Sella is a utility for finding first order saddle points
An example script
#!/usr/bin/env python3fromase.buildimportfcc111, add_adsorbatefromase.calculators.emtimportEMTfromsellaimportSella, Constraints# Set up your system as an ASE atoms objectslab=fcc111('Cu', (5, 5, 6), vacuum=7.5)
add_adsorbate(slab, 'Cu', 2.0, 'bridge')
# Optionally, create and populate a Constraints object.cons=Constraints(slab)
foratominslab:
ifatom.position[2] <slab.cell[2, 2] /2.:
cons.fix_translation(atom.index)
# Set up your calculatorslab.calc=EMT()
# Set up a Sella Dynamics objectdyn=Sella(
slab,
constraints=cons,
trajectory='test_emt.traj',
)
dyn.run(1e-3, 1000)If you are using Sella or you wish to use Sella, let me know!
For more information on how to use Sella, please check the wiki.
If you need help using Sella, please visit our gitter support channel, or open a GitHub issue.
If you use our code in publications, please cite the revelant work(s). (1) is recommended when Sella is used for solids or in heterogeneous catalysis, (3) is recommended for molecular systems.
- Hermes, E., Sargsyan, K., Najm, H. N., Zádor, J.: Accelerated saddle point refinement through full exploitation of partial Hessian diagonalization. Journal of Chemical Theory and Computation, 2019 15 6536-6549. https://pubs.acs.org/doi/full/10.1021/acs.jctc.9b00869
- Hermes, E. D., Sagsyan, K., Najm, H. N., Zádor, J.: A geodesic approach to internal coordinate optimization. The Journal of Chemical Physics, 2021 155 094105. https://aip.scitation.org/doi/10.1063/5.0060146
- Hermes, E. D., Sagsyan, K., Najm, H. N., Zádor, J.: Sella, an open-source automation-friendly molecular saddle point optimizer. Journal of Chemical Theory and Computation, 2022 18 6974–6988. https://pubs.acs.org/doi/10.1021/acs.jctc.2c00395
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.