How to misinterpret photosynthesis measurements and develop incorrect ecosystem models

At recent EGU General Assembly in Wien, I saw an interesting presentation by Professor Ian Colin Prentice (GS) entitled: How to misinterpret photosynthesis measurements and develop incorrect ecosystem models. I believe I already cited some of his papers (in our Precise proposal and “Can we trust Climate models?”), however, I did not faced his thinking directly. I would lie if I said that I understood his point. I am far too ignorant of the Carbon cycle and the way to measure it to understand. However, I accept the challenge to to start somewhere, because understanding the carbon cycle helps certainly to understand evapotranspiration. 

Please find below some relevant picture of his slides and, just after the paper(s) he cited. Probably reading those papers can be a starting point to understand.

I. C. Prentice, X. Liang, B. E. Medlyn , and Y.-P. Wang, Reliable, robust and realistic: the three R’s of next-generation land-surface modelling, ACP, 2015 

Hoffman, F. M., J. T. Randerson, V. K. Arora, Q. Bao, P. Cadule, D. Ji, C. D. Jones, M. Kawamiya, S. Khatiwala, K. Lindsay, A. Obata, E. Shevliakova, K. D. Six, J. F. Tjiputra, E. M. Volodin, and T. Wu (2014), Causes and implications of persistent atmospheric carbon dioxide biases in Earth System Models, J. Geophys. Res. Biogeosci., 119, 141–162, doi:10.1002/2013JG002381.

H. D. Graven, R. F. Keeling, S. C. Pipe, P. K. Patra, B. B. Stephens, S. C. Wofsy, L. R. Welp, C. Sweeney, P. P. Tans, J. J. Kelley, B. C. Daube, E. A. Kort, G. W. Santoni, J. D. Bent Enhanced Seasonal Exchange of CO2 by Northern Ecosystems Since 1960, Science 2013

Thomas, R. T., et al. (2016), Increased light-use efficiency in northern terrestrial ecosystems indicated by CO2 and greening observations, Geophys. Res. Lett., 43, 11,339–11,349, doi:10.1002/2016GL070710.

Wenzel, S., P. M. Cox, V. Eyring, andP. Friedlingstein (2014), Emergent constraints on climate-carbon cycle feedbacks in the CMIP5 Earth system models, J. Geophys. Res. Biogeosci., 119,794–807, doi:10.1002/2013JG002591 

Ainsworth EA1, Long SP, What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2., New Phytol. 2005 Feb;165(2):351-71.

Ning Dong, Iain Colin Prentice, Bradley J. Evans , Stefan Caddy-Retalic, Andrew J. Lowe, and Ian J. Wright, Leaf nitrogen from first principles: field evidence for adaptive variation with climate, Biogeosciences, 14, 481–495, 2017 doi:10.5194/bg-14-481-2017 

Zaehle, S., Medlyn, B. E., De Kauwe, M. G., Walker, A. P., Dietze, M. C., Hickler, T., Luo, Y., Wang, Y.-P., El-Masri, B., Thornton, P., Jain, A., Wang, S., Warlind, D., Weng, E., Parton, W., Iversen, C. M., Gallet-Budynek, A., McCarthy, H., Finzi, A., Hanson, P. J., Prentice, I. C., Oren, R. and Norby, R. J. (2014), Evaluation of 11 terrestrial carbon–nitrogen cycle models against observations from two temperate Free-Air CO2 Enrichment studies. New Phytol, 202: 803–822. doi:10.1111/nph.12697 

César Terrer, Sara Vicca,Bruce A. Hungate,Richard P. Phillips,I. Colin Prentice, Mycorrhizal association as a primary control of the CO2 fertilization effect, Science 2016 

A good (hydrological) model according to Thorsten Wagener

This is what Thorsten Wagener (GS) thinks is a good model. Almost no comment is necessary.

The best two 2016 papers in HESS

During the last EGU General Assembly, two paper were voted as the two best paper in HESS in 2016. They were:

• Anke Hildebrandt (RG), Axel Kleidon (GS), and Marcel Bechmann, A thermodynamic formulation of root water uptake
• Stanislaus J. Schymanski (GS) and Dani Or (GS),Leaf-scale experiments reveal an important omission in the Penman–Monteith equation

Which, because HESS is an open Journal can download from HESS’s site. The are from well known group and quite interesting, indeed.  

New Insights in Permafrost modelling (EGU Wien 2017)

This talk (and work) is another rearrangement of Niccolò Tubini work, and continues Matteo Dall'Amico Ph.D work. It derives the set of equations for water flow in freezing soils based on the same assumptions by Matteo but the results is slightly different at the end. 

Click on the figure above to see the presentation. Hope you enjoy it.

Dalton Prize 2017 to Dani Or

This is the video of Dani Or (GS) lecture for the prize he received at this year EGU Wien. Dani is an outstanding scientist and any of the things he does deserve attention and a reading. He talked about evaporation and others of his lectures were already linked in this blog.

Here below the video of the presentation of Dani.

Here his lecture (unfortunately a little out of focus, but still visible. I hope that there will be an official, professional record from EGU). You can find the PDF of the slides here.

Open-source software for simulating hillslope hydrology and stability

This is the material of the SC34/NH10.2 ECS: Open-source software for simulating hillslope hydrology and stability
by Giuseppe Formetta, Francesco Serafin, Riccardo Rigon, Raffaele Albano and Luigi Lombardo (co-conveners)

session of the  2017 EGU meeting in Wien.

For all of this work it is necessary to download a number of softwares.

• Docker GEOtop,
• Preliminari to any operation is to install GEOtop 2.0  on your machine. To avoid the complication implied by different platform GEOtop has been compiled against Docker which is a lightweight, well supported mini virtual machine which run on most operating systems.  The instructions on how to do it are available directly at: https://github.com/geotopmodel/docker (scroll down a little the page to see the instructions). Installing Docker is time consuming so, it is essential that participants to the pico session will download it before the session. An alternative little guide is on GrowWorkingHard.  Other information about the dockerized version of GEOtop can be found here.
• References: 
• Rigon, R., Bertoldi, G., & Over, T. M. (2006). GEOtop: A Distributed Hydrological Model with Coupled Water and Energy Budgets. Journal of Hydrometeorology, 7, 371–388.
• Endrizzi S., Gruber S., Dall’Amico M., Rigon R., GEOtop 2.0.: Simulating the combined energy and water balance at and below the land surface accounting for soil freezing, snow cover and terrain effects, Geosci. Model Dev., 2014
• Other GEOtop information can be found in the GEOtop essential post
• Next stuff require you to have installed the Java JDK (from Oracle site)
• Console OMS3, 
• OMS3 is a framework to build environmental models. It is Java native but it supports also the inclusion of C/C++ and FORTRAN codes. In our case, GEOtop is a C++ code and the hillslope stability code is a Java one. 
• First operation required in this case is the installation of OMS3 console. Its installation page is here.
• Further readings:
• David, O., Ascough II, J.C., Lloyd, W., Green, T.R., Rojas, K.W., Leavesley, G.H., Ahuja, L.R., 2013. A software engineering perspective on environmental modeling framework design: the Object Modeling System. Environ. Model. Softw. 39, 201e213
• Formetta, G., Antonello, A., Franceschi, S., David, O., & Rigon, R. (2014). Hydrological modelling with components: A GIS-based open source framework, 55(C), 190–200. http://doi.org/10.1016/j.envsoft.2014.01.019

• Hillslope Stability jars and data
• To download the .sim files to be used with OMS please go to https://zenodo.org/record/569354. Alternatively, the same material can be found here and here.
• This Stability analysis is novel unpublished material. So if you use it, the Author kindly ask to cite:
• Formetta G., S. Simoni, J. W. Godt, N. Lu, and R. Rigon (2016), Geomorphological control on variably saturated hillslope hydrology and slope instability, Water Resour. Res., 52, 4590?4607, doi:10.1002/2015WR017626.
• Further Readings
• Lu, N., & Likos, W. J. (2006). Suction Stress Characteristic Curve for Unsaturated Soil. Journal of Geotechnical and Geoenvironmental Engineering, 32, 131–142. 
• Lu, N., & Godt, J. (2008). Infinite slope stability under steady unsaturated seepage conditions. Water Resources Research, 44(11), 148–13. http://doi.org/10.1029/2008WR006976 
• Lu, N. & Godt, J.W., Hillslope Hydrology and Stability, Cambridge University Press, 2013, https://doi.org/10.1017/CBO9781139108164
• Running all of the examples
• At present here you have to types of runs:
• First you execute from the system console the command: 
  docker run --rm -v $(pwd):/work omslab/geotop 
Before launching it, please pay attention to have changed your directory that contains the initialisation files (geotop.inpts and io.ini), and then issue the command. (In the present case, you have to go in the "concave" directory that contains all these files and the input data file appropriately positioned)
• Secondly, please starts the OMS console, usually executing the "console" .sh or .bat files. Once in the console, you should upload the appropriate OMS project (OMS.landslide.prj) and you can execute Giuseppe's code for hillslope stability. It runs reading the outputs of GEOtop and does its job.