update according to donof2.0 submitting

docs/Installation.md

@@ -66,3 +66,22 @@ Current capabilities include:
 - **RUNTYP = DYN** - Born-Oppenheimer on-the-fly molecular dynamics
 
 Other common options include excited states calculation (`ERPA=T`) and NOF-MBPT calculations (`MBPT=T`).
+
+## Python and Julia
+
+PyNOF is a version of DoNOF written in Python. You can install it with
+```{margin}
+![PyNOF](./PyNOF.png)
+```
+~~~
+pip install pynof
+~~~
+
+Similarly, DoNOF.jl is a version of DoNOF written in the Julia language. You can install DoNOF.jl form REPL with
+```{margin}
+![DoNOF.jl](./DoNOFjl.png)
+```
+~~~
+add DoNOF
+~~~
+

docs/License.md

@@ -19,12 +19,17 @@ M. Piris, I. Mitxelena, DoNOF: an open-source implementation of natural-orbital-
 Comp. Phys. Comm. 259, 107651 (2021)
 
 [DOI:10.1016/j.cpc.2020.107651](https://doi.org/10.1016/j.cpc.2020.107651)
+
+J. F. H. Lew-Yee, I. Mitxelena, J. M. Campo, M. Piris; DoNOF 2.0: modern Open-Source Electronic Structure Program for Natural Orbital Functionals
+
+[arXiv:2512.13550](https://doi.org/10.48550/arXiv.2512.13550)
 :::
 
 ```{margin} arXiv
-You can find a preprint corresponding to this publication in:
+You can find the preprints corresponding to these publications in the next sites:
 ~~~
 https://arxiv.org/abs/2004.06142 
+https://arxiv.org/abs/2512.13550v1
 ~~~
 ```
 
@@ -39,4 +44,50 @@ You can also place the following in your bibtex file:
     volume = {259},
     year = {2021}
     }
+    @misc{Lewyee2025,
+    title={DoNOF 2.0: A modern Open-Source Electronic Structure Program for Natural Orbital Functionals}, 
+    author={Juan Felipe Huan Lew-Yee and Ion Mitxelena and Jorge M. del Campo and and Mario Piris},
+    year={2025},
+    eprint={2512.13550},
+    archivePrefix={arXiv},
+    primaryClass={physics.chem-ph},
+    url={https://arxiv.org/abs/2512.13550}, 
+}
 ~~~
+
+For specific calculations, additional citations are grateful:
+
+:::{admonition} Citation
+:class: tip
+Molecular dynamics ($RUNTYP='DYN'):
+
+A. Rivero-Santamaria, M. Piris; Time evolution of natural orbitals in ab initio molecular dynamics,
+J. Chem. Phys. 160, 071102 (2024)
+
+[doi.org/10.1063/5.0188491](https://doi.org/10.1063/5.0188491)
+
+and 
+
+M. Piris, X. Lopez, J. M. Ugalde; Time-Resolved Chemical Bonding Structure Evolution by Direct-Dynamics Chemical Simulations,
+
+[doi.org/10.1021/acs.jpclett.4c03010](https://pubs.acs.org/doi/10.1021/acs.jpclett.4c03010)
+
+Geometry Optimization:
+
+I. Mitxelena, M. Piris; Analytic gradients for spin multiplets in natural orbital functional theory,
+
+[doi.org/10.1063/5.0012897](https://doi.org/10.1063/5.0012897)
+
+and
+
+I. Mitxelena, M. Piris; Analytic gradients for spin multiplets in natural orbital functional theory,
+
+[doi.org/10.1063/1.4973271](https://doi.org/10.1063/1.4973271)
+
+Excited States:
+
+J. F. H. Lew-Yee, M. Piris; Excited States by Coupling Piris Natural Orbital Functionals with the Extended Random-Phase Approximation,
+
+[doi/10.1021/acs.jctc.3c01194](https://pubs.acs.org/doi/10.1021/acs.jctc.3c01194)
+:::
+

docs/NOF.md

@@ -196,7 +196,7 @@ Note real orbitals are assumed, so exchange (K) and time-inversion-exchange (L)
 [`Phys. Rev. Lett. 127(23), 233001 (2021).`](https://doi.org/10.1103/PhysRevLett.127.233001)
 ```
 
-In order to choose GNOF in DoNOF, you must set IPNOF=8 in the $NOFINP section of your input file.
+In order to choose GNOF in DoNOF, you must set IPNOF=8 and Imod=0 in the $NOFINP section of your input file.
 
 $$
     E_{el}^{gnof} = E^{intra} + E_{HF}^{inter} + E_{sta}^{inter} + E_{dyn}^{inter}
@@ -247,3 +247,22 @@ $$
 $$
 
 The maximum value of $n_p^d$ is around 0.012 in accordance with the Pulay’s criterion that establishes an occupancy deviation of approximately 0.01 with respect to 1 or 0 for a natural orbital to contribute to the dynamic correlation. Clearly, GNOF does not take into account dynamic correlation of the single electrons. Considering real spatial orbitals (L=K) and $n_p$ ~ $n_p^d$, it is not difficult to verify that the terms proportional to the product of the occupation numbers will cancel out, so that only those terms proportional to \Pi will contribute significantly to the energy.
+
+### GNOFm
+
+```{margin} Article
+[`Phys. Rev. Lett. 134(20), 206401 (2025).`](https://doi.org/10.1103/PhysRevLett.134.206401)
+```
+
+In order to choose GNOFm in DoNOF, you must set IPNOF=8 and Imod=1 in the $NOFINP section of your input file.
+
+$$
+    E_{el}^{gnofm} = E^{intra} + E_{HF}^{inter} + E_{sta}^{inter} + E_{dyn}^{inter}
+$$
+
+The modification of GNOFm with respect to its predecessor GNOF stands in the correlation energy term between different electron pairs
+
+$$
+    E _{sta}^{inter} = \sum\limits _{p,q}^{\mathrm{N}_B}\,'\, \mathcal{K}_{pq}
+$$ 
+