diff --git a/doc/src/fix_pafi.rst b/doc/src/fix_pafi.rst index 7cb0de0cc0..8f1d02ac49 100644 --- a/doc/src/fix_pafi.rst +++ b/doc/src/fix_pafi.rst @@ -40,14 +40,16 @@ Description Perform Brownian or Langevin integration whilst constraining the system to lie in some hyperplane, which is expected to be the tangent plane to some reference -pathway. The instantaneous value of a modified force projection is also -calculated, whose time integral can be shown to be equal to a free energy gradient -along the minimum free energy path local to the reference pathway. +pathway in a solid state system. The instantaneous value of a modified force +projection is also calculated, whose time integral can be shown to be equal to +the true free energy gradient along the minimum free energy path local to the reference pathway. A detailed discussion of the projection technique can be found in :ref:`(Swinburne) `. This fix can be used with LAMMPS as demonstrated in examples/USER/misc/pafi, -though it is primarily intended to be coupled with the PAFI C++ code, which is developed -at `https://github.com/tomswinburne/pafi `_. +though it is primarily intended to be coupled with the PAFI C++ code, developed +at `https://github.com/tomswinburne/pafi `_, +which distributes multiple LAMMPS workers in parallel to compute and collate +hyperplane-constrained averages, allowing the calculation of free energy barriers and pathways. A :doc:`compute property/atom ` must be provided with 9 fields per atom coordinate, which in order are the x,y,z coordinates of a configuration on the reference path, @@ -94,4 +96,4 @@ The option defaults are com = *yes*, overdamped = *no* .. _Swinburne: -**(Swinburne)** Swinburne and Marinica, Physical Review Letters, 276, 1 (2018). +**(Swinburne)** Swinburne and Marinica, Physical Review Letters, 120, 1 (2018) diff --git a/examples/USER/misc/pafi/README b/examples/USER/misc/pafi/README index 785a4abe97..f1a2b409f4 100644 --- a/examples/USER/misc/pafi/README +++ b/examples/USER/misc/pafi/README @@ -15,7 +15,7 @@ Unsupervised calculation of free energy barriers in large crystalline systems Physical Review Letters 276, 1 2018 -Also see https://github.com/tomswinburne/pafi/ for PAFI++ code which uses the USER-PAFI package when loading LAMMPS as a C++ library +Also see https://github.com/tomswinburne/pafi/ for PAFI code which uses the USER-PAFI package when loading LAMMPS as a C++ library To compile: @@ -28,4 +28,4 @@ To run the example from this folder: mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi ``` -To generate your own path, please see the PAFI++ documentation for more details +To generate your own path, please see the LAMMPS documentation for more details diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 079659fb7c..e901644fea 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -48,9 +48,9 @@ static const char cite_fix_pafi_package[] = "title={Unsupervised calculation of free energy barriers in large " "crystalline systems},\n" "journal={Physical Review Letters},\n" - "volume={276},\n" - "number={1},\n" - "pages={154-165},\n" + "volume={120},\n" + "number={13},\n" + "pages={135503},\n" "year={2018},\n" "publisher={APS}\n}\n" "Recommended to be coupled with PAFI++ code:\n"