Sella
Sella is a utility for finding first order saddle points
An example script
#!/usr/bin/env python3
from ase.build import fcc111, add_adsorbate
from ase.calculators.emt import EMT
from sella import Sella
# Set up your system as an ASE atoms object
slab = fcc111('Cu', (5, 5, 6), vacuum=7.5)
add_adsorbate(slab, 'Cu', 2.0, 'bridge')
# Define any constraints. Here we fix all atoms in the bottom half
# of the slab.
cart = [atom.index for atom in slab if atom.position[2] < slab.cell[2, 2] / 2.]
# Set up your calculator
slab.calc = EMT()
# Set up a Sella Dynamics object
dyn = Sella(slab,
constraints=dict(cart=cart),
trajectory='test_emt.traj')
dyn.run(1e-3, 1000)If you are using Sella or you wish to use Sella, let me know!
Documentation
For more information on how to use Sella, please check the wiki.
Support
If you need help using Sella, please visit our gitter support channel, or open a GitHub issue.
Acknowledgments
This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division, as part of the Computational Chemistry Sciences Program.