Update main paper reference

LICENSE.txt

@@ -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

README.md

@@ -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.

docs/source/citeus.md

@@ -4,8 +4,10 @@
 
 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.

docs/source/index.md

@@ -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:

docs/source/topics/formulation.md

@@ -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:
 
@@ -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).
 :::