# Citing SODA

When publishing results obtained with SODA, cite the SODA preprint, the workflow
methods, and the interatomic potential or model used in your calculation.
The workflows are separate scientific works with their own methods and
references. The SODA reference describes the supporting execution and
data-aggregation framework. Choose the references relevant to the calculation
you report.

## SODA preprint

Lopez, C., Lai, K. C., Rampp, M., and Scheurer, C.
“A scalable framework for goal-driven task-based simulations.” *ChemRxiv*,
preprint, version 1, 15 September 2026.
[doi:10.26434/chemrxiv.15008845/v1](https://doi.org/10.26434/chemrxiv.15008845/v1).

```bibtex
@article{lopez2026soda,
  author  = {Lopez, Carlos and Lai, King Chun and Rampp, Markus and Scheurer, Christoph},
  title   = {A scalable framework for goal-driven task-based simulations},
  journal = {ChemRxiv},
  year    = {2026},
  month   = sep,
  doi     = {10.26434/chemrxiv.15008845/v1},
  url     = {https://doi.org/10.26434/chemrxiv.15008845/v1},
  note    = {Preprint, version 1, posted 15 September 2026}
}
```

## SODA software

The repository's {repo}`CITATION.cff <CITATION.cff>` contains the software
citation metadata and the preprint as its preferred citation. Use the metadata
from the release or commit used for your results, and include its version and
repository URL in your software reference.
For a development checkout, record the full Git commit as well.

From the source directory used to build SODA, you can record the revision with:

```bash
git describe --tags --always --dirty
git rev-parse HEAD
```

Keep any local modifications with your research records. A commit identifier
alone does not capture changes made after that commit.

A methods statement can follow this pattern, replacing the bracketed text with
the details of your calculation and adding the corresponding references:

> Calculations used the [workflow] method, with [workflow software/version,
> where applicable]. SODA (Scalable Orchestration and Data Aggregation), version
> [version], commit [commit], provided parallel execution and data aggregation.
> Energy and force evaluations used [potential/model name and version].

## Workflow references

These references describe the independent methods and frameworks that can be
run through the available SODA integrations. The
{repo}`example READMEs <examples/README.md>` identify the references relevant
to particular example calculations.

### APE

Lai, K. C., et al. “Automatic Process Exploration through Machine Learning
Assisted Transition State Searches.” *Physical Review Letters* **134**, 096201
(2025). [doi:10.1103/PhysRevLett.134.096201](https://doi.org/10.1103/PhysRevLett.134.096201).

### EZGA

Lombardi, J. M., et al. *Computer Physics Communications* **328**, 110354
(2026). [doi:10.1016/j.cpc.2026.110354](https://doi.org/10.1016/j.cpc.2026.110354).

The {repo}`repository reference list <README.md#ezga>` also records the
[EZGA preprint, version 1](https://doi.org/10.26434/chemrxiv.15008068/v1).
Use the journal reference for the published work; use the preprint reference
when referring specifically to that version.

### NEBScape

Jung, H., et al. “From global optimization to transition state search: an
automated workflow for surface reaction barriers.” *npj Computational
Materials* **12**, 300 (2026).
[doi:10.1038/s41524-026-02298-1](https://doi.org/10.1038/s41524-026-02298-1).

(eon-references)=
### AKMC / EON

**AKMC method:** Xu, L., and Henkelman, G. “Adaptive kinetic Monte Carlo for
first-principles accelerated dynamics.” *The Journal of Chemical Physics* **129**(11), 114104
(2008). [doi:10.1063/1.2976010](https://doi.org/10.1063/1.2976010).

**EON software:** Chill, S. T., et al. “EON: software for long time simulations
of atomic scale systems.” *Modelling and Simulation in Materials Science and
Engineering* **22**(5), 055002 (2014).
[doi:10.1088/0965-0393/22/5/055002](https://doi.org/10.1088/0965-0393/22/5/055002).

**Source provenance:** SODA's EON-derived components are based on
[EON, SVN revision r2545](https://theory.cm.utexas.edu/svn/eon/?p=2545).
Identify this revision alongside the method and software references when
describing their origin. See [Third-party notices](third_party_notices.md#eon)
for the incorporated components and retained license.

## Potentials, models, and simulation engines

The workflow reference describes how structures or processes are explored.
Also cite the method and parameterization used to calculate their energies and
forces. Record the model name, version or checkpoint, and its source alongside
your input files.

| Used in your calculation | References to include |
| --- | --- |
| EAM | The [EAM review](#eam) and the publication for the actual EAM parameter file. For the Foiles–Baskes–Daw parameterization used in the examples, see the reference below. |
| GAP | The [GAP method](#gap) and the specific trained model. The Pd/O example model reference is listed below. |
| MACE | The [MACE method](#mace), any additional applicable [MACE references](https://github.com/ACEsuit/mace#references), and the publication or model card for the exact checkpoint, including the base model when fine-tuning. |
| Fairchem | The [FAIRChem software citation](#fairchem), plus the method, model, and dataset references provided with the chosen checkpoint in the [Fairchem project](https://github.com/facebookresearch/fairchem). |
| LAMMPS | Follow the [LAMMPS citation instructions](https://docs.lammps.org/Intro_citing.html), including references for the potential styles or algorithms used. |
| Other calculators or models | Follow the calculator's citation instructions and cite the specific potential, parameter set, or model used. |

### EAM

Daw, M. S., Foiles, S. M., and Baskes, M. I. “The embedded-atom method: a review
of theory and applications.” *Materials Science Reports* **9**(7–8), 251–310
(1993). [doi:10.1016/0920-2307(93)90001-U](https://doi.org/10.1016/0920-2307(93)90001-U).

### GAP

Bartók, A. P., Payne, M. C., Kondor, R., and Csányi, G. “Gaussian Approximation
Potentials: The Accuracy of Quantum Mechanics, without the Electrons.”
*Physical Review Letters* **104**(13), 136403 (2010).
[doi:10.1103/PhysRevLett.104.136403](https://doi.org/10.1103/PhysRevLett.104.136403).

### MACE

Batatia, I., Kovács, D. P., Simm, G. N. C., Ortner, C., and Csányi, G.
“MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and
Accurate Force Fields.” *Advances in Neural Information Processing Systems*
**35**, 11423–11436 (2022).
[doi:10.52202/068431-0830](https://doi.org/10.52202/068431-0830).

### Fairchem

Shuaibi, M., et al. *FAIRChem* [software]. Zenodo.
[doi:10.5281/zenodo.15587497](https://doi.org/10.5281/zenodo.15587497).

This follows the software citation in the project's
[CITATION.cff](https://github.com/facebookresearch/fairchem/blob/main/CITATION.cff).
Record the software version you use and also cite the selected model and
datasets according to its model card.

### EAM example parameterization

Foiles, S. M., Baskes, M. I., and Daw, M. S. *Physical Review B* **33**, 7983
(1986). [doi:10.1103/PhysRevB.33.7983](https://doi.org/10.1103/PhysRevB.33.7983).

### GAP example model

Poths, P., Lai, K. C., Cannizzaro, F., Scheurer, C., Matera, S., and Reuter, K.
“ML-Accelerated Automatic Process Exploration Reveals Facile O-Induced Pd
Step-Edge Restructuring on Catalytic Time Scales.” *ACS Catalysis* **15**(1),
514–522 (2025). [doi:10.1021/acscatal.4c06414](https://doi.org/10.1021/acscatal.4c06414).

These example references apply to those parameterizations. If you use a
different potential file or retrain a model, record and cite that choice.

For copyright notices, redistribution conditions, and the retained upstream
license texts, see [Third-party notices](third_party_notices.md).