ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

citation update

Browse Source
This commit is contained in:
Tom Swinburne
2020-05-01 16:19:03 +02:00
parent 2ff463cc6e
commit 64fdaaec3c
3 changed files with 13 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
doc/src/fix_pafi.rst
View File

@ -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)

4
examples/USER/misc/pafi/README
View File

@ -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

6
src/USER-MISC/fix_pafi.cpp
View File

@ -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"