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, Constraints
# 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')
# Optionally, create and populate a Constraints object.
cons = Constraints(slab)
for atom in slab:
if atom.position[2] < slab.cell[2, 2] / 2.:
cons.fix_translation(atom.index)
# Set up your calculator
slab.calc = EMT()
# Set up a Sella Dynamics object
dyn = 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!
Documentation
For more information on how to use Sella, please check the wiki.
How to cite
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
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.
Release files for sella 2.6.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| sella-2.6.0.tar.gz | 182.7 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sella-2.6.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 309.8 kB
Release files / sella-2.6.0.tar.gz
| Download URL | sella-2.6.0.tar.gz |
|---|---|
| Size | 182.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
7effc2a10f6d43c0bbdff11acb1fe36e16424cd9f01746660e87985662713384
|
|
BLAKE2b-256 checksum How to use checksums |
d5e84ee9960010ca9156ed794efe249ba071d161411c59e61aa7378ebe11d292
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.16
|
Release files / sella-2.6.0-py3-none-any.whl
| Download URL | sella-2.6.0-py3-none-any.whl |
|---|---|
| Size | 127.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
cce6594830cd6afb5d0f4c934a6dd8111ad422882477fdc9cfd04ce65ee544f9
|
|
BLAKE2b-256 checksum How to use checksums |
2086f06e254ea018baf0bf584369c0f25b5e3693f0b57242ed44bb3cbc39bada
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.11.16
|
Security for sella 2.6.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
