Showing posts with label Distributed Modeling. Show all posts
Showing posts with label Distributed Modeling. Show all posts

Friday, July 3, 2020

On Doing Large-Scale Hydrology with Lions: Realising the Value of Perceptual Models and Knowledge Accumulation A Review.

This is a review of the paper by Wagener, Thorsten, Tom Gleeson, Gemma Coxon, Andreas Hartmann, Nicholas Howden, Francesca Pianosi, Shams Rahman, Rafael Rosolem, Lina Stein, and Ross Woods. 2020. “On Doing Large-Scale Hydrology with Lions: Realising the Value of Perceptual Models and Knowledge Accumulation.” EarthArXiv. https://doi.org/10.31223/osf.io/zdy5n.

Since the Authors uploaded it to EarthArXiv making it available as Preprint, My review can be public too. 

The paper main statement can be formulated by saying that in global hydrology and related science there remain large areas of knowledge which could be easily explored because we have now the data and the tools to do it, but we do not do. There are unexplored geographical regions and substantially the Authors asks for a “everywhere modelling effort” by saying that as in the old maps where it was written “hic sunt leones” there are large areas on Earth whose hydrology is essentially unknown (a known unknown indeed).  They have a point.  The paper's language is good and the writing pleasant but I would prefer a more simpler organization which focuses more on the two or three main statements. A sound knowledge of literature is interesting for the general reader but it is not in my opinion used to focalise the issues. On the contrary there are a lot of paragraph that, reporting the state of art, let with the impression that there is no problem at all. This does not mean that those paragraph, read alone, are not well written, informed, or interesting but they do not serve to goal of highlighting well the issues. You get easily the main ideas but I had difficulties to grasp the whole paper contents, even after many readings. For instance, "the lions" refers to the known-unknown, I cited above, or to an unknown-unknown with regards models' structure and their granularity how the manuscript seems to indicate sometimes ?

I understand that the Authors invoke two main solutions for the issues they rise:
  • a larger sharing of perceptual models of catchments
  • better strategies for organization of the current knowledge which is seen as not efficient with systematic metadata, development of tools for knowledge harvesting, standardization of databases and data in general.

These two directions of work are remarked within two sections, and I would say that without this separation, I would have hard time to obtain this synthesis.

Understanding what a “perceptual model” is,  is  part of making the reader understand the concepts supported by the Authors. What a perceptual model is, however, is not clarified in the paper, and could remain obscure to non-hydrologists.   What is that ? Can they define it more precisely ? Is it a drawing ? Is a set of relations ? Has it a specific mathematical representation ? Overall,  I believe a little more should be said on what a hydrological models at large scale are, without fall into an annoying classification or taxonomy but discussing what these models are or should be. Recently, Frigg et al (2020) tried a general  discussion on scientific models from the point of view of philosophy of science which could help to clarify what these models are.

The domain of the paper is a little slippery. While the title of the paper and the main statements look at the large-scale hydrology, sometimes, the Authors indulge in observations that have to do with a finer granularity of the processes than the one required by this type of modelling. Maybe there is a lack of definition of what “large-scale hydrology” is, especially with respect to the methods, and the granularity of the processes described. The Authors should adopt or try one. Not that it cannot be partially deduced from what it is written in the present manuscript, but this knowledge should not be given for granted in readers who come from other disciplines.

A final comment have to be made on the advancement of science.  The Authors cite Popper and Kuhn but I do not think their topic is in the same domain, which is in my opinion in the area of theories and interpretations of  a theory, but in the application of a given theory (or a set of theories) to the cases to which it is thinkable they could apply. Therefore I would esclude a “Kuhnnian” direction here. Eventually the topic here could be the practice of Popperian theory of falsification. If the repeated application of the models reveals unsatisfactory in fact, it could bring to the necessity of a new theory or a new model.
But I guess this grows too philosophical for me and I do not want to pursue this argument further, I concede I do not have the understanding required to treat it properly.

Therefore, I like very much the issue the paper rises and I think that the topic is of interest for hydrologists and a wider audience. However, I think that the Author should make the effort to reframe and refocus a little bit more their manuscript.

Below some sparse comments on specific statements.

Page 6 - Line 1 “… for new scales of management …” What doest it means ? It seems to me, whatever it means, that it diverts the attention from the fact that “it also contains hydrologic lions" is the point by moving the thinking to the lateral issue of scale of analysis.

Page 8 - Line 5  - I think the main problems with pure data assimilation is that it tends to be erroneously inductive, without any   hypothesis to test. Some phrases that follow in the subsequent pages, seem to support that science advancement is not hypotetical-deductive but inductive.  This is, maybe, a marginal point in the context of the paper, but, because I think it is wrong, I ask the Authors to be more clear on it.

Page 9 - Line 12 - “As Mc Donnell et al. …” - Yes, correct, but: how this statement is coupled with large-scale hydrology ? Does it means a support to the reductionist view that, if we describe well all the hillslope of the world, we have the best large scale-model ? Secondly, it is used to support  inductivism ? Or to deny it ?

Page 9 - Line 44 - “How much can we reduce model uncertainty … “. This phrase conveys the idea that  large scale models should be constrained by some expected large scale behavior. But what does have to do with the hydrologic "lions" ?  I was expecting from the geographical example that these "lions" were referring to unexplored geographical areas, where data or modelling are scanty, not to the general aspect of modelling. Do the Authors mean that we apply our models to large areas but nevertheless we do not know well their validity and foundations (other Lions indeed) ? If it is so, maybe the concept of lions is not so clear too me, and the authors should clarify more its extent.

Page 9 - Line 48 - "Some studies have shown that simpler …” This regards again the “inner Lions” of the large scale hydrological modelling. It is a critique of the way such model are actually done and verified. The Authors suggest (probably with some unexpressed example in mind) a directions to better characterizing those models.  I agree with the single statements, but I do not feel the topic is properly prepared and introduced/discussed in the paper.

Page 9 - Is, to their knowledge, Boorman 1995 the unique paper that deals with conceptualised parameters of a model ?  It was 25 years ago though. Or did I misunderstand what you want to say ?

Page 9 - Line 55 - “It has been widely discussed … “ Frankly, I do not buy this statement. It is not exactly true that complex models, as those, for instance that solve partial differential equation have this degrees of freedom in practice. There are, at least,  two reasons for that: 1 - Models that conserve mass (and BTW energy) usually cannot be stretched to reproduce any measured time series as accurately as one desires (for instance, a model that solves Richards equations cannot reproduce macropores flow with any characterization of the soil parameters); 2 - Even if, in principle, optimization of the parameters of a spatially distributed model can involve arbitrary and different values of the parameters in each site, in practice the calibration is extremely time consuming and usually unfeasible even with a ten of them.  Therefore the possibility to really explore a large set of parameters in high dimension is simply not possible. I’ve tried it several times. If anything, the strength of physically based spatially distributed models is their physics,  the capability to accomodate heterogenous inputs and obtain spatially distributed outputs.

Page 11 - Line 8 - “Supervisors” I would better say “oral communication”, like for instance the one given by Tom Dunne.

Page 12 - line 51 - Among the experiences that merit to be cited in categorizing the hydrological description, at least two should be cited: the CF (https://cfconventions.org/) convention and the Basic Model Interface (now in its second version: https://bmi-spec.readthedocs.io/en/latest/).


References

Frigg, Roman, and Stephan Hartmann. 2020. “Models in Science.” In The Stanford Encyclopedia of Philosophy, edited by Edward N. Zalta, Spring 2020. Metaphysics Research Lab, Stanford University. https://plato.stanford.edu/archives/spr2020/entries/models-science/.

Sunday, August 26, 2018

Winter School on the GEOframe system

The course for doctoral students, post docs and young researchers in Hydrology, Forestry, and related disciplines will cover the simulation of the hydrological cycle of catchments of various sizes with the GEOframe system. To know about GEOframe and GEOframe-NewAGE, please refer to here.

They say that all models are wrong but useful. However, with better tools you forecast and decide better.

The course will enroll at most thirty students and will be held at the Department of Civil, Environmental and Mechanical Engineering of Trento from January 8 to January 18 included.
The course will be of totally 68 hours (8 a day) of which 34 (4 each day) will be dedicated to laboratory and personal work under the supervision of tutors. The course includes as option to get an exam certification, upon the completion of an exercise, to have doctoral credits.

Subscription at: https://webmagazine.unitn.it/en/evento/dicam/44808/geoframe-newage-winter-school

Instructors

  • Riccardo Rigon
  • Michele Bottazzi
  • Niccolò Tubini
with material prepared by
  • Giovanna Dalpiaz
  • Marialaura Bancheri


The  topics treated has been:


Why choosing GEOframe over other models/platforms ? I would say for:
  • Flexibility: GEOframe is not a model but a system of components that interact at run-time. You can chose among various components options for any of the processes.
  • Expandability: If you like to program, with a little investment in Java you can write your own component and make them to interact with the others without having to reinvent the wheel.
  • Parallelism. Components work in parallel when their tasks do not interact, but this is transparent for you (we call it implicit parallelism). 
  • Spatial discretisation. A catchment is subdivided in parts (HRU) which can be modeled separately and are computed in parallel. The network structure is used to achieve the spatial parallelism. Its spatial modularity can be used to add/cut part of the basins without having to redo the spatial analysis, for doing multisite calibration, to progress the analysis of a larger basin in parts that are assembled together eventually.
  • Beyond-state-of art components.  Besides traditional approach to processes, we implemented a few new ideas for all the processes we covered.
  • Reliability.  GEOframe is currently used for the flood forecasting in real time by Regione Basilicata. It is not just a system for research that does not work in real cases. 
  • Tracers studies. Not treated in the school are present tools for doing tracers studies,
  • Process based modelling.  Not treated in the school, we have tools for integrating Richards equation in 1D, and we are developing tools for integrating it in 2d and 3d coupling it with the energy budget. These components will be able to interact with the other. We also started new developments on freezing soil and snow modelling.

The cost of the course for early subscribers is 270 Euros which includes lunch and parsimonious coffee-breaks  Member of SII, The Italian hydrological Society have a discount of 20 Euros. Cost of late subscribers (after November 15, 2018) is 370 Euros. 

After November 15 some work will be required to participant in order to setup their tools for running GEOframe. Installation of Java (version 8), installation of the Object Modelling System console, Installation of Python and Python notebooks, testing the use of some file formats. After the accomplishment of the requirements, students will be allow to bring their own study cases at the School.

Who wants to have early information or clarifications can write to me: riccardo.rigon at unit.it. Subscription page at:

https://webmagazine.unitn.it/en/evento/dicam/44808/geoframe-newage-winter-school

Saturday, May 20, 2017

ARS-AGEs is finally public

That is a news that I was waiting since a long time. AGEs is one of the other models that is based on the Object Modelling System infrastructure, and therefore a possible source of available components in our modelling based on GEOframe and JGrass-NewAGE tools.  I always beg for they to do this step, in order to have a clear basis on which to start collaborations and convergences. Finally they did.
Please, click on the image above for accessing the Bitbucket public repository.  They write:

"The Agricultural Ecosystem Services (AgES) model is a modular, Java-based spatially distributed environmental model which implements hydrologic/water quality simulation components under the Java Connection Framework (JCF) environmental modeling framework."

Actually, I do not like the word "JCF" which I do not know what exactly means, but is, anyway, a step forward openess that I appreciate.

Monday, May 16, 2016

The JGrass-NewAGE system essentials: concepts, deployment, case studies and use cases

This is the talk I gave in Parma at ARPAE. In a mood for collaboration, I presented our modelling ssytem JGrass-NewAGE and out process-based model GEOtop 2.0. The presentation about GEOtop does not contain anything essentially new. It is a synthesis of the talk I gave in San Francisco in December 2013 (I and II). The presentation about JGrass-NewAGE, at the beginning, revisited a presentation I gave in 2008 at CUASHI biennial meeting (and includes now OMS instead than OpenMI)
However, it continues by showing and discussing some of the main components of the system, now documented in the GEOframe blog. Eventually shows some applications of the model and some ways to combine the components in modelling solutions.
The fact that many thoughts that I made at that time are still valid is reassuring. Obviously now we are much more close to the objective, and the codes are more robust and reliable than eight years ago.  Clicking on the figure above, please find the presentation on one of my channel in SlideShare. A longer version of the concepts part will be in a companion posts.

Saturday, May 14, 2016

PRECISE: PRocess-based ECohydrology In grasSland Ecosystems

We presented Project PRECISE to the last EUREGIO call. We know that competition is high but the project objctive are really important: of practical and theoretical use. Besides, they are based on existing experimental infrastructures and models, which would have the occasion to be maintained and evolved.  Collaborations inside the project would be of very high quality.

The overall goal of the project PRECISE is to advance ecohydrological modeling in mountain grassland ecosystems (with an eye to towards generalisation for other types of vegetation), in order to have quantitative instruments that supports management and impact assessment studies. In particular, we want to improve our understanding and modeling capability of the effects of climate, soil, topography and plant functional types on the water balance (with a particular focus on evapotranspiration - ET) and vegetation productivity in alpine grassland ecosystems in a range of scales from plot to hillslope.

We address the following research questions:

R1. How does plant functional diversity and plant water-use strategy influence the watervarying abiotic conditions (i.e. soil physics, topography, climate)?

R2. Which is the relative role of biotic (plant functional diversity) versus abiotic (soils, topography, climate) processes in determining the spatial and-temporal variability of ET from the plot to the hillslope scale?

R3. Which is the right level of complexity necessary in models to produce R3 at any scale of interest?
R4. How to take advantage of a combination of advanced multi-sensor, multi scale observations to better constrain and improve spatial accuracy in coupled, process based ecohydrological models?

1.2 State of the art

1.2.1 Ecohydrological modeling of plant-water interactions

In recent years, plant-physiology studies provided an increasingly detailed knowledge of the small details of plants behavior, but only some of which started to be inserted in ecohydrological models (Fatichi et al., 2015b). These include stomata actions and photosynthesis. Two main categories of models can be roughly individuated to this respect: those who approach the problem very mechanistically (Fatichi et al., 2012a), by adding detailed processes parameterizations, and those who make reference to optimality principles (Prentice et al., 2015), claiming that feedback mechanisms were discovered during plants evolution to maintain good performances under sub-optimal conditions (Prentice et al., 2015).
Most advanced plot-to-catchment scale models include a three-dimensional treatment of the water fluxes in soil, explicit spatial variability of atmospheric forcing and turbulence, and a well-balanced complexity in the formulation of the water and energy budgets. These aspects cannot be simply reduced to factors external to the vegetation dynamics, when focusing on the hydrological cycle, and not on a single plant. Among these models are GEOtop-dv (Della Chiesa et al., 2014; Endrizzi et al., 2014) and Tethys-Chloris (Fatichi et al., 2012a, 2012b).
To further develop this models, a new infrastructure is deemed necessary in order to enable comparisons of the alternative models that are emerging very fast from research. In fact, the monolithic informatics of traditional design (Rizzoli et al., 2004) hinder any change of the code and slow-down progresses of research. Fortunately, recently “component-oriented” modeling approaches (e.g. David et al., 2013; Formetta et al., 2014) were deployed. Such approaches make it easier to change modules simulating specific processes, while maintaining unchanged the others.
Three modeling challenges are faced by modelers. The first is to model water and carbon processes of a single plant in its entirety from roots to leafs, upscaling cellular micro-physiology at a reasonable coarse-grained level. The second challenge is to differentiate vegetation types in a sound way. Today this is addressed by abstracting plants in functional types (PFT, e.g. Bonan, 2002), which definition is widely criticized. More recently, however, research has focused on the definition of plant traits which correspond more closely to models’ parameters (Fyllas et al., 2014). The third challenge is to link plant physiology with the biosphere as a whole, considering the interactions with pedo- and atmosphere (including spatial and temporal patterns). This task, has, in turn, many aspects. It involves: (1) an appropriate modeling of the environmental conditions, especially turbulence (Bertoldi et al., 2007; Siqueira et al., 2009);(2) the mathematical description of soil water interaction with roots and the reciprocal influence of plants for accessing energy and nutrient resources (Manoli et al., 2014); (3) a more accurate separation of soil evaporation from transpiration (Jung et al., 2010; Lawrence et al., 2007); (4) and of plant transpiration from groundwater and streamflow (Evaristo et al., 2015); (5) and, finally, the need to upscale the mathematics of plants behavior at the hillslope scale, with the appropriate degree of complexity. This last point is a key issue, especially in mountain terrain, given the nonlinear dynamics inherent to hydrological and vegetation processes. Although, the process’ importance and heterogeneity clearly changes with the spatial scale, the conceptualization remains the same, and - so far - similar approaches have been used on very different scales (Pappas et al., 2015). On the other hand, the pool of observational data vastly expanded in the past couple decades, bearing opportunities for modellers to pursue quantitative explanations of what is observed, and predict the spatial variation of parameters. The challenge is now to make use of the extensive data pool to test hypotheses generated from optimality principles, select the one that gives the right answer, and finally meet the requirement of models reliability (Prentice et al., 2015).

1.2.2 Experimental estimation of plant-water interactions

In-depth understanding of plant-water interactions drives accurate quantification of the water budget, where biophysical parameters (e.g. biomass) play a key role. However, to correctly assess canopy stomatal conductance and biophysical parameters controlling the water balance equation, plant functional diversity (i.e. biomass abundance of grasses, herbs, legumes, dwarf shrubs) have to be considered. Regarding ET, which is the key part in the water budget driven by vegetation, plant water-use strategies of existing species within individual plant functional types significantly bias biomass-ET correlations (Della Chiesa et al., 2014; Leitinger et al., 2015). Mitchell et al., (2008) already defined ‘hydraulic functional types (HFT)’, which revealed promising results to characterize plant communities regarding their ecohydrological characteristics. However, although (1) methods to assess plant trait diversity in the field (Lavorel et al., 2008) and (2) a trait database with steadily increasing numbers of plant traits (Kattge et al., 2011) exist, this aspect is virtually inexistent in ecohydrological models. Moreover, once the implementation of plant functional diversity is satisfactorily achieved, the dynamics of ET under field conditions (i.e. soil moisture, and microclimate) have to be introduced to finally assess needed crop ET. When measuring ET, two types can be distinguished: (1) water budget- and (2) water vapour transfer measurements. Water budget methods measure incoming and outgoing fluxes of water, while water vapour transfer methods assess the flow of water vapour. Most known among the latter is Eddy Covariance, operating at field scale and not usable to fully address the water budget. Among the water budget methods, lysimeter measurements are of growing interest, as they operate at plot scale and with individual samples (also referred to as ‘sample’ scale). High precision lysimeters evaluate all the water budget components and are state-of-the-art to entangle biotic responses (Schrader et al., 2013). Accompanying phytosociological-, soil physical-, and soil hydrological data are needed to fully explore the relationship between biomass and crop ET. Moreover, lysimeters are suitable to separate evaporation from transpiration for varying micrometeorological conditions and soil characteristics ,providing valuable parameters for eco hydrological modeling. The overall aim of in-situ water budget analyses in PRECISE is to provide guidelines for ecohydrological model selection, considering sensitivity of model output to input parameters in order to subsequently detect structural deficits of the model itself (i.e. to reduce model complexity where possible and increase precision of system representation).

1.2.3 Use of proximal sensing of vegetation for ecohydrological modeling

Plant-water interactions can be addressed form the cellular up the global scale, and are studied by different scientific communities. There is an inconsistency – both in term of approaches and scales of interests - between the lysimeter community, focused on confined vegetation patches, the Eddy Covariance (EC) community (represented by the FLUXNET-ICOS networks), measuring carbon and water fluxes at the ecosystem level, the hydrological community working at watershed scale, and the remote sensing (RS) community working at regional scale (Fatichi et al., 2015b). If data from these communities can be interconnected, a step-change in the scientific understanding of ecohydrological cycling will be achievable. However, scale gaps first need to be bridged.
UAV platforms are a key instrument for solving many of the scale issues in measuring and modeling processes involving vegetation interactions with the earth and the atmosphere. First, UAV-borne observations can support ground measurements, allowing not only to upscale local observations to entire ecosystems, but also to interpret limited observations in a wider context. Second, they can be integrated with hydrological models both by providing high-resolution distributed input data, and for evaluating model performances. Third, they are a unique source of validation data for remote sensing observations.
UAV applications in geoscience, rely on the collection of multi-, hyper-spectral in the visible and near infrared portion of the spectrum and thermal imagery. The first allows retrieving information of vegetation structure, calculating vegetation indexes, like NDVI, and inverting radiative transfer models for retrieving spatially explicit information about biophysical parameters (Calderón et al., 2013; Duan et al., 2014; Zarco-Tejada et al., 2012). The second is useful for measuring land surface temperature (LST) at a very fine resolution, up to the single leaves (Gonzalez-Dugo et al., 2013).
The combination of an energy balance model with UAV thermal infrared data with a resolution of few centimetres offers a new perspective for ET and SM mapping. Involved processes can be addressed at a proper spatial scale. One promising approach is the two-source energy balance model (TSEB) (Kustas and Norman, 1999), and it extensions ALEXI/DisALEXI (Anderson et al., 2008), which computes the surface energy budget for the soil and canopy components directly from LST and LAI observations. From the point of view of the spatial and temporal resolution, the availability of UAVs allows a big improvement with respect to satellites (Hoffmann et al., 2015).
In this project, we want to exploit hi-resolution maps of vegetation properties, LST and surface energy fluxes for a spatially distributed validation of process-based, distributed ecohydrological models. The current research challenge is to directly implement in process-based models the possibility to use observations coming from remote and proximal sensing. In this sense, high resolution data integrated with the modular modeling system we will implement in this project will offer unforeseen chances for testing new hypotheses with different model formulations.

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Saturday, March 26, 2016

Process based simulation of the hydrological cycle

The one below is a concept paper (or a review, under certain aspects) of researchers that thought at a certain moment of their carrier that lumped models were not enough. Criticism was often raised on this type of models (sometimes by bad modellers or by researchers in love with their own products: nobody's perfect).  Who follows me knows that both lumped (yes, up to a point) and distributed models are in my past research. Whatever party you belong to,  I think the paper is a good reading which summarises a lot of issues and give a view of the current state-of-art.
Clicking on the picture above, please find the paper's pdf.

Saturday, March 21, 2015

Four interesting papers on Hydrological modelling

I met the first time Martyn Clark in Fort Collins last summer. USGS scientist Stacey Archfield organised a meeting for modellers (to which I was not invited :-( ), and Martyn was part of the crew.
I did not his work up to recently. and after our meeting, he came out with three Water Resources Research Papers, that I am listing here for subsequent readings.


Clark, M. P., Kavetski, D., & Fenicia, F. (2011). Pursuing the method of multiple working hypotheses for hydrological modeling. Water Resources Research, 47(9), n/a–n/a. doi:10.1029/2010WR009827

Pablo A. Mendoza, Martyn P. Clark, Michael Barlage, Balaji Rajagopalan, Luis Samaniego, Gab Abramowitz and Hoshin Gupta, Are we unnecessarily constraining the agility of complex process-based models? , Water Resources Research, Volume 51, Issue 1, pages 716–728, January 2015

Clark, M. P., B. Nijssen, J. Lundquist, D. Kavetski, D. E. Rupp, R. A. Woods, J. E. Freer, E. D. Gutmann, A. E. Wood, L. D. Brekke, J. A. Arnold, D. Gochis, R. Rasmussen. 2015. A unified approach for process-based hydrologic modeling: Part 1. Modeling concept, Water Resources Research, doi:10.1002/2015WR017198.

Clark, M. P., B. Nijssen, J. Lundquist, D. Kavetski, D. E. Rupp, R. A. Woods, E. D. Gutmann, A. W. Wood, D. Gochis, R. Rasmussen, D. Tarboton, V. Mahat, G. Flerschinger, D. Marks. 2015. A unified approach for process-based hydrologic modeling: Part 2. Model implementation and case studies, Water Resources Research, doi:10.1002/2015WR017200.


A late addition, the technical note regarding this SUMMA stuff.

Tuesday, February 10, 2015

GEOtop essentials

Being one of my more fruitful research products, GEOtop has so many posts that it can be really difficult to understand what it is in brief. GEOtop is a unique blend of a process-based hydrological model and a Land Surface Model. It in fact integrates both the water and energy budget: a characteristics that differentiate it from many other models. Recently there were many efforts in the same direction. However, these efforts combine different models together, while in GEOtop the processes description is intimately tied.

To start with GEOtop probably the best way is to read the two most general papers first.

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

A set of around 30 hours video lectures is available from here.

Subsequently a good reading could be the history of GEOtop, meaning understanding the motivation that guided us in building it:
Second part: Up to version 0.5
First Part: The addition of Land atmosphere interactions, and beyond.
The not-so-out-of-date manual, can be found here.

All the journal papers published in Journals, here.
The main presentations (mostly invited) about GEOtop can be found here. 

We were used to compile and provide executables of GEOtop code for any platform (see old Executables for Mac OS X Yosemite, Executables for Windows 7, Executables for Linux).

However, very recently, we "dockerised" the code, which is now available at the docker hub (this marks some difference with what explained in the video lectures).
There are two mailing for GEOtop:
Both of them contain relevant information and are the place where to ask for help (depending on which is your case) keeping in mind that GEOtop is an open source project with a very low financial support, so any answer is a courtesy not a duty.

The official repository of the code is on GIThub.
The overall set of information, including new directions, is here.
A set of matlab script for importing and exporting data is here.

Saturday, January 10, 2015

Matching process based modelling and remote sensing

This blog post summarizes a recent discussion I have had with Luca Brocca concerning the use of remote sensing data in hydrological applications. As you know, I have expertise on the description of the hydrological processes and on the development/implementation of physically-based hydrological models (i.e., GEOtop [1,2]). Luca has experience on the use and assimilation of remote sensing products of soil moisture and rainfall into hydrological model for improving hydrological predictions (e.g. flood [3] and landslide [4] forecasting).

Our starting viewpoints on remote sensing products are quite dissimilar. Luca has a lot of confidence on satellite data and he found in his research activity that remote sensing could be highly important for improving the modelling and prediction of hydrological processes (see, e.g., his recent interview on Research Gate and [5]). On my side, I believe that remote sensing products are derived from sensors data without strong reference to reasonable hydrological modelling. In fact, most of the times, remote sensing products are not the results of assimilation (or fusion) of data with hydrological models, but the outcome of procedures that may involve strong hydrological assumptions that remain implicit. This in my view constitutes a bad practice and a source of large mismatching between the results of the two communities.

In a recent post, it is highlighted how even physically-based and fully 3D hydrological models may fail in reproducing the spatial variability of soil moisture (e.g., [6]), and similar results were found in the comparison of satellite and modelled soil moisture data (e.g. [7]). Studies that attempted to used satellite rainfall data as input (see in [8]) or assimilated satellite soil moisture data [9] into rainfall-runoff models usually found several issues that still need to be addressed.

These issues can be addressed in two ways. I told Luca that a model of the sensor should be available from the side of the hydrological models, in which the process-based models can give all the information necessary to reproduce the expected results as seen from the sensors. In this way, a more direct assimilation could be made without undeclared passages that introduce bias in the products. Luca replied on the need to improve the structure of conceptual hydrological models (usually employed in most of the studies) to better fit what is measured from satellite sensors (see the discussion paragraph in [3]). In both cases, we are suggesting that the two communities, hydrologists and remote sensing scientists, should start a stronger and closer collaboration. It should not happen that hydrologists use satellite data simply as end-user without giving feedback to remote sensing scientists, and viceversa remote sensing scientists should take care of the suggestions and criticism made by hydrologists. From the close collaboration both communities can highly benefit providing improved models and satellite products each other!

REFERENCES

[1] Rigon, R., Bertoldi, G., and T.M. Over,  GEOtop: A distributed hydrological model with coupled water and energy budgets, Jour. of Hydrommet. , 7(3), 371-388, 2006

[2] Endrizzi, S., Gruber, S., Dall'Amico, M., and Rigon, R. (2014). GEOtop 2.0: simulating the combined energy and water balance at and below the land surface accounting for soil freezing, snow cover and terrain effect. Geosci. Model Dev., 7, 2831-2857, doi:10.5194/gmd-7-2831-2014.

[3] Brocca, L., Moramarco, T., Melone, F., Wagner, W., Hasenauer, S., Hahn, S. (2012). Assimilation of surface and root-zone ASCAT soil moisture products into rainfall-runoff modelling. IEEE Transactions on Geoscience and Remote Sensing, 50(7), 2542-2555, doi:10.1109/TGRS.2011.2177468.

[4] Brocca, L., Ponziani, F., Moramarco, T., Melone, F., Berni, N., Wagner, W. (2012). Improving landslide forecasting using ASCAT-derived soil moisture data: A case study of the Torgiovannetto landslide in central Italy. Remote Sensing, 4(5), 1232-1244, doi:10.3390/rs4051232.

[5] Brocca, L., Ciabatta, L., Massari, C., Moramarco, T., Hahn, S., Hasenauer, S., Kidd, R., Dorigo, W., Wagner, W., Levizzani, V. (2014). Soil as a natural rain gauge: estimating global rainfall from satellite soil moisture data. Journal of Geophysical Research, 119(9), 5128-5141, doi:10.1002/2014JD021489.

[6] Cornelissen, T., Diekkrüger, B. Bogena, H.R. (2014). Significance of scale and lower boundary condition in the 3D simulation of hydrological processes and soil moisture variability in a forested headwater catchment. Journal of Hydrology, 516, 140-153, doi: 10.1016/j.jhydrol.2014.01.060.

[7] Li, B. and Rodell, M. (2013). Spatial variability and its scale dependency of observed and modeled soil moisture over different climate regions. Hydrol. Earth Syst. Sci., 17, 1177-1188, doi:10.5194/hess-17-1177-2013.

[8] Alvarez-Garreton, C., Ryu, D., Western, A. W., Su, C.-H., Crow, W. T., Robertson, D. E., and Leahy, C. (2014). Improving operational flood ensemble prediction by the assimilation of satellite soil moisture: comparison between lumped and semi-distributed schemes. Hydrol. Earth Syst. Sci. Discuss., 11, 10635-10681, doi:10.5194/hessd-11-10635-2014.

Monday, December 29, 2014

MeteoIO

As known, we use MeteoIO in our GEOtop 2.0. Despite the fact that we implemented most of the same capabilities inside GEOtop directly. And despite we also reimplemented the same (and in some case more articulate possibilities inside JGrass-NewAGE). Many the reasons: having alternatives to compare is good; it is not possible to keep pace in every subject necessary to built a modeling system, and having someone doing things for you is the essence of the success of a open source project; the JGrass-NewAGE system is not yet at the stage to be interoperable with GEOtop tools. In any case Mathias Bavey and Thomas Egger did an excellent work in documenting MeteoIO with this paper appeared in GMD, one of our journals of election.

The project is open source, well designed, constantly maintained and evolved, in C++. Have a nice reading.

Monday, September 15, 2014

Opinions on the GEOtop roadmap

Just opinions indeed. For who landed here occasionally, information on GEOtop can be found here.

1 - Infrastructure

Mountain-eering and Exact-lab companies are doing a visible and positive effort in having a clean C++ code, after the huge work made by Stefano Endrizzi and Stephan Gruber to arrive to GEOtop 2.0. However, I believe the work on C++  should make some further steps, which I delineate in one of my previous posts here.
I deem necessary to do at least the first step described there, but the others would be also necessary in order that many people can work collaboratively on the project, and to maintain what we have while producing alternatives, and progress. My solution is, obviously just a proposal, and others (that I do not know) could exist. I plan to work myself part time on this from now to February, but if I can have help from someone this will be great. While changing the basic structure of the model's main( ), if  I will be really able to do it in this favourable astral conjunction,  I will take notes, and provide information to everybody. 

2 - Algorithms

On the side of the algorithms I believe we can work in several directions.  Using an unstructured grid will be a necessary intermediate step to pass through. 
Obviously this would imply a subsequent complete rewrite of the code, and in this rewriting we could take the occasion to: 1 - solve Richards equation with Casulli’s method, and 2 - better integrate surface waters with it. If resources would be available, even freezing soil could be rewritten, and the successful 2011 paper already contains how to do it.

3 - Processes

Among the processes, it would be important if the work by Stefano Dellachiesa on vegetation, and if the work of Florian Marshall on contaminant transport could be really embedded in the GEOtop main stream. My claim for more OO structure above, will go also in the direction to include these achievements, without cluttering the code and/or making more complicate the IO.
Personally, and in perspective, I am interested to include in GEOtop a modeling of the low atmosphere, integrating Navier-Stokes equation. I did some preliminary approach to the problem working conjointly with Dino Zardi and Michael Dumbser. A lot of resources are needed but I can work to grab them.

4 - OMS - Web services

My personal academic interest is also to push further  the evolution of GEOtop’s (beyond step 1) informatics for embedding GEOtop in OMS. This would allow splitting GEOtop  in components that can be joined at run-time through a scripting language, i.e. Groovy. This would enormously  increase the ability to run different modelling solutions, facilitate simulations reports, incapsulate even more the code. I am not claiming here, or pursuing, that this must be the main road followed by the GEOtop community. A certain “genetic variability” in the GEOtop versions and ecology would be indeed of benefit, and in favour of the model eventual survival. A passage necessary for OMS integration will be that task 1above will be pursued. That I think, should be really accomplished right away.

5 - Commitment and Executables

I already manifested my opinion to the developer group. Which is the following: in this moment using GEOtop require the total commitment of the guy/gal the want to embrace it. This is not acceptable if we want that our product would have some spreading. In this moment compiling GEOtop, still remains a challenge for a new users, and even for expert users, because they usually have a lot of other things to do, and they are pissed out when something that they consider trivial does not work as they expect. 
Downloading the source code directly from trunk should work for developers, but not for users. A tagged version, known to compile under the three major operating systems, should be used instead. More than that, a tarred zipped file, with the source code should be made available without passing through git. The best experience for a user would be, however, to download directly the executable for her/his machine and run it. I think that this move, together with improving the manual and documentation, will really boost GEOtop use. And, IMHO is the presence of a lot users that create a fertile soil for businesses.  Certainly a different pathway would be to implement GEOtop as a remote web-service. Recently at CSU,  I was impressed on what te eRams platform can offer, and how it helps in getting data and simulations together, and make easier collaborative work of groups.

6 -Testing

GEOtop comes with a series of tests, and, I verified, all of them compile, and all except one converge to the right solutions. This is useful for making users confident of what they are doing, and developers certain that they did not screwed up the system with their last minute modifications.  However, a special attention should be given to compare GEOtop with the tests provided by the increasing community of process-based model developers. They call their virtual experiment “the superslab” and you can find its definition here.  Being engaged with those guys would be really important, and would bring furhter recognition the our model. We could possibly be able also to challenge that community and propose tests that cope with the cryosphere, since none of its models does it. 

7 - Manual

The manual is not out-of -date but not up-to-date too. Efforts to get it improved would be necessary. I will try to put some students on it, if the occasion comes.

8 -License and Community

GEOtop is GPL and I believe it has to remain GPL. However, not in name of a single Author, but most probably in name of many. The creation of a GEOtop by components, could help in this direction, in the sense that single components, could be copyrighted then by single persons or group different from the original ones. The establishment of some GEOtop foundation with some organisation, and which determines some rules of behavior and/or an etiquette to follow for GEOtop use, will be a desired goal for future. I consider myself not eligible for any position in it though. 

9 - Courses

If a few of the conditions above would be met, it would not be difficult to start some schools either in Europe and in the Americas (or elsewhere). This also should be a goal to be pursued. Schools for Ph.D. students and Researchers, could not be very expensive, however some income can be generated.  Courses for professionals should be more expensive ... but maybe these could be directed to use web-services, and therefore the real income could arrive from subsequent use. 


10 - And then ?


Then it is matter to find resources and man/months to have all of it working. 

Wednesday, March 19, 2014

Ubiquitous Diffusion

These are the slides for the lecture I gave to Michael Dumbser' class on Environmental Modelling. I tried to show the non linear diffusion equations that can be found in analysing the water and energy budget of the soil-snow (with freezing soil) continuum. In practice I used the material from my class in hydrology (the whole stuff here) and other material from GEOtop's talks, and the presentation is, at the moment, in Italian and English.
Incidentally two of these equations present  discontinuities due to phase transitions and the three of them require special numerical methods to be integrated. Here I suggest that a good method could be the Nested Newton one, introduced recently by Casulli and Zanolli (for integrating Richards), and before by  Brugnano and Casulli (for integrating Boussinesq equation).
Below you can find also the audio (in Italian) of the lecture: Richards equation (21.9 Mb); Frozen Soil (18.4 Mb); Snow (7.1 Mb). I gave longer presentations on Richards equation, in Todini Symposium (here), and at the summer School on Landslide Modelling in Praia a Mare (here).
An update. A new treatment of part of this matter is given by Niccolo Tubini in his Master Thesis. The slides he used in the 2017 lecture are here.

Essential References

L. Brugnano and V. Casulli, Iterative solution of piecewise linear systems and applications
to flows in porous media, SIAM J. Sci. Comput., 31 (2009), pp. 1858–1873.

Casulli, V., and Zanolli, P., A Nested Newton-Type Algorithm for Finite Volume Methods Solving Richards' Equation in Mixed Form, SIAM J. Sci. Comput., 32(4), 2255–2273,  Volume 32, Issue 4, 2010.

Cordano E., and Rigon R., A mass-conservative method for the integration of the two-dimensional groundwater (Boussinesq) equation,  Water Resour. Res., 49, doi:10.1002/wrcr.20072, 2013.


Dall’Amico, M.; Endrizzi, S., Gruber, S; and Rigon, R. (2011), An energy-conserving model of freezing variably-saturated soil, The Cryosphere.

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., 2015

Monday, February 24, 2014

JGrass-NewAGE codes

Jgrass-NewAGE is going out from its infantry, and this is signed by its appearance in Github, where the code in development is going to be uploaded. The definitive repository for the code is the JGrasstools Github repository, however, since the requirement to fulfil the jgrasstools standards, were not followed during these first years of development, and because, at the same time, some of the functionalities required for the most recent components are not yet met by the actual version of the uDig Spatial Toolbox, we decided to open a series of new repositories receiving the code in development.
This step was decided also to boost the development of the documentation for the software, that is still kind of missing, at the moment. So here it is the list of the places where the main JGrass-NewAGE components can be found:

All the other components:
  • The Hymod component, 
  • The shortwave radiation component (by Giuseppe Formetta, starting from previous work by Daniele Andreis)
  • The snow water equivalent component (by Giuseppe Formetta)
  • The  evapotranspiration component (by Giuseppe Formetta)
can be found instead here, under the same general repository.

Tuesday, December 10, 2013

GEOtop 2.0 at AGU 2013 - II - The Cryosphere

In this marathon I am doing at this Fall AGU Meeting, I am also giving a second talk about GEOtop 2.0. But this time I talk about the simulations of the snow modelling and the soil freezing.
The presentation is mainly based on the work initiated with Stefano Endrizzi and Matteo Dall'Amico thesis, and subsequently pursed together with Stephan Gruber of Zurich University, now at Carleton University. The two reference papers are Dall'Amico et al. 2011 and Endrizzi et al., 2013, cited in the talk, but also the work in Gubler et al. 2013 is extremely relevant for all the testing it performed on the models
.
So clicking on the image, as usual, you will gain access to the presentation. While, in the first post I took the occasion for adding the References of GEOtop, in this case I just collect the main presentations on the topic that you can find below.

GEOtop relevant presentation

Especially important to understand GEOtop history (see also these post: I and II).
http://www.slideshare.net/GEOFRAMEcafe/geotop-2008

GEOtop, the making of version 1.45  (Summer school on Environmental Dynamics, 2011)
summarised concepts already present in GEOtop 2008 presentation.

GEOtop, the snow modelling (now actually obsolete ... but a good reading for the general concepts)


Monday, December 9, 2013

GEOtop 2.0 at AGU 2013

I was invited to talk at a Fall AGU Meeting section about High Resolution Hydrological modelling. This is the topic of the H21M session of the meeting.  The following, below (clicking on) the figure is my interpretation of the topic.

I describe GEOtop 2.0, present a few case studies, and took the occasion to do some synthesis of this work. All the merits go to my co-authors, that in the last years strongly believed and pushed GEOtop beyond what it was. The presentation does not cover the cryospheric part of the models, which will be the focus of the second presentation.

This other posts covers my second presentation at AGU, talking about how the cryosphere is modeled in GEOtop 2.0.

GEOtop bibliography (so far)

Bertoldi, G., Rigon, R., & Over, T. M. (2006). Impact of Watershed Geomorphic Characteristics on the Energy and Water Budgets. Journal of Hydrometeorology,, 7, 389–403.

Bertoldi, G., Notarnicola, C., Leitinger, G., Endrizzi, S., Della Chiesa, S., Zebisch, M., & Tappeiner, U. (2010). Topographical and ecohydrological controls on land surface temperature in an Alpine catchment. Ecohydrology, 3(doi:10.1002/eco.129), 189–204.

Bertoldi G.; Della Chiesa, S; Notarnicola, C.; Pasolli, L.; Niedrist, G; Tappeiner, U. (2013), Estimation of soil moisture patterns in mountain grasslands by means of SAR RADARSAT 2 images and hydrological modeling, submitted to Journal of Hydrology


Bertoldi, G., Della, S., Notarnicola, C., Pasolli, L., Niedrist, G., & Tappeiner, U. (2014). Estimation of soil moisture patterns in mountain grasslands by means of SAR RADARSAT2 images and hydrological modeling. Journal of Hydrology, 516, 245–257. https://doi.org/10.1016/j.jhydrol.2014.02.018
Dall’Amico, M.; Endrizzi, S., Gruber, S; and Rigon, R. (2011), An energy-conserving model of freezing variably-saturated soil, The Cryosphere.

Della Chiesa, S.; Bertoldi, G.; Niedrist G., Obojes, N.; Albertson, J. D.; Wohlfahrt,G.; Hörtnagl L., Tappeiner U.,  (2014),  Modelling changes in grassland hydrological cycling along an elevational gradient in the Alps, Ecohydrol. 7, 1453–1473 (2014), DOI: 10.1002/eco.1471

Eccel, E., Cordano, E., & Zottele, F. (2015). A project for climatologic mapping of soil water content in Trentino. Italian Journal of Agrometeorology, 1(500 m), 5–20.
Endrizzi S. and Marsh P. Observations and modeling of turbulent fluxes during melt at the shrub-tundra transition zone 1: point scale variations, (2010) Hydrology Research

Endrizzi S., Gruber S., Investigating the effects of lateral water flow on spatial patterns of ground temperature, depth of thaw and ice content, Peer reviewed proceedings of the 10th International Conference on Permafrost, 25–29 June 2012, Salekhard, Russia, 91–96, 2012

Endrizzi S., Gruber S., Dall’Amico M., Rigon R., GEOtop 2.0. (2014), Simulating the combined energy and water balance at and below the land surface accounting for soil freezing, snow cover and terrain effects, 7(6), 2831–2857. https://doi.org/10.5194/gmd-7-2831-2014

Fiddes, J., Endrizzi, S., & Gruber, S. (2015). Large-area land surface simulations in heterogeneous terrain driven by global data sets : application to mountain permafrost. The Cryosphere, 9, 411–426. https://doi.org/10.5194/tc-9-411-2015

Fiddes, J., & Gruber, S. (2012). TopoSUB: a tool for efficient large area numerical modelling in complex topography at sub-grid scales. Geoscientific Model Development, 5(5), 1245–1257. https://doi.org/10.5194/gmd-5-1245-2012

Formetta, G., Rigon R., David, O., Green, T. R., Capparelli, G. (2016), Integration of a spatial hydrological model (GEOtop) into the Object Modeling System (OMS), Water 8(1), 12

Gubler S., Endrizzi S., Gruber S., Purves R. S., Sensitivity and uncertainty of modeled ground temperatures and related variables in mountain environments, Geosci. Model Dev., 6, 1319–1336, 2013.

Gebremichael, M., Rigon, R., Bertoldi, G., & Over, T. M. (2009). On the scaling characteristics of observed and simulated spatial soil moisture fields, Nonlin. Processes Geophys., 16, 141–150.

Hingerl, L., Kunstmann, H., Wagner, S., Mauder, M., Bliefernicht, J., & Rigon, R. (2016). Spatio-temporal variability of water and energy fluxes - a case study for a mesoscale catchment in pre-alpine environment. Hydrological Processes. https://doi.org/10.1002/hyp.10893

Kunstmann, H.,  Hingerl, L., Mauder, M.,  Wagner, S., and Rigon, R., A combined water and energy flux observation and modelling study at the TERENO-preAlpine observatory, Climate and Land-surface Changes in Hydrology, Proceedings of H01, IAHS-IAPSO-IASPEI Assembly, Gothenburg, Sweden, July 2013 (IAHS Publ. 359, 2013)

Lewis, C., Albertson, J., Zi, T., Xu, X., & Kiely, G. (2013). How does afforestation affect the hydrology of a blanket peatland? A modelling study. Hydrological Processes, 27(25), 3577–3588. https://doi.org/10.1002/hyp.9486

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.

Simoni, S., Zanotti, F., Bertoldi, G., & Rigon, R. (2007). Modelling the probability of occurrence of shallow landslides and channelized debris flows using GEOtop-FS. Hydrological Processes, doi: 10.10.

Zanotti, F., Endrizzi, S., Bertoldi, G., & Rigon, R. (2004). The GEOtop snow module. Hydrol. Proc., 18, 3667–3679. DOI:10.1002/hyp.5794.

Zi, T., Kumar, M., Kiely, G., Lewis, C., & Albertson, J. (2016). Simulating the spatio-temporal dynamics of soil erosion, deposition , and yield using a coupled sediment dynamics and 3D distributed hydrologic model. Environmental Modelling and Software, 83, 310–325. https://doi.org/10.1016/j.envsoft.2016.06.004

Ph.D Thesis


Giacomo Bertoldi (2004) The water and energy balance at basin scale: a distributed modeling approach. Download PDF

Stefano Endrizzi (2009), Snow cover modelling at a local and distributed scale over complex terrain

Silvia Simoni (2009), A Comprehensive Approach to Landslide Triggering.

Matteo Dall'Amico (2011), Coupled Water and Heat Transfer in Permafrost Modeling.

Ageel Ibrahim Bushara (2011), Hydrological simulations at basin scale using distributed model and remote sensing with a focus of soil moisture.

GEOtop Manual

GEOtop Manual (a little out-of-date with respect to GEOtop 2.0 ... but not so much).