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Merge pull request #4157 from lab-cosmo/bugfix/ipi-neigh

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Performance improvements for fix_ipi
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Stan Moore
2024-05-28 15:06:15 -06:00
committed by GitHub
parent dad0d2651b 33351704a5
commit dedcfa157c
4 changed files with 70 additions and 21 deletions
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doc/src/fix_ipi.rst
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@ -35,23 +35,24 @@ Description
"""""""""""
This fix enables LAMMPS to be run as a client for the i-PI Python
wrapper :ref:`(IPI) <ipihome>` for performing a path integral molecular dynamics
(PIMD) simulation. The philosophy behind i-PI is described in the
following publication :ref:`(IPI-CPC) <IPICPC>`.
wrapper :ref:`(IPI) <ipihome>`. i-PI is a universal force engine,
designed to perform advanced molecular simulations, with a special
focus on path integral molecular dynamics (PIMD) simulation.
The philosophy behind i-PI is to separate the evaluation of the
energy and forces, which is delegated to the client, and the evolution
of the dynamics, that is the responsibility of i-PI. This approach also
simplifies combining energies computed from different codes, which
can for instance be useful to mix first-principles calculations,
empirical force fields or machine-learning potentials.
The following publication :ref:`(IPI-CPC-2014) <IPICPC>` discusses the
overall implementation of i-PI, and focuses on path-integral techniques,
while a later release :ref:`(IPI-CPC-2019) <IPICPC2>` introduces several
additional features and simulation schemes.
A version of the i-PI package, containing only files needed for use
with LAMMPS, is provided in the tools/i-pi directory. See the
tools/i-pi/manual.pdf for an introduction to i-PI. The
examples/PACKAGES/i-pi directory contains example scripts for using i-PI
with LAMMPS.
In brief, the path integral molecular dynamics is performed by the
Python wrapper, while the client (LAMMPS in this case) simply computes
forces and energy for each configuration. The communication between
the two components takes place using sockets, and is reduced to the
bare minimum. All the parameters of the dynamics are specified in the
input of i-PI, and all the parameters of the force field must be
specified as LAMMPS inputs, preceding the *fix ipi* command.
The communication between i-PI and LAMMPS takes place using sockets,
and is reduced to the bare minimum. All the parameters of the dynamics
are specified in the input of i-PI, and all the parameters of the force
field must be specified as LAMMPS inputs, preceding the *fix ipi* command.
The server address must be specified by the *address* argument, and
can be either the IP address, the fully-qualified name of the server,
@ -75,6 +76,14 @@ If the cell varies too wildly, it may be advisable to re-initialize
these interactions at each call. This behavior can be requested by
setting the *reset* switch.
Obtaining i-PI
""""""""""""""
A simple version of the i-PI package, containing only files needed for use
with LAMMPS, is provided in the tools/i-pi directory. We recommend you
obtain the latest stable version from the github repository of i-PI,
or from the python package index.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -111,9 +120,14 @@ Related commands
.. _IPICPC:
**(IPI-CPC)** Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,
**(IPI-CPC-2014)** Ceriotti, More and Manolopoulos, Comp Phys Comm 185,
1019-1026 (2014).
.. _IPICPC2:
**(IPI-CPC-2019)** Kapil et al., Comp Phys Comm 236, 214–223 (2019).
.. _ipihome:
**(IPI)**