Fixi

Fixi, so far, implements bond length constraints using the RATTLE algorithm [1]. Fixi is written in C++20 and has optional support for multi-threading with OpenMP. Fixi also provides an interface to ASE [2,3], so that that it can be used as a drop-in replacement for ASE's FixedBondLengths class (see also the example tests_python/test_water.py).

Installation

To install

pip install git+https://github.com/amro-tools/fixi.git@main

Or, alternatively, clone the repository and run pip install from inside the root folder:

pip install .

NOTE: The pip install command will try to compile the C++ source code and build a binary wheel. Hence, this step depends on your system being equipped with a working C++20 compiler and the necessary build tools.

Obtaining build dependencies

We use micromamba here, but conda or mamba will work just as well. First create the environment, then activate it.

micromamba create -f environment.yml # only once
micromamba activate fixienv # every time 

After you have activated the environment it shoudl be possible to install fixi with pip install .

Advanced building and running the tests

We use meson as the build system:

meson setup build
meson compile -C build

To run the C++ unit tests:

meson test -C build

To run the tests in Python (which are in pytest):

pytest -v

PYPI

TODO.

For now, you can just do this (without having to clone the repository first):

pip install git+https://github.com/amro-tools/fixi.git@main

Usage

fixi.FixBondLengths is a drop-in replacement for ase.constraints.FixBondLengths:

from pyfixi.constraints import FixBondLengths
from ase import Atoms
# ...

# Fix the pairwwise bond lengths between the first three atoms
atoms.set_constraint( FixBondLengths( [ [0,1], [0,2], [1,2] ], tolerance=1e-5) )
# ...

The tolerance and maxiter are optional, with default values equal to 1e-13 and 500, respectively.

The number of threads is controlled via the OMP_NUM_THREADS environment variable, e.g:

export OMP_NUM_THREADS=2

Known bugs

• The editable pip install doesn't work.

References

[1] Hans C Andersen, Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations, Journal of Computational Physics, Volume 52, Issue 1, 1983

[2] ASE (Atomic Simulation Environment), https://gitlab.com/ase/ase

[3] Ask Hjorth Larsen et al 2017 J. Phys.: Condens. Matter 29 2730022