of force/energy evaluations, used in quenching

  {time} value = {steps} or {clock}

    {steps} = simulation runs for N timesteps (default)

    {clock} = simulation runs until hyper time exceeds N timesteps

  {dump} value = dump-ID

    dump-ID = ID of dump to trigger whenever an event takes place

  {rebond} value = Nrebond

the system and runs dynamics on each independently with a normal

unbiased potential until an event occurs in one of the replicas.  The

time between events is reduced by a factor of Nr replicas.  For both

methods, per wall-clock second, more physical time elapses and more

events occur.  See the "prd"_prd.html doc page for more info about

PRD.

methods, per CPU second, more physical time elapses and more events

occur.  See the "prd"_prd.html doc page for more info about PRD.

An HD run has several stages, which are repeated each time an "event"

occurs, as explained below.  The logic for an HD run is as follows:

parameters for the quench.  Their meaning is the same

as for the "minimize"_minimize.html command

The {time} keyword determines how the {N} timesteps argument is

interpreted.  If {time} is set to {steps}, then hyperdynamics is run

for {N} timesteps.  If the time acceleration provided by the bias

potential is 10x, then that is the same as running a normal (unbiased)

MD simulation for 10N steps.  If {time} is set to {clock}, then

hyperdynamics would run for N/10 steps, since that would correspond to

an elapsed real time of N*dt.

The {dump} keyword can be used to trigger a specific dump command with

the specified {dump-ID} to output a snapshot each time an event is

detected.  It can be specified multiple times with different {dump-ID}

reduced by a factor of Nr replicas.  HD uses a single replica of the

system and accelerates time by biasing the interaction potential in a

manner such that each timestep is effectively longer.  For both

methods, per wall-clock second, more physical time elapses and more

events occur.  See the "hyper"_hyper.html doc page for more info about

HD.

methods, per CPU second, more physical time elapses and more events

occur.  See the "hyper"_hyper.html doc page for more info about HD.

In PRD, each replica runs on a partition of one or more processors.

Processor partitions are defined at run-time using the "-partition