Friday, July 21, 2017

Jackknife

I found this nice paper on Jackknife, worth to read. Easy also to understand the differences between the jackknife technique and the leave-one-out one.
You can click on the knife to download it. 


Tuesday, July 18, 2017

Hydrological Extremes and Human Societies

This presentation is part of the summer school “Hydrometeorological extremes: processes, models and human impacts”  just held at Cagliari University this July 12-16. It is a school well organised by Roberto Deidda and became over the year a standard appointment fo my Ph.D. students. This year, among the lecturer there was Giuliano di Baldassarre (GS, RG) who covered the topic on Hydrological Extremes and Human Societies. Unfortunately I could not have been present at his lecture, but I've got his slides (and the permission to publish them).  You can find them below, by clicking on the figure. 
He also suggested some readings related to the talk:

Bianchizza, C., & Frigerio, S. (2013). Domination of or Adaptation to Nature ? A lesson we can still learn from the Vajont. Italian Journal of Engineering Geology and Environment, 6, 523–530. http://doi.org/10.4408/IJEGE.2013-06.B-50

Delle Rose, M. (2012). Decision-making errors and socio-political disputes over the Vajont dam disaster. Disaster Advances, 5(3), 144–152.

Di Baldassarre, G., Martinez, F., Kalantari, Z., & Viglione, A. (2017). Drought and flood in the Anthropocene: feedback mechanisms in reservoir operation. Earth System Dynamics, 8(1), 225–233. http://doi.org/10.5194/esd-8-225-2017

Di Baldassarre, G., Viglione, A., Carr, G., Kuil, L., Yan, K., Brandimarte, L., & Blöschl, G. (2015). Debates-Perspectives on socio-hydrology: Capturing feedbacks between physical and social processes. Water Resources Research, 51(6), 4770–4781. http://doi.org/10.1002/2014WR016416

Montanari, A., Young, G., Savenije, H. H. G., Hughes, D., Wagener, T., Ren, L. L., et al. (2013). “Panta Rhei—Everything Flows”: Change in hydrology and society—The IAHS Scientific Decade 2013–2022. Hydrological Sciences Journal, 58(6), 1256–1275. http://doi.org/10.1080/02626667.2013.809088

Sunday, July 16, 2017

Iowa and operational hydrology

Or operational hydrology in Iowa. I do not know if I like the name, because it usually distinguished, since Sacramento model, models that work but kind of far from the edge of research. Obviously this was due to the fact that having a model running every day faces issues that researchers of my type seldom love, like dealing with unreliable data sets, managing, in any case huge amount of data, calibration of parameters, and, more recently, data assimilation. This obviously has to be done routinely, with no loss of forecasting, when it is easy not to have data, and so on. So the focus of these systems was (is) operativity and having reliable results with unreliable tools (an not, like I do, improving the tools).
Among the various experience I saw around the world, The Iowa's one, is remarkable, because never forgot the most recent research, thanks to the effort of Ricardo Gutierrez Mantilla (GS), and Witold Krajesky (GS).
Ricardo, which whom I share a paper, was so kind to show me what he is doing with all the group of people in Iowa in the recent EGU meeting in Wien, and I was surprised by the quality of the results he has, and the quality of the overall system. One remarkable fact is also the this system is, certainly based on the knowledge of current literature but, originally developed and different from any other. He finally sent to me the couple of his presentation that I (under his permission) am sharing with who is interested. 


Click on the figures to access the presentations. 

A recent publication about the systema was published on BAMS: Witold F. Krajewski, Daniel Ceynar, Ibrahim Demir, Radoslaw Goska, Anton Kruger, Carmen Langel, Ricardo Mantilla, James Niemeier, Felipe Quintero, Bong-Chul Seo, Scott J. Small, Larry J. Weber, and Nathan C. Young, Real-Time Flood Forecasting and Information System for the State of Iowa, Real-time flood forecasting and information system for the State of Iowa, Bull. Am. Meteorol. Soc., doi:10.1175/BAMS-D-15-00243.1, 2017.

Here you can find the  IFC official website.
Here a link to the Iowa Flood Information System (IFIS) which is the platform they use to disseminate flood related information


Enjoy.

Wednesday, July 12, 2017

Open call for a master course in High Performance Computing applied to Hydrological Modeling.


Dear all, I would like to advertise an unique opportunity for bright and motivated young people interested in both hydrology and learn on high-performance scientific computing.
The HPC-Tres program (see http://www.ogs.trieste.it/it/content/hpc-training-and-research-earth-sciences-hpc-tres) is just ready to open a call four (4) fellowship to attend the master in HPC (www.mhpc.it) and work on a thesis on earth science computational project.

One of these four project is dedicated to the development of high-performance parallel code for hydrological modelling, thanks to the cooperation among EURAC Bolzano www.eurac.edu , OGS (Istituto Nazionale di Oceanografia e Geofisica Sperimentale http://www.ogs.trieste.it/) and MHPC Master in High Scientific Computing http://www.mhpc.it/).

This is a great chance for a young graduated student to become an HPC professional and at the same time give an important contribution to advanced scientific packages.
One of the goals of the thesis is to make the hydrological model GEOtop (see also here) run in parallel and increase its speed and overall performance. See “Line C7. Development of a High Performance hydrological model” in the attached document.

To apply for the fellowship is mandatory to apply to the MHPC as well

Deadline has been updated to the 17 of July, see here: http://www.mhpc.it/how-apply

Please do not hesitate to contact Giacomo Bertoldi giacomo.bertoldi@eurac.edu for any further information on this.

Please circulate this opportunity among young and motivated collaborators interested in spending 12 month between Trieste and Bolzano fully paid to attend the master and work on HPC hydrological modelling.

Ing. Giacomo Bertoldi, Ph.D.

EURAC research

Istituto per l'ambiente alpino

Viale Druso 1, I-39100 Bolzano


t +39 0471 055 314
f +39 0471 055 399


Line C7. Development of a High Performance hydrological model


The GEOtop hydrological scientific package is an integrated hydrological model that simulates the heat and water budgets at and below the soil surface. It describes the three-dimensional water flow in the soil and the energy exchange with the atmosphere, considering the radiative and turbulent fluxes. Furthermore, it reproduces the highly non-linear interactions between the water and energy balance during soil freezing and thawing, and simulates the temporal evolution of snow cover, soil temperature and moisture. The core components of the package were presented in the 2.0 version (Endrizzi et al, 2014), which was released as Free Software Open-source project. However, despite the high scientific quality of the project, a modern software engineering approach was still missing. Such weakness hindered its scientific potential and its use both as a standalone package and, more importantly, in an integrate way with other hydrological software tools. In this research line we ail to concentrate software re - engineering efforts to create a robust and stable parallel scientific software package open to the hydrological community, easily usable by researchers and experts, and interoperable with other packages. The overall goal of the activity is to eventually reach a robust and stable software project that manages in a flexible way a complex state-of-the-art hydrological model like GEOtop and integrates it into wider workflows.

Monday, July 10, 2017

A look back to go forward with JGrass-NewAGE

Let's give a look to the last two papers to delineate what is missing. They are all about the use of the JGrass-NewAGE system.


The key aspect of the whole treatment of the water budget is the closure strategy based on the Budyko hypothesis. This has been obtained by a suitable adaptation of the previous Adige-Hymod component that has to be futher cleaned: closing the budget in this way should become more easy and "normal”.  Notably, the method implies that we cannot easily account for cc, unless we let TB increase or decrease with time. However, there is no clear way to obtain this sliding TB from cc simulations.
Another aspect that distinguishes Pp is the use of MODIS for assessing the snow cover. That method would require a better definition, and a standardization of procedures which, again, is missing.
A weak point of this procedure is that ET does not depends on soil cover  characteristics. These characteristics have to be introduced appropriately, for instance giving plants' properties, which include foliage and some plants and roots dimensions which  affect water flows.

Other questions  involve the amount of simplification made when considering an HRU as the basic unit, and how a forcing attributed to a single point (inside a HRU) is representative of the variability of the whole area. Esemplificative is the case of the ET response, obtained by a single point or a small group of points inside the HRU and not by processing all the points. 
With respect to this, the original (version 0) of JGrass-NewAGE was more farsighted by introducing the  energy index calculator components. This OMS component was set to estimate the ratio of radiation received a single pixel inside the basin in a prescribed amount of time (i.e. a month, a year) with respect to a reference pixels. Then, when working in “real time” this factor was used to estimate (approximately) the radiation of the whole HRU on the basis of the single estimate of the reference point and saving, therefore, a lot of computational time. This type of simplifications should/could be reintroduced back again and used when relevant (for instance in Pp this should have been irrelevant for temperature, since its small variation inside each HRU). 


Besides what already said for the Pp that is valid also for BNp, there is to talk, for this paper, about satellite data. All the procedures to obtain those data were performed by using R scripts which are not reproducible and/or not well designed and/or not designed to be available to third parties. To make that research really sparkling, it would be necessary that those scripts and procedures would become real OMS components to be connected with the other ones that constitutesthe core of the paper.

The second point, obviously, is the use of very large HRU that was made: more than 400 square kilometers each on average (not so big, just as large as a square of 20 times 20 km). Therefore the arguments used in Pp, where HRU are of a few kilometers estension, are much more important here: how the sub grid variability of forcings like radiation affects the final results ?
Another aspect not well investigated is how the routing scheme used  affects the results. Clearly in a so large basin, this has to be investigated more thoroughly. Our tools have several routing schemes, including an integrator of a 1d de Saint-Venant equation. Using them could have some importance for the final assessment of our work.

Beyond this, another question arises: can we use those data and those results (in Pp and BNp) as benchmarks for future develpments of our system ? If not, this would be a big wound in our claim to do replicable research.


So, Let's get our sleeves back. 

Friday, July 7, 2017

The Watsup project

This is the Watsup project. It is an integrate Life project, and, therefore, intended a very applicate ones. However, the technologies and the extent of the project would be exceptionally relevant also for science. In fact, its extent, its detail will bring unprecedented capabilities to the institutions that will adopt it.

Please click on the figure above to access the project proposal.

Tuesday, July 4, 2017

CLIMAWARE at the end

This post collects some of the contribution given in our final meetings about the CLIMAWARE project.  For the videoclip introducing the project see here. Some other scientific outcomes are here.


First comes the contribution by Riccardo Rigon (GS) group: here.
Contribution by Rocco Scolozzi and Davide Geneletti (GS) is here. Rocco's YouTube video.
Other contributions to come.

Thursday, June 29, 2017

Start it up again

I am reflecting about what to do in the next Fall. Last year was heavy but the workflow was following a given track, and I have not to think about what to do . This incoming Fall will be a little different.  Looking forward, I obviously have wishes, but reality are the people I am working with that keep me on more concrete goals. So I have four or five offsprings, since I am working directly with five students (let’s call them S1 to S5, they know who is who).



The first direction of work is the consolidation S1 work, but not limited to it. This work, during the last year, covered mainly the systematising of the theory of travel times, producing a (imho) beautiful paper which was not so much recognised yet. This happened because we could not access, so far, reliable-enough tracers' data to test the theory, improve details of our informatics accordingly, and continue the thread of publications in that research direction. One single publication on a topic is usually quite invisible if it is proposed by newcomers (as we are in this topic). 
We also redirected part of S1 work towards the building of an operational hydrological model, which is a task with its own pain. It was based on a (relatively) new partition of (lumped) hillslope fluxes that was necessary to test by itself. This work is at a good stage but the initial goals, of fully testing and have it operational, has been only partially accomplished so far. Much work is required in the Fall to arrive to a full completion of the task which would allow also an easy (without pain) reproducibility of the results (it is a long story.  To see models that work in papers and do not work so fairly in my implementation, is a constant of my research life). Getting a new cleaned version of the new model would mean also cleaning the Adige-Hymod component ("the old model"), to use it for comparison. Documentation of the new model has to be completed on the GEOframe blog too. This could involve distilling some of what already done for the 2017 hydrology class. Understanding the limitations of the new model would be also an achievement, especially regarding some details of the hydrographs that are reproduced systematically wrong. Hopefully this work would lead to a  paper on modelling*  (which could be under our - mine and student's- control) and others that the new arrangement of reservoirs allows in term of processes description (which is not fully under our control, since we need data produced by other researchers). S1 has to be pro-active in this.

Student 1 approach is very much based on a new engine to run modelling solutions described by graphs (to see what I mean, please see here). This task has been pretty much on the shoulders of S2 who did a good job in understanding how OMS works and in implementing a graph-based way to execute in parallel the models implemented in each node. This was constructed with the idea that graphs can describe many type of interaction, but the first implementations are to describe a river network hydrology, having hillslopes (or better HRU as, see the introduction of this paper). It cannot be considered a final work until the modifications he introduced will not flow into the OMS mainstream code. Besides, I am sure the idea is so fertile that several and several generalisation of the system will follow.

This informatics, behind the tree-graph engine, can produce a paper that could be written in the incoming Fall, especially if more than one exemplificative modelling solutions could be shown to work with it*. S2 tells me that the next main problem is to make the calibration machineries of OMS to work properly with various modeling solutions and spatial arrangements. But I am confident that, with the help of Olaf David (OD), this can be obtained reasonably soon. One further steep in informatics, would be to use the CSIP infrastructure to run our modelling solutions on the UNITN multiprocessor system.

Overall S2 has interaction with most of the other guys (see also below). His effort can be summarised in saying, that he is contributing practically and theoretically, in building an infrastructure for scientific productivity and science reproducibility. I think from his cooperative work, a new version of OMS will come out, and his work will also result in some new interesting papers.
The branch of the work in which S2 works is the one I know personally the least. I am conscious that this can cause frustration since he has to explore, mainly by himself, the unexplored. Hope that OD can fill the empty space, but I will try to do a little effort to reduce the gap myself, even if I cannot guarantee the results. 

S3 is working on finding his way. The idea is to work with him on the irrigation demand. This has two non hydrological aspects, the climatological and the plant’s one. The climatological regards the expectation one has in certain places to have certain temperature, radiation (CO2 contents); the plants' response has to do with their response/adaptation to the climate forcing. However, I left out, to mention now,  the third aspect, the hydrological one that has to do with water availability. This, in turn, has also two aspects, the natural one, which, in part, falls in the climatological area, and the human intervention. On the first, we dare to say,  we are experts, and have models to treat with it, especially GEOtop and its evolutions, but also JGrass-NewAGE. However, we should not give for granted  that the description of water movemente in “natural” settings, could not be improved. On the second, personally, I am a parvenù, and I have a lot to learn. Involving humans, accounting for  anthropic behavior and conflicts, could not be out of the horizon, but also how to connect the hydraulics of human infrastructures with the “natural" environment cannot given for granted. So S3 has a perspective to build and a focus to create on just a few of the aspects of this complex question (he, we, will not able to deal with everything): with the second year of the Ph.D incoming S3 has to search this  consistently and produce a couple of research questions to live along in the next two or three years. It could or could be not in one of the aspects I like the most (modelling, and thinking to the infrastructure -physics and informatics- to give answers) but he has (we have) to take decisions.

S4 is working on Richards equation (again!).  The roadmap is well traced, into enriching the actual 1d code with, among possible other aspects: 1- the energy budget; 2 - the freezing: 3- the withdraw either a- natural and b-human; 4 - the interaction with surface water (either as source of pressure or element where runoff is produced). A few others: a - to make explicit the vapour flux inside soil, and therefore, add a further budget; b - to include an explicit treatment of the water (molecules) age, according to theories well defined around year 2000; c - be more explicit in describing water functioning by introducing plants thermodynamics and hydraulics (a topic, the latter where convergence can be found with S3). We focused our first attention on freezing soil aspects, but the whole CZO studies are waiting for tools.
This roadmap is to be broken into steps  to  get along with  before to switch to a full 3D implementation. There are aspects of this research (also described from a different point o view here) that could represent possibilities with strong interactions with S2. S2 graph infrastructure, in fact, should be versatile enough to be able to run, at its node several of these codes, which exchanges, for instance, just water remaining at the surface. Besides, there remain the big problem on how to get the best computational parallel behavior in multiprocessor or multicores machines, under the hood, i.e. without the hydrologist has to take care too much about it (what we call implicit parallelism). But this is just one of the further possible directions to investigate on the informatics side. 
There are a lot of technical mini-issues in all of these topics (which are not mini, at the end). For instance why we do not adopt a more reliable method than CSV for input and output files (I know at least two: one is netcdf, the second is sqlite files/databases) ?

S5 is concerned with Urban Hydrology. His committment is about absorbing SWMM (its site here) concepts and organisation into a new system which include a designing tool compatible with it. It's just a master thesis, but I have expectations on his work. Today SWMM relies on old physics and, above all, is not a designing tool. For who is interested, we did some experience and work around by using different tools (GISWATER, QGIS, Docker) in the experiment we made with students last semester. I think was hard but fun, and we will see the results with the next week finals. Let's what we will be able to produce in future to bring the infrastructure into OMS (OD told me that he already has a ported version of SWMM, let's see if we can find it in some drawer).

Seen from the bottom, and the real work of people, all our enterprise seems matter of ordinary  work and, accordingly, of incremental work, while science, instead, is often said to be looking for paradigmatic changes. However, this is only an impression. There are only a few models (or models component) like ours and our model were conceived since long ago (here a brief compendium of ideas) to set the base for those paradigmatic changes just mentioned. Hydrology has been said to be a dilectantistic field, where physical issues are never really solved and people get accostumed with solutions that just work. My attention to informatics is for freeing people from the legacy of too much constraining tools, allowing third parties inspection of scientific work, and making easier the implementation of new modelling approaches and ideas. I think we are close to this, and we should perseverate on this road.

Before closing this, I just want to refocus on the two possible papers I mentioned above.

S1 paper cannot be justified itself by saying that it is "a new model". So the scientific question has to be a different one. For instance, 1 - which is the minimal set of reservoirs that allows to describe evapotranspiration correctly; 2 - How the introduction of these reservoirs alter the overall residence-travel time; 3 - Is the age of evapotranspirated water in this model different from the age of the runoff water ? 4 - can we say something abot the information that flows around ?

*S2 paper can be justified by saying that it make much more flexible the building of models, either because it is possible to include different types of "models" in each node and also because, we can add and delete nodes (and the relative connections) without altering the rest of the model structure at run time. For instance, in a spatially semi-distribute model, that  works for giving the proper water budget of a catchment, we can add an intake or a reservoir, to see what does change. Or, in the same way, maintaining the same spatial organisation, we can change the runoff production mode in each node wihout excessive reprogramming burden. Looking also how the performance scales with the number of nodes, for instance in comparison, with ADIGE Hymod, could also be of interest.


In any of the two case, we have to keep in mind that a paper is a narrative of something that can be (or should ?) be different from simply describing the tool we have in our hand and it became interesting only when it is finalise to fill a gap in our current knowledge or overcome the current state of art. (What can we do that before was not possible ? Why it is good for research ? Why it is good for operational systems ? How it affects performances ? How it affects performances of researchers ? 

Monday, June 5, 2017

A method for determining optimal observations for prediction

This is the seminar given in Trento on May 30th by Henk Dijkstra (GS). Henk is mainly an oceanographer but the methods he illustrates, especially the Bayesian tools he develops towards the end of his presentation can be useful also in hydrological cases, so I am very happy to host his talk here.
The discussion that followed is here:



The slides of the talk are here. And here is the paper by Kramer et al. (JPO 2012), Measuring the Impact of Observations on the Predictability of the Kuroshio Extension in a Shallow-Water Model.





Sunday, June 4, 2017

How to misinterpret photosynthesis measurements and develop incorrect ecosystem models

At recent EGU General Assembly in Wien, I saw an interesting presentation by Professor Ian Colin Prentice (GS) entitled: How to misinterpret photosynthesis measurements and develop incorrect ecosystem models. I believe I already cited some of his papers (in our Precise proposal and “Can we trust Climate models?”), however, I did not faced his thinking directly. I would lie if I said that I understood his point. I am far too ignorant of the Carbon cycle and the way to measure it to understand. However, I accept the challenge to to start somewhere, because understanding the carbon cycle helps certainly to understand evapotranspiration
Please find below some relevant picture of his slides and, just after the paper(s) he cited. Probably reading those papers can be a starting point to understand.
I. C. Prentice, X. Liang, B. E. Medlyn , and Y.-P. Wang, Reliable, robust and realistic: the three R’s of next-generation land-surface modelling, ACP, 2015 
Hoffman, F. M., J. T. Randerson, V. K. Arora, Q. Bao, P. Cadule, D. Ji, C. D. Jones, M. Kawamiya, S. Khatiwala, K. Lindsay, A. Obata, E. Shevliakova, K. D. Six, J. F. Tjiputra, E. M. Volodin, and T. Wu (2014), Causes and implications of persistent atmospheric carbon dioxide biases in Earth System Models, J. Geophys. Res. Biogeosci., 119, 141–162, doi:10.1002/2013JG002381.
H. D. Graven, R. F. Keeling, S. C. Pipe, P. K. Patra, B. B. Stephens, S. C. Wofsy, L. R. Welp, C. Sweeney, P. P. Tans, J. J. Kelley, B. C. Daube, E. A. Kort, G. W. Santoni, J. D. Bent Enhanced Seasonal Exchange of CO2 by Northern Ecosystems Since 1960, Science 2013
Wenzel, S., P. M. Cox, V. Eyring, andP. Friedlingstein (2014), Emergent constraints on climate-carbon cycle feedbacks in the CMIP5 Earth system models, J. Geophys. Res. Biogeosci., 119,794–807, doi:10.1002/2013JG002591 
Ainsworth EA1, Long SP, What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2., New Phytol. 2005 Feb;165(2):351-71.
Ning Dong, Iain Colin Prentice, Bradley J. Evans , Stefan Caddy-Retalic, Andrew J. Lowe, and Ian J. Wright, Leaf nitrogen from first principles: field evidence for adaptive variation with climate, Biogeosciences, 14, 481–495, 2017 doi:10.5194/bg-14-481-2017 
Zaehle, S., Medlyn, B. E., De Kauwe, M. G., Walker, A. P., Dietze, M. C., Hickler, T., Luo, Y., Wang, Y.-P., El-Masri, B., Thornton, P., Jain, A., Wang, S., Warlind, D., Weng, E., Parton, W., Iversen, C. M., Gallet-Budynek, A., McCarthy, H., Finzi, A., Hanson, P. J., Prentice, I. C., Oren, R. and Norby, R. J. (2014), Evaluation of 11 terrestrial carbon–nitrogen cycle models against observations from two temperate Free-Air CO2 Enrichment studies. New Phytol, 202: 803–822. doi:10.1111/nph.12697 

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

Wednesday, May 24, 2017


This video presents part of the so called “Hazard Map” of Trentino Province in Italy. This is a work started in 2004 that aimed to substitute and simplify previous hazard maps. these maps are used for a variety of scopes that goes from urban and regional planning to civil protection scopes.
As reported in the Province website relative to the Hazard map, the following hazards are mapped:

Hydrological and geological hazards about:
  •  rivers; 
  •  torrents; 
  •  hillslope; 
  •  snow avalanches. 
Other hazards:
  • sismicity; 
  • unexploded bombs (after second world war); 
  • forest fires
The seminar was part of a short course held by Ing. Claudio Bortolotti, a former director of Civil Protection in Trentino, entitled: Integrated Civil Protection Systems.

The speakers were: dott. Mauro Zambotto, directory of Trento province Geological Service (TPGS), dott. Franco Daminato, and dott. Riccardo Campana, geologists at TPGS

I think that the seminar was interesting and highlight the practical use of many tools that I try to popularize to my students.

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 8, 2017

Dolle's Water by Andrea Zanzotto

Now to console me 
with a long visit 
comes the water of Dolle 
that brought ten hills to the town 
fled among bees and their keen castles 
touched the sensitive shapes 
of an island of pure sand, 
now comes this water I long for 
because it shines through your 
twin limbs; 
because it lingered 
a long time in the shadowed coffer 
where the fig-tree stands guard 
and the sun no longer makes moss or fern, 
where the sky’s festive scenes 
are already open. 
Water ignorant of clay 
that already flows from its tangles, 
proud of the momentary red 
of flowers celebrated by this hour, 
you go lightly touching and probing 
the shyest solitudes: 
let it stay mine, 
for my snail’s lamp 
for the garden the dwarf sharecrops, 
water from the thickest alphabet 
water with its messages 
of noble invasion 
of stars returning from alps 
now heavy with silver, 
water promising 
a night cool as a tomorrow

(Translation form Italian from here)

Ora viene a consolarmi
con una lunga visita
l’acqua di Dolle
che portò dieci colline al paese
sfuggì tra le api e i lor castelli di acume
toccò le forme sensitive
di un’isola di pura sabbia,
ora viene quest’acqua ch’io sospiro
perché traspare dalle tue
membra gemelle;
perché a lungo
indugiò nello scrigno d’ombra
dove il fico s’affaccia guardiano
e il sole non fa più musco né felce,
dove sono già aperte
le scene da festa del cielo.
Acqua ignara della creta
che già fuoriesce dai suoi viluppi,
fiera del rosso momentaneo
dei fiori celebrati da quest’ora,
tu vai dovunque lambendo e tentando
le più ritrose solitudini:
lasciatemela mia,
per la mia lampadina di chiocciola
per l’orto di che il nano è mezzadro,
lei dal fittissimo alfabeto
lei che ha i messaggi
di nobili invasioni
degli astri che ritornano dalle alpi
ormai pingui d’argento,
lei che va promettendo
una notte fresca come un domani.

Friday, April 28, 2017

Quantify biological complexity - by John Baez

Just verbatim form the Azimuth blog (here). I place it also here for not forgetting it. Maybe later I will also comment it.

"Here’s a video of the talk I gave at the Stanford Complexity Group:


You can see slides here:

Biology as information dynamics.

Abstract. If biology is the study of self-replicating entities, and we want to understand the role of information, it makes sense to see how information theory is connected to the ‘replicator equation’ — a simple model of population dynamics for self-replicating entities. The relevant concept of information turns out to be the information of one probability distribution relative to another, also known as the Kullback–Liebler divergence. Using this we can get a new outlook on free energy, see evolution as a learning process, and give a clearer, more general formulation of Fisher’s fundamental theorem of natural selection.

I’d given a version of this talk earlier this year at a workshop on Quantifying biological complexity, but I’m glad this second try got videotaped and not the first, because I was a lot happier about my talk this time. And as you’ll see at the end, there were a lot of interesting questions. "

A new topic for a Ph.D. in Hydrology at University of Trento. Modelling water flows under phase transitions

This study starts from a pore scale view of flow in soil and aggregate it at the representative elementary volume, (REV), scale according to statistical assumptions, to obtain new forms of the Richards equation. Flows are assumed to happen under normal and/or freezing conditions and under evapotranspiration demand. Transitions from unsaturated to saturated conditions will be properly accounted in all types of flow. The theoretical work at the basis of this proposal is contained in Dall’Amico et al. 2011 and Tubini, 2017. At the beginning the system will be modeled by coupling the water budget equation and the energy budget equation, neglecting vapor mass budget, as usually done. The candidate should take care of integrating the equations with appropriate and sound numerical methods that guarantee mass and energy conservation, following the footsteps of the work by Casulli and Zanolli (2010) and work for possible extensions.

There are various possible further development of this research. One is to couple the water and energy budget with surface waters simultaneously solved, another is to deal with water vapor explicitly. Others developments could come ongoing.

The informatics behind the code will follow (and, in case co-develops) the developments pursued by dott. Serafin, Ph.D. work inside the Object Modelling System, version 3 or subsequent (OMS3, David et al., 2013), that will take care implicitly of execution of parallel processes and will provide various services to computation (e.g. Serafin, 2016).

All the code developed will be done in Github (or similar platform), inside the GEOframe community and will be Open Source according to the GPL v3 license.
The candidate will take care of implementing, besides the code, the appropriate procedures for continuous integration of the evolving source code, and s/he will be also asked to maintain a regular rate of commits to the common open platform. Despite these conditions, and being free and open source, the code will be intellectual property by the coder. This will be guaranteed also by the components-based infrastructure offered by OMS3, which allows to better define the contributions of anyone. (See also: For incoming students, The tales of open source codes).

The implementation part will be followed, accompanied by testing activities, either for mathematical consistency, than for physical consistency with experiments and field measurements. These will be made especially by Dr. Stephan Gruber (GS) group at Carleton University, where the candidate will be asked to spend some periods od his/her doctorate. Participation to experimental activities will not be intended to be purely passive, the candidate will be asked to actively participate as much as feasible and reasonable to any part of the research.

The Ph.D. student is intended to produce, besides working and tested codes, also at least three papers in major journals (VQR Class A), of which, at least one as first Author.  Duration of the doctoral studies could be three or four years.

This project can enter either the curriculum C (Environmental Engineering) or the curriculum A (Modelling and Simulation) of our doctoral school.

For information please refers to riccardo.rigon <at> unitn.it

Essential References

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

M. Dall’Amico, S. Endrizzi, S. Gruber, and R. Rigon, An energy-conserving model of freezing variably-saturated soil, The Cryosphere, 5, 469-484, 2011, doi:10.5194/tc-5-469-2011.

David, O., Ascough, J. C., II, Lloyd, W., Green, T. R., Rojas, K. W., Leavesley, G. H., & Ahuja, L. R. (2012). A software engineering perspective on environmental modeling framework design: The Object Modeling System. Environmental Modelling and Software, 39, 1–13. http://doi.org/10.1016/j.envsoft.2012.03.006

Serafin, F., About graphs, DSL and replicable research, 2016, http://abouthydrology.blogspot.co.at/2016/11/about-graphs-dsl-and-replicable.html

Tubini, N. (2017, March 31). Theoretical Progress in freezing-thawing process studies. (R. Rigon, F. Serafin, & S. Gruber, Advisors.).

Thursday, April 27, 2017

New Insights in Permafrost modelling (EGU Wien 2017)

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

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

Dalton Prize 2017 to Dani Or

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

Here below a presentation of Dani.


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

Monday, April 10, 2017

Open-source software for simulating hillslope hydrology and stability

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

session of the  2017 EGU meeting in Wien.
For all of this work it is necessary to download a number of softwares.

Thursday, March 30, 2017

Modelling discharge in an Alpine basin with JGrass-NewAGE

This and a related post reports about the Master thesis by Niccolò Tubini and Stefano Tasin. It was a couple years ago that I graduate my last Master guy, and I am happy with these two graduations.
Stefano thesis is in Italian. So I am summarising it a little bit below.
JGrass-NewAGE has a a snow module that was developed by Giuseppe Formetta (GS). Giuseppe developed also a component called  Adige-Hymod for runoff estimation. The two were not tested conjointly (well, they were), and we would like to have a new case to understand more about the behaviour of the model and sharpen the methods we use with it.
 
Stefano did it, making leverage on the NewAGE database of river Adige and using, side by side with NewAGE, GEOtop as the true to reproduce in matter of snow. Other directions could have taken, but Stefano chose this one with excellent results. He had in mind a relatively small basin in the Norther part of Italy that was known to be dominated by snow (and glacier melt) and he wanted to investigate how much of discharge depends upon snow melting. The figure above is one of his results, which shows an excellent discharge fitting and quite impressive demonstration of how snowmelt counts in this case. Thinking that snow on the Alps is going to almost disappear cause the climate change, the basin will go to a quite large change in the discharge regime. It is foreseeable that winter discharge will grow in place of the summer ones, with possible modifications of the discharges distributions.
The thesis and the simulations files used are here.

Theoretical progress in freezing-thawing processes studies

This and a related post reports about the Master thesis by Niccolò Tubini and Stefano Tasin. It was a couple years ago that I graduate my last Master guy, and I am happy with these two graduations.
Niccolò thesis is about modelling permafrost.

I already worked on it during the Ph.D. thesis by Matteo Dall'Amico, obtaining interesting results, which were published in this 2011 paper. From it we built. Initially the idea was that the work by Matteo dall’Amico was clear enough to go directly to a full three-dimensional implementation of 3D algorithms on a unstructured grid. That was actually not the case an we had to rework all the theory. I do not want to waste its reading. So, if you want to know the story, please click here

The presentation Niccolò gave for his Master (Laurea) degree is here.

Wednesday, March 29, 2017

A field trip to Posina catchment

Since a couple of years we started to work on modelling Posina catchment in the Italian pre-alpine area. There University of Padua colleagues, Marco Borga heading the group, started hydrological measurements since many years. Posina is a small catchment (116 km$^{2}$) located in the Alpine foothills of the Veneto Region in Italy. The elevation difference of the basin is 1820 meters. The climate is characterised as wet, with annual precipitation of 1,645 mm and annual runoff of 1000 mm. For a detailed report on its hydrological budget please see Abera's et al. paper.
Finally we had the occasion to visit it with Marco Borga himself and Giulia Zuecco on March 22 afternoon. Please here below find a photographic synthesis with  some comment.

1 - The position of the gauge station at the Stancari outlet.
2 - A view of the position of Bazzoni gauge position.
3 - A view of the Ressi sub-catchment top with a few of the buckets
4 -A more panoramic view (was not a sunny day)
5 - A panorama view with Giulia, Marco and Marialaura from left to right.
6 - Going inside the catchment, to explore these channels (?) or hollow. Soil depth is not very large here. Many trees just did not succeeded to stay still due to the limited roots development. Here and there the bedrock outcrops, but in other position, especially in the concave parts, soil seems to be deeper. 
7 - Here the bedrock channel is visible. We can see also the soil section with the roots of the tree in the foreground.
8 - The V-shaped weir where discharge and water level is measured
9 - The water sampler to do isotopes estimations
10 - A view of the sampler - weir area from below. Please observe the big fallen tree that just slightly touched the box with the sampler when falling. 
11- The throughfall measurement site. 500 hundred buckets for 500 hundred square meters
12 - The stemflow measurements 
It was a nice a pleasant trip! We hope to continue the collaboration further.