Run an example constrained sample for PAFI calculation

Author:
Thomas Swinburne, CNRS / CINaM, Marseille
swinburne@cinam.univ-mrs.fr
tomswinburne.github.io


PAFI performs constrained force averages on hyperplanes to a reference pathway in order to compute unbiased free energy barriers


Paper:
T. D. Swinburne and M. C. Marinica
Unsupervised calculation of free energy barriers in large crystalline systems
Physical Review Letters 276, 1 2018


Also see https://github.com/tomswinburne/pafi/ for the PAFI code which distributes
multiple LAMMPS workers in parallel to compute and collate fix pafi averages,
allowing the calculation of free energy barriers and minimum free energy paths.

To compile:

make yes-misc # for PAFI
make yes-manybody # for EAM potential
make machine # for binary (machine= e.g. mpi)

To run the example from this folder:
```
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
