citation update (64fdaaec) · Commits · 郑智淋 / lammps

doc/src/fix_pafi.rst

+8 −6

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		@@ -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) <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 <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 <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 <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)

examples/USER/misc/pafi/README

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		@@ -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

src/USER-MISC/fix_pafi.cpp

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		@@ -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"

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