Thursday, November 11, 2021

How to write a paper on a new hydrological model component

 Let’s try to keep the matter simple.  General rules apply:



Analyzing back the general scheme, in the case of software presenting, you need a specific part dedicated to the availability and delivery of the software. The main parts required here were already illustrated in explaining the Zero Notebook contents.

Because you are talking about scientific software your methodology has two parts. One related to the science you have to produce and one related to the science of writing good software.

Taking the example of Evapotranspiration. The science could be the one included in the sub-models you are implementing. Meaning, what is the science behind Priestley-Taylor, which the one behind FAO approach, and which the one one behind, for instance, our Prospero model ? Here the material is very large so you have to work usually by extracting the essentials and citing the literature. Part of it can easily fit actually inside the introduction. The informatics has to do with the way your system is built. Which is the framework you use, in our case, OMS3, and why you use it, instead of others. It also the system you are working with, like in our case GEOframe that provides ancillary tools. Finally the informatics can boil down to the algorithms and their organization in classes. Algorithms can be new or old and irrelevant. Just in the first case it is important to mention them with details, otherwise just a a little note can be done. Classes, assuming we are talking of some OO programming, have two scopes, one is to contain the algorithms, the other is to orchestrate the software relations in order to make easy the reuse of the softwares and their expansion. This part will be routine in future, maybe, but now it is not part of the common knowledge of hydrologist, and therefore it is worth to be explained if well engineered. In explaining classes and the overall working of the software using of UML diagrams is mandatory.

In a software paper, it is debatable what is the test of the contents. Let’s say that, because we are hydrologists, we need to test both the software running, and the models’ physics.

The software running test for who is programming in Java, like we do, is obtained through the appropriate Unit Tests and this part is commented, in case, inside the section which inherit from the Notebook Zero. For the physics we have, in turn, two modes. If we are solving problems, i.e. equations,  that have an analytical solution, then we have to reproduce the analytical results. Secondly the nasty reviewer, would also see that the model reproduces measurement. Getting some measurements to reproduce is then important. A third case is also ideally possible, which is that, no measurements are available and therefore eventually the model provide a possibility to test something that was never tried before. In this case it must be emphasized that the model makes possible something that before was not not, and we have to rely to some virtual, behavioural, experiment.

If measurements are involved, new methodological steps come in: explaining the case study, first. Secondly, not differently from other cases, we have to say if parameters to calibrate and to mention the techniques we use for doing it. Explaining how we assess the goodness of the results, and finally commenting the results are the rest of the story. An exceptionally good software that does not reproduce reality is simply not useful from the hydrology point of view, even if its implementation can still provide novelties worth to be explained. The physical test, however, should not extend to be very complicate but just functional to convince that the software is doing what it is designed to do. In the mentioned case of evapotranspiration, another issue is relevant, which is the comparison among sub-models or models alternative. It is clear that different models produce different results, so assessing in which case they work or work netter is important. However, that can be pursued with moderation in a “software presentation” paper, because this is clearly an argument which requires a paper by itself. For example , in a recent paper, Clark et al., 2021, they talk of “laugh test” for emphasizing this aspect.

At the end of the post, you have some ingredients and an idea of the procedure. To cook them together for a nice result is a little of art.  In general, a good example to follow is the WHETGEO paper.

Monday, November 8, 2021

GEOframe Winter School 2022 (GWS2022) - Save the dates Dec 20-22, 2021; January 10-14, 2022

December 20-22, 2021 - Installations and Informatics - Online

January 10 - 14 2022 - Onsite and Online

Scientific Committee: Prof. Riccardo Rigon, Ph.D.; Prof. Giuseppe Formetta, Ph.D; Ing. Niccolò Tubini, Ph.D., Ing. Marialaura Bancheri, Ph.D.

Organizing Committee: Ing. Concetta d’Amato, Eng. Shima Azimi, Ms. Sc. Martin Morlot, Ing. Daniele Andreis, Ing. Gaia Roati, Ing. Riccardo Busti (the fantastic group of our Ph.D. students)

Organizing Institutions:
  • Department of Civil, Environmental and Mechanical Engineering, University of Trento
  • Center Agriculture Food Environment, University of Trento
  • Institute for Agricultural and Forest Systems in the Mediterranean, National Research Council, Ercolano NA, Italy

GENERALITIES
GEOframe is a system for doing hydrology by computer. By saying that it is a system, we emphasize that it is not a model but an infrastructure that can contain many differentiated modelling solutions (some tens of that) that are built upon models components. This is because GEOframe leverage on the Object Modelling system-framework (v3) that allows to connect modelling components to solve a specific hydrological issue together and having many alternative for its mathematical/numerical description. This infrastructure allows adapting the tools to the problems and not viceversa. GEOframe has been applied to hydrological simulations from the point scale to large catchments as the Blue Nile, and among those is being deployed to the Po river (the largest in Italy) with great detail. GEOframe is open source and built with open source tools.

CONTENTS OF THE SCHOOL

GEOframe contains tens of components that cover rainfall-runoff, evaporation, transpiration, infiltration, terrain analysis tools, interpolation models, calibrations tools, and so on.
The Winter school is about using some of these tools to perform the hydrological budget of catchments. The core rainfall-runoff model are dynamical systems (systems of ordinary differential equations) and the school mainly treats their theory and their use in a contemporary way as summarized in these7 steps.
Besides the lectures and the hands-on sessions, the Summer School is the occasion for discussion and experience exchange among senior scholars and young researchers.

And Pizza party every night ! Just Kidding


PARTICIPANTS' BACKGROUND

Admissions are reserved to up to 30, PhD students and postdoctoral students, young researchers willing to learn the use of the GEOframe tools envisioned for the study of infiltration, energy budget, vegetation transpiration, water budget with process-based models
All students are asked to upload a CV and a motivation letter when applying.


WORKLOAD AND CREDITS

The Winter School which is to be held in English, consists of 8 hours/day of activities for 8 days. The first three days, 20-22 of December will be dedicate to the the installation of the new version of GEOframe-OMS system tools. Lectures will be brief, dedicated to informatics and the exploiting of the concepts of modeling by components, digital twin Earth and most of the time will be used for supporting participants’ installations.

The other five days (10-14 January) will cover:
  • Catchment and Hydrologic Response Unit delineation
  • Meteorological variables interpolation with Kriging techniques
  • Simple evapotranspiration methods
  • Rainfall-Runoff modelling (as explained in these 7 steps)

LOCATION & TIMING

University of Trento Polo Mesiano, H1 Room and Online. The three days on informatics and installations will be online. The others online and onsite. The time schedule will be 9-13 and 14-18 CET each of the days. Lectures and workout will be recorded and immediately post on the VIMEO Channel of the School and therefore they could be followed off line. Special agreement will be arranged for supporting abroad students with fuse issues.

PARTICIPATION COSTS

The cost is free for Students of the Hydrological Modelling Classes at the University of Trento, for Ph.D. students of the University of Trento DICAM and C3A programs, for the participants of the WATZON PRIN project and for all who wants to participate without having a certificate of GEOframe proficiency. Subscription to the class is necessary for anyone to receive the information to participate. For those who want the certificate, the Course costs 180 Euros. In any case the certificate is issued after the presentation of a small project of simulations for which appropriate tutoring will be given during and after the School.


CONTACTS

For further information write to: abouthydrology@google.com or to the Secretary of the Class dott. Lorena Galante, lorena.galante@unitn.it

OTHER INFORMATION

The GSS2022 talks and labs will be recorded and made publicly available during the School for self-training through the GEOframe blog (http://geoframe.blogspot.com). Information about past Schools can be found here.

GEOframe Soil Plants Atmosphere Continuum and hydrology Estimator (GEO-SPACE) essentials

GEO-SPACE (formerly known also as Lys-GEO in its its 1D implementation)  is intended to collect the growing set of GEOframe tools developed on the base of process-based philosophy. This can be found envisioned first in  Freeze and Harlan, 1969, and, fo instance well documented recently in Fatichi et al., 2016 and Paniconi and Putti, 2016. From a different point of view, it can be considered the upgrade of the GEOtop model, that still efficient and up-to-date, and more advanced than other similar models, was considered to be improvable from the algorithmic and informatics structure.  GEO-SPACE make leverage on the various common tools (components) shared with GEOframe-NewAGE and is made up  specifically of two main groups components, WHETGEO (mainly due, so far to the work of Niccolò Tubini) and the evaporation and transpiration, as follows from the work by Michele Bottazzi and Concetta D'Amato (ET-GEO). 



At present the development of GEO-SPACE (to become GEOtop 4.0) has still to achieve some goals, including the connection of plants treatment on WHETGEO 2D, the implementation of WHETGEO-3D, and so on. The current status of the project can be well described looking at the material presented at the Summer Schools on GEOframe that started in 2021 and will be held usually in week in middle June every year.  The most recent School addresses the more recent material. 

We remind here below, the general declaratory about GEOframe:

GEOframe is a system for doing hydrology by computer. By saying that it is a system, we emphasize that it is not a model but an infrastructure that can contain many differentiated modelling solutions (some tens of that) that are built upon models components. This is because GEOframe leverage on the Object Modelling system-framework (v3) that allows to connect modelling components to solve a specific hydrological issue together and having many alternative for its mathematical/numerical description. This infrastructure allows adapting the tools to the problems and not viceversa. In GEOframe particular attention has been dedicated to allow enhancements and additions writing the less code possible. The core code has been designed to open to addition and closed to modifications, thus allowing stability over time.  The systems contains tens of components that cover rainfall-runoff, evaporation, transpiration, infiltration, terrain analysis tools, interpolation models, calibrations tools, and so on. Every modelling paradigm is included, as, for instance process based modelling, lumped modelling, machine learning, or can be included. Spatially disjoint catchments can be modelled separately and joined together in a bigger model. GEOframe has been applied to hydrological simulations from the point scale to large catchments as the Blue Nile, and among those is being deployed to the Po river. GEOframe is open source and built with open source tools.

References

Fatichi, Simone, Enrique R. Vivoni, Fred L. Ogden, Valeriy Y. Ivanov, Benjamin Mirus, David Gochis, Charles W. Downer, et al. 2016. “An Overview of Current Applications, Challenges, and Future Trends in Distributed Process-Based Models in Hydrology.” Journal of Hydrology 537 (C): 45–60.

Freeze, R. Allan, and R. L. Harlan. 1969. “Blueprint for a Physically-Based, Digitally-Simulated Hydrologic Response Model.” Journal of Hydrology 9 (3): 237–58.

Paniconi, Claudio, and Mario Putti. 2015. “Physically Based Modeling in Catchment Hydrology at 50: Survey and Outlook.” Water Resources Research 51 (9): 7090–7129.

Tubini, Niccolò, and Riccardo Rigon. n.d. “Implementing the Water, HEat and Transport Model in GEOframe (WHETGEO): Algorithms, Informatics, Design Patterns, Open Science Features and 1D Deployment.Geoscientific Models Development Discussions.

Thursday, November 4, 2021

Seven Steps Into Catchments analysis by Hydrological models

 First step: Overall


Define the overall scope of the analysis. (e.g. Blöschl et al., 2019)
Document about the literature existing on the catchments. Including papers appeared in any type of studies.  Choose a large set of  performances indicators (depending on the model use and objectives) (Addor et al., 2017).  Set a strategy for assessing the results uncertainty and variability. (e.g. Clark et al., )

Second step: Geomorphology

Extract the catchment from DEM by state-of-art  analysis tools (as TauDEM or the Horton Machine Toolbox). Investigate if the surface catchment corresponds to the effective catchment (i.e. if including/excluding karst is an option). Control the surface water network extension (talk at the GSS2021). Analyze the presence and the number of lakes/reservoirs. Pay attention to endorheic catchments. Discuss the catchment connectivity.

Third step: Hydrological Data

Analyze the time series of available data and make a comparison  between rainfall and runoff amounts. Analyze any other time series or map time series, like  map of snow and evapotranspiration (Abera et al., 2017). Define the calibration set and the validation set.


Fourth step: Modelling Setup

Setup the space partitioning in hydrologic response units  (e.g. Dal Molin, 2021). Discuss the data density required (or possible) to give robust results or, viceversa, reduce your objectives to something achievable with the data available.   Choose the model among existing ones for adequacy not for legacy (Addor, 2019).  Choose a model structure as hypothesis zero (Fenicia and Kavetski, 2021, VimeoVideo).*  Setup the modelling solution (MS). Choose the better modelling structure (Clark et al., 2011).  Analyze the MS  parameters and discuss their variability.  Plan the model runs thinking to open science protocols (Hall et al., 2021). 

Fifth step: Modelling Execution

Executing the model, including discharges, snow and ET. Annotate the model performances issues. 

Sixth step: Results Delivery

Show the results appropriately (discharge analysis is not the only one quantity to watch at).  Analyze the performances of indicators. Add comments and discussion. Assess results confidence.

Seventh step: Deployment

Deploy the results for open science and public discussion (e.g. Hall et al., 2021). 

Notes

*With regards to the modelling structure, if you are using ODEs for modelling, consider a standard way to visualize and describe the model structure. As many know, the Extended Petri Net can be a sound way to do it. 

Some Slides and Videos about the above topics:

References

Abera, W., G. Formetta, and L. Brocca. 2017. “Modeling the Water Budget of the Upper Blue Nile Basin Using the JGrass-NewAge Model System and Satellite Data.” Hydrology and Earth System Sciences. http://nora.nerc.ac.uk/id/eprint/517346/.

Addor, Nans, Andrew J. Newman, Naoki Mizukami, and Martyn P. Clark. 2017. “The CAMELS Data Set: Catchment Attributes and Meteorology for Large-Sample Studies.” Hydrology and Earth System Sciences 21 (10): 5293–5313.

Addor, N., and L. A. Melsen. 2019. “Legacy, Rather Than Adequacy, Drives the Selection of Hydrological Models.” Water Resources Research 55 (1): 378–90.

Blöschl, Günter, Marc F. P. Bierkens, Antonio Chambel, Christophe Cudennec, Georgia Destouni, Aldo Fiori, James W. Kirchner, et al. 2019. “Twenty-Three Unsolved Problems in Hydrology (UPH) – a Community Perspective.” Hydrological Sciences Journal 64 (10): 1141–58.

Clark, Martyn P., Andrew G. Slater, David E. Rupp, Ross A. Woods, Jasper A. Vrugt, Hoshin V. Gupta, Thorsten Wagener, and Lauren E. Hay. 2008. “Framework for Understanding Structural Errors (FUSE): A Modular Framework to Diagnose Differences between Hydrological Models.” Water Resources Research, Water Sci. Appl., 44 (12): 2135.

Clark, Martyn P., Dmitri Kavetski, and Fabrizio Fenicia. 2011. “Pursuing the Method of Multiple Working Hypotheses for Hydrological Modeling: HYPOTHESIS TESTING IN HYDROLOGY.” Water Resources Research 47 (9). https://doi.org/10.1029/2010wr009827.

Dal Molin, Marco. 2021. “Improvement and Application of Flexible Frameworks for Modelling Regional Streamflow Variability.” Edited by Marco Schirmer Fabrizio Fenicia. Ph.D., Université de Neuchâtel.

Fenicia, Fabrizio, and Dmitri Kavetski. 2021. “Behind Every Robust Result Is a Robust Method: Perspectives from a Case Study and Publication Process in Hydrological Modelling.” Hydrological Processes 35 (8). https://doi.org/10.1002/hyp.14266.

Hall, Caitlyn A., Sheila M. Saia, Andrea L. Popp, Nilay Dogulu, Stanislaus J. Schymanski, Niels Drost, Tim van Emmerik, and Rolf Hut. 2021. “A Hydrologist’s Guide to Open Science.” Hydrol. Earth Syst. Sci. https://doi.org/10.5194/hess-2021-392.