minor changes to example

mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi

```

This example executes a hyperplane constrained overdamped Langevin simulation

whilst recording the projected free energy gradient, then minimizes in-plane, 

then removes the hyperplane constraint and minimizes the whole system.

If the temperature is too high the system will leave the local minima of

the constrained system; PAFI checks for this also.

To generate your own path, please see the LAMMPS documentation for more details

run 1000

minimize 0 0 1000 1000

variable s_pe equal ${pe}

variable s_apf equal ${apf}

variable s_adn equal ${adn}

variable s_maxjump equal ${maxjump}

unfix hp

unfix pa

unfix af

minimize 0 0 1000 1000

print """

---------- PAFI RESULTS --------

During run:

  Average Distance From Hyperplane = ${adn} A,

  Average Force Projection Along MFEP = ${apf} eV/A

  Average Distance From Hyperplane = ${s_adn}A (Should be very small, around 1e-5A),

  Average Force Projection Along MFEP = ${s_apf} eV/A

"""

print """

In-plane minimization post-run:

energy = ${pe} eV

energy = ${s_pe} eV

"""

if "${maxjump} > 0.1" then &

"print 'Max Atomic Displacement = ${maxjump}A > 0.1A'" &

if "${s_maxjump} > 0.1" then &

"print 'Max Atomic Displacement = ${s_maxjump}A > 0.1A'" &

"print ' => Possible shallow in-plane metastability: Reduce time in basin and/or decrease tdamp'" &

else &

"print 'Max Atomic Displacement = ${maxjump}A < 0.1A => No in-plane jumps'"

"print 'Max Atomic Displacement = ${s_maxjump}A < 0.1A => No in-plane jumps'"

print """

----- END PAFI ----

"""

Full minimization after removal of PAFI fixes:

energy = ${pe} eV

#  disable fix and minimize full system

# unfix hp

# unfix pa

# unfix af

# minimize 0 0 1000 1000

# print """

#   Full minimization post-run:

#   energy = ${pe} eV

# """

----- END PAFI ----

"""