Run an example constrained sample for USER-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-user-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