wiki:GroupActivities/CodeAvalaibilityPublication

Version 58 (modified by maignan, 17 months ago) (diff)

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Code availability associated to a publication

To answer the GMD editors' demands for a standard procedure for all submissions, the orchidee-project group has taken the following decisions.

  • A branch named "publications" is created where each publication has an associated directory containing the ORCHIDEE code used in the publication. See here ​https://forge.ipsl.jussieu.fr/orchidee/browser/branches/publications
  • On the bottom of this page (the one you're reading now), you should manually add a link towards a specific page that is related to the publication. This page should include:
    • the link to the code,
    • the explanation on how to download it,
    • a short description of the model,
    • other information (use one of the available links as a template for you to create this page)
  • The orchidee-project group centralizes the doi demands and the specific page (see above) will be sent to IPSL, to ask for a doi.
  • Prior to submission, the manuscript should be uploaded to ​https://sharebox.lsce.ipsl.fr/index.php/s/AhJk0Bk6rdySXKL and a mail should be send to the orchidee-project group to inform the group about this manuscript (standard demand from the Fair Use Policy).

How to create a new version in publications

Use following to copy revision X of version YYY into publications/ORCHIDEE_ZZZ: 

svn cp -r X svn://forge.ipsl.jussieu.fr/orchidee/YYY svn://forge.ipsl.jussieu.fr/orchidee/branches/publications/ORCHIDEE_ZZZ

where YYY can be branches/... or trunk/ORCHIDEE. For example: 

svn cp -r 4513 svn://forge.ipsl.jussieu.fr/orchidee/branches/ORCHIDEE-ROUTING/ORCHIDEE svn://forge.ipsl.jussieu.fr/orchidee/branches/publications/ORCHIDEE_gmd-2018-57

How to extract a version from publications

All versions copied into publications folder can be extracted with username anonymous with passwd anonymous. For example: 

> svn co --username anonymous svn://forge.ipsl.jussieu.fr/orchidee/branches/publications/ORCHIDEE_gmd-2018-57 ORCHIDEE
Domaine d'authentification : <svn://forge.ipsl.jussieu.fr:3690> f489ceea-5127-0410-b15c-c4a6149ed9a7
Mot de passe pour 'anonymous' :

answer anonymous.

Versions copied to publications

  • GroupActivities/CodeAvalaibilityPublication/ORCHIDEE_gmd-2023-05. This version of ORCHIDEE has been used in a paper entitled : Simulating Bark Beetle Outbreak Dynamics and their Influence on Carbon Balance Estimates with ORCHIDEE r7791, Guillaume Marie, Jina Jeong, Hervé Jactel, Gunnar Petter, Maxime Cailleret, Matthew J.McGrath?, Vladislav Bastrikov, Josefine Ghattas, Bertrand Guenet, Anne-Sofie Lansø, Kim Naudts, Aude Valade, Chao Yue, Sebastiaan Luyssaert. It include a new module that simu:ation abrupt mortality event from pest outbreak and its intyeraction with the windtrow mortality module.
  • ORCHIDEE_3_r6863. This version of ORCHIDEE has been used in two papers. Global carbon budget 2020" by P. Friedlingstein et al., 2020 and "Using free air CO2 enrichment data to constrain land surface model projections of the terrestrial carbon cycle" by N. Raoult, to be submitted
  • ORCHIDEE-Hillslope-r6515: This version of ORCHIDEE has been used in two papers, by Yi et al. on the effects of afforestation on wetland extents (under minor revision for Nature Communications in Nov 2021), and by Arboleda et al. on groundwater impact on climate chnage pathways (to be submitted in December 2021 to Earth Future)
  • ORCHIDEE_biochar:This version of ORCHIDEE has been used in "Pyrogenic carbon mineralisation the missing link in the global grassland-dominated fire carbon budget" by Bowring et al., (2021)
  • ORCHIDEE_CN-P_v1.3: This version of ORCHIDEE has been used in Carbon sink enhanced by atmospheric phosphorus deposition in simulations for tropical forest site in Central Africa (working title) by Goll et al., XXXX.
  • ORCHIDEE_MICT_BIOENERGY_r7298: This version of ORCHIDEE has been used in Global cooling induced by biophysical effects of bioenergy crop cultivation by Wang et al., 2021.
  • ORCHIDEE_gmd-2018-261: copy of revision 4999 of the branch ORCHIDEE-CN used in "Accounting for Carbon and Nitrogen interactions in the Global Terrestrial Ecosystem Model ORCHIDEE (rev 4999): multi-scale evaluation of gross primary production" by Nicolas Vuichard, Palmira Messina, Sebastiaan Luyssaert, Bertrand Guenet, Sönke Zaehle, Josefine Ghattas, Vladislav Bastrikov, Philippe Peylin
  • ORCHIDEE_gmd-2018-182: copy of revision 1311 of the Trunk used in "A generic pixel-to-point comparison for simulated large-scale ecosystem properties and ground-based observations: an example from the Amazon region" by Anja Rammig, Jens Heinke, Florian Hofhansl, Hans Verbeeck, Timothy R. Baker, Bradley Christoffersen, Phillipe Ciais, Hannes De Deurwaerder, Katrin Fleischer, David Galbraith, Matthieu Guimberteau, Andreas Huth, Michelle Johnson, Bart Krujit, Fanny Langerwisch, Patrick Meir, Phillip Papastefanou, Gilvan Sampaio, Kirsten Thonicke, Celso von Randow, Christian Zang, and Edna Rödig
  • ORCHIDEE-CN-P_grl_2018GL077736: copy of revision 4630 of branch ORCHIDEE-CN-P used in publication "Low phosphorus availability decreases susceptibility of tropical primary productivity to droughts" by Daniel S. GOLL, Emilie JOETZJER, Mengtian HUANG, and Philippe CIAIS 2019
  • ORCHIDEE-CN-P_v1.2_r5986: copy of revision 5986 of branch ORCHIDEE-CN-P used in publication Sun, Goll et al (in prep for GMD) which provides a global evaluation of the model.
  • ORCHIDEE_CAN_r2290: copy of revision 2290 of the ORCHIDEE-CAN branch used in "A vertically discretised canopy description for ORCHIDEE (SVN r2290) and the modifications to the energy, water and carbon fluxes" by K. Naudts, J. Ryder, M. J. McGrath, J. Otto, Y. Chen, A. Valade, V. Bellasen, G. Berhongaray, G. Bönisch, M. Campioli, J. Ghattas, T. De Groote, V. Haverd, J. Kattge, N. MacBean, F. Maignan, P. Merilä, J. Penuelas, P. Peylin, B. Pinty, H. Pretzsch, E. D. Schulze, D. Solyga, N. Vuichard, Y. Yan, and S. Luyssaert. Geosci. Model Dev., 8, 2035–2065, 2015. doi:10.5194/gmd-8-2035-2015
  • ORCHIDEE_CAN_r3069: copy of revision 3069 of the ORCHIDEE-CAN branch used in "Tradeoffs in using European forests to meet climate objectives" by Sebastiaan Luyssaert, Guillaume Marie, Aude Valade, Yi-Ying Chen, Sylvestre Njakou Djomo, James Ryder, Juliane Otto, Kim Naudts, Anne Sofie Lansø, Josefine Ghattas, and Matthew J. McGrath
  • ORCHIDEE_CN_CAN_r5698: copy of revision 5698 of the ORCHIDEE-CN-CAN branch used in "Using the International Tree-Ring Data Bank (ITRDB) records as century-long benchmarks for land-surface models" by Jina Jeong, Jonathan Barichivich, Philippe Peylin, Vanessa Haverd, Matthew J. McGrath, Nicolas Vuichard, Mike Evans, and Sebastiaan Luyssaert (to be submitted)
  • ORCHIDEE_gmd-2018-MICT-LEAK_r5459 This version of ORCHIDEE has been used in ORCHIDEE MICT-LEAK, a global model for the production, transport and transformation of DOC from Arctic permafrost regions by Bowring, S.P.K., Lauerwald, R., Guenet, B., Zhu, D., Guimberteau, M., Regnier, P., Tootchi, A., Ducharne, A. & Ciais, P. 2020. ORCHIDEE MICT-LEAK ( r5459 ), a global model for the production , transport , and transformation of dissolved organic carbon from Arctic permafrost regions – Part 2 : Model evaluation over the Lena River basin. Geoscientific Model Development, 13, 507–520.
  • ORCHIDEE_gmd-2018-14C This version of ORCHIDEE has been used in publication Tifafi, M., Camino-Serrano, M., Hatté, C., Morras, H., Moretti, L., Cornu, S. and Guenet, B.: The use of radiocarbon 14C to constrain soil carbon dynamics in the land surface model ORCHIDEE, Geosci. Model Dev., 11, 4711–4726, doi:10.5194/gmd-2018-102, 2018.
  • ORCHIDEE_SOM_13C_r4859 This version of ORCHIDEE has been used in Using stable carbon isotopes as an observational constraint on the dynamics of soil carbon in the land-surface model ORCHIDEE by Camino-Serrano, M., Tifafi, M., Balesdent, J., Hatté, C., Penuelas, J., Cornu, S. & Guenet, B. 2019. Including Stable Carbon Isotopes to Evaluate the Dynamics of Soil Carbon in the Land ‐ Surface Model ORCHIDEE. Journal of Advances in Modeling Earth Systems, 11.
  • ORCHIDEE_PEAT_V2 This version of ORCHIDEE has been used in "Modelling northern peatlands area and carbon dynamics since the Holocene with the ORCHIDEE-PEAT land surface model (SVN r5488)" by Qiu, C., Zhu, D., Ciais, P., Guenet, B., Krinner, G., Peng, S., Aurela, M., Bernhofer, C., Brümmer, C., Bret-Harte, S., Chu, H., Chen, J., Desai, A.R., Dušek, J., Euskirchen, E.S., Fortuniak, K., Flanagan, L.B., Friborg, T., Grygoruk, M., Gogo, S., Grünwald, T., Hansen, B.U., Holl, D., Humphreys, E., Hurkuck, M., Kiely, G., Klatt, J., Kutzbach, L., Largeron, C., Laggoun-Défarge, F., Lund, M., Lafleur, P.M., Li, X., Mammarella, I., Merbold, L., Nilsson, M.B., Olejnik, J., Ottosson-Löfvenius, M., Oechel, W., Parmentier, F.-J.W., Peichl, M., Pirk, N., Peltola, O., Pawlak, W., Rebmann, C., Rasse, D., Rinne, J., Shaver, G., Schmid, H.P., Sottocornola, M., Steinbrecher, R., Sachs, T., Urbaniak, M., Zona, D. & Ziemblinska, K. 2018. ORCHIDEE-PEAT (revision 4596), a model for northern peatland CO2 water and energy fluxes on daily to annual scales. Geoscientific Model Development, 11, 497–519.
  • ORCHIDEE-LEAK_r5919 This version of ORCHIDEE has been used in “How simulations of the land carbon sink are biased by ignoring fluvial carbon transfers – A case study for the Amazon basin” by R. Lauerwald, P. Regnier, B. Guenet, P. Friedlingstein, P. Ciais Lauerwald, R., Regnier, P., Guenet, B., Friedlingstein, P. and Ciais, P.: How Simulations of the Land Carbon Sink Are Biased by Ignoring Fluvial Carbon Transfers: A Case Study for the Amazon Basin, One Earth, 3(2), 226–236, doi:10.1016/j.oneear.2020.07.009, 2020.
  • ORCHIDEE-GMv3.2 This version of ORCHIDEE has been used in a publication Chang, J., Ciais, P., Gasser, T., Smith, P., Herrero, M., Havlík, P., Obersteiner, M., Guenet, B., Goll, D.S., Li, W., Naipal, V., Peng, S., Qiu, C., Tian, H., Viovy, N., Yue, C., Zhu, D., 2021. Climate warming from managed grasslands cancels the cooling effect of carbon sinks in sparsely grazed and natural grasslands. Nature Communications 12, 118.
  • ORCHIDEE-CN-P_v1.2_r5986 This version of ORCHIDEE has been used in publication "Global evaluation of nutrient enabled version land surface model ORCHIDEE-CNP v1.2 (r5986)" by Sun et al to be submitted to GMD. Reference and information will be added later
  • ORCHIDEE_IPSLCM5A2.1.r5307 This version of ORCHIDEE has been used in the coupled model IPSLCM5A2.1 for the publication in GMD with title "IPSL-CM5A2. An Earth System Model designed for multi-millennial climate simulation" by Pierre Sepulchre, A. Caubel, J-B. Ladant, L. Bopp, O. Boucher, P. Braconnot, P. Brockmann, A. Cozic, Y. Donnadieu, V. Estella-Perez, C. Ethé, F. Fluteau, M-A. Foujols, G. Gastineau, J. Ghattas, D. Hauglustaine, F. Hourdin, M. Kageyama, M. Khodri, O. Marti, Y. Meurdesoif, J. Mignot, A-C. Sarr, J. Servonnat, D. Swingedouw, S. Szopa, and D. Tardif
  • ORCHIDEE_MUSLE-r6129 This version of ORCHIDEE has been used in “SZhang, H., Lauerwald, R., Regnier, P., Ciais, P., Yuan, W., Naipal, V., Guenet, B., Van Oost, K. and Camino‐Serrano, M.: Simulating erosion‐induced soil and carbon delivery from uplands to rivers in a global land surface model, J. Adv. Model. Earth Syst., 1(C), 1–24, doi:10.1029/2020ms002121, 2020.
  • ORCHIDEE_DFv1.0_site This version of ORCHIDEE has been used in publication "Modeling the impacts of diffuse light fraction on photosynthesis in ORCHIDEE (v5453) land surface model" by Zhang et al to be submitted to GMD. Reference and information will be added later
  • ORCHIDEE-MICT-OP-r6850 This version of ORCHIDEE has been used in publication "Modelling oil palm growth and harvest using the global land-surface model ORCHIDEE-MICT" by Xu et al to be submitted to GMD. Reference and information will be added later.
  • ORCHIDEE_DFv1.0_DFforc This version of ORCHIDEE has been used in publication "How to reconstruct diffuse radiation scenario for simulating GPP in land surface models?" by Zhang et al. to be submitted to GMD. Reference and information will be added later
  • ORCHIDEE_mict_peat_ch4 This version of ORCHIDEE has been used in publication Assess methane emissions for northern peatlands in ORCHIDEE-PEAT revision 7020. Submitted to Geoscientific Model Development. by Salmon et al. to be submitted to GMD. Reference and information will be added later
  • GroupActivities/CodeAvalaibilityPublication/ORCHIDEE-Clateral This version of ORCHIDEE has been used in publication Estimating the lateral redistribution of organic carbon in Europe through rivers using a land surface model. Submitted to JAMES. by Zhang et al. Reference and information will be added later
  • GroupActivities/CodeAvalaibilityPublication/ORCHIDEELEAK-Gommet This version of ORCHIDEE has been used in publication Spatio-temporal patterns and drivers of terrestrial Dissolved Organic Carbon (DOC) leaching to the European river network. Submitted to Earth System Dynamic by Gommet et al. Reference and information will be added later
  • GroupActivities/CodeAvalaibilityPublication/ORCHIDEE_CAN_NHA This version of ORCHIDEE has been used in publication Forest fluxes and mortality response to drought: model description (ORCHIDEE-CAN-NHA, r7236) and evaluation at the Caxiuanã drought experiment Submitted to Geoscientific Model Development by Yitong Yao, Emilie Joetzjer, Philippe Ciais, Nicolas Viovy, Fabio Cresto Aleina, Jerome Chave, Lawren Sack, Megan Bartlett, Patrick Meir, Rosie Fisher, Sebastiaan Luyssaert.