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Update main paper reference
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The main paper on npj Comp. Mat. has been published, and all the
references to the arxiv are now updated to the corresponding
peer-reviewed publication.
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bastonero committed Mar 19, 2024
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5 changes: 3 additions & 2 deletions LICENSE.txt
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Expand Up @@ -53,8 +53,9 @@ by a person or an entity engaged in the commercial use, application or
exploitation of works similar to the PROGRAM.

5. LICENSEE agrees that he/she shall make the following acknowledgement in
publications resulting from the use of the PROGRAM: "Lorenzo Bastonero and Nicola
Marzari, Automated all-functionals infrared and Raman spectra, arXiv:2308.04308";
publications resulting from the use of the PROGRAM: "Lorenzo Bastonero and
Nicola Marzari, Automated all-functionals infrared and Raman spectra,
npj Computational Materials 10, 55 (2024), DOI: 10.1038/s41524-024-01236-3";
"Sebastiaan. P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid
Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V.
Yakutovich, Casper W. Andersen, Francisco F. Ramirez, Carl S. Adorf, Fernando
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12 changes: 12 additions & 0 deletions README.md
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Expand Up @@ -24,6 +24,18 @@ or when installing from source:
git clone https://github.com/bastonero/aiida-vibrosopy
pip install .

## How to cite

If you use this plugin for your research, please cite the following works:

* L. Bastonero and N. Marzari, [*Automated all-functionals infrared and Raman spectra*](https://doi.org/10.1038/s41524-024-01236-3), npj Computational Materials **10**, 55 (2024)

* S. P. Huber _et al._, [*AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance*](https://doi.org/10.1038/s41597-020-00638-4), Scientific Data **7**, 300 (2020)

* M. Uhrin _et al._, [*Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows*](https://www.sciencedirect.com/science/article/pii/S0010465522001746), Computational Materials Science **187**, 110086 (2021)

Please, also cite the underlying Quantum ESPRESSO and Phonopy codes references.

## License
The `aiida-vibroscopy` plugin package is released under a special academic license.
See the `LICENSE.txt` file for more details.
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4 changes: 3 additions & 1 deletion docs/source/citeus.md
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If you use this plugin for your research, please cite the following works:

> Lorenzo Bastonero and Nicola Marzari, [*Automated all-functionals infrared and Raman spectra*](https://arxiv.org/abs/2308.04308) (2023)
> Lorenzo Bastonero and Nicola Marzari, [*Automated all-functionals infrared and Raman spectra*](https://doi.org/10.1038/s41524-024-01236-3), npj Computational Materials **10**, 55 (2024)
> Sebastiaan. P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V. Yakutovich, Casper W. Andersen, Francisco F. Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar, Elsa Passaro, Conrad Johnston, Andrius Merkys, Andrea Cepellotti, Nicolas Mounet, Nicola Marzari, Boris Kozinsky, and Giovanni Pizzi, [*AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance*](https://doi.org/10.1038/s41597-020-00638-4), Scientific Data **7**, 300 (2020)
> Martin Uhrin, Sebastiaan. P. Huber, Jusong Yu, Nicola Marzari, and Giovanni Pizzi, [*Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows*](https://www.sciencedirect.com/science/article/pii/S0010465522001746), Computational Materials Science **187**, 110086 (2021)
Please, also cite the underlying Quantum ESPRESSO and Phonopy codes references.
6 changes: 4 additions & 2 deletions docs/source/index.md
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Expand Up @@ -100,14 +100,16 @@ To the tutorials

# How to cite

If you use this plugin for your research, please cite the following work:
If you use this plugin for your research, please cite the following works:

> Lorenzo Bastonero and Nicola Marzari, [*Automated all-functionals infrared and Raman spectra*](https://arxiv.org/abs/2308.04308) (2023)
> Lorenzo Bastonero and Nicola Marzari, [*Automated all-functionals infrared and Raman spectra*](https://doi.org/10.1038/s41524-024-01236-3), npj Computational Materials **10**, 55 (2024)
> Sebastiaan. P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V. Yakutovich, Casper W. Andersen, Francisco F. Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar, Elsa Passaro, Conrad Johnston, Andrius Merkys, Andrea Cepellotti, Nicolas Mounet, Nicola Marzari, Boris Kozinsky, and Giovanni Pizzi, [*AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance*](https://doi.org/10.1038/s41597-020-00638-4), Scientific Data **7**, 300 (2020)
> Martin Uhrin, Sebastiaan. P. Huber, Jusong Yu, Nicola Marzari, and Giovanni Pizzi, [*Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows*](https://doi.org/10.1016/j.commatsci.2020.110086), Computational Materials Science **187**, 110086 (2021)
Please, also cite the underlying Quantum ESPRESSO and Phonopy codes references.

# Acknowledgements

We acknowledge support from:
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4 changes: 2 additions & 2 deletions docs/source/topics/formulation.md
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Expand Up @@ -3,7 +3,7 @@
# Formulation

In this section we briefly explore the underlying theory and formulation made used in the workflows.
For a more in depth explanation, please refer to the [main paper of the package](https://arxiv.org/abs/2308.04308).
For a more in depth explanation, please refer to the [main paper of the package](https://doi.org/10.1038/s41524-024-01236-3).

Considered good sources are:

Expand All @@ -21,7 +21,7 @@ In the code, all properties are computed within the __Born-Oppenheimer__ and __h
The vibrational spectra are computed in the __first-order non-resonant__ regime: the infrared using the __dipole-dipole__ approximation, and the Raman using the __Placzek__ approximation.

:::{important}
These are considered __good approximations for insulators__. Nevertheless, a frequency dependent solution form is usually used also for the __resonant__ case and for __metals__. _Nevertheless_, one must be aware that in such cases (resonance, metals) these approximations might not hold, as multiphonon processes, non-adiabaticity, excitonic effects (i.e. electronic excitations), or even exciton-phonon interactions might be non negligible, thus comparison with experiments could result poor. If these effects are important for your case, you can refer to [S. Reichardt and L. Wirtz, _Science Advances_, __7__, 32 (__2020__)](https://www.science.org/doi/10.1126/sciadv.abb5915).
These are considered __good approximations for insulators__. Nevertheless, a frequency dependent solution form is usually used also for the __resonant__ case and for __metals__. _Nevertheless_, one must be aware that in such cases (resonance, metals) these approximations might not hold, as multiphonon processes, non-adiabaticity, excitonic effects (i.e. electronic excitations), or even exciton-phonon interactions might be non negligible, thus comparison with experiments could result poor. If these effects are important for your case, you can refer to [S. Reichardt and L. Wirtz, _Science Advances_, **7**, 32 (__2020__)](https://www.science.org/doi/10.1126/sciadv.abb5915).

Moreover, temperature effects can also play a crucial role, as __anharmonic__ effects (of ions) should be incorporate to the phonons. A state-of-the-art approach, which differs from the classical molecular dynamics solutions, can be found using the [time-dependent self-consistent harmonic approximation](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.103.104305).
:::
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