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 MinModeAtoms, optimize
# 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.
fix = [atom.index for atom in slab if atom.position[2] < slab.cell[2, 2] / 2.]
# Set up your calculator
calc = EMT()
# Create a Sella MinMode object
myminmode = MinModeAtoms(slab, # Your Atoms object
calc, # Your calculator
constraints=dict(fix=fix), # Your constraints
trajectory='test_emt.traj', # Optional trajectory
)
x1 = optimize(myminmode, # Your MinMode object
maxiter=500, # Maximum number of force evaluations
ftol=1e-3, # Norm of the force vector, convergence threshold
r_trust=0.1, # Initial trust radius (Angstrom)
order=1, # Order of saddle point to find (set to 0 for minimization)
dxL=1e-4, # Finite difference displacement magnitude (Angstrom)
maxres=0.1, # Maximum residual for eigensolver convergence (should be <= 1)
)Additional documentation forthcoming. All interfaces likely to change.
If you are using Sella or you wish to use Sella, let me know!