atooms-landscape 2.0.1

Energy landscape analysis tools built with atooms

Energy landscape

Energy landscape analysis tools built with atooms.

Quick start

Find the minimum of the potential energy surface (PES) of a Lennard-Jones trimer

from atooms.landscape import conjugate_gradient
from atooms.system import Particle, Cell, System
from atooms.models.f90 import Interaction

system = System()
system.particle = [Particle(species=1, position=[0., 0., 0.]),
                   Particle(species=1, position=[0.5, 1., -.1]),
                   Particle(species=1, position=[1.1, 0.1, 0.1])]
system.cell = Cell([10., 10., 10.])
system.interaction = Interaction('lennard_jones')
result = conjugate_gradient(system)
distance = sum(system.particle[0].distance(system.particle[1])**2)**0.5
assert abs(distance - 1.12246) < 1e-5

Features

• Optimization methods to find local minima of the PES
  • Steepest descent
  • Conjugate gradients
  • l-BFGS
  • Fast inertial relaxation engine (FIRE)
• Optimization methods to find stationary points of the PES
  • Eigenvector-following
  • Square-force minimization
• Normal modes analysis

Documentation

Check out the tutorial for more examples and the public API for full details.

Org-mode and jupyter notebooks are available under docs/. You can run the tutorial interactively on Binder.

Installation

From pypi

pip install atooms-landscape

You can clone the code repository and install from source

git clone https://framagit.org/atooms/landscape.git
cd landscape
make install

Contributing

Contributions to the project are welcome. If you wish to contribute, check out these guidelines.

Authors

Daniele Coslovich: https://www.units.it/daniele.coslovich/

Thanks go to Ginevra Lautizi for her contribution to code testing.