Wednesday, April 29, 2015

Earth Science Lectures at ICTP

ICTP stands for International Center for Theoretical Physics. The school is warranty of extremely high quality both in teaching and research. Looking at their product Eya for my using it in my classes, I saw their courses Tv. Among the many interesting things, to watch, there is a complete course on the Earth System that could be of interest also for hydrologist.  They derive from the


They say: "Disclaimer: ICTP publishes these lectures on the web and distribute them in digital form only for educational purposes. It will not endorse or sponsor any commercial product, service or activity, and does not permit the recorded material to be used for commercial purposes.
For more information about the courses, including the schedule of lessons, please visit the website of the ICTP Postgraduate Diploma Programme. "

Here they are the available topics for the Academic year 2014/2015

Mathematical Methods
(recorded hours: 12)
Mathematical Methods II
(recorded hours: 10)
Earth System Dynamics and Modelling I-II
(recorded hours: 48)
Wave Physics
(recorded hours: 24)
Earth System Thermodynamics
(recorded hours: 24)
Fluid Mechanics
(recorded hours: 24)
Physics of the Atmosphere
(recorded hours: 24)
Atmospheric Dynamics
(recorded hours: 24)
Physics of the Solid Earth
(recorded hours: 24)
Physics of the Oceans
(recorded hours: 20)
Space Geodesy and InSAR
(recorded hours: 24)
Theoretical Seismology
(recorded hours: 24)
Biogeochemical Cycles
(recorded hours: 28)
Observational and Computational Seismology
(recorded hours: 24)
Physics of Volcanoes
(recorded hours: 24)
Mechanics of Earthquakes and Tectonophysics
(recorded hours: 16)

(16 topics found, for a total of 374 hours)

Friday, April 17, 2015

The man who planted trees -part I

It was a few years ago that I came across the beautiful and inspiring movie  “The man who planted trees”  (in italian here)[1] . 
Read it or watch to it, it is a pleasure of a eco-novel which I find particularly adapt to Spring time. 
The novel raises several eco-hydrological issues, and in particular it poses a question to me: does planting trees change so greatly the hydrological cycle (and the ecosystem) ?  

Ecosystem Services (from the hydrological point of view)

From another point of view, a modern way to ask the same  question would be: which kind of ecosystem services can be obtained with a careful management of the environment, and  when the hydrological cycle is positively managed ? And, what kind of ecosystems services are activated or dumped as a consequence of soil cover change ?

Ecosystem services cover a broad range of agents, but in this case, I would restrict the focus to  understand the interactions between waters and vegetation (and, possibly opened to consider the carbon fluxes). 

It is believed that vegetation can serve for natural hazard and water cycle regulation. There is a generic consensus that forest ecosystems play a significant role in the prevention of soil erosion.  Specifically by cutting surface run-off and storing water they decrease the effects of extreme weather events and natural hazards like floods, storms, avalanches and landslides. Also they are believed to have an action of filtering waters producing cleaner waters and providing  groundwater recharge.  But how much of these beliefs can be quantitatively assessed ? 

The questions can be moved from forests to agricultural landscapes, a provisioning service themselves, without changing much of the hydrological aspects. The spatial unit, in this case is the cadastral unit, or something similar to it. As well as forests, agricultural fields can contribute to the carbon budget, to water quality, especially when they are riparian. 

Again the question is: how can we quantify it, in order to guide landscape management, precision agricolture, and doing forecasts on the effects of changes of soil use (and BTW the impacts of climate change) ?

So, why do not ask to  hydrologists [2] ;-) what they can say about the effects of vegetation on the hydrological cycle ? 

To any hydrologist it is clear that the key hydrological effects are related to evapotranspiration, of which I discussed in several posts. Dealing with it  there are several aspects to account for, among which I name three:

- Canopy transpiration (which can be differentiated in several layers: for instance, grass and plants are different for the way they uptake water). Usually it depends on the height of canopy, leaf area index (LAI), root depth, phenology  and plant's functional  specific parameters. Now there is quite an amount of literature on those parameters, but its real robustness and applicability is unknown.
Plants are different, but  plant types are really so different or it does exists an underlying optimization principle which ever optimize the use of water resources and therefore evapotranspiration for an ecosystem ? Some experimental evidence is going in this direction: but it is clearly a matter of equilibrium and time scales. Among plants there are differences, but it is not certainly possible to say that, for example, pine woods transpire more than larches: too many factors are playing a role. Dimension, characteristic and locations of the trees play possibly a major role than tree species and, this case may be it is the tree specific phenology the major source of difference among trees that share the same landscape.

- Soil evaporation (from bare soil and from below the canopy). It could appear pretty simple with respect to the thermodynamics of plants. Somehow pretty simple. However, whilst it affects only the surface layer, it is controlled by the water potential gradient of the soil column if atmospheric demand is sufficient. As recent papers by Dani Or and coworkers showed.   So very it is very coupled with bottom conditions. Evaporation from soils,  with their own biology,  is not always less than transpiration. In many conditions could be more, and separating it from canopy behaviour is not as simple. 
However, also the interactions,  with the overlaying atmosphere cannot be given for easily estimated. Either for soils and plants.

- Therefore, it is necessary to considering  a better description of the Boundary layer turbulence (which can be treated at different levels of approximations, also depending on the considered time and spatial scales).
 Per se, ET is a flux, a molecular diffusion driven flux, that we have at the surface of soil, of leaves, of water, or when it comes from sublimation, of snow or ice. The flux obeys to the laws of irreversibile thermodynamics processes, and is commanded by gradients of chemical potential. However, ET, as treated in hydrology, is  lumped together with transport, and theoretically derived from conceptualisations of the fluxes conceived a few decades ago. So, even if not simple, better quantitative estimates could derive by addressing fluxes and transport separately and numerically, which could actually benefit both the description of  stomatal and soil resistances, and of aerodynamics.

When me move out from science to application of science, perception of science products is important, as remarked by the post here

[1] - Giono, J. - The man who planted trees - L’uomo che piantava gli alberi, 1953
[2] - And I asked in particular to Giacomo Bertoldi

Wednesday, April 15, 2015

Best practices for Scientific Computing

I was actually looking for other stuff, but I across this paper on Plosone entitled:

Best practices for Scientific Computing, by Wilson et al., 2014

Enjoy it ! One of the Authors, Titus Brown has a blog that we follow (see the Related blog)

Wednesday, April 8, 2015


To who is learning Java I also suggest to apply to the two courses at Coursera called

They are the product of the work of  Kevin Wayne and Robert Sedgewick, and are a good example of how to implement algorithms in Object Oriented language (and in a scientific context), and examples are in Java. I listen to some of the classes and they are nicely implemented, even if programming always require a specific application, i.e. writing yourself the code, it is a nice exercise even just to listen to. Particularly interesting I found the use of generics and data structures, if you do want just to understand when it can be interesting to use them.

On Sedgewick's site, additional material can also be found.

Wednesday, April 1, 2015

Five steps into Reproducible Research

I am worried about Wuletawu being worried about the steep path in doing reproducible research. However,  taking inspiration from Tim-Berners Lee  five star/steps into open data I tried to implement a similar five steps sequence for RR:

@ Do not wait! Make your stuff available on the Web (whatever format) under an open license^1.

@@  Make it available with documentation (e.g. a README file for any data set and for any model)

@@@ Provide examples of runs, and give some reference. Structure your documentation. Include figures and their making. 

@@@@ Use URLs and providers like Github to store code and data, so people can point at your stuff, and browse it freely^2

@@@@@ Maintain a user group (and answer to questions when asked). Provide any run you do on the web with the appropriate metadata^3,4. 

Then you start to be a professional  of RR and you can face more complex task, and using structured tools like those presented in the COURSERA classes brought to my attention by Wuletawu.

1- Same as Tim Berners-Lee - Waiting to have it in better shape will delays the publication forever, and your contribution will be lost (like tears in rain).  
2 - Almost the same as in Tim Berners-Lee