41 lines
1.3 KiB
Plaintext
41 lines
1.3 KiB
Plaintext
Run an example constrained sample for PAFI calculation
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Author:
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Thomas Swinburne, CNRS / CINaM, Marseille
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swinburne@cinam.univ-mrs.fr
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tomswinburne.github.io
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PAFI performs constrained force averages on hyperplanes to a reference pathway in order to compute unbiased free energy barriers
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Paper:
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T. D. Swinburne and M. C. Marinica
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Unsupervised calculation of free energy barriers in large crystalline systems
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Physical Review Letters 276, 1 2018
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Also see https://github.com/tomswinburne/pafi/ for the PAFI code which distributes
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multiple LAMMPS workers in parallel to compute and collate fix pafi averages,
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allowing the calculation of free energy barriers and minimum free energy paths.
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To compile:
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make yes-misc # for PAFI
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make yes-manybody # for EAM potential
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make machine # for binary (machine= e.g. mpi)
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To run the example from this folder:
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```
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mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi
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```
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This example executes a hyperplane constrained overdamped Langevin simulation
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whilst recording the projected free energy gradient, then minimizes in-plane,
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then removes the hyperplane constraint and minimizes the whole system.
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If the temperature is too high the system will leave the local minima of
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the constrained system; PAFI checks for this also.
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To generate your own path, please see the LAMMPS documentation for more details
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