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

Merge branch 'develop' into remove-i-pi

Browse Source 
# Conflicts:
#	doc/src/fix_ipi.rst
This commit is contained in:
Axel Kohlmeyer
2024-05-28 18:03:03 -04:00
parent 2afbf229ff dedcfa157c
commit 05ba777c0a
4 changed files with 76 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

61
doc/src/fix_ipi.rst
View File

@ -35,30 +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.
Here are the commands to set up a virtual environment and install i-PI
into it with all its dependencies via the PyPi repository and the pip package manager.
.. code-block:: sh
python -m venv ipienv
source ipienv/bin/activate
pip install --upgrade pip
pip install 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,
@ -82,6 +76,20 @@ 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
""""""""""""""
Here are the commands to set up a virtual environment and install
i-PI into it with all its dependencies via the PyPi repository and
the pip package manager.
.. code-block:: sh
python -m venv ipienv
source ipienv/bin/activate
pip install --upgrade pip
pip install i-PI
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -118,9 +126,14 @@ 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)**