Merge pull request #78 from nichollsh/hn/citation

Citation

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Harrison"
   orcid: "https://orcid.org/0000-0002-8368-4641"
 title: "AGNI"
-version: 0.11.2
-doi: 10.xx/xx.xx
-date-released: 2024-11-29
+version: 1.0.0
+doi: 10.1093/mnras/stae2772
+date-released: 2024-12-17
 url: "https://github.com/nichollsh/AGNI"

Project.toml

@@ -1,7 +1,7 @@
 name = "AGNI"
 uuid = "ede838c1-9ec3-4ebe-8ae8-da4091b3f21c"
 authors = ["Harrison Nicholls <harrison.nicholls@physics.ox.ac.uk>"]
-version = "0.11.2"
+version = "1.0.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

README.md

@@ -14,6 +14,9 @@
   <a href="LICENSE.txt">
     <img src="https://img.shields.io/github/license/nichollsh/AGNI?label=License">
   </a>
+  <a href="https://doi.org/10.1093/mnras/stae2772">
+    <img src="https://img.shields.io/badge/DOI-10.1093%2Fmnras%2Fstae2772-blue">
+  </a>
 </p>
 
 <p align="center">
@@ -22,7 +25,6 @@
 
 
 ## Overview
-
 A numerical model for the atmospheres of hot rocky (exo)planets. AGNI's primary purpose is to simulate the evolving atmospheres of magma ocean planets, while ensuring that radiative-convective equilibrium is maintained throughout the atmosphere.
 
 AGNI models correlated-k radiative transfer including shortwave irradiation from the star, surface emission, gaseous absorption, Rayleigh scattering, parameterised clouds, and CIA. Mixing length theory is used to model convection. Together, energy transport processes allow for an energy-conserving calculation of the atmosphere's temperature profile.
@@ -31,12 +33,14 @@ Consult the [AGNI documentation](https://nichollsh.github.io/AGNI/) for informat
 
 Contact: `harrison[dot]nicholls[at]physics.ox.ac.uk`
 
-GitHub: https://github.com/nichollsh/AGNI
-
-
 ## Installation and usage
 See the [Getting Started](https://nichollsh.github.io/AGNI/dev/setup/) page in the documentation for information on installing and using the model.
 
+## Citation
+If you use AGNI, please cite the following papers:
+* Nicholls et al., (2024) - https://doi.org/10.1093/mnras/stae2772
+* Nicholls et al., (2025) - submitted to JOSS
+
 ## Repository structure
 * `agni.jl`         - The main AGNI executable
 * `LICENSE.txt`     - License for use and re-use
@@ -49,4 +53,4 @@ See the [Getting Started](https://nichollsh.github.io/AGNI/dev/setup/) page in t
 * `test/`           - Tests for the code
 * `tutorials/`      - Notebooks and tutorials
 
-This software is available under the GPLv3. Copyright (C) 2024 Harrison Nicholls.
+This software is available under GPLv3. Copyright (C) 2025 Harrison Nicholls.

codemeta.json

@@ -19,5 +19,5 @@
   "keywords": "physics, radiative transfer, exoplanets, astronomy, convection, radiation, planets, atmospheres",
   "license": "GPL v3.0",
   "title": "AGNI",
-  "version": "0.11.2"
+  "version": "1.0.0"
 }

docs/paper/paper.bib

@@ -317,6 +317,16 @@ @ARTICLE{hammond_photometric_2024
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
+@ARTICLE{nicholls_convection_2024,
+       author = {Harrison Nicholls and Raymond Pierrehumbert and Tim Lichtenberg and Laurent Soucasses and Stef Smeets},
+        title = "{Convective shutdown in the atmospheres of lava worlds}",
+      journal = {Monthly Notices of the Royal Astronomical Society},
+         year = 2024,
+        month = dec,
+          doi = {10.1093/mnras/stae2772},
+		  url = {https://arxiv.org/abs/2412.11987}
+}
+
 @ARTICLE{lichtenberg_review_2024,
        author = {{Lichtenberg}, Tim and {Miguel}, Yamila},
         title = "{Super-Earths and Earth-like Exoplanets}",

docs/paper/paper.md

@@ -57,7 +57,7 @@ AGNI is a new radiative-convective atmosphere model developed with the view of b
 * operate with sufficient speed that it may be participate in a wide parameter space,
 * constrain convective mass diffusivity using mixing length theory.
 
-This is possible due to the method by which AGNI numerically obtains a solution for atmospheric temperature structure and energy transport. Rather than time-stepping each model level according to radiative heating and applying convective adjustment (e.g. @malik_helios_2017, @selsis_cool_2023, @pierrehumbert_book_2010), AGNI uses the Newton-Raphson method to conserve energy fluxes through the column to a required tolerence. This is similar to the method applied by @drummond_effects_2016 and @goyal_library_2020. This means that the model takes tens or hundereds of iterations to obtain a solution, in comparison to thousands or tens of thousands.
+This is possible due to the method by which AGNI numerically obtains a solution for atmospheric temperature structure and energy transport (@nicholls_convection_2024). Rather than time-stepping each model level according to radiative heating and applying convective adjustment (e.g. @malik_helios_2017, @selsis_cool_2023, @pierrehumbert_book_2010), AGNI uses the Newton-Raphson method to conserve energy fluxes through the column to a required tolerence. This is similar to the method applied by @drummond_effects_2016 and @goyal_library_2020. This means that the model takes tens or hundereds of iterations to obtain a solution, in comparison to thousands or tens of thousands.
 
 Radiative transfer is performed under the correlated-k and two-stream approximations using SOCRATES[^3], a well established FORTRAN code developed by the UK Met Office [@manners_socrates_2024; @sergeev_socrates_2023; @amundsen_treatment_2017; @amundsen_radiation_2014]. Convection, condensation, and sensible heat transport are also modelled.
 
@@ -69,7 +69,6 @@ AGNI was used in @hammond_photometric_2024.
 
 # Acknowledgements
 
-HN is supported by the Clarendon Fund and the MT Scholarship Trust.
-We acknowledge the continuing hard work of the Julia developers and those of its many libraries [@julialang].
+We acknowledge the continuing work of the Julia developers and the developers of its many libraries [@julialang].
 
 # References

docs/src/index.md

@@ -7,7 +7,8 @@
 
 A numerical model for the atmospheres of hot rocky (exo)planets. AGNI's
 primary purpose is to simulate the evolving atmospheres of magma ocean planets, while
-ensuring that radiative-convective equilibrium is sufficiently maintained.
+ensuring that radiative-convective equilibrium is sufficiently maintained. Pronounced as
+_ag-nee_. Named after the fire deity of Hinduism.
 
 Follow [Getting started](@ref) for information on installing the code and
 obtaining results.
@@ -16,6 +17,8 @@ Contact: `harrison[dot]nicholls[at]physics.ox.ac.uk`
 
 GitHub: [https://github.com/nichollsh/AGNI](https://github.com/nichollsh/AGNI)
 
-Pronounced: _ag-nee_. Named after the fire deity of Hinduism.
+If you use AGNI, please cite the following papers:
+* Nicholls et al., (2024) - https://doi.org/10.1093/mnras/stae2772
+* Nicholls et al., (2025) - submitted to JOSS
 
-This software is available under the GPLv3. Copyright (C) 2024 Harrison Nicholls.
+This software is available under the GPLv3. Copyright (C) 2025 Harrison Nicholls.

src/atmosphere.jl

@@ -333,7 +333,7 @@ module atmosphere
         @info  "Setting-up a new atmosphere struct"
 
         # Code versions
-        atmos.AGNI_VERSION = "0.11.2"
+        atmos.AGNI_VERSION = "1.0.0"
         atmos.SOCRATES_VERSION = readchomp(joinpath(ENV["RAD_DIR"],"version"))
         @debug "AGNI VERSION = "*atmos.AGNI_VERSION
         @debug "Using SOCRATES at $(ENV["RAD_DIR"])"