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Project description
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.surfaces import potential_energy
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-6
Features
- Optimization methods to find local minima of the PES
- Steepest descent
- Conjugate gradients
- l-BFGS
- Optimization methods to find stationary points of the PES
- Eigenvector-following
- Square-force minimization
- Normal modes analysis
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/
Project details
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