Wednesday, October 19, 2016

Every breath you take

I found these photographies by Robert Dash of stomata and I could not avoid to share them in this blog. The collections of photo are, at least two:

They were taken with an electronic microscope but preserve artistic values. Clicking on the figures you are redirected to the whole collection.

Monday, October 17, 2016

Hillslope stability tools

Here I am on landslides. I gave some contributions to this topics, and I wrote also something about, however I never tried to put a list of models that can be used.

As a general reading I would suggest certainly 

It is one of the few books that have a modern approach to quantitative hillslope hydrology. Who starts from it, is already a few years behind others.  Fortunately, Ning Lu covered some of the book chapters in the summer school on landslides held in 2013, and you can also learn directly from his voice and video.

If you have red the book, you can then understand that having at least a 2D tool for assessing hillslope stability is a necessity that you cannot avoid. 

So here they are my favorite tools:

Jgrasstools (see also here) - They contain a SHALSTAB implementation that can be used for comparison. They also contains the necessary tools for terrain analysis. 
CISLAM -  model was originally implemented in R by Cristiano Lanni (GS), but it was ported to JGrasstools in a Google Summer of Code by Marco Foi. I cannot guarantee its quality, since I never used it, but it is built on the theory I co-developed with Cristiano that you can find addressed here. (Jgrasstools are migrated to the gvSIG 2.3 now or are available trough S.T.A.G.E.).

Boussinesq - This is not directly a tool for hillslope stability estimation. However, it serves to estimate the water content (neglecting at the moment, the vadose zone). There are two version of it:  a C version by Emanuele Cordano (stable and working) and a Java version by Francesco Serafin (that is in Java, for being inserted into OMS3, and still a project under construction).

RiDI. - This was developed by Fabio Ciervo in his Ph.D.  it has the peculiarity that it implements a double porosity soil water retention curve proposed by Nunzio Romano (GS) and coworkers.

GEOtop - It was used a lot to this scope, conjointly with simple and less simple hillslope stability analysis (we did some papers with it).

At present, all the tools require to become part of a consistent framework. But we (Giuseppe Formetta -GS-, Francesco Serafin and I) are working on it, looking forward to the next EGU General Assembly in Wien (April 2017). Stay tuned. 

Tuesday, October 11, 2016

Reservoirology no.2

Because, as we already noticed, often modelling the hydrological cycle is studying the mutual interactions of "reservoirs" of something (which I named "reservoirology"), I tried with my students to have a clean way to represent reservoirs. As we said in the slides below, we try to represent them in a way that, if it is not in a one to one correspondence with the equations that can be derived from the graphs, we are as close as possible to it.

Please find above this graphic collection and help us to improve it. One thing to notice is that our representation is mappable, with different expressivity of the concepts to the Petri Networks algebra, which puts in our hands several studies in mathematics, computer sciences, biology and other sciences. 

Friday, October 7, 2016

Freezing-thawing processes studying with numerical models

This is the presentation given by Niccolò Tubini at the Carleton University last October 6th. Niccolò in his Master Thesis is working for a new implementation of the theory of freezing and thawing already covered by Matteo Dall'Amico in his Ph.D. Thesis and in Dall'Amico et al., 2011.
This work is part of the GEOtop project and its new implementations (see also here). The intention is to use the new numerical method implemented by Casulli and Zanolli (2010, 2011) of the extended Richards equation (see also the video here). The new method promise to be faster than the older one, more stable, and implemented for unstructured grids, while at present, GEOtop 2.0 uses a structured grid. Hopefully, the new development will be made in OMS3


Casulli, V., & Zanolli, P (2010). A nested newton-type algorithm for finite colume methods solving Richards' equation in mixed form. SIAM J. SCI. Comput., 32(4), 2225–2273.

Casulli, V., & Zanolli, P. (2012). Iterative solutions of mildly non linear systems, Journal of Computational and Applied Mathematics, 236(16), 3937–3947.

Dall'Amico, M., Endrizzi, S., Gruber, S., & Rigon, R. (2011). A robust and energy-conserving model of freezing variably-saturated soil. The Cryosphere, 469–484.

Tuesday, October 4, 2016


Networks are pervasive in our world and represent often the way energy is dissipated from large to small scale. I have some past in the topics, especially if we look at river networks, for which a all-time reference is Rodriguez-Iturbe and Rinaldo book.
The news is that my research on networks could have some future. We are using networks for commanding our JGrass-NewAGE model, but with the idea that we can, by means of a chain of models, follow energy dissipation across the hydrological cycle.

John Baez  works on the mathematical theory of networks, seen under different perspectives. His blog, Azimuth, is a source of really exciting ideas brought with extreme competence and he and coworkers have interest in networks. This blog post is to bring attention  his page on network theory which is a huge font of information to be read.

Sunday, October 2, 2016

Non-equilibrium Thermodynamics

I am starting to rewrite S.R. de Groot and P. Mazur, (dGM) Non-equilibrium thermodynamics book. Better, at the moment, I am trying the rewrite its PART A. What do I mean for rewriting ? Mostly two things: the first that I want to learn what it says, driving a slower dance with it, and the second is that I do not fully endorse what I understand so far from it. My differentiation is especially about the role of entropy, which, I think, is treated in a way that strongly derives from the idiosyncrasies of the equilibrium thermodynamics. I already wrote jointly with Matteo Dall’Amico something about thermodynamics, and possibly the two flows could merge in one final product. My goal is not thermodynamics, per se, but the thermodynamics of the hydrological cycle, of which I am a scientist. I believe that thermodynamics has to evolve towards a science of dynamical structures that allows for describing fluxes of information, besides energy and mass, with the final goal to understand ”life organisation”. The latter, however, is for future people. I will attack only water movements, and, maybe, some related cycles, as the carbon cycle. However water flows through plants, an plants are life. So let’s see where I will could arrive in the next fifteen years.

In what follows, what between ” ” is a verbatim transcription of dGM book. I believe their material is copyrighted, however, mine is distributed under CC license 3.0

You can follow the growth of the book while I am writing it, and comment it, if you like. To this scope I am using the Authorea tools. So:

Non-equilibrium Thermodynamics

1- Introduction and motivation
2- Conservation of mass

Other chapters will follow.

Friday, September 30, 2016

EPAs for water

EPA, in this case, stands for Environmental Protection Agency (of the United States).
We use a couple of models developed there, especially in my class of Hydraulic Constructions.
These products are:

and they are available as open source.

There is  an organization of people gathering who are interested in working on them.  You can join them at:

I do not endorse them as the best models ever. But they are there, opens source, and have a community. I see them as a starting point for injecting new ideas and extensions.